# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 09:03:25 2022
#   Inital geometry file: a 118 line input string
#   Ligand name: 5'-O-[(R)-hydroxy{[(S)-hydroxy(phosphonomethyl)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)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
 ACP  ACP  5'-O-[(R)-hydroxy{[(S)-hydroxy(phosphonomethyl)phosphoryl]oxy}phosphoryl]adenosine  ligand  45  31  .  2020-10-23  2022-03-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_ACP
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
 ACP  PG    P  P      0   1.165   1.6097  -1.5526  -5.7527
 ACP  O1G   O  O      0  -0.908   2.3692  -0.3226  -6.2620
 ACP  O2G   O  OP    -1  -0.923   2.5116  -2.7767  -5.5252
 ACP  O3G   O  OP    -1  -0.914   0.3459  -1.8833  -6.5527
 ACP  PB    P  P      0   1.279   0.3747   0.5871  -3.8655
 ACP  O1B   O  O      0  -0.817  -0.6940   0.8826  -4.8828
 ACP  O2B   O  OP    -1  -0.828   1.4723   1.5909  -3.6263
 ACP  C3B   C  CH2    0  -0.998   1.0210  -1.0947  -4.0327
 ACP  PA    P  P      0   1.339  -0.6038   1.5314  -1.2589
 ACP  O1A   O  O      0  -0.811  -1.0951   2.8255  -1.8348
 ACP  O2A   O  OP    -1  -0.792   0.5629   1.5534  -0.3090
 ACP  O3A   O  O2     0  -0.755  -0.4317   0.3859  -2.3849
 ACP  O5'   O  O2     0  -0.624  -1.8743   0.7647  -0.5174
 ACP  C5'   C  CH2    0  -0.145  -2.2461   1.1691   0.7752
 ACP  C4'   C  CH1    0   0.008  -2.4840  -0.0426   1.6485
 ACP  O4'   O  O2     0  -0.489  -1.3048  -0.8422   1.7456
 ACP  C3'   C  CH1    0  -0.049  -2.8432   0.3308   3.0855
 ACP  O3'   O  OH1    0  -0.658  -4.2317   0.4642   3.2209
 ACP  C2'   C  CH1    0  -0.037  -2.2576  -0.8384   3.8837
 ACP  O2'   O  OH1    0  -0.667  -3.0927  -1.9616   3.8129
 ACP  C1'   C  CH1    0   0.176  -1.0045  -1.1473   3.0681
 ACP  N9    N  NR5    0  -0.544   0.1336  -0.3367   3.5021
 ACP  C8    C  CR15   0   0.060   0.8598   0.5600   2.7627
 ACP  N7    N  N      0  -0.460   1.8678   1.0631   3.4196
 ACP  C5    C  CR56   0  -0.004   1.8165   0.4591   4.6470
 ACP  C6    C  CR6    0   0.448   2.6192   0.5570   5.7980
 ACP  N6    N  NH2    0  -0.818   3.6833   1.3606   5.8680
 ACP  N1    N  N      0  -0.475   2.3011  -0.2018   6.8527
 ACP  C2    C  CR16   0   0.036   1.2502  -1.0145   6.7720
 ACP  N3    N  N      0  -0.459   0.4243  -1.1914   5.7561
 ACP  C4    C  CR56   0   0.484   0.7503  -0.4242   4.7156
 ACP  H3B1  H  HCH2   0   0.205   1.8473  -1.1986  -3.3225
 ACP  H3B2  H  HCH2   0   0.208   0.2559  -1.8117  -3.7184
 ACP  H5'1  H  HCH2   0   0.221  -3.1785   1.7466   0.7472
 ACP  H5'2  H  HCH2   0   0.203  -1.4912   1.8092   1.2444
 ACP  H4'   H  HCH1   0   0.243  -3.2824  -0.6558   1.2128
 ACP  H3'   H  HCH1   0   0.247  -2.3255   1.2548   3.3733
 ACP  HO3'  H  HOH1   0   0.468  -4.4163   0.9921   4.0043
 ACP  H2'   H  HCH1   0   0.260  -2.0260  -0.5679   4.9198
 ACP  HO2'  H  HOH1   0   0.451  -4.0056  -1.6482   3.8352
 ACP  H1'   H  HCH1   0   0.283  -0.7140  -2.1982   3.1550
 ACP  H8    H  HCR5   0   0.331   0.6179   0.7980   1.7333
 ACP  HN61  H  HNH2   0   0.402   4.1872   1.4582   6.7325
 ACP  HN62  H  HNH2   0   0.410   3.9021   1.9919   5.1178
 ACP  H2    H  HCR6   0   0.249   1.0502  -1.6062   7.6591

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
 ACP  PG   O1G   deloc     1.533  0.020  1.533
 ACP  PG   O2G   deloc     1.537  0.020  1.537
 ACP  PG   O3G   deloc     1.532  0.020  1.532
 ACP  PG   C3B   single    1.875  0.020  1.875
 ACP  PB   O1B   deloc     1.505  0.020  1.505
 ACP  PB   O2B   deloc     1.507  0.020  1.507
 ACP  PB   C3B   single    1.810  0.020  1.810
 ACP  PB   O3A   single    1.698  0.020  1.698
 ACP  C3B  H3B1  single    0.970  0.020  1.090
 ACP  C3B  H3B2  single    0.970  0.020  1.090
 ACP  PA   O1A   deloc     1.499  0.020  1.499
 ACP  PA   O2A   deloc     1.505  0.020  1.505
 ACP  PA   O3A   single    1.615  0.020  1.615
 ACP  PA   O5'   single    1.659  0.020  1.659
 ACP  O5'  C5'   single    1.404  0.020  1.404
 ACP  C5'  C4'   single    1.513  0.020  1.513
 ACP  C5'  H5'1  single    0.970  0.020  1.090
 ACP  C5'  H5'2  single    0.970  0.020  1.090
 ACP  C4'  O4'   single    1.428  0.020  1.428
 ACP  C4'  C3'   single    1.528  0.020  1.528
 ACP  C4'  H4'   single    0.970  0.020  1.090
 ACP  O4'  C1'   single    1.390  0.020  1.390
 ACP  C3'  O3'   single    1.401  0.020  1.401
 ACP  C3'  C2'   single    1.532  0.020  1.532
 ACP  C3'  H3'   single    0.970  0.020  1.090
 ACP  O3'  HO3'  single    0.850  0.020  0.980
 ACP  C2'  O2'   single    1.401  0.020  1.401
 ACP  C2'  C1'   single    1.527  0.020  1.527
 ACP  C2'  H2'   single    0.970  0.020  1.090
 ACP  O2'  HO2'  single    0.850  0.020  0.980
 ACP  C1'  N9    single    1.463  0.020  1.463
 ACP  C1'  H1'   single    0.970  0.020  1.090
 ACP  N9   C8    aromatic  1.371  0.020  1.371
 ACP  N9   C4    aromatic  1.364  0.020  1.364
 ACP  C8   N7    aromatic  1.304  0.020  1.304
 ACP  C8   H8    single    0.930  0.020  1.080
 ACP  N7   C5    aromatic  1.369  0.020  1.369
 ACP  C5   C6    aromatic  1.407  0.020  1.407
 ACP  C5   C4    aromatic  1.386  0.020  1.386
 ACP  C6   N6    single    1.335  0.020  1.335
 ACP  C6   N1    aromatic  1.338  0.020  1.338
 ACP  N6   HN61  single    0.860  0.020  1.020
 ACP  N6   HN62  single    0.860  0.020  1.020
 ACP  N1   C2    aromatic  1.331  0.020  1.331
 ACP  C2   N3    aromatic  1.321  0.020  1.321
 ACP  C2   H2    single    0.930  0.020  1.080
 ACP  N3   C4    aromatic  1.333  0.020  1.333

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
 ACP  C3B   PG   O3G   105.83  3.000
 ACP  C3B   PG   O2G   104.06  3.000
 ACP  O3G   PG   O2G   112.92  3.000
 ACP  C3B   PG   O1G   105.33  3.000
 ACP  O3G   PG   O1G   114.11  3.000
 ACP  O2G   PG   O1G   113.42  3.000
 ACP  O3A   PB   C3B    98.05  3.000
 ACP  O3A   PB   O2B   106.65  3.000
 ACP  C3B   PB   O2B   111.95  3.000
 ACP  O3A   PB   O1B   105.99  3.000
 ACP  C3B   PB   O1B   111.94  3.000
 ACP  O2B   PB   O1B   119.60  3.000
 ACP  H3B2  C3B  H3B1  106.21  3.000
 ACP  H3B2  C3B  PB    109.43  3.000
 ACP  H3B1  C3B  PB    107.33  3.000
 ACP  H3B2  C3B  PG    108.84  3.000
 ACP  H3B1  C3B  PG    109.58  3.000
 ACP  PB    C3B  PG    115.09  3.000
 ACP  O5'   PA   O3A    93.75  3.000
 ACP  O5'   PA   O2A   108.57  3.000
 ACP  O3A   PA   O2A   111.58  3.000
 ACP  O5'   PA   O1A   108.64  3.000
 ACP  O3A   PA   O1A   112.28  3.000
 ACP  O2A   PA   O1A   118.95  3.000
 ACP  PA    O3A  PB    125.06  3.000
 ACP  C5'   O5'  PA    118.75  3.000
 ACP  H5'2  C5'  H5'1  106.80  3.000
 ACP  H5'2  C5'  C4'   109.22  3.000
 ACP  H5'1  C5'  C4'   107.62  3.000
 ACP  H5'2  C5'  O5'   112.34  3.000
 ACP  H5'1  C5'  O5'   110.68  3.000
 ACP  C4'   C5'  O5'   110.02  3.000
 ACP  H4'   C4'  C3'   109.83  3.000
 ACP  H4'   C4'  O4'   108.36  3.000
 ACP  C3'   C4'  O4'   105.49  3.000
 ACP  H4'   C4'  C5'   109.45  3.000
 ACP  C3'   C4'  C5'   112.60  3.000
 ACP  O4'   C4'  C5'   110.98  3.000
 ACP  C1'   O4'  C4'   111.46  3.000
 ACP  H3'   C3'  C2'   109.00  3.000
 ACP  H3'   C3'  O3'   111.21  3.000
 ACP  C2'   C3'  O3'   113.64  3.000
 ACP  H3'   C3'  C4'   109.97  3.000
 ACP  C2'   C3'  C4'   102.34  3.000
 ACP  O3'   C3'  C4'   110.31  3.000
 ACP  HO3'  O3'  C3'   108.72  3.000
 ACP  H2'   C2'  C1'   112.44  3.000
 ACP  H2'   C2'  O2'   111.82  3.000
 ACP  C1'   C2'  O2'   107.45  3.000
 ACP  H2'   C2'  C3'   112.65  3.000
 ACP  C1'   C2'  C3'   100.94  3.000
 ACP  O2'   C2'  C3'   110.95  3.000
 ACP  HO2'  O2'  C2'   107.59  3.000
 ACP  H1'   C1'  N9    107.58  3.000
 ACP  H1'   C1'  C2'   111.72  3.000
 ACP  N9    C1'  C2'   111.59  3.000
 ACP  H1'   C1'  O4'   110.11  3.000
 ACP  N9    C1'  O4'   109.19  3.000
 ACP  C2'   C1'  O4'   106.65  3.000
 ACP  C4    N9   C8    106.40  3.000
 ACP  C4    N9   C1'   125.46  3.000
 ACP  C8    N9   C1'   127.93  3.000
 ACP  H8    C8   N7    124.49  3.000
 ACP  H8    C8   N9    122.54  3.000
 ACP  N7    C8   N9    112.97  3.000
 ACP  C5    N7   C8    104.63  3.000
 ACP  C4    C5   C6    116.28  3.000
 ACP  C4    C5   N7    110.75  3.000
 ACP  C6    C5   N7    132.96  3.000
 ACP  N1    C6   N6    119.32  3.000
 ACP  N1    C6   C5    118.03  3.000
 ACP  N6    C6   C5    122.65  3.000
 ACP  HN62  N6   HN61  118.16  3.000
 ACP  HN62  N6   C6    120.83  3.000
 ACP  HN61  N6   C6    120.19  3.000
 ACP  C2    N1   C6    119.11  3.000
 ACP  H2    C2   N3    116.14  3.000
 ACP  H2    C2   N1    115.41  3.000
 ACP  N3    C2   N1    128.46  3.000
 ACP  C4    N3   C2    111.73  3.000
 ACP  N3    C4   C5    126.40  3.000
 ACP  N3    C4   N9    128.36  3.000
 ACP  C5    C4   N9    105.24  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
 ACP  CONST_01  C5    N7   C8   N9      0.00   0.0  0
 ACP  CONST_02  N7    C5   C4   N9      0.00   0.0  0
 ACP  CONST_03  C6    C5   C4   N9    180.00   0.0  0
 ACP  CONST_04  C2    N3   C4   N9    180.00   0.0  0
 ACP  CONST_05  C5    C4   N9   C8      0.00   0.0  0
 ACP  CONST_06  N3    C4   N9   C8    180.00   0.0  0
 ACP  CONST_07  C6    C5   N7   C8    180.00   0.0  0
 ACP  CONST_08  C4    C5   N7   C8      0.00   0.0  0
 ACP  CONST_09  C4    N9   C8   N7      0.00   0.0  0
 ACP  CONST_10  N1    C6   C5   N7    180.00   0.0  0
 ACP  CONST_11  N3    C4   C5   N7    180.00   0.0  0
 ACP  CONST_12  C2    N1   C6   C5      0.00   0.0  0
 ACP  CONST_13  C2    N3   C4   C5      0.00   0.0  0
 ACP  CONST_14  N3    C4   C5   C6      0.00   0.0  0
 ACP  CONST_15  N3    C2   N1   C6      0.00   0.0  0
 ACP  CONST_16  C4    C5   C6   N1      0.00   0.0  0
 ACP  CONST_17  C4    N3   C2   N1      0.00   0.0  0
 ACP  CONST_18  N7    C8   N9   C1'   180.00   0.0  0
 ACP  CONST_19  C5    C4   N9   C1'   180.00   0.0  0
 ACP  CONST_20  N3    C4   N9   C1'     0.00   0.0  0
 ACP  CONST_21  N6    C6   C5   N7      0.00   0.0  0
 ACP  CONST_22  C4    C5   C6   N6    180.00   0.0  0
 ACP  CONST_23  C2    N1   C6   N6    180.00   0.0  0
 ACP  CONST_24  H8    C8   N9   C1'     0.00   0.0  0
 ACP  CONST_25  H2    C2   N1   C6    180.00   0.0  0
 ACP  CONST_26  HN61  N6   C6   C5    180.00   0.0  0
 ACP  CONST_27  HN62  N6   C6   C5      0.00   0.0  0
 ACP  Var_01    C4'   C5'  O5'  PA   -135.17  30.0  3
 ACP  Var_02    O1B   PB   C3B  PG     52.82  30.0  1
 ACP  Var_03    PB    C3B  PG   O1G    41.87  30.0  3
 ACP  Var_04    O1A   PA   O3A  PB     48.75  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
 ACP  chir_03  C4'  C5'  O4'  C3'  negativ
 ACP  chir_04  C3'  O3'  C4'  C2'  positiv
 ACP  chir_05  C2'  O2'  C3'  C1'  positiv
 ACP  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
 ACP  plan-1  C1'   0.020
 ACP  plan-1  N9    0.020
 ACP  plan-1  C8    0.020
 ACP  plan-1  N7    0.020
 ACP  plan-1  C5    0.020
 ACP  plan-1  C6    0.020
 ACP  plan-1  N6    0.020
 ACP  plan-1  N1    0.020
 ACP  plan-1  C2    0.020
 ACP  plan-1  N3    0.020
 ACP  plan-1  C4    0.020
 ACP  plan-1  H8    0.020
 ACP  plan-1  H2    0.020
 ACP  plan-2  C6    0.020
 ACP  plan-2  N6    0.020
 ACP  plan-2  HN61  0.020
 ACP  plan-2  HN62  0.020

