# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 02:02:06 2020
#   Inital geometry file: a 112 line input string
#   Ligand name: 2-[5-(4-chlorophenyl)-3-methyl-1-oxidanylidene-pyrimido[4,5-c]quinolin-2-yl]ethanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=Nc2c(nc3ccccc3c2C(=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
 AV5  AV5  '2-[5-(4-chlorophenyl)-3-methyl-1-oxidanylidene-pyrimido[4,5-c]quinolin-2-yl]ethanoic acid'  ligand  41  27  .  2022-03-11  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_AV5
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
 AV5  CL1  CL  CL    0  -0.125  -6.5294   1.2860   0.1595
 AV5  C16  C   CR6   0  -0.049  -4.9127   0.6656   0.1157
 AV5  C14  C   CR16  0  -0.201  -3.9064   1.3362   0.7936
 AV5  C12  C   CR16  0  -0.276  -2.6118   0.8442   0.7452
 AV5  C15  C   CR16  0  -0.200  -4.6466  -0.4943  -0.5946
 AV5  C13  C   CR16  0  -0.293  -3.3510  -0.9845  -0.6197
 AV5  C11  C   CR6   0   0.086  -2.3167  -0.3204   0.0378
 AV5  C10  C   CR6   0   0.118  -0.9616  -0.9147   0.0159
 AV5  N9   N   N     0  -0.436  -0.8897  -2.2003   0.1632
 AV5  C2   C   CR66  0   0.157   0.3123  -2.8325   0.1607
 AV5  C4   C   CR16  0  -0.292   0.2953  -4.2321   0.3171
 AV5  C6   C   CR16  0  -0.263   1.4661  -4.9426   0.3369
 AV5  C5   C   CR16  0  -0.232   2.6890  -4.2672   0.2046
 AV5  C3   C   CR16  0  -0.352   2.7337  -2.9028   0.0518
 AV5  C1   C   CR66  0   0.094   1.5429  -2.1441   0.0214
 AV5  C8   C   CR66  0   0.169   0.2166  -0.1124  -0.1928
 AV5  N19  N   N     0  -0.471   0.0426   1.2139  -0.4304
 AV5  C20  C   CR6   0   0.488   1.0711   1.9573  -0.6463
 AV5  C22  C   CH3   0  -0.781   0.8569   3.4084  -0.9184
 AV5  C7   C   CR66  0   0.013   1.4576  -0.7276  -0.1674
 AV5  C17  C   CR6   0   0.593   2.6250   0.1278  -0.3397
 AV5  O21  O   O     0  -0.452   3.7870  -0.2229  -0.2471
 AV5  N18  N   NR6   0  -0.542   2.3426   1.4571  -0.6414
 AV5  C23  C   CH2   0  -0.471   3.5014   2.3010  -0.8433
 AV5  C24  C   C     0   0.554   4.1465   2.6444   0.4818
 AV5  O26  O   OH1   0  -0.582   5.3525   3.1510   0.3030
 AV5  O25  O   O     0  -0.427   3.6073   2.5024   1.5464
 AV5  H1   H   HCR6  0   0.281  -4.1241   2.2338   1.3559
 AV5  H2   H   HCR6  0   0.265  -1.8366   1.3713   1.2817
 AV5  H3   H   HCR6  0   0.282  -5.4353  -1.0113  -1.1238
 AV5  H4   H   HCR6  0   0.265  -3.1426  -1.8929  -1.1691
 AV5  H5   H   HCR6  0   0.266  -0.6634  -4.7235   0.4214
 AV5  H6   H   HCR6  0   0.266   1.4511  -6.0178   0.4546
 AV5  H7   H   HCR6  0   0.266   3.6137  -4.8289   0.2230
 AV5  H8   H   HCR6  0   0.274   3.6890  -2.4163  -0.0496
 AV5  H9   H   HCH3  0   0.290  -0.2052   3.6193  -0.8410
 AV5  H10  H   HCH3  0   0.273   1.3887   4.0391  -0.2053
 AV5  H11  H   HCH3  0   0.282   1.1905   3.6833  -1.9200
 AV5  H12  H   HCH2  0   0.329   4.2139   1.8050  -1.5001
 AV5  H13  H   HCH2  0   0.344   3.2130   3.2233  -1.3439
 AV5  H14  H   HOH1  0   0.490   5.7430   3.4047   1.1533

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
 AV5  CL1  C16  single    1.732  0.020  1.732
 AV5  C15  C16  aromatic  1.386  0.020  1.386
 AV5  C15  C13  aromatic  1.385  0.020  1.385
 AV5  C16  C14  aromatic  1.386  0.020  1.386
 AV5  C22  C20  single    1.492  0.020  1.492
 AV5  C13  C11  aromatic  1.394  0.020  1.394
 AV5  C14  C12  aromatic  1.386  0.020  1.386
 AV5  C20  N19  double    1.287  0.020  1.287
 AV5  C20  N18  single    1.366  0.020  1.366
 AV5  N19  C8   single    1.359  0.020  1.359
 AV5  C11  C12  aromatic  1.394  0.020  1.394
 AV5  C11  C10  single    1.480  0.020  1.480
 AV5  C23  N18  single    1.448  0.020  1.448
 AV5  C23  C24  single    1.513  0.020  1.513
 AV5  N18  C17  single    1.392  0.020  1.392
 AV5  C8   C10  aromatic  1.441  0.020  1.441
 AV5  C8   C7   aromatic  1.385  0.020  1.385
 AV5  C24  O25  double    1.202  0.020  1.202
 AV5  C24  O26  single    1.320  0.020  1.320
 AV5  C10  N9   aromatic  1.296  0.020  1.296
 AV5  C17  C7   single    1.458  0.020  1.458
 AV5  C17  O21  double    1.217  0.020  1.217
 AV5  C7   C1   aromatic  1.432  0.020  1.432
 AV5  N9   C2   aromatic  1.358  0.020  1.358
 AV5  C2   C1   aromatic  1.417  0.020  1.417
 AV5  C2   C4   aromatic  1.408  0.020  1.408
 AV5  C1   C3   aromatic  1.412  0.020  1.412
 AV5  C4   C6   aromatic  1.370  0.020  1.370
 AV5  C3   C5   aromatic  1.374  0.020  1.374
 AV5  C6   C5   aromatic  1.403  0.020  1.403
 AV5  C14  H1   single    0.930  0.020  1.080
 AV5  C12  H2   single    0.930  0.020  1.080
 AV5  C15  H3   single    0.930  0.020  1.080
 AV5  C13  H4   single    0.930  0.020  1.080
 AV5  C4   H5   single    0.930  0.020  1.080
 AV5  C6   H6   single    0.930  0.020  1.080
 AV5  C5   H7   single    0.930  0.020  1.080
 AV5  C3   H8   single    0.930  0.020  1.080
 AV5  C22  H9   single    0.970  0.020  1.090
 AV5  C22  H10  single    0.970  0.020  1.090
 AV5  C22  H11  single    0.970  0.020  1.090
 AV5  C23  H12  single    0.970  0.020  1.090
 AV5  C23  H13  single    0.970  0.020  1.090
 AV5  O26  H14  single    0.850  0.020  0.980

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
 AV5  C15  C16  C14  121.07  3.000
 AV5  C14  C16  CL1  119.46  3.000
 AV5  C15  C16  CL1  119.47  3.000
 AV5  H1   C14  C12  120.06  3.000
 AV5  H1   C14  C16  120.64  3.000
 AV5  C12  C14  C16  119.30  3.000
 AV5  H2   C12  C11  120.51  3.000
 AV5  H2   C12  C14  118.68  3.000
 AV5  C11  C12  C14  120.79  3.000
 AV5  H3   C15  C13  120.26  3.000
 AV5  H3   C15  C16  120.73  3.000
 AV5  C13  C15  C16  119.01  3.000
 AV5  H4   C13  C11  119.78  3.000
 AV5  H4   C13  C15  119.10  3.000
 AV5  C11  C13  C15  121.12  3.000
 AV5  C10  C11  C13  118.76  3.000
 AV5  C10  C11  C12  122.46  3.000
 AV5  C13  C11  C12  118.70  3.000
 AV5  C8   C10  N9   121.57  3.000
 AV5  N9   C10  C11  116.58  3.000
 AV5  C8   C10  C11  121.83  3.000
 AV5  C2   N9   C10  120.70  3.000
 AV5  C1   C2   C4   120.28  3.000
 AV5  C4   C2   N9   116.85  3.000
 AV5  C1   C2   N9   122.87  3.000
 AV5  H5   C4   C6   121.35  3.000
 AV5  H5   C4   C2   118.20  3.000
 AV5  C6   C4   C2   120.45  3.000
 AV5  H6   C6   C5   120.04  3.000
 AV5  H6   C6   C4   120.35  3.000
 AV5  C5   C6   C4   119.60  3.000
 AV5  H7   C5   C3   119.32  3.000
 AV5  H7   C5   C6   119.56  3.000
 AV5  C3   C5   C6   121.12  3.000
 AV5  H8   C3   C1   120.22  3.000
 AV5  H8   C3   C5   119.21  3.000
 AV5  C1   C3   C5   120.57  3.000
 AV5  C7   C1   C3   125.78  3.000
 AV5  C3   C1   C2   117.98  3.000
 AV5  C7   C1   C2   116.23  3.000
 AV5  C7   C8   N19  123.47  3.000
 AV5  C7   C8   C10  118.86  3.000
 AV5  N19  C8   C10  117.66  3.000
 AV5  C20  N19  C8   119.39  3.000
 AV5  N18  C20  C22  119.36  3.000
 AV5  N18  C20  N19  122.11  3.000
 AV5  C22  C20  N19  118.53  3.000
 AV5  H11  C22  H10  107.79  3.000
 AV5  H11  C22  H9   108.40  3.000
 AV5  H10  C22  H9   108.55  3.000
 AV5  H11  C22  C20  111.63  3.000
 AV5  H10  C22  C20  111.92  3.000
 AV5  H9   C22  C20  108.45  3.000
 AV5  C17  C7   C8   117.05  3.000
 AV5  C17  C7   C1   123.27  3.000
 AV5  C8   C7   C1   119.68  3.000
 AV5  N18  C17  O21  119.03  3.000
 AV5  O21  C17  C7   125.91  3.000
 AV5  N18  C17  C7   115.06  3.000
 AV5  C23  N18  C17  115.12  3.000
 AV5  C17  N18  C20  122.63  3.000
 AV5  C23  N18  C20  122.07  3.000
 AV5  H13  C23  H12  106.38  3.000
 AV5  H13  C23  C24  108.87  3.000
 AV5  H12  C23  C24  110.65  3.000
 AV5  H13  C23  N18  110.25  3.000
 AV5  H12  C23  N18  110.02  3.000
 AV5  C24  C23  N18  110.57  3.000
 AV5  O25  C24  O26  125.11  3.000
 AV5  O26  C24  C23  110.97  3.000
 AV5  O25  C24  C23  123.89  3.000
 AV5  H14  O26  C24  110.47  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
 AV5  CONST_01  C11  C13  C15  C16    0.00   0.0  0
 AV5  CONST_02  C11  C12  C14  C16    0.00   0.0  0
 AV5  CONST_03  C13  C15  C16  C14    0.00   0.0  0
 AV5  CONST_04  C13  C11  C12  C14    0.00   0.0  0
 AV5  CONST_05  C10  C11  C12  C14  180.00   0.0  0
 AV5  CONST_06  C15  C16  C14  C12    0.00   0.0  0
 AV5  CONST_07  C15  C13  C11  C12    0.00   0.0  0
 AV5  CONST_10  C10  C11  C13  C15  180.00   0.0  0
 AV5  CONST_13  C7   C8   C10  C11  180.00   0.0  0
 AV5  CONST_14  C2   N9   C10  C11  180.00   0.0  0
 AV5  CONST_15  C1   C7   C8   C10    0.00   0.0  0
 AV5  CONST_16  C1   C2   N9   C10    0.00   0.0  0
 AV5  CONST_17  C4   C2   N9   C10  180.00   0.0  0
 AV5  CONST_18  C7   C8   C10  N9     0.00   0.0  0
 AV5  CONST_19  C7   C1   C2   N9     0.00   0.0  0
 AV5  CONST_20  C3   C1   C2   N9   180.00   0.0  0
 AV5  CONST_21  C6   C4   C2   N9   180.00   0.0  0
 AV5  CONST_22  C8   C10  N9   C2     0.00   0.0  0
 AV5  CONST_23  C8   C7   C1   C2     0.00   0.0  0
 AV5  CONST_24  C5   C3   C1   C2     0.00   0.0  0
 AV5  CONST_25  C5   C6   C4   C2     0.00   0.0  0
 AV5  CONST_26  C7   C1   C2   C4   180.00   0.0  0
 AV5  CONST_27  C3   C1   C2   C4     0.00   0.0  0
 AV5  CONST_28  C3   C5   C6   C4     0.00   0.0  0
 AV5  CONST_29  C1   C2   C4   C6     0.00   0.0  0
 AV5  CONST_30  C1   C3   C5   C6     0.00   0.0  0
 AV5  CONST_31  C7   C1   C3   C5   180.00   0.0  0
 AV5  CONST_32  C8   C7   C1   C3   180.00   0.0  0
 AV5  CONST_33  N19  C8   C10  C11    0.00   0.0  0
 AV5  CONST_34  N18  C20  N19  C8     0.00   0.0  0
 AV5  CONST_35  C17  N18  C20  N19    0.00   0.0  0
 AV5  CONST_36  C7   C17  N18  C20    0.00   0.0  0
 AV5  CONST_37  C13  C15  C16  CL1  180.00   0.0  0
 AV5  CONST_38  C12  C14  C16  CL1  180.00   0.0  0
 AV5  CONST_39  C22  C20  N19  C8   180.00   0.0  0
 AV5  CONST_40  C23  N18  C20  N19  180.00   0.0  0
 AV5  CONST_41  O21  C17  N18  C20  180.00   0.0  0
 AV5  CONST_42  C17  N18  C20  C22  180.00   0.0  0
 AV5  CONST_43  C23  N18  C17  C7   180.00   0.0  0
 AV5  CONST_44  H4   C13  C15  C16  180.00   0.0  0
 AV5  CONST_45  H2   C12  C14  C16  180.00   0.0  0
 AV5  CONST_46  H3   C15  C16  C14  180.00   0.0  0
 AV5  CONST_47  H1   C14  C16  C15  180.00   0.0  0
 AV5  CONST_48  H5   C4   C2   N9     0.00   0.0  0
 AV5  CONST_49  H8   C3   C1   C2   180.00   0.0  0
 AV5  CONST_50  H6   C6   C4   C2   180.00   0.0  0
 AV5  CONST_51  H7   C5   C6   C4   180.00   0.0  0
 AV5  CONST_52  C23  N18  C20  C22    0.00   0.0  0
 AV5  CONST_53  C23  N18  C17  O21    0.00   0.0  0
 AV5  CONST_54  H14  O26  C24  C23  180.00   0.0  0
 AV5  Var_01    C24  C23  N18  C20   99.44  30.0  2
 AV5  Var_02    H9   C22  C20  N19    2.60  30.0  3
 AV5  Var_03    O25  C24  C23  N18  -15.88  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
 AV5  plan-1  CL1  0.020
 AV5  plan-1  C16  0.020
 AV5  plan-1  C14  0.020
 AV5  plan-1  C12  0.020
 AV5  plan-1  C15  0.020
 AV5  plan-1  C13  0.020
 AV5  plan-1  C11  0.020
 AV5  plan-1  C10  0.020
 AV5  plan-1  H1   0.020
 AV5  plan-1  H2   0.020
 AV5  plan-1  H3   0.020
 AV5  plan-1  H4   0.020
 AV5  plan-2  C11  0.020
 AV5  plan-2  C10  0.020
 AV5  plan-2  N9   0.020
 AV5  plan-2  C2   0.020
 AV5  plan-2  C4   0.020
 AV5  plan-2  C6   0.020
 AV5  plan-2  C5   0.020
 AV5  plan-2  C3   0.020
 AV5  plan-2  C1   0.020
 AV5  plan-2  C8   0.020
 AV5  plan-2  N19  0.020
 AV5  plan-2  C20  0.020
 AV5  plan-2  C22  0.020
 AV5  plan-2  C7   0.020
 AV5  plan-2  C17  0.020
 AV5  plan-2  O21  0.020
 AV5  plan-2  N18  0.020
 AV5  plan-2  C23  0.020
 AV5  plan-2  H5   0.020
 AV5  plan-2  H6   0.020
 AV5  plan-2  H7   0.020
 AV5  plan-2  H8   0.020
 AV5  plan-3  C23  0.020
 AV5  plan-3  C24  0.020
 AV5  plan-3  O26  0.020
 AV5  plan-3  O25  0.020
 AV5  plan-3  H14  0.020

