# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Aug  1 02:27:14 2021
#   Inital geometry file: a 133 line input string
#   Ligand name: a 2 line input string
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P@](O)(=O)O[P](O)(O)=O)n2cnc3c(NCc4ccccc4)ncnc23
#
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
 NBS  NBS  'N-benzyladenosine 5'-(trihydrogen diphosphate)'  ligand  55  34  .  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_NBS
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
 NBS  PB    P  P     0   1.457  -4.8901  48.9085  -2.1874
 NBS  O4P   O  OH1   0  -0.711  -4.6833  49.0918  -3.7430
 NBS  O5P   O  OH1   0  -0.723  -6.1041  49.9037  -1.9751
 NBS  O6P   O  O     0  -0.685  -4.9881  47.5466  -1.6375
 NBS  PA    P  P     0   1.484  -3.3516  49.9325  -0.0006
 NBS  O1P   O  OH1   0  -0.740  -2.3445  51.1459   0.0282
 NBS  O2P   O  O     0  -0.682  -4.6073  50.1562   0.7339
 NBS  O3P   O  O2    0  -0.702  -3.5919  49.7063  -1.5902
 NBS  O5'   O  O2    0  -0.583  -2.5704  48.6428   0.4972
 NBS  C5'   C  CH2   0  -0.189  -1.6666  47.8197  -0.2428
 NBS  C4'   C  CH1   0  -0.085  -0.5607  48.5981  -0.9486
 NBS  O4'   O  O2    0  -0.542  -0.0971  49.6763  -0.1261
 NBS  C1'   C  CH1   0   0.245   1.1862  49.4139   0.3928
 NBS  N9    N  NR5   0  -0.550   1.2175  49.7752   1.7818
 NBS  C4    C  CR56  0   0.496   2.1600  50.5576   2.3866
 NBS  N3    N  N     0  -0.456   3.2178  51.1295   1.8235
 NBS  C2    C  CR16  0   0.048   3.9195  51.8239   2.7035
 NBS  N1    N  N     0  -0.478   3.6796  51.9871   3.9971
 NBS  C6    C  CR6   0   0.484   2.6069  51.4071   4.5565
 NBS  N6    N  NH1   0  -0.629   2.4238  51.6142   5.8651
 NBS  CB1   C  CH2   0  -0.366   1.3142  51.1686   6.6714
 NBS  CB2   C  CR6   0   0.109   0.2155  52.1950   6.8303
 NBS  CB3   C  CR16  0  -0.306  -0.4694  52.2850   8.0388
 NBS  CB4   C  CR16  0  -0.242  -1.5073  53.1930   8.2031
 NBS  CB5   C  CR16  0  -0.270  -1.8712  54.0294   7.1565
 NBS  CB6   C  CR16  0  -0.240  -1.1901  53.9495   5.9486
 NBS  CB7   C  CR16  0  -0.293  -0.1553  53.0384   5.7864
 NBS  C5    C  CR56  0  -0.016   1.7755  50.6319   3.7206
 NBS  N7    N  N     0  -0.449   0.6188  49.9162   3.9215
 NBS  C8    C  CR15  0   0.119   0.3232  49.4242   2.7592
 NBS  C2'   C  CH1   0  -0.059   1.4288  47.9284   0.1195
 NBS  O2'   O  OH1   0  -0.649   2.7986  47.6891   0.0323
 NBS  C3'   C  CH1   0  -0.021   0.6590  47.7230  -1.1914
 NBS  O3'   O  OH1   0  -0.661   1.3722  48.2407  -2.2789
 NBS  HOP4  H  HOH1  0   0.514  -4.3256  48.3145  -4.1939
 NBS  HOP5  H  HOH1  0   0.503  -6.3712  50.0225  -1.0514
 NBS  HOP1  H  HOH1  0   0.505  -1.3948  50.8987   0.0078
 NBS  H5'1  H  HCH2  0   0.269  -1.2545  47.1321   0.4954
 NBS  H5'2  H  HCH2  0   0.278  -2.2144  47.2257  -0.9769
 NBS  H4'   H  HCH1  0   0.297  -0.9303  49.0254  -1.8842
 NBS  H1'   H  HCH1  0   0.284   1.9435  50.0248  -0.1066
 NBS  H2    H  HCR6  0   0.255   4.8033  52.3249   2.3235
 NBS  H6    H  HNH1  0   0.397   3.0817  52.2471   6.2944
 NBS  HB11  H  HCH2  0   0.282   0.9036  50.2569   6.2394
 NBS  HB12  H  HCH2  0   0.277   1.7026  50.8992   7.6544
 NBS  HB3   H  HCR6  0   0.251  -0.1861  51.6409   8.8637
 NBS  HB4   H  HCR6  0   0.255  -2.0260  53.2513   9.1515
 NBS  HB5   H  HCR6  0   0.256  -2.6765  54.7418   7.2807
 NBS  HB6   H  HCR6  0   0.255  -1.4647  54.6001   5.1281
 NBS  HB7   H  HCR6  0   0.247   0.3652  52.9986   4.8374
 NBS  H8    H  HCR5  0   0.299  -0.5416  48.8110   2.5541
 NBS  H2'   H  HCH1  0   0.261   0.9636  47.3285   0.9117
 NBS  HO'2  H  HOH1  0   0.474   2.9651  46.7546   0.1934
 NBS  H3'   H  HCH1  0   0.269   0.3809  46.6713  -1.3425
 NBS  HO'3  H  HOH1  0   0.455   2.2866  47.9413  -2.2054

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
 NBS  PB   O4P   single    1.580  0.020  1.580
 NBS  PB   O5P   single    1.584  0.020  1.584
 NBS  PB   O6P   double    1.472  0.020  1.472
 NBS  PB   O3P   single    1.637  0.020  1.637
 NBS  O4P  HOP4  single    0.850  0.020  0.980
 NBS  O5P  HOP5  single    0.850  0.020  0.980
 NBS  PA   O1P   single    1.577  0.020  1.577
 NBS  PA   O2P   double    1.472  0.020  1.472
 NBS  PA   O3P   single    1.624  0.020  1.624
 NBS  PA   O5'   single    1.588  0.020  1.588
 NBS  O1P  HOP1  single    0.850  0.020  0.980
 NBS  O5'  C5'   single    1.429  0.020  1.429
 NBS  C5'  C4'   single    1.525  0.020  1.525
 NBS  C5'  H5'1  single    0.970  0.020  1.090
 NBS  C5'  H5'2  single    0.970  0.020  1.090
 NBS  C4'  O4'   single    1.433  0.020  1.433
 NBS  C4'  C3'   single    1.521  0.020  1.521
 NBS  C4'  H4'   single    0.970  0.020  1.090
 NBS  O4'  C1'   single    1.409  0.020  1.409
 NBS  C1'  N9    single    1.436  0.020  1.436
 NBS  C1'  C2'   single    1.530  0.020  1.530
 NBS  C1'  H1'   single    0.970  0.020  1.090
 NBS  N9   C4    aromatic  1.366  0.020  1.366
 NBS  N9   C8    aromatic  1.370  0.020  1.370
 NBS  C4   N3    aromatic  1.328  0.020  1.328
 NBS  C4   C5    aromatic  1.390  0.020  1.390
 NBS  N3   C2    aromatic  1.322  0.020  1.322
 NBS  C2   N1    aromatic  1.326  0.020  1.326
 NBS  C2   H2    single    0.930  0.020  1.080
 NBS  N1   C6    aromatic  1.342  0.020  1.342
 NBS  C6   N6    single    1.337  0.020  1.337
 NBS  C6   C5    aromatic  1.411  0.020  1.411
 NBS  N6   CB1   single    1.442  0.020  1.442
 NBS  N6   H6    single    0.860  0.020  1.020
 NBS  CB1  CB2   single    1.512  0.020  1.512
 NBS  CB1  HB11  single    0.970  0.020  1.090
 NBS  CB1  HB12  single    0.970  0.020  1.090
 NBS  CB2  CB3   aromatic  1.392  0.020  1.392
 NBS  CB2  CB7   aromatic  1.392  0.020  1.392
 NBS  CB3  CB4   aromatic  1.389  0.020  1.389
 NBS  CB3  HB3   single    0.930  0.020  1.080
 NBS  CB4  CB5   aromatic  1.388  0.020  1.388
 NBS  CB4  HB4   single    0.930  0.020  1.080
 NBS  CB5  CB6   aromatic  1.389  0.020  1.389
 NBS  CB5  HB5   single    0.930  0.020  1.080
 NBS  CB6  CB7   aromatic  1.388  0.020  1.388
 NBS  CB6  HB6   single    0.930  0.020  1.080
 NBS  CB7  HB7   single    0.930  0.020  1.080
 NBS  C5   N7    aromatic  1.375  0.020  1.375
 NBS  N7   C8    aromatic  1.296  0.020  1.296
 NBS  C8   H8    single    0.930  0.020  1.080
 NBS  C2'  O2'   single    1.393  0.020  1.393
 NBS  C2'  C3'   single    1.534  0.020  1.534
 NBS  C2'  H2'   single    0.970  0.020  1.090
 NBS  O2'  HO'2  single    0.850  0.020  0.980
 NBS  C3'  O3'   single    1.400  0.020  1.400
 NBS  C3'  H3'   single    0.970  0.020  1.090
 NBS  O3'  HO'3  single    0.850  0.020  0.980

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
 NBS  O3P   PB   O6P   111.56  3.000
 NBS  O3P   PB   O5P   104.64  3.000
 NBS  O6P   PB   O5P   118.70  3.000
 NBS  O3P   PB   O4P   101.47  3.000
 NBS  O6P   PB   O4P   118.94  3.000
 NBS  O5P   PB   O4P    99.17  3.000
 NBS  HOP4  O4P  PB    114.47  3.000
 NBS  HOP5  O5P  PB    114.59  3.000
 NBS  O5'   PA   O3P   105.46  3.000
 NBS  O5'   PA   O2P   112.75  3.000
 NBS  O3P   PA   O2P   112.55  3.000
 NBS  O5'   PA   O1P   107.76  3.000
 NBS  O3P   PA   O1P   102.69  3.000
 NBS  O2P   PA   O1P   114.76  3.000
 NBS  HOP1  O1P  PA    115.07  3.000
 NBS  PA    O3P  PB    122.86  3.000
 NBS  C5'   O5'  PA    128.08  3.000
 NBS  H5'2  C5'  H5'1  107.58  3.000
 NBS  H5'2  C5'  C4'   109.29  3.000
 NBS  H5'1  C5'  C4'   111.17  3.000
 NBS  H5'2  C5'  O5'   110.14  3.000
 NBS  H5'1  C5'  O5'   104.59  3.000
 NBS  C4'   C5'  O5'   113.84  3.000
 NBS  H4'   C4'  C3'   111.07  3.000
 NBS  H4'   C4'  O4'   107.85  3.000
 NBS  C3'   C4'  O4'   105.37  3.000
 NBS  H4'   C4'  C5'   110.51  3.000
 NBS  C3'   C4'  C5'   111.21  3.000
 NBS  O4'   C4'  C5'   110.66  3.000
 NBS  C1'   O4'  C4'   111.46  3.000
 NBS  H1'   C1'  C2'   110.55  3.000
 NBS  H1'   C1'  N9    106.63  3.000
 NBS  C2'   C1'  N9    114.44  3.000
 NBS  H1'   C1'  O4'   111.01  3.000
 NBS  C2'   C1'  O4'   105.04  3.000
 NBS  N9    C1'  O4'   109.23  3.000
 NBS  C8    N9   C4    106.33  3.000
 NBS  C8    N9   C1'   127.68  3.000
 NBS  C4    N9   C1'   125.98  3.000
 NBS  C5    C4   N3    127.17  3.000
 NBS  C5    C4   N9    105.34  3.000
 NBS  N3    C4   N9    127.49  3.000
 NBS  C2    N3   C4    111.52  3.000
 NBS  H2    C2   N1    115.62  3.000
 NBS  H2    C2   N3    116.22  3.000
 NBS  N1    C2   N3    128.16  3.000
 NBS  C6    N1   C2    119.89  3.000
 NBS  C5    C6   N6    125.73  3.000
 NBS  C5    C6   N1    117.49  3.000
 NBS  N6    C6   N1    116.78  3.000
 NBS  H6    N6   CB1   117.23  3.000
 NBS  H6    N6   C6    115.10  3.000
 NBS  CB1   N6   C6    127.20  3.000
 NBS  HB12  CB1  HB11  106.55  3.000
 NBS  HB12  CB1  CB2   109.37  3.000
 NBS  HB11  CB1  CB2   109.63  3.000
 NBS  HB12  CB1  N6    107.83  3.000
 NBS  HB11  CB1  N6    109.08  3.000
 NBS  CB2   CB1  N6    114.09  3.000
 NBS  CB7   CB2  CB3   118.73  3.000
 NBS  CB7   CB2  CB1   121.73  3.000
 NBS  CB3   CB2  CB1   119.52  3.000
 NBS  HB3   CB3  CB4   119.58  3.000
 NBS  HB3   CB3  CB2   119.57  3.000
 NBS  CB4   CB3  CB2   120.85  3.000
 NBS  HB4   CB4  CB5   120.16  3.000
 NBS  HB4   CB4  CB3   119.80  3.000
 NBS  CB5   CB4  CB3   120.04  3.000
 NBS  HB5   CB5  CB6   120.16  3.000
 NBS  HB5   CB5  CB4   120.34  3.000
 NBS  CB6   CB5  CB4   119.49  3.000
 NBS  HB6   CB6  CB7   119.66  3.000
 NBS  HB6   CB6  CB5   120.01  3.000
 NBS  CB7   CB6  CB5   120.33  3.000
 NBS  HB7   CB7  CB6   118.99  3.000
 NBS  HB7   CB7  CB2   120.45  3.000
 NBS  CB6   CB7  CB2   120.56  3.000
 NBS  N7    C5   C6    134.03  3.000
 NBS  N7    C5   C4    110.18  3.000
 NBS  C6    C5   C4    115.78  3.000
 NBS  C8    N7   C5    104.97  3.000
 NBS  H8    C8   N7    124.64  3.000
 NBS  H8    C8   N9    122.18  3.000
 NBS  N7    C8   N9    113.17  3.000
 NBS  H2'   C2'  C3'   109.33  3.000
 NBS  H2'   C2'  O2'   111.60  3.000
 NBS  C3'   C2'  O2'   114.64  3.000
 NBS  H2'   C2'  C1'   109.55  3.000
 NBS  C3'   C2'  C1'   101.72  3.000
 NBS  O2'   C2'  C1'   109.51  3.000
 NBS  HO'2  O2'  C2'   109.04  3.000
 NBS  H3'   C3'  O3'   112.11  3.000
 NBS  H3'   C3'  C2'   111.89  3.000
 NBS  O3'   C3'  C2'   111.02  3.000
 NBS  H3'   C3'  C4'   111.71  3.000
 NBS  O3'   C3'  C4'   108.66  3.000
 NBS  C2'   C3'  C4'   100.89  3.000
 NBS  HO'3  O3'  C3'   108.00  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
 NBS  CONST_01  C2   N3   C4   N9    180.00   0.0  0
 NBS  CONST_02  C6   C5   C4   N9    180.00   0.0  0
 NBS  CONST_03  N7   C5   C4   N9      0.00   0.0  0
 NBS  CONST_04  C5   N7   C8   N9      0.00   0.0  0
 NBS  CONST_05  N7   C8   N9   C4      0.00   0.0  0
 NBS  CONST_06  N1   C2   N3   C4      0.00   0.0  0
 NBS  CONST_07  N1   C6   C5   C4      0.00   0.0  0
 NBS  CONST_08  C8   N7   C5   C4      0.00   0.0  0
 NBS  CONST_09  C8   N9   C4   N3    180.00   0.0  0
 NBS  CONST_10  C6   C5   C4   N3      0.00   0.0  0
 NBS  CONST_11  N7   C5   C4   N3    180.00   0.0  0
 NBS  CONST_12  C6   N1   C2   N3      0.00   0.0  0
 NBS  CONST_13  C5   C4   N3   C2      0.00   0.0  0
 NBS  CONST_14  C5   C6   N1   C2      0.00   0.0  0
 NBS  CONST_15  N7   C5   C6   N1    180.00   0.0  0
 NBS  CONST_16  C8   N7   C5   C6    180.00   0.0  0
 NBS  CONST_17  CB5  CB4  CB3  CB2     0.00   0.0  0
 NBS  CONST_18  CB5  CB6  CB7  CB2     0.00   0.0  0
 NBS  CONST_19  CB6  CB7  CB2  CB3     0.00   0.0  0
 NBS  CONST_20  CB6  CB5  CB4  CB3     0.00   0.0  0
 NBS  CONST_21  CB7  CB2  CB3  CB4     0.00   0.0  0
 NBS  CONST_22  CB7  CB6  CB5  CB4     0.00   0.0  0
 NBS  CONST_23  C8   N9   C4   C5      0.00   0.0  0
 NBS  CONST_24  N3   C4   N9   C1'     0.00   0.0  0
 NBS  CONST_25  C5   C4   N9   C1'   180.00   0.0  0
 NBS  CONST_26  N7   C8   N9   C1'   180.00   0.0  0
 NBS  CONST_27  N6   C6   C5   C4    180.00   0.0  0
 NBS  CONST_28  N6   C6   N1   C2    180.00   0.0  0
 NBS  CONST_29  N7   C5   C6   N6      0.00   0.0  0
 NBS  CONST_30  CB4  CB3  CB2  CB1   180.00   0.0  0
 NBS  CONST_31  CB6  CB7  CB2  CB1   180.00   0.0  0
 NBS  CONST_32  H8   C8   N9   C1'     0.00   0.0  0
 NBS  CONST_33  H2   C2   N3   C4    180.00   0.0  0
 NBS  CONST_34  HB4  CB4  CB3  CB2   180.00   0.0  0
 NBS  CONST_35  HB6  CB6  CB7  CB2   180.00   0.0  0
 NBS  CONST_36  HB7  CB7  CB2  CB3   180.00   0.0  0
 NBS  CONST_37  HB5  CB5  CB4  CB3   180.00   0.0  0
 NBS  CONST_38  HB3  CB3  CB4  CB5   180.00   0.0  0
 NBS  CONST_39  CB1  N6   C6   N1    180.00   0.0  0
 NBS  CONST_40  C5   C6   N6   CB1     0.00   0.0  0
 NBS  CONST_41  H6   N6   C6   N1      0.00   0.0  0
 NBS  Var_01    CB2  CB1  N6   C6    -94.79  30.0  3
 NBS  Var_02    CB3  CB2  CB1  N6   -144.03  30.0  2
 NBS  Var_03    C4'  C5'  O5'  PA     51.11  30.0  3
 NBS  Var_04    O1P  PA   O3P  PB   -159.80  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
 NBS  chir_02  C4'  C5'  O4'  C3'  negativ
 NBS  chir_03  C1'  O4'  N9   C2'  negativ
 NBS  chir_04  C2'  O2'  C1'  C3'  negativ
 NBS  chir_05  C3'  O3'  C4'  C2'  positiv
 NBS  chir_06  PA   O2P  O3P  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
 NBS  plan-1  CB1  0.020
 NBS  plan-1  CB2  0.020
 NBS  plan-1  CB3  0.020
 NBS  plan-1  CB4  0.020
 NBS  plan-1  CB5  0.020
 NBS  plan-1  CB6  0.020
 NBS  plan-1  CB7  0.020
 NBS  plan-1  HB3  0.020
 NBS  plan-1  HB4  0.020
 NBS  plan-1  HB5  0.020
 NBS  plan-1  HB6  0.020
 NBS  plan-1  HB7  0.020
 NBS  plan-2  C1'  0.020
 NBS  plan-2  N9   0.020
 NBS  plan-2  C4   0.020
 NBS  plan-2  N3   0.020
 NBS  plan-2  C2   0.020
 NBS  plan-2  N1   0.020
 NBS  plan-2  C6   0.020
 NBS  plan-2  N6   0.020
 NBS  plan-2  C5   0.020
 NBS  plan-2  N7   0.020
 NBS  plan-2  C8   0.020
 NBS  plan-2  H2   0.020
 NBS  plan-2  H8   0.020
 NBS  plan-3  C6   0.020
 NBS  plan-3  N6   0.020
 NBS  plan-3  CB1  0.020
 NBS  plan-3  H6   0.020

