# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 08:47:11 2022
#   Inital geometry file: a 90 line input string
#   Ligand name: 2-azanyl-9-[(2~{R},3~{R},4~{S},5~{R})-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]-1-methyl-purin-6-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=Nc2n(cnc2C1=O)[C@@H]3O[C@H](CO)[C@@H](O)[C@H]3O)N
#
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
 H93  H93  "2-azanyl-9-[(2R,3R,4S,5R)-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]-1-methyl-purin-6-one"
  ligand  36  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 PERFECT
;

data_comp_H93
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
 H93  C01  C  CH3   0  -0.576  -11.8285  52.3611   1.1315
 H93  C03  C  CR6   0   0.525  -11.2104  52.2399   3.5075
 H93  C05  C  CR56  0  -0.079  -10.2463  51.7176   4.4141
 H93  C06  C  CR56  0   0.506   -9.2322  50.9165   3.9358
 H93  C08  C  CR6   0   0.710   -9.9064  51.0246   1.8223
 H93  C11  C  CR15  0   0.096   -9.0955  51.1985   6.1018
 H93  C13  C  CR15  0   0.213   -7.3077  49.7650   5.1134
 H93  C14  C  CR15  0  -0.037   -7.4585  48.3442   4.5560
 H93  C15  C  CR15  0  -0.042   -6.0019  48.0075   4.2498
 H93  C16  C  CR15  0  -0.017   -5.4793  49.3483   3.7427
 H93  C18  C  CH2   0  -0.155   -5.5642  49.4682   2.2351
 H93  N02  N  NR6   0  -0.578  -10.9470  51.8490   2.1729
 H93  N07  N  N     0  -0.520   -9.0305  50.5394   2.6697
 H93  N10  N  NR5   0  -0.549   -8.4936  50.5776   5.0331
 H93  N12  N  N     0  -0.443  -10.1457  51.8808   5.7734
 H93  O04  O  O     0  -0.468  -12.1652  52.9463   3.7806
 H93  O17  O  O     0  -0.487   -6.2706  50.3551   4.3825
 H93  O19  O  OH1   0  -0.664   -5.0958  50.7401   1.8609
 H93  O20  O  OH1   0  -0.664   -5.2954  47.6688   5.4166
 H93  O21  O  OH1   0  -0.657   -8.0089  47.4365   5.4619
 H93  H1   H  HCH3  0   0.289  -12.5247  53.0603   1.5776
 H93  H2   H  HCH3  0   0.266  -11.2535  52.8841   0.3686
 H93  H3   H  HCH3  0   0.264  -12.4009  51.5562   0.6700
 H93  H4   H  HCR5  0   0.292   -8.6957  51.0940   7.1001
 H93  H5   H  HCR5  0   0.250   -7.0621  49.7079   6.1812
 H93  H6   H  HCR5  0   0.254   -8.0217  48.3740   3.6161
 H93  H7   H  HCR5  0   0.251   -5.9183  47.2229   3.4869
 H93  H8   H  HCR5  0   0.251   -4.4362  49.4827   4.0494
 H93  H9   H  HCH2  0   0.205   -6.5968  49.3025   1.9038
 H93  H10  H  HCH2  0   0.201   -4.9522  48.6642   1.8051
 H93  H11  H  HNH2  0   0.412   -9.0575  50.0333   0.3045
 H93  H12  H  HNH2  0   0.423  -10.5063  50.8080  -0.1405
 H93  H13  H  HOH1  0   0.454   -5.2091  50.8336   0.9109
 H93  H14  H  HOH1  0   0.452   -5.7235  46.9056   5.8198
 H93  H15  H  HOH1  0   0.464   -8.9659  47.5360   5.4668
 H93  N09  N  NH2   0  -0.841   -9.7517  50.7300   0.5193

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
 H93  N09  C08  single    1.345  0.020  1.345
 H93  C01  N02  single    1.457  0.020  1.457
 H93  O19  C18  single    1.406  0.020  1.406
 H93  C08  N02  single    1.373  0.020  1.373
 H93  C08  N07  double    1.312  0.020  1.312
 H93  N02  C03  single    1.415  0.020  1.415
 H93  C18  C16  single    1.515  0.020  1.515
 H93  N07  C06  single    1.336  0.020  1.336
 H93  C03  O04  double    1.219  0.020  1.219
 H93  C03  C05  single    1.423  0.020  1.423
 H93  C16  O17  single    1.432  0.020  1.432
 H93  C16  C15  single    1.526  0.020  1.526
 H93  C06  C05  aromatic  1.378  0.020  1.378
 H93  C06  N10  aromatic  1.365  0.020  1.365
 H93  O17  C13  single    1.399  0.020  1.399
 H93  C05  N12  aromatic  1.373  0.020  1.373
 H93  C15  C14  single    1.526  0.020  1.526
 H93  C15  O20  single    1.405  0.020  1.405
 H93  C14  C13  single    1.534  0.020  1.534
 H93  C14  O21  single    1.396  0.020  1.396
 H93  C13  N10  single    1.440  0.020  1.440
 H93  N10  C11  aromatic  1.375  0.020  1.375
 H93  N12  C11  aromatic  1.295  0.020  1.295
 H93  C01  H1   single    0.970  0.020  1.090
 H93  C01  H2   single    0.970  0.020  1.090
 H93  C01  H3   single    0.970  0.020  1.090
 H93  C11  H4   single    0.930  0.020  1.080
 H93  C13  H5   single    0.970  0.020  1.090
 H93  C14  H6   single    0.970  0.020  1.090
 H93  C15  H7   single    0.970  0.020  1.090
 H93  C16  H8   single    0.970  0.020  1.090
 H93  C18  H9   single    0.970  0.020  1.090
 H93  C18  H10  single    0.970  0.020  1.090
 H93  N09  H11  single    0.890  0.020  1.040
 H93  N09  H12  single    0.890  0.020  1.040
 H93  O19  H13  single    0.850  0.020  0.980
 H93  O20  H14  single    0.850  0.020  0.980
 H93  O21  H15  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
 H93  H3   C01  H2   109.59  3.000
 H93  H3   C01  H1   108.27  3.000
 H93  H2   C01  H1   108.54  3.000
 H93  H3   C01  N02  111.14  3.000
 H93  H2   C01  N02  110.49  3.000
 H93  H1   C01  N02  108.75  3.000
 H93  O04  C03  N02  121.14  3.000
 H93  O04  C03  C05  126.93  3.000
 H93  N02  C03  C05  111.93  3.000
 H93  N12  C05  C06  111.04  3.000
 H93  N12  C05  C03  129.57  3.000
 H93  C06  C05  C03  119.40  3.000
 H93  N10  C06  N07  127.56  3.000
 H93  N10  C06  C05  105.27  3.000
 H93  N07  C06  C05  127.16  3.000
 H93  N09  C08  N07  117.91  3.000
 H93  N07  C08  N02  124.28  3.000
 H93  N09  C08  N02  117.78  3.000
 H93  H4   C11  N12  125.84  3.000
 H93  H4   C11  N10  120.83  3.000
 H93  N12  C11  N10  113.33  3.000
 H93  H5   C13  O17  111.37  3.000
 H93  H5   C13  N10  105.55  3.000
 H93  O17  C13  N10  110.08  3.000
 H93  H5   C13  C14  109.12  3.000
 H93  N10  C13  C14  114.93  3.000
 H93  O17  C13  C14  105.89  3.000
 H93  H6   C14  O21  111.82  3.000
 H93  H6   C14  C15  108.93  3.000
 H93  O21  C14  C15  111.29  3.000
 H93  H6   C14  C13  109.69  3.000
 H93  O21  C14  C13  113.92  3.000
 H93  C15  C14  C13  100.57  3.000
 H93  H7   C15  O20  111.50  3.000
 H93  H7   C15  C16  111.78  3.000
 H93  O20  C15  C16  108.39  3.000
 H93  H7   C15  C14  111.71  3.000
 H93  O20  C15  C14  111.50  3.000
 H93  C16  C15  C14  101.52  3.000
 H93  H8   C16  O17  108.35  3.000
 H93  H8   C16  C18  108.80  3.000
 H93  O17  C16  C18  110.98  3.000
 H93  H8   C16  C15  109.94  3.000
 H93  O17  C16  C15  106.27  3.000
 H93  C18  C16  C15  112.41  3.000
 H93  H10  C18  H9   107.20  3.000
 H93  H10  C18  O19  111.86  3.000
 H93  H9   C18  O19  111.70  3.000
 H93  H10  C18  C16  107.49  3.000
 H93  H9   C18  C16  109.96  3.000
 H93  O19  C18  C16  108.53  3.000
 H93  C08  N02  C03  123.20  3.000
 H93  C03  N02  C01  117.66  3.000
 H93  C08  N02  C01  119.14  3.000
 H93  C08  N07  C06  114.00  3.000
 H93  C13  N10  C11  124.90  3.000
 H93  C11  N10  C06  106.01  3.000
 H93  C13  N10  C06  129.08  3.000
 H93  C11  N12  C05  104.35  3.000
 H93  C16  O17  C13  110.27  3.000
 H93  H13  O19  C18  108.17  3.000
 H93  H14  O20  C15  108.36  3.000
 H93  H15  O21  C14  109.16  3.000
 H93  H12  N09  H11  115.55  3.000
 H93  H12  N09  C08  122.18  3.000
 H93  H11  N09  C08  115.96  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
 H93  CONST_01  C11  N10  C06  C05     0.00   0.0  0
 H93  CONST_02  N10  C11  N12  C05     0.00   0.0  0
 H93  CONST_03  C11  N12  C05  C06     0.00   0.0  0
 H93  CONST_04  N12  C11  N10  C06     0.00   0.0  0
 H93  CONST_05  N12  C05  C06  N10     0.00   0.0  0
 H93  CONST_06  C13  N10  C06  C05   180.00   0.0  0
 H93  CONST_07  N07  C06  N10  C13     0.00   0.0  0
 H93  CONST_08  N12  C11  N10  C13   180.00   0.0  0
 H93  CONST_09  N07  C08  N02  C03     0.00   0.0  0
 H93  CONST_10  C08  N02  C03  C05     0.00   0.0  0
 H93  CONST_11  N02  C08  N07  C06     0.00   0.0  0
 H93  CONST_12  N07  C08  N02  C01   180.00   0.0  0
 H93  CONST_13  C05  C03  N02  C01   180.00   0.0  0
 H93  CONST_14  N09  C08  N02  C03   180.00   0.0  0
 H93  CONST_15  N09  C08  N07  C06   180.00   0.0  0
 H93  CONST_16  O04  C03  N02  C08   180.00   0.0  0
 H93  CONST_17  H4   C11  N12  C05   180.00   0.0  0
 H93  CONST_18  H4   C11  N10  C06   180.00   0.0  0
 H93  CONST_19  H4   C11  N10  C13     0.00   0.0  0
 H93  CONST_20  N09  C08  N02  C01     0.00   0.0  0
 H93  CONST_21  O04  C03  N02  C01     0.00   0.0  0
 H93  CONST_22  H11  N09  C08  N02   180.00   0.0  0
 H93  CONST_24  H11  N09  C08  N07     0.00   0.0  0
 H93  Var_01    H1   C01  N02  C03     4.94  30.0  3
 H93  Var_02    H2   C01  N02  C03   123.97  30.0  3
 H93  Var_03    H3   C01  N02  C03  -114.15  30.0  3
 H93  Var_04    H1   C01  N02  C08  -174.73  30.0  3
 H93  Var_05    H2   C01  N02  C08   -55.70  30.0  3
 H93  Var_06    H3   C01  N02  C08    66.18  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
 H93  chir_01  C13  O17  C14  N10  positiv
 H93  chir_02  C14  O21  C13  C15  negativ
 H93  chir_03  C15  O20  C16  C14  positiv
 H93  chir_04  C16  O17  C15  C18  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
 H93  plan-1  C01  0.020
 H93  plan-1  C03  0.020
 H93  plan-1  C05  0.020
 H93  plan-1  C06  0.020
 H93  plan-1  C08  0.020
 H93  plan-1  C11  0.020
 H93  plan-1  C13  0.020
 H93  plan-1  N02  0.020
 H93  plan-1  N07  0.020
 H93  plan-1  N10  0.020
 H93  plan-1  N12  0.020
 H93  plan-1  O04  0.020
 H93  plan-1  H4   0.020
 H93  plan-1  H11  0.020
 H93  plan-1  H12  0.020
 H93  plan-1  N09  0.020

