# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 09:33:49 2022
#   Inital geometry file: a 101 line input string
#   Ligand name: 5'-O-[(R)-hydroxy(thiophosphonooxy)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)(S)=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
 AT4  AT4  5'-O-[(R)-hydroxy(thiophosphonooxy)phosphoryl]adenosine  ligand  40  27  .  2022-03-11  2022-03-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_AT4
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
 AT4  O5'   O  O2     0  -0.618  -1.8080   2.9880   1.8141
 AT4  C5'   C  CH2    0  -0.159  -0.5909   2.3977   1.4230
 AT4  C4'   C  CH1    0  -0.077  -0.1295   1.4549   2.5179
 AT4  O4'   O  O2     0  -0.490  -1.0844   0.4226   2.7845
 AT4  C3'   C  CH1    0  -0.024   1.1484   0.7126   2.1382
 AT4  O3'   O  OH1    0  -0.666   1.8221   0.2005   3.2558
 AT4  C2'   C  CH1    0  -0.015   0.5615  -0.4653   1.3596
 AT4  C1'   C  CH1    0   0.218  -0.7113  -0.7686   2.1651
 AT4  N1    N  N      0  -0.474  -2.8260  -4.7356  -0.2841
 AT4  C2    C  CR16   0   0.035  -1.7887  -4.6601   0.5476
 AT4  N3    N  N      0  -0.446  -1.3075  -3.5988   1.1691
 AT4  C4    C  CR56   0   0.477  -2.0045  -2.5007   0.8819
 AT4  C5    C  CR56   0   0.019  -3.1117  -2.4263   0.0504
 AT4  C6    C  CR6    0   0.458  -3.5216  -3.6271  -0.5564
 AT4  N6    N  NH2    0  -0.817  -4.5737  -3.6968  -1.3753
 AT4  N7    N  N      0  -0.471  -3.5927  -1.1457  -0.0018
 AT4  C8    C  CR15   0   0.100  -2.7960  -0.4626   0.7698
 AT4  N9    N  NR5    0  -0.539  -1.8110  -1.2261   1.3313
 AT4  O2'   O  OH1    0  -0.649   1.3540  -1.6042   1.2692
 AT4  PA    P  P      0   1.374  -2.4815   4.1574   0.8734
 AT4  O2A   O  O      0  -0.787  -3.5307   4.7986   1.7189
 AT4  O1A   O  OP    -1  -0.792  -1.3967   4.9384   0.2028
 AT4  O3A   O  O2     0  -0.748  -3.1842   3.2532  -0.3148
 AT4  PB    P  P      0   1.202  -4.7762   2.8245  -0.3136
 AT4  O1B   O  O      0  -0.772  -5.0788   2.0166   0.9070
 AT4  O2B   O  OP    -1  -0.774  -5.6092   3.9864  -0.7466
 AT4  S3B   S  S2     0  -0.546  -4.7702   1.5311  -2.0196
 AT4  H5'1  H  HCH2   0   0.206  -0.6971   1.8638   0.4698
 AT4  H5'2  H  HCH2   0   0.236   0.1897   3.1520   1.2809
 AT4  H4'   H  HCH1   0   0.265  -0.0033   2.0276   3.4416
 AT4  H3'   H  HCH1   0   0.252   1.8055   1.3284   1.5106
 AT4  HO3'  H  HOH1   0   0.457   2.1497   0.9398   3.7778
 AT4  H2'   H  HCH1   0   0.243   0.2689  -0.0998   0.3657
 AT4  H1'   H  HCH1   0   0.265  -0.5225  -1.5569   2.9012
 AT4  HN61  H  HNH2   0   0.408  -5.0762  -2.8686  -1.6414
 AT4  HN62  H  HNH2   0   0.402  -4.7832  -4.5540  -1.8570
 AT4  H8    H  HCR5   0   0.306  -2.9086   0.5891   0.9836
 AT4  HO2'  H  HOH1   0   0.462   2.0682  -1.4315   0.6478
 AT4  HS3B  H  HSH1   0   0.232  -4.3578   0.4073  -1.4065
 AT4  H2    H  HCR6   0   0.249  -1.2740  -5.5967   0.7340

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
 AT4  O5'  PA    single    1.645  0.020  1.645
 AT4  O5'  C5'   single    1.408  0.020  1.408
 AT4  C5'  C4'   single    1.517  0.020  1.517
 AT4  C5'  H5'1  single    0.970  0.020  1.090
 AT4  C5'  H5'2  single    0.970  0.020  1.090
 AT4  C4'  C3'   single    1.526  0.020  1.526
 AT4  C4'  O4'   single    1.431  0.020  1.431
 AT4  C4'  H4'   single    0.970  0.020  1.090
 AT4  O4'  C1'   single    1.393  0.020  1.393
 AT4  C3'  O3'   single    1.402  0.020  1.402
 AT4  C3'  C2'   single    1.529  0.020  1.529
 AT4  C3'  H3'   single    0.970  0.020  1.090
 AT4  O3'  HO3'  single    0.850  0.020  0.980
 AT4  C2'  O2'   single    1.390  0.020  1.390
 AT4  C2'  C1'   single    1.537  0.020  1.537
 AT4  C2'  H2'   single    0.970  0.020  1.090
 AT4  C1'  N9    single    1.454  0.020  1.454
 AT4  C1'  H1'   single    0.970  0.020  1.090
 AT4  N1   C2    aromatic  1.332  0.020  1.332
 AT4  N1   C6    aromatic  1.337  0.020  1.337
 AT4  C2   N3    aromatic  1.321  0.020  1.321
 AT4  C2   H2    single    0.930  0.020  1.080
 AT4  N3   C4    aromatic  1.332  0.020  1.332
 AT4  C4   N9    aromatic  1.365  0.020  1.365
 AT4  C4   C5    aromatic  1.387  0.020  1.387
 AT4  C5   N7    aromatic  1.369  0.020  1.369
 AT4  C5   C6    aromatic  1.406  0.020  1.406
 AT4  C6   N6    single    1.335  0.020  1.335
 AT4  N6   HN61  single    0.860  0.020  1.020
 AT4  N6   HN62  single    0.860  0.020  1.020
 AT4  N7   C8    aromatic  1.303  0.020  1.303
 AT4  C8   N9    aromatic  1.367  0.020  1.367
 AT4  C8   H8    single    0.930  0.020  1.080
 AT4  O2'  HO2'  single    0.850  0.020  0.980
 AT4  PA   O2A   deloc     1.492  0.020  1.492
 AT4  PA   O3A   single    1.650  0.020  1.650
 AT4  PA   O1A   deloc     1.495  0.020  1.495
 AT4  O3A  PB    single    1.649  0.020  1.649
 AT4  PB   S3B   single    2.141  0.020  2.141
 AT4  PB   O1B   deloc     1.495  0.020  1.495
 AT4  PB   O2B   deloc     1.494  0.020  1.494
 AT4  S3B  HS3B  single    1.200  0.020  1.300

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
 AT4  PA    O5'  C5'   119.54  3.000
 AT4  H5'2  C5'  H5'1  106.95  3.000
 AT4  H5'2  C5'  C4'   107.76  3.000
 AT4  H5'1  C5'  C4'   110.73  3.000
 AT4  H5'2  C5'  O5'   111.31  3.000
 AT4  H5'1  C5'  O5'   111.19  3.000
 AT4  C4'   C5'  O5'   108.85  3.000
 AT4  H4'   C4'  C3'   111.60  3.000
 AT4  H4'   C4'  O4'   107.28  3.000
 AT4  C3'   C4'  O4'   104.73  3.000
 AT4  H4'   C4'  C5'   108.62  3.000
 AT4  O4'   C4'  C5'   112.32  3.000
 AT4  C3'   C4'  C5'   112.18  3.000
 AT4  C1'   O4'  C4'   110.80  3.000
 AT4  H3'   C3'  C2'   111.76  3.000
 AT4  H3'   C3'  O3'   111.91  3.000
 AT4  C2'   C3'  O3'   108.00  3.000
 AT4  H3'   C3'  C4'   111.76  3.000
 AT4  C2'   C3'  C4'   100.37  3.000
 AT4  O3'   C3'  C4'   112.45  3.000
 AT4  HO3'  O3'  C3'   108.38  3.000
 AT4  H2'   C2'  O2'   111.44  3.000
 AT4  H2'   C2'  C1'   108.62  3.000
 AT4  O2'   C2'  C1'   110.15  3.000
 AT4  H2'   C2'  C3'   107.86  3.000
 AT4  C1'   C2'  C3'   101.71  3.000
 AT4  O2'   C2'  C3'   116.44  3.000
 AT4  H1'   C1'  N9    106.82  3.000
 AT4  H1'   C1'  C2'   110.59  3.000
 AT4  N9    C1'  C2'   112.83  3.000
 AT4  H1'   C1'  O4'   111.28  3.000
 AT4  N9    C1'  O4'   108.74  3.000
 AT4  C2'   C1'  O4'   106.63  3.000
 AT4  C6    N1   C2    119.04  3.000
 AT4  H2    C2   N3    116.11  3.000
 AT4  H2    C2   N1    115.33  3.000
 AT4  N3    C2   N1    128.56  3.000
 AT4  C4    N3   C2    111.74  3.000
 AT4  N9    C4   C5    105.10  3.000
 AT4  C5    C4   N3    126.25  3.000
 AT4  N9    C4   N3    128.65  3.000
 AT4  N7    C5   C6    132.83  3.000
 AT4  C6    C5   C4    116.46  3.000
 AT4  N7    C5   C4    110.71  3.000
 AT4  N6    C6   C5    122.61  3.000
 AT4  N6    C6   N1    119.45  3.000
 AT4  C5    C6   N1    117.94  3.000
 AT4  HN62  N6   HN61  118.15  3.000
 AT4  HN62  N6   C6    120.18  3.000
 AT4  HN61  N6   C6    120.90  3.000
 AT4  C8    N7   C5    104.66  3.000
 AT4  H8    C8   N9    122.56  3.000
 AT4  H8    C8   N7    124.38  3.000
 AT4  N9    C8   N7    113.03  3.000
 AT4  C8    N9   C4    106.51  3.000
 AT4  C8    N9   C1'   127.22  3.000
 AT4  C4    N9   C1'   126.14  3.000
 AT4  HO2'  O2'  C2'   108.54  3.000
 AT4  O3A   PA   O1A   105.79  3.000
 AT4  O1A   PA   O2A   122.66  3.000
 AT4  O3A   PA   O2A   110.12  3.000
 AT4  O1A   PA   O5'   109.31  3.000
 AT4  O3A   PA   O5'   101.34  3.000
 AT4  O2A   PA   O5'   105.62  3.000
 AT4  PB    O3A  PA    123.59  3.000
 AT4  S3B   PB   O2B   103.92  3.000
 AT4  O2B   PB   O1B   122.97  3.000
 AT4  S3B   PB   O1B   108.95  3.000
 AT4  O2B   PB   O3A   109.63  3.000
 AT4  O1B   PB   O3A   109.67  3.000
 AT4  S3B   PB   O3A    98.85  3.000
 AT4  HS3B  S3B  PB     98.19  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
 AT4  CONST_01  C4    N3   C2   N1      0.00   0.0  0
 AT4  CONST_02  C4    C5   C6   N1      0.00   0.0  0
 AT4  CONST_03  N7    C5   C6   N1    180.00   0.0  0
 AT4  CONST_04  C5    C6   N1   C2      0.00   0.0  0
 AT4  CONST_05  N9    C4   N3   C2    180.00   0.0  0
 AT4  CONST_06  C5    C4   N3   C2      0.00   0.0  0
 AT4  CONST_07  C6    N1   C2   N3      0.00   0.0  0
 AT4  CONST_08  C8    N9   C4   N3    180.00   0.0  0
 AT4  CONST_09  N7    C5   C4   N3    180.00   0.0  0
 AT4  CONST_10  C6    C5   C4   N3      0.00   0.0  0
 AT4  CONST_11  N7    C8   N9   C4      0.00   0.0  0
 AT4  CONST_12  C8    N7   C5   C4      0.00   0.0  0
 AT4  CONST_13  C8    N9   C4   C5      0.00   0.0  0
 AT4  CONST_14  N9    C8   N7   C5      0.00   0.0  0
 AT4  CONST_15  N9    C4   C5   C6    180.00   0.0  0
 AT4  CONST_16  C8    N7   C5   C6    180.00   0.0  0
 AT4  CONST_17  N9    C4   C5   N7      0.00   0.0  0
 AT4  CONST_18  N3    C4   N9   C1'     0.00   0.0  0
 AT4  CONST_19  C5    C4   N9   C1'   180.00   0.0  0
 AT4  CONST_20  N7    C8   N9   C1'   180.00   0.0  0
 AT4  CONST_21  N6    C6   N1   C2    180.00   0.0  0
 AT4  CONST_22  N6    C6   C5   C4    180.00   0.0  0
 AT4  CONST_23  N7    C5   C6   N6      0.00   0.0  0
 AT4  CONST_24  H8    C8   N9   C1'     0.00   0.0  0
 AT4  CONST_25  H2    C2   N3   C4    180.00   0.0  0
 AT4  CONST_26  HN61  N6   C6   N1    180.00   0.0  0
 AT4  CONST_27  HN62  N6   C6   N1      0.00   0.0  0
 AT4  Var_01    O2A   PA   O5'  C5'  -165.86  30.0  3
 AT4  Var_02    S3B   PB   O3A  PA   -173.91  30.0  3
 AT4  Var_03    H5'1  C5'  O5'  PA    -62.97  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
 AT4  chir_01  C4'  C5'  C3'  O4'  positiv
 AT4  chir_02  C3'  O3'  C2'  C4'  negativ
 AT4  chir_03  C2'  O2'  C1'  C3'  negativ
 AT4  chir_04  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
 AT4  plan-1  C1'   0.020
 AT4  plan-1  N1    0.020
 AT4  plan-1  C2    0.020
 AT4  plan-1  N3    0.020
 AT4  plan-1  C4    0.020
 AT4  plan-1  C5    0.020
 AT4  plan-1  C6    0.020
 AT4  plan-1  N6    0.020
 AT4  plan-1  N7    0.020
 AT4  plan-1  C8    0.020
 AT4  plan-1  N9    0.020
 AT4  plan-1  H8    0.020
 AT4  plan-1  H2    0.020
 AT4  plan-2  C6    0.020
 AT4  plan-2  N6    0.020
 AT4  plan-2  HN61  0.020
 AT4  plan-2  HN62  0.020

