# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 08:52:16 2020
#   Inital geometry file: a 72 line input string
#   Ligand name: (5R,7R,8S,9S,10R)-8,9,10-trihydroxy-7-(hydroxymethyl)-2-imino-6-oxa-1-thia-3-azaspiro[4.5]decan-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@@]2(SC(=N)NC2=O)[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
 MIF  MIF  (5R,7R,8S,9S,10R)-8,9,10-trihydroxy-7-(hydroxymethyl)-2-imino-6-oxa-1-thia-3-azaspiro[4.5]decan-4-one  ligand  29  17  .  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_MIF
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
 MIF  C2    C  CH1   0   0.030   0.0651  -1.3849  -0.4616
 MIF  O2    O  OH1   0  -0.659  -0.8589  -2.3164   0.0219
 MIF  C3    C  CH1   0   0.000   1.4541  -1.5480   0.1400
 MIF  O3    O  OH1   0  -0.670   1.9410  -2.7820  -0.3297
 MIF  C4    C  CH1   0  -0.012   2.3355  -0.3859  -0.2957
 MIF  C1    C  CR5   0  -0.096  -0.5266  -0.0056  -0.1600
 MIF  O4    O  OH1   0  -0.669   3.5904  -0.5435   0.3252
 MIF  C5    C  CH1   0  -0.023   1.6884   0.9384   0.1162
 MIF  C6    C  CH2   0  -0.156   2.4434   2.1292  -0.4321
 MIF  O6    O  OH1   0  -0.668   1.8822   3.3081   0.0905
 MIF  O5    O  O2    0  -0.470   0.3602   1.0356  -0.4051
 MIF  C8    C  CR5   0   0.278  -3.0940   0.4676   0.0973
 MIF  S1    S  S2    0   0.126  -1.9660   0.2781  -1.2456
 MIF  N1    N  NR15  0  -0.639  -2.4166   0.3176   1.2895
 MIF  C7    C  CR5   0   0.624  -1.0876   0.0641   1.2764
 MIF  O7    O  O     0  -0.419  -0.4003  -0.0548   2.2626
 MIF  H1    H  HNR5  0   0.431  -2.9196   0.4216   2.1621
 MIF  H21   H  H     0   0.363  -4.6758   0.7966  -0.8930
 MIF  H2    H  HCH1  0   0.258   0.1799  -1.4608  -1.5548
 MIF  H5    H  HCH1  0   0.242   1.6765   1.0008   1.2108
 MIF  H61C  H  HCH2  0   0.207   3.4960   2.0234  -0.1464
 MIF  H62C  H  HCH2  0   0.203   2.4025   2.1041  -1.5298
 MIF  H4    H  HCH1  0   0.232   2.4290  -0.4129  -1.3909
 MIF  H6    H  HOH1  0   0.458   2.4278   4.0473  -0.1922
 MIF  HA    H  HOH1  0   0.463   4.2783  -0.2404  -0.2735
 MIF  H3    H  HCH1  0   0.236   1.3877  -1.5493   1.2354
 MIF  HB    H  HOH1  0   0.459   2.7391  -3.0005   0.1618
 MIF  HC    H  HOH1  0   0.465  -0.5277  -3.2028  -0.1593
 MIF  N2    N  N     0  -0.592  -4.3283   0.7017   0.0536

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
 MIF  O7  C7    double  1.208  0.020  1.208
 MIF  C7  N1    single  1.353  0.020  1.353
 MIF  C7  C1    single  1.544  0.020  1.544
 MIF  N1  C8    single  1.379  0.020  1.379
 MIF  C8  N2    double  1.257  0.020  1.257
 MIF  C8  S1    single  1.764  0.020  1.764
 MIF  S1  C1    single  1.825  0.020  1.825
 MIF  C1  O5    single  1.389  0.020  1.389
 MIF  C1  C2    single  1.531  0.020  1.531
 MIF  O5  C5    single  1.430  0.020  1.430
 MIF  C5  C6    single  1.513  0.020  1.513
 MIF  C5  C4    single  1.530  0.020  1.530
 MIF  C6  O6    single  1.406  0.020  1.406
 MIF  C4  O4    single  1.409  0.020  1.409
 MIF  C4  C3    single  1.522  0.020  1.522
 MIF  C3  O3    single  1.407  0.020  1.407
 MIF  C3  C2    single  1.522  0.020  1.522
 MIF  C2  O2    single  1.398  0.020  1.398
 MIF  N1  H1    single  0.860  0.020  1.020
 MIF  N2  H21   single  0.890  0.020  1.040
 MIF  C2  H2    single  0.970  0.020  1.090
 MIF  C5  H5    single  0.970  0.020  1.090
 MIF  C6  H61C  single  0.970  0.020  1.090
 MIF  C6  H62C  single  0.970  0.020  1.090
 MIF  C4  H4    single  0.970  0.020  1.090
 MIF  O6  H6    single  0.850  0.020  0.980
 MIF  O4  HA    single  0.850  0.020  0.980
 MIF  C3  H3    single  0.970  0.020  1.090
 MIF  O3  HB    single  0.850  0.020  0.980
 MIF  O2  HC    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
 MIF  H2    C2  C1    107.33  3.000
 MIF  H2    C2  C3    106.84  3.000
 MIF  C1    C2  C3    111.80  3.000
 MIF  H2    C2  O2    111.47  3.000
 MIF  C3    C2  O2    113.26  3.000
 MIF  C1    C2  O2    106.06  3.000
 MIF  HC    O2  C2    108.70  3.000
 MIF  H3    C3  C4    108.77  3.000
 MIF  H3    C3  O3    110.67  3.000
 MIF  C4    C3  O3    111.93  3.000
 MIF  H3    C3  C2    109.83  3.000
 MIF  O3    C3  C2    106.12  3.000
 MIF  C4    C3  C2    109.48  3.000
 MIF  HB    O3  C3    108.39  3.000
 MIF  H4    C4  C5    108.99  3.000
 MIF  H4    C4  O4    111.13  3.000
 MIF  C5    C4  O4    110.78  3.000
 MIF  H4    C4  C3    108.40  3.000
 MIF  O4    C4  C3    107.71  3.000
 MIF  C5    C4  C3    109.80  3.000
 MIF  C7    C1  S1    105.06  3.000
 MIF  S1    C1  O5    106.38  3.000
 MIF  C7    C1  O5    111.24  3.000
 MIF  O5    C1  C2    113.18  3.000
 MIF  S1    C1  C2    109.13  3.000
 MIF  C7    C1  C2    111.37  3.000
 MIF  HA    O4  C4    109.13  3.000
 MIF  H5    C5  O5    110.48  3.000
 MIF  H5    C5  C6    108.81  3.000
 MIF  O5    C5  C6    106.14  3.000
 MIF  H5    C5  C4    108.82  3.000
 MIF  C6    C5  C4    111.87  3.000
 MIF  O5    C5  C4    110.69  3.000
 MIF  H62C  C6  H61C  107.10  3.000
 MIF  H62C  C6  O6    112.05  3.000
 MIF  H61C  C6  O6    111.55  3.000
 MIF  H62C  C6  C5    109.00  3.000
 MIF  H61C  C6  C5    107.99  3.000
 MIF  O6    C6  C5    109.02  3.000
 MIF  H6    O6  C6    107.99  3.000
 MIF  C5    O5  C1    118.53  3.000
 MIF  N1    C8  S1    109.41  3.000
 MIF  S1    C8  N2    128.42  3.000
 MIF  N1    C8  N2    122.18  3.000
 MIF  C8    S1  C1     93.91  3.000
 MIF  H1    N1  C7    121.03  3.000
 MIF  H1    N1  C8    119.32  3.000
 MIF  C7    N1  C8    119.63  3.000
 MIF  O7    C7  N1    124.71  3.000
 MIF  N1    C7  C1    111.99  3.000
 MIF  O7    C7  C1    123.26  3.000
 MIF  H21   N2  C8    112.76  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
 MIF  CONST_01  C8   N1  C7  C1    0.00  0.0  0
 MIF  CONST_02  C7   N1  C8  S1    0.00  0.0  0
 MIF  CONST_03  C7   N1  C8  N2  180.00  0.0  0
 MIF  CONST_04  O7   C7  N1  C8  180.00  0.0  0
 MIF  CONST_05  H1   N1  C7  C1  180.00  0.0  0
 MIF  CONST_06  H21  N2  C8  S1    0.00  0.0  0

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
 MIF  chir_01  C2  C1  C3  O2  negativ
 MIF  chir_02  C3  O3  C2  C4  positiv
 MIF  chir_03  C4  O4  C5  C3  positiv
 MIF  chir_04  C1  O5  C7  C2  positiv
 MIF  chir_05  C5  O5  C6  C4  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
 MIF  plan-1  C1   0.020
 MIF  plan-1  C8   0.020
 MIF  plan-1  S1   0.020
 MIF  plan-1  N1   0.020
 MIF  plan-1  C7   0.020
 MIF  plan-1  O7   0.020
 MIF  plan-1  H1   0.020
 MIF  plan-1  H21  0.020
 MIF  plan-1  N2   0.020

