# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 19:30:01 2020
#   Inital geometry file: a 105 line input string
#   Ligand name: N-[(2Z,5R,7R,8S,9S,10R)-8,9,10-trihydroxy-7-(hydroxymethyl)-4-oxo-6-oxa-1-thia-3-azaspiro[4.5]dec-2-ylidene]benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@@]2(SC(NC2=O)=NC(=O)c3ccccc3)[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
 M7C  M7C  N-[(2Z,5R,7R,8S,9S,10R)-8,9,10-trihydroxy-7-(hydroxymethyl)-4-oxo-6-oxa-1-thia-3-azaspiro[4.5]dec-2-ylidene]benzamide  ligand  41  25  .  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_M7C
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
 M7C  C15   C  CR16  0  -0.259  -5.4073   0.2382  -1.2904
 M7C  C14   C  CR16  0  -0.242  -6.7785   0.2293  -1.0972
 M7C  C13   C  CR16  0  -0.244  -7.3002   0.0994   0.1850
 M7C  C12   C  CR16  0  -0.240  -6.4461  -0.0201   1.2734
 M7C  C11   C  CR16  0  -0.269  -5.0727  -0.0093   1.0830
 M7C  C10   C  CR6   0  -0.068  -4.5430   0.1195  -0.2008
 M7C  C9    C  C     0   0.511  -3.0800   0.1288  -0.4365
 M7C  O8    O  O     0  -0.436  -2.6102   0.2115  -1.5606
 M7C  N2    N  N     0  -0.498  -2.3093   0.0383   0.7023
 M7C  C8    C  CR5   0   0.393  -1.0351   0.0190   0.5688
 M7C  S1    S  S2    0   0.200  -0.0947   0.0735  -0.8990
 M7C  N1    N  NR15  0  -0.662  -0.2381  -0.0431   1.6690
 M7C  C7    C  CR5   0   0.621   1.1160  -0.0635   1.5025
 M7C  O7    O  O     0  -0.396   1.9094  -0.0591   2.4081
 M7C  C1    C  CR5   0  -0.101   1.4912  -0.0565   0.0124
 M7C  O5    O  O2    0  -0.470   2.2245   1.0706  -0.3299
 M7C  C5    C  CH1   0  -0.028   3.6114   1.1088   0.0181
 M7C  C6    C  CH2   0  -0.157   4.1649   2.3751  -0.5971
 M7C  O6    O  OH1   0  -0.668   3.5454   3.4831   0.0077
 M7C  C4    C  CH1   0  -0.012   4.3290  -0.1392  -0.5007
 M7C  O4    O  OH1   0  -0.669   5.6651  -0.1726  -0.0565
 M7C  C3    C  CH1   0   0.006   3.6383  -1.3881   0.0295
 M7C  O3    O  OH1   0  -0.669   4.1847  -2.5634  -0.5160
 M7C  C2    C  CH1   0   0.027   2.1722  -1.3709  -0.3803
 M7C  O2    O  OH1   0  -0.660   1.4156  -2.3830   0.2196
 M7C  H15   H  HCR6  0   0.261  -5.0064   0.3396  -2.2901
 M7C  H14   H  HCR6  0   0.265  -7.4431   0.3237  -1.9456
 M7C  H13   H  HCR6  0   0.267  -8.3722   0.0920   0.3338
 M7C  H12   H  HCR6  0   0.264  -6.8497  -0.1220   2.2722
 M7C  H11   H  HCR6  0   0.265  -4.4098  -0.1015   1.9317
 M7C  H1    H  HNR5  0   0.437  -0.6575  -0.0454   2.5917
 M7C  H2    H  HCH1  0   0.262   2.1411  -1.4443  -1.4790
 M7C  H5    H  HCH1  0   0.244   3.7331   1.1625   1.1065
 M7C  H61C  H  HCH2  0   0.208   5.2496   2.3840  -0.4375
 M7C  H62C  H  HCH2  0   0.204   3.9985   2.3500  -1.6827
 M7C  H4    H  HCH1  0   0.232   4.2745  -0.1500  -1.5989
 M7C  H6    H  HOH1  0   0.458   3.9044   4.2807  -0.3916
 M7C  HA    H  HOH1  0   0.465   6.2320   0.2193  -0.7263
 M7C  H3    H  HCH1  0   0.234   3.7173  -1.3957   1.1252
 M7C  HB    H  HOH1  0   0.458   5.0870  -2.6567  -0.1931
 M7C  HC    H  HOH1  0   0.468   1.7643  -3.2388  -0.0521

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
 M7C  C15  C14   aromatic  1.385  0.020  1.385
 M7C  C15  C10   aromatic  1.396  0.020  1.396
 M7C  C14  C13   aromatic  1.390  0.020  1.390
 M7C  C13  C12   aromatic  1.389  0.020  1.389
 M7C  C12  C11   aromatic  1.387  0.020  1.387
 M7C  C11  C10   aromatic  1.395  0.020  1.395
 M7C  C10  C9    single    1.482  0.020  1.482
 M7C  C9   O8    double    1.221  0.020  1.221
 M7C  C9   N2    single    1.378  0.020  1.378
 M7C  N2   C8    double    1.281  0.020  1.281
 M7C  C8   S1    single    1.744  0.020  1.744
 M7C  C8   N1    single    1.360  0.020  1.360
 M7C  S1   C1    single    1.834  0.020  1.834
 M7C  N1   C7    single    1.364  0.020  1.364
 M7C  C7   O7    double    1.204  0.020  1.204
 M7C  C7   C1    single    1.537  0.020  1.537
 M7C  C1   O5    single    1.388  0.020  1.388
 M7C  C1   C2    single    1.531  0.020  1.531
 M7C  O5   C5    single    1.430  0.020  1.430
 M7C  C5   C6    single    1.513  0.020  1.513
 M7C  C5   C4    single    1.530  0.020  1.530
 M7C  C6   O6    single    1.406  0.020  1.406
 M7C  C4   O4    single    1.408  0.020  1.408
 M7C  C4   C3    single    1.522  0.020  1.522
 M7C  C3   O3    single    1.406  0.020  1.406
 M7C  C3   C2    single    1.522  0.020  1.522
 M7C  C2   O2    single    1.399  0.020  1.399
 M7C  C15  H15   single    0.930  0.020  1.080
 M7C  C14  H14   single    0.930  0.020  1.080
 M7C  C13  H13   single    0.930  0.020  1.080
 M7C  C12  H12   single    0.930  0.020  1.080
 M7C  C11  H11   single    0.930  0.020  1.080
 M7C  N1   H1    single    0.860  0.020  1.020
 M7C  C2   H2    single    0.970  0.020  1.090
 M7C  C5   H5    single    0.970  0.020  1.090
 M7C  C6   H61C  single    0.970  0.020  1.090
 M7C  C6   H62C  single    0.970  0.020  1.090
 M7C  C4   H4    single    0.970  0.020  1.090
 M7C  O6   H6    single    0.850  0.020  0.980
 M7C  O4   HA    single    0.850  0.020  0.980
 M7C  C3   H3    single    0.970  0.020  1.090
 M7C  O3   HB    single    0.850  0.020  0.980
 M7C  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
 M7C  H15   C15  C10   119.99  3.000
 M7C  H15   C15  C14   119.76  3.000
 M7C  C10   C15  C14   120.25  3.000
 M7C  H14   C14  C13   120.05  3.000
 M7C  H14   C14  C15   119.89  3.000
 M7C  C13   C14  C15   120.05  3.000
 M7C  H13   C13  C12   120.05  3.000
 M7C  H13   C13  C14   119.94  3.000
 M7C  C12   C13  C14   120.00  3.000
 M7C  H12   C12  C11   119.79  3.000
 M7C  H12   C12  C13   120.15  3.000
 M7C  C11   C12  C13   120.06  3.000
 M7C  H11   C11  C10   119.85  3.000
 M7C  H11   C11  C12   119.94  3.000
 M7C  C10   C11  C12   120.22  3.000
 M7C  C9    C10  C11   121.46  3.000
 M7C  C9    C10  C15   119.12  3.000
 M7C  C11   C10  C15   119.41  3.000
 M7C  N2    C9   O8    123.37  3.000
 M7C  N2    C9   C10   114.85  3.000
 M7C  O8    C9   C10   121.78  3.000
 M7C  C8    N2   C9    118.10  3.000
 M7C  N1    C8   S1    111.48  3.000
 M7C  N1    C8   N2    119.95  3.000
 M7C  S1    C8   N2    128.57  3.000
 M7C  C1    S1   C8     92.63  3.000
 M7C  H1    N1   C7    121.45  3.000
 M7C  H1    N1   C8    119.61  3.000
 M7C  C7    N1   C8    118.91  3.000
 M7C  C1    C7   O7    124.65  3.000
 M7C  C1    C7   N1    111.14  3.000
 M7C  O7    C7   N1    124.20  3.000
 M7C  C2    C1   O5    113.51  3.000
 M7C  C2    C1   C7    110.69  3.000
 M7C  O5    C1   C7    111.84  3.000
 M7C  C2    C1   S1    108.54  3.000
 M7C  O5    C1   S1    106.07  3.000
 M7C  C7    C1   S1    105.73  3.000
 M7C  C5    O5   C1    118.30  3.000
 M7C  H5    C5   C4    108.93  3.000
 M7C  H5    C5   C6    108.78  3.000
 M7C  C4    C5   C6    111.92  3.000
 M7C  H5    C5   O5    110.51  3.000
 M7C  C4    C5   O5    110.51  3.000
 M7C  C6    C5   O5    106.15  3.000
 M7C  H62C  C6   H61C  107.09  3.000
 M7C  H62C  C6   O6    112.10  3.000
 M7C  H61C  C6   O6    111.52  3.000
 M7C  H62C  C6   C5    109.11  3.000
 M7C  H61C  C6   C5    108.04  3.000
 M7C  O6    C6   C5    108.88  3.000
 M7C  H6    O6   C6    108.09  3.000
 M7C  H4    C4   C3    108.50  3.000
 M7C  H4    C4   O4    111.21  3.000
 M7C  C3    C4   O4    107.52  3.000
 M7C  H4    C4   C5    108.87  3.000
 M7C  C3    C4   C5    109.77  3.000
 M7C  O4    C4   C5    110.93  3.000
 M7C  HA    O4   C4    109.28  3.000
 M7C  H3    C3   C2    109.74  3.000
 M7C  H3    C3   O3    110.69  3.000
 M7C  C2    C3   O3    106.21  3.000
 M7C  H3    C3   C4    108.69  3.000
 M7C  C2    C3   C4    109.50  3.000
 M7C  O3    C3   C4    111.98  3.000
 M7C  HB    O3   C3    108.36  3.000
 M7C  H2    C2   O2    111.36  3.000
 M7C  H2    C2   C3    107.15  3.000
 M7C  O2    C2   C3    113.41  3.000
 M7C  H2    C2   C1    107.48  3.000
 M7C  O2    C2   C1    105.69  3.000
 M7C  C3    C2   C1    111.65  3.000
 M7C  HC    O2   C2    109.03  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
 M7C  CONST_01  C12  C13  C14  C15    0.00   0.0  0
 M7C  CONST_02  C12  C11  C10  C15    0.00   0.0  0
 M7C  CONST_03  C11  C10  C15  C14    0.00   0.0  0
 M7C  CONST_04  C11  C12  C13  C14    0.00   0.0  0
 M7C  CONST_05  C10  C15  C14  C13    0.00   0.0  0
 M7C  CONST_06  C10  C11  C12  C13    0.00   0.0  0
 M7C  CONST_07  C1   C7   N1   C8     0.00   0.0  0
 M7C  CONST_08  C7   N1   C8   S1     0.00   0.0  0
 M7C  CONST_09  C9   C10  C15  C14  180.00   0.0  0
 M7C  CONST_10  C9   C10  C11  C12  180.00   0.0  0
 M7C  CONST_11  C7   N1   C8   N2   180.00   0.0  0
 M7C  CONST_12  O7   C7   N1   C8   180.00   0.0  0
 M7C  CONST_13  H13  C13  C14  C15  180.00   0.0  0
 M7C  CONST_14  H11  C11  C10  C15  180.00   0.0  0
 M7C  CONST_15  H12  C12  C13  C14  180.00   0.0  0
 M7C  CONST_16  H15  C15  C14  C13  180.00   0.0  0
 M7C  CONST_17  H14  C14  C13  C12  180.00   0.0  0
 M7C  CONST_18  H1   N1   C8   S1   180.00   0.0  0
 M7C  CONST_19  C8   N2   C9   C10  180.00   0.0  0
 M7C  CONST_20  S1   C8   N2   C9     0.00   0.0  0
 M7C  CONST_21  N1   C8   N2   C9   180.00   0.0  0
 M7C  CONST_22  C8   N2   C9   O8     0.00   0.0  0
 M7C  Var_01    O8   C9   C10  C15   -1.44  30.0  2

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
 M7C  chir_01  C1  C7  O5  C2  negativ
 M7C  chir_02  C5  O5  C6  C4  positiv
 M7C  chir_03  C4  O4  C5  C3  positiv
 M7C  chir_04  C3  O3  C4  C2  negativ
 M7C  chir_05  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
 M7C  plan-1  C15  0.020
 M7C  plan-1  C14  0.020
 M7C  plan-1  C13  0.020
 M7C  plan-1  C12  0.020
 M7C  plan-1  C11  0.020
 M7C  plan-1  C10  0.020
 M7C  plan-1  C9   0.020
 M7C  plan-1  H15  0.020
 M7C  plan-1  H14  0.020
 M7C  plan-1  H13  0.020
 M7C  plan-1  H12  0.020
 M7C  plan-1  H11  0.020
 M7C  plan-2  C10  0.020
 M7C  plan-2  C9   0.020
 M7C  plan-2  O8   0.020
 M7C  plan-2  N2   0.020
 M7C  plan-2  C8   0.020
 M7C  plan-2  S1   0.020
 M7C  plan-2  N1   0.020
 M7C  plan-2  C7   0.020
 M7C  plan-2  O7   0.020
 M7C  plan-2  C1   0.020
 M7C  plan-2  H1   0.020

