# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 01:46:35 2020
#   Inital geometry file: a 106 line input string
#   Ligand name: (2S,4S,5S)-5-amino-6-cyclohexyl-4-hydroxy-2-(propan-2-yl)hexanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)[C@H](C[C@H](O)[C@@H](N)CC1CCCCC1)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
 CPV  CPV  '(2S,4S,5S)-5-amino-6-cyclohexyl-4-hydroxy-2-(propan-2-yl)hexanoic acid'  ligand  47  19  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_CPV
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
 CPV  C     C  C      0   0.406  -3.2990   1.1388  -0.8946
 CPV  N     N  NH2    0  -0.830   0.8709  -1.9784  -0.0157
 CPV  O     O  O      0  -0.625  -3.0323   2.1048  -0.1454
 CPV  CA    C  CH1    0  -0.128   0.7277  -0.5230   0.0048
 CPV  CB    C  CH2    0  -0.396   1.8608   0.1457  -0.7708
 CPV  CG    C  CH1    0  -0.257   3.2837  -0.1752  -0.3120
 CPV  CH    C  CH1    0   0.054  -0.6367  -0.1920  -0.6350
 CPV  OH    O  OH1    0  -0.686  -0.7638  -0.9088  -1.8443
 CPV  CZ    C  CH2    0  -0.428   5.9531   0.5869   0.7341
 CPV  CA'   C  CH1    0  -0.285  -3.1844  -0.2627  -0.2657
 CPV  CB'   C  CH1    0  -0.218  -4.2857  -0.4516   0.7953
 CPV  CB1   C  CH2    0  -0.441  -1.7894  -0.4780   0.3258
 CPV  CD1   C  CH2    0  -0.421   3.5130   0.1150   1.1726
 CPV  CD2   C  CH2    0  -0.407   4.2952   0.5973  -1.1604
 CPV  CE1   C  CH2    0  -0.428   4.9506  -0.1758   1.5934
 CPV  CE2   C  CH2    0  -0.432   5.7333   0.3032  -0.7486
 CPV  CG1   C  CH3    0  -0.657  -5.6771  -0.2229   0.2073
 CPV  CG2   C  CH3    0  -0.662  -4.2335  -1.8324   1.4461
 CPV  OXT   O  OC    -1  -0.618  -3.6550   1.2173  -2.0878
 CPV  HN    H  HNH2   0   0.364   1.8307  -2.2545   0.1421
 CPV  H2    H  HNH2   0   0.357   0.3383  -2.3953   0.7371
 CPV  H3    H  HCH1   0   0.213   0.7248  -0.1235   1.0281
 CPV  HB    H  HCH2   0   0.219   1.7675  -0.1109  -1.8311
 CPV  HBA   H  HCH2   0   0.215   1.7136   1.2292  -0.7030
 CPV  HG    H  HCH1   0   0.203   3.4820  -1.2432  -0.4817
 CPV  HH    H  HCH1   0   0.211  -0.6481   0.8757  -0.8799
 CPV  HOH   H  HOH1   0   0.429  -0.3106  -1.7491  -1.6603
 CPV  HZ    H  HCH2   0   0.206   5.8431   1.6616   0.9169
 CPV  HZA   H  HCH2   0   0.224   6.9745   0.3269   1.0231
 CPV  HA'   H  HCH1   0   0.181  -3.3492  -1.0125  -1.0471
 CPV  H12   H  HCH1   0   0.200  -4.1213   0.2996   1.5764
 CPV  HB1   H  HCH2   0   0.208  -1.7042  -1.5090   0.6844
 CPV  HB1A  H  HCH2   0   0.203  -1.6685   0.1657   1.2036
 CPV  HD1   H  HCH2   0   0.205   3.2765   1.1680   1.3693
 CPV  HD1A  H  HCH2   0   0.228   2.8263  -0.4732   1.7875
 CPV  HD2   H  HCH2   0   0.223   4.1489   0.3586  -2.2181
 CPV  HD2A  H  HCH2   0   0.204   4.1001   1.6721  -1.0573
 CPV  HE1   H  HCH2   0   0.207   5.1401  -1.2515   1.5034
 CPV  HE1A  H  HCH2   0   0.224   5.0891   0.0723   2.6488
 CPV  HE2   H  HCH2   0   0.224   6.4264   0.8930  -1.3537
 CPV  HE2A  H  HCH2   0   0.207   5.9619  -0.7482  -0.9546
 CPV  HG1   H  HCH3   0   0.207  -5.8776  -0.9214  -0.6092
 CPV  HG1A  H  HCH3   0   0.217  -6.4475  -0.3754   0.9659
 CPV  H25   H  HCH3   0   0.227  -5.8037   0.7871  -0.1829
 CPV  HG2   H  HCH3   0   0.225  -3.3074  -2.0004   1.9957
 CPV  HG2A  H  HCH3   0   0.222  -5.0548  -1.9605   2.1543
 CPV  HG2B  H  HCH3   0   0.209  -4.3203  -2.6219   0.6946

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
 CPV  C    O     deloc   1.251  0.020  1.251
 CPV  C    CA'   single  1.540  0.020  1.540
 CPV  CA   N     single  1.463  0.020  1.463
 CPV  CB   CA    single  1.527  0.020  1.527
 CPV  CG   CB    single  1.529  0.020  1.529
 CPV  CG   CD2   single  1.530  0.020  1.530
 CPV  CG   CD1   single  1.530  0.020  1.530
 CPV  CH   CA    single  1.543  0.020  1.543
 CPV  CH   OH    single  1.412  0.020  1.412
 CPV  CH   CB1   single  1.528  0.020  1.528
 CPV  CA'  CB1   single  1.530  0.020  1.530
 CPV  CA'  CB'   single  1.541  0.020  1.541
 CPV  CB'  CG2   single  1.527  0.020  1.527
 CPV  CE1  CZ    single  1.525  0.020  1.525
 CPV  CE1  CD1   single  1.526  0.020  1.526
 CPV  CE2  CZ    single  1.526  0.020  1.526
 CPV  CE2  CD2   single  1.525  0.020  1.525
 CPV  CG1  CB'   single  1.528  0.020  1.528
 CPV  C    OXT   deloc   1.248  0.020  1.248
 CPV  N    HN    single  0.890  0.020  1.040
 CPV  N    H2    single  0.890  0.020  1.040
 CPV  CA   H3    single  0.970  0.020  1.090
 CPV  CB   HB    single  0.970  0.020  1.090
 CPV  CB   HBA   single  0.970  0.020  1.090
 CPV  CG   HG    single  0.970  0.020  1.090
 CPV  CH   HH    single  0.970  0.020  1.090
 CPV  OH   HOH   single  0.850  0.020  0.980
 CPV  CZ   HZ    single  0.970  0.020  1.090
 CPV  CZ   HZA   single  0.970  0.020  1.090
 CPV  CA'  HA'   single  0.970  0.020  1.090
 CPV  CB'  H12   single  0.970  0.020  1.090
 CPV  CB1  HB1   single  0.970  0.020  1.090
 CPV  CB1  HB1A  single  0.970  0.020  1.090
 CPV  CD1  HD1   single  0.970  0.020  1.090
 CPV  CD1  HD1A  single  0.970  0.020  1.090
 CPV  CD2  HD2   single  0.970  0.020  1.090
 CPV  CD2  HD2A  single  0.970  0.020  1.090
 CPV  CE1  HE1   single  0.970  0.020  1.090
 CPV  CE1  HE1A  single  0.970  0.020  1.090
 CPV  CE2  HE2   single  0.970  0.020  1.090
 CPV  CE2  HE2A  single  0.970  0.020  1.090
 CPV  CG1  HG1   single  0.970  0.020  1.090
 CPV  CG1  HG1A  single  0.970  0.020  1.090
 CPV  CG1  H25   single  0.970  0.020  1.090
 CPV  CG2  HG2   single  0.970  0.020  1.090
 CPV  CG2  HG2A  single  0.970  0.020  1.090
 CPV  CG2  HG2B  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
 CPV  OXT   C    CA'   117.96  3.000
 CPV  OXT   C    O     125.79  3.000
 CPV  CA'   C    O     116.24  3.000
 CPV  H2    N    HN    105.72  3.000
 CPV  H2    N    CA    110.36  3.000
 CPV  HN    N    CA    111.26  3.000
 CPV  H3    CA   CH    107.82  3.000
 CPV  H3    CA   CB    108.41  3.000
 CPV  CH    CA   CB    110.58  3.000
 CPV  H3    CA   N     112.03  3.000
 CPV  CH    CA   N     107.11  3.000
 CPV  CB    CA   N     110.85  3.000
 CPV  HBA   CB   HB    106.28  3.000
 CPV  HBA   CB   CG    108.30  3.000
 CPV  HB    CB   CG    108.70  3.000
 CPV  HBA   CB   CA    107.57  3.000
 CPV  HB    CB   CA    109.02  3.000
 CPV  CG    CB   CA    116.50  3.000
 CPV  HG    CG   CD2   106.60  3.000
 CPV  HG    CG   CD1   107.88  3.000
 CPV  CD2   CG   CD1   110.08  3.000
 CPV  HG    CG   CB    108.99  3.000
 CPV  CD1   CG   CB    113.00  3.000
 CPV  CD2   CG   CB    110.06  3.000
 CPV  HH    CH   CB1   108.37  3.000
 CPV  HH    CH   OH    107.61  3.000
 CPV  CB1   CH   OH    112.07  3.000
 CPV  HH    CH   CA    108.12  3.000
 CPV  CB1   CH   CA    111.49  3.000
 CPV  OH    CH   CA    109.03  3.000
 CPV  HOH   OH   CH    103.57  3.000
 CPV  HZA   CZ   HZ    106.44  3.000
 CPV  HZA   CZ   CE2   110.33  3.000
 CPV  HZ    CZ   CE2   109.27  3.000
 CPV  HZA   CZ   CE1   110.27  3.000
 CPV  HZ    CZ   CE1   109.31  3.000
 CPV  CE2   CZ   CE1   111.10  3.000
 CPV  HA'   CA'  CB1   108.45  3.000
 CPV  HA'   CA'  CB'   107.45  3.000
 CPV  CB1   CA'  CB'   111.60  3.000
 CPV  HA'   CA'  C     108.68  3.000
 CPV  CB'   CA'  C     109.84  3.000
 CPV  CB1   CA'  C     110.70  3.000
 CPV  H12   CB'  CG2   108.11  3.000
 CPV  H12   CB'  CG1   107.96  3.000
 CPV  CG2   CB'  CG1   109.29  3.000
 CPV  H12   CB'  CA'   107.43  3.000
 CPV  CG1   CB'  CA'   111.57  3.000
 CPV  CG2   CB'  CA'   112.32  3.000
 CPV  HB1A  CB1  HB1   106.40  3.000
 CPV  HB1A  CB1  CA'   109.13  3.000
 CPV  HB1   CB1  CA'   109.27  3.000
 CPV  HB1A  CB1  CH    108.11  3.000
 CPV  HB1   CB1  CH    108.88  3.000
 CPV  CA'   CB1  CH    114.73  3.000
 CPV  HD1A  CD1  HD1   106.27  3.000
 CPV  HD1A  CD1  CE1   109.51  3.000
 CPV  HD1   CD1  CE1   109.67  3.000
 CPV  HD1A  CD1  CG    110.45  3.000
 CPV  HD1   CD1  CG    108.89  3.000
 CPV  CE1   CD1  CG    111.88  3.000
 CPV  HD2A  CD2  HD2   106.31  3.000
 CPV  HD2A  CD2  CE2   109.34  3.000
 CPV  HD2   CD2  CE2   110.19  3.000
 CPV  HD2A  CD2  CG    108.97  3.000
 CPV  HD2   CD2  CG    109.73  3.000
 CPV  CE2   CD2  CG    112.12  3.000
 CPV  HE1A  CE1  HE1   106.27  3.000
 CPV  HE1A  CE1  CD1   110.03  3.000
 CPV  HE1   CE1  CD1   109.11  3.000
 CPV  HE1A  CE1  CZ    110.32  3.000
 CPV  HE1   CE1  CZ    109.33  3.000
 CPV  CD1   CE1  CZ    111.63  3.000
 CPV  HE2A  CE2  HE2   106.35  3.000
 CPV  HE2A  CE2  CD2   109.34  3.000
 CPV  HE2   CE2  CD2   110.16  3.000
 CPV  HE2A  CE2  CZ    109.34  3.000
 CPV  HE2   CE2  CZ    110.27  3.000
 CPV  CD2   CE2  CZ    111.26  3.000
 CPV  H25   CG1  HG1A  107.23  3.000
 CPV  H25   CG1  HG1   107.67  3.000
 CPV  HG1A  CG1  HG1   107.47  3.000
 CPV  H25   CG1  CB'   112.47  3.000
 CPV  HG1A  CG1  CB'   110.75  3.000
 CPV  HG1   CG1  CB'   111.03  3.000
 CPV  HG2B  CG2  HG2A  107.54  3.000
 CPV  HG2B  CG2  HG2   107.62  3.000
 CPV  HG2A  CG2  HG2   107.09  3.000
 CPV  HG2B  CG2  CB'   110.93  3.000
 CPV  HG2A  CG2  CB'   110.90  3.000
 CPV  HG2   CG2  CB'   112.54  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
 CPV  Var_01  CZ   CE2  CD2  CG   -55.71  30.0  1
 CPV  Var_02  CZ   CE1  CD1  CG    55.32  30.0  1
 CPV  Var_03  CE2  CZ   CE1  CD1  -54.71  30.0  1
 CPV  Var_04  HG2  CG2  CB'  CA'   63.09  30.0  3
 CPV  Var_05  HG1  CG1  CB'  CA'   59.79  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
 CPV  chir_01  CA   N    CB   CH   negativ
 CPV  chir_02  CG   CB   CD2  CD1  negativ
 CPV  chir_03  CH   OH   CB1  CA   negativ
 CPV  chir_04  CA'  CB'  CB1  C    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
 CPV  plan-1  C    0.020
 CPV  plan-1  O    0.020
 CPV  plan-1  CA'  0.020
 CPV  plan-1  OXT  0.020

