# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Aug  3 04:24:19 2021
#   Inital geometry file: a 116 line input string
#   Ligand name: [[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-[hydroxy-(phosphonoamino)phosphoryl]oxy-phosphoryl]oxymagnesium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](=O)(O[Mg])O[P@](O)(=O)N[P](O)(O)=O)[C@@H](O)[C@H]3O
#
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
 MAP  MAP  '[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-[hydroxy-(phosphonoamino)phosphoryl]oxy-phosphoryl]oxymagnesium'  ligand  48  32  .  2021-08-14  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_MAP
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
 MAP  PG    P   P     0   1.521  33.0153  16.1816  24.0628
 MAP  O1G   O   O     0  -0.674  32.4462  17.3482  23.2997
 MAP  O2G   O   OH1   0  -0.624  34.5866  16.1808  23.8478
 MAP  O3G   O   OH1   0  -0.666  32.4006  14.8411  23.4958
 MAP  PB    P   P     0   1.538  32.7813  17.5904  26.6819
 MAP  O1B   O   O     0  -0.723  33.2122  18.6982  25.7233
 MAP  O2B   O   OH1   0  -0.584  33.5853  17.2906  27.8926
 MAP  N3B   N   NH1   0  -1.007  32.6508  16.2122  25.6745
 MAP  PA    P   P     0   1.418  29.9243  18.4068  26.3205
 MAP  O1A   O   O     0  -0.733  28.8843  17.3584  26.3138
 MAP  O2A   O   OC2   0  -0.667  30.4137  19.0016  24.9944
 MAP  O3A   O   O2    0  -0.586  31.2469  17.8595  27.1321
 MAP  O5'   O   O2    0  -0.576  29.4344  19.6111  27.2673
 MAP  C5'   C   CH2   0  -0.146  30.0657  20.8821  27.2909
 MAP  C4'   C   CH1   0  -0.043  29.3955  21.7158  28.3708
 MAP  O4'   O   O2    0  -0.443  29.5489  21.1467  29.6677
 MAP  C3'   C   CH1   0  -0.105  29.9937  23.1082  28.4849
 MAP  O3'   O   OH1   0  -0.664  29.0346  23.9333  29.0864
 MAP  C2'   C   CH1   0  -0.040  31.1777  22.8471  29.4137
 MAP  O2'   O   OH1   0  -0.687  31.5546  23.9998  30.1022
 MAP  C1'   C   CH1   0   0.198  30.6408  21.7161  30.3223
 MAP  N9    N   NR5   0  -0.590  31.6435  20.6947  30.5592
 MAP  C8    C   CR15  0  -0.150  31.6959  19.4553  29.8933
 MAP  N7    N   N     0  -0.508  32.9333  18.8949  30.2488
 MAP  C5    C   CR56  0   0.084  33.6888  19.8789  30.8558
 MAP  C6    C   CR6   0   0.231  35.0115  19.9988  31.2520
 MAP  N6    N   NH2   0  -0.863  35.9311  19.0028  31.1293
 MAP  N1    N   N     0  -0.452  35.4070  21.1577  31.8214
 MAP  C2    C   CR16  0  -0.100  34.5420  22.1374  31.9504
 MAP  N3    N   N     0  -0.281  33.2570  22.1426  31.5816
 MAP  C4    C   CR56  0   0.354  32.8694  20.9856  31.0550
 MAP  MG    MG  MG    0   1.163  32.1323  19.1002  24.1374
 MAP  HOG2  H   HOH1  0   0.533  35.1083  15.6372  24.4537
 MAP  HOG3  H   HOH1  0   0.512  32.9106  14.0291  23.6167
 MAP  HOB2  H   HOH1  0   0.513  33.3286  18.2195  29.5985
 MAP  HNB1  H   HNH1  0   0.437  32.4105  15.3310  26.1153
 MAP  H5'1  H   HCH2  0   0.182  31.1384  20.7756  27.4798
 MAP  H5'2  H   HCH2  0   0.253  29.9365  21.3905  26.3310
 MAP  H4'   H   HCH1  0   0.216  28.3240  21.7647  28.1581
 MAP  H3'   H   HCH1  0   0.263  30.3183  23.5032  27.5135
 MAP  HO3'  H   HOH1  0   0.455  29.4963  24.6476  29.5409
 MAP  H2'   H   HCH1  0   0.308  32.0080  22.4494  28.8125
 MAP  HO2'  H   HOH1  0   0.440  32.1988  23.7216  30.7763
 MAP  H1'   H   HCH1  0   0.263  30.3249  22.1189  31.2912
 MAP  H8    H   HCR5  0   0.202  30.8178  18.8227  29.8714
 MAP  HN61  H   HNH2  0   0.335  36.8958  19.2872  31.1853
 MAP  HN62  H   HNH2  0   0.326  35.7613  18.2822  30.4469
 MAP  H2    H   HCR6  0   0.167  34.9111  23.0545  32.3953

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
 MAP  PG   O1G   double    1.506  0.020  1.506
 MAP  PG   O2G   single    1.586  0.020  1.586
 MAP  PG   O3G   single    1.580  0.020  1.580
 MAP  PG   N3B   single    1.653  0.020  1.653
 MAP  O2G  HOG2  single    0.832  0.020  0.971
 MAP  O3G  HOG3  single    0.832  0.020  0.971
 MAP  PB   O1B   double    1.527  0.020  1.527
 MAP  PB   O2B   single    1.484  0.020  1.484
 MAP  PB   N3B   single    1.712  0.020  1.712
 MAP  PB   O3A   single    1.622  0.020  1.622
 MAP  O2B  HOB2  single    0.832  0.020  0.971
 MAP  N3B  HNB1  single    0.868  0.020  1.013
 MAP  PA   O1A   double    1.477  0.020  1.477
 MAP  PA   O2A   single    1.534  0.020  1.534
 MAP  PA   O3A   single    1.645  0.020  1.645
 MAP  PA   O5'   single    1.608  0.020  1.608
 MAP  O2A  MG    single    1.923  0.020  1.923
 MAP  O5'  C5'   single    1.419  0.020  1.419
 MAP  C5'  C4'   single    1.520  0.020  1.520
 MAP  C5'  H5'1  single    0.939  0.020  1.096
 MAP  C5'  H5'2  single    0.939  0.020  1.096
 MAP  C4'  O4'   single    1.425  0.020  1.425
 MAP  C4'  C3'   single    1.520  0.020  1.520
 MAP  C4'  H4'   single    0.939  0.020  1.096
 MAP  O4'  C1'   single    1.395  0.020  1.395
 MAP  C3'  O3'   single    1.401  0.020  1.401
 MAP  C3'  C2'   single    1.527  0.020  1.527
 MAP  C3'  H3'   single    0.939  0.020  1.096
 MAP  O3'  HO3'  single    0.832  0.020  0.971
 MAP  C2'  O2'   single    1.395  0.020  1.395
 MAP  C2'  C1'   single    1.547  0.020  1.547
 MAP  C2'  H2'   single    0.939  0.020  1.096
 MAP  O2'  HO2'  single    0.832  0.020  0.971
 MAP  C1'  N9    single    1.451  0.020  1.451
 MAP  C1'  H1'   single    0.939  0.020  1.096
 MAP  N9   C8    aromatic  1.408  0.020  1.408
 MAP  N9   C4    aromatic  1.354  0.020  1.354
 MAP  C8   N7    aromatic  1.404  0.020  1.404
 MAP  C8   H8    single    0.929  0.020  1.085
 MAP  N7   C5    aromatic  1.381  0.020  1.381
 MAP  C5   C6    aromatic  1.386  0.020  1.386
 MAP  C5   C4    aromatic  1.391  0.020  1.391
 MAP  C6   N6    single    1.361  0.020  1.361
 MAP  C6   N1    aromatic  1.350  0.020  1.350
 MAP  N6   HN61  single    0.868  0.020  1.013
 MAP  N6   HN62  single    0.868  0.020  1.013
 MAP  N1   C2    aromatic  1.313  0.020  1.313
 MAP  C2   N3    aromatic  1.337  0.020  1.337
 MAP  C2   H2    single    0.929  0.020  1.085
 MAP  N3   C4    aromatic  1.329  0.020  1.329

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
 MAP  N3B   PG   O3G   106.25  3.000
 MAP  N3B   PG   O2G   110.53  3.000
 MAP  O3G   PG   O2G   109.66  3.000
 MAP  N3B   PG   O1G   113.36  3.000
 MAP  O3G   PG   O1G   109.17  3.000
 MAP  O2G   PG   O1G   107.83  3.000
 MAP  HOG2  O2G  PG    116.74  3.000
 MAP  HOG3  O3G  PG    117.55  3.000
 MAP  O3A   PB   N3B   102.99  3.000
 MAP  O3A   PB   O2B   108.64  3.000
 MAP  N3B   PB   O2B   111.02  3.000
 MAP  O3A   PB   O1B   108.72  3.000
 MAP  N3B   PB   O1B   103.66  3.000
 MAP  O2B   PB   O1B   120.39  3.000
 MAP  HOB2  O2B  PB    122.93  3.000
 MAP  HNB1  N3B  PB    117.50  3.000
 MAP  HNB1  N3B  PG    117.39  3.000
 MAP  PB    N3B  PG    124.88  3.000
 MAP  O5'   PA   O3A   101.74  3.000
 MAP  O5'   PA   O2A   108.41  3.000
 MAP  O3A   PA   O2A   107.40  3.000
 MAP  O5'   PA   O1A   108.65  3.000
 MAP  O3A   PA   O1A   109.40  3.000
 MAP  O2A   PA   O1A   119.75  3.000
 MAP  MG    O2A  PA    133.67  3.000
 MAP  PA    O3A  PB    132.75  3.000
 MAP  C5'   O5'  PA    123.02  3.000
 MAP  H5'2  C5'  H5'1  108.21  3.000
 MAP  H5'2  C5'  C4'   108.45  3.000
 MAP  H5'1  C5'  C4'   111.27  3.000
 MAP  H5'2  C5'  O5'   110.43  3.000
 MAP  H5'1  C5'  O5'   110.59  3.000
 MAP  C4'   C5'  O5'   107.87  3.000
 MAP  H4'   C4'  C3'   111.06  3.000
 MAP  H4'   C4'  O4'   107.48  3.000
 MAP  C3'   C4'  O4'   104.79  3.000
 MAP  H4'   C4'  C5'   108.56  3.000
 MAP  C3'   C4'  C5'   112.48  3.000
 MAP  O4'   C4'  C5'   112.35  3.000
 MAP  C1'   O4'  C4'   110.39  3.000
 MAP  H3'   C3'  C2'   111.74  3.000
 MAP  H3'   C3'  O3'   111.75  3.000
 MAP  C2'   C3'  O3'   111.73  3.000
 MAP  H3'   C3'  C4'   112.31  3.000
 MAP  C2'   C3'  C4'   101.20  3.000
 MAP  O3'   C3'  C4'   107.60  3.000
 MAP  HO3'  O3'  C3'   108.11  3.000
 MAP  H2'   C2'  C1'   108.59  3.000
 MAP  H2'   C2'  O2'   111.40  3.000
 MAP  C1'   C2'  O2'   114.08  3.000
 MAP  H2'   C2'  C3'   108.34  3.000
 MAP  C1'   C2'  C3'   102.31  3.000
 MAP  O2'   C2'  C3'   111.62  3.000
 MAP  HO2'  O2'  C2'   106.54  3.000
 MAP  H1'   C1'  N9    108.28  3.000
 MAP  H1'   C1'  C2'   110.53  3.000
 MAP  N9    C1'  C2'   111.76  3.000
 MAP  H1'   C1'  O4'   109.84  3.000
 MAP  N9    C1'  O4'   109.29  3.000
 MAP  C2'   C1'  O4'   107.13  3.000
 MAP  C4    N9   C8    109.19  3.000
 MAP  C4    N9   C1'   122.30  3.000
 MAP  C8    N9   C1'   124.63  3.000
 MAP  H8    C8   N7    119.13  3.000
 MAP  H8    C8   N9    119.60  3.000
 MAP  N7    C8   N9    105.33  3.000
 MAP  C5    N7   C8    108.00  3.000
 MAP  C4    C5   C6    116.89  3.000
 MAP  C4    C5   N7    107.91  3.000
 MAP  C6    C5   N7    135.18  3.000
 MAP  N1    C6   N6    117.91  3.000
 MAP  N1    C6   C5    118.31  3.000
 MAP  N6    C6   C5    123.76  3.000
 MAP  HN62  N6   HN61  113.66  3.000
 MAP  HN62  N6   C6    118.09  3.000
 MAP  HN61  N6   C6    115.81  3.000
 MAP  C2    N1   C6    119.25  3.000
 MAP  H2    C2   N3    115.92  3.000
 MAP  H2    C2   N1    116.56  3.000
 MAP  N3    C2   N1    127.51  3.000
 MAP  C4    N3   C2    112.72  3.000
 MAP  N3    C4   C5    125.27  3.000
 MAP  N3    C4   N9    126.60  3.000
 MAP  C5    C4   N9    108.06  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
 MAP  CONST_01  C5    N7   C8   N9      0.00   0.0  0
 MAP  CONST_02  N7    C5   C4   N9      0.00   0.0  0
 MAP  CONST_03  C6    C5   C4   N9    180.00   0.0  0
 MAP  CONST_04  C2    N3   C4   N9    180.00   0.0  0
 MAP  CONST_05  C5    C4   N9   C8      0.00   0.0  0
 MAP  CONST_06  N3    C4   N9   C8    180.00   0.0  0
 MAP  CONST_07  C6    C5   N7   C8    180.00   0.0  0
 MAP  CONST_08  C4    C5   N7   C8      0.00   0.0  0
 MAP  CONST_09  C4    N9   C8   N7      0.00   0.0  0
 MAP  CONST_10  N1    C6   C5   N7    180.00   0.0  0
 MAP  CONST_11  N3    C4   C5   N7    180.00   0.0  0
 MAP  CONST_12  C2    N1   C6   C5      0.00   0.0  0
 MAP  CONST_13  C2    N3   C4   C5      0.00   0.0  0
 MAP  CONST_14  N3    C4   C5   C6      0.00   0.0  0
 MAP  CONST_15  N3    C2   N1   C6      0.00   0.0  0
 MAP  CONST_16  C4    C5   C6   N1      0.00   0.0  0
 MAP  CONST_17  C4    N3   C2   N1      0.00   0.0  0
 MAP  CONST_18  N7    C8   N9   C1'   180.00   0.0  0
 MAP  CONST_19  C5    C4   N9   C1'   180.00   0.0  0
 MAP  CONST_20  N3    C4   N9   C1'     0.00   0.0  0
 MAP  CONST_21  N6    C6   C5   N7      0.00   0.0  0
 MAP  CONST_22  C4    C5   C6   N6    180.00   0.0  0
 MAP  CONST_23  C2    N1   C6   N6    180.00   0.0  0
 MAP  CONST_25  H2    C2   N1   C6    180.00   0.0  0
 MAP  Var_01    HN61  N6   C6   C5    162.14  30.0  2
 MAP  Var_02    C4'   C5'  O5'  PA   -175.90  30.0  3
 MAP  Var_03    O1B   PB   N3B  PG      3.02  30.0  3
 MAP  Var_04    PB    N3B  PG   O1G   -45.96  30.0  3
 MAP  Var_05    O1A   PA   O3A  PB    117.69  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
 MAP  chir_03  C4'  C5'  O4'  C3'  negativ
 MAP  chir_04  C3'  O3'  C4'  C2'  positiv
 MAP  chir_05  C2'  O2'  C3'  C1'  positiv
 MAP  chir_06  C1'  O4'  N9   C2'  negativ
 MAP  chir_07  PB   O2B  N3B  O3A  both
 MAP  chir_08  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
 MAP  plan-1  C1'  0.020
 MAP  plan-1  N9   0.020
 MAP  plan-1  C8   0.020
 MAP  plan-1  N7   0.020
 MAP  plan-1  C5   0.020
 MAP  plan-1  C6   0.020
 MAP  plan-1  N6   0.020
 MAP  plan-1  N1   0.020
 MAP  plan-1  C2   0.020
 MAP  plan-1  N3   0.020
 MAP  plan-1  C4   0.020
 MAP  plan-1  H8   0.020
 MAP  plan-1  H2   0.020

