# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May 16 15:10:28 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: (1S,2R,5S)-5-methyl-2-(1-methylethyl)cyclohexyl hydrogen (S)-hexylphosphonate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCC[P@@](O)(=O)O[C@H]1C[C@@H](C)CC[C@@H]1C(C)C
#
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
 MPC  MPC  '(1S,2R,5S)-5-methyl-2-(1-methylethyl)cyclohexyl hydrogen (S)-hexylphosphonate'  ligand  53  20  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MPC
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
 MPC  C1    C  CH2   0  -0.729  -3.1310  -5.0268   3.3306
 MPC  C2    C  CH2   0  -0.434  -1.6326  -4.7320   3.2652
 MPC  C3    C  CH2   0  -0.407  -0.8349  -5.6563   4.1770
 MPC  C4    C  CH2   0  -0.408   0.6682  -5.4260   4.0883
 MPC  C5    C  CH2   0  -0.419   1.4683  -6.3287   5.0197
 MPC  C6    C  CH3   0  -0.662   2.9708  -6.1055   4.9165
 MPC  C7    C  CH1   0   0.073  -4.1918  -3.4242  -0.2154
 MPC  C8    C  CH2   0  -0.433  -3.8186  -1.9556  -0.3596
 MPC  C9    C  CH1   0  -0.240  -4.4281  -1.3452  -1.6194
 MPC  C10   C  CH2   0  -0.406  -4.0114  -2.1574  -2.8401
 MPC  C11   C  CH2   0  -0.446  -4.3654  -3.6323  -2.6873
 MPC  C12   C  CH1   0  -0.246  -3.7543  -4.2482  -1.4249
 MPC  C13   C  CH3   0  -0.653  -4.0502   0.1230  -1.7587
 MPC  C14   C  CH1   0  -0.219  -4.0429  -5.7552  -1.2729
 MPC  C15   C  CH3   0  -0.675  -5.5235  -6.0819  -1.0952
 MPC  C16   C  CH3   0  -0.661  -3.4509  -6.5537  -2.4322
 MPC  O1    O  O2    0  -0.611  -3.5636  -3.9907   0.9490
 MPC  O2    O  O     0  -0.718  -4.1422  -2.4483   2.9816
 MPC  P1    P  P     0   1.387  -4.1349  -3.8327   2.4375
 MPC  H11   H  HCH2  0   0.277  -3.3413  -6.0287   2.9483
 MPC  H12A  H  HCH2  0   0.276  -3.4770  -5.0058   4.3682
 MPC  H21   H  HCH2  0   0.229  -1.4428  -3.6929   3.5486
 MPC  H22   H  HCH2  0   0.233  -1.2837  -4.8440   2.2360
 MPC  H31   H  HCH2  0   0.214  -1.1661  -5.5153   5.2114
 MPC  H32   H  HCH2  0   0.214  -1.0591  -6.6978   3.9236
 MPC  H41   H  HCH2  0   0.209   0.8911  -4.3788   4.3199
 MPC  H42   H  HCH2  0   0.209   0.9989  -5.5860   3.0562
 MPC  H51   H  HCH2  0   0.211   1.1440  -6.1602   6.0511
 MPC  H52   H  HCH2  0   0.211   1.2370  -7.3747   4.7961
 MPC  H61   H  HCH3  0   0.226   3.5198  -6.7590   5.5953
 MPC  H62   H  HCH3  0   0.216   3.3312  -6.3020   3.9048
 MPC  H63   H  HCH3  0   0.216   3.2348  -5.0759   5.1643
 MPC  H7    H  HCH1  0   0.220  -5.2813  -3.5033  -0.1084
 MPC  H81   H  HCH2  0   0.215  -2.7269  -1.8636  -0.3993
 MPC  H82   H  HCH2  0   0.239  -4.1541  -1.4033   0.5212
 MPC  H9    H  HCH1  0   0.214  -5.5204  -1.4109  -1.5301
 MPC  H101  H  HCH2  0   0.207  -2.9295  -2.0543  -2.9864
 MPC  H102  H  HCH2  0   0.228  -4.4861  -1.7522  -3.7380
 MPC  H111  H  HCH2  0   0.216  -5.4553  -3.7397  -2.6682
 MPC  H112  H  HCH2  0   0.240  -4.0188  -4.1784  -3.5667
 MPC  H12   H  HCH1  0   0.218  -2.6632  -4.1392  -1.5065
 MPC  H131  H  HCH3  0   0.214  -2.9683   0.2396  -1.8558
 MPC  H132  H  HCH3  0   0.226  -4.5116   0.5663  -2.6429
 MPC  H133  H  HCH3  0   0.225  -4.3702   0.7020  -0.8905
 MPC  H14   H  HCH1  0   0.227  -3.5263  -6.0878  -0.3677
 MPC  H151  H  HCH3  0   0.216  -6.1153  -5.7700  -1.9576
 MPC  H152  H  HCH3  0   0.227  -5.6622  -7.1582  -0.9787
 MPC  H153  H  HCH3  0   0.229  -5.9457  -5.6064  -0.2094
 MPC  H161  H  HCH3  0   0.215  -3.9809  -6.3749  -3.3695
 MPC  H162  H  HCH3  0   0.228  -3.5082  -7.6244  -2.2290
 MPC  H163  H  HCH3  0   0.222  -2.3998  -6.3037  -2.5922
 MPC  O3    O  OH1   0  -0.749  -5.6021  -4.5063   2.3943
 MPC  H3    H  HOH1  0   0.488  -6.3155  -3.8807   2.5741

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
 MPC  C1   C2    single  1.529  0.020  1.529
 MPC  C1   P1    single  1.798  0.020  1.798
 MPC  C1   H11   single  0.970  0.020  1.090
 MPC  C1   H12A  single  0.970  0.020  1.090
 MPC  C2   C3    single  1.524  0.020  1.524
 MPC  C2   H21   single  0.970  0.020  1.090
 MPC  C2   H22   single  0.970  0.020  1.090
 MPC  C3   C4    single  1.523  0.020  1.523
 MPC  C3   H31   single  0.970  0.020  1.090
 MPC  C3   H32   single  0.970  0.020  1.090
 MPC  C4   C5    single  1.524  0.020  1.524
 MPC  C4   H41   single  0.970  0.020  1.090
 MPC  C4   H42   single  0.970  0.020  1.090
 MPC  C5   C6    single  1.523  0.020  1.523
 MPC  C5   H51   single  0.970  0.020  1.090
 MPC  C5   H52   single  0.970  0.020  1.090
 MPC  C6   H61   single  0.970  0.020  1.090
 MPC  C6   H62   single  0.970  0.020  1.090
 MPC  C6   H63   single  0.970  0.020  1.090
 MPC  C7   C8    single  1.522  0.020  1.522
 MPC  C7   C12   single  1.528  0.020  1.528
 MPC  C7   O1    single  1.439  0.020  1.439
 MPC  C7   H7    single  0.970  0.020  1.090
 MPC  C8   C9    single  1.527  0.020  1.527
 MPC  C8   H81   single  0.970  0.020  1.090
 MPC  C8   H82   single  0.970  0.020  1.090
 MPC  C9   C10   single  1.524  0.020  1.524
 MPC  C9   C13   single  1.522  0.020  1.522
 MPC  C9   H9    single  0.970  0.020  1.090
 MPC  C10  C11   single  1.524  0.020  1.524
 MPC  C10  H101  single  0.970  0.020  1.090
 MPC  C10  H102  single  0.970  0.020  1.090
 MPC  C11  C12   single  1.532  0.020  1.532
 MPC  C11  H111  single  0.970  0.020  1.090
 MPC  C11  H112  single  0.970  0.020  1.090
 MPC  C12  C14   single  1.542  0.020  1.542
 MPC  C12  H12   single  0.970  0.020  1.090
 MPC  C13  H131  single  0.970  0.020  1.090
 MPC  C13  H132  single  0.970  0.020  1.090
 MPC  C13  H133  single  0.970  0.020  1.090
 MPC  C14  C15   single  1.527  0.020  1.527
 MPC  C14  C16   single  1.527  0.020  1.527
 MPC  C14  H14   single  0.970  0.020  1.090
 MPC  C15  H151  single  0.970  0.020  1.090
 MPC  C15  H152  single  0.970  0.020  1.090
 MPC  C15  H153  single  0.970  0.020  1.090
 MPC  C16  H161  single  0.970  0.020  1.090
 MPC  C16  H162  single  0.970  0.020  1.090
 MPC  C16  H163  single  0.970  0.020  1.090
 MPC  O1   P1    single  1.602  0.020  1.602
 MPC  O2   P1    double  1.488  0.020  1.488
 MPC  O3   P1    single  1.615  0.020  1.615
 MPC  O3   H3    single  0.850  0.020  0.980

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
 MPC  H12A  C1   H11   106.77  3.000
 MPC  H12A  C1   P1    106.37  3.000
 MPC  H11   C1   P1    109.13  3.000
 MPC  H12A  C1   C2    110.30  3.000
 MPC  H11   C1   C2    110.52  3.000
 MPC  P1    C1   C2    113.46  3.000
 MPC  H22   C2   H21   106.62  3.000
 MPC  H22   C2   C3    109.53  3.000
 MPC  H21   C2   C3    109.29  3.000
 MPC  H22   C2   C1    109.49  3.000
 MPC  H21   C2   C1    110.02  3.000
 MPC  C3    C2   C1    111.75  3.000
 MPC  H32   C3   H31   106.21  3.000
 MPC  H32   C3   C4    109.41  3.000
 MPC  H31   C3   C4    109.51  3.000
 MPC  H32   C3   C2    109.34  3.000
 MPC  H31   C3   C2    109.19  3.000
 MPC  C4    C3   C2    112.95  3.000
 MPC  H42   C4   H41   106.10  3.000
 MPC  H42   C4   C5    109.32  3.000
 MPC  H41   C4   C5    109.28  3.000
 MPC  H42   C4   C3    109.31  3.000
 MPC  H41   C4   C3    109.45  3.000
 MPC  C5    C4   C3    113.14  3.000
 MPC  H52   C5   H51   106.09  3.000
 MPC  H52   C5   C6    109.57  3.000
 MPC  H51   C5   C6    109.50  3.000
 MPC  H52   C5   C4    109.29  3.000
 MPC  H51   C5   C4    109.23  3.000
 MPC  C6    C5   C4    112.94  3.000
 MPC  H63   C6   H62   107.48  3.000
 MPC  H63   C6   H61   107.59  3.000
 MPC  H62   C6   H61   107.62  3.000
 MPC  H63   C6   C5    111.20  3.000
 MPC  H62   C6   C5    111.23  3.000
 MPC  H61   C6   C5    111.51  3.000
 MPC  H7    C7   O1    109.03  3.000
 MPC  H7    C7   C12   108.82  3.000
 MPC  O1    C7   C12   107.66  3.000
 MPC  H7    C7   C8    108.79  3.000
 MPC  O1    C7   C8    110.45  3.000
 MPC  C12   C7   C8    112.04  3.000
 MPC  H82   C8   H81   107.01  3.000
 MPC  H82   C8   C9    109.91  3.000
 MPC  H81   C8   C9    109.52  3.000
 MPC  H82   C8   C7    109.64  3.000
 MPC  H81   C8   C7    109.18  3.000
 MPC  C9    C8   C7    111.47  3.000
 MPC  H9    C9   C13   108.19  3.000
 MPC  H9    C9   C10   107.78  3.000
 MPC  C13   C9   C10   111.89  3.000
 MPC  H9    C9   C8    107.82  3.000
 MPC  C13   C9   C8    111.22  3.000
 MPC  C10   C9   C8    109.80  3.000
 MPC  H102  C10  H101  106.49  3.000
 MPC  H102  C10  C11   109.88  3.000
 MPC  H101  C10  C11   109.48  3.000
 MPC  H102  C10  C9    109.96  3.000
 MPC  H101  C10  C9    109.06  3.000
 MPC  C11   C10  C9    111.82  3.000
 MPC  H112  C11  H111  106.32  3.000
 MPC  H112  C11  C12   109.64  3.000
 MPC  H111  C11  C12   110.07  3.000
 MPC  H112  C11  C10   109.24  3.000
 MPC  H111  C11  C10   109.13  3.000
 MPC  C12   C11  C10   112.27  3.000
 MPC  H12   C12  C14   106.85  3.000
 MPC  H12   C12  C11   107.15  3.000
 MPC  C14   C12  C11   113.55  3.000
 MPC  H12   C12  C7    106.83  3.000
 MPC  C14   C12  C7    113.30  3.000
 MPC  C11   C12  C7    108.75  3.000
 MPC  H133  C13  H132  107.76  3.000
 MPC  H133  C13  H131  107.73  3.000
 MPC  H132  C13  H131  107.65  3.000
 MPC  H133  C13  C9    111.47  3.000
 MPC  H132  C13  C9    111.15  3.000
 MPC  H131  C13  C9    110.91  3.000
 MPC  H14   C14  C16   106.62  3.000
 MPC  H14   C14  C15   107.26  3.000
 MPC  C16   C14  C15   110.64  3.000
 MPC  H14   C14  C12   106.88  3.000
 MPC  C16   C14  C12   111.32  3.000
 MPC  C15   C14  C12   113.71  3.000
 MPC  H153  C15  H152  107.11  3.000
 MPC  H153  C15  H151  107.90  3.000
 MPC  H152  C15  H151  107.29  3.000
 MPC  H153  C15  C14   112.13  3.000
 MPC  H152  C15  C14   110.28  3.000
 MPC  H151  C15  C14   111.88  3.000
 MPC  H163  C16  H162  107.61  3.000
 MPC  H163  C16  H161  107.70  3.000
 MPC  H162  C16  H161  107.17  3.000
 MPC  H163  C16  C14   111.38  3.000
 MPC  H162  C16  C14   110.56  3.000
 MPC  H161  C16  C14   112.20  3.000
 MPC  P1    O1   C7    123.86  3.000
 MPC  O3    P1   O2    113.17  3.000
 MPC  O3    P1   O1    104.95  3.000
 MPC  O2    P1   O1    115.68  3.000
 MPC  O3    P1   C1    104.10  3.000
 MPC  O2    P1   C1    116.06  3.000
 MPC  O1    P1   C1    101.36  3.000
 MPC  H3    O3   P1    113.32  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
 MPC  Var_01  C12   C11  C10  C9   -56.23  30.0  1
 MPC  Var_02  O2    P1   O1   C7   -65.19  30.0  3
 MPC  Var_03  H151  C15  C14  C12   61.48  30.0  3
 MPC  Var_04  H161  C16  C14  C12  -70.26  30.0  3
 MPC  Var_05  C4    C3   C2   C1   177.54  30.0  3
 MPC  Var_06  O1    P1   C1   C2    60.07  30.0  3
 MPC  Var_07  C5    C4   C3   C2   178.82  30.0  3
 MPC  Var_08  P1    C1   C2   C3   172.66  30.0  1
 MPC  Var_09  C6    C5   C4   C3   179.38  30.0  3
 MPC  Var_10  H61   C6   C5   C4   179.73  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
 MPC  chir_01  C7   C8   C12  O1   negativ
 MPC  chir_02  C9   C13  C10  C8   negativ
 MPC  chir_03  C12  C7   C11  C14  positiv
 MPC  chir_04  P1   O1   O2   O3   both

