# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 08:21:31 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: N~3~-cyclopropyl-N~4~'-(cyclopropylmethyl)-6-methylbiphenyl-3,4'-dicarboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(cc1c2ccc(cc2)C(=O)NCC3CC3)C(=O)NC4CC4
#
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
 GK5  GK5  N~3~-cyclopropyl-N~4~'-(cyclopropylmethyl)-6-methylbiphenyl-3,4'-dicarboxamide  ligand  50  26  .  2022-09-22  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_GK5
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
 GK5  C9    C  CH3   0  -0.745   1.0467   3.7823   0.8365
 GK5  C22   C  CH2   0  -0.512   7.7379  -1.9636   0.4562
 GK5  C21   C  CH2   0  -0.484   7.1005  -2.2982  -0.8573
 GK5  C18   C  CH1   0  -0.080   6.2656  -2.2054   0.3797
 GK5  C26   C  CH2   0  -0.489  -8.0289  -2.4509   0.4814
 GK5  C25   C  CH2   0  -0.482  -6.7776  -2.5213   1.3030
 GK5  C24   C  CH1   0  -0.302  -6.7117  -2.1014  -0.1350
 GK5  C4    C  CR6   0   0.071   1.8596   2.5509   0.5612
 GK5  C8    C  CR16  0  -0.281   3.2413   2.5893   0.7299
 GK5  C13   C  CR16  0  -0.286   4.0346   1.4730   0.5213
 GK5  C7    C  CR6   0  -0.033   3.4532   0.2707   0.1320
 GK5  C12   C  C     0   0.528   4.2477  -0.9649  -0.1370
 GK5  O16   O  O     0  -0.482   3.8602  -1.8112  -0.9295
 GK5  N15   N  NH1   0  -0.656   5.4041  -1.0815   0.5437
 GK5  C3    C  CR16  0  -0.311   2.0760   0.2246  -0.0533
 GK5  C1    C  CR6   0   0.068   1.2737   1.3404   0.1593
 GK5  C2    C  CR6   0   0.036  -0.1890   1.2026  -0.0275
 GK5  C5    C  CR16  0  -0.278  -0.8862   1.9931  -0.9407
 GK5  C10   C  CR16  0  -0.256  -2.2506   1.8384  -1.1142
 GK5  C14   C  CR6   0  -0.041  -2.9538   0.8774  -0.3914
 GK5  C11   C  CR16  0  -0.277  -2.2624   0.0881   0.5237
 GK5  C6    C  CR16  0  -0.281  -0.8972   0.2494   0.7012
 GK5  C17   C  C     0   0.533  -4.4297   0.7672  -0.6048
 GK5  O20   O  O     0  -0.495  -5.0853   1.7232  -1.0021
 GK5  N19   N  NH1   0  -0.652  -4.9834  -0.4237  -0.3406
 GK5  C23   C  CH2   0  -0.251  -6.4074  -0.6699  -0.4722
 GK5  H9    H  HCH3  0   0.255   0.7384   4.2766  -0.0860
 GK5  H9A   H  HCH3  0   0.250   0.1395   3.5520   1.3949
 GK5  H9B   H  HCH3  0   0.256   1.6243   4.5039   1.4120
 GK5  H22A  H  HCH2  0   0.258   8.0735  -0.9454   0.6090
 GK5  H21   H  HCH2  0   0.256   7.0023  -1.5027  -1.5841
 GK5  H21A  H  HCH2  0   0.256   7.2649  -3.2804  -1.2806
 GK5  H18   H  HCH1  0   0.268   5.8964  -3.1382   0.7950
 GK5  H26   H  HCH2  0   0.255  -8.4983  -3.3789   0.1818
 GK5  H26A  H  HCH2  0   0.249  -8.7271  -1.6477   0.6843
 GK5  H25   H  HCH2  0   0.248  -6.6251  -1.7604   2.0593
 GK5  H25A  H  HCH2  0   0.254  -6.3926  -3.4968   1.5696
 GK5  H24   H  HCH1  0   0.268  -6.3005  -2.8273  -0.8300
 GK5  H8    H  HCR6  0   0.258   3.7081   3.5162   1.0400
 GK5  H13   H  HCR6  0   0.259   5.1064   1.5630   0.6468
 GK5  HN15  H  HNH1  0   0.406   5.5793  -0.4623   1.3188
 GK5  H3    H  HCR6  0   0.256   1.6152  -0.7013  -0.3745
 GK5  H5    H  HCR6  0   0.261  -0.3580   2.7291  -1.5335
 GK5  H10   H  HCR6  0   0.260  -2.7712   2.4628  -1.8281
 GK5  H11   H  HCR6  0   0.258  -2.7788  -0.6422   1.1341
 GK5  H6    H  HCR6  0   0.261  -0.3808  -0.3624   1.4305
 GK5  HN19  H  HNH1  0   0.408  -4.3970  -1.2115  -0.1188
 GK5  H23   H  HCH2  0   0.246  -6.7353  -0.4441  -1.4906
 GK5  H23A  H  HCH2  0   0.235  -6.9594  -0.0020   0.1952
 GK5  H22   H  HCH2  0   0.260   8.3434  -2.7136   0.9472

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
 GK5  C9   C4    single    1.501  0.020  1.501
 GK5  C22  C21   single    1.498  0.020  1.498
 GK5  C22  C18   single    1.494  0.020  1.494
 GK5  C21  C18   single    1.495  0.020  1.495
 GK5  C18  N15   single    1.426  0.020  1.426
 GK5  C26  C25   single    1.499  0.020  1.499
 GK5  C26  C24   single    1.496  0.020  1.496
 GK5  C25  C24   single    1.499  0.020  1.499
 GK5  C24  C23   single    1.502  0.020  1.502
 GK5  C4   C8    aromatic  1.393  0.020  1.393
 GK5  C4   C1    aromatic  1.404  0.020  1.404
 GK5  C8   C13   aromatic  1.385  0.020  1.385
 GK5  C13  C7    aromatic  1.391  0.020  1.391
 GK5  C7   C12   single    1.493  0.020  1.493
 GK5  C7   C3    aromatic  1.390  0.020  1.390
 GK5  C12  O16   double    1.222  0.020  1.222
 GK5  C12  N15   single    1.347  0.020  1.347
 GK5  C3   C1    aromatic  1.391  0.020  1.391
 GK5  C1   C2    single    1.481  0.020  1.481
 GK5  C2   C5    aromatic  1.395  0.020  1.395
 GK5  C2   C6    aromatic  1.393  0.020  1.393
 GK5  C5   C10   aromatic  1.384  0.020  1.384
 GK5  C10  C14   aromatic  1.393  0.020  1.393
 GK5  C14  C11   aromatic  1.392  0.020  1.392
 GK5  C14  C17   single    1.495  0.020  1.495
 GK5  C11  C6    aromatic  1.386  0.020  1.386
 GK5  C17  O20   double    1.225  0.020  1.225
 GK5  C17  N19   single    1.340  0.020  1.340
 GK5  N19  C23   single    1.451  0.020  1.451
 GK5  C9   H9    single    0.970  0.020  1.090
 GK5  C9   H9A   single    0.970  0.020  1.090
 GK5  C9   H9B   single    0.970  0.020  1.090
 GK5  C22  H22   single    0.970  0.020  1.090
 GK5  C22  H22A  single    0.970  0.020  1.090
 GK5  C21  H21   single    0.970  0.020  1.090
 GK5  C21  H21A  single    0.970  0.020  1.090
 GK5  C18  H18   single    0.970  0.020  1.090
 GK5  C26  H26   single    0.970  0.020  1.090
 GK5  C26  H26A  single    0.970  0.020  1.090
 GK5  C25  H25   single    0.970  0.020  1.090
 GK5  C25  H25A  single    0.970  0.020  1.090
 GK5  C24  H24   single    0.970  0.020  1.090
 GK5  C8   H8    single    0.930  0.020  1.080
 GK5  C13  H13   single    0.930  0.020  1.080
 GK5  N15  HN15  single    0.860  0.020  1.020
 GK5  C3   H3    single    0.930  0.020  1.080
 GK5  C5   H5    single    0.930  0.020  1.080
 GK5  C10  H10   single    0.930  0.020  1.080
 GK5  C11  H11   single    0.930  0.020  1.080
 GK5  C6   H6    single    0.930  0.020  1.080
 GK5  N19  HN19  single    0.860  0.020  1.020
 GK5  C23  H23   single    0.970  0.020  1.090
 GK5  C23  H23A  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
 GK5  H9B   C9   H9A  108.11  3.000
 GK5  H9B   C9   H9   107.25  3.000
 GK5  H9A   C9   H9   107.08  3.000
 GK5  H9B   C9   C4   110.69  3.000
 GK5  H9A   C9   C4   111.81  3.000
 GK5  H9    C9   C4   111.69  3.000
 GK5  H22A  C22  H22  114.47  3.000
 GK5  H22A  C22  C18  117.70  3.000
 GK5  H22   C22  C18  117.56  3.000
 GK5  H22A  C22  C21  117.75  3.000
 GK5  H22   C22  C21  118.78  3.000
 GK5  C18   C22  C21   59.97  3.000
 GK5  H21A  C21  H21  114.73  3.000
 GK5  H21A  C21  C18  117.70  3.000
 GK5  H21   C21  C18  117.35  3.000
 GK5  H21A  C21  C22  118.76  3.000
 GK5  H21   C21  C22  117.61  3.000
 GK5  C18   C21  C22   59.89  3.000
 GK5  H18   C18  N15  115.33  3.000
 GK5  H18   C18  C21  116.94  3.000
 GK5  N15   C18  C21  118.79  3.000
 GK5  H18   C18  C22  117.03  3.000
 GK5  N15   C18  C22  117.52  3.000
 GK5  C21   C18  C22   60.14  3.000
 GK5  H26A  C26  H26  114.08  3.000
 GK5  H26A  C26  C24  118.13  3.000
 GK5  H26   C26  C24  117.92  3.000
 GK5  H26A  C26  C25  118.05  3.000
 GK5  H26   C26  C25  118.27  3.000
 GK5  C24   C26  C25   60.11  3.000
 GK5  H25A  C25  H25  114.27  3.000
 GK5  H25A  C25  C24  118.23  3.000
 GK5  H25   C25  C24  117.81  3.000
 GK5  H25A  C25  C26  118.33  3.000
 GK5  H25   C25  C26  117.85  3.000
 GK5  C24   C25  C26   59.85  3.000
 GK5  H24   C24  C23  114.63  3.000
 GK5  H24   C24  C25  116.32  3.000
 GK5  C23   C24  C25  119.41  3.000
 GK5  H24   C24  C26  116.17  3.000
 GK5  C23   C24  C26  119.58  3.000
 GK5  C25   C24  C26   60.04  3.000
 GK5  C1    C4   C8   118.20  3.000
 GK5  C1    C4   C9   122.27  3.000
 GK5  C8    C4   C9   119.51  3.000
 GK5  H8    C8   C13  119.07  3.000
 GK5  H8    C8   C4   119.07  3.000
 GK5  C13   C8   C4   121.85  3.000
 GK5  H13   C13  C7   121.19  3.000
 GK5  H13   C13  C8   118.84  3.000
 GK5  C7    C13  C8   119.96  3.000
 GK5  C3    C7   C12  118.40  3.000
 GK5  C3    C7   C13  118.68  3.000
 GK5  C12   C7   C13  122.90  3.000
 GK5  N15   C12  O16  122.68  3.000
 GK5  N15   C12  C7   115.93  3.000
 GK5  O16   C12  C7   121.39  3.000
 GK5  HN15  N15  C12  119.01  3.000
 GK5  HN15  N15  C18  117.91  3.000
 GK5  C12   N15  C18  121.93  3.000
 GK5  H3    C3   C1   119.07  3.000
 GK5  H3    C3   C7   119.30  3.000
 GK5  C1    C3   C7   121.63  3.000
 GK5  C2    C1   C3   118.42  3.000
 GK5  C2    C1   C4   121.91  3.000
 GK5  C3    C1   C4   119.67  3.000
 GK5  C6    C2   C5   118.44  3.000
 GK5  C6    C2   C1   119.98  3.000
 GK5  C5    C2   C1   121.58  3.000
 GK5  H5    C5   C10  119.23  3.000
 GK5  H5    C5   C2   119.99  3.000
 GK5  C10   C5   C2   120.77  3.000
 GK5  H10   C10  C14  119.84  3.000
 GK5  H10   C10  C5   119.51  3.000
 GK5  C14   C10  C5   120.65  3.000
 GK5  C17   C14  C11  122.83  3.000
 GK5  C17   C14  C10  118.36  3.000
 GK5  C11   C14  C10  118.78  3.000
 GK5  H11   C11  C6   118.42  3.000
 GK5  H11   C11  C14  121.07  3.000
 GK5  C6    C11  C14  120.49  3.000
 GK5  H6    C6   C11  119.35  3.000
 GK5  H6    C6   C2   119.76  3.000
 GK5  C11   C6   C2   120.88  3.000
 GK5  N19   C17  O20  122.44  3.000
 GK5  N19   C17  C14  116.44  3.000
 GK5  O20   C17  C14  121.12  3.000
 GK5  HN19  N19  C23  117.30  3.000
 GK5  HN19  N19  C17  119.89  3.000
 GK5  C23   N19  C17  122.58  3.000
 GK5  H23A  C23  H23  106.91  3.000
 GK5  H23A  C23  N19  109.65  3.000
 GK5  H23   C23  N19  110.10  3.000
 GK5  H23A  C23  C24  110.05  3.000
 GK5  H23   C23  C24  110.19  3.000
 GK5  N19   C23  C24  109.89  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
 GK5  CONST_01  C7    C13  C8   C4      0.00   0.0  0
 GK5  CONST_02  C7    C3   C1   C4      0.00   0.0  0
 GK5  CONST_05  C3    C1   C4   C8      0.00   0.0  0
 GK5  CONST_06  C2    C1   C4   C8    180.00   0.0  0
 GK5  CONST_07  C3    C7   C13  C8      0.00   0.0  0
 GK5  CONST_08  C1    C4   C8   C13     0.00   0.0  0
 GK5  CONST_09  C1    C3   C7   C13     0.00   0.0  0
 GK5  CONST_10  C2    C1   C3   C7    180.00   0.0  0
 GK5  CONST_13  C10   C5   C2   C1    180.00   0.0  0
 GK5  CONST_14  C11   C6   C2   C1    180.00   0.0  0
 GK5  CONST_15  C14   C10  C5   C2      0.00   0.0  0
 GK5  CONST_16  C14   C11  C6   C2      0.00   0.0  0
 GK5  CONST_17  C11   C6   C2   C5      0.00   0.0  0
 GK5  CONST_18  C11   C14  C10  C5      0.00   0.0  0
 GK5  CONST_19  C6    C2   C5   C10     0.00   0.0  0
 GK5  CONST_20  C6    C11  C14  C10     0.00   0.0  0
 GK5  CONST_21  C13   C8   C4   C9    180.00   0.0  0
 GK5  CONST_22  C3    C1   C4   C9    180.00   0.0  0
 GK5  CONST_23  C2    C1   C4   C9      0.00   0.0  0
 GK5  CONST_24  C12   C7   C13  C8    180.00   0.0  0
 GK5  CONST_25  C1    C3   C7   C12   180.00   0.0  0
 GK5  CONST_26  C17   C14  C10  C5    180.00   0.0  0
 GK5  CONST_27  C17   C14  C11  C6    180.00   0.0  0
 GK5  CONST_28  H13   C13  C8   C4    180.00   0.0  0
 GK5  CONST_29  H3    C3   C1   C4    180.00   0.0  0
 GK5  CONST_30  H8    C8   C13  C7    180.00   0.0  0
 GK5  CONST_31  H5    C5   C2   C1      0.00   0.0  0
 GK5  CONST_32  H6    C6   C2   C1      0.00   0.0  0
 GK5  CONST_33  H10   C10  C5   C2    180.00   0.0  0
 GK5  CONST_34  H11   C11  C6   C2    180.00   0.0  0
 GK5  CONST_35  C7    C12  N15  C18   180.00   0.0  0
 GK5  CONST_36  O16   C12  N15  C18     0.00   0.0  0
 GK5  CONST_37  C23   N19  C17  C14   180.00   0.0  0
 GK5  CONST_38  HN15  N15  C12  C7      0.00   0.0  0
 GK5  CONST_39  HN19  N19  C17  C14     0.00   0.0  0
 GK5  CONST_40  C23   N19  C17  O20     0.00   0.0  0
 GK5  Var_01    N15   C18  C21  C22   107.00  30.0  1
 GK5  Var_02    C23   C24  C25  C26   109.22  30.0  1
 GK5  Var_03    C12   N15  C18  C22   144.61  30.0  3
 GK5  Var_04    N19   C23  C24  C26   148.67  30.0  3
 GK5  Var_05    O16   C12  C7   C13  -151.40  30.0  2
 GK5  Var_06    O20   C17  C14  C10   -25.15  30.0  2
 GK5  Var_07    H9    C9   C4   C8    103.46  30.0  2
 GK5  Var_08    C17   N19  C23  C24   178.77  30.0  2

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 GK5  chir_01  C18  C22  C21  N15  both
 GK5  chir_02  C24  C26  C25  C23  both

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
 GK5  plan-1  C9    0.020
 GK5  plan-1  C4    0.020
 GK5  plan-1  C8    0.020
 GK5  plan-1  C13   0.020
 GK5  plan-1  C7    0.020
 GK5  plan-1  C12   0.020
 GK5  plan-1  C3    0.020
 GK5  plan-1  C1    0.020
 GK5  plan-1  C2    0.020
 GK5  plan-1  H8    0.020
 GK5  plan-1  H13   0.020
 GK5  plan-1  H3    0.020
 GK5  plan-2  C1    0.020
 GK5  plan-2  C2    0.020
 GK5  plan-2  C5    0.020
 GK5  plan-2  C10   0.020
 GK5  plan-2  C14   0.020
 GK5  plan-2  C11   0.020
 GK5  plan-2  C6    0.020
 GK5  plan-2  C17   0.020
 GK5  plan-2  H5    0.020
 GK5  plan-2  H10   0.020
 GK5  plan-2  H11   0.020
 GK5  plan-2  H6    0.020
 GK5  plan-3  C18   0.020
 GK5  plan-3  C7    0.020
 GK5  plan-3  C12   0.020
 GK5  plan-3  O16   0.020
 GK5  plan-3  N15   0.020
 GK5  plan-3  HN15  0.020
 GK5  plan-4  C14   0.020
 GK5  plan-4  C17   0.020
 GK5  plan-4  O20   0.020
 GK5  plan-4  N19   0.020
 GK5  plan-4  C23   0.020
 GK5  plan-4  HN19  0.020

