# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 12:37:09 2020
#   Inital geometry file: a 127 line input string
#   Ligand name: N-(3-cyanophenyl)-2'-methyl-5'-(5-methyl-1,3,4-oxadiazol-2-yl)biphenyl-4-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1oc(nn1)c2ccc(C)c(c2)c3ccc(cc3)C(=O)Nc4cccc(c4)C#N
#
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
 GK3  GK3  N-(3-cyanophenyl)-2'-methyl-5'-(5-methyl-1,3,4-oxadiazol-2-yl)biphenyl-4-carboxamide  ligand  48  30  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GK3
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
 GK3  N5    N  NS    0  -0.248  -8.9321  -1.3444  -2.2256
 GK3  C5    C  CSP   0   0.057  -8.2251  -1.1764  -1.3317
 GK3  C18   C  CR6   0   0.028  -7.3524  -0.9696  -0.2191
 GK3  C2    C  CR16  0  -0.266  -7.8392  -1.1550   1.0708
 GK3  C29   C  CR16  0  -0.221  -6.9739  -0.9468   2.1325
 GK3  C19   C  CR16  0  -0.315  -5.6637  -0.5686   1.9069
 GK3  C22   C  CR16  0  -0.311  -6.0348  -0.5876  -0.4682
 GK3  C15   C  CR6   0   0.417  -5.1757  -0.3882   0.6092
 GK3  N3    N  NH1   0  -0.760  -3.8334  -0.0342   0.4842
 GK3  C3    C  C     0   0.535  -3.1363   0.2947  -0.6380
 GK3  O1    O  O     0  -0.447  -3.6397   0.4035  -1.7399
 GK3  C25   C  CR6   0  -0.051  -1.6802   0.5276  -0.4166
 GK3  C9    C  CR16  0  -0.260  -0.9554  -0.1481   0.5611
 GK3  C10   C  CR16  0  -0.237  -1.0157   1.4173  -1.2574
 GK3  C16   C  CR16  0  -0.260   0.3380   1.6517  -1.0986
 GK3  C13   C  CR6   0   0.035   1.0672   0.9861  -0.1140
 GK3  C27   C  CR16  0  -0.259   0.4039   0.0766   0.7050
 GK3  C28   C  CR6   0   0.076   2.5235   1.2007   0.0446
 GK3  C14   C  CR16  0  -0.296   3.3689   0.1083  -0.0913
 GK3  C17   C  CR6   0  -0.014   4.7476   0.2376   0.0517
 GK3  C12   C  CR5   0   0.478   5.5884  -0.9350  -0.1082
 GK3  O2    O  O     0  -0.411   6.9206  -0.8284   0.0131
 GK3  C7    C  CR5   0   0.461   7.3614  -2.0822  -0.1956
 GK3  C21   C  CH3   0  -0.727   8.8083  -2.3622  -0.1426
 GK3  N4    N  N     0  -0.306   6.3857  -2.8868  -0.4244
 GK3  N7    N  N     0  -0.316   5.2362  -2.1460  -0.3678
 GK3  C20   C  CR16  0  -0.261   5.2821   1.4887   0.3439
 GK3  C26   C  CR16  0  -0.258   4.4379   2.5750   0.4913
 GK3  C23   C  CR6   0   0.079   3.0580   2.4632   0.3466
 GK3  C1    C  CH3   0  -0.720   2.1907   3.6717   0.5411
 GK3  H2    H  HCR6  0   0.296  -8.8625  -1.4595   1.2348
 GK3  H29   H  HCR6  0   0.265  -7.3210  -1.0817   3.1471
 GK3  H19   H  HCR6  0   0.260  -5.0065  -0.4149   2.7543
 GK3  H22   H  HCR6  0   0.302  -5.7024  -0.4546  -1.4840
 GK3  HN3   H  HNH1  0   0.406  -3.3352   0.0454   1.3569
 GK3  H9    H  HCR6  0   0.251  -1.4276  -0.8781   1.2067
 GK3  H10   H  HCR6  0   0.260  -1.5595   1.9326  -2.0374
 GK3  H16   H  HCR6  0   0.245   0.8361   2.3450  -1.7638
 GK3  H27   H  HCR6  0   0.241   0.9517  -0.4565   1.4711
 GK3  H14   H  HCR6  0   0.246   2.9484  -0.8604  -0.3305
 GK3  H21   H  HCH3  0   0.264   9.2183  -2.1197   0.8373
 GK3  H21A  H  HCH3  0   0.264   8.9808  -3.4156  -0.3419
 GK3  H21B  H  HCH3  0   0.264   9.3461  -1.7743  -0.8857
 GK3  H20   H  HCR6  0   0.243   6.3474   1.6275   0.4656
 GK3  H26   H  HCR6  0   0.236   4.8660   3.5378   0.7391
 GK3  H1    H  HCH3  0   0.244   1.8953   4.1121  -0.4123
 GK3  H1A   H  HCH3  0   0.245   1.2760   3.4338   1.0822
 GK3  H1B   H  HCH3  0   0.245   2.7204   4.4423   1.0987

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
 GK3  N5   C5    triple    1.152  0.020  1.152
 GK3  C5   C18   single    1.429  0.020  1.429
 GK3  C2   C18   aromatic  1.391  0.020  1.391
 GK3  C2   C29   aromatic  1.385  0.020  1.385
 GK3  C18  C22   aromatic  1.394  0.020  1.394
 GK3  C29  C19   aromatic  1.382  0.020  1.382
 GK3  C22  C15   aromatic  1.392  0.020  1.392
 GK3  C19  C15   aromatic  1.398  0.020  1.398
 GK3  C15  N3    single    1.394  0.020  1.394
 GK3  N3   C3    single    1.361  0.020  1.361
 GK3  C1   C23   single    1.500  0.020  1.500
 GK3  C3   O1    double    1.216  0.020  1.216
 GK3  C3   C25   single    1.491  0.020  1.491
 GK3  C9   C25   aromatic  1.392  0.020  1.392
 GK3  C9   C27   aromatic  1.385  0.020  1.385
 GK3  C25  C10   aromatic  1.393  0.020  1.393
 GK3  C27  C13   aromatic  1.392  0.020  1.392
 GK3  C23  C26   aromatic  1.392  0.020  1.392
 GK3  C23  C28   aromatic  1.404  0.020  1.404
 GK3  C26  C20   aromatic  1.384  0.020  1.384
 GK3  C10  C16   aromatic  1.383  0.020  1.383
 GK3  C13  C28   single    1.481  0.020  1.481
 GK3  C13  C16   aromatic  1.394  0.020  1.394
 GK3  C28  C14   aromatic  1.388  0.020  1.388
 GK3  C20  C17   aromatic  1.391  0.020  1.391
 GK3  C14  C17   aromatic  1.392  0.020  1.392
 GK3  C17  C12   single    1.452  0.020  1.452
 GK3  C12  O2    aromatic  1.342  0.020  1.342
 GK3  C12  N7    aromatic  1.288  0.020  1.288
 GK3  O2   C7    aromatic  1.345  0.020  1.345
 GK3  N7   N4    aromatic  1.369  0.020  1.369
 GK3  C7   C21   single    1.475  0.020  1.475
 GK3  C7   N4    aromatic  1.285  0.020  1.285
 GK3  C2   H2    single    0.930  0.020  1.080
 GK3  C29  H29   single    0.930  0.020  1.080
 GK3  C19  H19   single    0.930  0.020  1.080
 GK3  C22  H22   single    0.930  0.020  1.080
 GK3  N3   HN3   single    0.860  0.020  1.020
 GK3  C9   H9    single    0.930  0.020  1.080
 GK3  C10  H10   single    0.930  0.020  1.080
 GK3  C16  H16   single    0.930  0.020  1.080
 GK3  C27  H27   single    0.930  0.020  1.080
 GK3  C14  H14   single    0.930  0.020  1.080
 GK3  C21  H21   single    0.970  0.020  1.090
 GK3  C21  H21A  single    0.970  0.020  1.090
 GK3  C21  H21B  single    0.970  0.020  1.090
 GK3  C20  H20   single    0.930  0.020  1.080
 GK3  C26  H26   single    0.930  0.020  1.080
 GK3  C1   H1    single    0.970  0.020  1.090
 GK3  C1   H1A   single    0.970  0.020  1.090
 GK3  C1   H1B   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
 GK3  C18   C5   N5    180.00  3.000
 GK3  C22   C18  C2    122.20  3.000
 GK3  C22   C18  C5    118.53  3.000
 GK3  C2    C18  C5    119.27  3.000
 GK3  H2    C2   C29   121.18  3.000
 GK3  H2    C2   C18   120.65  3.000
 GK3  C29   C2   C18   118.16  3.000
 GK3  H29   C29  C19   119.46  3.000
 GK3  H29   C29  C2    120.01  3.000
 GK3  C19   C29  C2    120.54  3.000
 GK3  H19   C19  C15   119.74  3.000
 GK3  H19   C19  C29   119.09  3.000
 GK3  C15   C19  C29   121.17  3.000
 GK3  H22   C22  C15   121.45  3.000
 GK3  H22   C22  C18   119.60  3.000
 GK3  C15   C22  C18   118.95  3.000
 GK3  N3    C15  C22   124.13  3.000
 GK3  N3    C15  C19   116.88  3.000
 GK3  C22   C15  C19   118.98  3.000
 GK3  HN3   N3   C3    116.19  3.000
 GK3  HN3   N3   C15   114.73  3.000
 GK3  C3    N3   C15   128.93  3.000
 GK3  C25   C3   O1    121.64  3.000
 GK3  C25   C3   N3    114.54  3.000
 GK3  O1    C3   N3    123.81  3.000
 GK3  C10   C25  C9    119.05  3.000
 GK3  C10   C25  C3    118.42  3.000
 GK3  C9    C25  C3    122.48  3.000
 GK3  H9    C9   C27   118.38  3.000
 GK3  H9    C9   C25   121.26  3.000
 GK3  C27   C9   C25   120.35  3.000
 GK3  H10   C10  C16   119.61  3.000
 GK3  H10   C10  C25   119.99  3.000
 GK3  C16   C10  C25   120.40  3.000
 GK3  H16   C16  C13   119.94  3.000
 GK3  H16   C16  C10   119.25  3.000
 GK3  C13   C16  C10   120.80  3.000
 GK3  C28   C13  C27   120.02  3.000
 GK3  C28   C13  C16   121.39  3.000
 GK3  C27   C13  C16   118.56  3.000
 GK3  H27   C27  C13   119.81  3.000
 GK3  H27   C27  C9    119.36  3.000
 GK3  C13   C27  C9    120.82  3.000
 GK3  C23   C28  C14   119.80  3.000
 GK3  C14   C28  C13   118.33  3.000
 GK3  C23   C28  C13   121.86  3.000
 GK3  H14   C14  C17   119.37  3.000
 GK3  H14   C14  C28   119.29  3.000
 GK3  C17   C14  C28   121.33  3.000
 GK3  C20   C17  C12   121.80  3.000
 GK3  C12   C17  C14   119.16  3.000
 GK3  C20   C17  C14   119.04  3.000
 GK3  N7    C12  O2    111.38  3.000
 GK3  N7    C12  C17   128.57  3.000
 GK3  O2    C12  C17   120.05  3.000
 GK3  C7    O2   C12   103.72  3.000
 GK3  N4    C7   C21   129.22  3.000
 GK3  N4    C7   O2    111.24  3.000
 GK3  C21   C7   O2    119.53  3.000
 GK3  H21B  C21  H21A  108.65  3.000
 GK3  H21B  C21  H21   107.91  3.000
 GK3  H21A  C21  H21   108.74  3.000
 GK3  H21B  C21  C7    110.94  3.000
 GK3  H21A  C21  C7    109.48  3.000
 GK3  H21   C21  C7    111.06  3.000
 GK3  N7    N4   C7    106.94  3.000
 GK3  N4    N7   C12   106.71  3.000
 GK3  H20   C20  C26   119.23  3.000
 GK3  H20   C20  C17   121.17  3.000
 GK3  C26   C20  C17   119.60  3.000
 GK3  H26   C26  C23   119.16  3.000
 GK3  H26   C26  C20   118.78  3.000
 GK3  C23   C26  C20   122.05  3.000
 GK3  C1    C23  C26   119.67  3.000
 GK3  C26   C23  C28   118.16  3.000
 GK3  C1    C23  C28   122.16  3.000
 GK3  H1B   C1   H1A   107.99  3.000
 GK3  H1B   C1   H1    107.08  3.000
 GK3  H1A   C1   H1    107.15  3.000
 GK3  H1B   C1   C23   110.81  3.000
 GK3  H1A   C1   C23   111.96  3.000
 GK3  H1    C1   C23   111.61  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
 GK3  CONST_01  C19  C29  C2   C18    0.00   0.0  0
 GK3  CONST_02  C19  C15  C22  C18    0.00   0.0  0
 GK3  CONST_03  C15  C22  C18  C2     0.00   0.0  0
 GK3  CONST_04  C15  C19  C29  C2     0.00   0.0  0
 GK3  CONST_05  C22  C18  C2   C29    0.00   0.0  0
 GK3  CONST_06  C22  C15  C19  C29    0.00   0.0  0
 GK3  CONST_07  C13  C27  C9   C25    0.00   0.0  0
 GK3  CONST_08  C13  C16  C10  C25    0.00   0.0  0
 GK3  CONST_09  C16  C10  C25  C9     0.00   0.0  0
 GK3  CONST_10  C28  C13  C27  C9   180.00   0.0  0
 GK3  CONST_11  C16  C13  C27  C9     0.00   0.0  0
 GK3  CONST_12  C27  C9   C25  C10    0.00   0.0  0
 GK3  CONST_13  C27  C13  C16  C10    0.00   0.0  0
 GK3  CONST_14  C28  C13  C16  C10  180.00   0.0  0
 GK3  CONST_17  C26  C23  C28  C13  180.00   0.0  0
 GK3  CONST_18  C17  C14  C28  C13  180.00   0.0  0
 GK3  CONST_21  C20  C26  C23  C28    0.00   0.0  0
 GK3  CONST_22  C20  C17  C14  C28    0.00   0.0  0
 GK3  CONST_23  C12  C17  C14  C28  180.00   0.0  0
 GK3  CONST_24  C26  C23  C28  C14    0.00   0.0  0
 GK3  CONST_25  C26  C20  C17  C14    0.00   0.0  0
 GK3  CONST_26  O2   C12  C17  C14  180.00   0.0  0
 GK3  CONST_27  N7   C12  C17  C14    0.00   0.0  0
 GK3  CONST_28  C23  C26  C20  C17    0.00   0.0  0
 GK3  CONST_29  C23  C28  C14  C17    0.00   0.0  0
 GK3  CONST_30  C7   O2   C12  C17  180.00   0.0  0
 GK3  CONST_31  N4   N7   C12  C17  180.00   0.0  0
 GK3  CONST_32  C26  C20  C17  C12  180.00   0.0  0
 GK3  CONST_33  N4   C7   O2   C12    0.00   0.0  0
 GK3  CONST_34  C7   N4   N7   C12    0.00   0.0  0
 GK3  CONST_35  C20  C17  C12  O2     0.00   0.0  0
 GK3  CONST_36  N4   N7   C12  O2     0.00   0.0  0
 GK3  CONST_37  N7   N4   C7   O2     0.00   0.0  0
 GK3  CONST_38  N7   C12  O2   C7     0.00   0.0  0
 GK3  CONST_39  C20  C17  C12  N7   180.00   0.0  0
 GK3  CONST_40  C29  C2   C18  C5   180.00   0.0  0
 GK3  CONST_41  C15  C22  C18  C5   180.00   0.0  0
 GK3  CONST_42  N3   C15  C22  C18  180.00   0.0  0
 GK3  CONST_43  N3   C15  C19  C29  180.00   0.0  0
 GK3  CONST_44  C27  C9   C25  C3   180.00   0.0  0
 GK3  CONST_45  C16  C10  C25  C3   180.00   0.0  0
 GK3  CONST_46  C1   C23  C28  C13    0.00   0.0  0
 GK3  CONST_47  C1   C23  C28  C14  180.00   0.0  0
 GK3  CONST_48  C21  C7   O2   C12  180.00   0.0  0
 GK3  CONST_49  N7   N4   C7   C21  180.00   0.0  0
 GK3  CONST_50  C1   C23  C26  C20  180.00   0.0  0
 GK3  CONST_51  H29  C29  C2   C18  180.00   0.0  0
 GK3  CONST_52  H22  C22  C18  C2   180.00   0.0  0
 GK3  CONST_53  H19  C19  C29  C2   180.00   0.0  0
 GK3  CONST_54  H2   C2   C29  C19  180.00   0.0  0
 GK3  CONST_55  H27  C27  C9   C25  180.00   0.0  0
 GK3  CONST_56  H16  C16  C10  C25  180.00   0.0  0
 GK3  CONST_57  H10  C10  C25  C9   180.00   0.0  0
 GK3  CONST_58  H9   C9   C25  C10  180.00   0.0  0
 GK3  CONST_59  H14  C14  C28  C13    0.00   0.0  0
 GK3  CONST_60  H26  C26  C23  C28  180.00   0.0  0
 GK3  CONST_61  H20  C20  C17  C14  180.00   0.0  0
 GK3  CONST_62  C25  C3   N3   C15  180.00   0.0  0
 GK3  CONST_63  C3   N3   C15  C19  180.00   0.0  0
 GK3  CONST_64  C3   N3   C15  C22    0.00   0.0  0
 GK3  CONST_65  HN3  N3   C15  C19    0.00   0.0  0
 GK3  CONST_66  O1   C3   N3   C15    0.00   0.0  0
 GK3  Var_01    C9   C25  C3   N3    31.75  30.0  2
 GK3  Var_02    H1   C1   C23  C28  -80.92  30.0  2
 GK3  Var_03    H21  C21  C7   O2    60.43  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
 GK3  plan-1  C17  0.020
 GK3  plan-1  C12  0.020
 GK3  plan-1  O2   0.020
 GK3  plan-1  C7   0.020
 GK3  plan-1  C21  0.020
 GK3  plan-1  N4   0.020
 GK3  plan-1  N7   0.020
 GK3  plan-2  N5   0.020
 GK3  plan-2  C5   0.020
 GK3  plan-2  C18  0.020
 GK3  plan-2  C2   0.020
 GK3  plan-2  C29  0.020
 GK3  plan-2  C19  0.020
 GK3  plan-2  C22  0.020
 GK3  plan-2  C15  0.020
 GK3  plan-2  N3   0.020
 GK3  plan-2  H2   0.020
 GK3  plan-2  H29  0.020
 GK3  plan-2  H19  0.020
 GK3  plan-2  H22  0.020
 GK3  plan-3  C3   0.020
 GK3  plan-3  C25  0.020
 GK3  plan-3  C9   0.020
 GK3  plan-3  C10  0.020
 GK3  plan-3  C16  0.020
 GK3  plan-3  C13  0.020
 GK3  plan-3  C27  0.020
 GK3  plan-3  C28  0.020
 GK3  plan-3  H9   0.020
 GK3  plan-3  H10  0.020
 GK3  plan-3  H16  0.020
 GK3  plan-3  H27  0.020
 GK3  plan-4  C13  0.020
 GK3  plan-4  C28  0.020
 GK3  plan-4  C14  0.020
 GK3  plan-4  C17  0.020
 GK3  plan-4  C12  0.020
 GK3  plan-4  C20  0.020
 GK3  plan-4  C26  0.020
 GK3  plan-4  C23  0.020
 GK3  plan-4  C1   0.020
 GK3  plan-4  H14  0.020
 GK3  plan-4  H20  0.020
 GK3  plan-4  H26  0.020
 GK3  plan-5  C15  0.020
 GK3  plan-5  N3   0.020
 GK3  plan-5  C3   0.020
 GK3  plan-5  O1   0.020
 GK3  plan-5  C25  0.020
 GK3  plan-5  HN3  0.020

