# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 18:14:58 2022
#   Inital geometry file: a 126 line input string
#   Ligand name: (3R)-1-(3,4-dihydroxy-9,10-dioxo-9,10-dihydroanthracene-2-sulfonyl)piperidine-3-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@@H]1CCCN(C1)[S](=O)(=O)c2cc3C(=O)c4ccccc4C(=O)c3c(O)c2O
#
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
 I7V  I7V  "(3R)-1-(3,4-dihydroxy-9,10-dioxo-9,10-dihydroanthracene-2-sulfonyl)piperidine-3-carboxylic acid"  ligand  46  30  .  2022-08-10  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_I7V
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
 I7V  C2   C  CR6    0   0.319  -10.4633  -59.1244  41.2417
 I7V  C4   C  CR66   0  -0.038  -10.3505  -60.8944  42.9039
 I7V  C5   C  CR66   0  -0.175  -11.1021  -59.9794  42.1366
 I7V  C6   C  CR6    0   0.390  -12.5603  -59.9100  42.2731
 I7V  C8   C  CR16   0  -0.267  -14.6064  -60.7717  43.3622
 I7V  C9   C  CR16   0  -0.231  -15.2455  -61.6133  44.2567
 I7V  C10  C  CR16   0  -0.227  -14.5055  -62.5012  45.0286
 I7V  O7   O  OS     0  -0.669   -6.1212  -59.1404  40.9357
 I7V  O    O  OS     0  -0.626   -6.0175  -60.7489  42.8647
 I7V  N    N  N      0  -0.577   -6.4166  -61.5937  40.5516
 I7V  C19  C  CH2    0  -0.305   -6.9760  -61.4483  39.1989
 I7V  C17  C  CH1    0  -0.379   -6.0644  -62.1609  38.1954
 I7V  C18  C  C      0   0.428   -6.8202  -62.4520  36.8724
 I7V  O6   O  O      0  -0.599   -7.8286  -61.7519  36.6473
 I7V  O5   O  OC    -1  -0.597   -6.3394  -63.3242  36.1249
 I7V  C16  C  CH2    0  -0.430   -5.4225  -63.3957  38.8410
 I7V  C15  C  CH2    0  -0.492   -6.3299  -63.9541  39.9257
 I7V  C14  C  CH2    0  -0.272   -6.4547  -62.9663  41.0860
 I7V  C    C  CR6    0  -0.303   -8.3454  -60.1254  41.8314
 I7V  C3   C  CR16   0  -0.312   -8.9874  -60.9617  42.7468
 I7V  C13  C  CR6    0   0.319  -11.0002  -61.7797  43.8909
 I7V  O3   O  O      0  -0.370  -10.3512  -62.5377  44.5824
 I7V  C12  C  CR66   0  -0.022  -12.4760  -61.7093  44.0079
 I7V  C11  C  CR16   0  -0.269  -13.1268  -62.5488  44.9054
 I7V  C7   C  CR66   0  -0.005  -13.2212  -60.8154  43.2315
 I7V  O4   O  O      0  -0.430  -13.2197  -59.1213  41.6044
 I7V  O2   O  OH1    0  -0.594  -11.0863  -58.2267  40.4974
 I7V  C1   C  CR6    0   0.334   -9.0503  -59.1798  41.0933
 I7V  O1   O  OH1    0  -0.592   -8.5324  -58.3056  40.2455
 I7V  H3   H  HCR6   0   0.276  -15.1844  -60.0806  42.7643
 I7V  H4   H  HCR6   0   0.278  -16.3221  -61.5769  44.3542
 I7V  H5   H  HCR6   0   0.278  -15.0059  -63.1581  45.7274
 I7V  H15  H  HCH2   0   0.262   -7.0558  -60.3963  38.9383
 I7V  H16  H  HCH2   0   0.245   -7.9896  -61.8580  39.1815
 I7V  H13  H  HCH1   0   0.245   -5.2593  -61.4649  37.9301
 I7V  H11  H  HCH2   0   0.220   -4.4556  -63.1405  39.2834
 I7V  H12  H  HCH2   0   0.240   -5.2266  -64.1453  38.0759
 I7V  H9   H  HCH2   0   0.255   -5.9462  -64.8948  40.3229
 I7V  H10  H  HCH2   0   0.236   -7.3155  -64.1733  39.5074
 I7V  H8   H  HCH2   0   0.261   -5.6157  -63.0929  41.7679
 I7V  H7   H  HCH2   0   0.247   -7.3792  -63.1585  41.6409
 I7V  H2   H  HCR6   0   0.294   -8.4150  -61.6585  43.3438
 I7V  H6   H  HCR6   0   0.275  -12.5529  -63.2408  45.5065
 I7V  H1   H  HOH1   0   0.488  -12.0490  -58.2930  40.6899
 I7V  H    H  HOH1   0   0.489   -7.5547  -58.3404  40.2884
 I7V  S    S  S      0   1.403   -6.5998  -60.3586  41.5958

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
 I7V  O    S    double    1.450  0.020  1.450
 I7V  C    S    single    1.777  0.020  1.777
 I7V  C    C1   aromatic  1.391  0.020  1.391
 I7V  O1   C1   single    1.323  0.020  1.323
 I7V  C1   C2   aromatic  1.422  0.020  1.422
 I7V  O2   C2   single    1.322  0.020  1.322
 I7V  C3   C    aromatic  1.396  0.020  1.396
 I7V  C4   C3   aromatic  1.374  0.020  1.374
 I7V  C4   C5   aromatic  1.411  0.020  1.411
 I7V  C2   C5   aromatic  1.393  0.020  1.393
 I7V  C5   C6   single    1.466  0.020  1.466
 I7V  C6   C7   single    1.475  0.020  1.475
 I7V  C7   C8   aromatic  1.392  0.020  1.392
 I7V  C8   C9   aromatic  1.384  0.020  1.384
 I7V  C9   C10  aromatic  1.390  0.020  1.390
 I7V  C10  C11  aromatic  1.385  0.020  1.385
 I7V  C11  C12  aromatic  1.391  0.020  1.391
 I7V  C7   C12  aromatic  1.399  0.020  1.399
 I7V  C12  C13  single    1.482  0.020  1.482
 I7V  C13  C4   single    1.476  0.020  1.476
 I7V  O3   C13  double    1.214  0.020  1.214
 I7V  O4   C6   double    1.226  0.020  1.226
 I7V  N    S    single    1.628  0.020  1.628
 I7V  N    C14  single    1.473  0.020  1.473
 I7V  C14  C15  single    1.529  0.020  1.529
 I7V  C15  C16  single    1.521  0.020  1.521
 I7V  C16  C17  single    1.534  0.020  1.534
 I7V  C18  C17  single    1.551  0.020  1.551
 I7V  O5   C18  deloc     1.245  0.020  1.245
 I7V  O6   C18  deloc     1.248  0.020  1.248
 I7V  C17  C19  single    1.532  0.020  1.532
 I7V  C19  N    single    1.471  0.020  1.471
 I7V  S    O7   double    1.466  0.020  1.466
 I7V  C8   H3   single    0.930  0.020  1.080
 I7V  C9   H4   single    0.930  0.020  1.080
 I7V  C10  H5   single    0.930  0.020  1.080
 I7V  C19  H15  single    0.970  0.020  1.090
 I7V  C19  H16  single    0.970  0.020  1.090
 I7V  C17  H13  single    0.970  0.020  1.090
 I7V  C16  H11  single    0.970  0.020  1.090
 I7V  C16  H12  single    0.970  0.020  1.090
 I7V  C15  H9   single    0.970  0.020  1.090
 I7V  C15  H10  single    0.970  0.020  1.090
 I7V  C14  H8   single    0.970  0.020  1.090
 I7V  C14  H7   single    0.970  0.020  1.090
 I7V  C3   H2   single    0.930  0.020  1.080
 I7V  C11  H6   single    0.930  0.020  1.080
 I7V  O2   H1   single    0.850  0.020  0.980
 I7V  O1   H    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
 I7V  C1   C2   O2   115.85  3.000
 I7V  O2   C2   C5   124.23  3.000
 I7V  C1   C2   C5   119.93  3.000
 I7V  C13  C4   C3   118.92  3.000
 I7V  C13  C4   C5   121.19  3.000
 I7V  C3   C4   C5   119.88  3.000
 I7V  C6   C5   C4   120.66  3.000
 I7V  C6   C5   C2   119.13  3.000
 I7V  C4   C5   C2   120.21  3.000
 I7V  O4   C6   C7   120.54  3.000
 I7V  O4   C6   C5   120.96  3.000
 I7V  C7   C6   C5   118.50  3.000
 I7V  H3   C8   C7   120.00  3.000
 I7V  H3   C8   C9   119.93  3.000
 I7V  C7   C8   C9   120.06  3.000
 I7V  H4   C9   C10  120.09  3.000
 I7V  H4   C9   C8   119.82  3.000
 I7V  C10  C9   C8   120.09  3.000
 I7V  H5   C10  C11  119.80  3.000
 I7V  H5   C10  C9   120.03  3.000
 I7V  C11  C10  C9   120.17  3.000
 I7V  C14  N    C19  114.57  3.000
 I7V  C19  N    S    118.18  3.000
 I7V  C14  N    S    118.11  3.000
 I7V  H16  C19  H15  106.91  3.000
 I7V  H16  C19  C17  111.53  3.000
 I7V  H15  C19  C17  109.69  3.000
 I7V  H16  C19  N    109.28  3.000
 I7V  H15  C19  N    110.12  3.000
 I7V  C17  C19  N    109.28  3.000
 I7V  H13  C17  C16  107.78  3.000
 I7V  H13  C17  C18  105.68  3.000
 I7V  C16  C17  C18  114.32  3.000
 I7V  H13  C17  C19  107.47  3.000
 I7V  C18  C17  C19  110.86  3.000
 I7V  C16  C17  C19  110.35  3.000
 I7V  O5   C18  O6   126.63  3.000
 I7V  O6   C18  C17  116.25  3.000
 I7V  O5   C18  C17  117.08  3.000
 I7V  H12  C16  H11  106.61  3.000
 I7V  H12  C16  C15  110.84  3.000
 I7V  H11  C16  C15  108.95  3.000
 I7V  H12  C16  C17  109.49  3.000
 I7V  H11  C16  C17  110.64  3.000
 I7V  C15  C16  C17  110.25  3.000
 I7V  H10  C15  H9   106.48  3.000
 I7V  H10  C15  C14  110.27  3.000
 I7V  H9   C15  C14  108.03  3.000
 I7V  H10  C15  C16  109.80  3.000
 I7V  H9   C15  C16  111.50  3.000
 I7V  C14  C15  C16  110.66  3.000
 I7V  H7   C14  H8   108.23  3.000
 I7V  H7   C14  C15  109.87  3.000
 I7V  H8   C14  C15  109.72  3.000
 I7V  H7   C14  N    111.66  3.000
 I7V  H8   C14  N    108.40  3.000
 I7V  C15  C14  N    108.93  3.000
 I7V  C1   C    C3   121.46  3.000
 I7V  C3   C    S    117.39  3.000
 I7V  C1   C    S    121.10  3.000
 I7V  H2   C3   C    120.30  3.000
 I7V  H2   C3   C4   119.58  3.000
 I7V  C    C3   C4   120.12  3.000
 I7V  C12  C13  O3   121.13  3.000
 I7V  O3   C13  C4   121.32  3.000
 I7V  C12  C13  C4   117.55  3.000
 I7V  C7   C12  C11  119.65  3.000
 I7V  C7   C12  C13  121.13  3.000
 I7V  C11  C12  C13  119.23  3.000
 I7V  H6   C11  C12  119.78  3.000
 I7V  H6   C11  C10  120.06  3.000
 I7V  C12  C11  C10  120.16  3.000
 I7V  C12  C7   C8   119.87  3.000
 I7V  C12  C7   C6   120.94  3.000
 I7V  C8   C7   C6   119.19  3.000
 I7V  H1   O2   C2   107.76  3.000
 I7V  O1   C1   C    126.20  3.000
 I7V  O1   C1   C2   115.47  3.000
 I7V  C    C1   C2   118.33  3.000
 I7V  H    O1   C1   109.83  3.000
 I7V  C    S    N    107.17  3.000
 I7V  N    S    O    108.18  3.000
 I7V  C    S    O    108.30  3.000
 I7V  N    S    O7   107.75  3.000
 I7V  C    S    O7   105.75  3.000
 I7V  O    S    O7   119.13  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
 I7V  CONST_01  C3   C    C1   C2      0.00   0.0  0
 I7V  CONST_02  C3   C4   C5   C2      0.00   0.0  0
 I7V  CONST_03  C7   C6   C5   C2    180.00   0.0  0
 I7V  CONST_04  C1   C    C3   C4      0.00   0.0  0
 I7V  CONST_05  C1   C2   C5   C4      0.00   0.0  0
 I7V  CONST_06  C7   C6   C5   C4      0.00   0.0  0
 I7V  CONST_07  C11  C12  C13  C4    180.00   0.0  0
 I7V  CONST_08  C7   C12  C13  C4      0.00   0.0  0
 I7V  CONST_09  C    C3   C4   C5      0.00   0.0  0
 I7V  CONST_10  C12  C13  C4   C5      0.00   0.0  0
 I7V  CONST_11  C    C1   C2   C5      0.00   0.0  0
 I7V  CONST_12  C8   C7   C6   C5    180.00   0.0  0
 I7V  CONST_13  C12  C7   C6   C5      0.00   0.0  0
 I7V  CONST_14  C11  C12  C7   C8      0.00   0.0  0
 I7V  CONST_15  C11  C10  C9   C8      0.00   0.0  0
 I7V  CONST_16  C12  C7   C8   C9      0.00   0.0  0
 I7V  CONST_17  C12  C11  C10  C9      0.00   0.0  0
 I7V  CONST_18  C7   C8   C9   C10     0.00   0.0  0
 I7V  CONST_19  C7   C12  C11  C10     0.00   0.0  0
 I7V  CONST_20  C12  C13  C4   C3    180.00   0.0  0
 I7V  CONST_21  S    C    C1   C2    180.00   0.0  0
 I7V  CONST_22  O4   C6   C5   C2      0.00   0.0  0
 I7V  CONST_23  S    C    C3   C4    180.00   0.0  0
 I7V  CONST_24  O2   C2   C5   C4    180.00   0.0  0
 I7V  CONST_25  O4   C6   C5   C4    180.00   0.0  0
 I7V  CONST_26  O3   C13  C4   C5    180.00   0.0  0
 I7V  CONST_27  O1   C1   C2   C5    180.00   0.0  0
 I7V  CONST_28  O2   C2   C5   C6      0.00   0.0  0
 I7V  CONST_29  O4   C6   C7   C8      0.00   0.0  0
 I7V  CONST_30  O2   C2   C1   C     180.00   0.0  0
 I7V  CONST_31  O1   C1   C    C3    180.00   0.0  0
 I7V  CONST_32  O3   C13  C4   C3      0.00   0.0  0
 I7V  CONST_33  C11  C12  C13  O3      0.00   0.0  0
 I7V  CONST_34  C7   C12  C13  O3    180.00   0.0  0
 I7V  CONST_35  O4   C6   C7   C12   180.00   0.0  0
 I7V  CONST_36  H2   C3   C4   C5    180.00   0.0  0
 I7V  CONST_37  H3   C8   C7   C6      0.00   0.0  0
 I7V  CONST_38  H5   C10  C9   C8    180.00   0.0  0
 I7V  CONST_39  H6   C11  C10  C9    180.00   0.0  0
 I7V  CONST_40  H3   C8   C9   C10   180.00   0.0  0
 I7V  CONST_41  H6   C11  C12  C13     0.00   0.0  0
 I7V  CONST_42  H2   C3   C4   C13     0.00   0.0  0
 I7V  CONST_43  H5   C10  C11  C12   180.00   0.0  0
 I7V  CONST_44  H3   C8   C7   C12   180.00   0.0  0
 I7V  CONST_45  H4   C9   C10  C11   180.00   0.0  0
 I7V  CONST_46  H4   C9   C8   C7    180.00   0.0  0
 I7V  CONST_47  H6   C11  C12  C7    180.00   0.0  0
 I7V  CONST_48  H2   C3   C    C1    180.00   0.0  0
 I7V  Var_01    C16  C15  C14  N      34.34  30.0  1
 I7V  Var_02    C15  C14  N    C19    30.93  30.0  1
 I7V  Var_03    C14  C15  C16  C17   -66.01  30.0  1
 I7V  Var_04    C14  N    C19  C17   -68.28  30.0  1
 I7V  Var_05    C15  C14  N    S     177.33  30.0  1
 I7V  Var_06    C17  C19  N    S     145.35  30.0  1
 I7V  Var_07    C1   C    S    N     -95.61  30.0  1
 I7V  Var_08    C3   C    S    N      82.01  30.0  1
 I7V  Var_09    C    S    N    C19    61.33  30.0  3
 I7V  Var_10    C    S    N    C14   -83.85  30.0  3
 I7V  Var_11    H9   C15  C14  N     156.66  30.0  1
 I7V  Var_12    H10  C15  C14  N     -87.34  30.0  1
 I7V  Var_13    H8   C14  N    C19   150.27  30.0  1
 I7V  Var_14    H7   C14  N    C19   -90.60  30.0  1
 I7V  Var_15    H9   C15  C16  C17   173.72  30.0  1
 I7V  Var_16    H10  C15  C16  C17    55.95  30.0  1
 I7V  Var_17    H8   C14  C15  C16   -84.17  30.0  1
 I7V  Var_18    H7   C14  C15  C16   156.95  30.0  1
 I7V  Var_19    H15  C19  N    C14   171.16  30.0  1
 I7V  Var_20    H16  C19  N    C14    54.01  30.0  1
 I7V  Var_21    H11  C16  C15  C14    55.58  30.0  1
 I7V  Var_22    H12  C16  C15  C14   172.59  30.0  1
 I7V  Var_23    C1   C    S    O7     19.15  30.0  1
 I7V  Var_24    C3   C    S    O7   -163.23  30.0  1
 I7V  Var_25    C14  N    S    O7    162.75  30.0  1
 I7V  Var_26    C19  N    S    O7    -52.07  30.0  1
 I7V  Var_27    C1   C    S    O     147.90  30.0  1
 I7V  Var_28    C3   C    S    O     -34.49  30.0  1
 I7V  Var_29    C14  N    S    O      32.73  30.0  1
 I7V  Var_30    C19  N    S    O     177.90  30.0  1
 I7V  Var_31    H8   C14  N    S     -63.33  30.0  1
 I7V  Var_32    H7   C14  N    S      55.80  30.0  1
 I7V  Var_33    H15  C19  N    S      24.79  30.0  1
 I7V  Var_34    H16  C19  N    S     -92.36  30.0  1

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
 I7V  chir_01  C17  C16  C18  C19  negativ

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
 I7V  plan-1  C2   0.020
 I7V  plan-1  C4   0.020
 I7V  plan-1  C5   0.020
 I7V  plan-1  C6   0.020
 I7V  plan-1  C8   0.020
 I7V  plan-1  C9   0.020
 I7V  plan-1  C10  0.020
 I7V  plan-1  C    0.020
 I7V  plan-1  C3   0.020
 I7V  plan-1  C13  0.020
 I7V  plan-1  O3   0.020
 I7V  plan-1  C12  0.020
 I7V  plan-1  C11  0.020
 I7V  plan-1  C7   0.020
 I7V  plan-1  O4   0.020
 I7V  plan-1  O2   0.020
 I7V  plan-1  C1   0.020
 I7V  plan-1  O1   0.020
 I7V  plan-1  H3   0.020
 I7V  plan-1  H4   0.020
 I7V  plan-1  H5   0.020
 I7V  plan-1  H2   0.020
 I7V  plan-1  H6   0.020
 I7V  plan-1  S    0.020
 I7V  plan-2  C17  0.020
 I7V  plan-2  C18  0.020
 I7V  plan-2  O6   0.020
 I7V  plan-2  O5   0.020

