# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 20:18:22 2020
#   Inital geometry file: a 126 line input string
#   Ligand name: 3-(3-acetamidophenyl)-5-quinolin-7-yl-benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)Nc1cccc(c1)c2cc(cc(c2)c3ccc4cccnc4c3)C(O)=O
#
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
 AVM  AVM  '3-(3-acetamidophenyl)-5-quinolin-7-yl-benzoic acid'  ligand  46  29  .  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_AVM
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
 AVM  O2   O  O      0  -0.589  -1.1525   4.4289   0.5161
 AVM  C3   C  CR6    0   0.408  -4.6541  -0.8991   0.3166
 AVM  C4   C  C      0   0.501  -7.0258  -0.9709  -0.4601
 AVM  C5   C  CH3    0  -0.791  -7.9803  -0.1223  -1.2625
 AVM  C12  C  CR16   0  -0.375   1.2511   1.7529   0.1061
 AVM  C13  C  CR6    0  -0.061   0.0397   2.4002   0.3154
 AVM  C14  C  C      0   0.405  -0.0292   3.9248   0.3307
 AVM  C15  C  CR6    0   0.086   2.6253  -0.3143  -0.1473
 AVM  C17  C  CR16   0  -0.309   2.6759  -1.5180  -0.8971
 AVM  C18  C  CR16   0  -0.296   3.8612  -2.1536  -1.1341
 AVM  C19  C  CR6    0   0.057   5.0717  -1.6253  -0.6333
 AVM  C20  C  CR6    0   0.237   5.0368  -0.4245   0.1169
 AVM  C21  C  C1     0  -0.181   6.3271  -2.2332  -0.8461
 AVM  C22  C  C1     0  -0.329   7.4457  -1.6480  -0.3240
 AVM  C23  C  C1     0  -0.081   7.3015  -0.4522   0.4112
 AVM  O1   O  OC    -1  -0.589   1.0446   4.5304   0.1551
 AVM  N    N  NH1    0  -0.733  -5.8000  -0.3999  -0.3073
 AVM  C    C  CR16   0  -0.332  -2.2480  -1.7277   1.4718
 AVM  O    O  O      0  -0.467  -7.3317  -2.0549   0.0020
 AVM  C1   C  CR16   0  -0.231  -3.4106  -2.4581   1.6520
 AVM  C10  C  CR16   0  -0.394   0.1708  -0.3814   0.2845
 AVM  C11  C  CR6    0   0.142   1.3329   0.3617   0.0866
 AVM  C16  C  CR16   0  -0.370   3.7970   0.2096   0.3461
 AVM  C2   C  CR16   0  -0.329  -4.6152  -2.0626   1.0863
 AVM  C6   C  CR16   0  -0.426  -3.4817  -0.1613   0.1411
 AVM  C7   C  CR6    0   0.105  -2.2769  -0.5601   0.7085
 AVM  C8   C  CR6    0   0.131  -1.0554   0.2442   0.4972
 AVM  C9   C  CR16   0  -0.373  -1.1059   1.6370   0.5073
 AVM  N1   N  N      0  -0.435   6.1578   0.1401   0.6293
 AVM  H4   H  HCH3   0   0.269  -7.5650   0.1097  -2.2439
 AVM  H5   H  HCH3   0   0.267  -8.9244  -0.6430  -1.3954
 AVM  H6   H  HCH3   0   0.273  -8.1718   0.8257  -0.7577
 AVM  H10  H  HCR6   0   0.245   2.1384   2.3487  -0.0650
 AVM  H12  H  HCR6   0   0.261   1.7629  -1.9280  -1.3089
 AVM  H13  H  HCR6   0   0.264   3.8840  -3.0649  -1.7192
 AVM  H14  H  H      0   0.274   6.3899  -3.1509  -1.4182
 AVM  H15  H  H      0   0.273   8.4276  -2.0787  -0.4619
 AVM  H16  H  H      0   0.264   8.1833   0.0229   0.8287
 AVM  H3   H  HNH1   0   0.417  -5.6723   0.4897  -0.7659
 AVM  H    H  HCR6   0   0.253  -1.3282  -2.0516   1.9416
 AVM  H1   H  HCR6   0   0.259  -3.3885  -3.3566   2.2552
 AVM  H9   H  HCR6   0   0.254   0.2190  -1.4637   0.2733
 AVM  H11  H  HCR6   0   0.257   3.7945   1.1167   0.9385
 AVM  H2   H  HCR6   0   0.278  -5.5004  -2.6539   1.2498
 AVM  H7   H  HCR6   0   0.267  -3.5074   0.7330  -0.4722
 AVM  H8   H  HCR6   0   0.245  -2.0464   2.1416   0.6891

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
 AVM  O    C4   double    1.217  0.020  1.217
 AVM  C4   N    single    1.361  0.020  1.361
 AVM  C4   C5   single    1.508  0.020  1.508
 AVM  N    C3   single    1.397  0.020  1.397
 AVM  C3   C2   aromatic  1.396  0.020  1.396
 AVM  C3   C6   aromatic  1.396  0.020  1.396
 AVM  C2   C1   aromatic  1.388  0.020  1.388
 AVM  C6   C7   aromatic  1.390  0.020  1.390
 AVM  C1   C    aromatic  1.385  0.020  1.385
 AVM  C7   C    aromatic  1.395  0.020  1.395
 AVM  C7   C8   single    1.478  0.020  1.478
 AVM  C18  C17  aromatic  1.366  0.020  1.366
 AVM  C18  C19  aromatic  1.412  0.020  1.412
 AVM  C17  C15  aromatic  1.419  0.020  1.419
 AVM  C8   C10  aromatic  1.393  0.020  1.393
 AVM  C8   C9   aromatic  1.394  0.020  1.394
 AVM  C10  C11  aromatic  1.393  0.020  1.393
 AVM  C9   C13  aromatic  1.390  0.020  1.390
 AVM  C11  C15  single    1.477  0.020  1.477
 AVM  C11  C12  aromatic  1.394  0.020  1.394
 AVM  C15  C16  aromatic  1.375  0.020  1.375
 AVM  C19  C21  aromatic  1.411  0.020  1.411
 AVM  C19  C20  aromatic  1.416  0.020  1.416
 AVM  O2   C14  deloc     1.245  0.020  1.245
 AVM  C21  C22  aromatic  1.366  0.020  1.366
 AVM  C13  C12  aromatic  1.389  0.020  1.389
 AVM  C13  C14  single    1.526  0.020  1.526
 AVM  C14  O1   deloc     1.245  0.020  1.245
 AVM  C16  C20  aromatic  1.411  0.020  1.411
 AVM  C20  N1   aromatic  1.356  0.020  1.356
 AVM  C22  C23  aromatic  1.411  0.020  1.411
 AVM  C23  N1   aromatic  1.306  0.020  1.306
 AVM  C5   H4   single    0.970  0.020  1.090
 AVM  C5   H5   single    0.970  0.020  1.090
 AVM  C5   H6   single    0.970  0.020  1.090
 AVM  C12  H10  single    0.930  0.020  1.080
 AVM  C17  H12  single    0.930  0.020  1.080
 AVM  C18  H13  single    0.930  0.020  1.080
 AVM  C21  H14  single    0.930  0.020  1.080
 AVM  C22  H15  single    0.930  0.020  1.080
 AVM  C23  H16  single    0.930  0.020  1.080
 AVM  N    H3   single    0.860  0.020  1.020
 AVM  C    H    single    0.930  0.020  1.080
 AVM  C1   H1   single    0.930  0.020  1.080
 AVM  C10  H9   single    0.930  0.020  1.080
 AVM  C16  H11  single    0.930  0.020  1.080
 AVM  C2   H2   single    0.930  0.020  1.080
 AVM  C6   H7   single    0.930  0.020  1.080
 AVM  C9   H8   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
 AVM  C6   C3   C2   119.11  3.000
 AVM  C6   C3   N    116.35  3.000
 AVM  C2   C3   N    124.54  3.000
 AVM  O    C4   N    123.87  3.000
 AVM  N    C4   C5   113.18  3.000
 AVM  O    C4   C5   122.95  3.000
 AVM  H6   C5   H5   108.70  3.000
 AVM  H6   C5   H4   107.36  3.000
 AVM  H5   C5   H4   108.84  3.000
 AVM  H6   C5   C4   110.72  3.000
 AVM  H5   C5   C4   110.20  3.000
 AVM  H4   C5   C4   110.94  3.000
 AVM  H10  C12  C11  119.95  3.000
 AVM  H10  C12  C13  118.82  3.000
 AVM  C11  C12  C13  121.22  3.000
 AVM  C9   C13  C14  120.66  3.000
 AVM  C14  C13  C12  120.42  3.000
 AVM  C9   C13  C12  118.92  3.000
 AVM  O1   C14  C13  116.45  3.000
 AVM  O1   C14  O2   127.02  3.000
 AVM  C13  C14  O2   116.53  3.000
 AVM  C16  C15  C11  120.95  3.000
 AVM  C16  C15  C17  118.84  3.000
 AVM  C11  C15  C17  120.20  3.000
 AVM  H12  C17  C18  119.34  3.000
 AVM  H12  C17  C15  119.49  3.000
 AVM  C18  C17  C15  121.16  3.000
 AVM  H13  C18  C19  119.22  3.000
 AVM  H13  C18  C17  120.23  3.000
 AVM  C19  C18  C17  120.55  3.000
 AVM  C21  C19  C20  117.84  3.000
 AVM  C20  C19  C18  118.93  3.000
 AVM  C21  C19  C18  123.22  3.000
 AVM  N1   C20  C16  118.55  3.000
 AVM  N1   C20  C19  122.20  3.000
 AVM  C16  C20  C19  119.25  3.000
 AVM  H14  C21  C22  121.16  3.000
 AVM  H14  C21  C19  119.75  3.000
 AVM  C22  C21  C19  119.10  3.000
 AVM  H15  C22  C23  119.80  3.000
 AVM  H15  C22  C21  121.62  3.000
 AVM  C23  C22  C21  118.58  3.000
 AVM  H16  C23  N1   116.66  3.000
 AVM  H16  C23  C22  119.23  3.000
 AVM  N1   C23  C22  124.11  3.000
 AVM  H3   N    C4   115.65  3.000
 AVM  H3   N    C3   114.47  3.000
 AVM  C4   N    C3   129.72  3.000
 AVM  H    C    C7   120.36  3.000
 AVM  H    C    C1   119.94  3.000
 AVM  C7   C    C1   119.68  3.000
 AVM  H1   C1   C2   118.76  3.000
 AVM  H1   C1   C    119.55  3.000
 AVM  C2   C1   C    121.68  3.000
 AVM  H9   C10  C8   119.30  3.000
 AVM  H9   C10  C11  119.61  3.000
 AVM  C8   C10  C11  121.09  3.000
 AVM  C10  C11  C15  120.54  3.000
 AVM  C15  C11  C12  120.69  3.000
 AVM  C10  C11  C12  118.77  3.000
 AVM  H11  C16  C20  117.84  3.000
 AVM  H11  C16  C15  120.88  3.000
 AVM  C20  C16  C15  121.27  3.000
 AVM  H2   C2   C1   119.66  3.000
 AVM  H2   C2   C3   121.24  3.000
 AVM  C1   C2   C3   119.10  3.000
 AVM  H7   C6   C7   119.20  3.000
 AVM  H7   C6   C3   119.13  3.000
 AVM  C7   C6   C3   121.66  3.000
 AVM  C8   C7   C6   120.12  3.000
 AVM  C8   C7   C    121.11  3.000
 AVM  C6   C7   C    118.77  3.000
 AVM  C9   C8   C7   120.86  3.000
 AVM  C9   C8   C10  118.80  3.000
 AVM  C7   C8   C10  120.34  3.000
 AVM  H8   C9   C8   119.89  3.000
 AVM  H8   C9   C13  118.90  3.000
 AVM  C8   C9   C13  121.19  3.000
 AVM  C23  N1   C20  118.17  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
 AVM  CONST_01  C    C1   C2   C3     0.00   0.0  0
 AVM  CONST_02  C    C7   C6   C3     0.00   0.0  0
 AVM  CONST_03  C8   C7   C6   C3   180.00   0.0  0
 AVM  CONST_04  C8   C10  C11  C12    0.00   0.0  0
 AVM  CONST_07  C8   C9   C13  C12    0.00   0.0  0
 AVM  CONST_08  C7   C8   C9   C13  180.00   0.0  0
 AVM  CONST_09  C10  C8   C9   C13    0.00   0.0  0
 AVM  CONST_10  C10  C11  C12  C13    0.00   0.0  0
 AVM  CONST_11  C15  C11  C12  C13  180.00   0.0  0
 AVM  CONST_12  C19  C18  C17  C15    0.00   0.0  0
 AVM  CONST_13  C8   C10  C11  C15  180.00   0.0  0
 AVM  CONST_14  C19  C20  C16  C15    0.00   0.0  0
 AVM  CONST_15  N1   C20  C16  C15  180.00   0.0  0
 AVM  CONST_16  C21  C19  C18  C17  180.00   0.0  0
 AVM  CONST_17  C20  C19  C18  C17    0.00   0.0  0
 AVM  CONST_19  C20  C16  C15  C17    0.00   0.0  0
 AVM  CONST_20  C11  C15  C17  C18  180.00   0.0  0
 AVM  CONST_21  C16  C15  C17  C18    0.00   0.0  0
 AVM  CONST_22  C22  C21  C19  C18  180.00   0.0  0
 AVM  CONST_23  C16  C20  C19  C18    0.00   0.0  0
 AVM  CONST_24  N1   C20  C19  C18  180.00   0.0  0
 AVM  CONST_25  C23  C22  C21  C19    0.00   0.0  0
 AVM  CONST_26  C23  N1   C20  C19    0.00   0.0  0
 AVM  CONST_27  C22  C21  C19  C20    0.00   0.0  0
 AVM  CONST_28  C11  C15  C16  C20  180.00   0.0  0
 AVM  CONST_29  C22  C23  N1   C20    0.00   0.0  0
 AVM  CONST_30  C16  C20  C19  C21  180.00   0.0  0
 AVM  CONST_31  N1   C20  C19  C21    0.00   0.0  0
 AVM  CONST_32  N1   C23  C22  C21    0.00   0.0  0
 AVM  CONST_33  C16  C20  N1   C23  180.00   0.0  0
 AVM  CONST_36  C6   C3   C2   C1     0.00   0.0  0
 AVM  CONST_37  C6   C7   C    C1     0.00   0.0  0
 AVM  CONST_38  C8   C7   C    C1   180.00   0.0  0
 AVM  CONST_41  C7   C8   C10  C11  180.00   0.0  0
 AVM  CONST_42  C9   C8   C10  C11    0.00   0.0  0
 AVM  CONST_43  C9   C13  C12  C11    0.00   0.0  0
 AVM  CONST_44  C7   C6   C3   C2     0.00   0.0  0
 AVM  CONST_45  C7   C    C1   C2     0.00   0.0  0
 AVM  CONST_47  C8   C9   C13  C14  180.00   0.0  0
 AVM  CONST_48  C11  C12  C13  C14  180.00   0.0  0
 AVM  CONST_49  C1   C2   C3   N    180.00   0.0  0
 AVM  CONST_50  C7   C6   C3   N    180.00   0.0  0
 AVM  CONST_51  H1   C1   C2   C3   180.00   0.0  0
 AVM  CONST_52  H9   C10  C11  C12  180.00   0.0  0
 AVM  CONST_53  H8   C9   C13  C12  180.00   0.0  0
 AVM  CONST_54  H13  C18  C17  C15  180.00   0.0  0
 AVM  CONST_55  H10  C12  C11  C15    0.00   0.0  0
 AVM  CONST_56  H11  C16  C15  C17  180.00   0.0  0
 AVM  CONST_57  H14  C21  C19  C18    0.00   0.0  0
 AVM  CONST_58  H12  C17  C18  C19  180.00   0.0  0
 AVM  CONST_59  H15  C22  C21  C19  180.00   0.0  0
 AVM  CONST_60  H16  C23  N1   C20  180.00   0.0  0
 AVM  CONST_61  H2   C2   C1   C    180.00   0.0  0
 AVM  CONST_62  H7   C6   C7   C    180.00   0.0  0
 AVM  CONST_63  H    C    C1   C2   180.00   0.0  0
 AVM  CONST_64  C2   C3   N    C4     0.00   0.0  0
 AVM  CONST_65  C6   C3   N    C4   180.00   0.0  0
 AVM  CONST_66  H3   N    C3   C2   180.00   0.0  0
 AVM  CONST_67  O    C4   N    C3     0.00   0.0  0
 AVM  CONST_68  C5   C4   N    C3   180.00   0.0  0
 AVM  Var_01    C9   C13  C14  O2    -0.29  30.0  3
 AVM  Var_02    H4   C5   C4   N     56.65  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
 AVM  plan-1  C3   0.020
 AVM  plan-1  N    0.020
 AVM  plan-1  C    0.020
 AVM  plan-1  C1   0.020
 AVM  plan-1  C2   0.020
 AVM  plan-1  C6   0.020
 AVM  plan-1  C7   0.020
 AVM  plan-1  C8   0.020
 AVM  plan-1  H    0.020
 AVM  plan-1  H1   0.020
 AVM  plan-1  H2   0.020
 AVM  plan-1  H7   0.020
 AVM  plan-2  C12  0.020
 AVM  plan-2  C13  0.020
 AVM  plan-2  C14  0.020
 AVM  plan-2  C15  0.020
 AVM  plan-2  C10  0.020
 AVM  plan-2  C11  0.020
 AVM  plan-2  C7   0.020
 AVM  plan-2  C8   0.020
 AVM  plan-2  C9   0.020
 AVM  plan-2  H10  0.020
 AVM  plan-2  H9   0.020
 AVM  plan-2  H8   0.020
 AVM  plan-3  C15  0.020
 AVM  plan-3  C17  0.020
 AVM  plan-3  C18  0.020
 AVM  plan-3  C19  0.020
 AVM  plan-3  C20  0.020
 AVM  plan-3  C21  0.020
 AVM  plan-3  C22  0.020
 AVM  plan-3  C23  0.020
 AVM  plan-3  C11  0.020
 AVM  plan-3  C16  0.020
 AVM  plan-3  N1   0.020
 AVM  plan-3  H12  0.020
 AVM  plan-3  H13  0.020
 AVM  plan-3  H14  0.020
 AVM  plan-3  H15  0.020
 AVM  plan-3  H16  0.020
 AVM  plan-3  H11  0.020
 AVM  plan-4  C3   0.020
 AVM  plan-4  C4   0.020
 AVM  plan-4  C5   0.020
 AVM  plan-4  N    0.020
 AVM  plan-4  O    0.020
 AVM  plan-4  H3   0.020
 AVM  plan-5  O2   0.020
 AVM  plan-5  C13  0.020
 AVM  plan-5  C14  0.020
 AVM  plan-5  O1   0.020

