# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 12:26:28 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: (2R,4R)-4-methoxy-2-(4-methoxyphenyl)-2-[3-(pyridin-3-yl)phenyl]-3,4-dihydro-2H-pyrrol-5-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@@H]1C[C@@](N=C1N)(c2ccc(OC)cc2)c3cccc(c3)c4cccnc4
#
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
 KGG  KGG  (2R,4R)-4-methoxy-2-(4-methoxyphenyl)-2-[3-(pyridin-3-yl)phenyl]-3,4-dihydro-2H-pyrrol-5-amine  ligand  51  28  .  2021-08-12  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_KGG
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
 KGG  C1    C  CH3   0  -0.435  -4.2393   4.6409   0.1638
 KGG  O2    O  O2    0  -0.473  -3.5242   3.9056  -0.8072
 KGG  C3    C  CR6   0   0.362  -2.9082   2.7684  -0.4234
 KGG  C4    C  CR16  0  -0.326  -2.2500   2.0472  -1.4192
 KGG  C5    C  CR16  0  -0.297  -1.6012   0.8639  -1.1143
 KGG  C6    C  CR6   0   0.191  -1.5837   0.3553   0.1832
 KGG  C7    C  CR16  0  -0.305  -2.2308   1.0925   1.1661
 KGG  C8    C  CR16  0  -0.370  -2.8919   2.2817   0.8806
 KGG  C9    C  CR5   0  -0.080  -0.8221  -0.9298   0.5096
 KGG  C10   C  CH2   0  -0.495  -1.6234  -1.8831   1.4303
 KGG  C11   C  CR15  0  -0.040  -2.3714  -2.7650   0.4502
 KGG  C12   C  CR5   0   0.451  -1.4124  -2.6909  -0.7300
 KGG  N13   N  N     0  -0.426  -0.5996  -1.7052  -0.7025
 KGG  N14   N  NH2   0  -0.828  -1.5023  -3.5679  -1.7501
 KGG  O15   O  O2    0  -0.476  -3.6154  -2.1896   0.1357
 KGG  C16   C  CH3   0  -0.408  -4.4861  -3.0228  -0.5920
 KGG  C17   C  CR6   0   0.183   0.5124  -0.5269   1.1218
 KGG  C18   C  CR16  0  -0.330   0.6188  -0.2363   2.4796
 KGG  C19   C  CR16  0  -0.224   1.8308   0.1676   3.0208
 KGG  C20   C  CR16  0  -0.330   2.9537   0.2870   2.2171
 KGG  C21   C  CR6   0   0.118   2.8687   0.0031   0.8543
 KGG  C22   C  CR16  0  -0.381   1.6427  -0.3985   0.3233
 KGG  C23   C  CR6   0  -0.007   4.0570   0.1144  -0.0113
 KGG  C24   C  CR16  0  -0.197   5.0056   1.1208   0.1591
 KGG  C25   C  CR16  0  -0.316   6.1053   1.1683  -0.6808
 KGG  C26   C  CR16  0  -0.073   6.2248   0.2077  -1.6739
 KGG  N27   N  N     0  -0.399   5.3339  -0.7612  -1.8516
 KGG  C28   C  CR16  0  -0.103   4.2871  -0.8009  -1.0402
 KGG  H11C  H  HCH3  0   0.258  -4.6737   5.4945  -0.3509
 KGG  H12C  H  HCH3  0   0.226  -5.0455   4.0522   0.6103
 KGG  H13C  H  HCH3  0   0.226  -3.5898   5.0080   0.9633
 KGG  H4    H  HCR6  0   0.255  -2.2546   2.4171  -2.4375
 KGG  H8    H  HCR6  0   0.275  -3.3873   2.8062   1.6866
 KGG  H5    H  HCR6  0   0.246  -1.1038   0.3199  -1.9057
 KGG  H7    H  HCR6  0   0.243  -2.2380   0.7516   2.1942
 KGG  H101  H  HCH2  0   0.264  -0.9251  -2.5046   1.9941
 KGG  H102  H  HCH2  0   0.260  -2.2835  -1.3948   2.1457
 KGG  H11   H  HCR5  0   0.244  -2.5031  -3.7915   0.8201
 KGG  H141  H  HNH2  0   0.397  -1.9205  -4.4669  -1.5849
 KGG  H142  H  HNH2  0   0.389  -0.7863  -3.5496  -2.4583
 KGG  H161  H  HCH3  0   0.206  -4.6211  -3.9957  -0.1041
 KGG  H162  H  HCH3  0   0.237  -5.4545  -2.5256  -0.6355
 KGG  H163  H  HCH3  0   0.211  -4.1477  -3.1999  -1.6169
 KGG  H18   H  HCR6  0   0.254  -0.2425  -0.3249   3.1305
 KGG  H22   H  HCR6  0   0.247   1.5546  -0.6058  -0.7349
 KGG  H19   H  HCR6  0   0.257   1.9029   0.3782   4.0799
 KGG  H20   H  HCR6  0   0.253   3.8992   0.5779   2.6576
 KGG  H24   H  HCR6  0   0.270   4.8787   1.8694   0.9310
 KGG  H28   H  HCR6  0   0.260   3.5906  -1.6182  -1.1979
 KGG  H25   H  HCR6  0   0.273   6.8553   1.9398  -0.5743
 KGG  H26   H  HCR6  0   0.266   7.0719   0.2202  -2.3500

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
 KGG  C1   O2    single    1.412  0.020  1.412
 KGG  O2   C3    single    1.349  0.020  1.349
 KGG  C3   C4    aromatic  1.395  0.020  1.395
 KGG  C3   C8    aromatic  1.392  0.020  1.392
 KGG  C4   C5    aromatic  1.384  0.020  1.384
 KGG  C5   C6    aromatic  1.394  0.020  1.394
 KGG  C6   C7    aromatic  1.389  0.020  1.389
 KGG  C6   C9    single    1.529  0.020  1.529
 KGG  C7   C8    aromatic  1.390  0.020  1.390
 KGG  C9   C10   single    1.549  0.020  1.549
 KGG  C9   N13   single    1.456  0.020  1.456
 KGG  C9   C17   single    1.523  0.020  1.523
 KGG  C10  C11   single    1.516  0.020  1.516
 KGG  C11  C12   single    1.522  0.020  1.522
 KGG  C11  O15   single    1.406  0.020  1.406
 KGG  C12  N13   double    1.278  0.020  1.278
 KGG  C12  N14   single    1.348  0.020  1.348
 KGG  O15  C16   single    1.408  0.020  1.408
 KGG  C17  C18   aromatic  1.393  0.020  1.393
 KGG  C17  C22   aromatic  1.390  0.020  1.390
 KGG  C18  C19   aromatic  1.387  0.020  1.387
 KGG  C19  C20   aromatic  1.386  0.020  1.386
 KGG  C20  C21   aromatic  1.395  0.020  1.395
 KGG  C21  C22   aromatic  1.395  0.020  1.395
 KGG  C21  C23   single    1.474  0.020  1.474
 KGG  C23  C24   aromatic  1.393  0.020  1.393
 KGG  C23  C28   aromatic  1.396  0.020  1.396
 KGG  C24  C25   aromatic  1.385  0.020  1.385
 KGG  C25  C26   aromatic  1.387  0.020  1.387
 KGG  C26  N27   aromatic  1.328  0.020  1.328
 KGG  N27  C28   aromatic  1.325  0.020  1.325
 KGG  C1   H11C  single    0.970  0.020  1.090
 KGG  C1   H12C  single    0.970  0.020  1.090
 KGG  C1   H13C  single    0.970  0.020  1.090
 KGG  C4   H4    single    0.930  0.020  1.080
 KGG  C8   H8    single    0.930  0.020  1.080
 KGG  C5   H5    single    0.930  0.020  1.080
 KGG  C7   H7    single    0.930  0.020  1.080
 KGG  C10  H101  single    0.970  0.020  1.090
 KGG  C10  H102  single    0.970  0.020  1.090
 KGG  C11  H11   single    0.970  0.020  1.090
 KGG  N14  H141  single    0.890  0.020  1.040
 KGG  N14  H142  single    0.890  0.020  1.040
 KGG  C16  H161  single    0.970  0.020  1.090
 KGG  C16  H162  single    0.970  0.020  1.090
 KGG  C16  H163  single    0.970  0.020  1.090
 KGG  C18  H18   single    0.930  0.020  1.080
 KGG  C22  H22   single    0.930  0.020  1.080
 KGG  C19  H19   single    0.930  0.020  1.080
 KGG  C20  H20   single    0.930  0.020  1.080
 KGG  C24  H24   single    0.930  0.020  1.080
 KGG  C28  H28   single    0.930  0.020  1.080
 KGG  C25  H25   single    0.930  0.020  1.080
 KGG  C26  H26   single    0.930  0.020  1.080

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
 KGG  H13C  C1   H12C  108.67  3.000
 KGG  H13C  C1   H11C  108.66  3.000
 KGG  H12C  C1   H11C  108.74  3.000
 KGG  H13C  C1   O2    112.13  3.000
 KGG  H12C  C1   O2    111.94  3.000
 KGG  H11C  C1   O2    106.59  3.000
 KGG  C3    O2   C1    118.32  3.000
 KGG  C8    C3   C4    118.86  3.000
 KGG  C8    C3   O2    124.51  3.000
 KGG  C4    C3   O2    116.63  3.000
 KGG  H4    C4   C5    120.08  3.000
 KGG  H4    C4   C3    119.51  3.000
 KGG  C5    C4   C3    120.41  3.000
 KGG  H5    C5   C6    119.47  3.000
 KGG  H5    C5   C4    118.98  3.000
 KGG  C6    C5   C4    121.55  3.000
 KGG  C9    C6   C7    121.81  3.000
 KGG  C9    C6   C5    120.77  3.000
 KGG  C7    C6   C5    117.35  3.000
 KGG  H7    C7   C8    117.45  3.000
 KGG  H7    C7   C6    120.52  3.000
 KGG  C8    C7   C6    122.03  3.000
 KGG  H8    C8   C7    118.66  3.000
 KGG  H8    C8   C3    121.54  3.000
 KGG  C7    C8   C3    119.80  3.000
 KGG  C17   C9   N13   109.99  3.000
 KGG  C17   C9   C10   112.17  3.000
 KGG  N13   C9   C10   104.25  3.000
 KGG  C17   C9   C6    107.45  3.000
 KGG  N13   C9   C6    110.24  3.000
 KGG  C10   C9   C6    112.74  3.000
 KGG  H102  C10  H101  107.68  3.000
 KGG  H102  C10  C11   112.74  3.000
 KGG  H101  C10  C11   108.57  3.000
 KGG  H102  C10  C9    115.35  3.000
 KGG  H101  C10  C9    109.05  3.000
 KGG  C11   C10  C9    103.24  3.000
 KGG  H11   C11  O15   110.57  3.000
 KGG  H11   C11  C12   112.45  3.000
 KGG  O15   C11  C12   111.34  3.000
 KGG  H11   C11  C10   112.63  3.000
 KGG  O15   C11  C10   110.06  3.000
 KGG  C12   C11  C10    99.33  3.000
 KGG  N14   C12  N13   124.09  3.000
 KGG  N14   C12  C11   120.85  3.000
 KGG  N13   C12  C11   114.93  3.000
 KGG  C12   N13  C9    109.36  3.000
 KGG  H142  N14  H141  115.32  3.000
 KGG  H142  N14  C12   118.21  3.000
 KGG  H141  N14  C12   119.02  3.000
 KGG  C16   O15  C11   114.87  3.000
 KGG  H163  C16  H162  108.15  3.000
 KGG  H163  C16  H161  108.14  3.000
 KGG  H162  C16  H161  108.26  3.000
 KGG  H163  C16  O15   112.88  3.000
 KGG  H162  C16  O15   107.48  3.000
 KGG  H161  C16  O15   111.79  3.000
 KGG  C22   C17  C18   118.61  3.000
 KGG  C22   C17  C9    120.42  3.000
 KGG  C18   C17  C9    120.94  3.000
 KGG  H18   C18  C19   118.95  3.000
 KGG  H18   C18  C17   120.54  3.000
 KGG  C19   C18  C17   120.51  3.000
 KGG  H19   C19  C20   119.79  3.000
 KGG  H19   C19  C18   119.77  3.000
 KGG  C20   C19  C18   120.44  3.000
 KGG  H20   C20  C21   120.35  3.000
 KGG  H20   C20  C19   119.65  3.000
 KGG  C21   C20  C19   119.98  3.000
 KGG  C23   C21  C22   120.43  3.000
 KGG  C23   C21  C20   120.61  3.000
 KGG  C22   C21  C20   118.95  3.000
 KGG  H22   C22  C21   119.93  3.000
 KGG  H22   C22  C17   118.56  3.000
 KGG  C21   C22  C17   121.51  3.000
 KGG  C28   C23  C24   116.83  3.000
 KGG  C28   C23  C21   121.07  3.000
 KGG  C24   C23  C21   122.10  3.000
 KGG  H24   C24  C25   120.13  3.000
 KGG  H24   C24  C23   120.44  3.000
 KGG  C25   C24  C23   119.42  3.000
 KGG  H25   C25  C26   120.34  3.000
 KGG  H25   C25  C24   121.04  3.000
 KGG  C26   C25  C24   118.62  3.000
 KGG  H26   C26  N27   116.69  3.000
 KGG  H26   C26  C25   120.40  3.000
 KGG  N27   C26  C25   122.92  3.000
 KGG  C28   N27  C26   118.02  3.000
 KGG  H28   C28  N27   116.14  3.000
 KGG  H28   C28  C23   119.67  3.000
 KGG  N27   C28  C23   124.18  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
 KGG  CONST_01  C6    C5   C4   C3      0.00   0.0  0
 KGG  CONST_02  C6    C7   C8   C3      0.00   0.0  0
 KGG  CONST_03  C7    C8   C3   C4      0.00   0.0  0
 KGG  CONST_04  C7    C6   C5   C4      0.00   0.0  0
 KGG  CONST_05  C8    C3   C4   C5      0.00   0.0  0
 KGG  CONST_06  C8    C7   C6   C5      0.00   0.0  0
 KGG  CONST_07  C20   C19  C18  C17     0.00   0.0  0
 KGG  CONST_08  C20   C21  C22  C17     0.00   0.0  0
 KGG  CONST_09  C23   C21  C22  C17   180.00   0.0  0
 KGG  CONST_10  C21   C22  C17  C18     0.00   0.0  0
 KGG  CONST_11  C21   C20  C19  C18     0.00   0.0  0
 KGG  CONST_12  C22   C17  C18  C19     0.00   0.0  0
 KGG  CONST_13  C22   C21  C20  C19     0.00   0.0  0
 KGG  CONST_14  C23   C21  C20  C19   180.00   0.0  0
 KGG  CONST_17  C25   C24  C23  C21   180.00   0.0  0
 KGG  CONST_18  N27   C28  C23  C21   180.00   0.0  0
 KGG  CONST_21  C26   C25  C24  C23     0.00   0.0  0
 KGG  CONST_22  C26   N27  C28  C23     0.00   0.0  0
 KGG  CONST_23  N27   C28  C23  C24     0.00   0.0  0
 KGG  CONST_24  N27   C26  C25  C24     0.00   0.0  0
 KGG  CONST_25  C28   C23  C24  C25     0.00   0.0  0
 KGG  CONST_26  C28   N27  C26  C25     0.00   0.0  0
 KGG  CONST_27  C9    C6   C5   C4    180.00   0.0  0
 KGG  CONST_28  C9    C6   C7   C8    180.00   0.0  0
 KGG  CONST_29  C19   C18  C17  C9    180.00   0.0  0
 KGG  CONST_30  C21   C22  C17  C9    180.00   0.0  0
 KGG  CONST_31  C11   C12  N13  C9      0.00   0.0  0
 KGG  CONST_32  C5    C4   C3   O2    180.00   0.0  0
 KGG  CONST_33  C7    C8   C3   O2    180.00   0.0  0
 KGG  CONST_34  N14   C12  N13  C9    180.00   0.0  0
 KGG  CONST_35  H5    C5   C4   C3    180.00   0.0  0
 KGG  CONST_36  H7    C7   C8   C3    180.00   0.0  0
 KGG  CONST_37  H8    C8   C3   C4    180.00   0.0  0
 KGG  CONST_38  H4    C4   C5   C6    180.00   0.0  0
 KGG  CONST_39  H18   C18  C17  C9      0.00   0.0  0
 KGG  CONST_40  H22   C22  C17  C9      0.00   0.0  0
 KGG  CONST_41  H19   C19  C18  C17   180.00   0.0  0
 KGG  CONST_42  H20   C20  C19  C18   180.00   0.0  0
 KGG  CONST_43  H24   C24  C23  C21     0.00   0.0  0
 KGG  CONST_44  H28   C28  C23  C21     0.00   0.0  0
 KGG  CONST_45  H25   C25  C24  C23   180.00   0.0  0
 KGG  CONST_46  H26   C26  C25  C24   180.00   0.0  0
 KGG  CONST_48  H142  N14  C12  C11   180.00   0.0  0
 KGG  Var_01    C4    C3   O2   C1    177.93  30.0  2
 KGG  Var_02    H11C  C1   O2   C3   -178.59  30.0  3
 KGG  Var_03    H161  C16  O15  C11    52.77  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
 KGG  chir_01  C9   C10  N13  C17  positiv
 KGG  chir_02  C11  O15  C12  C10  negativ

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
 KGG  plan-1  O2    0.020
 KGG  plan-1  C3    0.020
 KGG  plan-1  C4    0.020
 KGG  plan-1  C5    0.020
 KGG  plan-1  C6    0.020
 KGG  plan-1  C7    0.020
 KGG  plan-1  C8    0.020
 KGG  plan-1  C9    0.020
 KGG  plan-1  H4    0.020
 KGG  plan-1  H8    0.020
 KGG  plan-1  H5    0.020
 KGG  plan-1  H7    0.020
 KGG  plan-2  C9    0.020
 KGG  plan-2  C11   0.020
 KGG  plan-2  C12   0.020
 KGG  plan-2  N13   0.020
 KGG  plan-2  N14   0.020
 KGG  plan-2  H141  0.020
 KGG  plan-2  H142  0.020
 KGG  plan-3  C9    0.020
 KGG  plan-3  C17   0.020
 KGG  plan-3  C18   0.020
 KGG  plan-3  C19   0.020
 KGG  plan-3  C20   0.020
 KGG  plan-3  C21   0.020
 KGG  plan-3  C22   0.020
 KGG  plan-3  C23   0.020
 KGG  plan-3  H18   0.020
 KGG  plan-3  H22   0.020
 KGG  plan-3  H19   0.020
 KGG  plan-3  H20   0.020
 KGG  plan-4  C21   0.020
 KGG  plan-4  C23   0.020
 KGG  plan-4  C24   0.020
 KGG  plan-4  C25   0.020
 KGG  plan-4  C26   0.020
 KGG  plan-4  N27   0.020
 KGG  plan-4  C28   0.020
 KGG  plan-4  H24   0.020
 KGG  plan-4  H28   0.020
 KGG  plan-4  H25   0.020
 KGG  plan-4  H26   0.020

