# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 15:09:34 2020
#   Inital geometry file: a 73 line input string
#   Ligand name: [(2S,3R,4R)-4-(6-amino-9H-purin-9-yl)oxetane-2,3-diyl]dimethanol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO)[C@H]3CO
#
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
 7D7  7D7  '[(2S,3R,4R)-4-(6-amino-9H-purin-9-yl)oxetane-2,3-diyl]dimethanol'  ligand  31  18  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_7D7
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
 7D7  O01  O  O     0  -0.510   1.8500  -0.5905  -1.1534
 7D7  C02  C  C     0   0.056   2.9426  -0.0200  -0.3948
 7D7  C03  C  CH2   0  -0.154   3.6927  -1.0245   0.4337
 7D7  O04  O  OH1   0  -0.667   4.4068  -1.8819  -0.4211
 7D7  C05  C  C     0  -0.435   1.9753   0.9038   0.3481
 7D7  C06  C  CH2   0  -0.138   2.2420   2.3874   0.3153
 7D7  O07  O  OH1   0  -0.666   3.3929   2.6293   1.0885
 7D7  C08  C  C     0   0.256   0.9431   0.3714  -0.6499
 7D7  N09  N  NR5   0  -0.538  -0.2566  -0.2289  -0.1408
 7D7  C10  C  CR15  0   0.114  -0.3526  -1.3070   0.6992
 7D7  N11  N  N     0  -0.449  -1.5773  -1.6267   0.9900
 7D7  C12  C  CR56  0  -0.015  -2.3403  -0.7114   0.3104
 7D7  C13  C  CR6   0   0.462  -3.7294  -0.5114   0.2065
 7D7  N14  N  NH2   0  -0.816  -4.6187  -1.2772   0.8387
 7D7  N15  N  N     0  -0.474  -4.1605   0.4979  -0.5592
 7D7  C16  C  CR16  0   0.047  -3.2710   1.2617  -1.1869
 7D7  N17  N  N     0  -0.457  -1.9521   1.1726  -1.1677
 7D7  C18  C  CR56  0   0.493  -1.5395   0.1651  -0.4030
 7D7  H1   H  H     0   0.241   3.6339   0.5145  -1.0569
 7D7  H2   H  HCH2  0   0.212   4.3528  -0.4578   1.1050
 7D7  H3   H  HCH2  0   0.197   2.9878  -1.5740   1.0720
 7D7  H4   H  HOH1  0   0.460   4.8889  -2.5142   0.1194
 7D7  H5   H  H     0   0.285   1.7762   0.5753   1.3729
 7D7  H6   H  HCH2  0   0.202   2.3771   2.7084  -0.7260
 7D7  H7   H  HCH2  0   0.215   1.3643   2.9208   0.7032
 7D7  H8   H  HOH1  0   0.459   3.6075   3.5646   1.0274
 7D7  H9   H  H     0   0.256   0.6305   1.1008  -1.4038
 7D7  H10  H  HCR5  0   0.296   0.5223  -1.8279   1.0583
 7D7  H11  H  HNH2  0   0.412  -4.3280  -2.0644   1.3911
 7D7  H12  H  HNH2  0   0.404  -5.6038  -1.1177   0.7159
 7D7  H13  H  HCR6  0   0.253  -3.6873   2.0604  -1.7916

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
 7D7  O07  C06  single    1.407  0.020  1.407
 7D7  C06  C05  single    1.508  0.020  1.508
 7D7  C02  C03  single    1.503  0.020  1.503
 7D7  C02  O01  single    1.447  0.020  1.447
 7D7  C02  C05  single    1.530  0.020  1.530
 7D7  C03  O04  single    1.406  0.020  1.406
 7D7  O01  C08  single    1.415  0.020  1.415
 7D7  C05  C08  single    1.531  0.020  1.531
 7D7  C08  N09  single    1.435  0.020  1.435
 7D7  N09  C18  aromatic  1.367  0.020  1.367
 7D7  N09  C10  aromatic  1.370  0.020  1.370
 7D7  N17  C18  aromatic  1.330  0.020  1.330
 7D7  N17  C16  aromatic  1.322  0.020  1.322
 7D7  C18  C12  aromatic  1.385  0.020  1.385
 7D7  C16  N15  aromatic  1.330  0.020  1.330
 7D7  C10  N11  aromatic  1.299  0.020  1.299
 7D7  C12  N11  aromatic  1.372  0.020  1.372
 7D7  C12  C13  aromatic  1.407  0.020  1.407
 7D7  N15  C13  aromatic  1.338  0.020  1.338
 7D7  C13  N14  single    1.333  0.020  1.333
 7D7  C02  H1   single    0.970  0.020  1.090
 7D7  C03  H2   single    0.970  0.020  1.090
 7D7  C03  H3   single    0.970  0.020  1.090
 7D7  O04  H4   single    0.850  0.020  0.980
 7D7  C05  H5   single    0.970  0.020  1.090
 7D7  C06  H6   single    0.970  0.020  1.090
 7D7  C06  H7   single    0.970  0.020  1.090
 7D7  O07  H8   single    0.850  0.020  0.980
 7D7  C08  H9   single    0.970  0.020  1.090
 7D7  C10  H10  single    0.930  0.020  1.080
 7D7  N14  H11  single    0.860  0.020  1.020
 7D7  N14  H12  single    0.860  0.020  1.020
 7D7  C16  H13  single    0.930  0.020  1.080

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
 7D7  C08  O01  C02   91.68  3.000
 7D7  H1   C02  C05  113.42  3.000
 7D7  H1   C02  C03  110.13  3.000
 7D7  C05  C02  C03  116.84  3.000
 7D7  H1   C02  O01  110.59  3.000
 7D7  C05  C02  O01   90.87  3.000
 7D7  C03  C02  O01  113.72  3.000
 7D7  H3   C03  H2   106.77  3.000
 7D7  H3   C03  O04  111.98  3.000
 7D7  H2   C03  O04  112.39  3.000
 7D7  H3   C03  C02  109.54  3.000
 7D7  H2   C03  C02  106.97  3.000
 7D7  O04  C03  C02  109.03  3.000
 7D7  H4   O04  C03  108.31  3.000
 7D7  H5   C05  C08  112.54  3.000
 7D7  H5   C05  C06  110.35  3.000
 7D7  C08  C05  C06  116.57  3.000
 7D7  H5   C05  C02  112.86  3.000
 7D7  C08  C05  C02   84.25  3.000
 7D7  C06  C05  C02  118.15  3.000
 7D7  H7   C06  H6   106.94  3.000
 7D7  H7   C06  O07  112.10  3.000
 7D7  H6   C06  O07  111.72  3.000
 7D7  H7   C06  C05  109.21  3.000
 7D7  H6   C06  C05  109.27  3.000
 7D7  O07  C06  C05  107.57  3.000
 7D7  H8   O07  C06  108.35  3.000
 7D7  H9   C08  N09  106.52  3.000
 7D7  H9   C08  C05  114.18  3.000
 7D7  N09  C08  C05  118.55  3.000
 7D7  H9   C08  O01  113.02  3.000
 7D7  N09  C08  O01  112.20  3.000
 7D7  C05  C08  O01   92.08  3.000
 7D7  C18  N09  C10  106.18  3.000
 7D7  C10  N09  C08  127.25  3.000
 7D7  C18  N09  C08  126.57  3.000
 7D7  H10  C10  N11  124.81  3.000
 7D7  H10  C10  N09  121.79  3.000
 7D7  N11  C10  N09  113.39  3.000
 7D7  C12  N11  C10  104.44  3.000
 7D7  C18  C12  C13  116.28  3.000
 7D7  C13  C12  N11  132.88  3.000
 7D7  C18  C12  N11  110.84  3.000
 7D7  N15  C13  N14  119.33  3.000
 7D7  N14  C13  C12  122.81  3.000
 7D7  N15  C13  C12  117.86  3.000
 7D7  H12  N14  H11  118.35  3.000
 7D7  H12  N14  C13  120.30  3.000
 7D7  H11  N14  C13  121.19  3.000
 7D7  C16  N15  C13  119.20  3.000
 7D7  H13  C16  N17  116.14  3.000
 7D7  H13  C16  N15  115.43  3.000
 7D7  N17  C16  N15  128.43  3.000
 7D7  C18  N17  C16  111.64  3.000
 7D7  N17  C18  C12  126.58  3.000
 7D7  C12  C18  N09  105.15  3.000
 7D7  N17  C18  N09  128.27  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
 7D7  CONST_01  C16  N17  C18  N09  180.00  0.0  0
 7D7  CONST_02  N11  C12  C18  N09    0.00  0.0  0
 7D7  CONST_03  C13  C12  C18  N09  180.00  0.0  0
 7D7  CONST_04  C12  N11  C10  N09    0.00  0.0  0
 7D7  CONST_05  N17  C18  N09  C10  180.00  0.0  0
 7D7  CONST_06  C12  C18  N09  C10    0.00  0.0  0
 7D7  CONST_07  C18  C12  N11  C10    0.00  0.0  0
 7D7  CONST_08  C13  C12  N11  C10  180.00  0.0  0
 7D7  CONST_09  C18  N09  C10  N11    0.00  0.0  0
 7D7  CONST_10  N17  C18  C12  N11  180.00  0.0  0
 7D7  CONST_11  N15  C13  C12  N11  180.00  0.0  0
 7D7  CONST_12  C16  N17  C18  C12    0.00  0.0  0
 7D7  CONST_13  C16  N15  C13  C12    0.00  0.0  0
 7D7  CONST_14  N17  C18  C12  C13    0.00  0.0  0
 7D7  CONST_15  N17  C16  N15  C13    0.00  0.0  0
 7D7  CONST_16  C18  N17  C16  N15    0.00  0.0  0
 7D7  CONST_17  C18  C12  C13  N15    0.00  0.0  0
 7D7  CONST_18  N17  C18  N09  C08    0.00  0.0  0
 7D7  CONST_19  C12  C18  N09  C08  180.00  0.0  0
 7D7  CONST_20  N11  C10  N09  C08  180.00  0.0  0
 7D7  CONST_21  N14  C13  C12  N11    0.00  0.0  0
 7D7  CONST_22  C18  C12  C13  N14  180.00  0.0  0
 7D7  CONST_23  C16  N15  C13  N14  180.00  0.0  0
 7D7  CONST_24  H10  C10  N09  C08    0.00  0.0  0
 7D7  CONST_25  H13  C16  N15  C13  180.00  0.0  0
 7D7  CONST_26  H11  N14  C13  C12    0.00  0.0  0
 7D7  CONST_27  H12  N14  C13  C12  180.00  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
 7D7  chir_01  C02  C03  O01  C05  negativ
 7D7  chir_02  C05  C08  C02  C06  negativ
 7D7  chir_03  C08  O01  N09  C05  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
 7D7  plan-1  C08  0.020
 7D7  plan-1  N09  0.020
 7D7  plan-1  C10  0.020
 7D7  plan-1  N11  0.020
 7D7  plan-1  C12  0.020
 7D7  plan-1  C13  0.020
 7D7  plan-1  N14  0.020
 7D7  plan-1  N15  0.020
 7D7  plan-1  C16  0.020
 7D7  plan-1  N17  0.020
 7D7  plan-1  C18  0.020
 7D7  plan-1  H10  0.020
 7D7  plan-1  H13  0.020
 7D7  plan-2  C13  0.020
 7D7  plan-2  N14  0.020
 7D7  plan-2  H11  0.020
 7D7  plan-2  H12  0.020

