# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 15:23:51 2020
#   Inital geometry file: a 127 line input string
#   Ligand name: 1-[4-(4-amino-5-oxopyrido[2,3-d]pyrimidin-8(5H)-yl)phenyl]-3-[2-fluoro-5-(trifluoromethyl)phenyl]urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2N(C=CC(=O)c12)c3ccc(NC(=O)Nc4cc(ccc4F)C(F)(F)F)cc3
#
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
 3WR  3WR  1-[4-(4-amino-5-oxopyrido[2,3-d]pyrimidin-8(5H)-yl)phenyl]-3-[2-fluoro-5-(trifluoromethyl)phenyl]urea  ligand  47  33  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3WR
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
 3WR  C1   C  CR66  0   0.529   5.1985  -0.2522  -0.1304
 3WR  C3   C  CR66  0  -0.308   6.5126   0.2251  -0.1865
 3WR  C7   C  CR6   0   0.464   6.8508   1.5829   0.2121
 3WR  C8   C  CR6   0   0.512   7.4769  -0.7152  -0.6640
 3WR  C9   C  CR16  0   0.071   5.8291  -2.2497  -0.9285
 3WR  C10  C  CR16  0  -0.241   2.4641  -0.7639   1.4090
 3WR  C11  C  CR16  0  -0.251   1.9104   0.5689  -0.5041
 3WR  C12  C  CR16  0  -0.483   5.7263   2.3677   0.6553
 3WR  C16  C  CR16  0  -0.357   1.1448  -1.1576   1.5072
 3WR  C20  C  C     0   0.734  -2.2688  -0.6597   0.2374
 3WR  C24  C  CR16  0  -0.312  -5.1779   0.2436   0.2056
 3WR  C27  C  CR16  0  -0.401  -6.8153  -1.8508  -0.6132
 3WR  C30  C  CT    0   1.056  -7.0037   1.8886  -0.2541
 3WR  N2   N  NR6   0  -0.624   4.1989   0.5682   0.3213
 3WR  N4   N  N     0  -0.467   4.8456  -1.4836  -0.5015
 3WR  C5   C  CR6   0   0.260   2.8482   0.1077   0.4014
 3WR  C6   C  CR16  0   0.043   4.4831   1.8459   0.6965
 3WR  O13  O  O     0  -0.496   8.0022   2.0335   0.1777
 3WR  N14  N  N     0  -0.465   7.1094  -1.9500  -1.0302
 3WR  N15  N  NH2   0  -0.814   8.7624  -0.4064  -0.7624
 3WR  C17  C  CR16  0  -0.317   0.5812   0.1813  -0.4104
 3WR  C18  C  CR6   0   0.392   0.1828  -0.6876   0.6059
 3WR  N19  N  NH1   0  -0.788  -1.1173  -1.1540   0.7836
 3WR  N21  N  NH1   0  -0.783  -3.3811  -1.3583   0.6370
 3WR  O22  O  O     0  -0.487  -2.3207   0.2949  -0.5137
 3WR  C23  C  CR6   0   0.217  -4.6720  -1.0529   0.2047
 3WR  C25  C  CR6   0   0.512  -5.5159  -2.0769  -0.2108
 3WR  C26  C  CR6   0  -0.209  -6.4770   0.4885  -0.2141
 3WR  F28  F  F     0  -0.300  -5.0437  -3.3286  -0.2058
 3WR  C29  C  CR16  0  -0.267  -7.2991  -0.5548  -0.6258
 3WR  F31  F  F     0  -0.302  -6.2808   2.7304   0.4905
 3WR  F32  F  F     0  -0.314  -7.0073   2.3789  -1.5032
 3WR  F33  F  F     0  -0.310  -8.2665   1.9587   0.1855
 3WR  H1   H  HCR6  0   0.262   5.5505  -3.2529  -1.2351
 3WR  H2   H  HCR6  0   0.274   3.1888  -1.1308   2.1236
 3WR  H3   H  HCR6  0   0.275   2.2090   1.2378  -1.3019
 3WR  H4   H  HCR6  0   0.280   5.8817   3.3896   0.9714
 3WR  H5   H  HCR6  0   0.279   0.8526  -1.8319   2.3032
 3WR  H6   H  HCR6  0   0.290  -4.5496   1.0501   0.5532
 3WR  H7   H  HCR6  0   0.296  -7.4365  -2.6802  -0.9236
 3WR  H8   H  HCR6  0   0.322   3.6365   2.4225   1.0413
 3WR  H9   H  HNH2  0   0.420   9.0815   0.5101  -0.4868
 3WR  H10  H  HNH2  0   0.403   9.4149  -1.0987  -1.0899
 3WR  H11  H  HCR6  0   0.286  -0.1221   0.5560  -1.1349
 3WR  H12  H  HNH1  0   0.418  -1.2120  -1.8772   1.4808
 3WR  H13  H  HNH1  0   0.417  -3.2555  -2.2447   1.1029
 3WR  H14  H  HCR6  0   0.286  -8.3151  -0.3764  -0.9510

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
 3WR  N15  C8   single    1.326  0.020  1.326
 3WR  O13  C7   double    1.237  0.020  1.237
 3WR  C7   C3   single    1.455  0.020  1.455
 3WR  C7   C12  single    1.441  0.020  1.441
 3WR  C8   C3   aromatic  1.429  0.020  1.429
 3WR  C8   N14  aromatic  1.339  0.020  1.339
 3WR  C3   C1   aromatic  1.399  0.020  1.399
 3WR  N14  C9   aromatic  1.319  0.020  1.319
 3WR  C12  C6   double    1.349  0.020  1.349
 3WR  C9   N4   aromatic  1.318  0.020  1.318
 3WR  C6   N2   single    1.362  0.020  1.362
 3WR  C1   N4   aromatic  1.334  0.020  1.334
 3WR  C1   N2   single    1.370  0.020  1.370
 3WR  N2   C5   single    1.429  0.020  1.429
 3WR  C5   C10  aromatic  1.387  0.020  1.387
 3WR  C5   C11  aromatic  1.383  0.020  1.383
 3WR  C10  C16  aromatic  1.380  0.020  1.380
 3WR  C11  C17  aromatic  1.388  0.020  1.388
 3WR  C16  C18  aromatic  1.399  0.020  1.399
 3WR  C17  C18  aromatic  1.395  0.020  1.395
 3WR  C18  N19  single    1.393  0.020  1.393
 3WR  N19  C20  single    1.367  0.020  1.367
 3WR  O22  C20  double    1.216  0.020  1.216
 3WR  C20  N21  single    1.373  0.020  1.373
 3WR  N21  C23  single    1.395  0.020  1.395
 3WR  F33  C30  single    1.339  0.020  1.339
 3WR  C24  C23  aromatic  1.392  0.020  1.392
 3WR  C24  C26  aromatic  1.387  0.020  1.387
 3WR  C23  C25  aromatic  1.390  0.020  1.390
 3WR  F31  C30  single    1.336  0.020  1.336
 3WR  C30  C26  single    1.496  0.020  1.496
 3WR  C30  F32  single    1.342  0.020  1.342
 3WR  C26  C29  aromatic  1.391  0.020  1.391
 3WR  C25  F28  single    1.338  0.020  1.338
 3WR  C25  C27  aromatic  1.379  0.020  1.379
 3WR  C29  C27  aromatic  1.383  0.020  1.383
 3WR  C9   H1   single    0.930  0.020  1.080
 3WR  C10  H2   single    0.930  0.020  1.080
 3WR  C11  H3   single    0.930  0.020  1.080
 3WR  C12  H4   single    0.930  0.020  1.080
 3WR  C16  H5   single    0.930  0.020  1.080
 3WR  C24  H6   single    0.930  0.020  1.080
 3WR  C27  H7   single    0.930  0.020  1.080
 3WR  C6   H8   single    0.930  0.020  1.080
 3WR  N15  H9   single    0.860  0.020  1.020
 3WR  N15  H10  single    0.860  0.020  1.020
 3WR  C17  H11  single    0.930  0.020  1.080
 3WR  N19  H12  single    0.860  0.020  1.020
 3WR  N21  H13  single    0.860  0.020  1.020
 3WR  C29  H14  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
 3WR  N4   C1   N2   116.85  3.000
 3WR  N2   C1   C3   119.62  3.000
 3WR  N4   C1   C3   123.53  3.000
 3WR  C8   C3   C7   123.28  3.000
 3WR  C8   C3   C1   115.00  3.000
 3WR  C7   C3   C1   121.71  3.000
 3WR  O13  C7   C12  122.44  3.000
 3WR  C12  C7   C3   114.28  3.000
 3WR  O13  C7   C3   123.28  3.000
 3WR  N15  C8   N14  117.42  3.000
 3WR  N14  C8   C3   120.85  3.000
 3WR  N15  C8   C3   121.72  3.000
 3WR  H1   C9   N14  115.94  3.000
 3WR  H1   C9   N4   115.94  3.000
 3WR  N14  C9   N4   128.12  3.000
 3WR  H2   C10  C5   120.50  3.000
 3WR  H2   C10  C16  119.78  3.000
 3WR  C5   C10  C16  119.72  3.000
 3WR  H3   C11  C17  119.09  3.000
 3WR  H3   C11  C5   120.09  3.000
 3WR  C17  C11  C5   120.82  3.000
 3WR  H4   C12  C6   119.30  3.000
 3WR  H4   C12  C7   119.51  3.000
 3WR  C6   C12  C7   121.19  3.000
 3WR  H5   C16  C18  119.80  3.000
 3WR  H5   C16  C10  119.18  3.000
 3WR  C18  C16  C10  121.02  3.000
 3WR  O22  C20  N21  123.01  3.000
 3WR  N21  C20  N19  112.47  3.000
 3WR  O22  C20  N19  124.52  3.000
 3WR  H6   C24  C26  120.70  3.000
 3WR  H6   C24  C23  118.98  3.000
 3WR  C26  C24  C23  120.31  3.000
 3WR  H7   C27  C29  120.99  3.000
 3WR  H7   C27  C25  119.94  3.000
 3WR  C29  C27  C25  119.06  3.000
 3WR  F33  C30  F32  106.50  3.000
 3WR  F32  C30  F31  106.85  3.000
 3WR  F33  C30  F31  107.11  3.000
 3WR  F32  C30  C26  111.57  3.000
 3WR  F31  C30  C26  112.59  3.000
 3WR  F33  C30  C26  111.86  3.000
 3WR  C6   N2   C5   118.96  3.000
 3WR  C5   N2   C1   121.00  3.000
 3WR  C6   N2   C1   120.04  3.000
 3WR  C9   N4   C1   115.44  3.000
 3WR  N2   C5   C11  119.78  3.000
 3WR  C11  C5   C10  119.84  3.000
 3WR  N2   C5   C10  120.34  3.000
 3WR  H8   C6   N2   115.15  3.000
 3WR  H8   C6   C12  121.69  3.000
 3WR  N2   C6   C12  123.16  3.000
 3WR  C9   N14  C8   117.05  3.000
 3WR  H10  N15  H9   120.59  3.000
 3WR  H10  N15  C8   119.52  3.000
 3WR  H9   N15  C8   119.87  3.000
 3WR  H11  C17  C18  121.35  3.000
 3WR  H11  C17  C11  118.88  3.000
 3WR  C18  C17  C11  119.77  3.000
 3WR  N19  C18  C17  124.62  3.000
 3WR  N19  C18  C16  116.55  3.000
 3WR  C17  C18  C16  118.82  3.000
 3WR  H12  N19  C18  114.57  3.000
 3WR  H12  N19  C20  117.14  3.000
 3WR  C18  N19  C20  127.90  3.000
 3WR  H13  N21  C23  116.77  3.000
 3WR  H13  N21  C20  118.71  3.000
 3WR  C23  N21  C20  123.24  3.000
 3WR  C25  C23  N21  119.54  3.000
 3WR  C25  C23  C24  117.75  3.000
 3WR  N21  C23  C24  122.68  3.000
 3WR  F28  C25  C23  118.27  3.000
 3WR  F28  C25  C27  119.15  3.000
 3WR  C23  C25  C27  122.58  3.000
 3WR  C29  C26  C30  119.07  3.000
 3WR  C29  C26  C24  120.72  3.000
 3WR  C30  C26  C24  120.20  3.000
 3WR  H14  C29  C26  121.37  3.000
 3WR  H14  C29  C27  119.06  3.000
 3WR  C26  C29  C27  119.57  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
 3WR  CONST_01  N14  C8   C3   C1      0.00   0.0  0
 3WR  CONST_02  N14  C9   N4   C1      0.00   0.0  0
 3WR  CONST_03  C9   N14  C8   C3      0.00   0.0  0
 3WR  CONST_04  C9   N4   C1   C3      0.00   0.0  0
 3WR  CONST_05  N4   C1   C3   C8      0.00   0.0  0
 3WR  CONST_06  N4   C9   N14  C8      0.00   0.0  0
 3WR  CONST_07  C17  C11  C5   C10     0.00   0.0  0
 3WR  CONST_08  C17  C18  C16  C10     0.00   0.0  0
 3WR  CONST_09  C16  C10  C5   C11     0.00   0.0  0
 3WR  CONST_10  C16  C18  C17  C11     0.00   0.0  0
 3WR  CONST_11  C27  C25  C23  C24     0.00   0.0  0
 3WR  CONST_12  C27  C29  C26  C24     0.00   0.0  0
 3WR  CONST_13  C18  C16  C10  C5      0.00   0.0  0
 3WR  CONST_14  C18  C17  C11  C5      0.00   0.0  0
 3WR  CONST_15  C29  C26  C24  C23     0.00   0.0  0
 3WR  CONST_16  C29  C27  C25  C23     0.00   0.0  0
 3WR  CONST_17  C26  C24  C23  C25     0.00   0.0  0
 3WR  CONST_18  C26  C29  C27  C25     0.00   0.0  0
 3WR  CONST_19  N2   C5   C10  C16   180.00   0.0  0
 3WR  CONST_20  C17  C11  C5   N2    180.00   0.0  0
 3WR  CONST_21  N15  C8   C3   C1    180.00   0.0  0
 3WR  CONST_22  N15  C8   C3   C7      0.00   0.0  0
 3WR  CONST_23  N15  C8   N14  C9    180.00   0.0  0
 3WR  CONST_24  N19  C18  C16  C10   180.00   0.0  0
 3WR  CONST_25  N19  C18  C17  C11   180.00   0.0  0
 3WR  CONST_26  F28  C25  C23  C24   180.00   0.0  0
 3WR  CONST_27  N21  C23  C25  C27   180.00   0.0  0
 3WR  CONST_28  C30  C26  C29  C27   180.00   0.0  0
 3WR  CONST_29  C23  C24  C26  C30   180.00   0.0  0
 3WR  CONST_30  C26  C24  C23  N21   180.00   0.0  0
 3WR  CONST_31  C29  C27  C25  F28   180.00   0.0  0
 3WR  CONST_32  H1   C9   N4   C1    180.00   0.0  0
 3WR  CONST_33  H3   C11  C5   C10   180.00   0.0  0
 3WR  CONST_34  H2   C10  C5   C11   180.00   0.0  0
 3WR  CONST_35  H11  C17  C18  C16   180.00   0.0  0
 3WR  CONST_36  H14  C29  C26  C24   180.00   0.0  0
 3WR  CONST_37  H5   C16  C10  C5    180.00   0.0  0
 3WR  CONST_38  H7   C27  C25  C23   180.00   0.0  0
 3WR  CONST_39  H6   C24  C23  C25   180.00   0.0  0
 3WR  CONST_40  C20  N19  C18  C16   180.00   0.0  0
 3WR  CONST_44  H9   N15  C8   C3      0.00   0.0  0
 3WR  CONST_45  H10  N15  C8   C3    180.00   0.0  0
 3WR  CONST_46  H12  N19  C18  C16     0.00   0.0  0
 3WR  CONST_48  O22  C20  N19  C18     0.00   0.0  0
 3WR  CONST_49  C23  N21  C20  O22     0.00   0.0  0
 3WR  CONST_50  N21  C20  N19  C18   180.00   0.0  0
 3WR  CONST_51  C23  N21  C20  N19   180.00   0.0  0
 3WR  Var_01    C10  C5   N2   C1     74.72  30.0  2
 3WR  Var_02    F33  C30  C26  C24  -139.06  30.0  3

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
 3WR  plan-1  C24  0.020
 3WR  plan-1  C27  0.020
 3WR  plan-1  C30  0.020
 3WR  plan-1  N21  0.020
 3WR  plan-1  C23  0.020
 3WR  plan-1  C25  0.020
 3WR  plan-1  C26  0.020
 3WR  plan-1  F28  0.020
 3WR  plan-1  C29  0.020
 3WR  plan-1  H6   0.020
 3WR  plan-1  H7   0.020
 3WR  plan-1  H14  0.020
 3WR  plan-2  C10  0.020
 3WR  plan-2  C11  0.020
 3WR  plan-2  C16  0.020
 3WR  plan-2  N2   0.020
 3WR  plan-2  C5   0.020
 3WR  plan-2  C17  0.020
 3WR  plan-2  C18  0.020
 3WR  plan-2  N19  0.020
 3WR  plan-2  H2   0.020
 3WR  plan-2  H3   0.020
 3WR  plan-2  H5   0.020
 3WR  plan-2  H11  0.020
 3WR  plan-3  C1   0.020
 3WR  plan-3  C3   0.020
 3WR  plan-3  C7   0.020
 3WR  plan-3  C8   0.020
 3WR  plan-3  C9   0.020
 3WR  plan-3  C12  0.020
 3WR  plan-3  N2   0.020
 3WR  plan-3  N4   0.020
 3WR  plan-3  C5   0.020
 3WR  plan-3  C6   0.020
 3WR  plan-3  O13  0.020
 3WR  plan-3  N14  0.020
 3WR  plan-3  N15  0.020
 3WR  plan-3  H1   0.020
 3WR  plan-3  H4   0.020
 3WR  plan-3  H8   0.020
 3WR  plan-4  C20  0.020
 3WR  plan-4  C18  0.020
 3WR  plan-4  N19  0.020
 3WR  plan-4  N21  0.020
 3WR  plan-4  O22  0.020
 3WR  plan-4  C23  0.020
 3WR  plan-4  H12  0.020
 3WR  plan-4  H13  0.020
 3WR  plan-5  C8   0.020
 3WR  plan-5  N15  0.020
 3WR  plan-5  H9   0.020
 3WR  plan-5  H10  0.020

