# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 03:35:28 2020
#   Inital geometry file: a 133 line input string
#   Ligand name: N-[5-({[(3-fluorophenyl)carbamoyl]amino}methyl)-2-methylphenyl]imidazo[1,2-a]pyridine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(CNC(=O)Nc2cccc(F)c2)cc1NC(=O)c3cnc4ccccn34
#
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
 4VD  4VD  N-[5-({[(3-fluorophenyl)carbamoyl]amino}methyl)-2-methylphenyl]imidazo[1,2-a]pyridine-3-carboxamide  ligand  51  31  .  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_4VD
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
 4VD  C1   C  CH3   0  -0.758   3.5884   3.2769  -0.5852
 4VD  C2   C  CR6   0   0.067   2.1243   3.2922  -0.2613
 4VD  C3   C  CR16  0  -0.303   1.3939   4.4726  -0.3169
 4VD  C5   C  CR6   0   0.103  -0.6324   3.3332   0.3144
 4VD  C6   C  CH2   0  -0.377  -2.1101   3.3532   0.6253
 4VD  C8   C  C     0   0.759  -3.2563   1.2013   0.3127
 4VD  O9   O  O     0  -0.521  -3.0778   0.8449   1.4683
 4VD  C11  C  CR6   0   0.397  -4.3832  -0.8650  -0.4958
 4VD  C12  C  CR16  0  -0.365  -4.8023  -1.5063  -1.6686
 4VD  C13  C  CR16  0  -0.231  -5.3302  -2.7832  -1.6237
 4VD  C14  C  CR16  0  -0.437  -5.4578  -3.4663  -0.4207
 4VD  C15  C  CR6   0   0.553  -5.0380  -2.8119   0.7183
 4VD  C19  C  CR6   0   0.311   1.4455   2.1205   0.0989
 4VD  C21  C  C     0   0.508   1.7724  -0.2843  -0.3050
 4VD  C23  C  CR5   0   0.130   2.6984  -1.4110  -0.1307
 4VD  C24  C  CR15  0  -0.181   2.3455  -2.7241   0.0941
 4VD  C26  C  CR56  0   0.538   4.4674  -2.7157   0.1426
 4VD  C27  C  CR16  0  -0.397   5.8393  -3.0222   0.2070
 4VD  C28  C  CR16  0  -0.145   6.7538  -2.0331  -0.0042
 4VD  C4   C  CR16  0  -0.303   0.0324   4.4963  -0.0469
 4VD  N7   N  NH1   0  -0.669  -2.8721   2.4116  -0.1596
 4VD  N10  N  NH1   0  -0.791  -3.8810   0.4227  -0.6323
 4VD  F16  F  F     0  -0.320  -5.1505  -3.4411   1.9011
 4VD  C17  C  CR16  0  -0.492  -4.5076  -1.5358   0.7224
 4VD  C18  C  CR16  0  -0.309   0.0896   2.1472   0.3963
 4VD  N20  N  NH1   0  -0.763   2.1817   0.9170   0.1815
 4VD  O22  O  O     0  -0.454   0.6873  -0.4657  -0.8296
 4VD  N25  N  N     0  -0.466   3.4160  -3.5122   0.2737
 4VD  C29  C  CR16  0  -0.389   6.3197  -0.7195  -0.3031
 4VD  C30  C  CR16  0   0.023   4.9959  -0.4293  -0.3585
 4VD  N31  N  N     0  -0.570   4.0798  -1.4101  -0.1067
 4VD  H34  H  HCH3  0   0.247   4.1975   2.9751   0.2705
 4VD  H33  H  HCH3  0   0.254   3.8101   2.5881  -1.4029
 4VD  H32  H  HCH3  0   0.268   3.9297   4.2652  -0.8873
 4VD  H35  H  HCR6  0   0.253   1.8969   5.3901  -0.5970
 4VD  H38  H  HCH2  0   0.269  -2.2773   3.1333   1.6793
 4VD  H37  H  HCH2  0   0.269  -2.5043   4.3548   0.4469
 4VD  H41  H  HCR6  0   0.272  -4.7071  -0.9986  -2.6209
 4VD  H42  H  HCR6  0   0.270  -5.6447  -3.2579  -2.5434
 4VD  H43  H  HCR6  0   0.275  -5.8680  -4.4658  -0.3738
 4VD  H47  H  HCR5  0   0.276   1.3377  -3.1071   0.1573
 4VD  H48  H  HCR6  0   0.287   6.1307  -4.0415   0.4172
 4VD  H49  H  HCR6  0   0.281   7.8120  -2.2492   0.0403
 4VD  H36  H  HCR6  0   0.253  -0.5130   5.4300  -0.1192
 4VD  H39  H  HNH1  0   0.401  -2.9653   2.6152  -1.1418
 4VD  H40  H  HNH1  0   0.412  -3.9331   0.7930  -1.5691
 4VD  H44  H  HCR6  0   0.297  -4.2071  -1.0863   1.6544
 4VD  H45  H  HCR6  0   0.260  -0.4037   1.2398   0.7141
 4VD  H46  H  HNH1  0   0.415   3.0223   0.9429   0.7395
 4VD  H50  H  HCR6  0   0.288   7.0329   0.0664  -0.5025
 4VD  H51  H  HCR6  0   0.307   4.6245   0.5470  -0.6262

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
 4VD  F16  C15  single    1.344  0.020  1.344
 4VD  C15  C14  aromatic  1.379  0.020  1.379
 4VD  C15  C17  aromatic  1.382  0.020  1.382
 4VD  C14  C13  aromatic  1.389  0.020  1.389
 4VD  C17  C11  aromatic  1.396  0.020  1.396
 4VD  C13  C12  aromatic  1.383  0.020  1.383
 4VD  N25  C24  aromatic  1.341  0.020  1.341
 4VD  N25  C26  aromatic  1.326  0.020  1.326
 4VD  C11  C12  aromatic  1.401  0.020  1.401
 4VD  C11  N10  single    1.389  0.020  1.389
 4VD  C24  C23  aromatic  1.378  0.020  1.378
 4VD  O9   C8   double    1.222  0.020  1.222
 4VD  C26  C27  aromatic  1.407  0.020  1.407
 4VD  C26  N31  aromatic  1.385  0.020  1.385
 4VD  C27  C28  aromatic  1.364  0.020  1.364
 4VD  N10  C8   single    1.375  0.020  1.375
 4VD  C8   N7   single    1.355  0.020  1.355
 4VD  C23  N31  aromatic  1.382  0.020  1.382
 4VD  C23  C21  single    1.469  0.020  1.469
 4VD  N31  C30  aromatic  1.366  0.020  1.366
 4VD  N20  C21  single    1.359  0.020  1.359
 4VD  N20  C19  single    1.413  0.020  1.413
 4VD  C28  C29  aromatic  1.415  0.020  1.415
 4VD  C21  O22  double    1.219  0.020  1.219
 4VD  N7   C6   single    1.443  0.020  1.443
 4VD  C19  C18  aromatic  1.388  0.020  1.388
 4VD  C19  C2   aromatic  1.401  0.020  1.401
 4VD  C18  C5   aromatic  1.391  0.020  1.391
 4VD  C30  C29  aromatic  1.356  0.020  1.356
 4VD  C6   C5   single    1.510  0.020  1.510
 4VD  C5   C4   aromatic  1.388  0.020  1.388
 4VD  C2   C1   single    1.500  0.020  1.500
 4VD  C2   C3   aromatic  1.389  0.020  1.389
 4VD  C4   C3   aromatic  1.388  0.020  1.388
 4VD  C1   H34  single    0.970  0.020  1.090
 4VD  C1   H33  single    0.970  0.020  1.090
 4VD  C1   H32  single    0.970  0.020  1.090
 4VD  C3   H35  single    0.930  0.020  1.080
 4VD  C6   H38  single    0.970  0.020  1.090
 4VD  C6   H37  single    0.970  0.020  1.090
 4VD  C12  H41  single    0.930  0.020  1.080
 4VD  C13  H42  single    0.930  0.020  1.080
 4VD  C14  H43  single    0.930  0.020  1.080
 4VD  C24  H47  single    0.930  0.020  1.080
 4VD  C27  H48  single    0.930  0.020  1.080
 4VD  C28  H49  single    0.930  0.020  1.080
 4VD  C4   H36  single    0.930  0.020  1.080
 4VD  N7   H39  single    0.860  0.020  1.020
 4VD  N10  H40  single    0.860  0.020  1.020
 4VD  C17  H44  single    0.930  0.020  1.080
 4VD  C18  H45  single    0.930  0.020  1.080
 4VD  N20  H46  single    0.860  0.020  1.020
 4VD  C29  H50  single    0.930  0.020  1.080
 4VD  C30  H51  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
 4VD  H32  C1   H33  107.54  3.000
 4VD  H32  C1   H34  107.05  3.000
 4VD  H33  C1   H34  107.40  3.000
 4VD  H32  C1   C2   110.91  3.000
 4VD  H33  C1   C2   111.50  3.000
 4VD  H34  C1   C2   112.20  3.000
 4VD  C19  C2   C3   117.78  3.000
 4VD  C3   C2   C1   120.89  3.000
 4VD  C19  C2   C1   121.33  3.000
 4VD  H35  C3   C4   119.42  3.000
 4VD  H35  C3   C2   119.08  3.000
 4VD  C4   C3   C2   121.49  3.000
 4VD  C18  C5   C4   118.77  3.000
 4VD  C4   C5   C6   120.75  3.000
 4VD  C18  C5   C6   120.47  3.000
 4VD  H37  C6   H38  106.74  3.000
 4VD  H37  C6   N7   108.62  3.000
 4VD  H38  C6   N7   108.26  3.000
 4VD  H37  C6   C5   109.39  3.000
 4VD  H38  C6   C5   110.28  3.000
 4VD  N7   C6   C5   113.33  3.000
 4VD  N10  C8   N7   113.28  3.000
 4VD  N7   C8   O9   123.27  3.000
 4VD  N10  C8   O9   123.44  3.000
 4VD  C17  C11  N10  124.29  3.000
 4VD  N10  C11  C12  116.76  3.000
 4VD  C17  C11  C12  118.94  3.000
 4VD  H41  C12  C13  119.67  3.000
 4VD  H41  C12  C11  119.67  3.000
 4VD  C13  C12  C11  120.65  3.000
 4VD  H42  C13  C14  119.59  3.000
 4VD  H42  C13  C12  119.25  3.000
 4VD  C14  C13  C12  121.16  3.000
 4VD  H43  C14  C15  121.21  3.000
 4VD  H43  C14  C13  121.79  3.000
 4VD  C15  C14  C13  116.99  3.000
 4VD  C17  C15  F16  117.49  3.000
 4VD  C17  C15  C14  123.88  3.000
 4VD  F16  C15  C14  118.63  3.000
 4VD  N20  C19  C18  120.84  3.000
 4VD  C18  C19  C2   120.80  3.000
 4VD  N20  C19  C2   118.35  3.000
 4VD  O22  C21  N20  123.62  3.000
 4VD  O22  C21  C23  119.88  3.000
 4VD  N20  C21  C23  116.47  3.000
 4VD  N31  C23  C24  104.71  3.000
 4VD  N31  C23  C21  129.19  3.000
 4VD  C24  C23  C21  126.07  3.000
 4VD  H47  C24  N25  121.91  3.000
 4VD  H47  C24  C23  125.90  3.000
 4VD  N25  C24  C23  112.17  3.000
 4VD  N31  C26  N25  111.25  3.000
 4VD  N31  C26  C27  119.12  3.000
 4VD  N25  C26  C27  129.63  3.000
 4VD  H48  C27  C28  122.23  3.000
 4VD  H48  C27  C26  118.51  3.000
 4VD  C28  C27  C26  119.26  3.000
 4VD  H49  C28  C29  119.63  3.000
 4VD  H49  C28  C27  120.35  3.000
 4VD  C29  C28  C27  120.01  3.000
 4VD  H36  C4   C5   119.89  3.000
 4VD  H36  C4   C3   119.69  3.000
 4VD  C5   C4   C3   120.42  3.000
 4VD  H39  N7   C8   119.61  3.000
 4VD  H39  N7   C6   116.57  3.000
 4VD  C8   N7   C6   122.89  3.000
 4VD  H40  N10  C11  114.40  3.000
 4VD  H40  N10  C8   117.00  3.000
 4VD  C11  N10  C8   128.46  3.000
 4VD  H44  C17  C15  119.66  3.000
 4VD  H44  C17  C11  121.96  3.000
 4VD  C15  C17  C11  118.37  3.000
 4VD  H45  C18  C19  119.52  3.000
 4VD  H45  C18  C5   119.76  3.000
 4VD  C19  C18  C5   120.71  3.000
 4VD  H46  N20  C21  118.12  3.000
 4VD  H46  N20  C19  116.38  3.000
 4VD  C21  N20  C19  125.09  3.000
 4VD  C26  N25  C24  105.47  3.000
 4VD  H50  C29  C30  118.77  3.000
 4VD  H50  C29  C28  120.78  3.000
 4VD  C30  C29  C28  120.44  3.000
 4VD  H51  C30  N31  117.71  3.000
 4VD  H51  C30  C29  122.68  3.000
 4VD  N31  C30  C29  119.57  3.000
 4VD  C30  N31  C26  121.51  3.000
 4VD  C30  N31  C23  131.92  3.000
 4VD  C26  N31  C23  106.40  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
 4VD  CONST_01  C5   C18  C19  C2     0.00   0.0  0
 4VD  CONST_02  C5   C4   C3   C2     0.00   0.0  0
 4VD  CONST_03  C18  C19  C2   C3     0.00   0.0  0
 4VD  CONST_04  C18  C5   C4   C3     0.00   0.0  0
 4VD  CONST_05  C14  C15  C17  C11    0.00   0.0  0
 4VD  CONST_06  C14  C13  C12  C11    0.00   0.0  0
 4VD  CONST_07  C15  C14  C13  C12    0.00   0.0  0
 4VD  CONST_08  C15  C17  C11  C12    0.00   0.0  0
 4VD  CONST_09  C17  C15  C14  C13    0.00   0.0  0
 4VD  CONST_10  C17  C11  C12  C13    0.00   0.0  0
 4VD  CONST_11  C4   C5   C18  C19    0.00   0.0  0
 4VD  CONST_12  C4   C3   C2   C19    0.00   0.0  0
 4VD  CONST_13  C26  N25  C24  C23    0.00   0.0  0
 4VD  CONST_14  N25  C26  N31  C23    0.00   0.0  0
 4VD  CONST_15  C27  C26  N31  C23  180.00   0.0  0
 4VD  CONST_16  C29  C30  N31  C23  180.00   0.0  0
 4VD  CONST_17  C27  C26  N25  C24  180.00   0.0  0
 4VD  CONST_18  N31  C26  N25  C24    0.00   0.0  0
 4VD  CONST_19  C26  N31  C23  C24    0.00   0.0  0
 4VD  CONST_20  C30  N31  C23  C24  180.00   0.0  0
 4VD  CONST_21  C29  C28  C27  C26    0.00   0.0  0
 4VD  CONST_22  C29  C30  N31  C26    0.00   0.0  0
 4VD  CONST_23  C30  N31  C26  C27    0.00   0.0  0
 4VD  CONST_24  C30  C29  C28  C27    0.00   0.0  0
 4VD  CONST_25  N25  C26  C27  C28  180.00   0.0  0
 4VD  CONST_26  N31  C26  C27  C28    0.00   0.0  0
 4VD  CONST_27  N31  C30  C29  C28    0.00   0.0  0
 4VD  CONST_28  N31  C23  C24  N25    0.00   0.0  0
 4VD  CONST_29  C30  N31  C26  N25  180.00   0.0  0
 4VD  CONST_30  C18  C19  C2   C1   180.00   0.0  0
 4VD  CONST_31  C4   C3   C2   C1   180.00   0.0  0
 4VD  CONST_32  N20  C19  C2   C3   180.00   0.0  0
 4VD  CONST_33  C6   C5   C4   C3   180.00   0.0  0
 4VD  CONST_34  N20  C19  C18  C5   180.00   0.0  0
 4VD  CONST_35  C19  C18  C5   C6   180.00   0.0  0
 4VD  CONST_36  F16  C15  C17  C11  180.00   0.0  0
 4VD  CONST_37  F16  C15  C14  C13  180.00   0.0  0
 4VD  CONST_38  N10  C11  C12  C13  180.00   0.0  0
 4VD  CONST_39  N10  C11  C17  C15  180.00   0.0  0
 4VD  CONST_40  N25  C24  C23  C21  180.00   0.0  0
 4VD  CONST_41  C26  N31  C23  C21  180.00   0.0  0
 4VD  CONST_42  C30  N31  C23  C21    0.00   0.0  0
 4VD  CONST_43  H45  C18  C19  C2   180.00   0.0  0
 4VD  CONST_44  H36  C4   C3   C2   180.00   0.0  0
 4VD  CONST_45  H35  C3   C4   C5   180.00   0.0  0
 4VD  CONST_46  H42  C13  C12  C11  180.00   0.0  0
 4VD  CONST_47  H43  C14  C13  C12  180.00   0.0  0
 4VD  CONST_48  H44  C17  C11  C12  180.00   0.0  0
 4VD  CONST_49  H41  C12  C13  C14  180.00   0.0  0
 4VD  CONST_50  H51  C30  N31  C23    0.00   0.0  0
 4VD  CONST_51  H47  C24  N25  C26  180.00   0.0  0
 4VD  CONST_52  H49  C28  C27  C26  180.00   0.0  0
 4VD  CONST_53  H50  C29  C28  C27  180.00   0.0  0
 4VD  CONST_54  H48  C27  C26  N25    0.00   0.0  0
 4VD  CONST_55  C23  C21  N20  C19  180.00   0.0  0
 4VD  CONST_57  C17  C11  N10  C8     0.00   0.0  0
 4VD  CONST_58  C12  C11  N10  C8   180.00   0.0  0
 4VD  CONST_61  H40  N10  C11  C12    0.00   0.0  0
 4VD  CONST_62  C11  N10  C8   O9     0.00   0.0  0
 4VD  CONST_63  O22  C21  N20  C19    0.00   0.0  0
 4VD  CONST_64  N7   C8   N10  C11  180.00   0.0  0
 4VD  CONST_65  O9   C8   N7   C6     0.00   0.0  0
 4VD  CONST_66  N10  C8   N7   C6   180.00   0.0  0
 4VD  CONST_67  H39  N7   C8   O9   180.00   0.0  0
 4VD  Var_01    N20  C21  C23  C24  145.80  30.0  2
 4VD  Var_02    N7   C6   C5   C4   125.27  30.0  2
 4VD  Var_03    H34  C1   C2   C3   117.35  30.0  2
 4VD  Var_04    C8   N7   C6   C5    99.13  30.0  1

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
 4VD  plan-1  C11  0.020
 4VD  plan-1  C12  0.020
 4VD  plan-1  C13  0.020
 4VD  plan-1  C14  0.020
 4VD  plan-1  C15  0.020
 4VD  plan-1  N10  0.020
 4VD  plan-1  F16  0.020
 4VD  plan-1  C17  0.020
 4VD  plan-1  H41  0.020
 4VD  plan-1  H42  0.020
 4VD  plan-1  H43  0.020
 4VD  plan-1  H44  0.020
 4VD  plan-2  C1   0.020
 4VD  plan-2  C2   0.020
 4VD  plan-2  C3   0.020
 4VD  plan-2  C5   0.020
 4VD  plan-2  C6   0.020
 4VD  plan-2  C19  0.020
 4VD  plan-2  C4   0.020
 4VD  plan-2  C18  0.020
 4VD  plan-2  N20  0.020
 4VD  plan-2  H35  0.020
 4VD  plan-2  H36  0.020
 4VD  plan-2  H45  0.020
 4VD  plan-3  C21  0.020
 4VD  plan-3  C23  0.020
 4VD  plan-3  C24  0.020
 4VD  plan-3  C26  0.020
 4VD  plan-3  C27  0.020
 4VD  plan-3  C28  0.020
 4VD  plan-3  N25  0.020
 4VD  plan-3  C29  0.020
 4VD  plan-3  C30  0.020
 4VD  plan-3  N31  0.020
 4VD  plan-3  H47  0.020
 4VD  plan-3  H48  0.020
 4VD  plan-3  H49  0.020
 4VD  plan-3  H50  0.020
 4VD  plan-3  H51  0.020
 4VD  plan-4  C6   0.020
 4VD  plan-4  C8   0.020
 4VD  plan-4  O9   0.020
 4VD  plan-4  C11  0.020
 4VD  plan-4  N7   0.020
 4VD  plan-4  N10  0.020
 4VD  plan-4  H39  0.020
 4VD  plan-4  H40  0.020
 4VD  plan-5  C19  0.020
 4VD  plan-5  C21  0.020
 4VD  plan-5  C23  0.020
 4VD  plan-5  N20  0.020
 4VD  plan-5  O22  0.020
 4VD  plan-5  H46  0.020

