# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Mon Jun 22 05:01:30 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: {5'-O-[(R)-{[(S)-amino(hydroxy-kappaO)phosphoryl]oxy}(hydroxy-kappaO)phosphoryl]adenosinato(2-)}magnesium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@]4(=O)O[Mg]O[P@](N)(=O)O4)[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
 APW  APW  {5'-O-[(R)-{[(S)-amino(hydroxy-kappaO)phosphoryl]oxy}(hydroxy-kappaO)phosphoryl]adenosinato(2-)}magnesium  ligand  42  28  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_APW
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
 APW  MG    MG  MG    0   1.072  -3.8303   1.7707  -0.8225
 APW  O2A   O   O2    0  -0.757  -3.2319   0.3648   0.3089
 APW  PA    P   P     0   1.514  -1.8103  -0.1539   0.5638
 APW  O1A   O   O     0  -0.689  -1.3120  -0.1832   1.9618
 APW  O3A   O   O2    0  -0.581  -0.8233   0.6720  -0.4319
 APW  PB    P   P     0   1.308  -0.8113   2.2872  -0.7501
 APW  O1B   O   O     0  -0.791   0.3505   2.5461  -1.6392
 APW  O2B   O   O2    0  -0.758  -2.2056   2.6510  -1.3115
 APW  N3B   N   NH2   0  -0.860  -0.7726   2.9196   0.8045
 APW  O5'   O   O2    0  -0.548  -1.7864  -1.6148  -0.1248
 APW  C5'   C   CH2   0  -0.242  -1.0354  -2.6770   0.4418
 APW  C4'   C   CH1   0  -0.046   0.2029  -2.9845  -0.3838
 APW  C3'   C   CH1   0   0.043   1.1755  -3.8411   0.4166
 APW  O3'   O   OH1   0  -0.589   1.9683  -4.5884  -0.4679
 APW  C2'   C   CH1   0  -0.125   2.0009  -2.7561   1.1200
 APW  O2'   O   OH1   0  -0.698   3.2711  -3.1544   1.5367
 APW  C1'   C   CH1   0   0.257   2.1126  -1.7176   0.0075
 APW  O4'   O   O2    0  -0.422   0.9042  -1.7874  -0.6987
 APW  N9    N   NR5   0  -0.527   2.3277  -0.3670   0.4518
 APW  C4    C   CR56  0   0.384   2.9096   0.6087  -0.3131
 APW  C5    C   CR56  0  -0.004   2.7276   1.7841   0.3891
 APW  N7    N   N     0  -0.460   2.0206   1.5530   1.5432
 APW  C8    C   CR15  0   0.149   1.7963   0.2723   1.5389
 APW  N3    N   N     0  -0.436   3.5223   0.4742  -1.4852
 APW  C2    C   CR16  0   0.044   3.9599   1.6342  -1.9421
 APW  N1    N   N     0  -0.430   3.8573   2.8355  -1.3811
 APW  C6    C   CR6   0   0.469   3.2280   2.9539  -0.2069
 APW  N6    N   NH2   0  -0.812   3.0937   4.1623   0.3424
 APW  H3B1  H   HNH2  0   0.405   0.0628   2.6709   1.3250
 APW  H3B2  H   HNH2  0   0.398  -0.9106   3.9220   0.8359
 APW  H5'1  H   HCH2  0   0.284  -1.6712  -3.5656   0.4593
 APW  H5'2  H   HCH2  0   0.249  -0.7730  -2.4510   1.4778
 APW  H4'   H   HCH1  0   0.264  -0.0808  -3.4760  -1.3191
 APW  H3'   H   HCH1  0   0.237   0.6546  -4.4864   1.1371
 APW  H2    H   HOH1  0   0.443   2.7453  -4.8957   0.0138
 APW  H1    H   HCH1  0   0.235   1.4078  -2.3604   1.9535
 APW  H2'   H   HOH1  0   0.442   3.1947  -3.5973   2.3877
 APW  H1'   H   HCH1  0   0.253   2.9576  -1.9584  -0.6459
 APW  H8    H   HCR5  0   0.262   1.2338  -0.2517   2.2950
 APW  H3    H   HCR6  0   0.267   4.4854   1.6058  -2.8909
 APW  HN61  H   HNH2  0   0.394   3.5423   4.9581  -0.0773
 APW  HN62  H   HNH2  0   0.401   2.7126   4.2723   1.2653

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
 APW  MG   O2A   single    1.901  0.020  1.901
 APW  MG   O2B   single    1.912  0.020  1.912
 APW  O2A  PA    single    1.535  0.020  1.535
 APW  PA   O1A   double    1.484  0.020  1.484
 APW  PA   O3A   single    1.627  0.020  1.627
 APW  PA   O5'   single    1.615  0.020  1.615
 APW  O3A  PB    single    1.646  0.020  1.646
 APW  PB   O1B   double    1.486  0.020  1.486
 APW  PB   O2B   single    1.546  0.020  1.546
 APW  PB   N3B   single    1.679  0.020  1.679
 APW  N3B  H3B1  single    0.890  0.020  1.040
 APW  N3B  H3B2  single    0.890  0.020  1.040
 APW  O5'  C5'   single    1.419  0.020  1.419
 APW  C5'  C4'   single    1.520  0.020  1.520
 APW  C5'  H5'1  single    0.970  0.020  1.090
 APW  C5'  H5'2  single    0.970  0.020  1.090
 APW  C4'  C3'   single    1.523  0.020  1.523
 APW  C4'  O4'   single    1.423  0.020  1.423
 APW  C4'  H4'   single    0.970  0.020  1.090
 APW  C3'  O3'   single    1.403  0.020  1.403
 APW  C3'  C2'   single    1.534  0.020  1.534
 APW  C3'  H3'   single    0.970  0.020  1.090
 APW  O3'  H2    single    0.850  0.020  0.980
 APW  C2'  O2'   single    1.395  0.020  1.395
 APW  C2'  C1'   single    1.526  0.020  1.526
 APW  C2'  H1    single    0.970  0.020  1.090
 APW  O2'  H2'   single    0.850  0.020  0.980
 APW  C1'  O4'   single    1.401  0.020  1.401
 APW  C1'  N9    single    1.438  0.020  1.438
 APW  C1'  H1'   single    0.970  0.020  1.090
 APW  N9   C4    aromatic  1.370  0.020  1.370
 APW  N9   C8    aromatic  1.369  0.020  1.369
 APW  C4   C5    aromatic  1.381  0.020  1.381
 APW  C4   N3    aromatic  1.329  0.020  1.329
 APW  C5   N7    aromatic  1.373  0.020  1.373
 APW  C5   C6    aromatic  1.405  0.020  1.405
 APW  N7   C8    aromatic  1.300  0.020  1.300
 APW  C8   H8    single    0.930  0.020  1.080
 APW  N3   C2    aromatic  1.321  0.020  1.321
 APW  C2   N1    aromatic  1.330  0.020  1.330
 APW  C2   H3    single    0.930  0.020  1.080
 APW  N1   C6    aromatic  1.337  0.020  1.337
 APW  C6   N6    single    1.334  0.020  1.334
 APW  N6   HN61  single    0.860  0.020  1.020
 APW  N6   HN62  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
 APW  O2B   MG   O2A   103.02  3.000
 APW  PA    O2A  MG    129.82  3.000
 APW  O5'   PA   O3A   100.90  3.000
 APW  O5'   PA   O1A   112.25  3.000
 APW  O3A   PA   O1A   112.50  3.000
 APW  O5'   PA   O2A   104.39  3.000
 APW  O3A   PA   O2A   106.78  3.000
 APW  O1A   PA   O2A   118.30  3.000
 APW  PB    O3A  PA    128.36  3.000
 APW  N3B   PB   O2B   105.57  3.000
 APW  N3B   PB   O1B   118.07  3.000
 APW  O2B   PB   O1B   116.54  3.000
 APW  N3B   PB   O3A   101.00  3.000
 APW  O2B   PB   O3A   107.12  3.000
 APW  O1B   PB   O3A   106.99  3.000
 APW  PB    O2B  MG    124.41  3.000
 APW  H3B2  N3B  H3B1  109.80  3.000
 APW  H3B2  N3B  PB    113.49  3.000
 APW  H3B1  N3B  PB    113.67  3.000
 APW  C5'   O5'  PA    120.97  3.000
 APW  H5'2  C5'  H5'1  107.02  3.000
 APW  H5'2  C5'  C4'   111.19  3.000
 APW  H5'1  C5'  C4'   108.56  3.000
 APW  H5'2  C5'  O5'   110.55  3.000
 APW  H5'1  C5'  O5'   107.89  3.000
 APW  C4'   C5'  O5'   111.46  3.000
 APW  H4'   C4'  O4'   108.46  3.000
 APW  H4'   C4'  C3'   111.23  3.000
 APW  O4'   C4'  C3'   105.95  3.000
 APW  H4'   C4'  C5'   110.13  3.000
 APW  O4'   C4'  C5'   110.59  3.000
 APW  C3'   C4'  C5'   110.40  3.000
 APW  H3'   C3'  C2'   111.71  3.000
 APW  H3'   C3'  O3'   111.62  3.000
 APW  C2'   C3'  O3'   111.20  3.000
 APW  H3'   C3'  C4'   111.85  3.000
 APW  C2'   C3'  C4'   100.76  3.000
 APW  O3'   C3'  C4'   109.20  3.000
 APW  H2    O3'  C3'   108.06  3.000
 APW  H1    C2'  C1'   110.37  3.000
 APW  H1    C2'  O2'   111.62  3.000
 APW  C1'   C2'  O2'   110.21  3.000
 APW  H1    C2'  C3'   108.22  3.000
 APW  C1'   C2'  C3'   100.75  3.000
 APW  O2'   C2'  C3'   115.15  3.000
 APW  H2'   O2'  C2'   108.86  3.000
 APW  H1'   C1'  N9    105.99  3.000
 APW  H1'   C1'  O4'   110.71  3.000
 APW  N9    C1'  O4'   109.36  3.000
 APW  H1'   C1'  C2'   109.99  3.000
 APW  N9    C1'  C2'   115.14  3.000
 APW  O4'   C1'  C2'   105.69  3.000
 APW  C1'   O4'  C4'   110.82  3.000
 APW  C8    N9   C4    106.01  3.000
 APW  C8    N9   C1'   128.76  3.000
 APW  C4    N9   C1'   124.07  3.000
 APW  N3    C4   C5    126.52  3.000
 APW  N3    C4   N9    128.04  3.000
 APW  C5    C4   N9    105.45  3.000
 APW  C6    C5   N7    132.85  3.000
 APW  C6    C5   C4    116.49  3.000
 APW  N7    C5   C4    110.60  3.000
 APW  C8    N7   C5    104.59  3.000
 APW  H8    C8   N7    124.49  3.000
 APW  H8    C8   N9    122.18  3.000
 APW  N7    C8   N9    113.32  3.000
 APW  C2    N3   C4    111.63  3.000
 APW  H3    C2   N1    115.46  3.000
 APW  H3    C2   N3    116.09  3.000
 APW  N1    C2   N3    128.44  3.000
 APW  C6    N1   C2    119.12  3.000
 APW  N6    C6   N1    119.28  3.000
 APW  N6    C6   C5    122.93  3.000
 APW  N1    C6   C5    117.79  3.000
 APW  HN62  N6   HN61  117.79  3.000
 APW  HN62  N6   C6    121.04  3.000
 APW  HN61  N6   C6    120.01  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
 APW  CONST_01  N7    C5   C4   N9      0.00   0.0  0
 APW  CONST_02  C6    C5   C4   N9    180.00   0.0  0
 APW  CONST_03  C2    N3   C4   N9    180.00   0.0  0
 APW  CONST_04  C5    N7   C8   N9      0.00   0.0  0
 APW  CONST_05  N7    C8   N9   C4      0.00   0.0  0
 APW  CONST_06  C8    N7   C5   C4      0.00   0.0  0
 APW  CONST_07  N1    C6   C5   C4      0.00   0.0  0
 APW  CONST_08  N1    C2   N3   C4      0.00   0.0  0
 APW  CONST_09  C8    N9   C4   C5      0.00   0.0  0
 APW  CONST_10  C2    N3   C4   C5      0.00   0.0  0
 APW  CONST_11  C2    N1   C6   C5      0.00   0.0  0
 APW  CONST_12  N3    C4   C5   N7    180.00   0.0  0
 APW  CONST_13  N1    C6   C5   N7    180.00   0.0  0
 APW  CONST_14  N3    C4   N9   C8    180.00   0.0  0
 APW  CONST_15  C6    C5   N7   C8    180.00   0.0  0
 APW  CONST_16  C6    C5   C4   N3      0.00   0.0  0
 APW  CONST_17  C6    N1   C2   N3      0.00   0.0  0
 APW  CONST_18  C5    C4   N9   C1'   180.00   0.0  0
 APW  CONST_19  N3    C4   N9   C1'     0.00   0.0  0
 APW  CONST_20  N7    C8   N9   C1'   180.00   0.0  0
 APW  CONST_21  N6    C6   C5   C4    180.00   0.0  0
 APW  CONST_22  N6    C6   C5   N7      0.00   0.0  0
 APW  CONST_23  N6    C6   N1   C2    180.00   0.0  0
 APW  CONST_24  H8    C8   N9   C1'     0.00   0.0  0
 APW  CONST_25  H3    C2   N3   C4    180.00   0.0  0
 APW  Var_01    O3A   PA   O2A  MG     -4.16  30.0  1
 APW  Var_02    O3A   PB   O2B  MG     31.28  30.0  1
 APW  Var_03    O2B   PB   O3A  PA    -58.81  30.0  1
 APW  Var_04    C4'   C5'  O5'  PA   -107.39  30.0  3
 APW  Var_05    H3B1  N3B  PB   O3A    62.87  30.0  3
 APW  Var_06    HN61  N6   C6   C5    174.28  30.0  2

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
 APW  chir_03  C4'  C5'  C3'  O4'  positiv
 APW  chir_04  C3'  O3'  C2'  C4'  negativ
 APW  chir_05  C2'  O2'  C1'  C3'  negativ
 APW  chir_06  C1'  O4'  N9   C2'  negativ
 APW  chir_07  PA   O1A  O3A  O5'  both
 APW  chir_08  PB   O1B  O2B  N3B  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
 APW  plan-1  C1'  0.020
 APW  plan-1  N9   0.020
 APW  plan-1  C4   0.020
 APW  plan-1  C5   0.020
 APW  plan-1  N7   0.020
 APW  plan-1  C8   0.020
 APW  plan-1  N3   0.020
 APW  plan-1  C2   0.020
 APW  plan-1  N1   0.020
 APW  plan-1  C6   0.020
 APW  plan-1  N6   0.020
 APW  plan-1  H8   0.020
 APW  plan-1  H3   0.020

