# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 20 05:36:39 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: (1S,2S)-2-ethyl-1-({[(3aS,4S,6R,7aS)-6-ethyl-1-oxooctahydro-1H-inden-4-yl]carbonyl}amino)cyclopropanecarboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@@H]1C[C@H]2[C@H](CCC2=O)[C@H](C1)C(=O)N[C@]3(C[C@@H]3CC)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
 OGK  OGK  '(1S,2S)-2-ethyl-1-({[(3aS,4S,6R,7aS)-6-ethyl-1-oxooctahydro-1H-inden-4-yl]carbonyl}amino)cyclopropanecarboxylic acid'  ligand  50  23  .  2022-09-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_OGK
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
 OGK  C01   C  CH3   0  -0.668  -1.0455   4.1447  -0.0046
 OGK  C02   C  CH2   0  -0.412  -2.2115   3.2055  -0.2862
 OGK  C03   C  CH1   0  -0.232  -1.8453   1.7216  -0.2507
 OGK  C04   C  CH2   0  -0.439  -1.4392   1.2671   1.1483
 OGK  C05   C  CH1   0  -0.403  -1.0310  -0.2128   1.1910
 OGK  C06   C  C     0   0.599   0.3054  -0.4284   0.4890
 OGK  O07   O  O     0  -0.473   0.4384  -1.1123  -0.5117
 OGK  N08   N  NH1   0  -0.677   1.3615   0.1845   1.0727
 OGK  C09   C  CT    0   0.027   2.6632   0.1338   0.5076
 OGK  C10   C  C     0   0.556   2.9284   1.0498  -0.6409
 OGK  O11   O  O     0  -0.451   4.0139   1.2207  -1.1442
 OGK  O12   O  OH1   0  -0.580   1.8393   1.6828  -1.0500
 OGK  C13   C  CH2   0  -0.474   3.8187  -0.1073   1.4539
 OGK  C14   C  CH1   0  -0.177   3.3672  -1.2107   0.5729
 OGK  C15   C  CH2   0  -0.450   4.2117  -1.8076  -0.5206
 OGK  C16   C  CH3   0  -0.664   5.1598  -2.8597   0.0435
 OGK  C17   C  CH1   0  -0.223  -2.1116  -1.1128   0.6003
 OGK  C18   C  CH2   0  -0.450  -3.3587  -1.2944   1.4775
 OGK  C19   C  CH2   0  -0.574  -4.3788  -1.9044   0.5177
 OGK  C20   C  C     0   0.426  -3.9863  -1.3911  -0.8539
 OGK  O21   O  O     0  -0.409  -4.6231  -1.5474  -1.8694
 OGK  C22   C  CH1   0  -0.379  -2.6839  -0.6312  -0.7379
 OGK  C23   C  CH2   0  -0.417  -3.0173   0.8714  -0.7315
 OGK  H01   H  HCH3  0   0.220  -0.6493   4.0210   1.0038
 OGK  H01A  H  HCH3  0   0.217  -0.2263   3.9706  -0.7040
 OGK  H02   H  HCH2  0   0.210  -3.0184   3.3934   0.4306
 OGK  H03   H  HCH1  0   0.226  -0.9987   1.5687  -0.9324
 OGK  H04   H  HCH2  0   0.242  -0.6333   1.8917   1.5383
 OGK  H04A  H  HCH2  0   0.235  -2.2830   1.4186   1.8296
 OGK  H05   H  HCH1  0   0.278  -0.8836  -0.4915   2.2418
 OGK  HN08  H  HNH1  0   0.400   1.2106   0.7886   1.8649
 OGK  HO12  H  HOH1  0   0.482   2.0636   2.2646  -1.7914
 OGK  H13   H  HCH2  0   0.268   4.7481   0.3946   1.2155
 OGK  H13A  H  HCH2  0   0.276   3.5809  -0.1429   2.5097
 OGK  H14   H  HCH1  0   0.270   2.7427  -1.9470   1.0691
 OGK  H15   H  HCH2  0   0.229   3.5501  -2.2652  -1.2611
 OGK  H15A  H  HCH2  0   0.235   4.7849  -1.0426  -1.0412
 OGK  H16   H  HCH3  0   0.232   5.7392  -3.3313  -0.7505
 OGK  H16A  H  HCH3  0   0.223   5.8627  -2.4145   0.7493
 OGK  H16B  H  HCH3  0   0.219   4.6165  -3.6465   0.5695
 OGK  H17   H  HCH1  0   0.251  -1.6874  -2.1096   0.4434
 OGK  H18   H  HCH2  0   0.250  -3.1586  -1.9295   2.3403
 OGK  H18A  H  HCH2  0   0.236  -3.7238  -0.3380   1.8586
 OGK  H19   H  HCH2  0   0.278  -4.2912  -2.9959   0.4983
 OGK  H19A  H  HCH2  0   0.276  -5.4206  -1.6750   0.7461
 OGK  H22   H  HCH1  0   0.274  -2.0204  -0.8432  -1.5780
 OGK  H23   H  HCH2  0   0.223  -3.8759   1.0741  -0.0794
 OGK  H23A  H  HCH2  0   0.246  -3.3198   1.1684  -1.7388
 OGK  H26   H  HCH3  0   0.229  -1.3522   5.1863  -0.1061
 OGK  H27   H  HCH2  0   0.222  -2.6219   3.4387  -1.2734

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
 OGK  C01  H01   single  0.970  0.020  1.090
 OGK  C01  H01A  single  0.970  0.020  1.090
 OGK  C02  C01   single  1.524  0.020  1.524
 OGK  C02  H02   single  0.970  0.020  1.090
 OGK  C03  C02   single  1.529  0.020  1.529
 OGK  C03  C23   single  1.526  0.020  1.526
 OGK  C03  H03   single  0.970  0.020  1.090
 OGK  C04  C03   single  1.526  0.020  1.526
 OGK  C04  H04   single  0.970  0.020  1.090
 OGK  C04  H04A  single  0.970  0.020  1.090
 OGK  C05  C04   single  1.536  0.020  1.536
 OGK  C05  H05   single  0.970  0.020  1.090
 OGK  C06  C05   single  1.525  0.020  1.525
 OGK  O07  C06   double  1.219  0.020  1.219
 OGK  N08  C06   single  1.353  0.020  1.353
 OGK  N08  HN08  single  0.860  0.020  1.020
 OGK  C09  N08   single  1.420  0.020  1.420
 OGK  C09  C14   single  1.519  0.020  1.519
 OGK  C09  C13   single  1.513  0.020  1.513
 OGK  C10  C09   single  1.493  0.020  1.493
 OGK  O11  C10   double  1.209  0.020  1.209
 OGK  O12  C10   single  1.325  0.020  1.325
 OGK  O12  HO12  single  0.850  0.020  0.980
 OGK  C13  H13   single  0.970  0.020  1.090
 OGK  C13  H13A  single  0.970  0.020  1.090
 OGK  C14  C13   single  1.482  0.020  1.482
 OGK  C14  H14   single  0.970  0.020  1.090
 OGK  C15  C14   single  1.505  0.020  1.505
 OGK  C15  C16   single  1.524  0.020  1.524
 OGK  C15  H15   single  0.970  0.020  1.090
 OGK  C15  H15A  single  0.970  0.020  1.090
 OGK  C16  H16   single  0.970  0.020  1.090
 OGK  C16  H16A  single  0.970  0.020  1.090
 OGK  C16  H16B  single  0.970  0.020  1.090
 OGK  C17  C05   single  1.525  0.020  1.525
 OGK  C17  C22   single  1.533  0.020  1.533
 OGK  C17  C18   single  1.536  0.020  1.536
 OGK  C17  H17   single  0.970  0.020  1.090
 OGK  C18  C19   single  1.528  0.020  1.528
 OGK  C18  H18   single  0.970  0.020  1.090
 OGK  C18  H18A  single  0.970  0.020  1.090
 OGK  C19  H19   single  0.970  0.020  1.090
 OGK  C19  H19A  single  0.970  0.020  1.090
 OGK  C20  C19   single  1.516  0.020  1.516
 OGK  C20  O21   double  1.209  0.020  1.209
 OGK  C22  C20   single  1.512  0.020  1.512
 OGK  C22  C23   single  1.539  0.020  1.539
 OGK  C22  H22   single  0.970  0.020  1.090
 OGK  C23  H23   single  0.970  0.020  1.090
 OGK  C23  H23A  single  0.970  0.020  1.090
 OGK  C01  H26   single  0.970  0.020  1.090
 OGK  C02  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
 OGK  H26   C01  H01A  107.69  3.000
 OGK  H26   C01  H01   107.26  3.000
 OGK  H01A  C01  H01   107.57  3.000
 OGK  H26   C01  C02   110.87  3.000
 OGK  H01A  C01  C02   110.96  3.000
 OGK  H01   C01  C02   112.27  3.000
 OGK  H27   C02  H02   106.11  3.000
 OGK  H27   C02  C03   108.52  3.000
 OGK  H02   C02  C03   109.13  3.000
 OGK  H27   C02  C01   108.81  3.000
 OGK  C03   C02  C01   114.25  3.000
 OGK  H02   C02  C01   109.69  3.000
 OGK  H03   C03  C23   108.61  3.000
 OGK  H03   C03  C04   108.82  3.000
 OGK  C23   C03  C04   109.11  3.000
 OGK  C04   C03  C02   111.97  3.000
 OGK  H03   C03  C02   107.79  3.000
 OGK  C23   C03  C02   110.46  3.000
 OGK  H04A  C04  H04   105.51  3.000
 OGK  H04A  C04  C05   108.72  3.000
 OGK  H04   C04  C05   110.19  3.000
 OGK  C05   C04  C03   112.53  3.000
 OGK  H04A  C04  C03   108.91  3.000
 OGK  H04   C04  C03   110.70  3.000
 OGK  H05   C05  C17   108.43  3.000
 OGK  C17   C05  C06   111.05  3.000
 OGK  H05   C05  C06   106.69  3.000
 OGK  C17   C05  C04   111.68  3.000
 OGK  C06   C05  C04   110.88  3.000
 OGK  H05   C05  C04   107.89  3.000
 OGK  N08   C06  O07   121.52  3.000
 OGK  N08   C06  C05   114.92  3.000
 OGK  O07   C06  C05   123.55  3.000
 OGK  HN08  N08  C09   118.13  3.000
 OGK  C09   N08  C06   121.84  3.000
 OGK  HN08  N08  C06   119.59  3.000
 OGK  C14   C09  C13    58.54  3.000
 OGK  C13   C09  C10   116.32  3.000
 OGK  C14   C09  C10   119.59  3.000
 OGK  C10   C09  N08   116.56  3.000
 OGK  C13   C09  N08   117.19  3.000
 OGK  C14   C09  N08   116.06  3.000
 OGK  O12   C10  O11   122.84  3.000
 OGK  O12   C10  C09   112.63  3.000
 OGK  O11   C10  C09   124.52  3.000
 OGK  HO12  O12  C10   109.45  3.000
 OGK  H13A  C13  H13   114.73  3.000
 OGK  H13A  C13  C14   119.22  3.000
 OGK  H13   C13  C14   118.39  3.000
 OGK  C14   C13  C09    60.94  3.000
 OGK  H13A  C13  C09   116.58  3.000
 OGK  H13   C13  C09   116.36  3.000
 OGK  H14   C14  C15   112.70  3.000
 OGK  C15   C14  C13   123.79  3.000
 OGK  H14   C14  C13   114.11  3.000
 OGK  C15   C14  C09   125.44  3.000
 OGK  H14   C14  C09   110.69  3.000
 OGK  C13   C14  C09    60.52  3.000
 OGK  H15A  C15  H15   106.79  3.000
 OGK  H15A  C15  C16   109.54  3.000
 OGK  H15   C15  C16   109.76  3.000
 OGK  H15A  C15  C14   111.36  3.000
 OGK  H15   C15  C14   108.58  3.000
 OGK  C16   C15  C14   110.72  3.000
 OGK  H16B  C16  H16A  107.64  3.000
 OGK  H16B  C16  H16   107.68  3.000
 OGK  H16A  C16  H16   107.78  3.000
 OGK  H16B  C16  C15   111.48  3.000
 OGK  H16A  C16  C15   111.01  3.000
 OGK  H16   C16  C15   111.07  3.000
 OGK  H17   C17  C22   107.79  3.000
 OGK  H17   C17  C18   106.79  3.000
 OGK  C22   C17  C18   103.45  3.000
 OGK  H17   C17  C05   108.56  3.000
 OGK  C18   C17  C05   115.08  3.000
 OGK  C22   C17  C05   114.66  3.000
 OGK  H18A  C18  H18   107.18  3.000
 OGK  H18A  C18  C19   110.22  3.000
 OGK  H18   C18  C19   112.79  3.000
 OGK  H18A  C18  C17   111.54  3.000
 OGK  H18   C18  C17   111.84  3.000
 OGK  C19   C18  C17   103.34  3.000
 OGK  H19A  C19  H19   106.84  3.000
 OGK  H19A  C19  C20   111.43  3.000
 OGK  H19   C19  C20   107.50  3.000
 OGK  C20   C19  C18   105.09  3.000
 OGK  H19A  C19  C18   114.97  3.000
 OGK  H19   C19  C18   110.84  3.000
 OGK  C22   C20  O21   125.67  3.000
 OGK  C22   C20  C19   108.89  3.000
 OGK  O21   C20  C19   125.44  3.000
 OGK  H22   C22  C23   108.94  3.000
 OGK  H22   C22  C20   111.53  3.000
 OGK  C23   C22  C20   107.72  3.000
 OGK  H22   C22  C17   112.58  3.000
 OGK  C23   C22  C17   112.57  3.000
 OGK  C20   C22  C17   103.33  3.000
 OGK  H23A  C23  H23   106.32  3.000
 OGK  H23A  C23  C22   108.75  3.000
 OGK  H23   C23  C22   110.63  3.000
 OGK  H23A  C23  C03   110.59  3.000
 OGK  H23   C23  C03   108.11  3.000
 OGK  C22   C23  C03   112.27  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
 OGK  CONST_01  C09   N08  C06  C05   180.00   0.0  0
 OGK  CONST_02  C09   N08  C06  O07     0.00   0.0  0
 OGK  CONST_03  HN08  N08  C06  C05     0.00   0.0  0
 OGK  CONST_04  HO12  O12  C10  C09   180.00   0.0  0
 OGK  Var_01    C20   C19  C18  C17   -28.31  30.0  1
 OGK  Var_02    C22   C20  C19  C18     6.26  30.0  1
 OGK  Var_03    C13   C14  C09  N08  -107.28  30.0  1
 OGK  Var_04    C15   C14  C13  C09   115.04  30.0  1
 OGK  Var_05    C14   C09  N08  C06   -70.68  30.0  2
 OGK  Var_06    C16   C15  C14  C09   158.66  30.0  1
 OGK  Var_07    H01   C01  C02  C03   -63.66  30.0  3
 OGK  Var_08    H16   C16  C15  C14   177.16  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
 OGK  chir_01  C03  C02  C23  C04  positiv
 OGK  chir_02  C05  C17  C06  C04  negativ
 OGK  chir_05  C17  C05  C22  C18  positiv
 OGK  chir_06  C22  C17  C20  C23  negativ
 OGK  chir_07  C09  C14  C13  C10  both
 OGK  chir_08  C14  C09  C13  C15  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
 OGK  plan-1  C05   0.020
 OGK  plan-1  C06   0.020
 OGK  plan-1  O07   0.020
 OGK  plan-1  N08   0.020
 OGK  plan-1  C09   0.020
 OGK  plan-1  HN08  0.020
 OGK  plan-2  C19   0.020
 OGK  plan-2  C20   0.020
 OGK  plan-2  O21   0.020
 OGK  plan-2  C22   0.020
 OGK  plan-3  C09   0.020
 OGK  plan-3  C10   0.020
 OGK  plan-3  O11   0.020
 OGK  plan-3  O12   0.020
 OGK  plan-3  HO12  0.020

