# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 05:33:54 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: 1-(5-chloro-2-methoxyphenyl)-3-{6-[(1S)-2-(dimethylamino)-1-methylethoxy]pyrazin-2-yl}urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(Cl)cc1NC(=O)Nc2cncc(O[C@@H](C)CN(C)C)n2
#
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
 77A  77A  1-(5-chloro-2-methoxyphenyl)-3-{6-[(1S)-2-(dimethylamino)-1-methylethoxy]pyrazin-2-yl}urea  ligand  48  26  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_77A
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
 77A  N1    N   NH1   0  -0.781  -3.4089   1.3795   5.4506
 77A  C2    C   CR6   0   0.293  -2.8125   2.3322   6.2729
 77A  C3    C   CR16  0  -0.276  -1.4875   2.2941   6.6880
 77A  C4    C   CR6   0  -0.051  -1.0023   3.2892   7.5271
 77A  C5    C   CR16  0  -0.226  -1.8026   4.3189   7.9721
 77A  C6    C   CR16  0  -0.384  -3.1325   4.3554   7.5659
 77A  C7    C   CR6   0   0.337  -3.6423   3.3815   6.7242
 77A  O8    O   O2    0  -0.482  -4.9126   3.3421   6.2802
 77A  C9    C   CH3   0  -0.434  -5.8188   4.3413   6.7090
 77A  CL10  CL  CL    0  -0.137   0.6601   3.2164   8.0240
 77A  C11   C   C     0   0.732  -2.7838   0.4266   4.6951
 77A  O12   O   O     0  -0.463  -1.5819   0.3214   4.5784
 77A  N13   N   NH1   0  -0.775  -3.6945  -0.4134   4.0836
 77A  C14   C   CR6   0   0.459  -3.3784  -1.4045   3.1711
 77A  N15   N   N     0  -0.423  -2.3657  -1.2130   2.3401
 77A  C16   C   CR6   0   0.472  -2.0936  -2.1685   1.4797
 77A  C17   C   CR16  0  -0.172  -2.8686  -3.3362   1.4077
 77A  N18   N   N     0  -0.338  -3.8903  -3.5031   2.2213
 77A  C19   C   CR16  0  -0.181  -4.1557  -2.5595   3.1136
 77A  O20   O   O2    0  -0.470  -1.0839  -2.0481   0.6298
 77A  C21   C   CH1   0  -0.016  -0.2859  -0.8534   0.6337
 77A  C22   C   CH2   0  -0.261   0.4005  -0.7953  -0.7203
 77A  N23   N   NT    0  -0.402  -0.5018  -0.8170  -1.8521
 77A  C24   C   CH3   0  -0.520   0.2413  -0.9601  -3.0857
 77A  C25   C   CH3   0  -0.688   0.7290  -0.8786   1.7618
 77A  C26   C   CH3   0  -0.530  -1.3684   0.3415  -1.9014
 77A  HN1   H   HNH1  0   0.417  -4.4109   1.4615   5.3604
 77A  H3    H   HCR6  0   0.298  -0.8329   1.5039   6.3598
 77A  H5    H   HCR6  0   0.280  -1.4155   5.0898   8.6235
 77A  H6    H   HCR6  0   0.293  -3.7575   5.1628   7.9215
 77A  H91   H   HCH3  0   0.234  -5.4989   5.3376   6.3951
 77A  H92   H   HCH3  0   0.234  -5.9455   4.3336   7.7942
 77A  H93   H   HCH3  0   0.265  -6.7719   4.1123   6.2402
 77A  HN13  H   HNH1  0   0.422  -4.6252  -0.4591   4.4717
 77A  H17   H   HCR6  0   0.272  -2.6456  -4.1138   0.6869
 77A  H19   H   HCR6  0   0.278  -4.9865  -2.7154   3.7918
 77A  H21   H   HCH1  0   0.242  -0.9410   0.0112   0.7651
 77A  H221  H   HCH2  0   0.201   1.0370   0.1075  -0.7201
 77A  H222  H   HCH2  0   0.236   1.0798  -1.6496  -0.8067
 77A  H241  H   HCH3  0   0.190   0.9353  -0.1261  -3.2782
 77A  H242  H   HCH3  0   0.233  -0.4451  -1.0214  -3.9313
 77A  H243  H   HCH3  0   0.233   0.8282  -1.8800  -3.0660
 77A  H251  H   HCH3  0   0.260   0.2389  -0.8803   2.7335
 77A  H252  H   HCH3  0   0.229   1.3781  -1.7521   1.6873
 77A  H253  H   HCH3  0   0.237   1.3549   0.0127   1.7101
 77A  H261  H   HCH3  0   0.192  -0.8176   1.2952  -1.9320
 77A  H262  H   HCH3  0   0.235  -2.0375   0.3700  -1.0411
 77A  H263  H   HCH3  0   0.236  -1.9944   0.2908  -2.7927

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
 77A  N1   C11   single    1.367  0.020  1.367
 77A  N1   C2    single    1.393  0.020  1.393
 77A  N1   HN1   single    0.860  0.020  1.020
 77A  C2   C3    aromatic  1.389  0.020  1.389
 77A  C2   C7    aromatic  1.412  0.020  1.412
 77A  C3   C4    aromatic  1.389  0.020  1.389
 77A  C3   H3    single    0.930  0.020  1.080
 77A  C4   CL10  single    1.737  0.020  1.737
 77A  C4   C5    aromatic  1.378  0.020  1.378
 77A  C5   C6    aromatic  1.391  0.020  1.391
 77A  C5   H5    single    0.930  0.020  1.080
 77A  C6   C7    aromatic  1.384  0.020  1.384
 77A  C6   H6    single    0.930  0.020  1.080
 77A  C7   O8    single    1.346  0.020  1.346
 77A  O8   C9    single    1.415  0.020  1.415
 77A  C9   H91   single    0.970  0.020  1.090
 77A  C9   H92   single    0.970  0.020  1.090
 77A  C9   H93   single    0.970  0.020  1.090
 77A  C11  O12   double    1.212  0.020  1.212
 77A  C11  N13   single    1.382  0.020  1.382
 77A  N13  C14   single    1.384  0.020  1.384
 77A  N13  HN13  single    0.860  0.020  1.020
 77A  C14  N15   aromatic  1.324  0.020  1.324
 77A  C14  C19   aromatic  1.393  0.020  1.393
 77A  N15  C16   aromatic  1.314  0.020  1.314
 77A  C16  O20   single    1.325  0.020  1.325
 77A  C16  C17   aromatic  1.403  0.020  1.403
 77A  C17  N18   aromatic  1.317  0.020  1.317
 77A  C17  H17   single    0.930  0.020  1.080
 77A  N18  C19   aromatic  1.326  0.020  1.326
 77A  C19  H19   single    0.930  0.020  1.080
 77A  O20  C21   single    1.437  0.020  1.437
 77A  C21  C25   single    1.518  0.020  1.518
 77A  C21  C22   single    1.519  0.020  1.519
 77A  C21  H21   single    0.970  0.020  1.090
 77A  C22  N23   single    1.448  0.020  1.448
 77A  C22  H221  single    0.970  0.020  1.090
 77A  C22  H222  single    0.970  0.020  1.090
 77A  N23  C26   single    1.448  0.020  1.448
 77A  N23  C24   single    1.447  0.020  1.447
 77A  C24  H241  single    0.970  0.020  1.090
 77A  C24  H242  single    0.970  0.020  1.090
 77A  C24  H243  single    0.970  0.020  1.090
 77A  C25  H251  single    0.970  0.020  1.090
 77A  C25  H252  single    0.970  0.020  1.090
 77A  C25  H253  single    0.970  0.020  1.090
 77A  C26  H261  single    0.970  0.020  1.090
 77A  C26  H262  single    0.970  0.020  1.090
 77A  C26  H263  single    0.970  0.020  1.090

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
 77A  HN1   N1   C11   117.46  3.000
 77A  HN1   N1   C2    114.98  3.000
 77A  C11   N1   C2    127.39  3.000
 77A  C7    C2   C3    119.05  3.000
 77A  C7    C2   N1    116.45  3.000
 77A  C3    C2   N1    124.49  3.000
 77A  H3    C3   C4    119.82  3.000
 77A  H3    C3   C2    120.57  3.000
 77A  C4    C3   C2    119.61  3.000
 77A  CL10  C4   C5    119.66  3.000
 77A  C5    C4   C3    121.84  3.000
 77A  CL10  C4   C3    118.50  3.000
 77A  H5    C5   C6    119.98  3.000
 77A  H5    C5   C4    121.30  3.000
 77A  C6    C5   C4    118.72  3.000
 77A  H6    C6   C7    120.82  3.000
 77A  H6    C6   C5    118.44  3.000
 77A  C7    C6   C5    120.74  3.000
 77A  O8    C7   C6    124.65  3.000
 77A  O8    C7   C2    115.31  3.000
 77A  C6    C7   C2    120.04  3.000
 77A  C9    O8   C7    118.92  3.000
 77A  H93   C9   H92   108.98  3.000
 77A  H93   C9   H91   108.97  3.000
 77A  H92   C9   H91   109.02  3.000
 77A  H93   C9   O8    106.38  3.000
 77A  H92   C9   O8    111.73  3.000
 77A  H91   C9   O8    111.67  3.000
 77A  N13   C11  O12   123.93  3.000
 77A  N13   C11  N1    111.53  3.000
 77A  O12   C11  N1    124.54  3.000
 77A  HN13  N13  C14   115.57  3.000
 77A  HN13  N13  C11   117.72  3.000
 77A  C14   N13  C11   125.22  3.000
 77A  C19   C14  N15   121.38  3.000
 77A  C19   C14  N13   119.57  3.000
 77A  N15   C14  N13   119.01  3.000
 77A  C16   N15  C14   117.65  3.000
 77A  O20   C16  C17   117.61  3.000
 77A  C17   C16  N15   121.61  3.000
 77A  O20   C16  N15   120.77  3.000
 77A  H17   C17  N18   118.67  3.000
 77A  H17   C17  C16   121.18  3.000
 77A  N18   C17  C16   120.15  3.000
 77A  C19   N18  C17   118.75  3.000
 77A  H19   C19  N18   118.18  3.000
 77A  H19   C19  C14   121.41  3.000
 77A  N18   C19  C14   120.41  3.000
 77A  C21   O20  C16   119.80  3.000
 77A  H21   C21  C25   108.94  3.000
 77A  H21   C21  C22   110.35  3.000
 77A  C25   C21  C22   111.16  3.000
 77A  H21   C21  O20   108.99  3.000
 77A  C22   C21  O20   106.29  3.000
 77A  C25   C21  O20   111.07  3.000
 77A  H222  C22  H221  106.28  3.000
 77A  H222  C22  N23   108.26  3.000
 77A  H221  C22  N23   111.81  3.000
 77A  H222  C22  C21   108.71  3.000
 77A  H221  C22  C21   106.95  3.000
 77A  N23   C22  C21   114.50  3.000
 77A  C26   N23  C24   110.95  3.000
 77A  C24   N23  C22   110.36  3.000
 77A  C26   N23  C22   112.81  3.000
 77A  H243  C24  H242  107.76  3.000
 77A  H243  C24  H241  107.60  3.000
 77A  H242  C24  H241  107.66  3.000
 77A  H243  C24  N23   110.13  3.000
 77A  H242  C24  N23   110.07  3.000
 77A  H241  C24  N23   113.42  3.000
 77A  H253  C25  H252  108.04  3.000
 77A  H253  C25  H251  107.59  3.000
 77A  H252  C25  H251  109.13  3.000
 77A  H253  C25  C21   109.57  3.000
 77A  H252  C25  C21   111.13  3.000
 77A  H251  C25  C21   111.26  3.000
 77A  H263  C26  H262  107.09  3.000
 77A  H263  C26  H261  107.73  3.000
 77A  H262  C26  H261  107.83  3.000
 77A  H263  C26  N23   109.53  3.000
 77A  H262  C26  N23   111.20  3.000
 77A  H261  C26  N23   113.22  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
 77A  CONST_01  C5    C4   C3   C2     0.00   0.0  0
 77A  CONST_02  C5    C6   C7   C2     0.00   0.0  0
 77A  CONST_03  C6    C7   C2   C3     0.00   0.0  0
 77A  CONST_04  C6    C5   C4   C3     0.00   0.0  0
 77A  CONST_05  C7    C2   C3   C4     0.00   0.0  0
 77A  CONST_06  C7    C6   C5   C4     0.00   0.0  0
 77A  CONST_07  C17   C16  N15  C14    0.00   0.0  0
 77A  CONST_08  C17   N18  C19  C14    0.00   0.0  0
 77A  CONST_09  N18   C19  C14  N15    0.00   0.0  0
 77A  CONST_10  N18   C17  C16  N15    0.00   0.0  0
 77A  CONST_11  C19   C14  N15  C16    0.00   0.0  0
 77A  CONST_12  C19   N18  C17  C16    0.00   0.0  0
 77A  CONST_13  C4    C3   C2   N1   180.00   0.0  0
 77A  CONST_14  C6    C7   C2   N1   180.00   0.0  0
 77A  CONST_15  CL10  C4   C3   C2   180.00   0.0  0
 77A  CONST_16  O8    C7   C2   C3   180.00   0.0  0
 77A  CONST_17  O8    C7   C6   C5   180.00   0.0  0
 77A  CONST_18  CL10  C4   C5   C6   180.00   0.0  0
 77A  CONST_19  C16   N15  C14  N13  180.00   0.0  0
 77A  CONST_20  N18   C19  C14  N13  180.00   0.0  0
 77A  CONST_21  O20   C16  N15  C14  180.00   0.0  0
 77A  CONST_22  O20   C16  C17  N18  180.00   0.0  0
 77A  CONST_23  H6    C6   C7   C2   180.00   0.0  0
 77A  CONST_24  H5    C5   C4   C3   180.00   0.0  0
 77A  CONST_25  H3    C3   C4   C5   180.00   0.0  0
 77A  CONST_26  H19   C19  C14  N15  180.00   0.0  0
 77A  CONST_27  H17   C17  C16  N15  180.00   0.0  0
 77A  CONST_28  C11   N1   C2   C3     0.00   0.0  0
 77A  CONST_29  C11   N1   C2   C7   180.00   0.0  0
 77A  CONST_32  HN1   N1   C2   C3   180.00   0.0  0
 77A  CONST_34  O12   C11  N1   C2     0.00   0.0  0
 77A  CONST_35  C14   N13  C11  O12    0.00   0.0  0
 77A  CONST_36  C14   N13  C11  N1   180.00   0.0  0
 77A  CONST_37  N13   C11  N1   C2   180.00   0.0  0
 77A  Var_01    H91   C9   O8   C7    61.61  30.0  3
 77A  Var_02    C26   N23  C22  C21   63.80  30.0  3
 77A  Var_03    H261  C26  N23  C22   57.45  30.0  3
 77A  Var_04    H241  C24  N23  C22  -61.87  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
 77A  chir_01  C21  O20  C25  C22  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
 77A  plan-1  N1    0.020
 77A  plan-1  C2    0.020
 77A  plan-1  C3    0.020
 77A  plan-1  C4    0.020
 77A  plan-1  C5    0.020
 77A  plan-1  C6    0.020
 77A  plan-1  C7    0.020
 77A  plan-1  O8    0.020
 77A  plan-1  CL10  0.020
 77A  plan-1  H3    0.020
 77A  plan-1  H5    0.020
 77A  plan-1  H6    0.020
 77A  plan-2  N13   0.020
 77A  plan-2  C14   0.020
 77A  plan-2  N15   0.020
 77A  plan-2  C16   0.020
 77A  plan-2  C17   0.020
 77A  plan-2  N18   0.020
 77A  plan-2  C19   0.020
 77A  plan-2  O20   0.020
 77A  plan-2  H17   0.020
 77A  plan-2  H19   0.020
 77A  plan-3  N1    0.020
 77A  plan-3  C2    0.020
 77A  plan-3  C11   0.020
 77A  plan-3  O12   0.020
 77A  plan-3  N13   0.020
 77A  plan-3  C14   0.020
 77A  plan-3  HN1   0.020
 77A  plan-3  HN13  0.020

