# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 02:00:12 2020
#   Inital geometry file: a 119 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]naphthalene-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@@]2(SC(NC2=O)=NC(=O)c3ccc4ccccc4c3)[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
 M8P  M8P  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]naphthalene-2-carboxamide  ligand  47  29  .  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_M8P
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
 M8P  C11   C  CR16  0  -0.330  -4.4025   0.1826  -0.9140
 M8P  C12   C  CR66  0   0.141  -5.7898   0.1477  -0.6668
 M8P  C13   C  CR16  0  -0.305  -6.7350   0.3027  -1.7096
 M8P  C14   C  CR16  0  -0.257  -8.0754   0.2644  -1.4424
 M8P  C15   C  CR16  0  -0.250  -8.5321   0.0685  -0.1212
 M8P  C16   C  CR16  0  -0.308  -7.6418  -0.0845   0.9069
 M8P  C17   C  CR66  0   0.117  -6.2501  -0.0481   0.6618
 M8P  C18   C  CR16  0  -0.298  -5.2989  -0.1991   1.6982
 M8P  C19   C  CR16  0  -0.272  -3.9602  -0.1570   1.4336
 M8P  C10   C  CR6   0  -0.074  -3.4959   0.0352   0.1092
 M8P  C9    C  C     0   0.515  -2.0471   0.0782  -0.2002
 M8P  O8    O  O     0  -0.437  -1.6327   0.1964  -1.3430
 M8P  N2    N  N     0  -0.501  -1.2230  -0.0210   0.8989
 M8P  C8    C  C     0   0.393   0.0443  -0.0166   0.7074
 M8P  S1    S  S2    0   0.202   0.9159   0.0746  -0.7998
 M8P  N1    N  NH1   0  -0.662   0.8902  -0.0801   1.7697
 M8P  C7    C  C     0   0.621   2.2356  -0.0757   1.5426
 M8P  O7    O  O     0  -0.395   3.0680  -0.0667   2.4122
 M8P  C1    C  CT    0  -0.101   2.5431  -0.0505   0.0370
 M8P  O5    O  O2    0  -0.471   3.2511   1.0850  -0.3293
 M8P  C5    C  CH1   0  -0.028   4.6514   1.1338  -0.0392
 M8P  C6    C  CH2   0  -0.157   5.1681   2.4068  -0.6722
 M8P  O6    O  OH1   0  -0.668   4.5539   3.5077  -0.0498
 M8P  C4    C  CH1   0  -0.011   5.3591  -0.1055  -0.5917
 M8P  O4    O  OH1   0  -0.669   6.7107  -0.1305  -0.1967
 M8P  C3    C  CH1   0   0.005   4.6987  -1.3635  -0.0453
 M8P  O3    O  OH1   0  -0.669   5.2325  -2.5304  -0.6208
 M8P  C2    C  CH1   0   0.028   3.2172  -1.3550  -0.3977
 M8P  O2    O  OH1   0  -0.659   2.4949  -2.3803   0.2213
 M8P  H11   H  HCR6  0   0.260  -4.0567   0.3317  -1.9297
 M8P  H13   H  HCR6  0   0.260  -6.3813   0.4536  -2.7223
 M8P  H14   H  HCR6  0   0.264  -8.7932   0.3841  -2.2430
 M8P  H15   H  HCR6  0   0.264  -9.5960   0.0399   0.0751
 M8P  H16   H  HCR6  0   0.260  -7.9951  -0.2353   1.9198
 M8P  H18   H  HCR6  0   0.260  -5.6460  -0.3499   2.7130
 M8P  H19   H  HCR6  0   0.263  -3.2458  -0.2717   2.2360
 M8P  H1    H  HNH1  0   0.438   0.5128  -0.1017   2.7101
 M8P  H2    H  HCH1  0   0.262   3.1437  -1.4164  -1.4951
 M8P  H5    H  HCH1  0   0.245   4.8163   1.1856   1.0434
 M8P  H61C  H  HCH2  0   0.209   6.2571   2.4293  -0.5470
 M8P  H62C  H  HCH2  0   0.204   4.9678   2.3782  -1.7522
 M8P  H4    H  HCH1  0   0.232   5.2653  -0.1099  -1.6872
 M8P  H6    H  HOH1  0   0.458   4.9207   4.3098  -0.4325
 M8P  HA    H  HOH1  0   0.465   7.2490   0.2732  -0.8828
 M8P  H3    H  HCH1  0   0.234   4.8193  -1.3792   1.0465
 M8P  HB    H  HOH1  0   0.458   6.1441  -2.6247  -0.3257
 M8P  HC    H  HOH1  0   0.468   2.8500  -3.2296  -0.0624

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
 M8P  C11  C12   aromatic  1.410  0.020  1.410
 M8P  C11  C10   aromatic  1.375  0.020  1.375
 M8P  C12  C13   aromatic  1.416  0.020  1.416
 M8P  C12  C17   aromatic  1.420  0.020  1.420
 M8P  C13  C14   aromatic  1.367  0.020  1.367
 M8P  C14  C15   aromatic  1.412  0.020  1.412
 M8P  C15  C16   aromatic  1.369  0.020  1.369
 M8P  C16  C17   aromatic  1.414  0.020  1.414
 M8P  C17  C18   aromatic  1.415  0.020  1.415
 M8P  C18  C19   aromatic  1.365  0.020  1.365
 M8P  C19  C10   aromatic  1.417  0.020  1.417
 M8P  C10  C9    single    1.482  0.020  1.482
 M8P  C9   O8    double    1.221  0.020  1.221
 M8P  C9   N2    single    1.377  0.020  1.377
 M8P  N2   C8    double    1.282  0.020  1.282
 M8P  C8   S1    single    1.743  0.020  1.743
 M8P  C8   N1    single    1.359  0.020  1.359
 M8P  S1   C1    single    1.834  0.020  1.834
 M8P  N1   C7    single    1.364  0.020  1.364
 M8P  C7   O7    double    1.204  0.020  1.204
 M8P  C7   C1    single    1.537  0.020  1.537
 M8P  C1   O5    single    1.387  0.020  1.387
 M8P  C1   C2    single    1.531  0.020  1.531
 M8P  O5   C5    single    1.431  0.020  1.431
 M8P  C5   C6    single    1.513  0.020  1.513
 M8P  C5   C4    single    1.530  0.020  1.530
 M8P  C6   O6    single    1.406  0.020  1.406
 M8P  C4   O4    single    1.408  0.020  1.408
 M8P  C4   C3    single    1.522  0.020  1.522
 M8P  C3   O3    single    1.406  0.020  1.406
 M8P  C3   C2    single    1.523  0.020  1.523
 M8P  C2   O2    single    1.399  0.020  1.399
 M8P  C11  H11   single    0.930  0.020  1.080
 M8P  C13  H13   single    0.930  0.020  1.080
 M8P  C14  H14   single    0.930  0.020  1.080
 M8P  C15  H15   single    0.930  0.020  1.080
 M8P  C16  H16   single    0.930  0.020  1.080
 M8P  C18  H18   single    0.930  0.020  1.080
 M8P  C19  H19   single    0.930  0.020  1.080
 M8P  N1   H1    single    0.860  0.020  1.020
 M8P  C2   H2    single    0.970  0.020  1.090
 M8P  C5   H5    single    0.970  0.020  1.090
 M8P  C6   H61C  single    0.970  0.020  1.090
 M8P  C6   H62C  single    0.970  0.020  1.090
 M8P  C4   H4    single    0.970  0.020  1.090
 M8P  O6   H6    single    0.850  0.020  0.980
 M8P  O4   HA    single    0.850  0.020  0.980
 M8P  C3   H3    single    0.970  0.020  1.090
 M8P  O3   HB    single    0.850  0.020  0.980
 M8P  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
 M8P  H11   C11  C10   120.13  3.000
 M8P  H11   C11  C12   118.82  3.000
 M8P  C10   C11  C12   121.05  3.000
 M8P  C17   C12  C13   119.21  3.000
 M8P  C17   C12  C11   119.12  3.000
 M8P  C13   C12  C11   121.68  3.000
 M8P  H13   C13  C14   120.44  3.000
 M8P  H13   C13  C12   119.06  3.000
 M8P  C14   C13  C12   120.49  3.000
 M8P  H14   C14  C15   119.56  3.000
 M8P  H14   C14  C13   120.18  3.000
 M8P  C15   C14  C13   120.26  3.000
 M8P  H15   C15  C16   120.02  3.000
 M8P  H15   C15  C14   119.44  3.000
 M8P  C16   C15  C14   120.54  3.000
 M8P  H16   C16  C17   119.12  3.000
 M8P  H16   C16  C15   120.38  3.000
 M8P  C17   C16  C15   120.49  3.000
 M8P  C18   C17  C16   122.15  3.000
 M8P  C18   C17  C12   118.84  3.000
 M8P  C16   C17  C12   119.01  3.000
 M8P  H18   C18  C19   120.01  3.000
 M8P  H18   C18  C17   119.06  3.000
 M8P  C19   C18  C17   120.93  3.000
 M8P  H19   C19  C10   119.48  3.000
 M8P  H19   C19  C18   120.07  3.000
 M8P  C10   C19  C18   120.45  3.000
 M8P  C9    C10  C19   121.30  3.000
 M8P  C9    C10  C11   119.09  3.000
 M8P  C19   C10  C11   119.61  3.000
 M8P  N2    C9   O8    123.41  3.000
 M8P  N2    C9   C10   114.60  3.000
 M8P  O8    C9   C10   121.99  3.000
 M8P  C8    N2   C9    118.17  3.000
 M8P  N1    C8   S1    111.53  3.000
 M8P  N1    C8   N2    119.89  3.000
 M8P  S1    C8   N2    128.58  3.000
 M8P  C1    S1   C8     92.61  3.000
 M8P  H1    N1   C7    121.45  3.000
 M8P  H1    N1   C8    119.63  3.000
 M8P  C7    N1   C8    118.90  3.000
 M8P  C1    C7   O7    124.70  3.000
 M8P  C1    C7   N1    111.13  3.000
 M8P  O7    C7   N1    124.16  3.000
 M8P  C2    C1   O5    113.43  3.000
 M8P  C2    C1   C7    110.62  3.000
 M8P  O5    C1   C7    111.98  3.000
 M8P  C2    C1   S1    108.61  3.000
 M8P  O5    C1   S1    106.05  3.000
 M8P  C7    C1   S1    105.70  3.000
 M8P  C5    O5   C1    118.28  3.000
 M8P  H5    C5   C4    108.98  3.000
 M8P  H5    C5   C6    108.79  3.000
 M8P  C4    C5   C6    111.86  3.000
 M8P  H5    C5   O5    110.43  3.000
 M8P  C4    C5   O5    110.59  3.000
 M8P  C6    C5   O5    106.15  3.000
 M8P  H62C  C6   H61C  107.09  3.000
 M8P  H62C  C6   O6    112.08  3.000
 M8P  H61C  C6   O6    111.54  3.000
 M8P  H62C  C6   C5    109.10  3.000
 M8P  H61C  C6   C5    107.99  3.000
 M8P  O6    C6   C5    108.93  3.000
 M8P  H6    O6   C6    108.08  3.000
 M8P  H4    C4   C3    108.50  3.000
 M8P  H4    C4   O4    111.18  3.000
 M8P  C3    C4   O4    107.52  3.000
 M8P  H4    C4   C5    108.87  3.000
 M8P  C3    C4   C5    109.82  3.000
 M8P  O4    C4   C5    110.91  3.000
 M8P  HA    O4   C4    109.26  3.000
 M8P  H3    C3   C2    109.69  3.000
 M8P  H3    C3   O3    110.68  3.000
 M8P  C2    C3   O3    106.21  3.000
 M8P  H3    C3   C4    108.72  3.000
 M8P  C2    C3   C4    109.53  3.000
 M8P  O3    C3   C4    111.97  3.000
 M8P  HB    O3   C3    108.37  3.000
 M8P  H2    C2   O2    111.44  3.000
 M8P  H2    C2   C3    107.17  3.000
 M8P  O2    C2   C3    113.32  3.000
 M8P  H2    C2   C1    107.51  3.000
 M8P  O2    C2   C1    105.75  3.000
 M8P  C3    C2   C1    111.55  3.000
 M8P  HC    O2   C2    109.00  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
 M8P  CONST_01  C14  C13  C12  C11  180.00   0.0  0
 M8P  CONST_02  C16  C17  C12  C11  180.00   0.0  0
 M8P  CONST_03  C18  C17  C12  C11    0.00   0.0  0
 M8P  CONST_04  C18  C19  C10  C11    0.00   0.0  0
 M8P  CONST_05  C19  C10  C11  C12    0.00   0.0  0
 M8P  CONST_06  C15  C14  C13  C12    0.00   0.0  0
 M8P  CONST_07  C15  C16  C17  C12    0.00   0.0  0
 M8P  CONST_08  C19  C18  C17  C12    0.00   0.0  0
 M8P  CONST_09  C10  C11  C12  C13  180.00   0.0  0
 M8P  CONST_10  C16  C17  C12  C13    0.00   0.0  0
 M8P  CONST_11  C18  C17  C12  C13  180.00   0.0  0
 M8P  CONST_12  C16  C15  C14  C13    0.00   0.0  0
 M8P  CONST_13  C17  C12  C13  C14    0.00   0.0  0
 M8P  CONST_14  C17  C16  C15  C14    0.00   0.0  0
 M8P  CONST_15  C18  C17  C16  C15  180.00   0.0  0
 M8P  CONST_16  C19  C18  C17  C16  180.00   0.0  0
 M8P  CONST_17  C10  C11  C12  C17    0.00   0.0  0
 M8P  CONST_18  C10  C19  C18  C17    0.00   0.0  0
 M8P  CONST_19  C1   C7   N1   C8     0.00   0.0  0
 M8P  CONST_20  C7   N1   C8   S1     0.00   0.0  0
 M8P  CONST_21  C9   C10  C11  C12  180.00   0.0  0
 M8P  CONST_22  C9   C10  C19  C18  180.00   0.0  0
 M8P  CONST_23  C7   N1   C8   N2   180.00   0.0  0
 M8P  CONST_24  O7   C7   N1   C8   180.00   0.0  0
 M8P  CONST_25  H13  C13  C12  C11    0.00   0.0  0
 M8P  CONST_26  H19  C19  C10  C11  180.00   0.0  0
 M8P  CONST_27  H14  C14  C13  C12  180.00   0.0  0
 M8P  CONST_28  H16  C16  C17  C12  180.00   0.0  0
 M8P  CONST_29  H18  C18  C17  C12  180.00   0.0  0
 M8P  CONST_30  H11  C11  C12  C13    0.00   0.0  0
 M8P  CONST_31  H15  C15  C14  C13  180.00   0.0  0
 M8P  CONST_32  H1   N1   C8   S1   180.00   0.0  0
 M8P  CONST_33  C8   N2   C9   C10  180.00   0.0  0
 M8P  CONST_34  S1   C8   N2   C9     0.00   0.0  0
 M8P  CONST_35  N1   C8   N2   C9   180.00   0.0  0
 M8P  CONST_36  C8   N2   C9   O8     0.00   0.0  0
 M8P  Var_01    O8   C9   C10  C11   -2.48  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
 M8P  chir_01  C1  C7  O5  C2  negativ
 M8P  chir_02  C5  O5  C6  C4  positiv
 M8P  chir_03  C4  O4  C5  C3  positiv
 M8P  chir_04  C3  O3  C4  C2  negativ
 M8P  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
 M8P  plan-1  C10  0.020
 M8P  plan-1  C9   0.020
 M8P  plan-1  O8   0.020
 M8P  plan-1  N2   0.020
 M8P  plan-1  C8   0.020
 M8P  plan-1  S1   0.020
 M8P  plan-1  N1   0.020
 M8P  plan-1  C7   0.020
 M8P  plan-1  O7   0.020
 M8P  plan-1  C1   0.020
 M8P  plan-1  H1   0.020
 M8P  plan-2  C11  0.020
 M8P  plan-2  C12  0.020
 M8P  plan-2  C13  0.020
 M8P  plan-2  C14  0.020
 M8P  plan-2  C15  0.020
 M8P  plan-2  C16  0.020
 M8P  plan-2  C17  0.020
 M8P  plan-2  C18  0.020
 M8P  plan-2  C19  0.020
 M8P  plan-2  C10  0.020
 M8P  plan-2  C9   0.020
 M8P  plan-2  H11  0.020
 M8P  plan-2  H13  0.020
 M8P  plan-2  H14  0.020
 M8P  plan-2  H15  0.020
 M8P  plan-2  H16  0.020
 M8P  plan-2  H18  0.020
 M8P  plan-2  H19  0.020

