# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Mon Jun  8 18:24:50 2020
#   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  2021-08-14  
;
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   1.431  -5.4780   0.7869  -0.8640
 MAP  O1G   O   O     0  -0.694  -6.6445   1.3669  -1.5539
 MAP  O2G   O   OH1   0  -0.738  -5.0045  -0.6624  -1.3520
 MAP  O3G   O   OH1   0  -0.756  -5.6868   0.6899   0.7105
 MAP  PB    P   P     0   1.471  -2.6866   1.4889  -0.1964
 MAP  O1B   O   O     0  -0.710  -2.9554   0.6995   1.0272
 MAP  O2B   O   OH1   0  -0.718  -2.1174   2.9312   0.1289
 MAP  N3B   N   NH1   0  -0.945  -4.0708   1.6805  -1.0948
 MAP  PA    P   P     0   1.563  -0.1751   0.2216  -0.8274
 MAP  O1A   O   O     0  -0.714   0.4077   0.9113   0.3449
 MAP  O2A   O   OC2   0  -0.776   0.5695   0.2147  -2.1618
 MAP  O3A   O   O2    0  -0.680  -1.6479   0.8362  -1.2362
 MAP  O5'   O   O2    0  -0.591  -0.6399  -1.2925  -0.5162
 MAP  C5'   C   CH2   0  -0.180   0.1338  -2.1367   0.3209
 MAP  C4'   C   CH1   0  -0.032   1.3468  -2.6925  -0.4033
 MAP  O4'   O   O2    0  -0.617   2.3074  -1.6392  -0.6838
 MAP  C3'   C   CH1   0  -0.008   2.1351  -3.6914   0.4237
 MAP  O3'   O   OH1   0  -0.656   2.8705  -4.5034  -0.4483
 MAP  C2'   C   CH1   0  -0.090   3.0580  -2.7682   1.2279
 MAP  O2'   O   OH1   0  -0.650   4.2079  -3.3839   1.7185
 MAP  C1'   C   CH1   0   0.284   3.4414  -1.7244   0.1847
 MAP  N9    N   NR5   0  -0.557   3.7326  -0.4300   0.7175
 MAP  C8    C   CR15  0   0.040   4.0297  -0.0759   2.0226
 MAP  N7    N   N     0  -0.454   4.4288   1.1659   2.0988
 MAP  C5    C   CR56  0  -0.043   4.3996   1.6456   0.8231
 MAP  C6    C   CR6   0   0.285   4.7349   2.9190   0.2447
 MAP  N6    N   NH2   0  -0.833   5.1044   3.9960   1.0427
 MAP  N1    N   N     0  -0.424   4.6276   3.0475  -1.0631
 MAP  C2    C   CR16  0  -0.036   4.1973   2.0562  -1.8338
 MAP  N3    N   N     0  -0.784   3.8023   0.7830  -1.3857
 MAP  C4    C   CR56  0   0.631   3.9729   0.6695  -0.0509
 MAP  MG    MG  MG    0   1.208   2.4060  -0.3560  -2.2974
 MAP  HOG2  H   HOH1  0   0.498  -5.6559  -1.3641  -1.2130
 MAP  HOG3  H   HOH1  0   0.490  -4.8524   0.5196   1.1923
 MAP  HOB2  H   HOH1  0   0.506  -1.7247   3.4292  -0.6011
 MAP  HNB1  H   HNH1  0   0.450  -4.0638   2.3045  -1.8943
 MAP  H5'1  H   HCH2  0   0.274  -0.5103  -2.9728   0.5944
 MAP  H5'2  H   HCH2  0   0.246   0.4167  -1.6168   1.2404
 MAP  H4'   H   HCH1  0   0.313   1.0383  -3.1208  -1.3596
 MAP  H3'   H   HCH1  0   0.271   1.4820  -4.2760   1.0831
 MAP  HO3'  H   HOH1  0   0.457   3.5837  -4.9149   0.0544
 MAP  H2'   H   HCH1  0   0.265   2.4714  -2.3004   2.0274
 MAP  HO2'  H   HOH1  0   0.476   4.0033  -3.7994   2.5628
 MAP  H1'   H   HCH1  0   0.301   4.2940  -2.0686  -0.4091
 MAP  H8    H   HCR5  0   0.276   3.9505  -0.7664   2.8457
 MAP  HN61  H   HNH2  0   0.361   5.5803   4.7200   0.5242
 MAP  HN62  H   HNH2  0   0.365   5.6548   3.7283   1.8467
 MAP  H2    H   HCR6  0   0.227   4.1288   2.2279  -2.8995

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    1.474  0.020  1.474
 MAP  PG   O2G   single    1.601  0.020  1.601
 MAP  PG   O3G   single    1.591  0.020  1.591
 MAP  PG   N3B   single    1.683  0.020  1.683
 MAP  O2G  HOG2  single    0.850  0.020  0.980
 MAP  O3G  HOG3  single    0.850  0.020  0.980
 MAP  PB   O1B   double    1.481  0.020  1.481
 MAP  PB   O2B   single    1.584  0.020  1.584
 MAP  PB   N3B   single    1.661  0.020  1.661
 MAP  PB   O3A   single    1.608  0.020  1.608
 MAP  O2B  HOB2  single    0.850  0.020  0.980
 MAP  N3B  HNB1  single    0.860  0.020  1.020
 MAP  PA   O1A   double    1.480  0.020  1.480
 MAP  PA   O2A   single    1.528  0.020  1.528
 MAP  PA   O3A   single    1.647  0.020  1.647
 MAP  PA   O5'   single    1.614  0.020  1.614
 MAP  O2A  MG    single    1.928  0.020  1.928
 MAP  O5'  C5'   single    1.418  0.020  1.418
 MAP  C5'  C4'   single    1.518  0.020  1.518
 MAP  C5'  H5'1  single    0.970  0.020  1.090
 MAP  C5'  H5'2  single    0.970  0.020  1.090
 MAP  C4'  O4'   single    1.453  0.020  1.453
 MAP  C4'  C3'   single    1.518  0.020  1.518
 MAP  C4'  H4'   single    0.970  0.020  1.090
 MAP  O4'  C1'   single    1.431  0.020  1.431
 MAP  C3'  O3'   single    1.400  0.020  1.400
 MAP  C3'  C2'   single    1.533  0.020  1.533
 MAP  C3'  H3'   single    0.970  0.020  1.090
 MAP  O3'  HO3'  single    0.850  0.020  0.980
 MAP  C2'  O2'   single    1.394  0.020  1.394
 MAP  C2'  C1'   single    1.525  0.020  1.525
 MAP  C2'  H2'   single    0.970  0.020  1.090
 MAP  O2'  HO2'  single    0.850  0.020  0.980
 MAP  C1'  N9    single    1.430  0.020  1.430
 MAP  C1'  H1'   single    0.970  0.020  1.090
 MAP  N9   C8    aromatic  1.385  0.020  1.385
 MAP  N9   C4    aromatic  1.363  0.020  1.363
 MAP  C8   N7    aromatic  1.307  0.020  1.307
 MAP  C8   H8    single    0.930  0.020  1.080
 MAP  N7   C5    aromatic  1.363  0.020  1.363
 MAP  C5   C6    aromatic  1.438  0.020  1.438
 MAP  C5   C4    aromatic  1.378  0.020  1.378
 MAP  C6   N6    single    1.391  0.020  1.391
 MAP  C6   N1    aromatic  1.319  0.020  1.319
 MAP  N6   HN61  single    0.890  0.020  1.040
 MAP  N6   HN62  single    0.890  0.020  1.040
 MAP  N1   C2    aromatic  1.327  0.020  1.327
 MAP  C2   N3    aromatic  1.406  0.020  1.406
 MAP  C2   H2    single    0.930  0.020  1.080
 MAP  N3   C4    aromatic  1.350  0.020  1.350

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   106.13  3.000
 MAP  N3B   PG   O2G   101.04  3.000
 MAP  O3G   PG   O2G   106.57  3.000
 MAP  N3B   PG   O1G   112.87  3.000
 MAP  O3G   PG   O1G   112.54  3.000
 MAP  O2G   PG   O1G   116.59  3.000
 MAP  HOG2  O2G  PG    114.43  3.000
 MAP  HOG3  O3G  PG    112.71  3.000
 MAP  O3A   PB   N3B   103.61  3.000
 MAP  O3A   PB   O2B   105.68  3.000
 MAP  N3B   PB   O2B   107.78  3.000
 MAP  O3A   PB   O1B   115.79  3.000
 MAP  N3B   PB   O1B   110.92  3.000
 MAP  O2B   PB   O1B   112.39  3.000
 MAP  HOB2  O2B  PB    117.37  3.000
 MAP  HNB1  N3B  PB    119.44  3.000
 MAP  HNB1  N3B  PG    116.14  3.000
 MAP  PB    N3B  PG    124.15  3.000
 MAP  O5'   PA   O3A    98.07  3.000
 MAP  O5'   PA   O2A   107.73  3.000
 MAP  O3A   PA   O2A   102.75  3.000
 MAP  O5'   PA   O1A   113.44  3.000
 MAP  O3A   PA   O1A   112.01  3.000
 MAP  O2A   PA   O1A   120.13  3.000
 MAP  MG    O2A  PA    121.80  3.000
 MAP  PA    O3A  PB    124.64  3.000
 MAP  C5'   O5'  PA    121.00  3.000
 MAP  H5'2  C5'  H5'1  107.85  3.000
 MAP  H5'2  C5'  C4'   111.62  3.000
 MAP  H5'1  C5'  C4'   108.12  3.000
 MAP  H5'2  C5'  O5'   110.76  3.000
 MAP  H5'1  C5'  O5'   106.39  3.000
 MAP  C4'   C5'  O5'   111.85  3.000
 MAP  H4'   C4'  C3'   111.45  3.000
 MAP  H4'   C4'  O4'   107.57  3.000
 MAP  C3'   C4'  O4'   103.82  3.000
 MAP  H4'   C4'  C5'   109.61  3.000
 MAP  C3'   C4'  C5'   113.33  3.000
 MAP  O4'   C4'  C5'   110.79  3.000
 MAP  C1'   O4'  C4'   111.32  3.000
 MAP  H3'   C3'  C2'   111.35  3.000
 MAP  H3'   C3'  O3'   112.21  3.000
 MAP  C2'   C3'  O3'   111.08  3.000
 MAP  H3'   C3'  C4'   111.66  3.000
 MAP  C2'   C3'  C4'   101.66  3.000
 MAP  O3'   C3'  C4'   108.37  3.000
 MAP  HO3'  O3'  C3'   108.13  3.000
 MAP  H2'   C2'  C1'   109.96  3.000
 MAP  H2'   C2'  O2'   111.91  3.000
 MAP  C1'   C2'  O2'   109.62  3.000
 MAP  H2'   C2'  C3'   108.50  3.000
 MAP  C1'   C2'  C3'   101.81  3.000
 MAP  O2'   C2'  C3'   114.54  3.000
 MAP  HO2'  O2'  C2'   108.91  3.000
 MAP  H1'   C1'  N9    109.16  3.000
 MAP  H1'   C1'  C2'   110.60  3.000
 MAP  N9    C1'  C2'   114.58  3.000
 MAP  H1'   C1'  O4'   107.87  3.000
 MAP  N9    C1'  O4'   109.49  3.000
 MAP  C2'   C1'  O4'   104.88  3.000
 MAP  C4    N9   C8    106.69  3.000
 MAP  C4    N9   C1'   123.80  3.000
 MAP  C8    N9   C1'   128.80  3.000
 MAP  H8    C8   N7    125.95  3.000
 MAP  H8    C8   N9    122.71  3.000
 MAP  N7    C8   N9    111.32  3.000
 MAP  C5    N7   C8    105.86  3.000
 MAP  C4    C5   C6    116.38  3.000
 MAP  C4    C5   N7    110.54  3.000
 MAP  C6    C5   N7    133.07  3.000
 MAP  N1    C6   N6    121.03  3.000
 MAP  N1    C6   C5    117.79  3.000
 MAP  N6    C6   C5    121.13  3.000
 MAP  HN62  N6   HN61  109.99  3.000
 MAP  HN62  N6   C6    113.34  3.000
 MAP  HN61  N6   C6    112.70  3.000
 MAP  C2    N1   C6    121.97  3.000
 MAP  H2    C2   N3    116.10  3.000
 MAP  H2    C2   N1    118.30  3.000
 MAP  N3    C2   N1    125.60  3.000
 MAP  C4    N3   C2    110.83  3.000
 MAP  N3    C4   C5    127.33  3.000
 MAP  N3    C4   N9    127.08  3.000
 MAP  C5    C4   N9    105.58  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_24  H8    C8   N9   C1'    0.00   0.0  0
 MAP  CONST_25  H2    C2   N1   C6   180.00   0.0  0
 MAP  Var_01    HN61  N6   C6   C5   162.17  30.0  2
 MAP  Var_02    C4'   C5'  O5'  PA   -77.64  30.0  3
 MAP  Var_03    O1B   PB   N3B  PG   -14.42  30.0  3
 MAP  Var_04    PB    N3B  PG   O1G  165.93  30.0  3
 MAP  Var_05    O1A   PA   O3A  PB   -30.07  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
 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

