# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 00:23:09 2020
#   Inital geometry file: a 55 line input string
#   Ligand name: (1R,2R,3R,4S,5R)-4-amino-5-(methylsulfanyl)cyclopentane-1,2,3-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CS[C@@H]1[C@@H](N)[C@@H](O)[C@@H](O)[C@H]1O
#
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
 MSN  MSN  (1R,2R,3R,4S,5R)-4-amino-5-(methylsulfanyl)cyclopentane-1,2,3-triol  ligand  24  11  .  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_MSN
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
 MSN  C5    C  CH1   0  -0.079  -0.1949  -1.3721  -0.3944
 MSN  N5    N  NH2   0  -0.796   0.0254  -2.5969   0.3443
 MSN  C4    C  CH1   0  -0.002  -1.6265  -0.8520  -0.3304
 MSN  O4    O  OH1   0  -0.668  -2.0744  -0.8347   1.0009
 MSN  C3    C  CH1   0  -0.012  -1.4419   0.5645  -0.8779
 MSN  O3    O  OH1   0  -0.670  -2.5084   1.4336  -0.5988
 MSN  C2    C  CH1   0   0.068  -0.1375   1.0809  -0.2238
 MSN  O2    O  OH1   0  -0.666  -0.3543   1.8518   0.9307
 MSN  C1    C  CH1   0  -0.407   0.6158  -0.2001   0.1743
 MSN  S6    S  S2    0  -0.026   2.3311  -0.3004  -0.3956
 MSN  C7    C  CH3   0  -0.764   3.0981   0.9693   0.6348
 MSN  H5    H  HCH1  0   0.223   0.0419  -1.4701  -1.4674
 MSN  HN51  H  HNH2  0   0.348  -0.4755  -3.3551  -0.1028
 MSN  HN52  H  HNH2  0   0.343   1.0053  -2.8466   0.2828
 MSN  H4    H  HCH1  0   0.221  -2.2979  -1.4491  -0.9655
 MSN  HO4   H  HOH1  0   0.442  -2.7015  -0.1072   1.0842
 MSN  H3    H  HCH1  0   0.232  -1.2641   0.4833  -1.9577
 MSN  HO3   H  HOH1  0   0.463  -3.2179   1.2650  -1.2268
 MSN  H2    H  HCH1  0   0.221   0.4354   1.6534  -0.9640
 MSN  HO2   H  HOH1  0   0.449  -0.8597   2.6320   0.6805
 MSN  H1    H  HCH1  0   0.281   0.6111  -0.2804   1.2648
 MSN  H71   H  HCH3  0   0.274   4.1684   0.9474   0.4387
 MSN  H72   H  HCH3  0   0.263   2.7215   1.9612   0.3915
 MSN  H73   H  HCH3  0   0.262   2.9314   0.7683   1.6918

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
 MSN  C5  N5    single  1.447  0.020  1.447
 MSN  C5  C4    single  1.525  0.020  1.525
 MSN  C5  C1    single  1.534  0.020  1.534
 MSN  C5  H5    single  0.970  0.020  1.090
 MSN  N5  HN51  single  0.890  0.020  1.040
 MSN  N5  HN52  single  0.890  0.020  1.040
 MSN  C4  O4    single  1.405  0.020  1.405
 MSN  C4  C3    single  1.530  0.020  1.530
 MSN  C4  H4    single  0.970  0.020  1.090
 MSN  O4  HO4   single  0.850  0.020  0.980
 MSN  C3  O3    single  1.404  0.020  1.404
 MSN  C3  C2    single  1.548  0.020  1.548
 MSN  C3  H3    single  0.970  0.020  1.090
 MSN  O3  HO3   single  0.850  0.020  0.980
 MSN  C2  O2    single  1.405  0.020  1.405
 MSN  C2  C1    single  1.538  0.020  1.538
 MSN  C2  H2    single  0.970  0.020  1.090
 MSN  O2  HO2   single  0.850  0.020  0.980
 MSN  C1  S6    single  1.810  0.020  1.810
 MSN  C1  H1    single  0.970  0.020  1.090
 MSN  S6  C7    single  1.806  0.020  1.806
 MSN  C7  H71   single  0.970  0.020  1.090
 MSN  C7  H72   single  0.970  0.020  1.090
 MSN  C7  H73   single  0.970  0.020  1.090

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
 MSN  H5    C5  C1    108.36  3.000
 MSN  H5    C5  C4    105.82  3.000
 MSN  C1    C5  C4    102.71  3.000
 MSN  H5    C5  N5    112.87  3.000
 MSN  C1    C5  N5    112.14  3.000
 MSN  C4    C5  N5    114.22  3.000
 MSN  HN52  N5  HN51  105.49  3.000
 MSN  HN52  N5  C5    108.96  3.000
 MSN  HN51  N5  C5    109.44  3.000
 MSN  H4    C4  C3    111.69  3.000
 MSN  H4    C4  O4    111.05  3.000
 MSN  C3    C4  O4    111.48  3.000
 MSN  H4    C4  C5    111.33  3.000
 MSN  C3    C4  C5    100.81  3.000
 MSN  O4    C4  C5    110.08  3.000
 MSN  HO4   O4  C4    107.38  3.000
 MSN  H3    C3  C2    107.69  3.000
 MSN  H3    C3  O3    111.38  3.000
 MSN  C2    C3  O3    110.46  3.000
 MSN  H3    C3  C4    107.65  3.000
 MSN  C2    C3  C4    105.03  3.000
 MSN  O3    C3  C4    114.23  3.000
 MSN  HO3   O3  C3    108.78  3.000
 MSN  H2    C2  C1    110.69  3.000
 MSN  H2    C2  O2    110.40  3.000
 MSN  C1    C2  O2    108.65  3.000
 MSN  H2    C2  C3    109.21  3.000
 MSN  C1    C2  C3    104.13  3.000
 MSN  O2    C2  C3    113.59  3.000
 MSN  HO2   O2  C2    108.19  3.000
 MSN  H1    C1  S6    108.29  3.000
 MSN  H1    C1  C2    108.49  3.000
 MSN  S6    C1  C2    115.38  3.000
 MSN  H1    C1  C5    108.13  3.000
 MSN  S6    C1  C5    109.98  3.000
 MSN  C2    C1  C5    106.35  3.000
 MSN  C7    S6  C1    100.60  3.000
 MSN  H73   C7  H72   109.41  3.000
 MSN  H73   C7  H71   108.77  3.000
 MSN  H72   C7  H71   108.56  3.000
 MSN  H73   C7  S6    111.04  3.000
 MSN  H72   C7  S6    111.48  3.000
 MSN  H71   C7  S6    107.50  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
 MSN  Var_01  H71  C7  S6  C1  175.36  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
 MSN  chir_01  C5  N5  C4  C1  negativ
 MSN  chir_02  C4  O4  C3  C5  negativ
 MSN  chir_03  C3  O3  C2  C4  negativ
 MSN  chir_04  C2  O2  C1  C3  negativ
 MSN  chir_05  C1  S6  C5  C2  positiv

