# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 29 22:57:11 2021
#   Inital geometry file: a 101 line input string
#   Ligand name: a 2 line input string
#   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)=O)[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
 ABP  ABP  '8-bromoadenosine 5'-(trihydrogen diphosphate)'  ligand  42  28  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_ABP
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
 ABP  PB    P   P     0   1.364  -14.2570  44.9665  17.7709
 ABP  O1B   O   O     0  -0.680  -14.6290  46.3495  17.4333
 ABP  O2B   O   OH1   0  -0.622  -12.7068  44.8518  18.0727
 ABP  O3B   O   OH1   0  -0.666  -15.0395  44.3082  18.9758
 ABP  PA    P   P     0   1.356  -15.5828  42.7921  16.2873
 ABP  O1A   O   O     0  -0.717  -16.0758  42.2780  17.5879
 ABP  O2A   O   OH1   0  -0.606  -14.8843  41.7087  15.3977
 ABP  O3A   O   O2    0  -0.658  -14.4690  43.9423  16.5152
 ABP  O5'   O   O2    0  -0.577  -16.6632  43.5636  15.4160
 ABP  C5'   C   CH2   0  -0.246  -17.2001  43.0775  14.1799
 ABP  C4'   C   CH1   0   0.021  -16.5279  43.6909  12.9744
 ABP  O4'   O   O2    0  -0.483  -16.9687  45.0185  12.7593
 ABP  C3'   C   CH1   0  -0.042  -15.0135  43.8643  13.0205
 ABP  O3'   O   OH1   0  -0.658  -14.3637  42.6138  12.9552
 ABP  C2'   C   CH1   0  -0.064  -14.7750  44.8244  11.8455
 ABP  O2'   O   OH1   0  -0.696  -14.6152  44.1665  10.6213
 ABP  C1'   C   CH1   0   0.220  -16.1323  45.5702  11.7781
 ABP  N9    N   NR5   0  -0.592  -16.0893  47.0004  11.9343
 ABP  C8    C   CR5   0   0.318  -15.7762  47.7903  13.0169
 ABP  BR8   BR  BR    0   0.043  -15.3137  47.1242  14.6830
 ABP  N7    N   N     0  -0.455  -15.8512  49.0584  12.7767
 ABP  C5    C   CR56  0  -0.035  -16.2321  49.1382  11.4626
 ABP  C6    C   CR6   0   0.426  -16.4865  50.2253  10.6054
 ABP  N6    N   NH2   0  -0.818  -16.3706  51.4939  10.9918
 ABP  N1    N   N     0  -0.390  -16.8591  49.9516   9.3495
 ABP  C2    C   CR16  0   0.015  -16.9724  48.6841   8.9668
 ABP  N3    N   N     0  -0.426  -16.7575  47.5895   9.6785
 ABP  C4    C   CR56  0   0.557  -16.3903  47.8774  10.9214
 ABP  HOB2  H   HOH1  0   0.534  -12.3915  43.9878  18.3731
 ABP  HOB3  H   HOH1  0   0.501  -15.5016  43.4615  18.7612
 ABP  HOA2  H   HOH1  0   0.423  -14.6288  41.9463  14.4597
 ABP  H5'1  H   HCH2  0   0.261  -17.1197  41.9918  14.1150
 ABP  H5'2  H   HCH2  0   0.290  -18.2621  43.3206  14.1783
 ABP  H4'   H   HCH1  0   0.256  -16.7961  43.0544  12.1178
 ABP  H3'   H   HCH1  0   0.284  -14.7295  44.3941  13.9329
 ABP  HO3'  H   HOH1  0   0.483  -13.4060  42.7441  12.9500
 ABP  H2'   H   HCH1  0   0.291  -13.9436  45.5085  12.0467
 ABP  HO2'  H   HOH1  0   0.457  -13.7306  43.7906  10.5756
 ABP  H1'   H   HCH1  0   0.303  -16.5410  45.4063  10.7749
 ABP  HN61  H   HNH2  0   0.430  -16.0989  51.7326  11.9293
 ABP  HN62  H   HNH2  0   0.403  -16.5771  52.2401  10.3503
 ABP  H2    H   HCR6  0   0.199  -17.2796  48.5315   7.9380

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
 ABP  PB   O1B   double    1.471  0.020  1.471
 ABP  PB   O2B   single    1.583  0.020  1.583
 ABP  PB   O3B   single    1.580  0.020  1.580
 ABP  PB   O3A   single    1.634  0.020  1.634
 ABP  O2B  HOB2  single    0.850  0.020  0.980
 ABP  O3B  HOB3  single    0.850  0.020  0.980
 ABP  PA   O1A   double    1.483  0.020  1.483
 ABP  PA   O2A   single    1.566  0.020  1.566
 ABP  PA   O3A   single    1.617  0.020  1.617
 ABP  PA   O5'   single    1.588  0.020  1.588
 ABP  O2A  HOA2  single    0.850  0.020  0.980
 ABP  O5'  C5'   single    1.433  0.020  1.433
 ABP  C5'  C4'   single    1.510  0.020  1.510
 ABP  C5'  H5'1  single    0.970  0.020  1.090
 ABP  C5'  H5'2  single    0.970  0.020  1.090
 ABP  C4'  O4'   single    1.415  0.020  1.415
 ABP  C4'  C3'   single    1.525  0.020  1.525
 ABP  C4'  H4'   single    0.970  0.020  1.090
 ABP  O4'  C1'   single    1.402  0.020  1.402
 ABP  C3'  O3'   single    1.411  0.020  1.411
 ABP  C3'  C2'   single    1.536  0.020  1.536
 ABP  C3'  H3'   single    0.970  0.020  1.090
 ABP  O3'  HO3'  single    0.850  0.020  0.980
 ABP  C2'  O2'   single    1.399  0.020  1.399
 ABP  C2'  C1'   single    1.550  0.020  1.550
 ABP  C2'  H2'   single    0.970  0.020  1.090
 ABP  O2'  HO2'  single    0.850  0.020  0.980
 ABP  C1'  N9    single    1.439  0.020  1.439
 ABP  C1'  H1'   single    0.970  0.020  1.090
 ABP  N9   C8    aromatic  1.376  0.020  1.376
 ABP  N9   C4    aromatic  1.373  0.020  1.373
 ABP  C8   BR8   single    1.853  0.020  1.853
 ABP  C8   N7    aromatic  1.293  0.020  1.293
 ABP  N7   C5    aromatic  1.371  0.020  1.371
 ABP  C5   C6    aromatic  1.408  0.020  1.408
 ABP  C5   C4    aromatic  1.381  0.020  1.381
 ABP  C6   N6    single    1.331  0.020  1.331
 ABP  C6   N1    aromatic  1.338  0.020  1.338
 ABP  N6   HN61  single    0.860  0.020  1.020
 ABP  N6   HN62  single    0.860  0.020  1.020
 ABP  N1   C2    aromatic  1.329  0.020  1.329
 ABP  C2   N3    aromatic  1.323  0.020  1.323
 ABP  C2   H2    single    0.930  0.020  1.080
 ABP  N3   C4    aromatic  1.328  0.020  1.328

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
 ABP  O3A   PB   O3B   105.10  3.000
 ABP  O3A   PB   O2B   103.18  3.000
 ABP  O3B   PB   O2B   108.02  3.000
 ABP  O3A   PB   O1B   112.33  3.000
 ABP  O3B   PB   O1B   116.19  3.000
 ABP  O2B   PB   O1B   111.06  3.000
 ABP  HOB2  O2B  PB    116.29  3.000
 ABP  HOB3  O3B  PB    115.01  3.000
 ABP  O5'   PA   O3A   101.56  3.000
 ABP  O5'   PA   O2A   109.14  3.000
 ABP  O3A   PA   O2A   105.35  3.000
 ABP  O5'   PA   O1A   115.06  3.000
 ABP  O3A   PA   O1A   110.61  3.000
 ABP  O2A   PA   O1A   113.99  3.000
 ABP  HOA2  O2A  PA    118.82  3.000
 ABP  PA    O3A  PB    130.04  3.000
 ABP  C5'   O5'  PA    124.30  3.000
 ABP  H5'2  C5'  H5'1  107.09  3.000
 ABP  H5'2  C5'  C4'   110.01  3.000
 ABP  H5'1  C5'  C4'   108.90  3.000
 ABP  H5'2  C5'  O5'   106.91  3.000
 ABP  H5'1  C5'  O5'   111.19  3.000
 ABP  C4'   C5'  O5'   112.58  3.000
 ABP  H4'   C4'  C3'   109.35  3.000
 ABP  H4'   C4'  O4'   110.39  3.000
 ABP  C3'   C4'  O4'   101.96  3.000
 ABP  H4'   C4'  C5'   106.13  3.000
 ABP  C3'   C4'  C5'   117.65  3.000
 ABP  O4'   C4'  C5'   111.32  3.000
 ABP  C1'   O4'  C4'   106.84  3.000
 ABP  H3'   C3'  C2'   107.18  3.000
 ABP  H3'   C3'  O3'   110.42  3.000
 ABP  C2'   C3'  O3'   116.56  3.000
 ABP  H3'   C3'  C4'   109.78  3.000
 ABP  C2'   C3'  C4'   101.66  3.000
 ABP  O3'   C3'  C4'   110.81  3.000
 ABP  HO3'  O3'  C3'   109.70  3.000
 ABP  H2'   C2'  C1'   111.84  3.000
 ABP  H2'   C2'  O2'   111.58  3.000
 ABP  C1'   C2'  O2'   106.75  3.000
 ABP  H2'   C2'  C3'   111.58  3.000
 ABP  C1'   C2'  C3'   101.42  3.000
 ABP  O2'   C2'  C3'   113.16  3.000
 ABP  HO2'  O2'  C2'   109.29  3.000
 ABP  H1'   C1'  N9    105.03  3.000
 ABP  H1'   C1'  C2'   107.13  3.000
 ABP  N9    C1'  C2'   116.56  3.000
 ABP  H1'   C1'  O4'   111.06  3.000
 ABP  N9    C1'  O4'   109.44  3.000
 ABP  C2'   C1'  O4'   107.60  3.000
 ABP  C4    N9   C8    105.28  3.000
 ABP  C4    N9   C1'   123.23  3.000
 ABP  C8    N9   C1'   131.49  3.000
 ABP  N7    C8   BR8   122.28  3.000
 ABP  N7    C8   N9    113.81  3.000
 ABP  BR8   C8   N9    123.90  3.000
 ABP  C5    N7   C8    104.56  3.000
 ABP  C4    C5   C6    116.47  3.000
 ABP  C4    C5   N7    110.76  3.000
 ABP  C6    C5   N7    132.78  3.000
 ABP  N1    C6   N6    119.45  3.000
 ABP  N1    C6   C5    117.64  3.000
 ABP  N6    C6   C5    122.92  3.000
 ABP  HN62  N6   HN61  118.33  3.000
 ABP  HN62  N6   C6    120.27  3.000
 ABP  HN61  N6   C6    121.39  3.000
 ABP  C2    N1   C6    119.28  3.000
 ABP  H2    C2   N3    116.10  3.000
 ABP  H2    C2   N1    115.57  3.000
 ABP  N3    C2   N1    128.34  3.000
 ABP  C4    N3   C2    111.66  3.000
 ABP  N3    C4   C5    126.62  3.000
 ABP  N3    C4   N9    127.78  3.000
 ABP  C5    C4   N9    105.60  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
 ABP  CONST_01  C5    N7   C8   N9     0.00   0.0  0
 ABP  CONST_02  N7    C5   C4   N9     0.00   0.0  0
 ABP  CONST_03  C6    C5   C4   N9   180.00   0.0  0
 ABP  CONST_04  C2    N3   C4   N9   180.00   0.0  0
 ABP  CONST_05  C5    C4   N9   C8     0.00   0.0  0
 ABP  CONST_06  N3    C4   N9   C8   180.00   0.0  0
 ABP  CONST_07  C6    C5   N7   C8   180.00   0.0  0
 ABP  CONST_08  C4    C5   N7   C8     0.00   0.0  0
 ABP  CONST_09  C4    N9   C8   N7     0.00   0.0  0
 ABP  CONST_10  N1    C6   C5   N7   180.00   0.0  0
 ABP  CONST_11  N3    C4   C5   N7   180.00   0.0  0
 ABP  CONST_12  C2    N1   C6   C5     0.00   0.0  0
 ABP  CONST_13  C2    N3   C4   C5     0.00   0.0  0
 ABP  CONST_14  N3    C4   C5   C6     0.00   0.0  0
 ABP  CONST_15  N3    C2   N1   C6     0.00   0.0  0
 ABP  CONST_16  C4    C5   C6   N1     0.00   0.0  0
 ABP  CONST_17  C4    N3   C2   N1     0.00   0.0  0
 ABP  CONST_18  N7    C8   N9   C1'  180.00   0.0  0
 ABP  CONST_19  C5    C4   N9   C1'  180.00   0.0  0
 ABP  CONST_20  N3    C4   N9   C1'    0.00   0.0  0
 ABP  CONST_21  BR8   C8   N9   C1'    0.00   0.0  0
 ABP  CONST_22  C4    N9   C8   BR8  180.00   0.0  0
 ABP  CONST_23  C5    N7   C8   BR8  180.00   0.0  0
 ABP  CONST_24  N6    C6   C5   N7     0.00   0.0  0
 ABP  CONST_25  C4    C5   C6   N6   180.00   0.0  0
 ABP  CONST_26  C2    N1   C6   N6   180.00   0.0  0
 ABP  CONST_27  H2    C2   N1   C6   180.00   0.0  0
 ABP  CONST_28  HN61  N6   C6   C5     0.00   0.0  0
 ABP  CONST_29  HN62  N6   C6   C5   180.00   0.0  0
 ABP  Var_01    C4'   C5'  O5'  PA   -98.74  30.0  3
 ABP  Var_02    O1A   PA   O3A  PB   -26.75  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
 ABP  chir_02  C4'  C5'  O4'  C3'  negativ
 ABP  chir_03  C3'  O3'  C4'  C2'  positiv
 ABP  chir_04  C2'  O2'  C3'  C1'  positiv
 ABP  chir_05  C1'  O4'  N9   C2'  negativ
 ABP  chir_06  PA   O2A  O3A  O5'  both

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
 ABP  plan-1  C1'   0.020
 ABP  plan-1  N9    0.020
 ABP  plan-1  C8    0.020
 ABP  plan-1  BR8   0.020
 ABP  plan-1  N7    0.020
 ABP  plan-1  C5    0.020
 ABP  plan-1  C6    0.020
 ABP  plan-1  N6    0.020
 ABP  plan-1  N1    0.020
 ABP  plan-1  C2    0.020
 ABP  plan-1  N3    0.020
 ABP  plan-1  C4    0.020
 ABP  plan-1  H2    0.020
 ABP  plan-2  C6    0.020
 ABP  plan-2  N6    0.020
 ABP  plan-2  HN61  0.020
 ABP  plan-2  HN62  0.020

