Hello, While trying to prepare a ligand for further calculations I find that one that contains a morpholine substituent is not protonated properly. At physiological pH I would expect the nitrogen on the morpholine to be protonated. Is this incorrect? The coordinates are given below for the heavy atoms.
The aliphatic nitrogen seems to be protonated properly. Thank you. Brian ATOM 3529 C5 TIM A 401 3.037 1.145 51.139 1.00 45.16 C ATOM 3530 C6 TIM A 401 3.227 1.181 52.657 1.00 57.05 C ATOM 3531 O1 TIM A 401 2.525 0.109 53.257 1.00 58.33 O ATOM 3532 C2 TIM A 401 1.125 0.224 53.044 1.00 53.51 C ATOM 3533 C3 TIM A 401 0.710 0.379 51.570 1.00 51.17 C ATOM 3534 N4 TIM A 401 1.640 1.118 50.754 1.00 50.77 N ATOM 3535 C7 TIM A 401 1.306 1.594 49.509 1.00 53.55 C ATOM 3536 N8 TIM A 401 0.645 0.822 48.631 1.00 58.54 N ATOM 3537 S9 TIM A 401 0.376 1.667 47.251 1.00 55.87 S ATOM 3538 N10 TIM A 401 1.084 3.083 47.666 1.00 49.53 N ATOM 3539 C11 TIM A 401 1.554 2.967 48.898 1.00 52.80 C ATOM 3540 O12 TIM A 401 2.233 3.973 49.543 1.00 52.38 O ATOM 3541 C13 TIM A 401 2.227 5.300 48.941 1.00 43.69 C ATOM 3542 C14 TIM A 401 3.213 6.032 49.863 1.00 42.67 C ATOM 3543 O15 TIM A 401 3.888 7.083 49.235 1.00 42.10 O ATOM 3544 C16 TIM A 401 2.480 6.515 51.102 1.00 44.11 C ATOM 3545 N17 TIM A 401 3.043 7.593 51.881 1.00 48.54 N ATOM 3546 C18 TIM A 401 2.542 7.436 53.270 1.00 41.41 C ATOM 3547 C19 TIM A 401 2.600 8.757 54.024 1.00 44.38 C ATOM 3548 C20 TIM A 401 1.067 6.963 53.216 1.00 36.66 C ATOM 3549 C21 TIM A 401 3.404 6.393 54.011 1.00 46.82 C ------------------------------------------------------------------------------ Get 100% visibility into Java/.NET code with AppDynamics Lite! It's a free troubleshooting tool designed for production. Get down to code-level detail for bottlenecks, with <2% overhead. Download for free and get started troubleshooting in minutes. http://pubads.g.doubleclick.net/gampad/clk?id=48897031&iu=/4140/ostg.clktrk _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
