# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 09:45:09 2022
#   Inital geometry file: a 133 line input string
#   Ligand name: [(2R,3S,4R,5R)-5-(6-amino-8-bromo-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl [(2R,3S,4S)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n([C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)OC[C@H]4OC[C@H](O)[C@@H]4O)[C@@H](O)[C@H]3O)c(Br)nc12
#
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
 AV1  AV1  '[(2R,3S,4R,5R)-5-(6-amino-8-bromo-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl [(2R,3S,4S)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name)'  ligand  56  36  .  2022-03-11  2022-03-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_AV1
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
 AV1  BR1   BR  BR     0   0.047  -1.7016   0.2999   1.3521
 AV1  O3    O   O2     0  -0.735   2.0779   0.8003  -0.1065
 AV1  PA    P   P      0   1.377   1.1633   2.1322   0.1553
 AV1  PN    P   P      0   1.342   3.0036   0.0968   1.0545
 AV1  C1'   C   CR15   0   0.233  -3.6564   0.4624  -1.3815
 AV1  N1A   N   N      0  -0.471  -6.4650  -3.5087   0.0546
 AV1  O1A   O   OP    -1  -0.787   1.9195   3.3685  -0.2137
 AV1  C1D   C   CH2    0  -0.174   7.8099  -0.9125  -1.5757
 AV1  O1N   O   O      0  -0.785   2.2743  -1.0506   1.6757
 AV1  C2'   C   CR15   0  -0.040  -4.1181   1.8719  -1.0244
 AV1  O2'   O   OH1    0  -0.652  -5.5087   1.9540  -1.1024
 AV1  C2A   C   CR16   0   0.046  -6.4711  -2.7522  -1.0391
 AV1  O2A   O   O      0  -0.792   0.4781   2.0497   1.4893
 AV1  C2D   C   CH1    0  -0.018   8.2105  -1.6632  -0.3092
 AV1  O2D   O   OH1    0  -0.668   9.4665  -2.2795  -0.3517
 AV1  O2N   O   OP    -1  -0.802   3.6485   1.1428   1.9084
 AV1  C3'   C   CR15   0  -0.047  -3.3602   2.6783  -2.0872
 AV1  O3'   O   OH1    0  -0.668  -3.9834   2.5699  -3.3404
 AV1  N3A   N   N      0  -0.458  -5.6861  -1.7306  -1.3361
 AV1  C3D   C   CH1    0  -0.036   7.0981  -2.7085  -0.2215
 AV1  O3D   O   OH1    0  -0.671   7.3073  -3.7666  -1.1240
 AV1  C4'   C   CR15   0  -0.027  -2.0279   1.9361  -2.1245
 AV1  O4'   O   O      0  -0.489  -2.3127   0.5858  -1.7356
 AV1  C4A   C   CR56   0   0.503  -4.7989  -1.4942  -0.3750
 AV1  C4D   C   CH1    0  -0.024   5.8929  -1.9005  -0.6896
 AV1  O4D   O   O2     0  -0.498   6.3949  -0.8970  -1.5680
 AV1  C5'   C   CH2    0  -0.154  -1.0208   2.5968  -1.1986
 AV1  O5'   O   O2     0  -0.615   0.1015   1.7638  -1.0487
 AV1  C5A   C   CR56   0  -0.000  -4.6674  -2.1969   0.8084
 AV1  C5D   C   CH2    0  -0.145   5.1518  -1.2680   0.4732
 AV1  O5D   O   O2     0  -0.617   4.0970  -0.4828  -0.0345
 AV1  C6A   C   CR6    0   0.453  -5.5655  -3.2596   1.0127
 AV1  N6A   N   NH2    0  -0.816  -5.5393  -4.0270   2.1041
 AV1  N7A   N   N      0  -0.434  -3.6382  -1.6948   1.5606
 AV1  C8A   C   CR5    0   0.278  -3.1698  -0.7138   0.8561
 AV1  N9A   N   NR5    0  -0.566  -3.8263  -0.5280  -0.3401
 AV1  H1'   H   HCR5   0   0.258  -4.2632   0.0903  -2.2157
 AV1  H2'   H   HCR5   0   0.247  -3.7493   2.1490  -0.0294
 AV1  HO2'  H   HOH1   0   0.469  -5.8028   2.7246  -0.6065
 AV1  H2A   H   HCR6   0   0.253  -7.2200  -3.0094  -1.7806
 AV1  H2D   H   HCH1   0   0.223   8.1237  -0.9917   0.5551
 AV1  HO2D  H   HOH1   0   0.463  10.1479  -1.6007  -0.3544
 AV1  H3'   H   HCR5   0   0.253  -3.2319   3.7275  -1.7891
 AV1  HO3'  H   HOH1   0   0.449  -4.9219   2.7577  -3.2229
 AV1  H3D   H   HCH1   0   0.240   6.9668  -3.0795   0.8038
 AV1  HO3D  H   HOH1   0   0.450   8.1801  -4.1373  -0.9559
 AV1  H4'   H   HCR5   0   0.258  -1.6234   1.9150  -3.1410
 AV1  H4D   H   HCH1   0   0.243   5.1954  -2.5427  -1.2396
 AV1  H5'   H   HCH2   0   0.229  -0.7491   3.5583  -1.6522
 AV1  H5'A  H   HCH2   0   0.210  -1.4814   2.8232  -0.2307
 AV1  H5D   H   HCH2   0   0.212   4.7763  -2.0728   1.1164
 AV1  H5DA  H   HCH2   0   0.206   5.8382  -0.6616   1.0790
 AV1  HN6A  H   HNH2   0   0.404  -6.2557  -4.7174   2.2501
 AV1  HN6B  H   HNH2   0   0.412  -4.9413  -3.7987   2.8789
 AV1  H1D   H   HCH2   0   0.230   8.1789   0.1154  -1.5960
 AV1  H1DA  H   HCH2   0   0.204   8.2000  -1.4313  -2.4600

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
 AV1  BR1  C8A   single    1.852  0.020  1.852
 AV1  O3   PA    single    1.637  0.020  1.637
 AV1  O3   PN    single    1.643  0.020  1.643
 AV1  PA   O1A   deloc     1.496  0.020  1.496
 AV1  PA   O2A   deloc     1.502  0.020  1.502
 AV1  PA   O5'   single    1.647  0.020  1.647
 AV1  PN   O1N   deloc     1.495  0.020  1.495
 AV1  PN   O2N   deloc     1.496  0.020  1.496
 AV1  PN   O5D   single    1.648  0.020  1.648
 AV1  C1'  C2'   single    1.526  0.020  1.526
 AV1  C1'  O4'   single    1.395  0.020  1.395
 AV1  C1'  N9A   single    1.447  0.020  1.447
 AV1  N1A  C2A   aromatic  1.330  0.020  1.330
 AV1  N1A  C6A   aromatic  1.338  0.020  1.338
 AV1  C1D  C2D   single    1.526  0.020  1.526
 AV1  C1D  O4D   single    1.415  0.020  1.415
 AV1  C2'  O2'   single    1.395  0.020  1.395
 AV1  C2'  C3'   single    1.534  0.020  1.534
 AV1  C2A  N3A   aromatic  1.322  0.020  1.322
 AV1  C2D  O2D   single    1.400  0.020  1.400
 AV1  C2D  C3D   single    1.529  0.020  1.529
 AV1  C3'  O3'   single    1.404  0.020  1.404
 AV1  C3'  C4'   single    1.526  0.020  1.526
 AV1  N3A  C4A   aromatic  1.329  0.020  1.329
 AV1  C3D  O3D   single    1.406  0.020  1.406
 AV1  C3D  C4D   single    1.525  0.020  1.525
 AV1  C4'  O4'   single    1.434  0.020  1.434
 AV1  C4'  C5'   single    1.519  0.020  1.519
 AV1  C4A  C5A   aromatic  1.383  0.020  1.383
 AV1  C4A  N9A   aromatic  1.371  0.020  1.371
 AV1  C4D  O4D   single    1.425  0.020  1.425
 AV1  C4D  C5D   single    1.517  0.020  1.517
 AV1  C5'  O5'   single    1.406  0.020  1.406
 AV1  C5A  C6A   aromatic  1.406  0.020  1.406
 AV1  C5A  N7A   aromatic  1.370  0.020  1.370
 AV1  C5D  O5D   single    1.410  0.020  1.410
 AV1  C6A  N6A   single    1.334  0.020  1.334
 AV1  N7A  C8A   aromatic  1.295  0.020  1.295
 AV1  C8A  N9A   aromatic  1.377  0.020  1.377
 AV1  C1'  H1'   single    0.970  0.020  1.090
 AV1  C1D  H1D   single    0.970  0.020  1.090
 AV1  C1D  H1DA  single    0.970  0.020  1.090
 AV1  C2'  H2'   single    0.970  0.020  1.090
 AV1  O2'  HO2'  single    0.850  0.020  0.980
 AV1  C2A  H2A   single    0.930  0.020  1.080
 AV1  C2D  H2D   single    0.970  0.020  1.090
 AV1  O2D  HO2D  single    0.850  0.020  0.980
 AV1  C3'  H3'   single    0.970  0.020  1.090
 AV1  O3'  HO3'  single    0.850  0.020  0.980
 AV1  C3D  H3D   single    0.970  0.020  1.090
 AV1  O3D  HO3D  single    0.850  0.020  0.980
 AV1  C4'  H4'   single    0.970  0.020  1.090
 AV1  C4D  H4D   single    0.970  0.020  1.090
 AV1  C5'  H5'   single    0.970  0.020  1.090
 AV1  C5'  H5'A  single    0.970  0.020  1.090
 AV1  C5D  H5D   single    0.970  0.020  1.090
 AV1  C5D  H5DA  single    0.970  0.020  1.090
 AV1  N6A  HN6A  single    0.860  0.020  1.020
 AV1  N6A  HN6B  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
 AV1  PN    O3   PA    123.38  3.000
 AV1  O5'   PA   O2A   110.05  3.000
 AV1  O5'   PA   O1A   109.30  3.000
 AV1  O2A   PA   O1A   119.69  3.000
 AV1  O5'   PA   O3     93.52  3.000
 AV1  O2A   PA   O3    110.63  3.000
 AV1  O1A   PA   O3    110.53  3.000
 AV1  O5D   PN   O2N   109.69  3.000
 AV1  O5D   PN   O1N   109.17  3.000
 AV1  O2N   PN   O1N   120.64  3.000
 AV1  O5D   PN   O3     93.29  3.000
 AV1  O2N   PN   O3    110.28  3.000
 AV1  O1N   PN   O3    110.33  3.000
 AV1  H1'   C1'  N9A   104.50  3.000
 AV1  H1'   C1'  O4'   111.71  3.000
 AV1  N9A   C1'  O4'   110.87  3.000
 AV1  H1'   C1'  C2'   108.91  3.000
 AV1  N9A   C1'  C2'   115.36  3.000
 AV1  O4'   C1'  C2'   105.62  3.000
 AV1  C6A   N1A  C2A   119.10  3.000
 AV1  H1DA  C1D  H1D   108.06  3.000
 AV1  H1DA  C1D  O4D   111.42  3.000
 AV1  H1D   C1D  O4D   109.12  3.000
 AV1  H1DA  C1D  C2D   110.06  3.000
 AV1  H1D   C1D  C2D   112.94  3.000
 AV1  O4D   C1D  C2D   105.27  3.000
 AV1  H2'   C2'  C3'   109.24  3.000
 AV1  H2'   C2'  O2'   111.78  3.000
 AV1  C3'   C2'  O2'   115.01  3.000
 AV1  H2'   C2'  C1'   110.12  3.000
 AV1  C3'   C2'  C1'   100.02  3.000
 AV1  O2'   C2'  C1'   110.05  3.000
 AV1  HO2'  O2'  C2'   108.83  3.000
 AV1  H2A   C2A  N3A   116.07  3.000
 AV1  H2A   C2A  N1A   115.49  3.000
 AV1  N3A   C2A  N1A   128.43  3.000
 AV1  H2D   C2D  C3D   108.39  3.000
 AV1  H2D   C2D  O2D   111.35  3.000
 AV1  C3D   C2D  O2D   110.71  3.000
 AV1  H2D   C2D  C1D   109.37  3.000
 AV1  C3D   C2D  C1D   101.13  3.000
 AV1  O2D   C2D  C1D   115.28  3.000
 AV1  HO2D  O2D  C2D   108.97  3.000
 AV1  H3'   C3'  C4'   111.67  3.000
 AV1  H3'   C3'  O3'   111.59  3.000
 AV1  C4'   C3'  O3'   109.16  3.000
 AV1  H3'   C3'  C2'   111.83  3.000
 AV1  C4'   C3'  C2'   101.11  3.000
 AV1  O3'   C3'  C2'   111.01  3.000
 AV1  HO3'  O3'  C3'   107.96  3.000
 AV1  C4A   N3A  C2A   111.79  3.000
 AV1  H3D   C3D  C4D   111.79  3.000
 AV1  H3D   C3D  O3D   111.27  3.000
 AV1  C4D   C3D  O3D   108.62  3.000
 AV1  H3D   C3D  C2D   111.81  3.000
 AV1  C4D   C3D  C2D   101.26  3.000
 AV1  O3D   C3D  C2D   111.67  3.000
 AV1  HO3D  O3D  C3D   108.20  3.000
 AV1  H4'   C4'  C5'   109.24  3.000
 AV1  H4'   C4'  O4'   107.90  3.000
 AV1  C5'   C4'  O4'   112.08  3.000
 AV1  H4'   C4'  C3'   110.80  3.000
 AV1  C5'   C4'  C3'   110.64  3.000
 AV1  O4'   C4'  C3'   106.14  3.000
 AV1  C4'   O4'  C1'   110.09  3.000
 AV1  N9A   C4A  C5A   105.59  3.000
 AV1  N9A   C4A  N3A   128.10  3.000
 AV1  C5A   C4A  N3A   126.30  3.000
 AV1  H4D   C4D  C5D   108.54  3.000
 AV1  H4D   C4D  O4D   109.11  3.000
 AV1  C5D   C4D  O4D   110.54  3.000
 AV1  H4D   C4D  C3D   110.28  3.000
 AV1  C5D   C4D  C3D   111.83  3.000
 AV1  O4D   C4D  C3D   106.50  3.000
 AV1  C4D   O4D  C1D   110.36  3.000
 AV1  H5'A  C5'  H5'   106.75  3.000
 AV1  H5'A  C5'  O5'   111.34  3.000
 AV1  H5'   C5'  O5'   111.45  3.000
 AV1  H5'A  C5'  C4'   110.46  3.000
 AV1  H5'   C5'  C4'   107.06  3.000
 AV1  O5'   C5'  C4'   109.67  3.000
 AV1  C5'   O5'  PA    117.40  3.000
 AV1  N7A   C5A  C6A   132.60  3.000
 AV1  N7A   C5A  C4A   110.80  3.000
 AV1  C6A   C5A  C4A   116.60  3.000
 AV1  H5DA  C5D  H5D   107.20  3.000
 AV1  H5DA  C5D  O5D   111.03  3.000
 AV1  H5D   C5D  O5D   111.34  3.000
 AV1  H5DA  C5D  C4D   110.35  3.000
 AV1  H5D   C5D  C4D   108.11  3.000
 AV1  O5D   C5D  C4D   108.77  3.000
 AV1  C5D   O5D  PN    117.01  3.000
 AV1  N6A   C6A  C5A   122.74  3.000
 AV1  N6A   C6A  N1A   119.47  3.000
 AV1  C5A   C6A  N1A   117.78  3.000
 AV1  HN6B  N6A  HN6A  117.89  3.000
 AV1  HN6B  N6A  C6A   120.77  3.000
 AV1  HN6A  N6A  C6A   119.98  3.000
 AV1  C8A   N7A  C5A   104.52  3.000
 AV1  N9A   C8A  N7A   113.71  3.000
 AV1  N9A   C8A  BR1   122.46  3.000
 AV1  N7A   C8A  BR1   123.75  3.000
 AV1  C8A   N9A  C4A   105.38  3.000
 AV1  C8A   N9A  C1'   131.41  3.000
 AV1  C4A   N9A  C1'   123.17  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
 AV1  CONST_01  C4A   N3A  C2A  N1A     0.00   0.0  0
 AV1  CONST_02  C4A   C5A  C6A  N1A     0.00   0.0  0
 AV1  CONST_03  N7A   C5A  C6A  N1A   180.00   0.0  0
 AV1  CONST_04  C5A   C6A  N1A  C2A     0.00   0.0  0
 AV1  CONST_05  C5A   C4A  N3A  C2A     0.00   0.0  0
 AV1  CONST_06  N9A   C4A  N3A  C2A   180.00   0.0  0
 AV1  CONST_07  C6A   N1A  C2A  N3A     0.00   0.0  0
 AV1  CONST_08  C6A   C5A  C4A  N3A     0.00   0.0  0
 AV1  CONST_09  N7A   C5A  C4A  N3A   180.00   0.0  0
 AV1  CONST_10  C8A   N9A  C4A  N3A   180.00   0.0  0
 AV1  CONST_11  C8A   N7A  C5A  C4A     0.00   0.0  0
 AV1  CONST_12  N7A   C8A  N9A  C4A     0.00   0.0  0
 AV1  CONST_13  C8A   N9A  C4A  C5A     0.00   0.0  0
 AV1  CONST_14  N9A   C8A  N7A  C5A     0.00   0.0  0
 AV1  CONST_15  N9A   C4A  C5A  C6A   180.00   0.0  0
 AV1  CONST_16  C8A   N7A  C5A  C6A   180.00   0.0  0
 AV1  CONST_17  N9A   C4A  C5A  N7A     0.00   0.0  0
 AV1  CONST_18  N3A   C4A  N9A  C1'     0.00   0.0  0
 AV1  CONST_19  C5A   C4A  N9A  C1'   180.00   0.0  0
 AV1  CONST_20  N7A   C8A  N9A  C1'   180.00   0.0  0
 AV1  CONST_21  C5A   N7A  C8A  BR1   180.00   0.0  0
 AV1  CONST_22  C1'   N9A  C8A  BR1     0.00   0.0  0
 AV1  CONST_23  C4A   N9A  C8A  BR1   180.00   0.0  0
 AV1  CONST_24  N6A   C6A  N1A  C2A   180.00   0.0  0
 AV1  CONST_25  N6A   C6A  C5A  C4A   180.00   0.0  0
 AV1  CONST_26  N7A   C5A  C6A  N6A     0.00   0.0  0
 AV1  CONST_27  H2A   C2A  N3A  C4A   180.00   0.0  0
 AV1  CONST_28  HN6A  N6A  C6A  N1A     0.00   0.0  0
 AV1  CONST_29  HN6B  N6A  C6A  N1A   180.00   0.0  0
 AV1  Var_01    H1D   C1D  O4D  C4D  -140.06  30.0  1
 AV1  Var_02    C4'   C5'  O5'  PA   -167.20  30.0  2
 AV1  Var_03    C4D   C5D  O5D  PN    170.06  30.0  1
 AV1  Var_04    O1N   PN   O3   PA     96.92  30.0  3
 AV1  Var_05    O1A   PA   O3   PN     93.70  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
 AV1  chir_03  C1'  C2'  O4'  N9A  negativ
 AV1  chir_04  C2'  O2'  C3'  C1'  positiv
 AV1  chir_05  C2D  C1D  O2D  C3D  positiv
 AV1  chir_06  C3'  C2'  O3'  C4'  positiv
 AV1  chir_07  C3D  C2D  O3D  C4D  positiv
 AV1  chir_08  C4'  C3'  O4'  C5'  positiv
 AV1  chir_09  C4D  C3D  O4D  C5D  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
 AV1  plan-1  C6A   0.020
 AV1  plan-1  N6A   0.020
 AV1  plan-1  HN6A  0.020
 AV1  plan-1  HN6B  0.020
 AV1  plan-2  BR1   0.020
 AV1  plan-2  C1'   0.020
 AV1  plan-2  N1A   0.020
 AV1  plan-2  C2A   0.020
 AV1  plan-2  N3A   0.020
 AV1  plan-2  C4A   0.020
 AV1  plan-2  C5A   0.020
 AV1  plan-2  C6A   0.020
 AV1  plan-2  N6A   0.020
 AV1  plan-2  N7A   0.020
 AV1  plan-2  C8A   0.020
 AV1  plan-2  N9A   0.020
 AV1  plan-2  H2A   0.020

