# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 16:42:20 2022
#   Inital geometry file: a 79 line input string
#   Ligand name: (1R,2S,3R,5R)-3-(6-amino-9H-purin-9-yl)-5-(hydroxymethyl)cyclopentane-1,2-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@@H]3C[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
 7CY  7CY  (1R,2S,3R,5R)-3-(6-amino-9H-purin-9-yl)-5-(hydroxymethyl)cyclopentane-1,2-diol  ligand  34  19  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_7CY
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
 7CY  N1   N  N     0  -0.476  -4.2495  -0.8570   0.5510
 7CY  C2   C  CR16  0   0.043  -3.2279  -1.5740   1.0142
 7CY  C4   C  CR56  0   0.482  -1.7009  -0.2009   0.2360
 7CY  C5   C  CR56  0  -0.014  -2.6563   0.6482  -0.3029
 7CY  C6   C  CR6   0   0.456  -4.0001   0.2730  -0.1200
 7CY  C8   C  CR15  0   0.100  -0.7878   1.5111  -0.7581
 7CY  O2'  O  OH1   0  -0.659   1.1488  -1.5095  -1.6979
 7CY  C2'  C  CH1   0   0.027   1.6726  -0.4438  -0.9565
 7CY  C3'  C  CH1   0   0.017   3.0441  -0.7079  -0.3265
 7CY  O3'  O  OH1   0  -0.677   3.0838  -1.9958   0.2463
 7CY  C4'  C  CH1   0  -0.288   3.1369   0.3349   0.8015
 7CY  C5'  C  CH2   0  -0.152   4.0073   1.5264   0.4447
 7CY  O5'  O  OH1   0  -0.670   5.3445   1.1020   0.3199
 7CY  C1'  C  CH1   0  -0.120   0.8082  -0.1529   0.2632
 7CY  C6'  C  CH2   0  -0.467   1.6858   0.7877   1.0860
 7CY  N9   N  NR5   0  -0.509  -0.5005   0.3711  -0.0625
 7CY  N7   N  N     0  -0.453  -2.0626   1.7157  -0.9234
 7CY  N3   N  N     0  -0.457  -1.9348  -1.3278   0.9065
 7CY  N6   N  NH2   0  -0.818  -5.0202   0.9966  -0.5840
 7CY  H1   H  HCR6  0   0.250  -3.4996  -2.4779   1.5494
 7CY  H2   H  HCR5  0   0.294  -0.0072   2.1618  -1.1240
 7CY  H3   H  HOH1  0   0.463   1.5492  -1.5051  -2.5731
 7CY  H4   H  HCH1  0   0.223   1.7432   0.4700  -1.5646
 7CY  H5   H  HCH1  0   0.228   3.8473  -0.5849  -1.0642
 7CY  H6   H  HOH1  0   0.443   2.7488  -2.6185  -0.4094
 7CY  H7   H  HCH1  0   0.260   3.5630  -0.1450   1.6864
 7CY  H8   H  HCH2  0   0.193   3.6409   1.9829  -0.4864
 7CY  H9   H  HCH2  0   0.212   3.8974   2.2871   1.2292
 7CY  H10  H  HOH1  0   0.455   5.8659   1.8415  -0.0042
 7CY  H11  H  HCH1  0   0.282   0.6351  -1.0825   0.8084
 7CY  H12  H  HCH2  0   0.271   1.4354   0.7624   2.1451
 7CY  H13  H  HCH2  0   0.245   1.5370   1.8193   0.7510
 7CY  H14  H  HNH2  0   0.411  -4.8638   1.8403  -1.1065
 7CY  H15  H  HNH2  0   0.403  -5.9666   0.6862  -0.4486

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
 7CY  N7   C8   aromatic  1.302  0.020  1.302
 7CY  N7   C5   aromatic  1.370  0.020  1.370
 7CY  C8   N9   aromatic  1.366  0.020  1.366
 7CY  C2'  O2'  single    1.400  0.020  1.400
 7CY  C2'  C3'  single    1.532  0.020  1.532
 7CY  C2'  C1'  single    1.523  0.020  1.523
 7CY  O3'  C3'  single    1.410  0.020  1.410
 7CY  C3'  C4'  single    1.539  0.020  1.539
 7CY  N6   C6   single    1.334  0.020  1.334
 7CY  C5   C6   aromatic  1.407  0.020  1.407
 7CY  C5   C4   aromatic  1.387  0.020  1.387
 7CY  N9   C1'  single    1.447  0.020  1.447
 7CY  N9   C4   aromatic  1.363  0.020  1.363
 7CY  C1'  C6'  single    1.527  0.020  1.527
 7CY  C6   N1   aromatic  1.338  0.020  1.338
 7CY  C4   N3   aromatic  1.332  0.020  1.332
 7CY  C4'  C6'  single    1.547  0.020  1.547
 7CY  C4'  C5'  single    1.518  0.020  1.518
 7CY  C5'  O5'  single    1.408  0.020  1.408
 7CY  N1   C2   aromatic  1.331  0.020  1.331
 7CY  N3   C2   aromatic  1.321  0.020  1.321
 7CY  C2   H1   single    0.930  0.020  1.080
 7CY  C8   H2   single    0.930  0.020  1.080
 7CY  O2'  H3   single    0.850  0.020  0.980
 7CY  C2'  H4   single    0.970  0.020  1.090
 7CY  C3'  H5   single    0.970  0.020  1.090
 7CY  O3'  H6   single    0.850  0.020  0.980
 7CY  C4'  H7   single    0.970  0.020  1.090
 7CY  C5'  H8   single    0.970  0.020  1.090
 7CY  C5'  H9   single    0.970  0.020  1.090
 7CY  O5'  H10  single    0.850  0.020  0.980
 7CY  C1'  H11  single    0.970  0.020  1.090
 7CY  C6'  H12  single    0.970  0.020  1.090
 7CY  C6'  H13  single    0.970  0.020  1.090
 7CY  N6   H14  single    0.860  0.020  1.020
 7CY  N6   H15  single    0.860  0.020  1.020

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
 7CY  C6   N1   C2   119.11  3.000
 7CY  H1   C2   N3   116.15  3.000
 7CY  H1   C2   N1   115.35  3.000
 7CY  N3   C2   N1   128.50  3.000
 7CY  N3   C4   N9   128.31  3.000
 7CY  N3   C4   C5   126.34  3.000
 7CY  N9   C4   C5   105.35  3.000
 7CY  N7   C5   C6   132.88  3.000
 7CY  C6   C5   C4   116.36  3.000
 7CY  N7   C5   C4   110.76  3.000
 7CY  N6   C6   C5   122.72  3.000
 7CY  C5   C6   N1   117.94  3.000
 7CY  N6   C6   N1   119.34  3.000
 7CY  H2   C8   N7   124.76  3.000
 7CY  H2   C8   N9   121.55  3.000
 7CY  N7   C8   N9   113.69  3.000
 7CY  H3   O2'  C2'  108.81  3.000
 7CY  H4   C2'  C1'  108.70  3.000
 7CY  H4   C2'  C3'  108.25  3.000
 7CY  C1'  C2'  C3'  102.22  3.000
 7CY  H4   C2'  O2'  111.32  3.000
 7CY  C1'  C2'  O2'  110.92  3.000
 7CY  C3'  C2'  O2'  114.93  3.000
 7CY  H5   C3'  C4'  111.87  3.000
 7CY  H5   C3'  O3'  110.78  3.000
 7CY  C4'  C3'  O3'  108.63  3.000
 7CY  H5   C3'  C2'  111.07  3.000
 7CY  C4'  C3'  C2'  103.80  3.000
 7CY  O3'  C3'  C2'  110.47  3.000
 7CY  H6   O3'  C3'  107.69  3.000
 7CY  H7   C4'  C6'  110.20  3.000
 7CY  H7   C4'  C5'  108.14  3.000
 7CY  C6'  C4'  C5'  110.57  3.000
 7CY  H7   C4'  C3'  108.63  3.000
 7CY  C5'  C4'  C3'  113.21  3.000
 7CY  C6'  C4'  C3'  106.06  3.000
 7CY  H9   C5'  H8   106.49  3.000
 7CY  H9   C5'  O5'  111.53  3.000
 7CY  H8   C5'  O5'  111.49  3.000
 7CY  H9   C5'  C4'  108.56  3.000
 7CY  H8   C5'  C4'  109.50  3.000
 7CY  O5'  C5'  C4'  109.19  3.000
 7CY  H10  O5'  C5'  108.25  3.000
 7CY  H11  C1'  N9   106.11  3.000
 7CY  H11  C1'  C6'  110.28  3.000
 7CY  N9   C1'  C6'  114.71  3.000
 7CY  H11  C1'  C2'  109.11  3.000
 7CY  C6'  C1'  C2'  102.88  3.000
 7CY  N9   C1'  C2'  113.72  3.000
 7CY  H13  C6'  H12  106.76  3.000
 7CY  H13  C6'  C1'  109.72  3.000
 7CY  H12  C6'  C1'  112.19  3.000
 7CY  H13  C6'  C4'  110.31  3.000
 7CY  H12  C6'  C4'  112.83  3.000
 7CY  C1'  C6'  C4'  105.06  3.000
 7CY  C1'  N9   C8   127.38  3.000
 7CY  C1'  N9   C4   126.55  3.000
 7CY  C8   N9   C4   106.05  3.000
 7CY  C8   N7   C5   104.15  3.000
 7CY  C4   N3   C2   111.76  3.000
 7CY  H15  N6   H14  118.43  3.000
 7CY  H15  N6   C6   120.37  3.000
 7CY  H14  N6   C6   121.15  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
 7CY  CONST_01  N7   C5  C6  N1   180.00  0.0  0
 7CY  CONST_02  C4   C5  C6  N1     0.00  0.0  0
 7CY  CONST_03  C4   N3  C2  N1     0.00  0.0  0
 7CY  CONST_04  C5   C6  N1  C2     0.00  0.0  0
 7CY  CONST_05  C5   C4  N3  C2     0.00  0.0  0
 7CY  CONST_06  N9   C4  N3  C2   180.00  0.0  0
 7CY  CONST_07  C8   N7  C5  C4     0.00  0.0  0
 7CY  CONST_08  N7   C8  N9  C4     0.00  0.0  0
 7CY  CONST_09  N9   C8  N7  C5     0.00  0.0  0
 7CY  CONST_10  C8   N9  C4  C5     0.00  0.0  0
 7CY  CONST_11  C8   N7  C5  C6   180.00  0.0  0
 7CY  CONST_12  N9   C4  C5  C6   180.00  0.0  0
 7CY  CONST_13  N3   C4  C5  C6     0.00  0.0  0
 7CY  CONST_14  N3   C2  N1  C6     0.00  0.0  0
 7CY  CONST_15  N3   C4  N9  C8   180.00  0.0  0
 7CY  CONST_16  N7   C5  C4  N9     0.00  0.0  0
 7CY  CONST_17  N3   C4  C5  N7   180.00  0.0  0
 7CY  CONST_18  C1'  N9  C4  C5   180.00  0.0  0
 7CY  CONST_19  N7   C8  N9  C1'  180.00  0.0  0
 7CY  CONST_20  N3   C4  N9  C1'    0.00  0.0  0
 7CY  CONST_21  N6   C6  N1  C2   180.00  0.0  0
 7CY  CONST_22  N6   C6  C5  C4   180.00  0.0  0
 7CY  CONST_23  N6   C6  C5  N7     0.00  0.0  0
 7CY  CONST_24  H2   C8  N9  C4   180.00  0.0  0
 7CY  CONST_25  H1   C2  N3  C4   180.00  0.0  0
 7CY  CONST_26  H14  N6  C6  N1   180.00  0.0  0
 7CY  CONST_27  H15  N6  C6  N1     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
 7CY  chir_01  C2'  O2'  C3'  C1'  positiv
 7CY  chir_02  C3'  O3'  C4'  C2'  positiv
 7CY  chir_03  C4'  C3'  C6'  C5'  positiv
 7CY  chir_04  C1'  N9   C2'  C6'  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
 7CY  plan-1  N1   0.020
 7CY  plan-1  C2   0.020
 7CY  plan-1  C4   0.020
 7CY  plan-1  C5   0.020
 7CY  plan-1  C6   0.020
 7CY  plan-1  C8   0.020
 7CY  plan-1  C1'  0.020
 7CY  plan-1  N9   0.020
 7CY  plan-1  N7   0.020
 7CY  plan-1  N3   0.020
 7CY  plan-1  N6   0.020
 7CY  plan-1  H1   0.020
 7CY  plan-1  H2   0.020
 7CY  plan-2  C6   0.020
 7CY  plan-2  N6   0.020
 7CY  plan-2  H14  0.020
 7CY  plan-2  H15  0.020

