# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Nov 23 00:58:38 2022
#   Inital geometry file: a 105 line input string
#   Ligand name: (2R)-2-[2-(4-tert-butylphenyl)ethyl]-2-hydroxybutanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(C)c1ccc(CC[C@@](O)(CC(O)=O)C(O)=O)cc1
#
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
 X3M  X3M  "(2R)-2-[2-(4-tert-butylphenyl)ethyl]-2-hydroxybutanedioic acid"  ligand  43  21  .  2023-02-16  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_X3M
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
 X3M  C11   C  CH2   0  -0.515  157.0411  158.2114  145.0282
 X3M  C10   C  CR16  0  -0.322  155.1390  157.0699  148.1215
 X3M  C12   C  CH2   0  -0.482  156.8911  159.7195  144.8339
 X3M  C18   C  C     0   0.522  157.0946  161.7577  143.4970
 X3M  C14   C  CH2   0  -0.593  156.4099  159.6790  142.3091
 X3M  C01   C  CH3   0  -0.630  156.1649  157.8298  151.4919
 X3M  C03   C  CH3   0  -0.663  154.3791  156.2615  150.7771
 X3M  C04   C  CH3   0  -0.630  156.7202  155.4533  150.9164
 X3M  C05   C  CR6   0   0.179  156.1155  157.0690  149.1139
 X3M  C06   C  CR16  0  -0.296  157.4029  157.4605  148.7359
 X3M  C07   C  CR16  0  -0.292  157.6985  157.8242  147.4328
 X3M  C08   C  CR6   0   0.120  156.7191  157.8129  146.4415
 X3M  C09   C  CR16  0  -0.292  155.4356  157.4346  146.8124
 X3M  C13   C  CT    0   0.158  157.3090  160.2397  143.4450
 X3M  O19   O  O     0  -0.433  155.9997  162.2607  143.5245
 X3M  O20   O  OH1   0  -0.576  158.2242  162.4415  143.5479
 X3M  O21   O  OH1   0  -0.654  158.6314  159.9045  143.1332
 X3M  H112  H  HCH2  0   0.255  156.3828  157.6793  144.3410
 X3M  H111  H  HCH2  0   0.243  158.0615  157.9045  144.7900
 X3M  H101  H  HCR6  0   0.245  154.1230  156.7775  148.3504
 X3M  H122  H  HCH2  0   0.262  157.4943  160.2358  145.5905
 X3M  H121  H  HCH2  0   0.259  155.8545  160.0091  145.0180
 X3M  H141  H  HCH2  0   0.290  156.1724  160.4627  141.5898
 X3M  H142  H  HCH2  0   0.293  155.4642  159.3302  142.7228
 X3M  H013  H  HCH3  0   0.225  155.9707  157.5521  152.5301
 X3M  H012  H  HCH3  0   0.227  157.2109  158.1307  151.4229
 X3M  H011  H  HCH3  0   0.226  155.5498  158.7002  151.2569
 X3M  H033  H  HCH3  0   0.236  154.2306  155.9813  151.8213
 X3M  H032  H  HCH3  0   0.228  153.6919  157.0814  150.5599
 X3M  H031  H  HCH3  0   0.228  154.0882  155.4047  150.1664
 X3M  H043  H  HCH3  0   0.225  156.5355  155.1397  151.9460
 X3M  H042  H  HCH3  0   0.226  156.5053  154.6041  150.2654
 X3M  H041  H  HCH3  0   0.227  157.7830  155.6821  150.8286
 X3M  H061  H  HCR6  0   0.243  158.2012  157.4773  149.4685
 X3M  H071  H  HCR6  0   0.239  158.7126  158.1126  147.1786
 X3M  H091  H  HCR6  0   0.239  154.6480  157.4137  146.0672
 X3M  H1    H  HOH1  0   0.476  158.1437  158.2169  140.0454
 X3M  H2    H  HOH1  0   0.484  158.0326  163.3896  143.6231
 X3M  H211  H  HOH1  0   0.460  159.1963  160.0456  143.9018
 X3M  C15   C  C     0   0.545  157.0660  158.5403  141.5646
 X3M  C02   C  CT    0  -0.168  155.8388  156.6573  150.5565
 X3M  O16   O  O     0  -0.431  156.9858  157.3751  141.8613
 X3M  O17   O  OH1   0  -0.585  157.7302  158.9683  140.4972

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
 X3M  O16  C15   double    1.205  0.020  1.205
 X3M  C15  C14   single    1.510  0.020  1.510
 X3M  C15  O17   single    1.328  0.020  1.328
 X3M  C14  C13   single    1.553  0.020  1.553
 X3M  O19  C18   double    1.205  0.020  1.205
 X3M  C18  O20   single    1.321  0.020  1.321
 X3M  C18  C13   single    1.534  0.020  1.534
 X3M  O21  C13   single    1.399  0.020  1.399
 X3M  C13  C12   single    1.541  0.020  1.541
 X3M  C12  C11   single    1.528  0.020  1.528
 X3M  C11  C08   single    1.503  0.020  1.503
 X3M  C08  C07   aromatic  1.394  0.020  1.394
 X3M  C08  C09   aromatic  1.388  0.020  1.388
 X3M  C07  C06   aromatic  1.385  0.020  1.385
 X3M  C09  C10   aromatic  1.391  0.020  1.391
 X3M  C06  C05   aromatic  1.398  0.020  1.398
 X3M  C10  C05   aromatic  1.392  0.020  1.392
 X3M  C05  C02   single    1.525  0.020  1.525
 X3M  C02  C04   single    1.535  0.020  1.535
 X3M  C02  C03   single    1.528  0.020  1.528
 X3M  C02  C01   single    1.535  0.020  1.535
 X3M  C11  H112  single    0.970  0.020  1.090
 X3M  C11  H111  single    0.970  0.020  1.090
 X3M  C10  H101  single    0.930  0.020  1.080
 X3M  C12  H122  single    0.970  0.020  1.090
 X3M  C12  H121  single    0.970  0.020  1.090
 X3M  C14  H141  single    0.970  0.020  1.090
 X3M  C14  H142  single    0.970  0.020  1.090
 X3M  C01  H013  single    0.970  0.020  1.090
 X3M  C01  H012  single    0.970  0.020  1.090
 X3M  C01  H011  single    0.970  0.020  1.090
 X3M  C03  H033  single    0.970  0.020  1.090
 X3M  C03  H032  single    0.970  0.020  1.090
 X3M  C03  H031  single    0.970  0.020  1.090
 X3M  C04  H043  single    0.970  0.020  1.090
 X3M  C04  H042  single    0.970  0.020  1.090
 X3M  C04  H041  single    0.970  0.020  1.090
 X3M  C06  H061  single    0.930  0.020  1.080
 X3M  C07  H071  single    0.930  0.020  1.080
 X3M  C09  H091  single    0.930  0.020  1.080
 X3M  O17  H1    single    0.850  0.020  0.980
 X3M  O20  H2    single    0.850  0.020  0.980
 X3M  O21  H211  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
 X3M  H111  C11  H112  106.84  3.000
 X3M  H111  C11  C08   109.32  3.000
 X3M  H112  C11  C08   109.50  3.000
 X3M  H111  C11  C12   109.97  3.000
 X3M  H112  C11  C12   110.02  3.000
 X3M  C08   C11  C12   111.11  3.000
 X3M  H101  C10  C09   118.05  3.000
 X3M  H101  C10  C05   120.51  3.000
 X3M  C09   C10  C05   121.43  3.000
 X3M  H121  C12  H122  106.31  3.000
 X3M  H121  C12  C13   108.66  3.000
 X3M  H122  C12  C13   108.28  3.000
 X3M  H121  C12  C11   109.49  3.000
 X3M  H122  C12  C11   108.84  3.000
 X3M  C13   C12  C11   114.91  3.000
 X3M  O20   C18  O19   124.04  3.000
 X3M  O20   C18  C13   113.20  3.000
 X3M  O19   C18  C13   122.73  3.000
 X3M  H142  C14  H141  106.96  3.000
 X3M  H142  C14  C13   109.89  3.000
 X3M  H141  C14  C13   110.43  3.000
 X3M  H142  C14  C15   108.83  3.000
 X3M  H141  C14  C15   108.15  3.000
 X3M  C13   C14  C15   112.40  3.000
 X3M  H011  C01  H012  107.87  3.000
 X3M  H011  C01  H013  107.90  3.000
 X3M  H012  C01  H013  107.51  3.000
 X3M  H011  C01  C02   110.99  3.000
 X3M  H012  C01  C02   112.08  3.000
 X3M  H013  C01  C02   110.32  3.000
 X3M  H031  C03  H032  108.08  3.000
 X3M  H031  C03  H033  107.31  3.000
 X3M  H032  C03  H033  107.31  3.000
 X3M  H031  C03  C02   112.15  3.000
 X3M  H032  C03  C02   112.21  3.000
 X3M  H033  C03  C02   109.55  3.000
 X3M  H041  C04  H042  107.88  3.000
 X3M  H041  C04  H043  107.51  3.000
 X3M  H042  C04  H043  107.79  3.000
 X3M  H041  C04  C02   112.10  3.000
 X3M  H042  C04  C02   110.94  3.000
 X3M  H043  C04  C02   110.44  3.000
 X3M  C06   C05  C02   119.90  3.000
 X3M  C02   C05  C10   123.16  3.000
 X3M  C06   C05  C10   116.94  3.000
 X3M  H061  C06  C07   118.35  3.000
 X3M  H061  C06  C05   120.00  3.000
 X3M  C07   C06  C05   121.65  3.000
 X3M  H071  C07  C08   119.52  3.000
 X3M  H071  C07  C06   119.34  3.000
 X3M  C08   C07  C06   121.14  3.000
 X3M  C09   C08  C07   117.51  3.000
 X3M  C09   C08  C11   121.43  3.000
 X3M  C07   C08  C11   121.06  3.000
 X3M  H091  C09  C08   119.54  3.000
 X3M  H091  C09  C10   119.13  3.000
 X3M  C08   C09  C10   121.33  3.000
 X3M  O21   C13  C14   107.31  3.000
 X3M  O21   C13  C18   112.13  3.000
 X3M  C14   C13  C18   107.52  3.000
 X3M  O21   C13  C12   112.10  3.000
 X3M  C18   C13  C12   105.41  3.000
 X3M  C14   C13  C12   112.35  3.000
 X3M  H2    O20  C18   109.87  3.000
 X3M  H211  O21  C13   109.94  3.000
 X3M  O17   C15  O16   122.88  3.000
 X3M  O17   C15  C14   111.74  3.000
 X3M  O16   C15  C14   125.36  3.000
 X3M  C05   C02  C04   109.23  3.000
 X3M  C04   C02  C03   108.14  3.000
 X3M  C05   C02  C03   112.31  3.000
 X3M  C03   C02  C01   108.22  3.000
 X3M  C04   C02  C01   109.53  3.000
 X3M  C05   C02  C01   109.37  3.000
 X3M  H1    O17  C15   109.76  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
 X3M  CONST_01  C07   C08  C09  C10     0.00   0.0  0
 X3M  CONST_02  C07   C06  C05  C10     0.00   0.0  0
 X3M  CONST_03  C08   C07  C06  C05     0.00   0.0  0
 X3M  CONST_04  C08   C09  C10  C05     0.00   0.0  0
 X3M  CONST_05  C09   C08  C07  C06     0.00   0.0  0
 X3M  CONST_06  C09   C10  C05  C06     0.00   0.0  0
 X3M  CONST_07  C06   C07  C08  C11   180.00   0.0  0
 X3M  CONST_08  C10   C09  C08  C11   180.00   0.0  0
 X3M  CONST_09  C07   C06  C05  C02   180.00   0.0  0
 X3M  CONST_10  C09   C10  C05  C02   180.00   0.0  0
 X3M  CONST_11  H061  C06  C05  C10   180.00   0.0  0
 X3M  CONST_12  H071  C07  C06  C05   180.00   0.0  0
 X3M  CONST_13  H091  C09  C10  C05   180.00   0.0  0
 X3M  CONST_14  H101  C10  C05  C06   180.00   0.0  0
 X3M  CONST_15  H091  C09  C08  C07   180.00   0.0  0
 X3M  CONST_16  H061  C06  C07  C08   180.00   0.0  0
 X3M  CONST_17  H101  C10  C09  C08   180.00   0.0  0
 X3M  CONST_18  H071  C07  C08  C09   180.00   0.0  0
 X3M  CONST_19  H1    O17  C15  C14   180.00   0.0  0
 X3M  CONST_20  H2    O20  C18  C13   180.00   0.0  0
 X3M  CONST_21  H1    O17  C15  O16     0.00   0.0  0
 X3M  CONST_22  H2    O20  C18  O19     0.00   0.0  0
 X3M  Var_01    C04   C02  C05  C10   119.58  30.0  2
 X3M  Var_02    C03   C02  C05  C10    -0.39  30.0  2
 X3M  Var_03    C01   C02  C05  C10  -120.56  30.0  2
 X3M  Var_04    C07   C08  C11  C12   -87.53  30.0  2
 X3M  Var_05    C09   C08  C11  C12    91.75  30.0  2
 X3M  Var_06    C06   C05  C02  C01    59.91  30.0  2
 X3M  Var_07    C06   C05  C02  C03  -179.93  30.0  2
 X3M  Var_08    C06   C05  C02  C04   -59.95  30.0  2
 X3M  Var_09    H112  C11  C08  C07   150.74  30.0  2
 X3M  Var_10    H111  C11  C08  C07    34.02  30.0  2
 X3M  Var_11    H112  C11  C08  C09   -29.98  30.0  2
 X3M  Var_12    H111  C11  C08  C09  -146.70  30.0  2
 X3M  Var_13    C13   C12  C11  C08   175.34  30.0  2
 X3M  Var_14    H043  C04  C02  C05  -179.83  30.0  3
 X3M  Var_15    H042  C04  C02  C05   -60.37  30.0  3
 X3M  Var_16    H041  C04  C02  C05    60.31  30.0  3
 X3M  Var_17    H033  C03  C02  C05  -179.70  30.0  3
 X3M  Var_18    H032  C03  C02  C05   -60.62  30.0  3
 X3M  Var_19    H031  C03  C02  C05    61.26  30.0  3
 X3M  Var_20    H013  C01  C02  C05   179.92  30.0  3
 X3M  Var_21    H012  C01  C02  C05   -60.32  30.0  3
 X3M  Var_22    H011  C01  C02  C05    60.37  30.0  3
 X3M  Var_23    H122  C12  C11  C08    53.74  30.0  2
 X3M  Var_24    H121  C12  C11  C08   -62.08  30.0  2
 X3M  Var_25    O16   C15  C14  C13    89.01  30.0  2
 X3M  Var_26    O17   C15  C14  C13   -92.72  30.0  2
 X3M  Var_27    H043  C04  C02  C01    60.41  30.0  3
 X3M  Var_28    H042  C04  C02  C01   179.87  30.0  3
 X3M  Var_29    H041  C04  C02  C01   -59.45  30.0  3
 X3M  Var_30    H033  C03  C02  C01   -58.87  30.0  3
 X3M  Var_31    H032  C03  C02  C01    60.21  30.0  3
 X3M  Var_32    H031  C03  C02  C01  -177.91  30.0  3
 X3M  Var_33    H043  C04  C02  C03   -57.32  30.0  3
 X3M  Var_34    H042  C04  C02  C03    62.14  30.0  3
 X3M  Var_35    H041  C04  C02  C03  -177.18  30.0  3
 X3M  Var_36    H013  C01  C02  C03    57.28  30.0  3
 X3M  Var_37    H012  C01  C02  C03   177.04  30.0  3
 X3M  Var_38    H011  C01  C02  C03   -62.27  30.0  3
 X3M  Var_39    H033  C03  C02  C04    59.70  30.0  3
 X3M  Var_40    H032  C03  C02  C04   178.78  30.0  3
 X3M  Var_41    H031  C03  C02  C04   -59.34  30.0  3
 X3M  Var_42    H013  C01  C02  C04   -60.41  30.0  3
 X3M  Var_43    H012  C01  C02  C04    59.36  30.0  3
 X3M  Var_44    H011  C01  C02  C04  -179.96  30.0  3
 X3M  Var_45    H112  C11  C12  C13   -63.24  30.0  3
 X3M  Var_46    H111  C11  C12  C13    54.17  30.0  3
 X3M  Var_47    H141  C14  C15  O16  -148.82  30.0  3
 X3M  Var_48    H142  C14  C15  O16   -32.96  30.0  3
 X3M  Var_49    H141  C14  C15  O17    29.45  30.0  3
 X3M  Var_50    H142  C14  C15  O17   145.31  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
 X3M  chir_01  C13  C18  O21  C12  negativ

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
 X3M  plan-1  C11   0.020
 X3M  plan-1  C10   0.020
 X3M  plan-1  C05   0.020
 X3M  plan-1  C06   0.020
 X3M  plan-1  C07   0.020
 X3M  plan-1  C08   0.020
 X3M  plan-1  C09   0.020
 X3M  plan-1  H101  0.020
 X3M  plan-1  H061  0.020
 X3M  plan-1  H071  0.020
 X3M  plan-1  H091  0.020
 X3M  plan-1  C02   0.020
 X3M  plan-2  C18   0.020
 X3M  plan-2  C13   0.020
 X3M  plan-2  O19   0.020
 X3M  plan-2  O20   0.020
 X3M  plan-2  H2    0.020
 X3M  plan-3  C14   0.020
 X3M  plan-3  H1    0.020
 X3M  plan-3  C15   0.020
 X3M  plan-3  O16   0.020
 X3M  plan-3  O17   0.020

