# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 00:59:50 2020
#   Inital geometry file: a 105 line input string
#   Ligand name: 5'-O-[(S)-hydroxy(phosphonomethyl)phosphoryl]adenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)C[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
 A12  A12  5'-O-[(S)-hydroxy(phosphonomethyl)phosphoryl]adenosine  ligand  41  27  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_A12
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
 A12  PB    P  P      0   1.151  -3.6385   2.6111  -0.5752
 A12  O1B   O  O      0  -0.893  -5.1011   2.1581  -0.5626
 A12  O2B   O  OP    -1  -0.943  -3.1539   3.2065   0.7504
 A12  O3B   O  OP    -1  -0.869  -3.2908   3.4774  -1.7969
 A12  PA    P  P      0   1.237  -2.4203   0.0342   0.6468
 A12  O1A   O  O      0  -0.807  -3.7307  -0.3116   1.3032
 A12  O2A   O  OP    -1  -0.893  -1.2920   0.5211   1.5337
 A12  C3A   C  CH2    0  -0.994  -2.6239   1.0558  -0.8249
 A12  O5'   O  O2     0  -0.605  -1.8696  -1.3723  -0.1113
 A12  C5'   C  CH2    0  -0.154  -1.0663  -2.2651   0.6015
 A12  C4'   C  CH1    0  -0.017   0.0556  -2.7721  -0.2898
 A12  O4'   O  O2     0  -0.471   0.7854  -1.6833  -0.8667
 A12  C3'   C  CH1    0  -0.083   1.0787  -3.5822   0.4927
 A12  O3'   O  OH1    0  -0.690   1.7063  -4.4956  -0.3703
 A12  C2'   C  CH1    0   0.021   2.0542  -2.4823   0.9203
 A12  O2'   O  OH1    0  -0.608   3.3447  -2.9262   1.2195
 A12  C1'   C  CH1    0   0.192   2.0718  -1.6093  -0.3338
 A12  N9    N  NR5    0  -0.544   2.4060  -0.2275  -0.0897
 A12  C8    C  CR15   0   0.072   1.6132   0.7298   0.4929
 A12  N7    N  N      0  -0.412   2.1984   1.8923   0.5632
 A12  C5    C  CR56   0   0.008   3.4324   1.6967   0.0013
 A12  C6    C  CR6    0   0.405   4.5174   2.5545  -0.2420
 A12  N6    N  NH2    0  -0.787   4.5148   3.8410   0.1283
 A12  N1    N  N      0  -0.511   5.5967   2.0514  -0.8496
 A12  C2    C  CR16   0   0.046   5.6002   0.7657  -1.1912
 A12  N3    N  N      0  -0.491   4.6523  -0.1373  -1.0120
 A12  C4    C  CR56   0   0.518   3.5817   0.3824  -0.4140
 A12  H3A1  H  HCH2   0   0.242  -1.6218   1.3224  -1.1740
 A12  H3A2  H  HCH2   0   0.221  -3.0843   0.4593  -1.6189
 A12  H5'1  H  HCH2   0   0.184  -1.6405  -3.1410   0.9347
 A12  H5'2  H  HCH2   0   0.219  -0.6499  -1.7979   1.5016
 A12  H4'   H  HCH1   0   0.229  -0.3680  -3.3631  -1.1080
 A12  H3'   H  HCH1   0   0.263   0.6278  -4.0883   1.3570
 A12  HO3'  H  HOH1   0   0.428   2.5581  -4.7272   0.0160
 A12  H2'   H  HCH1   0   0.249   1.6182  -1.9179   1.7543
 A12  HO2'  H  HOH1   0   0.449   3.3667  -3.2021   2.1397
 A12  H1'   H  HCH1   0   0.239   2.8257  -1.9844  -1.0361
 A12  H8    H  HCR5   0   0.302   0.5978   0.5265   0.8336
 A12  HN61  H  HNH2   0   0.401   5.2450   4.4500  -0.1959
 A12  HN62  H  HNH2   0   0.419   3.6631   4.2724   0.4398
 A12  H2    H  HCR6   0   0.278   6.5046   0.4182  -1.6805

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
 A12  PB   O1B   deloc     1.531  0.020  1.531
 A12  PB   O2B   deloc     1.532  0.020  1.532
 A12  PB   O3B   deloc     1.538  0.020  1.538
 A12  PB   C3A   single    1.874  0.020  1.874
 A12  PA   O1A   deloc     1.506  0.020  1.506
 A12  PA   O2A   deloc     1.515  0.020  1.515
 A12  PA   C3A   single    1.803  0.020  1.803
 A12  PA   O5'   single    1.690  0.020  1.690
 A12  C3A  H3A1  single    0.970  0.020  1.090
 A12  C3A  H3A2  single    0.970  0.020  1.090
 A12  O5'  C5'   single    1.397  0.020  1.397
 A12  C5'  C4'   single    1.520  0.020  1.520
 A12  C5'  H5'1  single    0.970  0.020  1.090
 A12  C5'  H5'2  single    0.970  0.020  1.090
 A12  C4'  O4'   single    1.432  0.020  1.432
 A12  C4'  C3'   single    1.522  0.020  1.522
 A12  C4'  H4'   single    0.970  0.020  1.090
 A12  O4'  C1'   single    1.394  0.020  1.394
 A12  C3'  O3'   single    1.405  0.020  1.405
 A12  C3'  C2'   single    1.531  0.020  1.531
 A12  C3'  H3'   single    0.970  0.020  1.090
 A12  O3'  HO3'  single    0.850  0.020  0.980
 A12  C2'  O2'   single    1.397  0.020  1.397
 A12  C2'  C1'   single    1.528  0.020  1.528
 A12  C2'  H2'   single    0.970  0.020  1.090
 A12  O2'  HO2'  single    0.850  0.020  0.980
 A12  C1'  N9    single    1.442  0.020  1.442
 A12  C1'  H1'   single    0.970  0.020  1.090
 A12  N9   C8    aromatic  1.373  0.020  1.373
 A12  N9   C4    aromatic  1.364  0.020  1.364
 A12  C8   N7    aromatic  1.303  0.020  1.303
 A12  C8   H8    single    0.930  0.020  1.080
 A12  N7   C5    aromatic  1.370  0.020  1.370
 A12  C5   C6    aromatic  1.404  0.020  1.404
 A12  C5   C4    aromatic  1.386  0.020  1.386
 A12  C6   N6    single    1.339  0.020  1.339
 A12  C6   N1    aromatic  1.337  0.020  1.337
 A12  N6   HN61  single    0.890  0.020  1.040
 A12  N6   HN62  single    0.890  0.020  1.040
 A12  N1   C2    aromatic  1.330  0.020  1.330
 A12  C2   N3    aromatic  1.321  0.020  1.321
 A12  C2   H2    single    0.930  0.020  1.080
 A12  N3   C4    aromatic  1.332  0.020  1.332

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
 A12  C3A   PB   O3B   103.85  3.000
 A12  C3A   PB   O2B   105.47  3.000
 A12  O3B   PB   O2B   113.39  3.000
 A12  C3A   PB   O1B   105.83  3.000
 A12  O3B   PB   O1B   112.91  3.000
 A12  O2B   PB   O1B   114.21  3.000
 A12  O5'   PA   C3A    98.17  3.000
 A12  O5'   PA   O2A   106.70  3.000
 A12  C3A   PA   O2A   112.32  3.000
 A12  O5'   PA   O1A   106.73  3.000
 A12  C3A   PA   O1A   112.81  3.000
 A12  O2A   PA   O1A   117.82  3.000
 A12  H3A2  C3A  H3A1  106.66  3.000
 A12  H3A2  C3A  PA    109.32  3.000
 A12  H3A1  C3A  PA    107.16  3.000
 A12  H3A2  C3A  PB    108.74  3.000
 A12  H3A1  C3A  PB    109.64  3.000
 A12  PA    C3A  PB    115.00  3.000
 A12  C5'   O5'  PA    119.38  3.000
 A12  H5'2  C5'  H5'1  106.81  3.000
 A12  H5'2  C5'  C4'   110.08  3.000
 A12  H5'1  C5'  C4'   107.31  3.000
 A12  H5'2  C5'  O5'   111.41  3.000
 A12  H5'1  C5'  O5'   111.33  3.000
 A12  C4'   C5'  O5'   109.79  3.000
 A12  H4'   C4'  C3'   110.93  3.000
 A12  H4'   C4'  O4'   107.86  3.000
 A12  C3'   C4'  O4'   105.62  3.000
 A12  H4'   C4'  C5'   109.43  3.000
 A12  C3'   C4'  C5'   111.86  3.000
 A12  O4'   C4'  C5'   111.03  3.000
 A12  C1'   O4'  C4'   110.89  3.000
 A12  H3'   C3'  C2'   111.89  3.000
 A12  H3'   C3'  O3'   111.54  3.000
 A12  C2'   C3'  O3'   110.74  3.000
 A12  H3'   C3'  C4'   111.96  3.000
 A12  C2'   C3'  C4'   100.92  3.000
 A12  O3'   C3'  C4'   109.31  3.000
 A12  HO3'  O3'  C3'   107.75  3.000
 A12  H2'   C2'  C1'   109.54  3.000
 A12  H2'   C2'  O2'   111.57  3.000
 A12  C1'   C2'  O2'   110.28  3.000
 A12  H2'   C2'  C3'   109.18  3.000
 A12  C1'   C2'  C3'   100.87  3.000
 A12  O2'   C2'  C3'   114.83  3.000
 A12  HO2'  O2'  C2'   108.51  3.000
 A12  H1'   C1'  N9    106.07  3.000
 A12  H1'   C1'  C2'   109.76  3.000
 A12  N9    C1'  C2'   114.27  3.000
 A12  H1'   C1'  O4'   111.80  3.000
 A12  N9    C1'  O4'   109.23  3.000
 A12  C2'   C1'  O4'   105.82  3.000
 A12  C4    N9   C8    106.68  3.000
 A12  C4    N9   C1'   126.01  3.000
 A12  C8    N9   C1'   127.31  3.000
 A12  H8    C8   N7    124.59  3.000
 A12  H8    C8   N9    122.72  3.000
 A12  N7    C8   N9    112.68  3.000
 A12  C5    N7   C8    104.77  3.000
 A12  C4    C5   C6    116.36  3.000
 A12  C4    C5   N7    110.80  3.000
 A12  C6    C5   N7    132.82  3.000
 A12  N1    C6   N6    119.27  3.000
 A12  N1    C6   C5    118.20  3.000
 A12  N6    C6   C5    122.52  3.000
 A12  HN62  N6   HN61  117.14  3.000
 A12  HN62  N6   C6    120.01  3.000
 A12  HN61  N6   C6    119.47  3.000
 A12  C2    N1   C6    118.85  3.000
 A12  H2    C2   N3    116.11  3.000
 A12  H2    C2   N1    115.30  3.000
 A12  N3    C2   N1    128.59  3.000
 A12  C4    N3   C2    111.77  3.000
 A12  N3    C4   C5    126.23  3.000
 A12  N3    C4   N9    128.70  3.000
 A12  C5    C4   N9    105.07  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
 A12  CONST_01  C5    N7   C8   N9      0.00   0.0  0
 A12  CONST_02  N7    C5   C4   N9      0.00   0.0  0
 A12  CONST_03  C6    C5   C4   N9    180.00   0.0  0
 A12  CONST_04  C2    N3   C4   N9    180.00   0.0  0
 A12  CONST_05  C5    C4   N9   C8      0.00   0.0  0
 A12  CONST_06  N3    C4   N9   C8    180.00   0.0  0
 A12  CONST_07  C6    C5   N7   C8    180.00   0.0  0
 A12  CONST_08  C4    C5   N7   C8      0.00   0.0  0
 A12  CONST_09  C4    N9   C8   N7      0.00   0.0  0
 A12  CONST_10  N1    C6   C5   N7    180.00   0.0  0
 A12  CONST_11  N3    C4   C5   N7    180.00   0.0  0
 A12  CONST_12  C2    N1   C6   C5      0.00   0.0  0
 A12  CONST_13  C2    N3   C4   C5      0.00   0.0  0
 A12  CONST_14  N3    C4   C5   C6      0.00   0.0  0
 A12  CONST_15  N3    C2   N1   C6      0.00   0.0  0
 A12  CONST_16  C4    C5   C6   N1      0.00   0.0  0
 A12  CONST_17  C4    N3   C2   N1      0.00   0.0  0
 A12  CONST_18  N7    C8   N9   C1'   180.00   0.0  0
 A12  CONST_19  C5    C4   N9   C1'   180.00   0.0  0
 A12  CONST_20  N3    C4   N9   C1'     0.00   0.0  0
 A12  CONST_21  N6    C6   C5   N7      0.00   0.0  0
 A12  CONST_22  C4    C5   C6   N6    180.00   0.0  0
 A12  CONST_23  C2    N1   C6   N6    180.00   0.0  0
 A12  CONST_24  H8    C8   N9   C1'     0.00   0.0  0
 A12  CONST_25  H2    C2   N1   C6    180.00   0.0  0
 A12  CONST_26  HN61  N6   C6   C5    180.00   0.0  0
 A12  CONST_27  HN62  N6   C6   C5      0.00   0.0  0
 A12  Var_01    C4'   C5'  O5'  PA   -138.60  30.0  3
 A12  Var_02    O1A   PA   C3A  PB     53.02  30.0  1
 A12  Var_03    PA    C3A  PB   O1B   -77.97  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
 A12  chir_02  C4'  C5'  O4'  C3'  negativ
 A12  chir_03  C3'  O3'  C4'  C2'  positiv
 A12  chir_04  C2'  O2'  C3'  C1'  positiv
 A12  chir_05  C1'  O4'  N9   C2'  negativ

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
 A12  plan-1  C1'   0.020
 A12  plan-1  N9    0.020
 A12  plan-1  C8    0.020
 A12  plan-1  N7    0.020
 A12  plan-1  C5    0.020
 A12  plan-1  C6    0.020
 A12  plan-1  N6    0.020
 A12  plan-1  N1    0.020
 A12  plan-1  C2    0.020
 A12  plan-1  N3    0.020
 A12  plan-1  C4    0.020
 A12  plan-1  H8    0.020
 A12  plan-1  H2    0.020
 A12  plan-2  C6    0.020
 A12  plan-2  N6    0.020
 A12  plan-2  HN61  0.020
 A12  plan-2  HN62  0.020

