HI Cheng,
What is the return value of EmbedMolecule() in these cases? That function
returns the new conformation id... if that value is -1 it means that the
embedding failed.
I suspect that this is what's happening in your case, at least it's what
happens for me:
In [5]: m =
Chem.MolFromSmiles('N#C/C(=C\\c1ccc(s1)c1ccc(s1)c1ccc(cc1)N(c1ccc(cc1)/C=C/c1cc2ccc(cc2oc1=O)N(CC)CC)c1ccc(cc1)/C=C/
...: c1cc2ccc(cc2oc1=O)N(CC)CC)/C(=O)O')
In [6]: mh = Chem.AddHs(m)
In [7]: AllChem.EmbedMolecule(mh)
Out[7]: -1
A solution that often works for larger molecules like this one is to try
embedding from random coordinates:
In [8]: ps = AllChem.ETKDG()
In [9]: ps.useRandomCoords = True
In [10]: AllChem.EmbedMolecule(mh,ps)
Out[10]: 0
As you can see, that worked.
-greg
On Thu, Feb 28, 2019 at 9:37 AM Chencheng Fan <s8chf...@stud.uni-saarland.de>
wrote:
> Hi,
>
> I use python2.7 and rdkit. I am trying to use
> "AllChem.EmbedMolecule()" function to generate 3D structure. However,
> the output molecule is wrongly 2D structure. All the z-coordinates are
> 0, specially in the output mol file, it is written "2D" in the second
> line. Could you help me to solve the problem?
>
>
> My codes and Smiles string are as followings:
>
> from __future__ import print_function
> from rdkit import Chem
> from rdkit.Chem import AllChem
>
>
> Smiles_1='N#C/C(=C\\c1ccc(s1)c1ccc(s1)c1ccc(cc1)N(c1ccc(cc1)/C=C/c1cc2ccc(cc2oc1=O)N(CC)CC)c1ccc(cc1)/C=C/c1cc2ccc(cc2oc1=O)N(CC)CC)/C(=O)O'
> m=Chem.MolFromSmiles(Smiles_1)
> m3=Chem.AddHs(m)
> AllChem.EmbedMolecule(m3)
> print(Chem.MolToMolBlock(m3))
>
>
>
> Smiles_2='CCCCCCCCOc1cccc(c1/C/1=C/2\\C=CC(=N2)/C(=c/2\\n3[Zn]n4c1ccc4/C(=C\\1/C=CC(=N1)/C(=c\\3/cc2)/c1c(OCCCCCCCC)cccc1OCCCCCCCC)/C#Cc1cccc(c1)C(=O)O)/C#Cc1ccc2c(c1)c1ccccc1n2CC)OCCCCCCCC'
> m=Chem.MolFromSmiles(Smiles_2)
> m3=Chem.AddHs(m)
> AllChem.EmbedMolecule(m3)
> print(Chem.MolToMolBlock(m3))
>
> The results are as followings:
>
>
> RDKit 2D
>
> 122130 0 0 0 0 0 0 0 0999 V2000
> 16.3301 -2.8145 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
> 17.0801 -4.1135 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 17.8301 -5.4126 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 17.0801 -6.7116 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 15.5801 -6.7116 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 14.6984 -5.4981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 13.2718 -5.9616 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 13.2718 -7.4616 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 14.6984 -7.9251 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0
> 12.0583 -8.3433 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 12.0583 -9.8433 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 10.6317 -10.3068 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 9.7500 -9.0933 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 10.6317 -7.8797 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0
> 8.2500 -9.0933 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 7.5000 -7.7942 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 6.0000 -7.7942 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 5.2500 -9.0933 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 6.0000 -10.3923 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 7.5000 -10.3923 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 3.7500 -9.0933 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
> 3.0000 -7.7942 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 1.5000 -7.7942 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 0.7500 -6.4952 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 1.5000 -5.1962 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 3.0000 -5.1962 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 3.7500 -6.4952 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 0.7500 -3.8971 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -0.7500 -3.8971 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -1.5000 -2.5981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -3.0000 -2.5981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -3.7500 -1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -5.2500 -1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -6.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -5.2500 1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -3.7500 1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -3.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -1.5000 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
> -0.7500 -1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 0.7500 -1.2990 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
> -6.0000 2.5981 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
> -7.5000 2.5981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -9.0000 2.5981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -5.2500 3.8971 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -4.5000 5.1962 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 3.0000 -10.3923 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 1.5000 -10.3923 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 0.7500 -11.6913 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 1.5000 -12.9904 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 3.0000 -12.9904 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 3.7500 -11.6913 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 0.7500 -14.2894 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 1.5000 -15.5885 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 0.7500 -16.8875 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 1.5000 -18.1865 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 0.7500 -19.4856 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 1.5000 -20.7846 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 0.7500 -22.0836 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -0.7500 -22.0836 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -1.5000 -20.7846 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -0.7500 -19.4856 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -1.5000 -18.1865 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
> -0.7500 -16.8875 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -1.5000 -15.5885 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
> -1.5000 -23.3827 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
> -3.0000 -23.3827 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -4.5000 -23.3827 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -0.7500 -24.6817 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -0.0000 -25.9808 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 19.3301 -5.4126 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 20.0801 -6.7116 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
> 20.0801 -4.1135 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
> 17.8301 -8.0106 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 15.1619 -4.0715 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 12.0583 -5.0799 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 13.2718 -10.7249 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 10.1682 -11.7334 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 8.2500 -6.4952 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 5.6155 -6.8883 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 5.6155 -11.2982 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 8.2500 -11.6913 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 0.9077 -8.5802 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -0.7500 -6.4952 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 3.7500 -3.8971 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 4.7268 -6.3752 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 1.5000 -2.5981 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -1.5000 -5.1962 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -3.7500 -3.8971 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -6.0000 -2.5981 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -7.5000 0.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -3.0000 2.5981 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -7.5000 4.0981 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -7.5000 1.0981 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -9.0000 1.0981 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -9.0000 4.0981 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -10.5000 2.5981 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -6.5490 4.6471 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -3.9510 3.1471 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -5.7990 5.9462 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -3.2010 4.4462 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -3.7500 6.4952 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 0.9077 -9.6063 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -0.7500 -11.6913 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 3.7500 -14.2894 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 4.7268 -11.8113 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -0.7500 -14.2894 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 3.0000 -15.5885 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 3.0000 -18.1865 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 3.0000 -20.7846 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 1.5000 -23.3827 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -3.0000 -20.7846 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -3.0000 -24.8827 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -3.0000 -21.8827 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -4.5000 -21.8827 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -4.5000 -24.8827 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -6.0000 -23.3827 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -2.0490 -25.4317 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 0.5490 -23.9317 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -1.2990 -26.7308 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 1.2990 -25.2308 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 0.7500 -27.2798 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 21.5801 -4.1135 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 1 2 3 0
> 2 3 1 0
> 3 4 2 0
> 4 5 1 0
> 5 6 2 0
> 6 7 1 0
> 7 8 2 0
> 8 9 1 0
> 8 10 1 0
> 10 11 2 0
> 11 12 1 0
> 12 13 2 0
> 13 14 1 0
> 13 15 1 0
> 15 16 2 0
> 16 17 1 0
> 17 18 2 0
> 18 19 1 0
> 19 20 2 0
> 18 21 1 0
> 21 22 1 0
> 22 23 2 0
> 23 24 1 0
> 24 25 2 0
> 25 26 1 0
> 26 27 2 0
> 25 28 1 0
> 28 29 2 0
> 29 30 1 0
> 30 31 2 0
> 31 32 1 0
> 32 33 2 0
> 33 34 1 0
> 34 35 2 0
> 35 36 1 0
> 36 37 2 0
> 37 38 1 0
> 38 39 1 0
> 39 40 2 0
> 35 41 1 0
> 41 42 1 0
> 42 43 1 0
> 41 44 1 0
> 44 45 1 0
> 21 46 1 0
> 46 47 2 0
> 47 48 1 0
> 48 49 2 0
> 49 50 1 0
> 50 51 2 0
> 49 52 1 0
> 52 53 2 0
> 53 54 1 0
> 54 55 2 0
> 55 56 1 0
> 56 57 2 0
> 57 58 1 0
> 58 59 2 0
> 59 60 1 0
> 60 61 2 0
> 61 62 1 0
> 62 63 1 0
> 63 64 2 0
> 59 65 1 0
> 65 66 1 0
> 66 67 1 0
> 65 68 1 0
> 68 69 1 0
> 3 70 1 0
> 70 71 2 0
> 70 72 1 0
> 9 5 1 0
> 14 10 1 0
> 20 15 1 0
> 27 22 1 0
> 39 30 1 0
> 51 46 1 0
> 63 54 1 0
> 37 32 1 0
> 61 56 1 0
> 4 73 1 0
> 6 74 1 0
> 7 75 1 0
> 11 76 1 0
> 12 77 1 0
> 16 78 1 0
> 17 79 1 0
> 19 80 1 0
> 20 81 1 0
> 23 82 1 0
> 24 83 1 0
> 26 84 1 0
> 27 85 1 0
> 28 86 1 0
> 29 87 1 0
> 31 88 1 0
> 33 89 1 0
> 34 90 1 0
> 36 91 1 0
> 42 92 1 0
> 42 93 1 0
> 43 94 1 0
> 43 95 1 0
> 43 96 1 0
> 44 97 1 0
> 44 98 1 0
> 45 99 1 0
> 45100 1 0
> 45101 1 0
> 47102 1 0
> 48103 1 0
> 50104 1 0
> 51105 1 0
> 52106 1 0
> 53107 1 0
> 55108 1 0
> 57109 1 0
> 58110 1 0
> 60111 1 0
> 66112 1 0
> 66113 1 0
> 67114 1 0
> 67115 1 0
> 67116 1 0
> 68117 1 0
> 68118 1 0
> 69119 1 0
> 69120 1 0
> 69121 1 0
> 72122 1 0
> M END
>
> [15:07:38] UFFTYPER: Unrecognized atom type: Zn1+2 (24)
>
> RDKit 2D
>
> 200211 0 0 0 0 0 0 0 0999 V2000
> 13.6340 -3.4609 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 12.2636 -2.8508 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 10.8933 -2.2407 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 9.5230 -1.6306 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 8.1527 -1.0205 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 6.7824 -0.4104 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 5.4120 0.1997 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 4.0417 0.8098 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 2.6714 1.4199 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
> 2.5146 2.9117 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 3.7281 3.7934 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 3.5713 5.2851 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 2.2010 5.8952 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 0.9875 5.0136 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 1.1443 3.5218 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -0.0692 2.6401 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 0.3943 1.2135 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 1.2760 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 0.3943 -1.2135 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -1.0323 -0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -1.0323 0.7500 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
> -2.7828 -1.0947 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -3.9963 -0.2131 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -4.4598 1.2135 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
> -3.9963 2.6401 0.0000 Zn 0 0 0 0 0 2 0 0 0 0 0 0
> -2.7828 3.5218 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
> -1.2828 3.5218 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -0.8192 4.9484 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -2.0328 5.8301 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -3.2463 4.9484 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -4.4598 5.8301 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -5.9598 5.8301 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -7.3864 6.2936 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -8.2681 5.0801 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -7.6369 3.5218 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -7.1733 4.9484 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
> -7.1733 2.0952 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -5.9598 1.2135 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -6.4233 -0.2131 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -5.2098 -1.0947 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -8.3869 1.2135 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -9.7572 1.8236 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -9.9140 3.3154 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
> -11.2843 3.9255 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -12.6546 4.5356 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -14.0249 5.1457 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -15.3952 5.7558 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -16.7656 6.3659 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -18.1359 6.9760 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -19.5062 7.5861 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -20.8765 8.1963 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -10.9707 0.9420 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -10.8139 -0.5498 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -9.4436 -1.1599 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -8.2301 -0.2783 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -6.8597 -0.8884 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
> -6.7030 -2.3801 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -6.5462 -3.8719 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -6.3894 -5.3637 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -6.2326 -6.8555 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -6.0758 -8.3473 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -5.9190 -9.8391 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -5.7622 -11.3308 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -5.6054 -12.8226 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -3.9963 7.2566 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -3.5328 8.6832 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -3.0692 10.1098 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -1.6020 10.4217 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -1.1385 11.8483 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -2.1422 12.9630 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -3.6094 12.6511 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -4.0729 11.2245 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -4.6131 13.7658 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -4.1496 15.1924 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
> -6.0803 13.4540 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
> -3.2463 -2.5213 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -3.7098 -3.9479 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -4.1733 -5.3745 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -5.6406 -5.6864 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -6.1041 -7.1129 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -5.1004 -8.2277 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -3.6332 -7.9158 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -3.1696 -6.4892 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -2.8832 -9.2148 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -1.4159 -9.5267 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -0.9524 -10.9533 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -1.9561 -12.0680 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -3.4233 -11.7561 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -3.8869 -10.3295 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -5.2572 -9.7194 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
> -6.5562 -10.4694 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -7.8552 -11.2194 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -0.3828 5.6237 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
> -0.5396 7.1155 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -0.6964 8.6072 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -0.8532 10.0990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -1.0100 11.5908 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -1.1668 13.0826 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -1.3236 14.5744 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -1.4804 16.0662 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -1.6372 17.5579 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 14.2441 -2.0906 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 13.0238 -4.8313 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 15.0043 -4.0710 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 12.8737 -1.4805 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 11.6535 -4.2212 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 11.5034 -0.8704 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 10.2832 -3.6110 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 10.1331 -0.2603 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 8.9129 -3.0009 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 8.7628 0.3498 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 7.5426 -2.3908 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 7.3925 0.9599 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 6.1723 -1.7807 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 6.0222 1.5700 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 4.8019 -1.1706 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 3.6032 -0.6247 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 4.6518 2.1801 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 5.0985 3.1833 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 4.7849 6.1668 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 2.0442 7.3870 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 2.7648 -0.1828 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 0.8578 -2.6401 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 0.4528 5.7433 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -2.2156 7.3189 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -7.8499 7.7202 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -9.7681 5.0801 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -7.6954 -1.0080 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -5.0270 -2.5836 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -10.6742 5.2958 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -11.8944 2.5552 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -13.2647 3.1653 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -12.0445 5.9059 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -13.4148 6.5160 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -14.6350 3.7754 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -16.0053 4.3855 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -14.7851 7.1262 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -16.1555 7.7363 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -17.3757 4.9956 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -18.7460 5.6057 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -17.5258 8.3464 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -18.8961 8.9565 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -20.1163 6.2158 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -21.4866 6.8259 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -20.2664 9.5666 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -22.2468 8.8064 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -12.3410 1.5521 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -12.0274 -1.4315 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -9.2868 -2.6517 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -5.2032 -2.4064 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -8.1947 -2.5369 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -8.0379 -4.0287 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -5.0544 -3.7151 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -4.9040 -5.5726 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -7.8811 -5.5205 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -4.7408 -6.6987 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -7.7323 -6.8293 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -4.5904 -8.5561 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -7.5756 -8.3211 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -4.4336 -10.0479 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -7.4188 -9.8128 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -4.2704 -11.1740 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -7.1717 -11.8439 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -4.1056 -12.8488 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -7.0669 -13.1601 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -5.4486 -14.3144 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -0.3584 9.5830 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 0.2798 12.3366 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -2.0376 14.4593 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -5.5401 10.9127 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -7.0840 14.5687 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -6.8842 -4.8476 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -7.5223 -7.6013 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -1.7024 -6.1773 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -0.4122 -8.4120 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 0.5148 -11.2652 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -1.4926 -13.4946 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -4.2837 -12.9849 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -7.5983 -9.3905 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -6.1428 -11.9114 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -7.2692 -12.6002 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -8.6052 -9.9204 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -9.1543 -11.9694 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -2.0394 7.1417 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 0.9522 7.2723 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 0.7954 8.7640 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -2.1882 8.4504 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -2.3386 10.3079 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 0.6386 10.2558 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 0.4898 11.5646 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -2.5018 11.4340 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -2.6522 13.2914 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 0.3250 13.2394 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 0.1682 14.7312 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -2.8154 14.4176 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -2.9721 15.9094 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 0.0114 16.2229 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -0.1454 17.7147 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -3.1289 17.4011 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> -1.7939 19.0497 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
> 1 2 1 0
> 2 3 1 0
> 3 4 1 0
> 4 5 1 0
> 5 6 1 0
> 6 7 1 0
> 7 8 1 0
> 8 9 1 0
> 9 10 1 0
> 10 11 2 0
> 11 12 1 0
> 12 13 2 0
> 13 14 1 0
> 14 15 2 0
> 15 16 1 0
> 16 17 2 0
> 17 18 1 0
> 18 19 2 0
> 19 20 1 0
> 20 21 2 0
> 20 22 1 0
> 22 23 2 0
> 23 24 1 0
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> 27 28 2 0
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> 29 30 2 0
> 30 31 1 0
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> 41 42 2 0
> 42 43 1 0
> 43 44 1 0
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> 73 75 1 0
> 22 76 1 0
> 76 77 3 0
> 77 78 1 0
> 78 79 2 0
> 79 80 1 0
> 80 81 2 0
> 81 82 1 0
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> 85 86 1 0
> 86 87 2 0
> 87 88 1 0
> 88 89 2 0
> 89 90 1 0
> 90 91 1 0
> 91 92 1 0
> 14 93 1 0
> 93 94 1 0
> 94 95 1 0
> 95 96 1 0
> 96 97 1 0
> 97 98 1 0
> 98 99 1 0
> 99100 1 0
> 100101 1 0
> 15 10 1 0
> 16 27 1 0
> 32 36 1 0
> 55 41 1 0
> 72 67 1 0
> 83 78 1 0
> 89 84 1 0
> 17 21 1 0
> 23 40 1 0
> 90 81 1 0
> 38 24 1 0
> 30 26 1 0
> 1102 1 0
> 1103 1 0
> 1104 1 0
> 2105 1 0
> 2106 1 0
> 3107 1 0
> 3108 1 0
> 4109 1 0
> 4110 1 0
> 5111 1 0
> 5112 1 0
> 6113 1 0
> 6114 1 0
> 7115 1 0
> 7116 1 0
> 8117 1 0
> 8118 1 0
> 11119 1 0
> 12120 1 0
> 13121 1 0
> 18122 1 0
> 19123 1 0
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> 33126 1 0
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> 39128 1 0
> 40129 1 0
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> 46135 1 0
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> 47137 1 0
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> 51145 1 0
> 51146 1 0
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> 57150 1 0
> 57151 1 0
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> 58153 1 0
> 59154 1 0
> 59155 1 0
> 60156 1 0
> 60157 1 0
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> 61159 1 0
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> 62161 1 0
> 63162 1 0
> 63163 1 0
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> 64165 1 0
> 64166 1 0
> 68167 1 0
> 69168 1 0
> 70169 1 0
> 72170 1 0
> 75171 1 0
> 79172 1 0
> 80173 1 0
> 83174 1 0
> 85175 1 0
> 86176 1 0
> 87177 1 0
> 88178 1 0
> 91179 1 0
> 91180 1 0
> 92181 1 0
> 92182 1 0
> 92183 1 0
> 94184 1 0
> 94185 1 0
> 95186 1 0
> 95187 1 0
> 96188 1 0
> 96189 1 0
> 97190 1 0
> 97191 1 0
> 98192 1 0
> 98193 1 0
> 99194 1 0
> 99195 1 0
> 100196 1 0
> 100197 1 0
> 101198 1 0
> 101199 1 0
> 101200 1 0
> M END
>
> Best regards
> Cheng
>
>
>
>
>
>
> _______________________________________________
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