# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 05:56:06 2022
#   Inital geometry file: a 87 line input string
#   Ligand name: 9-[(2~{R},3~{R},4~{R})-5-(hydroxymethyl)-3-methoxy-4-oxidanyl-oxolan-2-yl]-3~{H}-purine-2,6-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@@H]1[C@H](O)[C@@H](CO)O[C@H]1n2cnc3C(=O)NC(=O)Nc23
#
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
 H5C  H5C  "9-[(2R,3R,4R)-5-(hydroxymethyl)-3-methoxy-4-oxidanyl-oxolan-2-yl]-3H-purine-2,6-dione"
  ligand  35  21  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_H5C
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
 H5C  C02  C  CR6   0   0.524  -11.0942  -52.0385  -2.4110
 H5C  C03  C  CR56  0  -0.080  -10.4160  -51.4976  -3.5538
 H5C  C05  C  CR15  0   0.103   -9.6482  -51.0895  -5.4811
 H5C  C07  C  CH1   0   0.186   -8.2643  -49.0277  -5.0527
 H5C  C08  C  CH1   0   0.003   -6.9200  -49.4776  -5.6526
 H5C  C10  C  CH3   0  -0.414   -5.9980  -51.0371  -4.1405
 H5C  C11  C  CH1   0  -0.039   -6.5820  -48.2691  -6.5161
 H5C  C13  C  CH1   0  -0.039   -7.9628  -47.9043  -7.0659
 H5C  C14  C  CH2   0  -0.155   -8.2748  -48.5826  -8.3841
 H5C  C17  C  CR56  0   0.642   -9.6336  -50.3799  -3.4232
 H5C  C19  C  CR6   0   0.666  -10.0510  -50.1675  -1.1043
 H5C  N04  N  N     0  -0.431  -10.4133  -51.9236  -4.8554
 H5C  N06  N  NR5   0  -0.526   -9.1313  -50.1156  -4.6513
 H5C  N18  N  NR16  0  -0.743   -9.4346  -49.7247  -2.2513
 H5C  N20  N  NR16  0  -0.735  -10.8292  -51.2940  -1.2593
 H5C  O01  O  O     0  -0.440  -11.8197  -53.0106  -2.3753
 H5C  O09  O  O2    0  -0.472   -5.9235  -49.7571  -4.7316
 H5C  O12  O  OH1   0  -0.662   -6.0628  -47.2752  -5.6725
 H5C  O15  O  OH1   0  -0.662   -9.5654  -48.1974  -8.7832
 H5C  O16  O  O2    0  -0.481   -8.9014  -48.2976  -6.0564
 H5C  O21  O  O     0  -0.460   -9.9162  -49.6071  -0.0389
 H5C  H1   H  HCR5  0   0.307   -9.4191  -51.1118  -6.5357
 H5C  H2   H  HCH1  0   0.261   -8.0773  -48.4135  -4.1648
 H5C  H3   H  HCH1  0   0.254   -7.0940  -50.3366  -6.3192
 H5C  H4   H  HCH3  0   0.244   -5.0451  -51.2227  -3.6472
 H5C  H5   H  HCH3  0   0.216   -6.7874  -51.1121  -3.3867
 H5C  H6   H  HCH3  0   0.216   -6.1604  -51.8216  -4.8874
 H5C  H7   H  HCH1  0   0.258   -5.8825  -48.5274  -7.3208
 H5C  H8   H  HCH1  0   0.260   -8.0481  -46.8208  -7.2047
 H5C  H10  H  HCH2  0   0.210   -7.5102  -48.2692  -9.1071
 H5C  H11  H  HCH2  0   0.205   -8.1877  -49.6728  -8.2795
 H5C  H12  H  HNR6  0   0.444   -8.8566  -48.8993  -2.1733
 H5C  H13  H  HNR6  0   0.427  -11.2783  -51.6152  -0.4103
 H5C  H14  H  HOH1  0   0.457   -5.9088  -46.4808  -6.1943
 H5C  H15  H  HOH1  0   0.456   -9.7653  -48.6303  -9.6179

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
 H5C  C02  C03  single    1.435  0.020  1.435
 H5C  C02  N20  single    1.397  0.020  1.397
 H5C  C02  O01  double    1.214  0.020  1.214
 H5C  C03  C17  aromatic  1.371  0.020  1.371
 H5C  C03  N04  aromatic  1.370  0.020  1.370
 H5C  C05  N04  aromatic  1.293  0.020  1.293
 H5C  C05  N06  aromatic  1.380  0.020  1.380
 H5C  C07  C08  single    1.539  0.020  1.539
 H5C  C07  N06  single    1.448  0.020  1.448
 H5C  C07  O16  single    1.395  0.020  1.395
 H5C  C08  C11  single    1.523  0.020  1.523
 H5C  C08  O09  single    1.385  0.020  1.385
 H5C  C10  O09  single    1.412  0.020  1.412
 H5C  C11  C13  single    1.530  0.020  1.530
 H5C  C11  O12  single    1.403  0.020  1.403
 H5C  C13  C14  single    1.515  0.020  1.515
 H5C  C14  O15  single    1.405  0.020  1.405
 H5C  C17  N06  aromatic  1.353  0.020  1.353
 H5C  C17  N18  single    1.357  0.020  1.357
 H5C  C19  N18  single    1.375  0.020  1.375
 H5C  C19  N20  single    1.378  0.020  1.378
 H5C  C19  O21  double    1.211  0.020  1.211
 H5C  C05  H1   single    0.930  0.020  1.080
 H5C  C07  H2   single    0.970  0.020  1.090
 H5C  C08  H3   single    0.970  0.020  1.090
 H5C  C10  H4   single    0.970  0.020  1.090
 H5C  C10  H5   single    0.970  0.020  1.090
 H5C  C10  H6   single    0.970  0.020  1.090
 H5C  C11  H7   single    0.970  0.020  1.090
 H5C  C13  H8   single    0.970  0.020  1.090
 H5C  C14  H10  single    0.970  0.020  1.090
 H5C  C14  H11  single    0.970  0.020  1.090
 H5C  N18  H12  single    0.860  0.020  1.020
 H5C  N20  H13  single    0.860  0.020  1.020
 H5C  O12  H14  single    0.850  0.020  0.980
 H5C  O15  H15  single    0.850  0.020  0.980
 H5C  O16  C13  single    1.433  0.020  1.433

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
 H5C  O01  C02  N20  121.07  3.000
 H5C  O01  C02  C03  127.45  3.000
 H5C  N20  C02  C03  111.48  3.000
 H5C  N04  C03  C17  110.06  3.000
 H5C  N04  C03  C02  129.84  3.000
 H5C  C17  C03  C02  120.09  3.000
 H5C  H1   C05  N06  121.51  3.000
 H5C  H1   C05  N04  125.80  3.000
 H5C  N06  C05  N04  112.69  3.000
 H5C  H2   C07  O16  111.57  3.000
 H5C  H2   C07  N06  107.38  3.000
 H5C  O16  C07  N06  108.62  3.000
 H5C  H2   C07  C08  109.31  3.000
 H5C  O16  C07  C08  105.75  3.000
 H5C  N06  C07  C08  114.29  3.000
 H5C  H3   C08  O09  111.02  3.000
 H5C  H3   C08  C11  108.11  3.000
 H5C  O09  C08  C11  112.16  3.000
 H5C  H3   C08  C07  109.03  3.000
 H5C  O09  C08  C07  115.34  3.000
 H5C  C11  C08  C07  100.53  3.000
 H5C  H6   C10  H5   108.28  3.000
 H5C  H6   C10  H4   108.46  3.000
 H5C  H5   C10  H4   107.92  3.000
 H5C  H6   C10  O09  111.82  3.000
 H5C  H5   C10  O09  112.87  3.000
 H5C  H4   C10  O09  107.34  3.000
 H5C  H7   C11  O12  111.83  3.000
 H5C  H7   C11  C13  111.59  3.000
 H5C  O12  C11  C13  112.39  3.000
 H5C  H7   C11  C08  111.74  3.000
 H5C  O12  C11  C08  107.65  3.000
 H5C  C13  C11  C08  101.10  3.000
 H5C  H8   C13  O16  108.04  3.000
 H5C  O16  C13  C14  110.80  3.000
 H5C  H8   C13  C14  108.45  3.000
 H5C  O16  C13  C11  105.80  3.000
 H5C  H8   C13  C11  110.58  3.000
 H5C  C14  C13  C11  113.06  3.000
 H5C  H11  C14  H10  106.90  3.000
 H5C  H11  C14  O15  111.83  3.000
 H5C  H10  C14  O15  111.99  3.000
 H5C  H11  C14  C13  110.20  3.000
 H5C  H10  C14  C13  107.56  3.000
 H5C  O15  C14  C13  108.28  3.000
 H5C  N18  C17  N06  129.42  3.000
 H5C  N18  C17  C03  124.03  3.000
 H5C  N06  C17  C03  106.55  3.000
 H5C  O21  C19  N20  122.69  3.000
 H5C  O21  C19  N18  122.33  3.000
 H5C  N20  C19  N18  114.99  3.000
 H5C  C05  N04  C03  105.09  3.000
 H5C  C17  N06  C07  128.38  3.000
 H5C  C17  N06  C05  105.59  3.000
 H5C  C07  N06  C05  126.00  3.000
 H5C  H12  N18  C19  117.05  3.000
 H5C  H12  N18  C17  123.00  3.000
 H5C  C19  N18  C17  119.93  3.000
 H5C  H13  N20  C19  114.54  3.000
 H5C  H13  N20  C02  115.98  3.000
 H5C  C19  N20  C02  129.47  3.000
 H5C  C10  O09  C08  115.04  3.000
 H5C  H14  O12  C11  108.53  3.000
 H5C  H15  O15  C14  108.32  3.000
 H5C  C13  O16  C07  110.57  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
 H5C  CONST_01  C05  N06  C17  C03    0.00   0.0  0
 H5C  CONST_02  N06  C05  N04  C03    0.00   0.0  0
 H5C  CONST_03  C17  C03  N04  C05    0.00   0.0  0
 H5C  CONST_04  N04  C05  N06  C17    0.00   0.0  0
 H5C  CONST_05  N06  C17  C03  N04    0.00   0.0  0
 H5C  CONST_06  C07  N06  C17  C03  180.00   0.0  0
 H5C  CONST_07  N04  C05  N06  C07  180.00   0.0  0
 H5C  CONST_08  N18  C17  N06  C07    0.00   0.0  0
 H5C  CONST_09  N18  C19  N20  C02    0.00   0.0  0
 H5C  CONST_10  C19  N20  C02  C03    0.00   0.0  0
 H5C  CONST_11  N20  C19  N18  C17    0.00   0.0  0
 H5C  CONST_12  O21  C19  N20  C02  180.00   0.0  0
 H5C  CONST_13  O21  C19  N18  C17  180.00   0.0  0
 H5C  CONST_14  O01  C02  N20  C19  180.00   0.0  0
 H5C  CONST_15  H1   C05  N04  C03  180.00   0.0  0
 H5C  CONST_16  H1   C05  N06  C07    0.00   0.0  0
 H5C  CONST_17  H1   C05  N06  C17  180.00   0.0  0
 H5C  CONST_18  H13  N20  C02  C03  180.00   0.0  0
 H5C  CONST_19  H13  N20  C19  N18  180.00   0.0  0
 H5C  CONST_20  H12  N18  C19  N20  180.00   0.0  0
 H5C  CONST_21  H13  N20  C02  O01    0.00   0.0  0
 H5C  CONST_22  H12  N18  C19  O21    0.00   0.0  0
 H5C  CONST_23  H13  N20  C19  O21    0.00   0.0  0
 H5C  Var_01    H4   C10  O09  C08  165.91  30.0  3
 H5C  Var_02    H5   C10  O09  C08  -75.31  30.0  3
 H5C  Var_03    H6   C10  O09  C08   47.07  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
 H5C  chir_01  C07  C08  N06  O16  positiv
 H5C  chir_02  C08  O09  C11  C07  positiv
 H5C  chir_03  C11  O12  C13  C08  positiv
 H5C  chir_04  C13  O16  C14  C11  positiv

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
 H5C  plan-1  C02  0.020
 H5C  plan-1  C03  0.020
 H5C  plan-1  C05  0.020
 H5C  plan-1  C07  0.020
 H5C  plan-1  C17  0.020
 H5C  plan-1  C19  0.020
 H5C  plan-1  N04  0.020
 H5C  plan-1  N06  0.020
 H5C  plan-1  N18  0.020
 H5C  plan-1  N20  0.020
 H5C  plan-1  O01  0.020
 H5C  plan-1  O21  0.020
 H5C  plan-1  H1   0.020
 H5C  plan-1  H12  0.020
 H5C  plan-1  H13  0.020

