# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 08:46:40 2022
#   Inital geometry file: a 87 line input string
#   Ligand name: 2-azanyl-7-[(2~{R},3~{R},4~{S},5~{R})-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]-3~{H}-pyrrolo[2,3-d]pyrimidin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=Nc2n(ccc2C(=O)N1)[C@@H]3O[C@H](CO)[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
 HD3  HD3  "2-azanyl-7-[(2R,3R,4S,5R)-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]-3H-pyrrolo[2,3-d]pyrimidin-4-one"
  ligand  34  20  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HD3
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
 HD3  C05  C  CR56  0  -0.189  -49.9707  -17.0923  -3.4991
 HD3  C06  C  CR6   0   0.499  -50.8230  -16.7738  -2.4030
 HD3  C01  C  CR15  0  -0.420  -50.1133  -17.0040  -4.9144
 HD3  C02  C  CR15  0  -0.025  -48.9544  -17.4748  -5.4418
 HD3  C04  C  CR56  0   0.534  -48.7123  -17.6196  -3.2307
 HD3  C12  C  CH1   0   0.220  -46.7993  -18.4219  -4.6597
 HD3  C09  C  CR6   0   0.671  -48.9621  -17.5728  -1.0166
 HD3  C13  C  CH1   0  -0.005  -45.6207  -17.7794  -3.9365
 HD3  C14  C  CH1   0  -0.061  -44.5597  -18.8708  -4.1136
 HD3  C15  C  CH1   0   0.009  -45.4137  -20.1578  -4.0519
 HD3  C17  C  CH2   0  -0.184  -45.2686  -20.9597  -2.7797
 HD3  N03  N  NR5   0  -0.565  -48.0926  -17.8475  -4.4208
 HD3  N08  N  NR16  0  -0.722  -50.2137  -17.0517  -1.1757
 HD3  N10  N  N     0  -0.514  -48.1842  -17.8721  -2.0201
 HD3  N11  N  NH2   0  -0.830  -48.5187  -17.7383   0.2447
 HD3  O07  O  O     0  -0.470  -51.9541  -16.3144  -2.4377
 HD3  O16  O  O2    0  -0.495  -46.7734  -19.7600  -4.2462
 HD3  O18  O  OH1   0  -0.664  -45.4706  -20.1422  -1.6541
 HD3  O19  O  OH1   0  -0.665  -43.9499  -18.6906  -5.3675
 HD3  O20  O  OH1   0  -0.656  -45.3398  -16.5364  -4.5021
 HD3  H1   H  HCR5  0   0.252  -50.9632  -16.6385  -5.4674
 HD3  H2   H  HCR5  0   0.289  -48.6493  -17.5811  -6.4704
 HD3  H3   H  HCH1  0   0.240  -46.6390  -18.3352  -5.7431
 HD3  H4   H  HCH1  0   0.252  -45.8544  -17.7051  -2.8702
 HD3  H5   H  HCH1  0   0.241  -43.8161  -18.8475  -3.3082
 HD3  H6   H  HCH1  0   0.241  -45.1150  -20.8209  -4.8740
 HD3  H7   H  HCH2  0   0.214  -45.9743  -21.8009  -2.8064
 HD3  H8   H  HCH2  0   0.204  -44.2611  -21.3953  -2.7933
 HD3  H9   H  HNR6  0   0.421  -50.7628  -16.8389  -0.3520
 HD3  H10  H  HNH2  0   0.405  -47.6811  -18.2854   0.3549
 HD3  H11  H  HNH2  0   0.409  -49.1685  -17.7797   1.0122
 HD3  H12  H  HOH1  0   0.458  -45.3073  -20.6662  -0.8652
 HD3  H13  H  HOH1  0   0.452  -43.3074  -19.3954  -5.4959
 HD3  H14  H  HOH1  0   0.457  -44.6977  -16.0823  -3.9484

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
 HD3  O19  C14  single    1.406  0.020  1.406
 HD3  C02  C01  aromatic  1.357  0.020  1.357
 HD3  C02  N03  aromatic  1.387  0.020  1.387
 HD3  O20  C13  single    1.394  0.020  1.394
 HD3  C01  C05  aromatic  1.425  0.020  1.425
 HD3  C12  N03  single    1.435  0.020  1.435
 HD3  C12  C13  single    1.525  0.020  1.525
 HD3  C12  O16  single    1.401  0.020  1.401
 HD3  C14  C13  single    1.532  0.020  1.532
 HD3  C14  C15  single    1.546  0.020  1.546
 HD3  N03  C04  aromatic  1.361  0.020  1.361
 HD3  C15  O16  single    1.430  0.020  1.430
 HD3  C15  C17  single    1.511  0.020  1.511
 HD3  C05  C04  aromatic  1.391  0.020  1.391
 HD3  C05  C06  single    1.424  0.020  1.424
 HD3  C04  N10  single    1.345  0.020  1.345
 HD3  C17  O18  single    1.406  0.020  1.406
 HD3  O07  C06  double    1.221  0.020  1.221
 HD3  C06  N08  single    1.398  0.020  1.398
 HD3  N10  C09  double    1.305  0.020  1.305
 HD3  N08  C09  single    1.365  0.020  1.365
 HD3  C09  N11  single    1.347  0.020  1.347
 HD3  C01  H1   single    0.930  0.020  1.080
 HD3  C02  H2   single    0.930  0.020  1.080
 HD3  C12  H3   single    0.970  0.020  1.090
 HD3  C13  H4   single    0.970  0.020  1.090
 HD3  C14  H5   single    0.970  0.020  1.090
 HD3  C15  H6   single    0.970  0.020  1.090
 HD3  C17  H7   single    0.970  0.020  1.090
 HD3  C17  H8   single    0.970  0.020  1.090
 HD3  N08  H9   single    0.860  0.020  1.020
 HD3  N11  H10  single    0.890  0.020  1.040
 HD3  N11  H11  single    0.890  0.020  1.040
 HD3  O18  H12  single    0.850  0.020  0.980
 HD3  O19  H13  single    0.850  0.020  0.980
 HD3  O20  H14  single    0.850  0.020  0.980

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
 HD3  C04  C05  C01  107.80  3.000
 HD3  C04  C05  C06  118.54  3.000
 HD3  C01  C05  C06  133.66  3.000
 HD3  O07  C06  N08  120.22  3.000
 HD3  N08  C06  C05  111.73  3.000
 HD3  O07  C06  C05  128.05  3.000
 HD3  H1   C01  C02  126.26  3.000
 HD3  H1   C01  C05  127.55  3.000
 HD3  C02  C01  C05  106.20  3.000
 HD3  H2   C02  N03  119.99  3.000
 HD3  H2   C02  C01  130.27  3.000
 HD3  N03  C02  C01  109.73  3.000
 HD3  N10  C04  N03  125.24  3.000
 HD3  N10  C04  C05  126.90  3.000
 HD3  N03  C04  C05  107.86  3.000
 HD3  H3   C12  O16  111.33  3.000
 HD3  H3   C12  N03  105.31  3.000
 HD3  O16  C12  N03  110.48  3.000
 HD3  H3   C12  C13  108.76  3.000
 HD3  O16  C12  C13  104.37  3.000
 HD3  N03  C12  C13  116.68  3.000
 HD3  N11  C09  N10  119.72  3.000
 HD3  N11  C09  N08  117.25  3.000
 HD3  N10  C09  N08  123.01  3.000
 HD3  H4   C13  O20  112.20  3.000
 HD3  H4   C13  C14  107.99  3.000
 HD3  O20  C13  C14  116.65  3.000
 HD3  H4   C13  C12  109.01  3.000
 HD3  C14  C13  C12  100.39  3.000
 HD3  O20  C13  C12  109.82  3.000
 HD3  H5   C14  O19  111.00  3.000
 HD3  H5   C14  C15  111.29  3.000
 HD3  O19  C14  C15  112.45  3.000
 HD3  H5   C14  C13  111.69  3.000
 HD3  C15  C14  C13  101.88  3.000
 HD3  O19  C14  C13  108.18  3.000
 HD3  H6   C15  O16  108.97  3.000
 HD3  H6   C15  C17  106.50  3.000
 HD3  O16  C15  C17  110.69  3.000
 HD3  H6   C15  C14  108.83  3.000
 HD3  C17  C15  C14  114.99  3.000
 HD3  O16  C15  C14  106.76  3.000
 HD3  H8   C17  H7   106.58  3.000
 HD3  H8   C17  O18  111.88  3.000
 HD3  H7   C17  O18  111.87  3.000
 HD3  H8   C17  C15  106.76  3.000
 HD3  H7   C17  C15  108.92  3.000
 HD3  O18  C17  C15  110.60  3.000
 HD3  C12  N03  C04  128.53  3.000
 HD3  C04  N03  C02  108.41  3.000
 HD3  C12  N03  C02  123.02  3.000
 HD3  H9   N08  C09  118.85  3.000
 HD3  H9   N08  C06  115.85  3.000
 HD3  C09  N08  C06  125.29  3.000
 HD3  C09  N10  C04  114.53  3.000
 HD3  H11  N11  H10  115.55  3.000
 HD3  H11  N11  C09  120.43  3.000
 HD3  H10  N11  C09  116.31  3.000
 HD3  C15  O16  C12  108.87  3.000
 HD3  H12  O18  C17  108.40  3.000
 HD3  H13  O19  C14  108.34  3.000
 HD3  H14  O20  C13  108.77  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
 HD3  CONST_01  N03  C02  C01  C05    0.00  0.0  0
 HD3  CONST_02  C02  N03  C04  C05    0.00  0.0  0
 HD3  CONST_03  C04  N03  C02  C01    0.00  0.0  0
 HD3  CONST_04  N03  C04  C05  C01    0.00  0.0  0
 HD3  CONST_05  C04  C05  C01  C02    0.00  0.0  0
 HD3  CONST_06  C12  N03  C04  C05  180.00  0.0  0
 HD3  CONST_07  C12  N03  C02  C01  180.00  0.0  0
 HD3  CONST_08  N10  C04  N03  C12    0.00  0.0  0
 HD3  CONST_09  C09  N08  C06  C05    0.00  0.0  0
 HD3  CONST_10  N10  C09  N08  C06    0.00  0.0  0
 HD3  CONST_11  N08  C09  N10  C04    0.00  0.0  0
 HD3  CONST_12  N11  C09  N08  C06  180.00  0.0  0
 HD3  CONST_13  N11  C09  N10  C04  180.00  0.0  0
 HD3  CONST_14  O07  C06  N08  C09  180.00  0.0  0
 HD3  CONST_15  H2   C02  C01  C05  180.00  0.0  0
 HD3  CONST_16  H1   C01  C05  C06    0.00  0.0  0
 HD3  CONST_17  H2   C02  N03  C04  180.00  0.0  0
 HD3  CONST_18  H1   C01  C05  C04  180.00  0.0  0
 HD3  CONST_19  H2   C02  N03  C12    0.00  0.0  0
 HD3  CONST_20  H1   C01  C02  N03  180.00  0.0  0
 HD3  CONST_21  H9   N08  C06  C05  180.00  0.0  0
 HD3  CONST_22  H9   N08  C09  N10  180.00  0.0  0
 HD3  CONST_23  H10  N11  C09  N08  180.00  0.0  0
 HD3  CONST_25  H10  N11  C09  N10    0.00  0.0  0
 HD3  CONST_27  H9   N08  C09  N11    0.00  0.0  0
 HD3  CONST_28  H9   N08  C06  O07    0.00  0.0  0

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
 HD3  chir_01  C12  N03  C13  O16  negativ
 HD3  chir_02  C13  O20  C14  C12  positiv
 HD3  chir_03  C14  O19  C15  C13  positiv
 HD3  chir_04  C15  O16  C14  C17  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
 HD3  plan-1  C05  0.020
 HD3  plan-1  C06  0.020
 HD3  plan-1  C01  0.020
 HD3  plan-1  C02  0.020
 HD3  plan-1  C04  0.020
 HD3  plan-1  C12  0.020
 HD3  plan-1  C09  0.020
 HD3  plan-1  N03  0.020
 HD3  plan-1  N08  0.020
 HD3  plan-1  N10  0.020
 HD3  plan-1  N11  0.020
 HD3  plan-1  O07  0.020
 HD3  plan-1  H1   0.020
 HD3  plan-1  H2   0.020
 HD3  plan-1  H9   0.020
 HD3  plan-1  H10  0.020
 HD3  plan-1  H11  0.020

