# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 24 12:51:21 2021
#   Inital geometry file: a 122 line input string
#   Ligand name: 7-cyclopropyl-N-[trans-4-(2-hydroxypropan-2-yl)cyclohexyl]-1,8-naphthyridine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(O)[C@H]1CC[C@@H](CC1)NC(=O)c2cnc3nc(ccc3c2)C4CC4
#
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
 TJG  TJG  7-cyclopropyl-N-[trans-4-(2-hydroxypropan-2-yl)cyclohexyl]-1,8-naphthyridine-3-carboxamide  ligand  53  26  .  2022-07-22  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_TJG
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
 TJG  C17  C  CR16  0  -0.063  10.6655   8.9764   5.1031
 TJG  C21  C  CR6   0   0.313  10.3537  10.6086   9.3617
 TJG  C22  C  CR16  0  -0.321  10.7608   9.3845   9.9543
 TJG  C24  C  CR66  0  -0.011  10.9527   8.4723   7.7535
 TJG  C26  C  CH1   0  -0.369  10.0246  11.7553  10.2293
 TJG  C28  C  CH2   0  -0.461   8.9158  12.6943   9.8225
 TJG  C01  C  CH3   0  -0.675  14.7165  -0.1979   2.9571
 TJG  C02  C  CT    0   0.235  13.4479   0.4759   2.4296
 TJG  C03  C  CH3   0  -0.678  13.6229   0.8047   0.9519
 TJG  O04  O  OH1   0  -0.678  12.3739  -0.4576   2.4880
 TJG  C05  C  CH1   0  -0.250  13.0985   1.7190   3.2844
 TJG  C07  C  CH2   0  -0.446  14.1727   2.8093   3.2591
 TJG  C08  C  CH2   0  -0.455  13.8268   3.9757   4.1791
 TJG  C09  C  CH1   0  -0.036  12.4683   4.5699   3.8308
 TJG  C11  C  CH2   0  -0.429  11.3925   3.4882   3.8695
 TJG  C12  C  CH2   0  -0.428  11.7421   2.3361   2.9333
 TJG  N13  N  NH1   0  -0.669  12.1721   5.6698   4.7319
 TJG  O15  O  O     0  -0.491  10.7908   6.7829   3.3347
 TJG  C16  C  CR6   0  -0.126  11.1003   7.6873   5.4944
 TJG  N18  N  N     0  -0.406  10.4049   9.9530   5.9279
 TJG  C19  C  CR66  0   0.319  10.5390   9.7296   7.2533
 TJG  N20  N  N     0  -0.453  10.2518  10.7627   8.0627
 TJG  C23  C  CR16  0  -0.182  11.0572   8.3234   9.1531
 TJG  C25  C  CR16  0  -0.242  11.2338   7.4445   6.8375
 TJG  C27  C  CH2   0  -0.460  10.3246  13.1563   9.7574
 TJG  H1   H  HCR6  0   0.274  10.5408   9.1895   4.0472
 TJG  H2   H  HCR6  0   0.274  10.8306   9.3064  11.0307
 TJG  H3   H  HCH1  0   0.270  10.1360  11.5681  11.2903
 TJG  H4   H  HCH2  0   0.256   8.4122  12.4715   8.8911
 TJG  H5   H  HCH2  0   0.262   8.2790  13.0727  10.6112
 TJG  H6   H  HCH3  0   0.224  14.6163  -0.4527   4.0154
 TJG  H7   H  HCH3  0   0.233  14.9154  -1.1189   2.4064
 TJG  H8   H  HCH3  0   0.226  15.5958   0.4378   2.8557
 TJG  H9   H  HCH3  0   0.234  12.7184   1.2304   0.5158
 TJG  H10  H  HCH3  0   0.228  14.4323   1.5183   0.8020
 TJG  H11  H  HCH3  0   0.233  13.8728  -0.0965   0.3892
 TJG  H12  H  HOH1  0   0.439  12.2447  -0.7091   3.4090
 TJG  H13  H  HCH1  0   0.210  13.0323   1.3613   4.3246
 TJG  H14  H  HCH2  0   0.241  15.1441   2.4119   3.5578
 TJG  H15  H  HCH2  0   0.221  14.2928   3.1899   2.2394
 TJG  H16  H  HCH2  0   0.223  13.8130   3.6290   5.2192
 TJG  H17  H  HCH2  0   0.246  14.5998   4.7448   4.1097
 TJG  H18  H  HCH1  0   0.237  12.5170   4.9755   2.8152
 TJG  H19  H  HCH2  0   0.238  10.4248   3.9130   3.5935
 TJG  H20  H  HCH2  0   0.215  11.2970   3.1174   4.8960
 TJG  H21  H  HCH2  0   0.215  11.7594   2.7100   1.9036
 TJG  H22  H  HCH2  0   0.234  10.9548   1.5830   2.9772
 TJG  H23  H  HNH1  0   0.408  12.6293   5.6644   5.6297
 TJG  H24  H  HCR6  0   0.279  11.3725   7.3759   9.5721
 TJG  H25  H  HCR6  0   0.278  11.5308   6.4759   7.2233
 TJG  H26  H  HCH2  0   0.256  10.7836  13.2529   8.7820
 TJG  H27  H  HCH2  0   0.262  10.6758  13.8583  10.5023
 TJG  C14  C  C     0   0.544  11.3364   6.6704   4.4257

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
 TJG  C03  C02  single    1.524  0.020  1.524
 TJG  C02  C01  single    1.530  0.020  1.530
 TJG  C02  O04  single    1.424  0.020  1.424
 TJG  C02  C05  single    1.549  0.020  1.549
 TJG  C07  C05  single    1.531  0.020  1.531
 TJG  C07  C08  single    1.525  0.020  1.525
 TJG  C12  C05  single    1.531  0.020  1.531
 TJG  C12  C11  single    1.525  0.020  1.525
 TJG  O15  C14  double    1.225  0.020  1.225
 TJG  C08  C09  single    1.523  0.020  1.523
 TJG  C09  C11  single    1.526  0.020  1.526
 TJG  C09  N13  single    1.452  0.020  1.452
 TJG  C14  N13  single    1.339  0.020  1.339
 TJG  C14  C16  single    1.494  0.020  1.494
 TJG  C17  C16  aromatic  1.416  0.020  1.416
 TJG  C17  N18  aromatic  1.305  0.020  1.305
 TJG  C16  C25  aromatic  1.371  0.020  1.371
 TJG  N18  C19  aromatic  1.351  0.020  1.351
 TJG  C25  C24  aromatic  1.405  0.020  1.405
 TJG  C19  C24  aromatic  1.415  0.020  1.415
 TJG  C19  N20  aromatic  1.344  0.020  1.344
 TJG  C24  C23  aromatic  1.411  0.020  1.411
 TJG  N20  C21  aromatic  1.312  0.020  1.312
 TJG  C23  C22  aromatic  1.362  0.020  1.362
 TJG  C21  C22  aromatic  1.420  0.020  1.420
 TJG  C21  C26  single    1.475  0.020  1.475
 TJG  C28  C26  single    1.509  0.020  1.509
 TJG  C28  C27  single    1.484  0.020  1.484
 TJG  C26  C27  single    1.508  0.020  1.508
 TJG  C17  H1   single    0.930  0.020  1.080
 TJG  C22  H2   single    0.930  0.020  1.080
 TJG  C26  H3   single    0.970  0.020  1.090
 TJG  C28  H4   single    0.970  0.020  1.090
 TJG  C28  H5   single    0.970  0.020  1.090
 TJG  C01  H6   single    0.970  0.020  1.090
 TJG  C01  H7   single    0.970  0.020  1.090
 TJG  C01  H8   single    0.970  0.020  1.090
 TJG  C03  H9   single    0.970  0.020  1.090
 TJG  C03  H10  single    0.970  0.020  1.090
 TJG  C03  H11  single    0.970  0.020  1.090
 TJG  O04  H12  single    0.850  0.020  0.980
 TJG  C05  H13  single    0.970  0.020  1.090
 TJG  C07  H14  single    0.970  0.020  1.090
 TJG  C07  H15  single    0.970  0.020  1.090
 TJG  C08  H16  single    0.970  0.020  1.090
 TJG  C08  H17  single    0.970  0.020  1.090
 TJG  C09  H18  single    0.970  0.020  1.090
 TJG  C11  H19  single    0.970  0.020  1.090
 TJG  C11  H20  single    0.970  0.020  1.090
 TJG  C12  H21  single    0.970  0.020  1.090
 TJG  C12  H22  single    0.970  0.020  1.090
 TJG  N13  H23  single    0.860  0.020  1.020
 TJG  C23  H24  single    0.930  0.020  1.080
 TJG  C25  H25  single    0.930  0.020  1.080
 TJG  C27  H26  single    0.970  0.020  1.090
 TJG  C27  H27  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
 TJG  H1   C17  N18  116.46  3.000
 TJG  H1   C17  C16  118.91  3.000
 TJG  N18  C17  C16  124.63  3.000
 TJG  N20  C21  C26  118.27  3.000
 TJG  C26  C21  C22  119.26  3.000
 TJG  N20  C21  C22  122.47  3.000
 TJG  H2   C22  C23  121.00  3.000
 TJG  H2   C22  C21  119.75  3.000
 TJG  C23  C22  C21  119.24  3.000
 TJG  C25  C24  C23  123.67  3.000
 TJG  C23  C24  C19  117.77  3.000
 TJG  C25  C24  C19  118.56  3.000
 TJG  H3   C26  C27  116.52  3.000
 TJG  H3   C26  C28  116.57  3.000
 TJG  C27  C26  C28   58.92  3.000
 TJG  H3   C26  C21  114.76  3.000
 TJG  C27  C26  C21  119.58  3.000
 TJG  C28  C26  C21  119.28  3.000
 TJG  H5   C28  H4   115.18  3.000
 TJG  H5   C28  C27  118.81  3.000
 TJG  H4   C28  C27  117.92  3.000
 TJG  H5   C28  C26  116.97  3.000
 TJG  H4   C28  C26  116.49  3.000
 TJG  C27  C28  C26   60.53  3.000
 TJG  H8   C01  H7   107.35  3.000
 TJG  H8   C01  H6   107.46  3.000
 TJG  H7   C01  H6   107.97  3.000
 TJG  H8   C01  C02  112.33  3.000
 TJG  H7   C01  C02  110.41  3.000
 TJG  H6   C01  C02  111.12  3.000
 TJG  C05  C02  O04  109.47  3.000
 TJG  C05  C02  C03  112.83  3.000
 TJG  O04  C02  C03  105.53  3.000
 TJG  C05  C02  C01  110.50  3.000
 TJG  O04  C02  C01  108.81  3.000
 TJG  C03  C02  C01  109.52  3.000
 TJG  H11  C03  H10  107.44  3.000
 TJG  H11  C03  H9   107.82  3.000
 TJG  H10  C03  H9   107.79  3.000
 TJG  H11  C03  C02  110.37  3.000
 TJG  H10  C03  C02  111.10  3.000
 TJG  H9   C03  C02  112.13  3.000
 TJG  H12  O04  C02  108.14  3.000
 TJG  H13  C05  C12  107.10  3.000
 TJG  H13  C05  C07  106.80  3.000
 TJG  C12  C05  C07  109.31  3.000
 TJG  H13  C05  C02  105.91  3.000
 TJG  C12  C05  C02  113.38  3.000
 TJG  C07  C05  C02  113.85  3.000
 TJG  H15  C07  H14  106.49  3.000
 TJG  H15  C07  C08  108.71  3.000
 TJG  H14  C07  C08  108.37  3.000
 TJG  H15  C07  C05  109.88  3.000
 TJG  H14  C07  C05  111.15  3.000
 TJG  C08  C07  C05  112.06  3.000
 TJG  H17  C08  H16  106.96  3.000
 TJG  H17  C08  C09  109.99  3.000
 TJG  H16  C08  C09  109.21  3.000
 TJG  H17  C08  C07  109.85  3.000
 TJG  H16  C08  C07  109.47  3.000
 TJG  C09  C08  C07  111.27  3.000
 TJG  H18  C09  N13  107.71  3.000
 TJG  H18  C09  C11  108.51  3.000
 TJG  N13  C09  C11  112.17  3.000
 TJG  H18  C09  C08  108.48  3.000
 TJG  N13  C09  C08  109.60  3.000
 TJG  C11  C09  C08  110.27  3.000
 TJG  H20  C11  H19  106.93  3.000
 TJG  H20  C11  C12  109.85  3.000
 TJG  H19  C11  C12  109.99  3.000
 TJG  H20  C11  C09  108.97  3.000
 TJG  H19  C11  C09  110.02  3.000
 TJG  C12  C11  C09  110.99  3.000
 TJG  H22  C12  H21  106.55  3.000
 TJG  H22  C12  C11  109.35  3.000
 TJG  H21  C12  C11  108.83  3.000
 TJG  H22  C12  C05  110.62  3.000
 TJG  H21  C12  C05  109.83  3.000
 TJG  C11  C12  C05  111.52  3.000
 TJG  H23  N13  C14  119.41  3.000
 TJG  H23  N13  C09  117.14  3.000
 TJG  C14  N13  C09  123.45  3.000
 TJG  C25  C16  C14  124.39  3.000
 TJG  C25  C16  C17  117.51  3.000
 TJG  C14  C16  C17  118.07  3.000
 TJG  C19  N18  C17  118.47  3.000
 TJG  N20  C19  N18  116.27  3.000
 TJG  N20  C19  C24  122.20  3.000
 TJG  N18  C19  C24  121.53  3.000
 TJG  C19  N20  C21  119.31  3.000
 TJG  H24  C23  C24  119.84  3.000
 TJG  H24  C23  C22  121.15  3.000
 TJG  C24  C23  C22  119.01  3.000
 TJG  H25  C25  C16  122.23  3.000
 TJG  H25  C25  C24  118.45  3.000
 TJG  C16  C25  C24  119.31  3.000
 TJG  H27  C27  H26  115.14  3.000
 TJG  H27  C27  C28  118.67  3.000
 TJG  H26  C27  C28  118.03  3.000
 TJG  H27  C27  C26  116.85  3.000
 TJG  H26  C27  C26  116.69  3.000
 TJG  C28  C27  C26   60.55  3.000
 TJG  C16  C14  O15  120.28  3.000
 TJG  C16  C14  N13  116.33  3.000
 TJG  O15  C14  N13  123.38  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
 TJG  CONST_01  C24  C25  C16  C17     0.00   0.0  0
 TJG  CONST_02  C24  C19  N18  C17     0.00   0.0  0
 TJG  CONST_03  N20  C19  N18  C17   180.00   0.0  0
 TJG  CONST_04  N18  C19  N20  C21   180.00   0.0  0
 TJG  CONST_05  C24  C19  N20  C21     0.00   0.0  0
 TJG  CONST_06  C24  C23  C22  C21     0.00   0.0  0
 TJG  CONST_07  C25  C24  C23  C22   180.00   0.0  0
 TJG  CONST_08  C19  C24  C23  C22     0.00   0.0  0
 TJG  CONST_09  C19  N20  C21  C22     0.00   0.0  0
 TJG  CONST_10  C19  N18  C17  C16     0.00   0.0  0
 TJG  CONST_11  C19  C24  C25  C16     0.00   0.0  0
 TJG  CONST_12  C23  C24  C25  C16   180.00   0.0  0
 TJG  CONST_13  C25  C16  C17  N18     0.00   0.0  0
 TJG  CONST_14  C25  C24  C19  N18     0.00   0.0  0
 TJG  CONST_15  C23  C24  C19  N18   180.00   0.0  0
 TJG  CONST_16  C25  C24  C19  N20   180.00   0.0  0
 TJG  CONST_17  C23  C24  C19  N20     0.00   0.0  0
 TJG  CONST_18  C23  C22  C21  N20     0.00   0.0  0
 TJG  CONST_19  C19  N20  C21  C26   180.00   0.0  0
 TJG  CONST_20  C23  C22  C21  C26   180.00   0.0  0
 TJG  CONST_21  C14  C16  C25  C24   180.00   0.0  0
 TJG  CONST_22  N18  C17  C16  C14   180.00   0.0  0
 TJG  CONST_23  H25  C25  C16  C17   180.00   0.0  0
 TJG  CONST_24  H24  C23  C22  C21   180.00   0.0  0
 TJG  CONST_25  H2   C22  C23  C24   180.00   0.0  0
 TJG  CONST_26  H1   C17  N18  C19   180.00   0.0  0
 TJG  CONST_27  C16  C14  N13  C09   180.00   0.0  0
 TJG  CONST_28  O15  C14  N13  C09     0.00   0.0  0
 TJG  CONST_29  H23  N13  C14  C16     0.00   0.0  0
 TJG  Var_01    C27  C28  C26  C21  -108.83  30.0  1
 TJG  Var_02    C28  C26  C21  C22  -144.68  30.0  2
 TJG  Var_03    C09  C08  C07  C05   -56.21  30.0  1
 TJG  Var_04    C09  C11  C12  C05    57.68  30.0  1
 TJG  Var_05    O15  C14  C16  C17   -22.52  30.0  2
 TJG  Var_06    H9   C03  C02  C05   -60.08  30.0  3
 TJG  Var_07    H6   C01  C02  C05    55.55  30.0  3

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
 TJG  chir_02  C05  C02  C07  C12  negativ
 TJG  chir_03  C09  N13  C08  C11  negativ
 TJG  chir_04  C26  C21  C28  C27  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
 TJG  plan-1  C09  0.020
 TJG  plan-1  N13  0.020
 TJG  plan-1  O15  0.020
 TJG  plan-1  C16  0.020
 TJG  plan-1  H23  0.020
 TJG  plan-1  C14  0.020
 TJG  plan-2  C17  0.020
 TJG  plan-2  C21  0.020
 TJG  plan-2  C22  0.020
 TJG  plan-2  C24  0.020
 TJG  plan-2  C26  0.020
 TJG  plan-2  C16  0.020
 TJG  plan-2  N18  0.020
 TJG  plan-2  C19  0.020
 TJG  plan-2  N20  0.020
 TJG  plan-2  C23  0.020
 TJG  plan-2  C25  0.020
 TJG  plan-2  H1   0.020
 TJG  plan-2  H2   0.020
 TJG  plan-2  H24  0.020
 TJG  plan-2  H25  0.020
 TJG  plan-2  C14  0.020

