# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 14:21:25 2020
#   Inital geometry file: a 74 line input string
#   Ligand name: (2S)-2-amino-4-(methylsulfanyl)-1-pyridin-2-ylbutane-1,1-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CSCC[C@H](N)C(O)(O)c1ccccn1
#
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
 M2C  M2C  (2S)-2-amino-4-(methylsulfanyl)-1-pyridin-2-ylbutane-1,1-diol  ligand  31  15  .  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_M2C
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
 M2C  OA    O  OH1   0  -0.678  -1.4369  -1.5935  -0.6038
 M2C  C7    C  CT    0   0.521  -0.9597  -0.3081  -0.8225
 M2C  O8    O  OH1   0  -0.679  -2.0458   0.5566  -0.8202
 M2C  C9    C  CH1   0  -0.166   0.0333   0.1330   0.2989
 M2C  C11   C  CH2   0  -0.432  -0.4740  -0.2489   1.6882
 M2C  C12   C  CH2   0  -0.559   0.5578   0.0297   2.7755
 M2C  S13   S  S2    0  -0.038  -0.0498  -0.6093   4.3620
 M2C  C14   C  CH3   0  -0.764   1.2659  -0.0263   5.4529
 M2C  N10   N  NH2   0  -0.826   0.1683   1.5811   0.1910
 M2C  C1    C  CR6   0   0.188  -0.2308  -0.2790  -2.1680
 M2C  C2    C  CR16  0  -0.344  -0.1615   0.8543  -2.9674
 M2C  C3    C  CR16  0  -0.142   0.5648   0.7848  -4.1472
 M2C  C4    C  CR16  0  -0.332   1.1843  -0.4069  -4.4924
 M2C  C5    C  CR16  0  -0.059   1.0449  -1.4876  -3.6361
 M2C  N6    N  N     0  -0.459   0.3583  -1.4212  -2.5031
 M2C  HOA   H  HOH1  0   0.450  -0.8964  -2.1896  -1.1463
 M2C  HO8   H  HOH1  0   0.450  -1.7013   1.3838  -0.4319
 M2C  H9    H  HCH1  0   0.238   0.9840  -0.3915   0.1301
 M2C  H111  H  HCH2  0   0.254  -0.7104  -1.3128   1.6937
 M2C  H112  H  HCH2  0   0.236  -1.3999   0.2877   1.9147
 M2C  H121  H  HCH2  0   0.255   0.7491   1.0984   2.8953
 M2C  H122  H  HCH2  0   0.262   1.5074  -0.4531   2.5321
 M2C  H141  H  HCH3  0   0.274   1.0303  -0.3565   6.4628
 M2C  H142  H  HCH3  0   0.261   2.2298  -0.4439   5.1654
 M2C  H143  H  HCH3  0   0.261   1.3275   1.0612   5.4467
 M2C  H101  H  HNH2  0   0.370   0.4866   1.9913   1.0581
 M2C  H102  H  HNH2  0   0.369   0.8533   1.8365  -0.5089
 M2C  H2    H  HCR6  0   0.270  -0.6651   1.7693  -2.6885
 M2C  H3    H  HCR6  0   0.278   0.6408   1.6504  -4.7918
 M2C  H4    H  HCR6  0   0.274   1.7575  -0.5020  -5.4040
 M2C  H5    H  HCR6  0   0.271   1.5021  -2.4417  -3.8717

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
 M2C  OA   C7    single    1.388  0.020  1.388
 M2C  OA   HOA   single    0.850  0.020  0.980
 M2C  C7   O8    single    1.388  0.020  1.388
 M2C  C7   C9    single    1.562  0.020  1.562
 M2C  C7   C1    single    1.531  0.020  1.531
 M2C  O8   HO8   single    0.850  0.020  0.980
 M2C  C9   C11   single    1.528  0.020  1.528
 M2C  C9   N10   single    1.458  0.020  1.458
 M2C  C9   H9    single    0.970  0.020  1.090
 M2C  C11  C12   single    1.525  0.020  1.525
 M2C  C11  H111  single    0.970  0.020  1.090
 M2C  C11  H112  single    0.970  0.020  1.090
 M2C  C12  S13   single    1.815  0.020  1.815
 M2C  C12  H121  single    0.970  0.020  1.090
 M2C  C12  H122  single    0.970  0.020  1.090
 M2C  S13  C14   single    1.806  0.020  1.806
 M2C  C14  H141  single    0.970  0.020  1.090
 M2C  C14  H142  single    0.970  0.020  1.090
 M2C  C14  H143  single    0.970  0.020  1.090
 M2C  N10  H101  single    0.890  0.020  1.040
 M2C  N10  H102  single    0.890  0.020  1.040
 M2C  C1   C2    aromatic  1.389  0.020  1.389
 M2C  C1   N6    aromatic  1.328  0.020  1.328
 M2C  C2   C3    aromatic  1.387  0.020  1.387
 M2C  C2   H2    single    0.930  0.020  1.080
 M2C  C3   C4    aromatic  1.387  0.020  1.387
 M2C  C3   H3    single    0.930  0.020  1.080
 M2C  C4   C5    aromatic  1.386  0.020  1.386
 M2C  C4   H4    single    0.930  0.020  1.080
 M2C  C5   N6    aromatic  1.326  0.020  1.326
 M2C  C5   H5    single    0.930  0.020  1.080

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
 M2C  HOA   OA   C7    106.80  3.000
 M2C  C1    C7   C9    108.85  3.000
 M2C  C1    C7   O8    111.24  3.000
 M2C  C9    C7   O8    108.69  3.000
 M2C  C1    C7   OA    108.65  3.000
 M2C  C9    C7   OA    111.53  3.000
 M2C  O8    C7   OA    107.90  3.000
 M2C  HO8   O8   C7    104.61  3.000
 M2C  H9    C9   N10   112.49  3.000
 M2C  H9    C9   C11   107.92  3.000
 M2C  N10   C9   C11   110.26  3.000
 M2C  H9    C9   C7    107.76  3.000
 M2C  N10   C9   C7    106.63  3.000
 M2C  C11   C9   C7    111.80  3.000
 M2C  H112  C11  H111  107.11  3.000
 M2C  H112  C11  C12   109.61  3.000
 M2C  H111  C11  C12   108.76  3.000
 M2C  H112  C11  C9    110.29  3.000
 M2C  H111  C11  C9    108.70  3.000
 M2C  C12   C11  C9    112.22  3.000
 M2C  H122  C12  H121  107.73  3.000
 M2C  H122  C12  S13   109.28  3.000
 M2C  H121  C12  S13   107.89  3.000
 M2C  H122  C12  C11   110.39  3.000
 M2C  H121  C12  C11   112.05  3.000
 M2C  S13   C12  C11   109.42  3.000
 M2C  C14   S13  C12    99.81  3.000
 M2C  H143  C14  H142  109.34  3.000
 M2C  H143  C14  H141  108.69  3.000
 M2C  H142  C14  H141  108.67  3.000
 M2C  H143  C14  S13   111.11  3.000
 M2C  H142  C14  S13   111.20  3.000
 M2C  H141  C14  S13   107.75  3.000
 M2C  H102  N10  H101  106.13  3.000
 M2C  H102  N10  C9    111.37  3.000
 M2C  H101  N10  C9    111.64  3.000
 M2C  N6    C1   C2    122.31  3.000
 M2C  N6    C1   C7    114.62  3.000
 M2C  C2    C1   C7    123.05  3.000
 M2C  H2    C2   C3    120.38  3.000
 M2C  H2    C2   C1    121.26  3.000
 M2C  C3    C2   C1    118.35  3.000
 M2C  H3    C3   C4    120.52  3.000
 M2C  H3    C3   C2    120.23  3.000
 M2C  C4    C3   C2    119.26  3.000
 M2C  H4    C4   C5    120.38  3.000
 M2C  H4    C4   C3    121.50  3.000
 M2C  C5    C4   C3    118.12  3.000
 M2C  H5    C5   N6    116.62  3.000
 M2C  H5    C5   C4    120.64  3.000
 M2C  N6    C5   C4    122.74  3.000
 M2C  C5    N6   C1    119.22  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
 M2C  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 M2C  CONST_02  C4    C5   N6   C1      0.00   0.0  0
 M2C  CONST_03  C5    N6   C1   C2      0.00   0.0  0
 M2C  CONST_04  C5    C4   C3   C2      0.00   0.0  0
 M2C  CONST_05  N6    C1   C2   C3      0.00   0.0  0
 M2C  CONST_06  N6    C5   C4   C3      0.00   0.0  0
 M2C  CONST_07  C3    C2   C1   C7    180.00   0.0  0
 M2C  CONST_08  C5    N6   C1   C7    180.00   0.0  0
 M2C  CONST_09  H3    C3   C2   C1    180.00   0.0  0
 M2C  CONST_10  H5    C5   N6   C1    180.00   0.0  0
 M2C  CONST_11  H4    C4   C3   C2    180.00   0.0  0
 M2C  CONST_12  H2    C2   C3   C4    180.00   0.0  0
 M2C  Var_01    C2    C1   C7   OA    150.18  30.0  2
 M2C  Var_02    S13   C12  C11  C9   -174.09  30.0  3
 M2C  Var_03    H141  C14  S13  C12  -179.40  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
 M2C  chir_01  C9  C7  C11  N10  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
 M2C  plan-1  C7  0.020
 M2C  plan-1  C1  0.020
 M2C  plan-1  C2  0.020
 M2C  plan-1  C3  0.020
 M2C  plan-1  C4  0.020
 M2C  plan-1  C5  0.020
 M2C  plan-1  N6  0.020
 M2C  plan-1  H2  0.020
 M2C  plan-1  H3  0.020
 M2C  plan-1  H4  0.020
 M2C  plan-1  H5  0.020

