# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 12:55:51 2021
#   Inital geometry file: a 75 line input string
#   Ligand name: N-(6-methylpyridin-2-yl)-L-prolinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cccc(NC(=O)[C@@H]2CCCN2)n1
#
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
 WN4  WN4  N-(6-methylpyridin-2-yl)-L-prolinamide  ligand  30  15  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_WN4
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
 WN4  C10  C  CH1   0  -0.250  -39.1674  21.6080   0.0950
 WN4  C13  C  CH2   0  -0.320  -39.7584  21.8468   2.3394
 WN4  C01  C  CH3   0  -0.715  -35.1320  22.9124  -5.3978
 WN4  C02  C  CR6   0   0.244  -34.9884  22.5553  -3.9503
 WN4  C03  C  CR16  0  -0.358  -33.7413  22.4277  -3.3510
 WN4  C04  C  CR16  0  -0.141  -33.6898  22.0769  -2.0103
 WN4  C05  C  CR16  0  -0.382  -34.8561  21.8659  -1.2970
 WN4  C06  C  CR6   0   0.475  -36.0596  22.0254  -1.9863
 WN4  C08  C  C     0   0.550  -37.6686  21.5258  -0.1442
 WN4  C11  C  CH2   0  -0.475  -39.5671  23.1021   0.3239
 WN4  C12  C  CH2   0  -0.453  -40.3428  23.0725   1.6407
 WN4  N07  N  NH1   0  -0.710  -37.3194  21.8659  -1.4172
 WN4  N14  N  NH1   0  -0.575  -39.5514  20.8628   1.2821
 WN4  N15  N  N     0  -0.475  -36.1141  22.3564  -3.2700
 WN4  O09  O  O     0  -0.452  -36.8721  21.2355   0.7249
 WN4  H1   H  HCH1  0   0.282  -39.6872  21.2041  -0.7773
 WN4  H2   H  HCH2  0   0.240  -40.4003  21.4382   3.1200
 WN4  H3   H  HCH2  0   0.224  -38.7982  22.0944   2.8004
 WN4  H4   H  HCH3  0   0.251  -35.8234  23.7455  -5.5256
 WN4  H5   H  HCH3  0   0.245  -34.1759  23.1863  -5.8401
 WN4  H6   H  HCH3  0   0.254  -35.5341  22.0693  -5.9625
 WN4  H8   H  HCR6  0   0.271  -32.7351  21.9660  -1.5127
 WN4  H9   H  HCR6  0   0.283  -34.8294  21.5940  -0.2556
 WN4  H10  H  HCH2  0   0.246  -38.6857  23.7405   0.4153
 WN4  H11  H  HCH2  0   0.254  -40.1522  23.4894  -0.5093
 WN4  H12  H  HCH2  0   0.236  -40.2323  23.9930   2.2151
 WN4  H13  H  HCH2  0   0.229  -41.4089  22.9209   1.4566
 WN4  H14  H  HNH1  0   0.406  -38.0704  22.0435  -2.0697
 WN4  H15  H  HNH1  0   0.355  -40.4328  20.4037   1.0942
 WN4  H7   H  HCR6  0   0.262  -32.8373  22.5989  -3.9193

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
 WN4  C01  C02  single    1.498  0.020  1.498
 WN4  C02  C03  aromatic  1.390  0.020  1.390
 WN4  C02  N15  aromatic  1.330  0.020  1.330
 WN4  C03  C04  aromatic  1.387  0.020  1.387
 WN4  N15  C06  aromatic  1.327  0.020  1.327
 WN4  C04  C05  aromatic  1.383  0.020  1.383
 WN4  C06  N07  single    1.392  0.020  1.392
 WN4  C06  C05  aromatic  1.396  0.020  1.396
 WN4  N07  C08  single    1.363  0.020  1.363
 WN4  C08  C10  single    1.520  0.020  1.520
 WN4  C08  O09  double    1.214  0.020  1.214
 WN4  C10  C11  single    1.563  0.020  1.563
 WN4  C10  N14  single    1.453  0.020  1.453
 WN4  C11  C12  single    1.529  0.020  1.529
 WN4  N14  C13  single    1.459  0.020  1.459
 WN4  C12  C13  single    1.527  0.020  1.527
 WN4  C10  H1   single    0.970  0.020  1.090
 WN4  C13  H2   single    0.970  0.020  1.090
 WN4  C13  H3   single    0.970  0.020  1.090
 WN4  C01  H4   single    0.970  0.020  1.090
 WN4  C01  H5   single    0.970  0.020  1.090
 WN4  C01  H6   single    0.970  0.020  1.090
 WN4  C03  H7   single    0.930  0.020  1.080
 WN4  C04  H8   single    0.930  0.020  1.080
 WN4  C05  H9   single    0.930  0.020  1.080
 WN4  C11  H10  single    0.970  0.020  1.090
 WN4  C11  H11  single    0.970  0.020  1.090
 WN4  C12  H12  single    0.970  0.020  1.090
 WN4  C12  H13  single    0.970  0.020  1.090
 WN4  N07  H14  single    0.860  0.020  1.020
 WN4  N14  H15  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
 WN4  H1   C10  N14  109.68  3.000
 WN4  H1   C10  C11  110.39  3.000
 WN4  N14  C10  C11  107.63  3.000
 WN4  H1   C10  C08  108.87  3.000
 WN4  N14  C10  C08  111.18  3.000
 WN4  C11  C10  C08  109.08  3.000
 WN4  H3   C13  H2   107.46  3.000
 WN4  H3   C13  N14  109.49  3.000
 WN4  H2   C13  N14  110.46  3.000
 WN4  H3   C13  C12  110.31  3.000
 WN4  H2   C13  C12  113.78  3.000
 WN4  N14  C13  C12  105.31  3.000
 WN4  H6   C01  H5   107.92  3.000
 WN4  H6   C01  H4   107.22  3.000
 WN4  H5   C01  H4   108.49  3.000
 WN4  H6   C01  C02  110.56  3.000
 WN4  H5   C01  C02  111.62  3.000
 WN4  H4   C01  C02  110.88  3.000
 WN4  N15  C02  C03  121.68  3.000
 WN4  N15  C02  C01  116.66  3.000
 WN4  C03  C02  C01  121.65  3.000
 WN4  H7   C03  C04  121.14  3.000
 WN4  H7   C03  C02  120.60  3.000
 WN4  C04  C03  C02  118.26  3.000
 WN4  H8   C04  C05  119.41  3.000
 WN4  H8   C04  C03  120.21  3.000
 WN4  C05  C04  C03  120.38  3.000
 WN4  H9   C05  C06  121.86  3.000
 WN4  H9   C05  C04  121.09  3.000
 WN4  C06  C05  C04  117.05  3.000
 WN4  N15  C06  N07  112.77  3.000
 WN4  N07  C06  C05  124.43  3.000
 WN4  N15  C06  C05  122.80  3.000
 WN4  O09  C08  N07  124.07  3.000
 WN4  O09  C08  C10  123.17  3.000
 WN4  N07  C08  C10  112.71  3.000
 WN4  H11  C11  H10  106.84  3.000
 WN4  H11  C11  C12  113.16  3.000
 WN4  H10  C11  C12  110.41  3.000
 WN4  H11  C11  C10  111.41  3.000
 WN4  H10  C11  C10  111.38  3.000
 WN4  C12  C11  C10  103.73  3.000
 WN4  H13  C12  H12  107.74  3.000
 WN4  H13  C12  C11  110.65  3.000
 WN4  H12  C12  C11  112.70  3.000
 WN4  H13  C12  C13  109.83  3.000
 WN4  H12  C12  C13  113.44  3.000
 WN4  C11  C12  C13  102.45  3.000
 WN4  H14  N07  C08  117.16  3.000
 WN4  H14  N07  C06  112.87  3.000
 WN4  C08  N07  C06  129.97  3.000
 WN4  H15  N14  C13  108.49  3.000
 WN4  H15  N14  C10  108.14  3.000
 WN4  C13  N14  C10  106.47  3.000
 WN4  C06  N15  C02  119.82  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
 WN4  CONST_01  C05  C04  C03  C02     0.00   0.0  0
 WN4  CONST_02  C05  C06  N15  C02     0.00   0.0  0
 WN4  CONST_03  C06  N15  C02  C03     0.00   0.0  0
 WN4  CONST_04  C06  C05  C04  C03     0.00   0.0  0
 WN4  CONST_05  N15  C02  C03  C04     0.00   0.0  0
 WN4  CONST_06  N15  C06  C05  C04     0.00   0.0  0
 WN4  CONST_07  C04  C03  C02  C01   180.00   0.0  0
 WN4  CONST_08  C06  N15  C02  C01   180.00   0.0  0
 WN4  CONST_09  N07  C06  N15  C02   180.00   0.0  0
 WN4  CONST_10  N07  C06  C05  C04   180.00   0.0  0
 WN4  CONST_11  H8   C04  C03  C02   180.00   0.0  0
 WN4  CONST_12  H9   C05  C04  C03   180.00   0.0  0
 WN4  CONST_13  H7   C03  C04  C05   180.00   0.0  0
 WN4  CONST_14  C06  N07  C08  C10   180.00   0.0  0
 WN4  CONST_15  C08  N07  C06  C05     0.00   0.0  0
 WN4  CONST_16  N15  C06  N07  C08   180.00   0.0  0
 WN4  CONST_17  H14  N07  C06  C05   180.00   0.0  0
 WN4  CONST_18  O09  C08  N07  C06     0.00   0.0  0
 WN4  Var_01    C13  C12  C11  C10    26.49  30.0  1
 WN4  Var_02    C12  C13  N14  C10    34.85  30.0  1
 WN4  Var_03    N14  C13  C12  C11   -38.21  30.0  1
 WN4  Var_04    H4   C01  C02  C03  -129.23  30.0  2

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
 WN4  chir_01  C10  C08  C11  N14  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
 WN4  plan-1  C01  0.020
 WN4  plan-1  C02  0.020
 WN4  plan-1  C03  0.020
 WN4  plan-1  C04  0.020
 WN4  plan-1  C05  0.020
 WN4  plan-1  C06  0.020
 WN4  plan-1  N07  0.020
 WN4  plan-1  N15  0.020
 WN4  plan-1  H8   0.020
 WN4  plan-1  H9   0.020
 WN4  plan-1  H7   0.020
 WN4  plan-2  C10  0.020
 WN4  plan-2  C06  0.020
 WN4  plan-2  C08  0.020
 WN4  plan-2  N07  0.020
 WN4  plan-2  O09  0.020
 WN4  plan-2  H14  0.020

