# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 02:55:29 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: 2-[(1~{R})-5-(4-chlorophenyl)-9-fluoranyl-3-methyl-1-oxidanyl-1~{H}-pyrimido[4,5-c]quinolin-2-yl]ethanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=Nc2c(nc3ccc(F)cc3c2[C@@H](O)N1CC(O)=O)c4ccc(Cl)cc4
#
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
 AW8  AW8  '2-[(1~{R})-5-(4-chlorophenyl)-9-fluoranyl-3-methyl-1-oxidanyl-1~{H}-pyrimido[4,5-c]quinolin-2-yl]ethanoic acid'  ligand  42  28  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_AW8
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
 AW8  CL1  CL  CL     0  -0.130  -6.8387  -0.4111   0.1839
 AW8  C16  C   CR6    0  -0.051  -5.1117  -0.5448   0.1278
 AW8  C14  C   CR16   0  -0.201  -4.5320  -1.6681  -0.4402
 AW8  C12  C   CR16   0  -0.298  -3.1504  -1.7657  -0.4757
 AW8  C15  C   CR16   0  -0.202  -4.3309   0.4722   0.6540
 AW8  C13  C   CR16   0  -0.281  -2.9497   0.3685   0.5959
 AW8  C11  C   CR6    0   0.083  -2.3385  -0.7505   0.0303
 AW8  C10  C   CR6    0   0.106  -0.8688  -0.9347   0.0036
 AW8  N9   N   N      0  -0.448  -0.4439  -2.1373   0.2700
 AW8  C2   C   CR66   0   0.150   0.8809  -2.4108   0.2620
 AW8  C4   C   CR16   0  -0.279   1.2906  -3.7264   0.5661
 AW8  C6   C   CR16   0  -0.428   2.6167  -4.0641   0.5746
 AW8  C5   C   CR6    0   0.565   3.5591  -3.0721   0.2737
 AW8  F27  F   F      0  -0.315   4.8551  -3.4201   0.2860
 AW8  C3   C   CR16   0  -0.529   3.2184  -1.7882  -0.0352
 AW8  C8   C   CR6    0   0.155   0.0299   0.1382  -0.3304
 AW8  N19  N   N      0  -0.515  -0.4875   1.3727  -0.6104
 AW8  C20  C   C      0   0.473   0.3431   2.3639  -0.7383
 AW8  C22  C   CH3    0  -0.771  -0.2441   3.7300  -0.9020
 AW8  N18  N   NT     0  -0.461   1.6806   2.2355  -0.7282
 AW8  C17  C   CH1    0   0.113   2.3214   0.9443  -0.7844
 AW8  O21  O   OH1    0  -0.652   2.7429   0.6317  -2.0923
 AW8  C7   C   CR6    0   0.120   1.3793  -0.1305  -0.3510
 AW8  C1   C   CR66   0   0.107   1.8525  -1.4278  -0.0415
 AW8  C23  C   CH2    0  -0.484   2.5609   3.3782  -0.5922
 AW8  C24  C   C      0   0.421   2.7267   3.8704   0.8670
 AW8  O25  O   OC    -1  -0.613   3.5456   4.7980   1.0020
 AW8  O26  O   O      0  -0.588   2.0401   3.3168   1.7388
 AW8  H1   H   HCR6   0   0.279  -5.1446  -2.4592  -0.8507
 AW8  H2   H   HCR6   0   0.261  -2.6978  -2.6453  -0.9132
 AW8  H3   H   HCR6   0   0.278  -4.7903   1.3405   1.1060
 AW8  H4   H   HCR6   0   0.262  -2.3513   1.1669   1.0072
 AW8  H5   H   HCR6   0   0.272   0.5320  -4.4643   0.7926
 AW8  H6   H   HCR6   0   0.283   2.9407  -5.0698   0.8063
 AW8  H7   H   HCR6   0   0.275   3.9948  -1.0728  -0.2704
 AW8  H8   H   HCH3   0   0.269  -1.3252   3.6428  -0.9582
 AW8  H9   H   HCH3   0   0.264   0.0038   4.3704  -0.0548
 AW8  H10  H   HCH3   0   0.260   0.1165   4.2246  -1.8050
 AW8  H11  H   HCH1   0   0.251   3.1874   0.9810  -0.1137
 AW8  H12  H   HOH1   0   0.461   3.6271   0.9850  -2.2379
 AW8  H13  H   HCH2   0   0.264   3.5412   3.1152  -0.9940
 AW8  H14  H   HCH2   0   0.274   2.2131   4.2059  -1.2122

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
 AW8  CL1  C16  single    1.733  0.020  1.733
 AW8  C16  C15  aromatic  1.386  0.020  1.386
 AW8  C16  C14  aromatic  1.386  0.020  1.386
 AW8  C22  C20  single    1.496  0.020  1.496
 AW8  C15  C13  aromatic  1.386  0.020  1.386
 AW8  C14  C12  aromatic  1.385  0.020  1.385
 AW8  C13  C11  aromatic  1.395  0.020  1.395
 AW8  C20  N19  double    1.299  0.020  1.299
 AW8  C20  N18  single    1.344  0.020  1.344
 AW8  N19  C8   single    1.368  0.020  1.368
 AW8  C12  C11  aromatic  1.395  0.020  1.395
 AW8  C11  C10  single    1.481  0.020  1.481
 AW8  C23  N18  single    1.449  0.020  1.449
 AW8  C23  C24  single    1.549  0.020  1.549
 AW8  N18  C17  single    1.443  0.020  1.443
 AW8  C24  O26  deloc     1.240  0.020  1.240
 AW8  C24  O25  deloc     1.245  0.020  1.245
 AW8  C8   C10  aromatic  1.439  0.020  1.439
 AW8  C8   C7   aromatic  1.376  0.020  1.376
 AW8  C10  N9   aromatic  1.303  0.020  1.303
 AW8  C17  C7   single    1.493  0.020  1.493
 AW8  C17  O21  single    1.409  0.020  1.409
 AW8  C7   C1   aromatic  1.415  0.020  1.415
 AW8  N9   C2   aromatic  1.353  0.020  1.353
 AW8  C2   C1   aromatic  1.415  0.020  1.415
 AW8  C2   C4   aromatic  1.411  0.020  1.411
 AW8  C1   C3   aromatic  1.413  0.020  1.413
 AW8  C4   C6   aromatic  1.368  0.020  1.368
 AW8  C3   C5   aromatic  1.364  0.020  1.364
 AW8  C6   C5   aromatic  1.401  0.020  1.401
 AW8  C5   F27  single    1.342  0.020  1.342
 AW8  C14  H1   single    0.930  0.020  1.080
 AW8  C12  H2   single    0.930  0.020  1.080
 AW8  C15  H3   single    0.930  0.020  1.080
 AW8  C13  H4   single    0.930  0.020  1.080
 AW8  C4   H5   single    0.930  0.020  1.080
 AW8  C6   H6   single    0.930  0.020  1.080
 AW8  C3   H7   single    0.930  0.020  1.080
 AW8  C22  H8   single    0.970  0.020  1.090
 AW8  C22  H9   single    0.970  0.020  1.090
 AW8  C22  H10  single    0.970  0.020  1.090
 AW8  C17  H11  single    0.970  0.020  1.090
 AW8  O21  H12  single    0.850  0.020  0.980
 AW8  C23  H13  single    0.970  0.020  1.090
 AW8  C23  H14  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
 AW8  C15  C16  C14  120.98  3.000
 AW8  C14  C16  CL1  119.51  3.000
 AW8  C15  C16  CL1  119.51  3.000
 AW8  H1   C14  C12  120.24  3.000
 AW8  H1   C14  C16  120.77  3.000
 AW8  C12  C14  C16  118.99  3.000
 AW8  H2   C12  C11  119.67  3.000
 AW8  H2   C12  C14  119.01  3.000
 AW8  C11  C12  C14  121.32  3.000
 AW8  H3   C15  C13  120.05  3.000
 AW8  H3   C15  C16  120.57  3.000
 AW8  C13  C15  C16  119.37  3.000
 AW8  H4   C13  C11  120.33  3.000
 AW8  H4   C13  C15  118.76  3.000
 AW8  C11  C13  C15  120.90  3.000
 AW8  C10  C11  C13  122.80  3.000
 AW8  C10  C11  C12  118.72  3.000
 AW8  C13  C11  C12  118.41  3.000
 AW8  C8   C10  N9   122.13  3.000
 AW8  N9   C10  C11  115.76  3.000
 AW8  C8   C10  C11  122.09  3.000
 AW8  C2   N9   C10  120.32  3.000
 AW8  C1   C2   C4   119.64  3.000
 AW8  C4   C2   N9   118.14  3.000
 AW8  C1   C2   N9   122.22  3.000
 AW8  H5   C4   C6   120.65  3.000
 AW8  H5   C4   C2   118.51  3.000
 AW8  C6   C4   C2   120.85  3.000
 AW8  H6   C6   C5   120.19  3.000
 AW8  H6   C6   C4   121.40  3.000
 AW8  C5   C6   C4   118.41  3.000
 AW8  C3   C5   F27  119.17  3.000
 AW8  F27  C5   C6   117.65  3.000
 AW8  C3   C5   C6   123.18  3.000
 AW8  H7   C3   C1   121.62  3.000
 AW8  H7   C3   C5   119.52  3.000
 AW8  C1   C3   C5   118.86  3.000
 AW8  C7   C8   N19  122.97  3.000
 AW8  C7   C8   C10  118.06  3.000
 AW8  N19  C8   C10  118.97  3.000
 AW8  C20  N19  C8   117.84  3.000
 AW8  N18  C20  C22  118.61  3.000
 AW8  N18  C20  N19  124.23  3.000
 AW8  C22  C20  N19  117.16  3.000
 AW8  H10  C22  H9   107.56  3.000
 AW8  H10  C22  H8   108.82  3.000
 AW8  H9   C22  H8   108.28  3.000
 AW8  H10  C22  C20  112.02  3.000
 AW8  H9   C22  C20  111.23  3.000
 AW8  H8   C22  C20  108.85  3.000
 AW8  C23  N18  C17  116.09  3.000
 AW8  C17  N18  C20  121.83  3.000
 AW8  C23  N18  C20  122.01  3.000
 AW8  H11  C17  C7   110.18  3.000
 AW8  H11  C17  O21  109.81  3.000
 AW8  C7   C17  O21  107.36  3.000
 AW8  H11  C17  N18  107.28  3.000
 AW8  O21  C17  N18  111.57  3.000
 AW8  C7   C17  N18  110.65  3.000
 AW8  H12  O21  C17  109.49  3.000
 AW8  C1   C7   C17  120.81  3.000
 AW8  C1   C7   C8   120.24  3.000
 AW8  C17  C7   C8   118.84  3.000
 AW8  C7   C1   C3   123.93  3.000
 AW8  C3   C1   C2   119.06  3.000
 AW8  C7   C1   C2   117.01  3.000
 AW8  H14  C23  H13  105.06  3.000
 AW8  H14  C23  C24  109.17  3.000
 AW8  H13  C23  C24  109.10  3.000
 AW8  H14  C23  N18  110.57  3.000
 AW8  H13  C23  N18  108.73  3.000
 AW8  C24  C23  N18  113.84  3.000
 AW8  O26  C24  O25  128.37  3.000
 AW8  O25  C24  C23  114.17  3.000
 AW8  O26  C24  C23  117.46  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
 AW8  CONST_01  C11  C13  C15  C16    0.00   0.0  0
 AW8  CONST_02  C11  C12  C14  C16    0.00   0.0  0
 AW8  CONST_03  C13  C15  C16  C14    0.00   0.0  0
 AW8  CONST_04  C13  C11  C12  C14    0.00   0.0  0
 AW8  CONST_05  C10  C11  C12  C14  180.00   0.0  0
 AW8  CONST_06  C15  C16  C14  C12    0.00   0.0  0
 AW8  CONST_07  C15  C13  C11  C12    0.00   0.0  0
 AW8  CONST_10  C10  C11  C13  C15  180.00   0.0  0
 AW8  CONST_13  C7   C8   C10  C11  180.00   0.0  0
 AW8  CONST_14  C2   N9   C10  C11  180.00   0.0  0
 AW8  CONST_15  C1   C7   C8   C10    0.00   0.0  0
 AW8  CONST_16  C1   C2   N9   C10    0.00   0.0  0
 AW8  CONST_17  C4   C2   N9   C10  180.00   0.0  0
 AW8  CONST_18  C7   C8   C10  N9     0.00   0.0  0
 AW8  CONST_19  C7   C1   C2   N9     0.00   0.0  0
 AW8  CONST_20  C3   C1   C2   N9   180.00   0.0  0
 AW8  CONST_21  C6   C4   C2   N9   180.00   0.0  0
 AW8  CONST_22  C8   C10  N9   C2     0.00   0.0  0
 AW8  CONST_23  C8   C7   C1   C2     0.00   0.0  0
 AW8  CONST_24  C5   C3   C1   C2     0.00   0.0  0
 AW8  CONST_25  C5   C6   C4   C2     0.00   0.0  0
 AW8  CONST_26  C7   C1   C2   C4   180.00   0.0  0
 AW8  CONST_27  C3   C1   C2   C4     0.00   0.0  0
 AW8  CONST_28  C3   C5   C6   C4     0.00   0.0  0
 AW8  CONST_29  C1   C2   C4   C6     0.00   0.0  0
 AW8  CONST_30  C1   C3   C5   C6     0.00   0.0  0
 AW8  CONST_31  C7   C1   C3   C5   180.00   0.0  0
 AW8  CONST_32  C8   C7   C1   C3   180.00   0.0  0
 AW8  CONST_33  N19  C8   C10  C11    0.00   0.0  0
 AW8  CONST_34  N18  C20  N19  C8     0.00   0.0  0
 AW8  CONST_35  C17  N18  C20  N19    0.00   0.0  0
 AW8  CONST_36  C13  C15  C16  CL1  180.00   0.0  0
 AW8  CONST_37  C12  C14  C16  CL1  180.00   0.0  0
 AW8  CONST_38  F27  C5   C6   C4   180.00   0.0  0
 AW8  CONST_39  C1   C3   C5   F27  180.00   0.0  0
 AW8  CONST_40  C22  C20  N19  C8   180.00   0.0  0
 AW8  CONST_41  C23  N18  C20  N19  180.00   0.0  0
 AW8  CONST_42  C17  N18  C20  C22  180.00   0.0  0
 AW8  CONST_43  H4   C13  C15  C16  180.00   0.0  0
 AW8  CONST_44  H2   C12  C14  C16  180.00   0.0  0
 AW8  CONST_45  H3   C15  C16  C14  180.00   0.0  0
 AW8  CONST_46  H1   C14  C16  C15  180.00   0.0  0
 AW8  CONST_47  H5   C4   C2   N9     0.00   0.0  0
 AW8  CONST_48  H7   C3   C1   C2   180.00   0.0  0
 AW8  CONST_49  H6   C6   C4   C2   180.00   0.0  0
 AW8  CONST_50  C23  N18  C20  C22    0.00   0.0  0
 AW8  Var_01    C24  C23  N18  C20   80.28  30.0  2
 AW8  Var_02    H8   C22  C20  N19   -4.14  30.0  3
 AW8  Var_03    O26  C24  C23  N18   -4.76  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
 AW8  chir_01  C17  N18  C7  O21  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
 AW8  plan-1  CL1  0.020
 AW8  plan-1  C16  0.020
 AW8  plan-1  C14  0.020
 AW8  plan-1  C12  0.020
 AW8  plan-1  C15  0.020
 AW8  plan-1  C13  0.020
 AW8  plan-1  C11  0.020
 AW8  plan-1  C10  0.020
 AW8  plan-1  H1   0.020
 AW8  plan-1  H2   0.020
 AW8  plan-1  H3   0.020
 AW8  plan-1  H4   0.020
 AW8  plan-2  C11  0.020
 AW8  plan-2  C10  0.020
 AW8  plan-2  N9   0.020
 AW8  plan-2  C2   0.020
 AW8  plan-2  C4   0.020
 AW8  plan-2  C6   0.020
 AW8  plan-2  C5   0.020
 AW8  plan-2  F27  0.020
 AW8  plan-2  C3   0.020
 AW8  plan-2  C8   0.020
 AW8  plan-2  N19  0.020
 AW8  plan-2  C20  0.020
 AW8  plan-2  C22  0.020
 AW8  plan-2  N18  0.020
 AW8  plan-2  C17  0.020
 AW8  plan-2  C7   0.020
 AW8  plan-2  C1   0.020
 AW8  plan-2  C23  0.020
 AW8  plan-2  H5   0.020
 AW8  plan-2  H6   0.020
 AW8  plan-2  H7   0.020
 AW8  plan-3  C23  0.020
 AW8  plan-3  C24  0.020
 AW8  plan-3  O25  0.020
 AW8  plan-3  O26  0.020

