# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 20:05:58 2022
#   Inital geometry file: a 60 line input string
#   Ligand name: (1R,2R,3R,4S,5R)-4-amino-5-[(R)-methylsulfinyl]cyclopentane-1,2,3-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[S@@](=O)[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
 MZB  MZB  (1R,2R,3R,4S,5R)-4-amino-5-[(R)-methylsulfinyl]cyclopentane-1,2,3-triol  ligand  25  12  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_MZB
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
 MZB  O6    O  O     0  -0.780  -2.8271  -1.0318   0.2452
 MZB  S6    S  S3    0   0.734  -2.0286   0.2180   0.5513
 MZB  C7    C  CH3   0  -0.803  -2.6041   1.4851  -0.5949
 MZB  C1    C  CH1   0  -0.463  -0.3712  -0.0148  -0.1527
 MZB  C5    C  CH1   0  -0.076   0.2713  -1.3005   0.3892
 MZB  N5    N  NH2   0  -0.800  -0.0917  -2.4607  -0.3937
 MZB  C4    C  CH1   0  -0.007   1.7594  -0.9661   0.3440
 MZB  O4    O  OH1   0  -0.665   2.2090  -0.9892  -0.9859
 MZB  C3    C  CH1   0   0.002   1.7625   0.4545   0.9058
 MZB  O3    O  OH1   0  -0.667   2.9370   1.1764   0.6513
 MZB  C2    C  CH1   0   0.033   0.5537   1.1494   0.2355
 MZB  O2    O  OH1   0  -0.657   0.8750   1.8735  -0.9204
 MZB  H7    H  HCH3  0   0.292  -3.6197   1.7515  -0.3088
 MZB  H7A   H  HCH3  0   0.281  -1.9691   2.3672  -0.5298
 MZB  H7B   H  HCH3  0   0.283  -2.5921   1.0855  -1.6080
 MZB  H1    H  HCH1  0   0.310  -0.4648  -0.0867  -1.2397
 MZB  H5    H  HCH1  0   0.233   0.0161  -1.4022   1.4578
 MZB  HN5   H  HNH2  0   0.347   0.3097  -3.2887   0.0293
 MZB  HN5A  H  HNH2  0   0.346  -1.0961  -2.5789  -0.3420
 MZB  H4    H  HCH1  0   0.226   2.3417  -1.6548   0.9737
 MZB  HO4   H  HOH1  0   0.443   2.9545  -0.3813  -1.0492
 MZB  H3    H  HCH1  0   0.235   1.5552   0.3902   1.9816
 MZB  HO3   H  HOH1  0   0.464   3.6047   0.9195   1.2950
 MZB  H2    H  HCH1  0   0.236   0.0740   1.8085   0.9745
 MZB  HO2   H  HOH1  0   0.453   1.4253   2.6206  -0.6640

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
 MZB  S6  O6    double  1.514  0.020  1.514
 MZB  S6  C1    single  1.816  0.020  1.816
 MZB  C7  S6    single  1.803  0.020  1.803
 MZB  C7  H7    single  0.970  0.020  1.090
 MZB  C7  H7A   single  0.970  0.020  1.090
 MZB  C7  H7B   single  0.970  0.020  1.090
 MZB  C1  C5    single  1.536  0.020  1.536
 MZB  C1  H1    single  0.970  0.020  1.090
 MZB  C5  C4    single  1.526  0.020  1.526
 MZB  C5  N5    single  1.446  0.020  1.446
 MZB  C5  H5    single  0.970  0.020  1.090
 MZB  N5  HN5   single  0.890  0.020  1.040
 MZB  N5  HN5A  single  0.890  0.020  1.040
 MZB  C4  O4    single  1.404  0.020  1.404
 MZB  C4  H4    single  0.970  0.020  1.090
 MZB  O4  HO4   single  0.850  0.020  0.980
 MZB  C3  C4    single  1.528  0.020  1.528
 MZB  C3  H3    single  0.970  0.020  1.090
 MZB  O3  C3    single  1.402  0.020  1.402
 MZB  O3  HO3   single  0.850  0.020  0.980
 MZB  C2  C1    single  1.537  0.020  1.537
 MZB  C2  C3    single  1.547  0.020  1.547
 MZB  C2  H2    single  0.970  0.020  1.090
 MZB  O2  C2    single  1.401  0.020  1.401
 MZB  O2  HO2   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
 MZB  C1    S6  C7    97.76  3.000
 MZB  C7    S6  O6   106.45  3.000
 MZB  C1    S6  O6   107.29  3.000
 MZB  H7B   C7  H7A  110.27  3.000
 MZB  H7B   C7  H7   110.16  3.000
 MZB  H7A   C7  H7   109.28  3.000
 MZB  H7B   C7  S6   109.27  3.000
 MZB  H7A   C7  S6   110.19  3.000
 MZB  H7    C7  S6   107.62  3.000
 MZB  H1    C1  C2   110.64  3.000
 MZB  C2    C1  C5   107.05  3.000
 MZB  H1    C1  C5   109.36  3.000
 MZB  C2    C1  S6   110.76  3.000
 MZB  H1    C1  S6   108.41  3.000
 MZB  C5    C1  S6   110.63  3.000
 MZB  H5    C5  C4   105.93  3.000
 MZB  H5    C5  N5   113.11  3.000
 MZB  C4    C5  N5   113.87  3.000
 MZB  H5    C5  C1   108.79  3.000
 MZB  N5    C5  C1   112.06  3.000
 MZB  C4    C5  C1   102.36  3.000
 MZB  HN5A  N5  HN5  106.04  3.000
 MZB  HN5A  N5  C5   108.36  3.000
 MZB  HN5   N5  C5   109.29  3.000
 MZB  H4    C4  C3   111.75  3.000
 MZB  C3    C4  O4   111.29  3.000
 MZB  H4    C4  O4   111.24  3.000
 MZB  C3    C4  C5   101.24  3.000
 MZB  H4    C4  C5   111.23  3.000
 MZB  O4    C4  C5   109.68  3.000
 MZB  HO4   O4  C4   107.43  3.000
 MZB  H3    C3  C2   107.66  3.000
 MZB  C2    C3  O3   110.16  3.000
 MZB  H3    C3  O3   111.50  3.000
 MZB  C2    C3  C4   104.87  3.000
 MZB  O3    C3  C4   114.45  3.000
 MZB  H3    C3  C4   107.80  3.000
 MZB  HO3   O3  C3   108.80  3.000
 MZB  H2    C2  O2   110.15  3.000
 MZB  O2    C2  C3   114.22  3.000
 MZB  H2    C2  C3   108.58  3.000
 MZB  O2    C2  C1   108.73  3.000
 MZB  H2    C2  C1   111.17  3.000
 MZB  C3    C2  C1   103.86  3.000
 MZB  HO2   O2  C2   108.20  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
 MZB  Var_01  H7  C7  S6  C1  180.00  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
 MZB  chir_02  C1  S6  C5  C2  positiv
 MZB  chir_03  C5  N5  C4  C1  negativ
 MZB  chir_04  C4  O4  C3  C5  negativ
 MZB  chir_05  C3  O3  C4  C2  positiv
 MZB  chir_06  C2  O2  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
 MZB  plan-1  O6  0.020
 MZB  plan-1  S6  0.020
 MZB  plan-1  C7  0.020
 MZB  plan-1  C1  0.020

