# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  2 23:04:15 2021
#   Inital geometry file: a 152 line input string
#   Ligand name: 5-[(4,6-diamino-1,3,5-triazin-2-yl)amino]-4-hydroxy-3-[(E)-(2-sulfophenyl)diazenyl]naphthalene-2,7-disulfonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nc(N)nc(Nc2cc(cc3cc(c(N=Nc4ccccc4[S](O)(=O)=O)c(O)c23)[S](O)(=O)=O)[S](O)(=O)=O)n1
#
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
 RR1  RR1  '5-[(4,6-diamino-1,3,5-triazin-2-yl)amino]-4-hydroxy-3-[(E)-(2-sulfophenyl)diazenyl]naphthalene-2,7-disulfonic acid'  ligand  56  40  .  2022-03-23  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_RR1
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
 RR1  O89   O  OS    0  -0.698  26.5372  17.2663  56.8104
 RR1  O90   O  OS    0  -0.609  27.8832  19.2543  56.5194
 RR1  O92   O  OS    0  -0.639  26.2035  19.1661  58.3675
 RR1  S85   S  S     0   1.477  26.5894  18.8462  57.0068
 RR1  C10   C  CR6   0  -0.296  25.3083  19.4430  55.9315
 RR1  C11   C  CR16  0  -0.232  24.2245  20.1014  56.4893
 RR1  C12   C  CR16  0  -0.242  23.2392  20.6209  55.6603
 RR1  C13   C  CR16  0  -0.232  23.3460  20.4878  54.2839
 RR1  C14   C  CR16  0  -0.282  24.4382  19.8430  53.7244
 RR1  C4    C  CR6   0   0.325  25.4333  19.3206  54.5436
 RR1  C5    C  CR6   0   0.366  28.8848  17.4629  52.9963
 RR1  C3    C  CR6   0   0.273  28.0796  18.4342  52.4021
 RR1  C9    C  CR6   0  -0.305  28.4514  18.9560  51.1320
 RR1  C8    C  CR16  0  -0.334  29.5743  18.5669  50.4811
 RR1  C7    C  CR66  0   0.101  30.4576  17.6632  51.1232
 RR1  C6    C  CR66  0   0.010  30.1605  17.1594  52.4095
 RR1  C15   C  CR6   0   0.336  31.1338  16.3613  53.0680
 RR1  C16   C  CR16  0  -0.253  32.2799  15.9872  52.4197
 RR1  C17   C  CR6   0  -0.234  32.5051  16.4243  51.1063
 RR1  C18   C  CR16  0  -0.298  31.6413  17.2690  50.4701
 RR1  O37   O  OS    0  -0.710  33.5463  14.4436  49.9259
 RR1  O38   O  OS    0  -0.631  35.0742  15.8768  51.2626
 RR1  O41   O  OS    0  -0.625  34.1720  16.7037  49.0886
 RR1  S36   S  S     0   1.482  33.9951  15.9296  50.2980
 RR1  O39   O  OS    0  -0.707  27.1570  21.2555  51.3053
 RR1  O40   O  OS    0  -0.628  27.9953  20.6191  49.1395
 RR1  O42   O  OS    0  -0.627  26.0701  19.3573  50.1113
 RR1  S35   S  S     0   1.459  27.3305  20.0472  50.2875
 RR1  N1    N  N     0  -0.220  26.5302  18.6066  54.0494
 RR1  N2    N  N     0  -0.335  26.9654  19.0342  52.9715
 RR1  N19   N  NH1   0  -0.821  30.9373  15.9686  54.4122
 RR1  C20   C  CR6   0   0.564  31.1404  16.8848  55.4381
 RR1  N21   N  N     0  -0.509  31.2666  16.3652  56.6447
 RR1  C22   C  CR6   0   0.571  31.3920  17.2851  57.6138
 RR1  N23   N  N     0  -0.511  31.3759  18.6037  57.4253
 RR1  C24   C  CR6   0   0.596  31.2363  18.9875  56.1595
 RR1  N25   N  N     0  -0.488  31.1351  18.1579  55.1098
 RR1  NL1   N  NH2   0  -0.815  31.2333  20.2971  55.8969
 RR1  NL2   N  NH2   0  -0.816  31.5303  16.8366  58.8628
 RR1  H89   H  H     0   0.502  25.7893  16.8693  57.2871
 RR1  H11   H  HCR6  0   0.295  24.1383  20.2128  57.5607
 RR1  H12   H  HCR6  0   0.282  22.3870  21.1230  56.0962
 RR1  H13   H  HCR6  0   0.284  22.5713  20.8812  53.6399
 RR1  H14   H  HCR6  0   0.283  24.5028  19.7076  52.6526
 RR1  HC8   H  HCR6  0   0.301  29.8214  18.9342  49.4952
 RR1  H16   H  HCR6  0   0.306  33.0134  15.3859  52.9410
 RR1  H18   H  HCR6  0   0.302  31.8436  17.6450  49.4763
 RR1  H28   H  HOH1  0   0.501  29.1177  16.2108  54.3856
 RR1  H37   H  H     0   0.510  34.3091  13.8835  49.6946
 RR1  H39   H  H     0   0.497  26.7954  20.9032  52.1469
 RR1  H19   H  HNH1  0   0.417  31.2417  15.0317  54.6420
 RR1  HL11  H  HNH2  0   0.399  30.9698  20.6125  54.9798
 RR1  HL12  H  HNH2  0   0.399  31.1708  20.9539  56.6549
 RR1  HL21  H  HNH2  0   0.403  31.6868  17.4794  59.6188
 RR1  HL22  H  HNH2  0   0.403  31.5979  15.8508  59.0442
 RR1  O28   O  OH1   0  -0.547  28.4436  16.8436  54.0637

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
 RR1  O89  S85   single    1.593  0.020  1.593
 RR1  O89  H89   single    0.850  0.020  0.980
 RR1  O90  S85   double    1.442  0.020  1.442
 RR1  O92  S85   double    1.450  0.020  1.450
 RR1  S85  C10   single    1.776  0.020  1.776
 RR1  C10  C11   aromatic  1.385  0.020  1.385
 RR1  C10  C4    aromatic  1.399  0.020  1.399
 RR1  C11  C12   aromatic  1.389  0.020  1.389
 RR1  C11  H11   single    0.930  0.020  1.080
 RR1  C12  C13   aromatic  1.387  0.020  1.387
 RR1  C12  H12   single    0.930  0.020  1.080
 RR1  C13  C14   aromatic  1.386  0.020  1.386
 RR1  C13  H13   single    0.930  0.020  1.080
 RR1  C14  C4    aromatic  1.391  0.020  1.391
 RR1  C14  H14   single    0.930  0.020  1.080
 RR1  C4   N1    single    1.399  0.020  1.399
 RR1  C5   C3    aromatic  1.395  0.020  1.395
 RR1  C5   C6    aromatic  1.437  0.020  1.437
 RR1  C5   O28   single    1.311  0.020  1.311
 RR1  C3   C9    aromatic  1.423  0.020  1.423
 RR1  C3   N2    single    1.388  0.020  1.388
 RR1  C9   C8    aromatic  1.355  0.020  1.355
 RR1  C9   S35   single    1.778  0.020  1.778
 RR1  C8   C7    aromatic  1.417  0.020  1.417
 RR1  C8   HC8   single    0.930  0.020  1.080
 RR1  C7   C6    aromatic  1.413  0.020  1.413
 RR1  C7   C18   aromatic  1.408  0.020  1.408
 RR1  C6   C15   aromatic  1.421  0.020  1.421
 RR1  C15  C16   aromatic  1.369  0.020  1.369
 RR1  C15  N19   single    1.414  0.020  1.414
 RR1  C16  C17   aromatic  1.402  0.020  1.402
 RR1  C16  H16   single    0.930  0.020  1.080
 RR1  C17  C18   aromatic  1.365  0.020  1.365
 RR1  C17  S36   single    1.766  0.020  1.766
 RR1  C18  H18   single    0.930  0.020  1.080
 RR1  O28  H28   single    0.850  0.020  0.980
 RR1  O37  S36   single    1.596  0.020  1.596
 RR1  O37  H37   single    0.850  0.020  0.980
 RR1  O38  S36   double    1.448  0.020  1.448
 RR1  O41  S36   double    1.447  0.020  1.447
 RR1  O39  S35   single    1.589  0.020  1.589
 RR1  O39  H39   single    0.850  0.020  0.980
 RR1  O40  S35   double    1.445  0.020  1.445
 RR1  O42  S35   double    1.448  0.020  1.448
 RR1  N1   N2    double    1.239  0.020  1.239
 RR1  N19  C20   single    1.390  0.020  1.390
 RR1  N19  H19   single    0.890  0.020  1.040
 RR1  C20  N21   aromatic  1.320  0.020  1.320
 RR1  C20  N25   aromatic  1.315  0.020  1.315
 RR1  N21  C22   aromatic  1.342  0.020  1.342
 RR1  C22  N23   aromatic  1.332  0.020  1.332
 RR1  C22  NL2   single    1.334  0.020  1.334
 RR1  N23  C24   aromatic  1.330  0.020  1.330
 RR1  C24  N25   aromatic  1.342  0.020  1.342
 RR1  C24  NL1   single    1.336  0.020  1.336
 RR1  NL1  HL11  single    0.890  0.020  1.040
 RR1  NL1  HL12  single    0.890  0.020  1.040
 RR1  NL2  HL21  single    0.860  0.020  1.020
 RR1  NL2  HL22  single    0.860  0.020  1.020

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
 RR1  H89   O89  S85   111.71  3.000
 RR1  C10   S85  O92   107.58  3.000
 RR1  C10   S85  O90   110.34  3.000
 RR1  O92   S85  O90   119.58  3.000
 RR1  C10   S85  O89   103.60  3.000
 RR1  O92   S85  O89   109.01  3.000
 RR1  O90   S85  O89   105.58  3.000
 RR1  C4    C10  C11   120.73  3.000
 RR1  C4    C10  S85   120.46  3.000
 RR1  C11   C10  S85   118.71  3.000
 RR1  H11   C11  C12   119.79  3.000
 RR1  H11   C11  C10   120.70  3.000
 RR1  C12   C11  C10   119.51  3.000
 RR1  H12   C12  C13   120.37  3.000
 RR1  H12   C12  C11   119.50  3.000
 RR1  C13   C12  C11   120.13  3.000
 RR1  H13   C13  C14   119.55  3.000
 RR1  H13   C13  C12   120.06  3.000
 RR1  C14   C13  C12   120.39  3.000
 RR1  H14   C14  C4    119.58  3.000
 RR1  H14   C14  C13   120.33  3.000
 RR1  C4    C14  C13   120.05  3.000
 RR1  N1    C4   C14   123.00  3.000
 RR1  N1    C4   C10   117.72  3.000
 RR1  C14   C4   C10   119.19  3.000
 RR1  O28   C5   C6    122.13  3.000
 RR1  O28   C5   C3    118.80  3.000
 RR1  C6    C5   C3    119.07  3.000
 RR1  N2    C3   C9    114.69  3.000
 RR1  N2    C3   C5    126.15  3.000
 RR1  C9    C3   C5    119.01  3.000
 RR1  S35   C9   C8    118.08  3.000
 RR1  S35   C9   C3    118.98  3.000
 RR1  C8    C9   C3    122.69  3.000
 RR1  HC8   C8   C7    119.17  3.000
 RR1  HC8   C8   C9    122.01  3.000
 RR1  C7    C8   C9    118.82  3.000
 RR1  C18   C7   C6    119.94  3.000
 RR1  C18   C7   C8    119.49  3.000
 RR1  C6    C7   C8    120.57  3.000
 RR1  C15   C6   C7    118.56  3.000
 RR1  C15   C6   C5    122.54  3.000
 RR1  C7    C6   C5    118.90  3.000
 RR1  N19   C15  C16   119.39  3.000
 RR1  N19   C15  C6    120.09  3.000
 RR1  C16   C15  C6    120.51  3.000
 RR1  H16   C16  C17   121.03  3.000
 RR1  H16   C16  C15   119.42  3.000
 RR1  C17   C16  C15   119.53  3.000
 RR1  S36   C17  C18   119.59  3.000
 RR1  S36   C17  C16   118.48  3.000
 RR1  C18   C17  C16   121.84  3.000
 RR1  H18   C18  C17   121.66  3.000
 RR1  H18   C18  C7    119.07  3.000
 RR1  C17   C18  C7    119.27  3.000
 RR1  H37   O37  S36   111.74  3.000
 RR1  O41   S36  O38   119.02  3.000
 RR1  O41   S36  O37   109.73  3.000
 RR1  O38   S36  O37   109.31  3.000
 RR1  O41   S36  C17   109.63  3.000
 RR1  O38   S36  C17   109.51  3.000
 RR1  O37   S36  C17    97.48  3.000
 RR1  H39   O39  S35   108.45  3.000
 RR1  O42   S35  O40   119.51  3.000
 RR1  O42   S35  O39   110.20  3.000
 RR1  O40   S35  O39   104.96  3.000
 RR1  O42   S35  C9    108.32  3.000
 RR1  O40   S35  C9    109.29  3.000
 RR1  O39   S35  C9    103.37  3.000
 RR1  N2    N1   C4    114.00  3.000
 RR1  N1    N2   C3    119.34  3.000
 RR1  H19   N19  C20   113.50  3.000
 RR1  H19   N19  C15   115.55  3.000
 RR1  C20   N19  C15   119.88  3.000
 RR1  N25   C20  N21   127.58  3.000
 RR1  N25   C20  N19   116.95  3.000
 RR1  N21   C20  N19   115.41  3.000
 RR1  C22   N21  C20   113.53  3.000
 RR1  NL2   C22  N23   117.81  3.000
 RR1  NL2   C22  N21   117.08  3.000
 RR1  N23   C22  N21   125.11  3.000
 RR1  C24   N23  C22   114.94  3.000
 RR1  NL1   C24  N25   116.89  3.000
 RR1  NL1   C24  N23   118.05  3.000
 RR1  N25   C24  N23   125.03  3.000
 RR1  C24   N25  C20   113.77  3.000
 RR1  HL12  NL1  HL11  117.84  3.000
 RR1  HL12  NL1  C24   119.51  3.000
 RR1  HL11  NL1  C24   119.19  3.000
 RR1  HL22  NL2  HL21  118.78  3.000
 RR1  HL22  NL2  C22   120.39  3.000
 RR1  HL21  NL2  C22   120.36  3.000
 RR1  H28   O28  C5    109.96  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
 RR1  CONST_01  C13   C12  C11  C10     0.00   0.0  0
 RR1  CONST_02  C13   C14  C4   C10     0.00   0.0  0
 RR1  CONST_03  C14   C4   C10  C11     0.00   0.0  0
 RR1  CONST_04  C14   C13  C12  C11     0.00   0.0  0
 RR1  CONST_05  C4    C10  C11  C12     0.00   0.0  0
 RR1  CONST_06  C4    C14  C13  C12     0.00   0.0  0
 RR1  CONST_07  C8    C9   C3   C5      0.00   0.0  0
 RR1  CONST_08  C8    C7   C6   C5      0.00   0.0  0
 RR1  CONST_09  C18   C7   C6   C5    180.00   0.0  0
 RR1  CONST_10  C16   C15  C6   C5    180.00   0.0  0
 RR1  CONST_11  C7    C6   C5   C3      0.00   0.0  0
 RR1  CONST_12  C15   C6   C5   C3    180.00   0.0  0
 RR1  CONST_13  C7    C8   C9   C3      0.00   0.0  0
 RR1  CONST_14  C6    C5   C3   C9      0.00   0.0  0
 RR1  CONST_15  C6    C7   C8   C9      0.00   0.0  0
 RR1  CONST_16  C18   C7   C8   C9    180.00   0.0  0
 RR1  CONST_17  C15   C6   C7   C8    180.00   0.0  0
 RR1  CONST_18  C17   C18  C7   C8    180.00   0.0  0
 RR1  CONST_19  C16   C15  C6   C7      0.00   0.0  0
 RR1  CONST_20  C16   C17  C18  C7      0.00   0.0  0
 RR1  CONST_21  C17   C18  C7   C6      0.00   0.0  0
 RR1  CONST_22  C17   C16  C15  C6      0.00   0.0  0
 RR1  CONST_23  C18   C7   C6   C15     0.00   0.0  0
 RR1  CONST_24  C18   C17  C16  C15     0.00   0.0  0
 RR1  CONST_25  N23   C22  N21  C20     0.00   0.0  0
 RR1  CONST_26  N23   C24  N25  C20     0.00   0.0  0
 RR1  CONST_27  C24   N25  C20  N21     0.00   0.0  0
 RR1  CONST_28  C24   N23  C22  N21     0.00   0.0  0
 RR1  CONST_29  N25   C20  N21  C22     0.00   0.0  0
 RR1  CONST_30  N25   C24  N23  C22     0.00   0.0  0
 RR1  CONST_31  C12   C11  C10  S85   180.00   0.0  0
 RR1  CONST_32  C14   C4   C10  S85   180.00   0.0  0
 RR1  CONST_33  N1    C4   C10  C11   180.00   0.0  0
 RR1  CONST_34  N1    C4   C14  C13   180.00   0.0  0
 RR1  CONST_35  S35   C9   C3   C5    180.00   0.0  0
 RR1  CONST_36  N19   C15  C6   C5      0.00   0.0  0
 RR1  CONST_37  O28   C5   C3   C9    180.00   0.0  0
 RR1  CONST_38  N2    C3   C9   C8    180.00   0.0  0
 RR1  CONST_39  S35   C9   C8   C7    180.00   0.0  0
 RR1  CONST_40  O28   C5   C6   C7    180.00   0.0  0
 RR1  CONST_41  N19   C15  C6   C7    180.00   0.0  0
 RR1  CONST_42  S36   C17  C18  C7    180.00   0.0  0
 RR1  CONST_43  N2    C3   C5   C6    180.00   0.0  0
 RR1  CONST_44  O28   C5   C6   C15     0.00   0.0  0
 RR1  CONST_45  S36   C17  C16  C15   180.00   0.0  0
 RR1  CONST_46  N19   C15  C16  C17   180.00   0.0  0
 RR1  CONST_47  C22   N21  C20  N19   180.00   0.0  0
 RR1  CONST_48  C24   N25  C20  N19   180.00   0.0  0
 RR1  CONST_49  NL2   C22  N21  C20   180.00   0.0  0
 RR1  CONST_50  NL1   C24  N25  C20   180.00   0.0  0
 RR1  CONST_51  NL1   C24  N23  C22   180.00   0.0  0
 RR1  CONST_52  NL2   C22  N23  C24   180.00   0.0  0
 RR1  CONST_53  H12   C12  C11  C10   180.00   0.0  0
 RR1  CONST_54  H14   C14  C4   C10   180.00   0.0  0
 RR1  CONST_55  H13   C13  C12  C11   180.00   0.0  0
 RR1  CONST_56  H11   C11  C12  C13   180.00   0.0  0
 RR1  CONST_57  HC8   C8   C9   C3    180.00   0.0  0
 RR1  CONST_58  H18   C18  C7   C8      0.00   0.0  0
 RR1  CONST_59  H16   C16  C15  C6    180.00   0.0  0
 RR1  CONST_62  N1    N2   C3   C5      0.00   0.0  0
 RR1  CONST_63  N1    N2   C3   C9    180.00   0.0  0
 RR1  CONST_64  HL21  NL2  C22  N21   180.00   0.0  0
 RR1  CONST_65  HL22  NL2  C22  N21     0.00   0.0  0
 RR1  CONST_66  HL11  NL1  C24  N23   180.00   0.0  0
 RR1  CONST_67  HL12  NL1  C24  N23     0.00   0.0  0
 RR1  Var_01    C20   N19  C15  C6    -76.29  30.0  2
 RR1  Var_02    N21   C20  N19  C15  -163.60  30.0  2
 RR1  Var_03    C11   C10  S85  O89   116.65  30.0  2
 RR1  Var_04    O39   S35  C9   C3     59.38  30.0  2
 RR1  Var_05    O37   S36  C17  C16    78.14  30.0  2

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
 RR1  plan-1  S85   0.020
 RR1  plan-1  C10   0.020
 RR1  plan-1  C11   0.020
 RR1  plan-1  C12   0.020
 RR1  plan-1  C13   0.020
 RR1  plan-1  C14   0.020
 RR1  plan-1  C4    0.020
 RR1  plan-1  C3    0.020
 RR1  plan-1  N1    0.020
 RR1  plan-1  N2    0.020
 RR1  plan-1  H11   0.020
 RR1  plan-1  H12   0.020
 RR1  plan-1  H13   0.020
 RR1  plan-1  H14   0.020
 RR1  plan-2  N19   0.020
 RR1  plan-2  C20   0.020
 RR1  plan-2  N21   0.020
 RR1  plan-2  C22   0.020
 RR1  plan-2  N23   0.020
 RR1  plan-2  C24   0.020
 RR1  plan-2  N25   0.020
 RR1  plan-2  NL1   0.020
 RR1  plan-2  NL2   0.020
 RR1  plan-3  C5    0.020
 RR1  plan-3  C3    0.020
 RR1  plan-3  C9    0.020
 RR1  plan-3  C8    0.020
 RR1  plan-3  C7    0.020
 RR1  plan-3  C6    0.020
 RR1  plan-3  C15   0.020
 RR1  plan-3  C16   0.020
 RR1  plan-3  C17   0.020
 RR1  plan-3  C18   0.020
 RR1  plan-3  S36   0.020
 RR1  plan-3  S35   0.020
 RR1  plan-3  N1    0.020
 RR1  plan-3  N2    0.020
 RR1  plan-3  N19   0.020
 RR1  plan-3  HC8   0.020
 RR1  plan-3  H16   0.020
 RR1  plan-3  H18   0.020
 RR1  plan-3  O28   0.020
 RR1  plan-4  C24   0.020
 RR1  plan-4  NL1   0.020
 RR1  plan-4  HL11  0.020
 RR1  plan-4  HL12  0.020
 RR1  plan-5  C22   0.020
 RR1  plan-5  NL2   0.020
 RR1  plan-5  HL21  0.020
 RR1  plan-5  HL22  0.020

