# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 18:15:15 2020
#   Inital geometry file: a 126 line input string
#   Ligand name: [(2~{S},3~{S})-5-[8-azanyl-7-methyl-2,4-bis(oxidanylidene)-1~{H}-benzo[g]pteridin-10-ium-10-yl]-2,3-bis(oxidanyl)-4-oxidanylidene-pentyl] dihydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc2nc3C(=O)NC(=O)Nc3[n+](CC(=O)[C@@H](O)[C@@H](O)CO[P](O)(O)=O)c2cc1N
#
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
 8DP  8DP  '[(2~{S},3~{S})-5-[8-azanyl-7-methyl-2,4-bis(oxidanylidene)-1~{H}-benzo[g]pteridin-10-ium-10-yl]-2,3-bis(oxidanyl)-4-oxidanylidene-pentyl] dihydrogen phosphate'  ligand  48  31  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_8DP
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
 8DP  C4   C  C      0   0.362  -0.2198   1.4195  -0.6329
 8DP  C5   C  CH2    0  -0.497   0.4948   1.2385   0.6879
 8DP  C8   C  CR6    0   0.404   4.3769   3.0586   0.3324
 8DP  N3   N  N      0  -0.349   3.9929  -1.0445   0.2241
 8DP  C2   C  CH1    0  -0.039  -2.5361   0.4785  -0.5429
 8DP  N2   N  NH2    0  -0.843   4.5138   4.3853   0.3436
 8DP  N1   N  NR6    1  -0.567   1.7204   0.4886   0.5186
 8DP  C6   C  CR66   0   0.466   2.9410   1.1159   0.4095
 8DP  O6   O  OH1    0  -0.647  -2.0328   2.5847  -1.6803
 8DP  N4   N  NH1    0  -0.644   0.4019  -1.3899   0.3678
 8DP  C12  C  CR66   0   0.163   4.0874   0.2790   0.2837
 8DP  C13  C  CR6    0   0.645   1.6025  -0.8594   0.3775
 8DP  C14  C  CR6    0  -0.090   2.8133  -1.6008   0.2578
 8DP  C15  C  C      0   0.547   2.7122  -3.0614   0.1584
 8DP  C16  C  C      0   0.617   0.2689  -2.7435   0.2709
 8DP  C1   C  CH2    0  -0.163  -4.0180   0.8188  -0.4720
 8DP  C3   C  CH1    0  -0.073  -1.6951   1.7827  -0.5878
 8DP  C7   C  CR16   0  -0.456   3.0989   2.4879   0.4235
 8DP  C9   C  CR6    0   0.048   5.5439   2.2278   0.2222
 8DP  O1   O  OP    -1  -0.805  -6.5159  -2.0612  -0.1677
 8DP  P1   P  P      0   1.318  -5.3646  -1.3235   0.4387
 8DP  O2   O  O      0  -0.810  -5.5140  -0.5589   1.7196
 8DP  O3   O  OP    -1  -0.817  -4.1408  -2.3996   0.5483
 8DP  O4   O  O2     0  -0.624  -4.8307  -0.3007  -0.7439
 8DP  O5   O  OH1    0  -0.708  -2.2090  -0.3086   0.5774
 8DP  O7   O  O      0  -0.362   0.3581   1.2871  -1.6819
 8DP  C10  C  CH3    0  -0.754   6.9002   2.8516   0.1258
 8DP  C11  C  CR16   0  -0.358   5.3668   0.8808   0.2002
 8DP  O8   O  O      0  -0.436   3.6642  -3.8072   0.0681
 8DP  N5   N  NH1    0  -0.718   1.4208  -3.5142   0.1769
 8DP  O9   O  O      0  -0.470  -0.8183  -3.2885   0.2652
 8DP  H1   H  HCH2   0   0.349   0.7029   2.2244   1.1032
 8DP  H2   H  HCH2   0   0.331  -0.1390   0.7512   1.4266
 8DP  H3   H  HCH1   0   0.227  -2.3455  -0.0688  -1.4790
 8DP  H4   H  HNH2   0   0.425   5.4108   4.8310   0.2641
 8DP  H5   H  HNH2   0   0.418   3.7145   4.9902   0.4249
 8DP  H6   H  HOH1   0   0.452  -1.7527   2.1443  -2.4917
 8DP  H7   H  HNH1   0   0.498  -1.3303  -0.7257   0.4589
 8DP  H8   H  HCH2   0   0.215  -4.2416   1.2466   0.5111
 8DP  H9   H  HCH2   0   0.234  -4.2475   1.5746  -1.2235
 8DP  H10  H  HCH1   0   0.276  -1.8983   2.3636   0.3187
 8DP  H11  H  HCR6   0   0.288   2.2569   3.1617   0.4844
 8DP  H14  H  HOH1   0   0.461  -3.2940  -1.9467   0.6925
 8DP  H15  H  HCH3   0   0.258   7.1303   3.4552   1.0068
 8DP  H16  H  HCH3   0   0.270   7.6703   2.0881   0.0396
 8DP  H17  H  HCH3   0   0.257   6.9823   3.5037  -0.7469
 8DP  H18  H  HCR6   0   0.279   6.2185   0.2181   0.1107
 8DP  H19  H  HNH1   0   0.422   1.2846  -4.5157   0.1135

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
 8DP  O2   P1   deloc     1.499  0.020  1.499
 8DP  O5   C2   single    1.408  0.020  1.408
 8DP  O4   P1   single    1.652  0.020  1.652
 8DP  O4   C1   single    1.410  0.020  1.410
 8DP  O3   P1   deloc     1.633  0.020  1.633
 8DP  P1   O1   deloc     1.496  0.020  1.496
 8DP  O9   C16  double    1.216  0.020  1.216
 8DP  C2   C1   single    1.522  0.020  1.522
 8DP  C2   C3   single    1.552  0.020  1.552
 8DP  O7   C4   double    1.205  0.020  1.205
 8DP  C16  N4   single    1.364  0.020  1.364
 8DP  C16  N5   single    1.389  0.020  1.389
 8DP  C4   C3   single    1.520  0.020  1.520
 8DP  C4   C5   single    1.513  0.020  1.513
 8DP  C3   O6   single    1.397  0.020  1.397
 8DP  N4   C13  single    1.313  0.020  1.313
 8DP  N5   C15  single    1.369  0.020  1.369
 8DP  C5   N1   single    1.447  0.020  1.447
 8DP  C13  N1   aromatic  1.360  0.020  1.360
 8DP  C13  C14  aromatic  1.425  0.020  1.425
 8DP  C15  C14  single    1.467  0.020  1.467
 8DP  C15  O8   double    1.213  0.020  1.213
 8DP  N1   C6   aromatic  1.377  0.020  1.377
 8DP  C14  N3   aromatic  1.305  0.020  1.305
 8DP  C6   C7   aromatic  1.381  0.020  1.381
 8DP  C6   C12  aromatic  1.425  0.020  1.425
 8DP  N3   C12  aromatic  1.328  0.020  1.328
 8DP  C7   C8   aromatic  1.403  0.020  1.403
 8DP  C12  C11  aromatic  1.416  0.020  1.416
 8DP  C8   N2   single    1.334  0.020  1.334
 8DP  C8   C9   aromatic  1.437  0.020  1.437
 8DP  C11  C9   aromatic  1.359  0.020  1.359
 8DP  C9   C10  single    1.496  0.020  1.496
 8DP  C5   H1   single    0.970  0.020  1.090
 8DP  C5   H2   single    0.970  0.020  1.090
 8DP  C2   H3   single    0.970  0.020  1.090
 8DP  N2   H4   single    0.860  0.020  1.020
 8DP  N2   H5   single    0.860  0.020  1.020
 8DP  O6   H6   single    0.850  0.020  0.980
 8DP  N4   H7   single    0.860  0.020  1.020
 8DP  C1   H8   single    0.970  0.020  1.090
 8DP  C1   H9   single    0.970  0.020  1.090
 8DP  C3   H10  single    0.970  0.020  1.090
 8DP  C7   H11  single    0.930  0.020  1.080
 8DP  O5   H14  single    0.850  0.020  0.980
 8DP  C10  H15  single    0.970  0.020  1.090
 8DP  C10  H16  single    0.970  0.020  1.090
 8DP  C10  H17  single    0.970  0.020  1.090
 8DP  C11  H18  single    0.930  0.020  1.080
 8DP  N5   H19  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
 8DP  O7   C4   C3   121.17  3.000
 8DP  C3   C4   C5   117.47  3.000
 8DP  O7   C4   C5   121.36  3.000
 8DP  H2   C5   H1   104.92  3.000
 8DP  H2   C5   N1   109.91  3.000
 8DP  H1   C5   N1   110.60  3.000
 8DP  H2   C5   C4   111.78  3.000
 8DP  H1   C5   C4   108.34  3.000
 8DP  N1   C5   C4   111.11  3.000
 8DP  C9   C8   C7   120.65  3.000
 8DP  C9   C8   N2   119.50  3.000
 8DP  C7   C8   N2   119.85  3.000
 8DP  C14  N3   C12  119.21  3.000
 8DP  H3   C2   O5   111.01  3.000
 8DP  H3   C2   C3   107.41  3.000
 8DP  O5   C2   C3   111.52  3.000
 8DP  H3   C2   C1   108.62  3.000
 8DP  C3   C2   C1   109.93  3.000
 8DP  O5   C2   C1   108.31  3.000
 8DP  H5   N2   H4   116.69  3.000
 8DP  H5   N2   C8   121.16  3.000
 8DP  H4   N2   C8   122.15  3.000
 8DP  C13  N1   C6   121.34  3.000
 8DP  C6   N1   C5   121.61  3.000
 8DP  C13  N1   C5   116.90  3.000
 8DP  C7   C6   C12  119.50  3.000
 8DP  C12  C6   N1   116.91  3.000
 8DP  C7   C6   N1   123.59  3.000
 8DP  H6   O6   C3   108.99  3.000
 8DP  H7   N4   C16  105.51  3.000
 8DP  H7   N4   C13  135.08  3.000
 8DP  C16  N4   C13  119.40  3.000
 8DP  C11  C12  C6   118.84  3.000
 8DP  C11  C12  N3   119.01  3.000
 8DP  C6   C12  N3   122.14  3.000
 8DP  C14  C13  N4   124.50  3.000
 8DP  C14  C13  N1   116.79  3.000
 8DP  N4   C13  N1   118.71  3.000
 8DP  C15  C14  C13  117.71  3.000
 8DP  C15  C14  N3   119.01  3.000
 8DP  C13  C14  N3   123.28  3.000
 8DP  N5   C15  O8   122.56  3.000
 8DP  O8   C15  C14  124.27  3.000
 8DP  N5   C15  C14  113.17  3.000
 8DP  O9   C16  N5   119.49  3.000
 8DP  N5   C16  N4   118.34  3.000
 8DP  O9   C16  N4   122.17  3.000
 8DP  H9   C1   H8   107.76  3.000
 8DP  H9   C1   O4   107.22  3.000
 8DP  H8   C1   O4   111.44  3.000
 8DP  H9   C1   C2   109.14  3.000
 8DP  H8   C1   C2   109.15  3.000
 8DP  O4   C1   C2   112.00  3.000
 8DP  H10  C3   O6   107.33  3.000
 8DP  H10  C3   C2   108.72  3.000
 8DP  O6   C3   C2   111.97  3.000
 8DP  H10  C3   C4   109.34  3.000
 8DP  O6   C3   C4   110.40  3.000
 8DP  C2   C3   C4   109.02  3.000
 8DP  H11  C7   C6   122.08  3.000
 8DP  H11  C7   C8   117.40  3.000
 8DP  C6   C7   C8   120.51  3.000
 8DP  C11  C9   C10  122.04  3.000
 8DP  C10  C9   C8   120.02  3.000
 8DP  C11  C9   C8   117.95  3.000
 8DP  O4   P1   O3   102.35  3.000
 8DP  O3   P1   O2   110.69  3.000
 8DP  O4   P1   O2   109.15  3.000
 8DP  O3   P1   O1   106.20  3.000
 8DP  O4   P1   O1   105.30  3.000
 8DP  O2   P1   O1   121.41  3.000
 8DP  P1   O4   C1   122.67  3.000
 8DP  H14  O5   C2   112.57  3.000
 8DP  H17  C10  H16  107.61  3.000
 8DP  H17  C10  H15  107.37  3.000
 8DP  H16  C10  H15  107.61  3.000
 8DP  H17  C10  C9   111.62  3.000
 8DP  H16  C10  C9   110.74  3.000
 8DP  H15  C10  C9   111.67  3.000
 8DP  H18  C11  C9   120.37  3.000
 8DP  H18  C11  C12  117.08  3.000
 8DP  C9   C11  C12  122.55  3.000
 8DP  H19  N5   C16  116.19  3.000
 8DP  H19  N5   C15  116.96  3.000
 8DP  C16  N5   C15  126.85  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
 8DP  CONST_01  N1   C6   C7   C8   180.00   0.0  0
 8DP  CONST_02  C12  C6   C7   C8     0.00   0.0  0
 8DP  CONST_03  C12  C11  C9   C8     0.00   0.0  0
 8DP  CONST_04  N1   C13  C14  N3     0.00   0.0  0
 8DP  CONST_05  N1   C6   C12  N3     0.00   0.0  0
 8DP  CONST_06  C7   C6   C12  N3   180.00   0.0  0
 8DP  CONST_07  C9   C11  C12  N3   180.00   0.0  0
 8DP  CONST_08  C11  C12  C6   N1   180.00   0.0  0
 8DP  CONST_09  C14  C13  N1   C6     0.00   0.0  0
 8DP  CONST_10  C9   C8   C7   C6     0.00   0.0  0
 8DP  CONST_11  C14  N3   C12  C6     0.00   0.0  0
 8DP  CONST_12  C9   C11  C12  C6     0.00   0.0  0
 8DP  CONST_13  C13  N1   C6   C12    0.00   0.0  0
 8DP  CONST_14  C13  C14  N3   C12    0.00   0.0  0
 8DP  CONST_15  C7   C6   N1   C13  180.00   0.0  0
 8DP  CONST_16  C11  C12  N3   C14  180.00   0.0  0
 8DP  CONST_17  C11  C12  C6   C7     0.00   0.0  0
 8DP  CONST_18  C11  C9   C8   C7     0.00   0.0  0
 8DP  CONST_19  C15  N5   C16  N4     0.00   0.0  0
 8DP  CONST_20  N5   C16  N4   C13    0.00   0.0  0
 8DP  CONST_21  C16  N5   C15  C14    0.00   0.0  0
 8DP  CONST_22  N4   C13  N1   C5     0.00   0.0  0
 8DP  CONST_23  C14  C13  N1   C5   180.00   0.0  0
 8DP  CONST_24  C7   C6   N1   C5     0.00   0.0  0
 8DP  CONST_25  C12  C6   N1   C5   180.00   0.0  0
 8DP  CONST_26  C6   C7   C8   N2   180.00   0.0  0
 8DP  CONST_27  C11  C9   C8   N2   180.00   0.0  0
 8DP  CONST_28  C10  C9   C11  C12  180.00   0.0  0
 8DP  CONST_29  C10  C9   C8   C7   180.00   0.0  0
 8DP  CONST_30  O9   C16  N4   C13  180.00   0.0  0
 8DP  CONST_31  O9   C16  N5   C15  180.00   0.0  0
 8DP  CONST_32  O8   C15  N5   C16  180.00   0.0  0
 8DP  CONST_33  H18  C11  C9   C8   180.00   0.0  0
 8DP  CONST_34  H11  C7   C6   N1     0.00   0.0  0
 8DP  CONST_35  H19  N5   C16  N4   180.00   0.0  0
 8DP  CONST_36  H7   N4   C16  N5   180.00   0.0  0
 8DP  CONST_37  H4   N2   C8   C7   180.00   0.0  0
 8DP  CONST_38  H5   N2   C8   C7     0.00   0.0  0
 8DP  Var_01    C13  N1   C5   C4   -77.80  30.0  2
 8DP  Var_02    H15  C10  C9   C8    60.60  30.0  2
 8DP  Var_03    O7   C4   C5   N1   -19.16  30.0  2
 8DP  Var_04    O2   P1   O4   C1    29.91  30.0  3
 8DP  Var_05    H8   C1   O4   P1   -32.07  30.0  3

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
 8DP  chir_01  C2  O5  C1  C3  negativ
 8DP  chir_02  C3  O6  C2  C4  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
 8DP  plan-1  C5   0.020
 8DP  plan-1  C8   0.020
 8DP  plan-1  N3   0.020
 8DP  plan-1  N2   0.020
 8DP  plan-1  N1   0.020
 8DP  plan-1  C6   0.020
 8DP  plan-1  N4   0.020
 8DP  plan-1  C12  0.020
 8DP  plan-1  C13  0.020
 8DP  plan-1  C14  0.020
 8DP  plan-1  C15  0.020
 8DP  plan-1  C16  0.020
 8DP  plan-1  C7   0.020
 8DP  plan-1  C9   0.020
 8DP  plan-1  C10  0.020
 8DP  plan-1  C11  0.020
 8DP  plan-1  O8   0.020
 8DP  plan-1  N5   0.020
 8DP  plan-1  O9   0.020
 8DP  plan-1  H7   0.020
 8DP  plan-1  H11  0.020
 8DP  plan-1  H18  0.020
 8DP  plan-1  H19  0.020
 8DP  plan-2  C8   0.020
 8DP  plan-2  N2   0.020
 8DP  plan-2  H4   0.020
 8DP  plan-2  H5   0.020
 8DP  plan-3  C4   0.020
 8DP  plan-3  C5   0.020
 8DP  plan-3  C3   0.020
 8DP  plan-3  O7   0.020

