# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 13:25:04 2021
#   Inital geometry file: a 78 line input string
#   Ligand name: (2S)-5-phenyl-2-(sulfanylmethyl)pentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@@H](CS)CCCc1ccccc1
#
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
 M5P  M5P  '(2S)-5-phenyl-2-(sulfanylmethyl)pentanoic acid'  ligand  31  15  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_M5P
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
 M5P  C1    C  CR16  0  -0.317  34.9876   5.9305  107.2146
 M5P  C2    C  CR16  0  -0.239  36.1517   5.1826  107.0924
 M5P  C3    C  CR16  0  -0.275  37.1192   5.2310  108.0874
 M5P  C4    C  CR16  0  -0.239  36.9124   6.0326  109.2033
 M5P  C5    C  CR16  0  -0.310  35.7469   6.7777  109.3203
 M5P  C6    C  CR6   0   0.139  34.7672   6.7366  108.3291
 M5P  C7    C  CH2   0  -0.506  33.5279   7.5787  108.4401
 M5P  C8    C  CH2   0  -0.407  33.7579   9.0055  107.9360
 M5P  C9    C  CH2   0  -0.433  32.4952   9.8470  108.0670
 M5P  C10   C  CH1   0  -0.327  32.5762  11.2388  107.4186
 M5P  C12   C  C     0   0.537  31.1965  11.8575  107.4406
 M5P  O2    O  O     0  -0.440  30.4898  11.9972  106.4733
 M5P  O1    O  OH1   0  -0.590  30.8297  12.2218  108.6645
 M5P  C11   C  CH2   0  -0.579  33.5935  12.1774  108.0869
 M5P  S1    S  S2    0  -0.234  35.2905  12.0215  107.4467
 M5P  H1    H  HCR6  0   0.245  34.2378   5.8841  106.4329
 M5P  H2    H  HCR6  0   0.252  36.3019   4.5592  106.2199
 M5P  H3    H  HCR6  0   0.252  38.0260   4.6470  107.9962
 M5P  H4    H  HCR6  0   0.252  37.6593   6.0758  109.9858
 M5P  H5    H  HCR6  0   0.244  35.5932   7.3981  110.1964
 M5P  H71   H  HCH2  0   0.239  32.7161   7.1214  107.8679
 M5P  H72   H  HCH2  0   0.239  33.1952   7.6148  109.4814
 M5P  H81   H  HCH2  0   0.232  34.5808   9.4532  108.4973
 M5P  H82   H  HCH2  0   0.226  34.0804   8.9757  106.8916
 M5P  H91   H  HCH2  0   0.241  31.6685   9.3001  107.6019
 M5P  H92   H  HCH2  0   0.237  32.2378   9.9530  109.1247
 M5P  H10   H  HCH1  0   0.275  32.8362  11.1193  106.3644
 M5P  HO1   H  HOH1  0   0.483  29.9432  12.6132  108.6460
 M5P  H111  H  HCH2  0   0.296  33.3055  13.2226  107.9775
 M5P  H112  H  HCH2  0   0.287  33.6615  11.9794  109.1575
 M5P  HS1   H  HSH1  0   0.222  35.0783  12.6298  106.2740

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
 M5P  C1   C2    aromatic  1.389  0.020  1.389
 M5P  C1   C6    aromatic  1.393  0.020  1.393
 M5P  C1   H1    single    0.930  0.020  1.080
 M5P  C2   C3    aromatic  1.389  0.020  1.389
 M5P  C2   H2    single    0.930  0.020  1.080
 M5P  C3   C4    aromatic  1.389  0.020  1.389
 M5P  C3   H3    single    0.930  0.020  1.080
 M5P  C4   C5    aromatic  1.388  0.020  1.388
 M5P  C4   H4    single    0.930  0.020  1.080
 M5P  C5   C6    aromatic  1.394  0.020  1.394
 M5P  C5   H5    single    0.930  0.020  1.080
 M5P  C6   C7    single    1.502  0.020  1.502
 M5P  C7   C8    single    1.531  0.020  1.531
 M5P  C7   H71   single    0.970  0.020  1.090
 M5P  C7   H72   single    0.970  0.020  1.090
 M5P  C8   C9    single    1.523  0.020  1.523
 M5P  C8   H81   single    0.970  0.020  1.090
 M5P  C8   H82   single    0.970  0.020  1.090
 M5P  C9   C10   single    1.538  0.020  1.538
 M5P  C9   H91   single    0.970  0.020  1.090
 M5P  C9   H92   single    0.970  0.020  1.090
 M5P  C10  C12   single    1.512  0.020  1.512
 M5P  C10  C11   single    1.537  0.020  1.537
 M5P  C10  H10   single    0.970  0.020  1.090
 M5P  C12  O2    double    1.206  0.020  1.206
 M5P  C12  O1    single    1.329  0.020  1.329
 M5P  O1   HO1   single    0.850  0.020  0.980
 M5P  C11  S1    single    1.820  0.020  1.820
 M5P  C11  H111  single    0.970  0.020  1.090
 M5P  C11  H112  single    0.970  0.020  1.090
 M5P  S1   HS1   single    1.200  0.020  1.300

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
 M5P  H1    C1   C6    119.49  3.000
 M5P  H1    C1   C2    119.55  3.000
 M5P  C6    C1   C2    120.97  3.000
 M5P  H2    C2   C3    120.06  3.000
 M5P  H2    C2   C1    119.81  3.000
 M5P  C3    C2   C1    120.13  3.000
 M5P  H3    C3   C4    120.24  3.000
 M5P  H3    C3   C2    120.29  3.000
 M5P  C4    C3   C2    119.47  3.000
 M5P  H4    C4   C5    119.80  3.000
 M5P  H4    C4   C3    120.05  3.000
 M5P  C5    C4   C3    120.15  3.000
 M5P  H5    C5   C6    119.44  3.000
 M5P  H5    C5   C4    119.61  3.000
 M5P  C6    C5   C4    120.95  3.000
 M5P  C7    C6   C5    120.70  3.000
 M5P  C7    C6   C1    120.93  3.000
 M5P  C5    C6   C1    118.33  3.000
 M5P  H72   C7   H71   106.63  3.000
 M5P  H72   C7   C8    109.18  3.000
 M5P  H71   C7   C8    109.21  3.000
 M5P  H72   C7   C6    109.86  3.000
 M5P  H71   C7   C6    109.84  3.000
 M5P  C8    C7   C6    111.97  3.000
 M5P  H82   C8   H81   106.25  3.000
 M5P  H82   C8   C9    109.98  3.000
 M5P  H81   C8   C9    110.73  3.000
 M5P  H82   C8   C7    109.48  3.000
 M5P  H81   C8   C7    109.03  3.000
 M5P  C9    C8   C7    111.23  3.000
 M5P  H92   C9   H91   106.35  3.000
 M5P  H92   C9   C10   109.42  3.000
 M5P  H91   C9   C10   108.23  3.000
 M5P  H92   C9   C8    109.38  3.000
 M5P  H91   C9   C8    108.26  3.000
 M5P  C10   C9   C8    114.85  3.000
 M5P  H10   C10  C11   109.20  3.000
 M5P  H10   C10  C12   106.02  3.000
 M5P  C11   C10  C12   110.35  3.000
 M5P  H10   C10  C9    108.69  3.000
 M5P  C11   C10  C9    113.84  3.000
 M5P  C12   C10  C9    108.43  3.000
 M5P  O1    C12  O2    123.04  3.000
 M5P  O1    C12  C10   112.18  3.000
 M5P  O2    C12  C10   124.77  3.000
 M5P  HO1   O1   C12   110.22  3.000
 M5P  H112  C11  H111  106.80  3.000
 M5P  H112  C11  S1    105.75  3.000
 M5P  H111  C11  S1    107.05  3.000
 M5P  H112  C11  C10   110.93  3.000
 M5P  H111  C11  C10   111.54  3.000
 M5P  S1    C11  C10   114.32  3.000
 M5P  HS1   S1   C11    96.97  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
 M5P  CONST_01  C4   C3  C2   C1      0.00   0.0  0
 M5P  CONST_02  C4   C5  C6   C1      0.00   0.0  0
 M5P  CONST_03  C5   C6  C1   C2      0.00   0.0  0
 M5P  CONST_04  C5   C4  C3   C2      0.00   0.0  0
 M5P  CONST_05  C6   C1  C2   C3      0.00   0.0  0
 M5P  CONST_06  C6   C5  C4   C3      0.00   0.0  0
 M5P  CONST_07  C7   C6  C1   C2    180.00   0.0  0
 M5P  CONST_08  C7   C6  C5   C4    180.00   0.0  0
 M5P  CONST_09  H3   C3  C2   C1    180.00   0.0  0
 M5P  CONST_10  H5   C5  C6   C1    180.00   0.0  0
 M5P  CONST_11  H4   C4  C3   C2    180.00   0.0  0
 M5P  CONST_12  H1   C1  C2   C3    180.00   0.0  0
 M5P  CONST_13  H2   C2  C3   C4    180.00   0.0  0
 M5P  CONST_14  HO1  O1  C12  C10   180.00   0.0  0
 M5P  Var_01    C8   C7  C6   C1    -94.31  30.0  2
 M5P  Var_02    C9   C8  C7   C6   -179.52  30.0  3
 M5P  Var_03    C10  C9  C8   C7   -172.41  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
 M5P  chir_01  C10  C9  C12  C11  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
 M5P  plan-1  C1   0.020
 M5P  plan-1  C2   0.020
 M5P  plan-1  C3   0.020
 M5P  plan-1  C4   0.020
 M5P  plan-1  C5   0.020
 M5P  plan-1  C6   0.020
 M5P  plan-1  C7   0.020
 M5P  plan-1  H1   0.020
 M5P  plan-1  H2   0.020
 M5P  plan-1  H3   0.020
 M5P  plan-1  H4   0.020
 M5P  plan-1  H5   0.020
 M5P  plan-2  C10  0.020
 M5P  plan-2  C12  0.020
 M5P  plan-2  O2   0.020
 M5P  plan-2  O1   0.020
 M5P  plan-2  HO1  0.020

