# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 02:45:44 2020
#   Inital geometry file: a 71 line input string
#   Ligand name: 1-[(2S)-2-methyl-3-sulfanylpropanoyl]-D-proline
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](CS)C(=O)N1CCC[C@@H]1C(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
 MCO  MCO  1-[(2S)-2-methyl-3-sulfanylpropanoyl]-D-proline  ligand  28  14  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_MCO
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
 MCO  O2    O  O      0  -0.601   1.8247   1.6624   1.0445
 MCO  C9    C  C      0   0.405   2.4602   1.2310   0.0685
 MCO  O3    O  OC    -1  -0.621   3.3931   1.7950  -0.5385
 MCO  C8    C  CH1    0  -0.144   2.1437  -0.2006  -0.4094
 MCO  C7    C  CH2    0  -0.490   3.0161  -1.2166   0.3431
 MCO  C6    C  CH2    0  -0.464   2.1294  -2.4490   0.4665
 MCO  C5    C  CH2    0  -0.283   0.7522  -1.8480   0.7058
 MCO  N     N  NT     0  -0.472   0.7879  -0.6379  -0.1053
 MCO  C4    C  C      0   0.590  -0.2620   0.0435  -0.5759
 MCO  O1    O  O      0  -0.519  -0.1292   0.9918  -1.3440
 MCO  C2    C  CH1    0  -0.392  -1.6519  -0.4314  -0.1705
 MCO  C3    C  CH3    0  -0.652  -2.1842  -1.3683  -1.2578
 MCO  C1    C  CH2    0  -0.529  -2.5464   0.7876   0.0402
 MCO  S     S  S2     0  -0.263  -4.1628   0.2455   0.6973
 MCO  HC81  H  HCH1   0   0.227   2.3219  -0.2752  -1.4868
 MCO  HC71  H  HCH2   0   0.249   3.9573  -1.4101  -0.1694
 MCO  HC72  H  HCH2   0   0.233   3.2545  -0.8399   1.3413
 MCO  HC61  H  HCH2   0   0.236   2.1290  -3.0193  -0.4652
 MCO  HC62  H  HCH2   0   0.247   2.4320  -3.1218   1.2686
 MCO  HC51  H  HCH2   0   0.249  -0.0462  -2.5222   0.3972
 MCO  HC52  H  HCH2   0   0.236   0.6048  -1.6105   1.7644
 MCO  HC21  H  HCH1   0   0.267  -1.6042  -0.9760   0.7759
 MCO  HC31  H  HCH3   0   0.242  -1.5230  -2.2237  -1.4015
 MCO  HC32  H  HCH3   0   0.244  -3.1686  -1.7587  -1.0016
 MCO  HC33  H  HCH3   0   0.234  -2.2671  -0.8407  -2.2090
 MCO  HC11  H  HCH2   0   0.278  -2.0922   1.4687   0.7594
 MCO  HC12  H  HCH2   0   0.266  -2.6954   1.3225  -0.8960
 MCO  HS1   H  HSH1   0   0.226  -4.6739   1.4628   0.9074

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
 MCO  O2  C9    deloc   1.242  0.020  1.242
 MCO  C9  O3    deloc   1.248  0.020  1.248
 MCO  C9  C8    single  1.542  0.020  1.542
 MCO  C8  C7    single  1.536  0.020  1.536
 MCO  C8  N     single  1.457  0.020  1.457
 MCO  C8  HC81  single  0.970  0.020  1.090
 MCO  C7  C6    single  1.523  0.020  1.523
 MCO  C7  HC71  single  0.970  0.020  1.090
 MCO  C7  HC72  single  0.970  0.020  1.090
 MCO  C6  C5    single  1.522  0.020  1.522
 MCO  C6  HC61  single  0.970  0.020  1.090
 MCO  C6  HC62  single  0.970  0.020  1.090
 MCO  C5  N     single  1.457  0.020  1.457
 MCO  C5  HC51  single  0.970  0.020  1.090
 MCO  C5  HC52  single  0.970  0.020  1.090
 MCO  N   C4    single  1.337  0.020  1.337
 MCO  C4  O1    double  1.228  0.020  1.228
 MCO  C4  C2    single  1.524  0.020  1.524
 MCO  C2  C3    single  1.531  0.020  1.531
 MCO  C2  C1    single  1.527  0.020  1.527
 MCO  C2  HC21  single  0.970  0.020  1.090
 MCO  C3  HC31  single  0.970  0.020  1.090
 MCO  C3  HC32  single  0.970  0.020  1.090
 MCO  C3  HC33  single  0.970  0.020  1.090
 MCO  C1  S     single  1.827  0.020  1.827
 MCO  C1  HC11  single  0.970  0.020  1.090
 MCO  C1  HC12  single  0.970  0.020  1.090
 MCO  S   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
 MCO  C8    C9  O3    114.98  3.000
 MCO  C8    C9  O2    117.45  3.000
 MCO  O3    C9  O2    127.44  3.000
 MCO  HC81  C8  N     109.67  3.000
 MCO  HC81  C8  C7    110.16  3.000
 MCO  N     C8  C7    103.16  3.000
 MCO  HC81  C8  C9    109.56  3.000
 MCO  N     C8  C9    113.89  3.000
 MCO  C7    C8  C9    110.22  3.000
 MCO  HC72  C7  HC71  107.60  3.000
 MCO  HC72  C7  C6    109.37  3.000
 MCO  HC71  C7  C6    113.42  3.000
 MCO  HC72  C7  C8    110.08  3.000
 MCO  HC71  C7  C8    112.20  3.000
 MCO  C6    C7  C8    104.14  3.000
 MCO  HC62  C6  HC61  107.80  3.000
 MCO  HC62  C6  C5    112.30  3.000
 MCO  HC61  C6  C5    109.88  3.000
 MCO  HC62  C6  C7    113.42  3.000
 MCO  HC61  C6  C7    110.70  3.000
 MCO  C5    C6  C7    102.71  3.000
 MCO  HC52  C5  HC51  108.02  3.000
 MCO  HC52  C5  N     111.18  3.000
 MCO  HC51  C5  N     111.97  3.000
 MCO  HC52  C5  C6    111.08  3.000
 MCO  HC51  C5  C6    111.98  3.000
 MCO  N     C5  C6    102.61  3.000
 MCO  C4    N   C5    126.86  3.000
 MCO  C4    N   C8    120.28  3.000
 MCO  C5    N   C8    112.85  3.000
 MCO  C2    C4  O1    120.39  3.000
 MCO  C2    C4  N     117.63  3.000
 MCO  O1    C4  N     121.94  3.000
 MCO  HC21  C2  C1    107.69  3.000
 MCO  HC21  C2  C3    108.99  3.000
 MCO  C1    C2  C3    112.52  3.000
 MCO  HC21  C2  C4    110.23  3.000
 MCO  C1    C2  C4    108.80  3.000
 MCO  C3    C2  C4    108.60  3.000
 MCO  HC33  C3  HC32  108.04  3.000
 MCO  HC33  C3  HC31  108.09  3.000
 MCO  HC32  C3  HC31  107.32  3.000
 MCO  HC33  C3  C2    110.48  3.000
 MCO  HC32  C3  C2    111.50  3.000
 MCO  HC31  C3  C2    111.28  3.000
 MCO  HC12  C1  HC11  108.51  3.000
 MCO  HC12  C1  S     109.51  3.000
 MCO  HC11  C1  S     108.47  3.000
 MCO  HC12  C1  C2    110.73  3.000
 MCO  HC11  C1  C2    110.24  3.000
 MCO  S     C1  C2    109.33  3.000
 MCO  HS1   S   C1     97.16  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
 MCO  CONST_01  O1  C4  N   C8    0.00   0.0  0
 MCO  CONST_02  C2  C4  N   C8  180.00   0.0  0
 MCO  CONST_03  O1  C4  N   C5  180.00   0.0  0
 MCO  CONST_04  C2  C4  N   C5    0.00   0.0  0
 MCO  Var_01    C5  C6  C7  C8  -37.35  30.0  1
 MCO  Var_02    N   C5  C6  C7   35.06  30.0  1

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
 MCO  chir_01  C8  C9  C7  N   negativ
 MCO  chir_02  C2  C4  C3  C1  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
 MCO  plan-1  C8  0.020
 MCO  plan-1  C5  0.020
 MCO  plan-1  N   0.020
 MCO  plan-1  C4  0.020
 MCO  plan-1  O1  0.020
 MCO  plan-1  C2  0.020
 MCO  plan-2  O2  0.020
 MCO  plan-2  C9  0.020
 MCO  plan-2  O3  0.020
 MCO  plan-2  C8  0.020

