# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 17 02:56:27 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: (1R,2S,5R)-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
 MPA  MPA  '(1R,2S,5R)-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_MPA
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
 MPA  C1    C  CH2   0  -0.771   2.6764   3.3212   5.1765
 MPA  C2    C  CH2   0  -0.432   2.9891   3.6716   6.6324
 MPA  C3    C  CH2   0  -0.407   1.7905   4.2981   7.3337
 MPA  C4    C  CH2   0  -0.408   2.0807   4.6679   8.7830
 MPA  C5    C  CH2   0  -0.420   0.8808   5.2778   9.4973
 MPA  C6    C  CH3   0  -0.662   1.1807   5.6473  10.9436
 MPA  C7    C  CH1   0   0.068   2.4197   1.9989   2.2914
 MPA  C8    C  CH2   0  -0.443   2.1770   0.5181   2.5508
 MPA  C9    C  CH1   0  -0.240   0.8378   0.0582   1.9795
 MPA  C10   C  CH2   0  -0.405   0.7628   0.4018   0.4964
 MPA  C11   C  CH2   0  -0.449   1.0257   1.8825   0.2484
 MPA  C12   C  CH1   0  -0.242   2.3830   2.3280   0.8004
 MPA  C13   C  CH3   0  -0.652   0.6150  -1.4270   2.2301
 MPA  C14   C  CH1   0  -0.222   2.7223   3.7978   0.4878
 MPA  C15   C  CH3   0  -0.662   2.8795   4.0211  -1.0142
 MPA  C16   C  CH3   0  -0.674   1.7315   4.7963   1.0812
 MPA  O1    O  O2    0  -0.601   3.7014   2.4086   2.8007
 MPA  O2    O  O     0  -0.718   4.4689   1.2254   5.0137
 MPA  P1    P  P     0   1.382   4.0585   2.4958   4.3607
 MPA  H11   H  HCH2  0   0.274   1.8102   2.6540   5.1408
 MPA  H12A  H  HCH2  0   0.280   2.4077   4.2208   4.6159
 MPA  H21   H  HCH2  0   0.232   3.8367   4.3614   6.6731
 MPA  H22   H  HCH2  0   0.234   3.2918   2.7694   7.1701
 MPA  H31   H  HCH2  0   0.215   1.4735   5.1909   6.7845
 MPA  H32   H  HCH2  0   0.215   0.9476   3.5998   7.2988
 MPA  H41   H  HCH2  0   0.209   2.9193   5.3718   8.8173
 MPA  H42   H  HCH2  0   0.209   2.4092   3.7753   9.3268
 MPA  H51   H  HCH2  0   0.211   0.5489   6.1664   8.9517
 MPA  H52   H  HCH2  0   0.211   0.0448   4.5722   9.4672
 MPA  H61   H  HCH3  0   0.226   0.3053   6.0656  11.4415
 MPA  H62   H  HCH3  0   0.216   1.4978   4.7729  11.5155
 MPA  H63   H  HCH3  0   0.216   1.9805   6.3874  11.0058
 MPA  H7    H  HCH1  0   0.225   1.6363   2.5796   2.7948
 MPA  H81   H  HCH2  0   0.236   2.2052   0.3132   3.6249
 MPA  H82   H  HCH2  0   0.223   2.9897  -0.0607   2.0962
 MPA  H9    H  HCH1  0   0.217   0.0409   0.6119   2.4922
 MPA  H101  H  HCH2  0   0.229  -0.2182   0.1271   0.0985
 MPA  H102  H  HCH2  0   0.209   1.5004  -0.1981  -0.0495
 MPA  H111  H  HCH2  0   0.241   0.9749   2.0897  -0.8222
 MPA  H112  H  HCH2  0   0.218   0.2247   2.4677   0.7130
 MPA  H12   H  HCH1  0   0.222   3.1531   1.7105   0.3167
 MPA  H131  H  HCH3  0   0.227  -0.3464  -1.7523   1.8292
 MPA  H132  H  HCH3  0   0.215   1.3941  -2.0261   1.7530
 MPA  H133  H  HCH3  0   0.226   0.6254  -1.6585   3.2966
 MPA  H14   H  HCH1  0   0.229   3.6989   4.0039   0.9347
 MPA  H151  H  HCH3  0   0.217   1.9406   3.8913  -1.5554
 MPA  H152  H  HCH3  0   0.228   3.2314   5.0342  -1.2156
 MPA  H153  H  HCH3  0   0.224   3.6073   3.3293  -1.4436
 MPA  H161  H  HCH3  0   0.220   0.7255   4.6666   0.6777
 MPA  H162  H  HCH3  0   0.231   2.0411   5.8179   0.8546
 MPA  H163  H  HCH3  0   0.226   1.6632   4.7158   2.1677
 MPA  O3    O  OH1   0  -0.742   5.2322   3.5933   4.2572
 MPA  H3    H  HOH1  0   0.492   5.9626   3.4199   4.8647

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
 MPA  C1   C2    single  1.530  0.020  1.530
 MPA  C1   P1    single  1.805  0.020  1.805
 MPA  C1   H11   single  0.970  0.020  1.090
 MPA  C1   H12A  single  0.970  0.020  1.090
 MPA  C2   C3    single  1.524  0.020  1.524
 MPA  C2   H21   single  0.970  0.020  1.090
 MPA  C2   H22   single  0.970  0.020  1.090
 MPA  C3   C4    single  1.524  0.020  1.524
 MPA  C3   H31   single  0.970  0.020  1.090
 MPA  C3   H32   single  0.970  0.020  1.090
 MPA  C4   C5    single  1.524  0.020  1.524
 MPA  C4   H41   single  0.970  0.020  1.090
 MPA  C4   H42   single  0.970  0.020  1.090
 MPA  C5   C6    single  1.523  0.020  1.523
 MPA  C5   H51   single  0.970  0.020  1.090
 MPA  C5   H52   single  0.970  0.020  1.090
 MPA  C6   H61   single  0.970  0.020  1.090
 MPA  C6   H62   single  0.970  0.020  1.090
 MPA  C6   H63   single  0.970  0.020  1.090
 MPA  C7   C8    single  1.523  0.020  1.523
 MPA  C7   C12   single  1.527  0.020  1.527
 MPA  C7   O1    single  1.439  0.020  1.439
 MPA  C7   H7    single  0.970  0.020  1.090
 MPA  C8   C9    single  1.527  0.020  1.527
 MPA  C8   H81   single  0.970  0.020  1.090
 MPA  C8   H82   single  0.970  0.020  1.090
 MPA  C9   C10   single  1.524  0.020  1.524
 MPA  C9   C13   single  1.523  0.020  1.523
 MPA  C9   H9    single  0.970  0.020  1.090
 MPA  C10  C11   single  1.524  0.020  1.524
 MPA  C10  H101  single  0.970  0.020  1.090
 MPA  C10  H102  single  0.970  0.020  1.090
 MPA  C11  C12   single  1.532  0.020  1.532
 MPA  C11  H111  single  0.970  0.020  1.090
 MPA  C11  H112  single  0.970  0.020  1.090
 MPA  C12  C14   single  1.540  0.020  1.540
 MPA  C12  H12   single  0.970  0.020  1.090
 MPA  C13  H131  single  0.970  0.020  1.090
 MPA  C13  H132  single  0.970  0.020  1.090
 MPA  C13  H133  single  0.970  0.020  1.090
 MPA  C14  C15   single  1.527  0.020  1.527
 MPA  C14  C16   single  1.527  0.020  1.527
 MPA  C14  H14   single  0.970  0.020  1.090
 MPA  C15  H151  single  0.970  0.020  1.090
 MPA  C15  H152  single  0.970  0.020  1.090
 MPA  C15  H153  single  0.970  0.020  1.090
 MPA  C16  H161  single  0.970  0.020  1.090
 MPA  C16  H162  single  0.970  0.020  1.090
 MPA  C16  H163  single  0.970  0.020  1.090
 MPA  O1   P1    single  1.603  0.020  1.603
 MPA  O2   P1    double  1.486  0.020  1.486
 MPA  O3   P1    single  1.610  0.020  1.610
 MPA  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
 MPA  H12A  C1   H11   106.88  3.000
 MPA  H12A  C1   P1    109.44  3.000
 MPA  H11   C1   P1    108.22  3.000
 MPA  H12A  C1   C2    110.46  3.000
 MPA  H11   C1   C2    109.43  3.000
 MPA  P1    C1   C2    112.24  3.000
 MPA  H22   C2   H21   106.72  3.000
 MPA  H22   C2   C3    109.32  3.000
 MPA  H21   C2   C3    109.47  3.000
 MPA  H22   C2   C1    109.61  3.000
 MPA  H21   C2   C1    109.78  3.000
 MPA  C3    C2   C1    111.81  3.000
 MPA  H32   C3   H31   106.32  3.000
 MPA  H32   C3   C4    109.37  3.000
 MPA  H31   C3   C4    109.53  3.000
 MPA  H32   C3   C2    109.19  3.000
 MPA  H31   C3   C2    109.40  3.000
 MPA  C4    C3   C2    112.82  3.000
 MPA  H42   C4   H41   106.16  3.000
 MPA  H42   C4   C5    109.24  3.000
 MPA  H41   C4   C5    109.33  3.000
 MPA  H42   C4   C3    109.36  3.000
 MPA  H41   C4   C3    109.37  3.000
 MPA  C5    C4   C3    113.15  3.000
 MPA  H52   C5   H51   106.15  3.000
 MPA  H52   C5   C6    109.46  3.000
 MPA  H51   C5   C6    109.65  3.000
 MPA  H52   C5   C4    109.30  3.000
 MPA  H51   C5   C4    109.27  3.000
 MPA  C6    C5   C4    112.79  3.000
 MPA  H63   C6   H62   107.48  3.000
 MPA  H63   C6   H61   107.58  3.000
 MPA  H62   C6   H61   107.53  3.000
 MPA  H63   C6   C5    111.29  3.000
 MPA  H62   C6   C5    111.12  3.000
 MPA  H61   C6   C5    111.63  3.000
 MPA  H7    C7   O1    108.83  3.000
 MPA  H7    C7   C12   108.46  3.000
 MPA  O1    C7   C12   107.80  3.000
 MPA  H7    C7   C8    108.82  3.000
 MPA  O1    C7   C8    111.01  3.000
 MPA  C12   C7   C8    111.84  3.000
 MPA  H82   C8   H81   106.81  3.000
 MPA  H82   C8   C9    109.63  3.000
 MPA  H81   C8   C9    109.48  3.000
 MPA  H82   C8   C7    108.94  3.000
 MPA  H81   C8   C7    110.20  3.000
 MPA  C9    C8   C7    111.65  3.000
 MPA  H9    C9   C13   108.00  3.000
 MPA  H9    C9   C10   107.76  3.000
 MPA  C13   C9   C10   111.89  3.000
 MPA  H9    C9   C8    108.07  3.000
 MPA  C13   C9   C8    111.14  3.000
 MPA  C10   C9   C8    109.83  3.000
 MPA  H102  C10  H101  106.55  3.000
 MPA  H102  C10  C11   109.55  3.000
 MPA  H101  C10  C11   109.85  3.000
 MPA  H102  C10  C9    109.15  3.000
 MPA  H101  C10  C9    109.97  3.000
 MPA  C11   C10  C9    111.64  3.000
 MPA  H112  C11  H111  106.29  3.000
 MPA  H112  C11  C12   109.86  3.000
 MPA  H111  C11  C12   109.85  3.000
 MPA  H112  C11  C10   108.90  3.000
 MPA  H111  C11  C10   109.63  3.000
 MPA  C12   C11  C10   112.14  3.000
 MPA  H12   C12  C14   107.00  3.000
 MPA  H12   C12  C11   107.39  3.000
 MPA  C14   C12  C11   113.55  3.000
 MPA  H12   C12  C7    106.96  3.000
 MPA  C14   C12  C7    113.48  3.000
 MPA  C11   C12  C7    108.09  3.000
 MPA  H133  C13  H132  107.68  3.000
 MPA  H133  C13  H131  107.71  3.000
 MPA  H132  C13  H131  107.73  3.000
 MPA  H133  C13  C9    111.48  3.000
 MPA  H132  C13  C9    111.02  3.000
 MPA  H131  C13  C9    111.05  3.000
 MPA  H14   C14  C16   107.31  3.000
 MPA  H14   C14  C15   106.41  3.000
 MPA  C16   C14  C15   110.71  3.000
 MPA  H14   C14  C12   107.07  3.000
 MPA  C16   C14  C12   113.72  3.000
 MPA  C15   C14  C12   111.21  3.000
 MPA  H153  C15  H152  107.50  3.000
 MPA  H153  C15  H151  107.64  3.000
 MPA  H152  C15  H151  107.23  3.000
 MPA  H153  C15  C14   111.27  3.000
 MPA  H152  C15  C14   110.52  3.000
 MPA  H151  C15  C14   112.45  3.000
 MPA  H163  C16  H162  107.07  3.000
 MPA  H163  C16  H161  107.55  3.000
 MPA  H162  C16  H161  107.21  3.000
 MPA  H163  C16  C14   112.29  3.000
 MPA  H162  C16  C14   110.33  3.000
 MPA  H161  C16  C14   112.13  3.000
 MPA  P1    O1   C7    123.96  3.000
 MPA  O3    P1   O2    114.18  3.000
 MPA  O3    P1   O1     97.87  3.000
 MPA  O2    P1   O1    116.28  3.000
 MPA  O3    P1   C1    105.99  3.000
 MPA  O2    P1   C1    113.82  3.000
 MPA  O1    P1   C1    107.11  3.000
 MPA  H3    O3   P1    112.86  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
 MPA  Var_01  C12   C11  C10  C9     57.10  30.0  1
 MPA  Var_02  O2    P1   O1   C7     83.11  30.0  3
 MPA  Var_03  H151  C15  C14  C12    66.73  30.0  3
 MPA  Var_04  H161  C16  C14  C12   -62.41  30.0  3
 MPA  Var_05  C4    C3   C2   C1   -179.49  30.0  3
 MPA  Var_06  O1    P1   C1   C2   -170.68  30.0  3
 MPA  Var_07  C5    C4   C3   C2   -179.22  30.0  3
 MPA  Var_08  P1    C1   C2   C3   -176.86  30.0  2
 MPA  Var_09  C6    C5   C4   C3   -179.86  30.0  3
 MPA  Var_10  H61   C6   C5   C4   -179.02  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
 MPA  chir_01  C7   C8   C12  O1   positiv
 MPA  chir_02  C9   C13  C10  C8   positiv
 MPA  chir_03  C12  C7   C11  C14  negativ
 MPA  chir_04  P1   O1   O2   O3   both

