# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 03:57:45 2022
#   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  53  40  .  2022-03-23  2022-03-23
;
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    -1  -0.745   2.7927   0.8011  -2.9848
 RR1  O90   O  OS     0  -0.735   3.9501  -0.4979  -4.7191
 RR1  O92   O  OS     0  -0.746   2.5062  -1.6455  -3.0945
 RR1  S85   S  S      0   1.433   2.7787  -0.4029  -3.8325
 RR1  C10   C  C      0  -0.273   1.3711  -0.1910  -4.9357
 RR1  C11   C  C1     0  -0.267   1.5798  -0.1774  -6.3073
 RR1  C12   C  C1     0  -0.243   0.5110  -0.0278  -7.1796
 RR1  C13   C  C1     0  -0.251  -0.7783   0.1094  -6.6807
 RR1  C14   C  C1     0  -0.286  -1.0009   0.0931  -5.3154
 RR1  C4    C  C      0   0.329   0.0709  -0.0631  -4.4347
 RR1  C5    C  CR6    0   0.430  -0.5237  -0.0197  -0.3253
 RR1  C3    C  CR6    0   0.178  -1.5265  -0.1315  -1.2995
 RR1  C9    C  CR6    0  -0.302  -2.8900  -0.2207  -0.9099
 RR1  C8    C  CR16   0  -0.367  -3.2187  -0.1978   0.4044
 RR1  C7    C  CR66   0   0.121  -2.2212  -0.0867   1.4099
 RR1  C6    C  CR66   0  -0.125  -0.8460   0.0030   1.0677
 RR1  C15   C  CR6    0   0.392   0.1226   0.1109   2.1313
 RR1  C16   C  CR16   0  -0.330  -0.3224   0.1314   3.4394
 RR1  C17   C  CR6    0  -0.186  -1.6856   0.0456   3.7395
 RR1  C18   C  CR16   0  -0.378  -2.6271  -0.0637   2.7561
 RR1  S36   S  S      0   1.419  -2.1601   0.1029   5.4680
 RR1  S35   S  S      0   1.441  -4.1910  -0.3507  -2.1535
 RR1  N1    N  N      0  -0.409  -0.1014  -0.0691  -3.0409
 RR1  N2    N  N      0  -0.200  -1.2846  -0.1568  -2.6543
 RR1  N19   N  NH1    0  -0.794   1.4651   0.1830   1.8054
 RR1  C20   C  C      0   0.613   2.5862   0.2989   2.5726
 RR1  N21   N  N      0  -0.529   3.7105   0.3123   1.8581
 RR1  C22   C  C      0   0.561   4.8252   0.4269   2.5819
 RR1  N23   N  N      0  -0.518   4.8747   0.5288   3.9129
 RR1  C24   C  C      0   0.583   3.6883   0.5053   4.5109
 RR1  N25   N  N      0  -0.535   2.5056   0.3892   3.8889
 RR1  NL1   N  NH2    0  -0.816   3.6594   0.5877   5.8457
 RR1  NL2   N  NH2    0  -0.818   5.9873   0.4337   1.9220
 RR1  H11   H  H      0   0.272   2.5820  -0.2830  -6.6980
 RR1  H12   H  H      0   0.266   0.6864  -0.0144  -8.2470
 RR1  H13   H  H      0   0.267  -1.6126   0.2343  -7.3581
 RR1  H14   H  H      0   0.287  -2.0004   0.2100  -4.9162
 RR1  HC8   H  HCR6   0   0.269  -4.2513  -0.2622   0.7181
 RR1  H16   H  HCR6   0   0.308   0.4017   0.2090   4.2335
 RR1  H18   H  HCR6   0   0.266  -3.6811  -0.1334   2.9888
 RR1  H28   H  HOH1   0   0.516   0.8041   0.0418  -1.6987
 RR1  H19   H  HNH1   0   0.429   1.6739   0.1468   0.8169
 RR1  HL11  H  HNH2   0   0.400   4.5011   0.8024   6.3508
 RR1  HL12  H  HNH2   0   0.401   2.7805   0.7064   6.3181
 RR1  HL21  H  HNH2   0   0.400   6.8509   0.5722   2.4155
 RR1  HL22  H  HNH2   0   0.401   6.0008   0.4169   0.9180
 RR1  O28   O  OH1    0  -0.658   0.7421   0.0689  -0.6950
 RR1  O37   O  OS    -1  -0.751  -1.7116   1.4269   5.9287
 RR1  O38   O  OS     0  -0.741  -3.6229  -0.0624   5.4912
 RR1  O41   O  OS     0  -0.750  -1.4344  -1.0125   6.0968
 RR1  O39   O  OS    -1  -0.743  -4.0754   0.8680  -2.9683
 RR1  O40   O  OS     0  -0.744  -3.9199  -1.5980  -2.8806
 RR1  O42   O  OS     0  -0.739  -5.4414  -0.4020  -1.3745

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   deloc     1.473  0.020  1.473
 RR1  O90  S85   deloc     1.472  0.020  1.472
 RR1  O92  S85   deloc     1.471  0.020  1.471
 RR1  S85  C10   single    1.801  0.020  1.801
 RR1  C10  C11   aromatic  1.387  0.020  1.387
 RR1  C10  C4    aromatic  1.399  0.020  1.399
 RR1  C11  C12   aromatic  1.388  0.020  1.388
 RR1  C11  H11   single    0.930  0.020  1.080
 RR1  C12  C13   aromatic  1.389  0.020  1.389
 RR1  C12  H12   single    0.930  0.020  1.080
 RR1  C13  C14   aromatic  1.383  0.020  1.383
 RR1  C13  H13   single    0.930  0.020  1.080
 RR1  C14  C4    aromatic  1.396  0.020  1.396
 RR1  C14  H14   single    0.930  0.020  1.080
 RR1  C4   N1    single    1.404  0.020  1.404
 RR1  C5   C3    aromatic  1.403  0.020  1.403
 RR1  C5   C6    aromatic  1.430  0.020  1.430
 RR1  C5   O28   single    1.322  0.020  1.322
 RR1  C3   C9    aromatic  1.421  0.020  1.421
 RR1  C3   N2    single    1.377  0.020  1.377
 RR1  C9   C8    aromatic  1.355  0.020  1.355
 RR1  C9   S35   single    1.805  0.020  1.805
 RR1  C8   C7    aromatic  1.421  0.020  1.421
 RR1  C8   HC8   single    0.930  0.020  1.080
 RR1  C7   C6    aromatic  1.420  0.020  1.420
 RR1  C7   C18   aromatic  1.406  0.020  1.406
 RR1  C6   C15   aromatic  1.443  0.020  1.443
 RR1  C15  C16   aromatic  1.382  0.020  1.382
 RR1  C15  N19   single    1.383  0.020  1.383
 RR1  C16  C17   aromatic  1.399  0.020  1.399
 RR1  C16  H16   single    0.930  0.020  1.080
 RR1  C17  C18   aromatic  1.366  0.020  1.366
 RR1  C17  S36   single    1.793  0.020  1.793
 RR1  C18  H18   single    0.930  0.020  1.080
 RR1  O28  H28   single    0.850  0.020  0.980
 RR1  O37  S36   deloc     1.472  0.020  1.472
 RR1  O38  S36   deloc     1.472  0.020  1.472
 RR1  O41  S36   deloc     1.472  0.020  1.472
 RR1  O39  S35   deloc     1.471  0.020  1.471
 RR1  O40  S35   deloc     1.469  0.020  1.469
 RR1  O42  S35   deloc     1.474  0.020  1.474
 RR1  N1   N2    double    1.248  0.020  1.248
 RR1  N19  C20   single    1.363  0.020  1.363
 RR1  N19  H19   single    0.860  0.020  1.020
 RR1  C20  N21   aromatic  1.332  0.020  1.332
 RR1  C20  N25   aromatic  1.322  0.020  1.322
 RR1  N21  C22   aromatic  1.334  0.020  1.334
 RR1  C22  N23   aromatic  1.336  0.020  1.336
 RR1  C22  NL2   single    1.336  0.020  1.336
 RR1  N23  C24   aromatic  1.329  0.020  1.329
 RR1  C24  N25   aromatic  1.341  0.020  1.341
 RR1  C24  NL1   single    1.338  0.020  1.338
 RR1  NL1  HL11  single    0.860  0.020  1.020
 RR1  NL1  HL12  single    0.860  0.020  1.020
 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  C10   S85  O92   105.19  3.000
 RR1  C10   S85  O90   105.10  3.000
 RR1  O92   S85  O90   113.27  3.000
 RR1  C10   S85  O89   105.30  3.000
 RR1  O92   S85  O89   113.81  3.000
 RR1  O90   S85  O89   113.07  3.000
 RR1  C4    C10  C11   119.53  3.000
 RR1  C4    C10  S85   121.18  3.000
 RR1  C11   C10  S85   119.29  3.000
 RR1  H11   C11  C12   119.84  3.000
 RR1  H11   C11  C10   119.73  3.000
 RR1  C12   C11  C10   120.44  3.000
 RR1  H12   C12  C13   120.24  3.000
 RR1  H12   C12  C11   119.78  3.000
 RR1  C13   C12  C11   119.98  3.000
 RR1  H13   C13  C14   119.68  3.000
 RR1  H13   C13  C12   120.15  3.000
 RR1  C14   C13  C12   120.17  3.000
 RR1  H14   C14  C4    119.23  3.000
 RR1  H14   C14  C13   120.75  3.000
 RR1  C4    C14  C13   120.02  3.000
 RR1  N1    C4   C14   122.16  3.000
 RR1  N1    C4   C10   117.97  3.000
 RR1  C14   C4   C10   119.86  3.000
 RR1  O28   C5   C6    119.16  3.000
 RR1  O28   C5   C3    119.73  3.000
 RR1  C6    C5   C3    121.11  3.000
 RR1  N2    C3   C9    115.93  3.000
 RR1  N2    C3   C5    124.02  3.000
 RR1  C9    C3   C5    120.05  3.000
 RR1  S35   C9   C8    119.66  3.000
 RR1  S35   C9   C3    120.49  3.000
 RR1  C8    C9   C3    119.85  3.000
 RR1  HC8   C8   C7    118.03  3.000
 RR1  HC8   C8   C9    120.81  3.000
 RR1  C7    C8   C9    121.16  3.000
 RR1  C18   C7   C6    120.61  3.000
 RR1  C18   C7   C8    118.43  3.000
 RR1  C6    C7   C8    120.95  3.000
 RR1  C15   C6   C7    118.51  3.000
 RR1  C15   C6   C5    124.62  3.000
 RR1  C7    C6   C5    116.88  3.000
 RR1  N19   C15  C16   122.33  3.000
 RR1  N19   C15  C6    118.80  3.000
 RR1  C16   C15  C6    118.87  3.000
 RR1  H16   C16  C17   120.09  3.000
 RR1  H16   C16  C15   118.84  3.000
 RR1  C17   C16  C15   121.07  3.000
 RR1  S36   C17  C18   120.94  3.000
 RR1  S36   C17  C16   117.57  3.000
 RR1  C18   C17  C16   121.49  3.000
 RR1  H18   C18  C17   121.46  3.000
 RR1  H18   C18  C7    119.09  3.000
 RR1  C17   C18  C7    119.45  3.000
 RR1  O41   S36  O38   113.46  3.000
 RR1  O41   S36  O37   113.44  3.000
 RR1  O38   S36  O37   113.50  3.000
 RR1  O41   S36  C17   104.90  3.000
 RR1  O38   S36  C17   105.93  3.000
 RR1  O37   S36  C17   104.46  3.000
 RR1  O42   S35  O40   112.86  3.000
 RR1  O42   S35  O39   112.85  3.000
 RR1  O40   S35  O39   114.52  3.000
 RR1  O42   S35  C9    104.47  3.000
 RR1  O40   S35  C9    105.62  3.000
 RR1  O39   S35  C9    105.40  3.000
 RR1  N2    N1   C4    115.09  3.000
 RR1  N1    N2   C3    118.05  3.000
 RR1  H19   N19  C20   112.55  3.000
 RR1  H19   N19  C15   115.40  3.000
 RR1  C20   N19  C15   132.06  3.000
 RR1  N25   C20  N21   125.80  3.000
 RR1  N25   C20  N19   121.06  3.000
 RR1  N21   C20  N19   113.14  3.000
 RR1  C22   N21  C20   114.52  3.000
 RR1  NL2   C22  N23   117.34  3.000
 RR1  NL2   C22  N21   117.33  3.000
 RR1  N23   C22  N21   125.32  3.000
 RR1  C24   N23  C22   114.45  3.000
 RR1  NL1   C24  N25   116.68  3.000
 RR1  NL1   C24  N23   117.85  3.000
 RR1  N25   C24  N23   125.46  3.000
 RR1  C24   N25  C20   114.45  3.000
 RR1  HL12  NL1  HL11  118.11  3.000
 RR1  HL12  NL1  C24   119.69  3.000
 RR1  HL11  NL1  C24   119.78  3.000
 RR1  HL22  NL2  HL21  118.82  3.000
 RR1  HL22  NL2  C22   120.35  3.000
 RR1  HL21  NL2  C22   120.39  3.000
 RR1  H28   O28  C5    109.65  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_60  N2    N1   C4   C10  180.00   0.0  0
 RR1  CONST_61  N2    N1   C4   C14    0.00   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    0.00   0.0  0
 RR1  CONST_67  HL12  NL1  C24  N23  180.00   0.0  0
 RR1  Var_01    C20   N19  C15  C6   179.38  30.0  2
 RR1  Var_02    N21   C20  N19  C15  178.91  30.0  2
 RR1  Var_03    C11   C10  S85  O89  120.78  30.0  2
 RR1  Var_04    O39   S35  C9   C3   -60.10  30.0  2
 RR1  Var_05    O37   S36  C17  C16   62.18  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

