# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 11:36:16 2022
#   Inital geometry file: a 119 line input string
#   Ligand name: 3-{6-[2-(2,4-difluorophenyl)ethyl][1,2,4]triazolo[4,3-a]pyridin-3-yl}-4-methylbenzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(cc1c2nnc3ccc(CCc4ccc(F)cc4F)cn23)C(N)=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
 L9G  L9G  3-{6-[2-(2,4-difluorophenyl)ethyl][1,2,4]triazolo[4,3-a]pyridin-3-yl}-4-methylbenzamide  ligand  47  29  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_L9G
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
 L9G  C1    C  CR16  0  -0.373  -0.6615   3.8481  -0.6457
 L9G  C2    C  CR56  0   0.473  -1.8619   3.1046  -0.5842
 L9G  N3    N  N     0  -0.555  -1.8108   1.7986  -0.1621
 L9G  C4    C  CR16  0  -0.018  -0.6468   1.1888   0.2301
 L9G  C5    C  CR6   0  -0.008   0.5155   1.8813   0.1765
 L9G  C6    C  CR16  0  -0.172   0.4940   3.2383  -0.2793
 L9G  C7    C  CR5   0   0.344  -3.1066   1.3627  -0.2124
 L9G  N8    N  N     0  -0.353  -3.1073   3.4280  -0.8639
 L9G  N9    N  N     0  -0.303  -3.8620   2.3452  -0.6301
 L9G  C10   C  CH2   0  -0.512   1.8160   1.2404   0.5606
 L9G  C11   C  CH2   0  -0.506   2.6855   0.9462  -0.6703
 L9G  C12   C  CR6   0  -0.078   4.0314   0.3968  -0.2945
 L9G  C13   C  CR6   0   0.531   4.2198  -0.9433   0.0109
 L9G  C14   C  CR16  0  -0.552   5.4380  -1.4787   0.3825
 L9G  C15   C  CR6   0   0.528   6.5141  -0.6153   0.4536
 L9G  C16   C  CR16  0  -0.410   6.3983   0.7303   0.1673
 L9G  C17   C  CR16  0  -0.275   5.1524   1.2169  -0.2012
 L9G  F18   F  F     0  -0.307   3.1676  -1.7732  -0.0602
 L9G  F19   F  F     0  -0.311   7.7088  -1.1098   0.8063
 L9G  C20   C  CR6   0   0.030  -3.5383   0.0039   0.1258
 L9G  C21   C  CR16  0  -0.314  -2.9136  -1.0717  -0.4953
 L9G  C22   C  CR6   0  -0.038  -3.2796  -2.3837  -0.2176
 L9G  C23   C  CR16  0  -0.267  -4.3120  -2.6013   0.6898
 L9G  C24   C  CR16  0  -0.284  -4.9425  -1.5318   1.3040
 L9G  C25   C  CR6   0   0.095  -4.5721  -0.2152   1.0482
 L9G  C26   C  C     0   0.505  -2.5422  -3.4729  -0.9351
 L9G  N27   N  NH2   0  -0.824  -2.8085  -4.7332  -0.5695
 L9G  O28   O  O     0  -0.480  -1.7316  -3.2013  -1.8116
 L9G  C29   C  CH3   0  -0.738  -5.2697   0.9098   1.7498
 L9G  H1    H  HCR6  0   0.289  -0.6923   4.8761  -0.9771
 L9G  H4    H  HCR6  0   0.313  -0.7222   0.1681   0.5763
 L9G  H6    H  HCR6  0   0.274   1.4240   3.7915  -0.3174
 L9G  H10   H  HCH2  0   0.265   2.3611   1.9074   1.2336
 L9G  H10A  H  HCH2  0   0.263   1.6283   0.3190   1.1146
 L9G  H11   H  HCH2  0   0.263   2.1546   0.2580  -1.3312
 L9G  H11A  H  HCH2  0   0.264   2.8314   1.8664  -1.2404
 L9G  H14   H  HCR6  0   0.301   5.5425  -2.5321   0.6073
 L9G  H16   H  HCR6  0   0.284   7.2576   1.3845   0.2218
 L9G  H17   H  HCR6  0   0.272   5.0478   2.2697  -0.4316
 L9G  H21   H  HCR6  0   0.276  -2.1332  -0.8927  -1.2246
 L9G  H23   H  HCR6  0   0.255  -4.6614  -3.5966   0.9316
 L9G  H24   H  HCR6  0   0.265  -5.7408  -1.7248   2.0096
 L9G  HN27  H  HNH2  0   0.416  -3.4365  -4.9769   0.1749
 L9G  HN2A  H  HNH2  0   0.407  -2.3248  -5.4928  -1.0203
 L9G  H29   H  HCH3  0   0.259  -5.8837   1.4880   1.0602
 L9G  H29A  H  HCH3  0   0.253  -5.9148   0.5289   2.5395
 L9G  H29B  H  HCH3  0   0.251  -4.5580   1.6032   2.1996

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
 L9G  C6   C1    aromatic  1.357  0.020  1.357
 L9G  C1   C2    aromatic  1.413  0.020  1.413
 L9G  C1   H1    single    0.930  0.020  1.080
 L9G  C2   N8    aromatic  1.317  0.020  1.317
 L9G  C2   N3    aromatic  1.374  0.020  1.374
 L9G  C4   N3    aromatic  1.371  0.020  1.371
 L9G  N3   C7    aromatic  1.368  0.020  1.368
 L9G  C5   C4    aromatic  1.354  0.020  1.354
 L9G  C4   H4    single    0.930  0.020  1.080
 L9G  C6   C5    aromatic  1.432  0.020  1.432
 L9G  C10  C5    single    1.500  0.020  1.500
 L9G  C6   H6    single    0.930  0.020  1.080
 L9G  N9   C7    aromatic  1.308  0.020  1.308
 L9G  C7   C20   single    1.465  0.020  1.465
 L9G  N8   N9    aromatic  1.340  0.020  1.340
 L9G  C11  C10   single    1.536  0.020  1.536
 L9G  C10  H10   single    0.970  0.020  1.090
 L9G  C10  H10A  single    0.970  0.020  1.090
 L9G  C12  C11   single    1.502  0.020  1.502
 L9G  C11  H11   single    0.970  0.020  1.090
 L9G  C11  H11A  single    0.970  0.020  1.090
 L9G  C17  C12   aromatic  1.392  0.020  1.392
 L9G  C12  C13   aromatic  1.387  0.020  1.387
 L9G  C14  C13   aromatic  1.382  0.020  1.382
 L9G  C13  F18   single    1.342  0.020  1.342
 L9G  C15  C14   aromatic  1.382  0.020  1.382
 L9G  C14  H14   single    0.930  0.020  1.080
 L9G  F19  C15   single    1.340  0.020  1.340
 L9G  C16  C15   aromatic  1.381  0.020  1.381
 L9G  C16  C17   aromatic  1.387  0.020  1.387
 L9G  C16  H16   single    0.930  0.020  1.080
 L9G  C17  H17   single    0.930  0.020  1.080
 L9G  C20  C25   aromatic  1.403  0.020  1.403
 L9G  C20  C21   aromatic  1.390  0.020  1.390
 L9G  C21  C22   aromatic  1.390  0.020  1.390
 L9G  C21  H21   single    0.930  0.020  1.080
 L9G  C22  C23   aromatic  1.392  0.020  1.392
 L9G  C22  C26   single    1.498  0.020  1.498
 L9G  C24  C23   aromatic  1.385  0.020  1.385
 L9G  C23  H23   single    0.930  0.020  1.080
 L9G  C25  C24   aromatic  1.391  0.020  1.391
 L9G  C24  H24   single    0.930  0.020  1.080
 L9G  C29  C25   single    1.498  0.020  1.498
 L9G  O28  C26   double    1.224  0.020  1.224
 L9G  C26  N27   single    1.339  0.020  1.339
 L9G  N27  HN27  single    0.860  0.020  1.020
 L9G  N27  HN2A  single    0.860  0.020  1.020
 L9G  C29  H29   single    0.970  0.020  1.090
 L9G  C29  H29A  single    0.970  0.020  1.090
 L9G  C29  H29B  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
 L9G  H1    C1   C6    122.33  3.000
 L9G  H1    C1   C2    119.31  3.000
 L9G  C6    C1   C2    118.36  3.000
 L9G  N8    C2   N3    109.51  3.000
 L9G  N3    C2   C1    118.81  3.000
 L9G  N8    C2   C1    131.68  3.000
 L9G  C7    N3   C4    132.29  3.000
 L9G  C7    N3   C2    104.86  3.000
 L9G  C4    N3   C2    122.84  3.000
 L9G  H4    C4   C5    123.76  3.000
 L9G  H4    C4   N3    116.90  3.000
 L9G  C5    C4   N3    119.34  3.000
 L9G  C10   C5   C6    119.98  3.000
 L9G  C10   C5   C4    121.04  3.000
 L9G  C6    C5   C4    118.98  3.000
 L9G  H6    C6   C5    118.85  3.000
 L9G  H6    C6   C1    119.49  3.000
 L9G  C5    C6   C1    121.65  3.000
 L9G  C20   C7   N9    126.89  3.000
 L9G  C20   C7   N3    124.47  3.000
 L9G  N9    C7   N3    108.63  3.000
 L9G  N9    N8   C2    107.28  3.000
 L9G  N8    N9   C7    109.72  3.000
 L9G  H10A  C10  H10   106.77  3.000
 L9G  H10A  C10  C11   110.03  3.000
 L9G  H10   C10  C11   109.16  3.000
 L9G  H10A  C10  C5    109.98  3.000
 L9G  H10   C10  C5    109.22  3.000
 L9G  C11   C10  C5    111.56  3.000
 L9G  H11A  C11  H11   106.27  3.000
 L9G  H11A  C11  C12   108.61  3.000
 L9G  H11   C11  C12   110.90  3.000
 L9G  H11A  C11  C10   109.43  3.000
 L9G  H11   C11  C10   109.31  3.000
 L9G  C12   C11  C10   112.15  3.000
 L9G  C17   C12  C13   116.42  3.000
 L9G  C13   C12  C11   122.02  3.000
 L9G  C17   C12  C11   121.54  3.000
 L9G  F18   C13  C14   117.77  3.000
 L9G  F18   C13  C12   118.64  3.000
 L9G  C14   C13  C12   123.59  3.000
 L9G  H14   C14  C15   121.50  3.000
 L9G  H14   C14  C13   121.21  3.000
 L9G  C15   C14  C13   117.29  3.000
 L9G  F19   C15  C16   119.28  3.000
 L9G  C16   C15  C14   122.22  3.000
 L9G  F19   C15  C14   118.51  3.000
 L9G  H16   C16  C17   120.99  3.000
 L9G  H16   C16  C15   120.83  3.000
 L9G  C17   C16  C15   118.18  3.000
 L9G  H17   C17  C16   118.96  3.000
 L9G  H17   C17  C12   118.74  3.000
 L9G  C16   C17  C12   122.30  3.000
 L9G  C25   C20  C21   120.27  3.000
 L9G  C21   C20  C7    118.81  3.000
 L9G  C25   C20  C7    120.91  3.000
 L9G  H21   C21  C22   118.70  3.000
 L9G  H21   C21  C20   119.78  3.000
 L9G  C22   C21  C20   121.51  3.000
 L9G  C26   C22  C23   124.31  3.000
 L9G  C26   C22  C21   117.44  3.000
 L9G  C23   C22  C21   118.24  3.000
 L9G  H23   C23  C24   117.65  3.000
 L9G  H23   C23  C22   121.94  3.000
 L9G  C24   C23  C22   120.41  3.000
 L9G  H24   C24  C25   118.99  3.000
 L9G  H24   C24  C23   119.14  3.000
 L9G  C25   C24  C23   121.86  3.000
 L9G  C29   C25  C24   120.03  3.000
 L9G  C29   C25  C20   122.27  3.000
 L9G  C24   C25  C20   117.70  3.000
 L9G  O28   C26  N27   122.41  3.000
 L9G  N27   C26  C22   117.10  3.000
 L9G  O28   C26  C22   120.49  3.000
 L9G  HN2A  N27  HN27  116.70  3.000
 L9G  HN2A  N27  C26   119.49  3.000
 L9G  HN27  N27  C26   123.73  3.000
 L9G  H29B  C29  H29A  108.06  3.000
 L9G  H29B  C29  H29   106.94  3.000
 L9G  H29A  C29  H29   108.11  3.000
 L9G  H29B  C29  C25   111.51  3.000
 L9G  H29A  C29  C25   110.67  3.000
 L9G  H29   C29  C25   111.38  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
 L9G  CONST_01  C4    C5   C6   C1     0.00   0.0  0
 L9G  CONST_02  N9    N8   C2   C1   180.00   0.0  0
 L9G  CONST_03  C4    N3   C2   C1     0.00   0.0  0
 L9G  CONST_04  C7    N3   C2   C1   180.00   0.0  0
 L9G  CONST_05  C5    C6   C1   C2     0.00   0.0  0
 L9G  CONST_06  C7    N9   N8   C2     0.00   0.0  0
 L9G  CONST_07  C5    C4   N3   C2     0.00   0.0  0
 L9G  CONST_08  N9    C7   N3   C2     0.00   0.0  0
 L9G  CONST_09  C20   C7   N3   C2   180.00   0.0  0
 L9G  CONST_10  C6    C1   C2   N3     0.00   0.0  0
 L9G  CONST_11  N9    N8   C2   N3     0.00   0.0  0
 L9G  CONST_12  C6    C5   C4   N3     0.00   0.0  0
 L9G  CONST_13  N8    N9   C7   N3     0.00   0.0  0
 L9G  CONST_16  N8    C2   N3   C4   180.00   0.0  0
 L9G  CONST_17  N9    C7   N3   C4   180.00   0.0  0
 L9G  CONST_18  C20   C7   N3   C4     0.00   0.0  0
 L9G  CONST_19  C7    N3   C4   C5   180.00   0.0  0
 L9G  CONST_20  N8    C2   C1   C6   180.00   0.0  0
 L9G  CONST_21  N8    C2   N3   C7     0.00   0.0  0
 L9G  CONST_22  C24   C25  C20  C7   180.00   0.0  0
 L9G  CONST_23  C22   C21  C20  C7   180.00   0.0  0
 L9G  CONST_24  C20   C7   N9   N8   180.00   0.0  0
 L9G  CONST_27  C15   C16  C17  C12    0.00   0.0  0
 L9G  CONST_28  C15   C14  C13  C12    0.00   0.0  0
 L9G  CONST_29  C16   C17  C12  C13    0.00   0.0  0
 L9G  CONST_30  C16   C15  C14  C13    0.00   0.0  0
 L9G  CONST_31  C17   C12  C13  C14    0.00   0.0  0
 L9G  CONST_32  C17   C16  C15  C14    0.00   0.0  0
 L9G  CONST_33  C23   C24  C25  C20    0.00   0.0  0
 L9G  CONST_34  C23   C22  C21  C20    0.00   0.0  0
 L9G  CONST_35  C24   C25  C20  C21    0.00   0.0  0
 L9G  CONST_36  C24   C23  C22  C21    0.00   0.0  0
 L9G  CONST_37  C25   C20  C21  C22    0.00   0.0  0
 L9G  CONST_38  C25   C24  C23  C22    0.00   0.0  0
 L9G  CONST_39  C10   C5   C6   C1   180.00   0.0  0
 L9G  CONST_40  C10   C5   C4   N3   180.00   0.0  0
 L9G  CONST_41  C29   C25  C20  C7     0.00   0.0  0
 L9G  CONST_42  C16   C17  C12  C11  180.00   0.0  0
 L9G  CONST_43  C14   C13  C12  C11  180.00   0.0  0
 L9G  CONST_44  F19   C15  C14  C13  180.00   0.0  0
 L9G  CONST_45  F18   C13  C14  C15  180.00   0.0  0
 L9G  CONST_46  F18   C13  C12  C17  180.00   0.0  0
 L9G  CONST_47  F19   C15  C16  C17  180.00   0.0  0
 L9G  CONST_48  C26   C22  C21  C20  180.00   0.0  0
 L9G  CONST_49  C29   C25  C20  C21  180.00   0.0  0
 L9G  CONST_50  C29   C25  C24  C23  180.00   0.0  0
 L9G  CONST_51  C26   C22  C23  C24  180.00   0.0  0
 L9G  CONST_52  H6    C6   C1   C2   180.00   0.0  0
 L9G  CONST_53  H4    C4   N3   C2   180.00   0.0  0
 L9G  CONST_54  H1    C1   C2   N3   180.00   0.0  0
 L9G  CONST_55  H21   C21  C20  C7     0.00   0.0  0
 L9G  CONST_56  H16   C16  C17  C12  180.00   0.0  0
 L9G  CONST_57  H14   C14  C13  C12  180.00   0.0  0
 L9G  CONST_58  H17   C17  C12  C13  180.00   0.0  0
 L9G  CONST_59  H24   C24  C25  C20  180.00   0.0  0
 L9G  CONST_60  H23   C23  C22  C21  180.00   0.0  0
 L9G  CONST_61  HN27  N27  C26  C22    0.00   0.0  0
 L9G  CONST_62  HN2A  N27  C26  C22  180.00   0.0  0
 L9G  Var_01    C11   C10  C5   C4   106.80  30.0  1
 L9G  Var_02    C12   C11  C10  C5   175.83  30.0  1
 L9G  Var_03    C17   C12  C11  C10  -96.70  30.0  2
 L9G  Var_04    O28   C26  C22  C21   -6.03  30.0  2
 L9G  Var_05    H29   C29  C25  C20   69.30  30.0  2

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
 L9G  plan-1  C11   0.020
 L9G  plan-1  C12   0.020
 L9G  plan-1  C13   0.020
 L9G  plan-1  C14   0.020
 L9G  plan-1  C15   0.020
 L9G  plan-1  C16   0.020
 L9G  plan-1  C17   0.020
 L9G  plan-1  F18   0.020
 L9G  plan-1  F19   0.020
 L9G  plan-1  H14   0.020
 L9G  plan-1  H16   0.020
 L9G  plan-1  H17   0.020
 L9G  plan-2  C7    0.020
 L9G  plan-2  C20   0.020
 L9G  plan-2  C21   0.020
 L9G  plan-2  C22   0.020
 L9G  plan-2  C23   0.020
 L9G  plan-2  C24   0.020
 L9G  plan-2  C25   0.020
 L9G  plan-2  C26   0.020
 L9G  plan-2  C29   0.020
 L9G  plan-2  H21   0.020
 L9G  plan-2  H23   0.020
 L9G  plan-2  H24   0.020
 L9G  plan-3  C1    0.020
 L9G  plan-3  C2    0.020
 L9G  plan-3  N3    0.020
 L9G  plan-3  C4    0.020
 L9G  plan-3  C5    0.020
 L9G  plan-3  C6    0.020
 L9G  plan-3  C7    0.020
 L9G  plan-3  N8    0.020
 L9G  plan-3  N9    0.020
 L9G  plan-3  C10   0.020
 L9G  plan-3  C20   0.020
 L9G  plan-3  H1    0.020
 L9G  plan-3  H4    0.020
 L9G  plan-3  H6    0.020
 L9G  plan-4  C22   0.020
 L9G  plan-4  C26   0.020
 L9G  plan-4  N27   0.020
 L9G  plan-4  O28   0.020
 L9G  plan-4  HN27  0.020
 L9G  plan-4  HN2A  0.020

