# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Thu Jun  4 17:26:09 2020
#   Inital geometry file: a 52 line input string
#   Ligand name: (3~{S})-~{N}-methylpyrrolidine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=O)[C@H]1CCNC1
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 M6W  M6W  (3~{S})-~{N}-methylpyrrolidine-3-carboxamide  ligand  21  9  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_M6W
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 M6W  C01  C  CH3   0  -0.513   3.3920  -0.2571   0.0035
 M6W  C03  C  C     0   0.559   0.9790   0.0399  -0.2299
 M6W  C04  C  CR15  0  -0.403  -0.3775  -0.2591   0.3657
 M6W  C05  C  CH2   0  -0.301  -1.2376  -1.1546  -0.5507
 M6W  C07  C  CH2   0  -0.318  -2.6636   0.5445   0.0537
 M6W  C08  C  CH2   0  -0.462  -1.2635   0.9887   0.5470
 M6W  N02  N  NH1   0  -0.626   2.0319  -0.4267   0.4552
 M6W  N06  N  NR15  0  -0.581  -2.6146  -0.8960  -0.1740
 M6W  O09  O  O     0  -0.508   1.1062   0.6536  -1.2838
 M6W  H1   H  HCH3  0   0.236   3.5760  -0.7764  -0.9383
 M6W  H2   H  HCH3  0   0.237   3.6391   0.7959  -0.1343
 M6W  H3   H  HCH3  0   0.249   4.0589  -0.6682   0.7561
 M6W  H4   H  HCR5  0   0.260  -0.2637  -0.7646   1.3290
 M6W  H5   H  HCH2  0   0.227  -1.0882  -0.8614  -1.5942
 M6W  H6   H  HCH2  0   0.249  -0.9950  -2.2137  -0.4617
 M6W  H7   H  HCH2  0   0.237  -3.4590   0.7905   0.7568
 M6W  H8   H  HCH2  0   0.226  -2.8982   1.0471  -0.8879
 M6W  H9   H  HCH2  0   0.243  -1.2799   1.3010   1.5910
 M6W  H10  H  HCH2  0   0.242  -0.8948   1.8318  -0.0375
 M6W  H11  H  HNH1  0   0.403   1.8715  -0.9394   1.3051
 M6W  H12  H  HNR5  0   0.345  -2.8017  -1.3708   0.7015

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 M6W  C04  C05  single  1.543  0.020  1.543
 M6W  C04  C08  single  1.541  0.020  1.541
 M6W  C04  C03  single  1.511  0.020  1.511
 M6W  N06  C07  single  1.459  0.020  1.459
 M6W  N06  C05  single  1.451  0.020  1.451
 M6W  C07  C08  single  1.550  0.020  1.550
 M6W  N02  C03  single  1.340  0.020  1.340
 M6W  N02  C01  single  1.443  0.020  1.443
 M6W  C03  O09  double  1.226  0.020  1.226
 M6W  C01  H1   single  0.970  0.020  1.090
 M6W  C01  H2   single  0.970  0.020  1.090
 M6W  C01  H3   single  0.970  0.020  1.090
 M6W  C04  H4   single  0.970  0.020  1.090
 M6W  C05  H5   single  0.970  0.020  1.090
 M6W  C05  H6   single  0.970  0.020  1.090
 M6W  C07  H7   single  0.970  0.020  1.090
 M6W  C07  H8   single  0.970  0.020  1.090
 M6W  C08  H9   single  0.970  0.020  1.090
 M6W  C08  H10  single  0.970  0.020  1.090
 M6W  N02  H11  single  0.860  0.020  1.020
 M6W  N06  H12  single  0.890  0.020  1.040

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 M6W  H3   C01  H2   108.30  3.000
 M6W  H3   C01  H1   108.33  3.000
 M6W  H2   C01  H1   108.20  3.000
 M6W  H3   C01  N02  108.50  3.000
 M6W  H2   C01  N02  111.50  3.000
 M6W  H1   C01  N02  111.91  3.000
 M6W  O09  C03  N02  122.15  3.000
 M6W  O09  C03  C04  122.07  3.000
 M6W  N02  C03  C04  115.78  3.000
 M6W  H4   C04  C08  109.29  3.000
 M6W  H4   C04  C05  108.23  3.000
 M6W  C08  C04  C05  102.67  3.000
 M6W  H4   C04  C03  110.19  3.000
 M6W  C08  C04  C03  113.71  3.000
 M6W  C05  C04  C03  112.40  3.000
 M6W  H6   C05  H5   107.93  3.000
 M6W  H6   C05  N06  111.30  3.000
 M6W  H5   C05  N06  109.24  3.000
 M6W  H6   C05  C04  113.03  3.000
 M6W  H5   C05  C04  109.55  3.000
 M6W  N06  C05  C04  105.75  3.000
 M6W  H8   C07  H7   107.18  3.000
 M6W  H8   C07  N06  109.07  3.000
 M6W  H7   C07  N06  110.37  3.000
 M6W  H8   C07  C08  109.65  3.000
 M6W  H7   C07  C08  112.92  3.000
 M6W  N06  C07  C08  107.60  3.000
 M6W  H10  C08  H9   107.29  3.000
 M6W  H10  C08  C07  110.89  3.000
 M6W  H9   C08  C07  111.93  3.000
 M6W  H10  C08  C04  111.64  3.000
 M6W  H9   C08  C04  110.69  3.000
 M6W  C07  C08  C04  104.47  3.000
 M6W  H11  N02  C03  118.97  3.000
 M6W  H11  N02  C01  118.35  3.000
 M6W  C03  N02  C01  122.66  3.000
 M6W  H12  N06  C07  108.75  3.000
 M6W  H12  N06  C05  108.42  3.000
 M6W  C07  N06  C05  104.38  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 M6W  CONST_01  C04  C03  N02  C01  180.00   0.0  0
 M6W  CONST_02  H11  N02  C03  C04    0.00   0.0  0
 M6W  CONST_03  O09  C03  N02  C01    0.00   0.0  0
 M6W  Var_01    C07  N06  C05  C04   40.00  30.0  1
 M6W  Var_02    C08  C07  N06  C05  -30.08  30.0  1
 M6W  Var_03    H1   C01  N02  C03  -63.83  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 M6W  chir_01  C04  C05  C08  C03  positiv

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 M6W  plan-1  C01  0.020
 M6W  plan-1  C03  0.020
 M6W  plan-1  C04  0.020
 M6W  plan-1  N02  0.020
 M6W  plan-1  O09  0.020
 M6W  plan-1  H11  0.020

