# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 10 20:55:48 2022
#   Inital geometry file: a 116 line input string
#   Ligand name: 5'-O-[(S)-hydroxy{[(R)-hydroxy(phosphonoamino)phosphoryl]oxy}phosphoryl]adenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)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
 ANP  ANP  5'-O-[(S)-hydroxy{[(R)-hydroxy(phosphonoamino)phosphoryl]oxy}phosphoryl]adenosine  ligand  44  31  .  2012-08-31  2022-03-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_ANP
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
 ANP  PG    P  P      0   1.028  18.9705   1.3205  29.9393
 ANP  O1G   O  O      0  -0.998  19.2329  -0.1753  29.7529
 ANP  O2G   O  OP    -1  -0.863  20.0782   2.2286  29.4023
 ANP  O3G   O  OP    -1  -0.967  17.5580   1.7524  29.5494
 ANP  PB    P  P      0   1.202  18.5735   0.6405  32.9372
 ANP  O1B   O  O      0  -0.733  17.3202  -0.0906  32.5517
 ANP  O2B   O  OP    -1  -0.897  19.7059  -0.1000  33.6029
 ANP  N3B   N  NH1    0  -0.894  19.0908   1.6364  31.7020
 ANP  PA    P  P      0   1.334  18.9551   2.4945  35.1926
 ANP  O1A   O  O      0  -0.684  19.1541   1.6541  36.4112
 ANP  O2A   O  OP    -1  -0.823  20.1448   3.1485  34.5143
 ANP  O3A   O  O2     0  -0.754  18.0321   1.7731  34.0840
 ANP  O5'   O  O2     0  -0.557  17.8881   3.6734  35.6525
 ANP  C5'   C  CH2    0  -0.172  17.8910   4.9335  35.0213
 ANP  C4'   C  CH1    0  -0.026  18.6523   5.9809  35.8092
 ANP  O4'   O  O2     0  -0.522  17.9225   6.3827  36.9728
 ANP  C3'   C  CH1    0  -0.036  20.0132   5.5481  36.3628
 ANP  O3'   O  OH1    0  -0.647  21.0213   5.4645  35.4157
 ANP  C2'   C  CH1    0  -0.084  20.2272   6.5793  37.4586
 ANP  O2'   O  OH1    0  -0.691  20.6096   7.7961  36.8827
 ANP  C1'   C  CH1    0   0.143  18.7951   6.6555  38.0256
 ANP  N9    N  NR5    0  -0.526  18.5740   5.6782  39.0863
 ANP  C8    C  CR15   0   0.116  18.0114   4.4337  38.9910
 ANP  N7    N  N      0  -0.520  17.9836   3.7928  40.1241
 ANP  C5    C  CR56   0   0.087  18.5638   4.6537  41.0175
 ANP  C6    C  CR6    0   0.336  18.8320   4.5707  42.3944
 ANP  N6    N  NH2    0  -0.825  18.5483   3.4824  43.1230
 ANP  N1    N  N      0  -0.410  19.4253   5.6135  42.9833
 ANP  C2    C  CR16   0   0.048  19.7364   6.6811  42.2516
 ANP  N3    N  N      0  -0.416  19.5343   6.8785  40.9609
 ANP  C4    C  CR56   0   0.476  18.9416   5.8315  40.3897
 ANP  HNB1  H  HNH1   0   0.379  19.9259   2.1517  31.9439
 ANP  H5'1  H  HCH2   0   0.202  18.3296   4.8926  34.0202
 ANP  H5'2  H  HCH2   0   0.280  16.8537   5.2577  34.8952
 ANP  H4'   H  HCH1   0   0.251  18.7819   6.8474  35.1477
 ANP  H3'   H  HCH1   0   0.306  19.8850   4.5890  36.8851
 ANP  HO3'  H  HOH1   0   0.451  20.8443   4.5991  34.9705
 ANP  H2'   H  HCH1   0   0.302  20.9386   6.2435  38.2225
 ANP  HO2'  H  HOH1   0   0.447  20.7700   8.4353  37.5843
 ANP  H1'   H  HCH1   0   0.322  18.5851   7.6402  38.4555
 ANP  H8    H  HCR5   0   0.320  17.6377   4.0483  38.0553
 ANP  HN61  H  HNH2   0   0.339  18.5951   3.5473  44.1259
 ANP  HN62  H  HNH2   0   0.381  17.9337   2.7816  42.7457
 ANP  H2    H  HCR6   0   0.291  20.2165   7.4914  42.7901

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
 ANP  PG   O1G   deloc     1.530  0.020  1.530
 ANP  PG   O2G   deloc     1.530  0.020  1.530
 ANP  PG   O3G   deloc     1.528  0.020  1.528
 ANP  PG   N3B   single    1.795  0.020  1.795
 ANP  PB   O1B   deloc     1.501  0.020  1.501
 ANP  PB   O2B   deloc     1.508  0.020  1.508
 ANP  PB   N3B   single    1.669  0.020  1.669
 ANP  PB   O3A   single    1.700  0.020  1.700
 ANP  N3B  HNB1  single    0.890  0.020  1.040
 ANP  PA   O1A   deloc     1.494  0.020  1.494
 ANP  PA   O2A   deloc     1.518  0.020  1.518
 ANP  PA   O3A   single    1.613  0.020  1.613
 ANP  PA   O5'   single    1.655  0.020  1.655
 ANP  O5'  C5'   single    1.409  0.020  1.409
 ANP  C5'  C4'   single    1.516  0.020  1.516
 ANP  C5'  H5'1  single    0.970  0.020  1.090
 ANP  C5'  H5'2  single    0.970  0.020  1.090
 ANP  C4'  O4'   single    1.431  0.020  1.431
 ANP  C4'  C3'   single    1.532  0.020  1.532
 ANP  C4'  H4'   single    0.970  0.020  1.090
 ANP  O4'  C1'   single    1.394  0.020  1.394
 ANP  C3'  O3'   single    1.386  0.020  1.386
 ANP  C3'  C2'   single    1.520  0.020  1.520
 ANP  C3'  H3'   single    0.970  0.020  1.090
 ANP  O3'  HO3'  single    0.850  0.020  0.980
 ANP  C2'  O2'   single    1.399  0.020  1.399
 ANP  C2'  C1'   single    1.542  0.020  1.542
 ANP  C2'  H2'   single    0.970  0.020  1.090
 ANP  O2'  HO2'  single    0.850  0.020  0.980
 ANP  C1'  N9    single    1.459  0.020  1.459
 ANP  C1'  H1'   single    0.970  0.020  1.090
 ANP  N9   C8    aromatic  1.369  0.020  1.369
 ANP  N9   C4    aromatic  1.363  0.020  1.363
 ANP  C8   N7    aromatic  1.302  0.020  1.302
 ANP  C8   H8    single    0.930  0.020  1.080
 ANP  N7   C5    aromatic  1.370  0.020  1.370
 ANP  C5   C6    aromatic  1.405  0.020  1.405
 ANP  C5   C4    aromatic  1.387  0.020  1.387
 ANP  C6   N6    single    1.340  0.020  1.340
 ANP  C6   N1    aromatic  1.336  0.020  1.336
 ANP  N6   HN61  single    0.890  0.020  1.040
 ANP  N6   HN62  single    0.890  0.020  1.040
 ANP  N1   C2    aromatic  1.331  0.020  1.331
 ANP  C2   N3    aromatic  1.321  0.020  1.321
 ANP  C2   H2    single    0.930  0.020  1.080
 ANP  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
 ANP  N3B   PG   O3G   105.24  3.000
 ANP  N3B   PG   O2G   101.05  3.000
 ANP  O3G   PG   O2G   114.34  3.000
 ANP  N3B   PG   O1G   106.28  3.000
 ANP  O3G   PG   O1G   113.82  3.000
 ANP  O2G   PG   O1G   114.42  3.000
 ANP  O3A   PB   N3B   101.56  3.000
 ANP  O3A   PB   O2B   105.57  3.000
 ANP  N3B   PB   O2B   112.77  3.000
 ANP  O3A   PB   O1B   103.40  3.000
 ANP  N3B   PB   O1B   111.06  3.000
 ANP  O2B   PB   O1B   120.08  3.000
 ANP  HNB1  N3B  PB    112.53  3.000
 ANP  HNB1  N3B  PG    112.35  3.000
 ANP  PB    N3B  PG    126.95  3.000
 ANP  O5'   PA   O3A    98.09  3.000
 ANP  O5'   PA   O2A   108.82  3.000
 ANP  O3A   PA   O2A   109.52  3.000
 ANP  O5'   PA   O1A   105.07  3.000
 ANP  O3A   PA   O1A   112.67  3.000
 ANP  O2A   PA   O1A   120.18  3.000
 ANP  PA    O3A  PB    125.41  3.000
 ANP  C5'   O5'  PA    120.74  3.000
 ANP  H5'2  C5'  H5'1  106.60  3.000
 ANP  H5'2  C5'  C4'   109.35  3.000
 ANP  H5'1  C5'  C4'   107.46  3.000
 ANP  H5'2  C5'  O5'   108.34  3.000
 ANP  H5'1  C5'  O5'   112.17  3.000
 ANP  C4'   C5'  O5'   112.71  3.000
 ANP  H4'   C4'  C3'   109.63  3.000
 ANP  H4'   C4'  O4'   109.18  3.000
 ANP  C3'   C4'  O4'   103.81  3.000
 ANP  H4'   C4'  C5'   106.95  3.000
 ANP  C3'   C4'  C5'   116.03  3.000
 ANP  O4'   C4'  C5'   111.13  3.000
 ANP  C1'   O4'  C4'   110.47  3.000
 ANP  H3'   C3'  C2'   105.41  3.000
 ANP  H3'   C3'  O3'   110.91  3.000
 ANP  C2'   C3'  O3'   115.55  3.000
 ANP  H3'   C3'  C4'   108.34  3.000
 ANP  C2'   C3'  C4'   101.18  3.000
 ANP  O3'   C3'  C4'   114.61  3.000
 ANP  HO3'  O3'  C3'   103.31  3.000
 ANP  H2'   C2'  C1'   111.20  3.000
 ANP  H2'   C2'  O2'   112.06  3.000
 ANP  C1'   C2'  O2'   111.23  3.000
 ANP  H2'   C2'  C3'   112.69  3.000
 ANP  C1'   C2'  C3'    99.67  3.000
 ANP  O2'   C2'  C3'   109.37  3.000
 ANP  HO2'  O2'  C2'   108.84  3.000
 ANP  H1'   C1'  N9    106.73  3.000
 ANP  H1'   C1'  C2'   111.53  3.000
 ANP  N9    C1'  C2'   112.01  3.000
 ANP  H1'   C1'  O4'   110.64  3.000
 ANP  N9    C1'  O4'   108.85  3.000
 ANP  C2'   C1'  O4'   107.09  3.000
 ANP  C4    N9   C8    106.24  3.000
 ANP  C4    N9   C1'   125.38  3.000
 ANP  C8    N9   C1'   128.35  3.000
 ANP  H8    C8   N7    124.86  3.000
 ANP  H8    C8   N9    121.84  3.000
 ANP  N7    C8   N9    113.30  3.000
 ANP  C5    N7   C8    104.43  3.000
 ANP  C4    C5   C6    116.21  3.000
 ANP  C4    C5   N7    110.72  3.000
 ANP  C6    C5   N7    133.07  3.000
 ANP  N1    C6   N6    119.21  3.000
 ANP  N1    C6   C5    118.06  3.000
 ANP  N6    C6   C5    122.71  3.000
 ANP  HN62  N6   HN61  116.58  3.000
 ANP  HN62  N6   C6    119.43  3.000
 ANP  HN61  N6   C6    118.67  3.000
 ANP  C2    N1   C6    119.17  3.000
 ANP  H2    C2   N3    116.16  3.000
 ANP  H2    C2   N1    115.45  3.000
 ANP  N3    C2   N1    128.39  3.000
 ANP  C4    N3   C2    111.69  3.000
 ANP  N3    C4   C5    126.48  3.000
 ANP  N3    C4   N9    128.22  3.000
 ANP  C5    C4   N9    105.30  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
 ANP  CONST_01  C5    N7   C8   N9     0.00   0.0  0
 ANP  CONST_02  N7    C5   C4   N9     0.00   0.0  0
 ANP  CONST_03  C6    C5   C4   N9   180.00   0.0  0
 ANP  CONST_04  C2    N3   C4   N9   180.00   0.0  0
 ANP  CONST_05  C5    C4   N9   C8     0.00   0.0  0
 ANP  CONST_06  N3    C4   N9   C8   180.00   0.0  0
 ANP  CONST_07  C6    C5   N7   C8   180.00   0.0  0
 ANP  CONST_08  C4    C5   N7   C8     0.00   0.0  0
 ANP  CONST_09  C4    N9   C8   N7     0.00   0.0  0
 ANP  CONST_10  N1    C6   C5   N7   180.00   0.0  0
 ANP  CONST_11  N3    C4   C5   N7   180.00   0.0  0
 ANP  CONST_12  C2    N1   C6   C5     0.00   0.0  0
 ANP  CONST_13  C2    N3   C4   C5     0.00   0.0  0
 ANP  CONST_14  N3    C4   C5   C6     0.00   0.0  0
 ANP  CONST_15  N3    C2   N1   C6     0.00   0.0  0
 ANP  CONST_16  C4    C5   C6   N1     0.00   0.0  0
 ANP  CONST_17  C4    N3   C2   N1     0.00   0.0  0
 ANP  CONST_18  N7    C8   N9   C1'  180.00   0.0  0
 ANP  CONST_19  C5    C4   N9   C1'  180.00   0.0  0
 ANP  CONST_20  N3    C4   N9   C1'    0.00   0.0  0
 ANP  CONST_21  N6    C6   C5   N7     0.00   0.0  0
 ANP  CONST_22  C4    C5   C6   N6   180.00   0.0  0
 ANP  CONST_23  C2    N1   C6   N6   180.00   0.0  0
 ANP  CONST_24  H8    C8   N9   C1'    0.00   0.0  0
 ANP  CONST_25  H2    C2   N1   C6   180.00   0.0  0
 ANP  CONST_26  HN61  N6   C6   C5   180.00   0.0  0
 ANP  CONST_27  HN62  N6   C6   C5     0.00   0.0  0
 ANP  Var_01    C4'   C5'  O5'  PA   -98.38  30.0  3
 ANP  Var_02    O1B   PB   N3B  PG   -35.15  30.0  1
 ANP  Var_03    PB    N3B  PG   O1G  -37.51  30.0  3
 ANP  Var_04    O1A   PA   O3A  PB   -83.11  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
 ANP  chir_03  C4'  C5'  O4'  C3'  negativ
 ANP  chir_04  C3'  O3'  C4'  C2'  positiv
 ANP  chir_05  C2'  O2'  C3'  C1'  positiv
 ANP  chir_06  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
 ANP  plan-1  C1'   0.020
 ANP  plan-1  N9    0.020
 ANP  plan-1  C8    0.020
 ANP  plan-1  N7    0.020
 ANP  plan-1  C5    0.020
 ANP  plan-1  C6    0.020
 ANP  plan-1  N6    0.020
 ANP  plan-1  N1    0.020
 ANP  plan-1  C2    0.020
 ANP  plan-1  N3    0.020
 ANP  plan-1  C4    0.020
 ANP  plan-1  H8    0.020
 ANP  plan-1  H2    0.020
 ANP  plan-2  C6    0.020
 ANP  plan-2  N6    0.020
 ANP  plan-2  HN61  0.020
 ANP  plan-2  HN62  0.020

