# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 10:48:29 2022
#   Inital geometry file: a 125 line input string
#   Ligand name: (2~{S})-2-(5-cyclohexylpentanoylamino)-3-phenyl-propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@H](Cc1ccccc1)NC(=O)CCCCC2CCCCC2
#
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
 GKX  GKX  "(2~{S})-2-(5-cyclohexylpentanoylamino)-3-phenyl-propanoic acid"  ligand  52  24  .  2022-08-10  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_GKX
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
 GKX  C1   C  CH2    0  -0.429  22.2955   -4.1790  10.0702
 GKX  C2   C  CH2    0  -0.426  22.9835   -2.8549   9.7583
 GKX  C4   C  CH2    0  -0.419  22.6913   -3.3060   7.2936
 GKX  C5   C  CH1    0  -0.220  22.0090   -4.6411   7.5933
 GKX  C6   C  CH2    0  -0.412  21.3285   -4.5791   8.9609
 GKX  C7   C  CH2    0  -0.400  21.0156   -5.0531   6.5086
 GKX  C10  C  CH2    0  -0.564  21.2170   -6.1828   2.7793
 GKX  C11  C  C      0   0.537  22.0354   -7.4571   2.8454
 GKX  C12  C  CH1    0  -0.205  24.2264   -8.4557   2.3266
 GKX  C13  C  C      0   0.427  25.6716   -7.9046   2.2219
 GKX  C14  C  CH2    0  -0.514  23.9168   -9.4112   1.1574
 GKX  C15  C  CR6    0   0.133  23.9715   -8.7416  -0.1858
 GKX  C16  C  CR16   0  -0.297  25.1650   -8.6698  -0.9032
 GKX  C17  C  CR16   0  -0.242  25.2231   -8.0283  -2.1332
 GKX  C18  C  CR16   0  -0.272  24.0841   -7.4415  -2.6691
 GKX  O3   O  O      0  -0.596  26.5703   -8.7622   2.2789
 GKX  O2   O  OC    -1  -0.589  25.8007   -6.6735   2.0820
 GKX  C20  C  CR16   0  -0.313  22.8351   -8.1522  -0.7377
 GKX  C19  C  CR16   0  -0.240  22.8879   -7.5070  -1.9667
 GKX  N1   N  NH1    0  -0.623  23.2890   -7.3630   2.3890
 GKX  O1   O  O      0  -0.513  21.5553   -8.5000   3.2808
 GKX  C9   C  CH2    0  -0.424  20.6058   -5.8145   4.1275
 GKX  C8   C  CH2    0  -0.423  21.6423   -5.3893   5.1607
 GKX  C3   C  CH2    0  -0.426  23.6654   -2.9003   8.3959
 GKX  H1   H  HCH2   0   0.221  21.7679   -4.1177  11.0253
 GKX  H2   H  HCH2   0   0.205  23.0536   -4.9617  10.1860
 GKX  H3   H  HCH2   0   0.222  23.7092   -2.6109  10.5384
 GKX  H4   H  HCH2   0   0.205  22.2396   -2.0506   9.7639
 GKX  H5   H  HCH2   0   0.226  23.2193   -3.3492   6.3377
 GKX  H6   H  HCH2   0   0.200  21.9209   -2.5319   7.1856
 GKX  H7   H  HCH1   0   0.199  22.7916   -5.4116   7.6487
 GKX  H8   H  HCH2   0   0.201  20.5045   -3.8558   8.9168
 GKX  H9   H  HCH2   0   0.219  20.8748   -5.5475   9.1918
 GKX  H10  H  HCH2   0   0.203  20.2718   -4.2575   6.3794
 GKX  H11  H  HCH2   0   0.212  20.4597   -5.9303   6.8583
 GKX  H12  H  HCH2   0   0.239  21.8120   -5.3487   2.3991
 GKX  H13  H  HCH2   0   0.261  20.4205   -6.3529   2.0489
 GKX  H14  H  HCH1   0   0.243  24.1548   -9.0407   3.2490
 GKX  H15  H  HCH2   0   0.243  22.9262   -9.8418   1.3141
 GKX  H16  H  HCH2   0   0.243  24.6288  -10.2368   1.1983
 GKX  H17  H  HCR6   0   0.239  26.0596   -9.1202  -0.4909
 GKX  H18  H  HCR6   0   0.247  26.1597   -7.9882  -2.6751
 GKX  H19  H  HCR6   0   0.248  24.1266   -6.9426  -3.6290
 GKX  H21  H  HCR6   0   0.242  21.8929   -8.2110  -0.2053
 GKX  H22  H  HCR6   0   0.247  21.9922   -7.0586  -2.3780
 GKX  H23  H  HNH1   0   0.382  23.6634   -6.4683   2.1094
 GKX  H24  H  HCH2   0   0.226  19.8926   -4.9993   3.9779
 GKX  H25  H  HCH2   0   0.218  20.0256   -6.6597   4.5069
 GKX  H26  H  HCH2   0   0.213  22.3813   -6.1856   5.3041
 GKX  H27  H  HCH2   0   0.215  22.1955   -4.5300   4.7702
 GKX  H28  H  HCH2   0   0.206  24.4913   -3.6198   8.4288
 GKX  H29  H  HCH2   0   0.222  24.1117   -1.9303   8.1626

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
 GKX  C18  C19  aromatic  1.389  0.020  1.389
 GKX  C18  C17  aromatic  1.389  0.020  1.389
 GKX  C19  C20  aromatic  1.389  0.020  1.389
 GKX  C17  C16  aromatic  1.388  0.020  1.388
 GKX  C20  C15  aromatic  1.394  0.020  1.394
 GKX  C16  C15  aromatic  1.394  0.020  1.394
 GKX  C15  C14  single    1.502  0.020  1.502
 GKX  C14  C12  single    1.541  0.020  1.541
 GKX  N1   C12  single    1.441  0.020  1.441
 GKX  N1   C11  single    1.337  0.020  1.337
 GKX  C12  C13  single    1.550  0.020  1.550
 GKX  O3   C13  deloc     1.244  0.020  1.244
 GKX  C13  O2   deloc     1.246  0.020  1.246
 GKX  C10  C11  single    1.516  0.020  1.516
 GKX  C10  C9   single    1.525  0.020  1.525
 GKX  C11  O1   double    1.228  0.020  1.228
 GKX  C9   C8   single    1.524  0.020  1.524
 GKX  C8   C7   single    1.524  0.020  1.524
 GKX  C7   C5   single    1.527  0.020  1.527
 GKX  C4   C5   single    1.529  0.020  1.529
 GKX  C4   C3   single    1.526  0.020  1.526
 GKX  C5   C6   single    1.529  0.020  1.529
 GKX  C3   C2   single    1.524  0.020  1.524
 GKX  C6   C1   single    1.525  0.020  1.525
 GKX  C2   C1   single    1.524  0.020  1.524
 GKX  C1   H1   single    0.970  0.020  1.090
 GKX  C1   H2   single    0.970  0.020  1.090
 GKX  C2   H3   single    0.970  0.020  1.090
 GKX  C2   H4   single    0.970  0.020  1.090
 GKX  C4   H5   single    0.970  0.020  1.090
 GKX  C4   H6   single    0.970  0.020  1.090
 GKX  C5   H7   single    0.970  0.020  1.090
 GKX  C6   H8   single    0.970  0.020  1.090
 GKX  C6   H9   single    0.970  0.020  1.090
 GKX  C7   H10  single    0.970  0.020  1.090
 GKX  C7   H11  single    0.970  0.020  1.090
 GKX  C10  H12  single    0.970  0.020  1.090
 GKX  C10  H13  single    0.970  0.020  1.090
 GKX  C12  H14  single    0.970  0.020  1.090
 GKX  C14  H15  single    0.970  0.020  1.090
 GKX  C14  H16  single    0.970  0.020  1.090
 GKX  C16  H17  single    0.930  0.020  1.080
 GKX  C17  H18  single    0.930  0.020  1.080
 GKX  C18  H19  single    0.930  0.020  1.080
 GKX  C20  H21  single    0.930  0.020  1.080
 GKX  C19  H22  single    0.930  0.020  1.080
 GKX  N1   H23  single    0.860  0.020  1.020
 GKX  C9   H24  single    0.970  0.020  1.090
 GKX  C9   H25  single    0.970  0.020  1.090
 GKX  C8   H26  single    0.970  0.020  1.090
 GKX  C8   H27  single    0.970  0.020  1.090
 GKX  C3   H28  single    0.970  0.020  1.090
 GKX  C3   H29  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
 GKX  H2   C1   H1   106.36  3.000
 GKX  H2   C1   C6   109.16  3.000
 GKX  H1   C1   C6   110.13  3.000
 GKX  H2   C1   C2   109.26  3.000
 GKX  H1   C1   C2   110.36  3.000
 GKX  C6   C1   C2   111.42  3.000
 GKX  H4   C2   H3   106.45  3.000
 GKX  H4   C2   C3   109.28  3.000
 GKX  H3   C2   C3   110.34  3.000
 GKX  H4   C2   C1   109.28  3.000
 GKX  H3   C2   C1   110.33  3.000
 GKX  C3   C2   C1   111.03  3.000
 GKX  H6   C4   H5   106.33  3.000
 GKX  H6   C4   C3   109.37  3.000
 GKX  H5   C4   C3   109.51  3.000
 GKX  H6   C4   C5   108.78  3.000
 GKX  H5   C4   C5   110.64  3.000
 GKX  C3   C4   C5   112.05  3.000
 GKX  H7   C5   C7   108.04  3.000
 GKX  H7   C5   C6   107.47  3.000
 GKX  C7   C5   C6   110.90  3.000
 GKX  H7   C5   C4   107.70  3.000
 GKX  C6   C5   C4   109.79  3.000
 GKX  C7   C5   C4   112.74  3.000
 GKX  H9   C6   H8   106.30  3.000
 GKX  H9   C6   C5   109.72  3.000
 GKX  H8   C6   C5   108.96  3.000
 GKX  H9   C6   C1   109.98  3.000
 GKX  H8   C6   C1   109.42  3.000
 GKX  C5   C6   C1   112.27  3.000
 GKX  H11  C7   H10  105.92  3.000
 GKX  H11  C7   C8   108.31  3.000
 GKX  H10  C7   C8   109.56  3.000
 GKX  H11  C7   C5   108.62  3.000
 GKX  H10  C7   C5   109.21  3.000
 GKX  C8   C7   C5   114.84  3.000
 GKX  H13  C10  H12  106.43  3.000
 GKX  H13  C10  C9   109.63  3.000
 GKX  H12  C10  C9   109.96  3.000
 GKX  H13  C10  C11  106.95  3.000
 GKX  H12  C10  C11  111.27  3.000
 GKX  C9   C10  C11  112.38  3.000
 GKX  O1   C11  N1   123.18  3.000
 GKX  O1   C11  C10  121.23  3.000
 GKX  N1   C11  C10  115.60  3.000
 GKX  H14  C12  N1   109.03  3.000
 GKX  H14  C12  C14  107.15  3.000
 GKX  N1   C12  C14  111.85  3.000
 GKX  H14  C12  C13  107.93  3.000
 GKX  N1   C12  C13  109.86  3.000
 GKX  C14  C12  C13  110.88  3.000
 GKX  O2   C13  O3   127.71  3.000
 GKX  O2   C13  C12  117.10  3.000
 GKX  O3   C13  C12  115.18  3.000
 GKX  H16  C14  H15  106.76  3.000
 GKX  H16  C14  C15  110.32  3.000
 GKX  H15  C14  C15  109.72  3.000
 GKX  H16  C14  C12  108.03  3.000
 GKX  H15  C14  C12  108.54  3.000
 GKX  C15  C14  C12  113.25  3.000
 GKX  C20  C15  C16  118.18  3.000
 GKX  C16  C15  C14  120.95  3.000
 GKX  C20  C15  C14  120.86  3.000
 GKX  H17  C16  C17  119.65  3.000
 GKX  H17  C16  C15  119.32  3.000
 GKX  C17  C16  C15  121.03  3.000
 GKX  H18  C17  C18  120.04  3.000
 GKX  H18  C17  C16  119.79  3.000
 GKX  C18  C17  C16  120.18  3.000
 GKX  H19  C18  C19  120.27  3.000
 GKX  H19  C18  C17  120.30  3.000
 GKX  C19  C18  C17  119.42  3.000
 GKX  H21  C20  C19  119.53  3.000
 GKX  H21  C20  C15  119.42  3.000
 GKX  C19  C20  C15  121.04  3.000
 GKX  H22  C19  C20  119.80  3.000
 GKX  H22  C19  C18  120.05  3.000
 GKX  C20  C19  C18  120.15  3.000
 GKX  H23  N1   C12  114.76  3.000
 GKX  H23  N1   C11  120.30  3.000
 GKX  C12  N1   C11  124.83  3.000
 GKX  H25  C9   H24  106.13  3.000
 GKX  H25  C9   C8   109.96  3.000
 GKX  H24  C9   C8   109.17  3.000
 GKX  H25  C9   C10  109.44  3.000
 GKX  H24  C9   C10  108.68  3.000
 GKX  C8   C9   C10  113.20  3.000
 GKX  H27  C8   H26  106.05  3.000
 GKX  H27  C8   C9   108.73  3.000
 GKX  H26  C8   C9   110.16  3.000
 GKX  H27  C8   C7   110.51  3.000
 GKX  H26  C8   C7   108.77  3.000
 GKX  C9   C8   C7   112.42  3.000
 GKX  H29  C3   H28  106.34  3.000
 GKX  H29  C3   C4   110.03  3.000
 GKX  H28  C3   C4   109.16  3.000
 GKX  H29  C3   C2   110.30  3.000
 GKX  H28  C3   C2   109.26  3.000
 GKX  C4   C3   C2   111.60  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
 GKX  CONST_01  C18  C19  C20  C15     0.00   0.0  0
 GKX  CONST_02  C18  C17  C16  C15     0.00   0.0  0
 GKX  CONST_03  C19  C18  C17  C16     0.00   0.0  0
 GKX  CONST_04  C19  C20  C15  C16     0.00   0.0  0
 GKX  CONST_05  C20  C19  C18  C17     0.00   0.0  0
 GKX  CONST_06  C20  C15  C16  C17     0.00   0.0  0
 GKX  CONST_07  C19  C20  C15  C14   180.00   0.0  0
 GKX  CONST_08  C17  C16  C15  C14   180.00   0.0  0
 GKX  CONST_09  H22  C19  C20  C15   180.00   0.0  0
 GKX  CONST_10  H18  C17  C16  C15   180.00   0.0  0
 GKX  CONST_11  H19  C18  C17  C16   180.00   0.0  0
 GKX  CONST_12  H21  C20  C15  C16   180.00   0.0  0
 GKX  CONST_13  H22  C19  C18  C17   180.00   0.0  0
 GKX  CONST_14  H21  C20  C19  C18   180.00   0.0  0
 GKX  CONST_15  H17  C16  C17  C18   180.00   0.0  0
 GKX  CONST_16  H19  C18  C19  C20   180.00   0.0  0
 GKX  CONST_17  H17  C16  C15  C20   180.00   0.0  0
 GKX  CONST_18  H18  C17  C18  C19   180.00   0.0  0
 GKX  CONST_19  C12  N1   C11  C10   180.00   0.0  0
 GKX  CONST_20  O1   C11  N1   C12     0.00   0.0  0
 GKX  CONST_21  H23  N1   C11  C10     0.00   0.0  0
 GKX  CONST_22  H23  N1   C11  O1    180.00   0.0  0
 GKX  Var_01    C4   C3   C2   C1     54.55  30.0  1
 GKX  Var_02    C5   C4   C3   C2    -55.59  30.0  1
 GKX  Var_03    C5   C6   C1   C2     55.56  30.0  1
 GKX  Var_04    C3   C2   C1   C6    -54.43  30.0  1
 GKX  Var_05    H28  C3   C2   C1    -66.27  30.0  1
 GKX  Var_06    H29  C3   C2   C1    177.18  30.0  1
 GKX  Var_07    H5   C4   C3   C2   -178.75  30.0  1
 GKX  Var_08    H6   C4   C3   C2     65.11  30.0  1
 GKX  Var_09    H8   C6   C1   C2    -65.55  30.0  1
 GKX  Var_10    H9   C6   C1   C2    178.04  30.0  1
 GKX  Var_11    H3   C2   C3   C4    177.21  30.0  1
 GKX  Var_12    H4   C2   C3   C4    -66.06  30.0  1
 GKX  Var_13    H28  C3   C4   C5     65.28  30.0  1
 GKX  Var_14    H29  C3   C4   C5   -178.38  30.0  1
 GKX  Var_15    H1   C1   C6   C5    178.38  30.0  1
 GKX  Var_16    H2   C1   C6   C5    -65.20  30.0  1
 GKX  Var_17    H3   C2   C1   C6   -177.10  30.0  1
 GKX  Var_18    H4   C2   C1   C6     66.18  30.0  1
 GKX  Var_19    H1   C1   C2   C3   -177.12  30.0  1
 GKX  Var_20    H2   C1   C2   C3     66.27  30.0  1
 GKX  Var_21    C20  C15  C14  C12   -89.96  30.0  2
 GKX  Var_22    C16  C15  C14  C12    88.79  30.0  2
 GKX  Var_23    H15  C14  C15  C16  -149.77  30.0  2
 GKX  Var_24    H16  C14  C15  C16   -32.43  30.0  2
 GKX  Var_25    H15  C14  C15  C20    31.48  30.0  2
 GKX  Var_26    H16  C14  C15  C20   148.82  30.0  2
 GKX  Var_27    C9   C8   C7   C5    179.06  30.0  1
 GKX  Var_28    H26  C8   C7   C5     56.77  30.0  1
 GKX  Var_29    H27  C8   C7   C5    -59.27  30.0  1
 GKX  Var_30    C10  C9   C8   C7   -178.83  30.0  2
 GKX  Var_31    C8   C9   C10  C11    68.45  30.0  3
 GKX  Var_32    C9   C10  C11  N1   -126.47  30.0  2
 GKX  Var_33    C9   C10  C11  O1     54.21  30.0  2
 GKX  Var_34    H24  C9   C8   C7     59.97  30.0  2
 GKX  Var_35    H25  C9   C8   C7    -56.08  30.0  2
 GKX  Var_36    H26  C8   C9   C10   -57.33  30.0  3
 GKX  Var_37    H27  C8   C9   C10    58.49  30.0  3
 GKX  Var_38    H24  C9   C10  C11  -170.08  30.0  3
 GKX  Var_39    H25  C9   C10  C11   -54.59  30.0  3
 GKX  Var_40    H12  C10  C11  N1     -2.66  30.0  2
 GKX  Var_41    H13  C10  C11  N1    113.19  30.0  2
 GKX  Var_42    H12  C10  C11  O1    178.03  30.0  2
 GKX  Var_43    H13  C10  C11  O1    -66.13  30.0  2
 GKX  Var_44    H10  C7   C8   C9    -57.62  30.0  3
 GKX  Var_45    H11  C7   C8   C9     57.47  30.0  3
 GKX  Var_46    H12  C10  C9   C8    -56.09  30.0  1
 GKX  Var_47    H13  C10  C9   C8   -172.77  30.0  1

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
 GKX  chir_01  C5   C7   C4  C6   negativ
 GKX  chir_02  C12  C14  N1  C13  positiv

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
 GKX  plan-1  C14  0.020
 GKX  plan-1  C15  0.020
 GKX  plan-1  C16  0.020
 GKX  plan-1  C17  0.020
 GKX  plan-1  C18  0.020
 GKX  plan-1  C20  0.020
 GKX  plan-1  C19  0.020
 GKX  plan-1  H17  0.020
 GKX  plan-1  H18  0.020
 GKX  plan-1  H19  0.020
 GKX  plan-1  H21  0.020
 GKX  plan-1  H22  0.020
 GKX  plan-2  C10  0.020
 GKX  plan-2  C11  0.020
 GKX  plan-2  C12  0.020
 GKX  plan-2  N1   0.020
 GKX  plan-2  O1   0.020
 GKX  plan-2  H23  0.020
 GKX  plan-3  C12  0.020
 GKX  plan-3  C13  0.020
 GKX  plan-3  O3   0.020
 GKX  plan-3  O2   0.020

