# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 17:02:17 2020
#   Inital geometry file: a 79 line input string
#   Ligand name: (1S,2S,3R,5S)-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
 NOC  NOC  (1S,2S,3R,5S)-3-(6-amino-9H-purin-9-yl)-5-(hydroxymethyl)cyclopentane-1,2-diol  ligand  34  19  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NOC
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
 NOC  C6'   C  CH2   0  -0.142  -3.9888   1.4852   0.8459
 NOC  O6'   O  OH1   0  -0.670  -5.3118   1.1452   0.5078
 NOC  C5'   C  CH2   0  -0.459  -1.6327   0.6090   1.0935
 NOC  C4'   C  CH1   0  -0.300  -3.0954   0.2670   0.7225
 NOC  C3'   C  CH1   0   0.059  -3.0179  -0.3372  -0.6834
 NOC  O3'   O  OH1   0  -0.669  -4.0682  -1.2396  -0.9126
 NOC  C2'   C  CH1   0   0.021  -1.6295  -0.9780  -0.7123
 NOC  O2'   O  OH1   0  -0.663  -1.1463  -1.3206  -1.9813
 NOC  C1'   C  CH1   0  -0.130  -0.7823   0.1164  -0.0843
 NOC  N9    N  NR5   0  -0.510   0.5566  -0.3004   0.2694
 NOC  C8    C  CR15  0   0.101   0.9173  -1.3487   1.0676
 NOC  N7    N  N     0  -0.453   2.2048  -1.4771   1.2113
 NOC  C5    C  CR56  0  -0.013   2.7290  -0.4539   0.4666
 NOC  C6    C  CR6   0   0.456   4.0471  -0.0324   0.2122
 NOC  N6    N  NH2   0  -0.818   5.1130  -0.6524   0.7210
 NOC  N1    N  N     0  -0.476   4.2232   1.0370  -0.5720
 NOC  C2    C  CR16  0   0.044   3.1561   1.6530  -1.0759
 NOC  N3    N  N     0  -0.458   1.8800   1.3545  -0.9105
 NOC  C4    C  CR56  0   0.481   1.7197   0.2890  -0.1275
 NOC  H6'1  H  HCH2  0   0.207  -3.9219   1.8640   1.8748
 NOC  H6'2  H  HCH2  0   0.189  -3.5954   2.2786   0.1933
 NOC  HO6'  H  HOH1  0   0.453  -5.8635   1.9206   0.6436
 NOC  H5'1  H  HCH2  0   0.261  -1.3413   0.1074   2.0167
 NOC  H5'2  H  HCH2  0   0.260  -1.4835   1.6776   1.2570
 NOC  HC4'  H  HCH1  0   0.251  -3.4616  -0.5108   1.4006
 NOC  HC3'  H  HCH1  0   0.203  -3.0253   0.4753  -1.4286
 NOC  HO3'  H  HOH1  0   0.449  -4.0585  -1.4909  -1.8413
 NOC  HC2'  H  HCH1  0   0.222  -1.6487  -1.8522  -0.0437
 NOC  HO2'  H  HOH1  0   0.459  -1.4614  -2.1998  -2.2088
 NOC  HC1'  H  HCH1  0   0.286  -0.6600   0.9185  -0.8163
 NOC  HC8   H  HCR5  0   0.297   0.1808  -1.9928   1.5249
 NOC  HN61  H  HNH2  0   0.403   6.0393  -0.3152   0.5249
 NOC  HN62  H  HNH2  0   0.411   5.0126  -1.4590   1.3114
 NOC  HC2   H  HCR6  0   0.250   3.3685   2.5132  -1.7023

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
 NOC  C6'  O6'   single    1.407  0.020  1.407
 NOC  C6'  C4'   single    1.516  0.020  1.516
 NOC  C6'  H6'1  single    0.970  0.020  1.090
 NOC  C6'  H6'2  single    0.970  0.020  1.090
 NOC  O6'  HO6'  single    0.850  0.020  0.980
 NOC  C5'  C4'   single    1.547  0.020  1.547
 NOC  C5'  C1'   single    1.534  0.020  1.534
 NOC  C5'  H5'1  single    0.970  0.020  1.090
 NOC  C5'  H5'2  single    0.970  0.020  1.090
 NOC  C4'  C3'   single    1.532  0.020  1.532
 NOC  C4'  HC4'  single    0.970  0.020  1.090
 NOC  C3'  O3'   single    1.404  0.020  1.404
 NOC  C3'  C2'   single    1.529  0.020  1.529
 NOC  C3'  HC3'  single    0.970  0.020  1.090
 NOC  O3'  HO3'  single    0.850  0.020  0.980
 NOC  C2'  O2'   single    1.401  0.020  1.401
 NOC  C2'  C1'   single    1.520  0.020  1.520
 NOC  C2'  HC2'  single    0.970  0.020  1.090
 NOC  O2'  HO2'  single    0.850  0.020  0.980
 NOC  C1'  N9    single    1.446  0.020  1.446
 NOC  C1'  HC1'  single    0.970  0.020  1.090
 NOC  N9   C8    aromatic  1.366  0.020  1.366
 NOC  N9   C4    aromatic  1.363  0.020  1.363
 NOC  C8   N7    aromatic  1.302  0.020  1.302
 NOC  C8   HC8   single    0.930  0.020  1.080
 NOC  N7   C5    aromatic  1.370  0.020  1.370
 NOC  C5   C6    aromatic  1.407  0.020  1.407
 NOC  C5   C4    aromatic  1.387  0.020  1.387
 NOC  C6   N6    single    1.334  0.020  1.334
 NOC  C6   N1    aromatic  1.338  0.020  1.338
 NOC  N6   HN61  single    0.860  0.020  1.020
 NOC  N6   HN62  single    0.860  0.020  1.020
 NOC  N1   C2    aromatic  1.331  0.020  1.331
 NOC  C2   N3    aromatic  1.321  0.020  1.321
 NOC  C2   HC2   single    0.930  0.020  1.080
 NOC  N3   C4    aromatic  1.332  0.020  1.332

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
 NOC  H6'2  C6'  H6'1  106.57  3.000
 NOC  H6'2  C6'  C4'   108.70  3.000
 NOC  H6'1  C6'  C4'   108.52  3.000
 NOC  H6'2  C6'  O6'   111.58  3.000
 NOC  H6'1  C6'  O6'   111.44  3.000
 NOC  C4'   C6'  O6'   109.90  3.000
 NOC  HO6'  O6'  C6'   108.11  3.000
 NOC  H5'2  C5'  H5'1  106.69  3.000
 NOC  H5'2  C5'  C1'   110.71  3.000
 NOC  H5'1  C5'  C1'   110.75  3.000
 NOC  H5'2  C5'  C4'   112.44  3.000
 NOC  H5'1  C5'  C4'   110.73  3.000
 NOC  C1'   C5'  C4'   105.60  3.000
 NOC  HC4'  C4'  C3'   107.77  3.000
 NOC  HC4'  C4'  C5'   108.95  3.000
 NOC  C3'   C4'  C5'   105.03  3.000
 NOC  HC4'  C4'  C6'   108.87  3.000
 NOC  C3'   C4'  C6'   114.93  3.000
 NOC  C5'   C4'  C6'   111.10  3.000
 NOC  HC3'  C3'  C2'   107.59  3.000
 NOC  HC3'  C3'  O3'   111.00  3.000
 NOC  C2'   C3'  O3'   114.00  3.000
 NOC  HC3'  C3'  C4'   109.23  3.000
 NOC  C2'   C3'  C4'   103.20  3.000
 NOC  O3'   C3'  C4'   111.44  3.000
 NOC  HO3'  O3'  C3'   108.54  3.000
 NOC  HC2'  C2'  C1'   109.31  3.000
 NOC  HC2'  C2'  O2'   111.23  3.000
 NOC  C1'   C2'  O2'   110.99  3.000
 NOC  HC2'  C2'  C3'   107.79  3.000
 NOC  C1'   C2'  C3'   101.33  3.000
 NOC  O2'   C2'  C3'   115.65  3.000
 NOC  HO2'  O2'  C2'   108.97  3.000
 NOC  HC1'  C1'  N9    105.77  3.000
 NOC  HC1'  C1'  C2'   108.31  3.000
 NOC  N9    C1'  C2'   114.18  3.000
 NOC  HC1'  C1'  C5'   109.92  3.000
 NOC  N9    C1'  C5'   114.71  3.000
 NOC  C2'   C1'  C5'   103.85  3.000
 NOC  C4    N9   C8    106.06  3.000
 NOC  C4    N9   C1'   126.46  3.000
 NOC  C8    N9   C1'   127.48  3.000
 NOC  HC8   C8   N7    124.68  3.000
 NOC  HC8   C8   N9    121.67  3.000
 NOC  N7    C8   N9    113.65  3.000
 NOC  C5    N7   C8    104.17  3.000
 NOC  C4    C5   C6    116.35  3.000
 NOC  C4    C5   N7    110.76  3.000
 NOC  C6    C5   N7    132.89  3.000
 NOC  N1    C6   N6    119.34  3.000
 NOC  N1    C6   C5    117.95  3.000
 NOC  N6    C6   C5    122.71  3.000
 NOC  HN62  N6   HN61  118.43  3.000
 NOC  HN62  N6   C6    121.17  3.000
 NOC  HN61  N6   C6    120.40  3.000
 NOC  C2    N1   C6    119.10  3.000
 NOC  HC2   C2   N3    116.13  3.000
 NOC  HC2   C2   N1    115.37  3.000
 NOC  N3    C2   N1    128.49  3.000
 NOC  C4    N3   C2    111.75  3.000
 NOC  N3    C4   C5    126.35  3.000
 NOC  N3    C4   N9    128.30  3.000
 NOC  C5    C4   N9    105.35  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
 NOC  CONST_01  C5    N7  C8  N9     0.00  0.0  0
 NOC  CONST_02  N7    C5  C4  N9     0.00  0.0  0
 NOC  CONST_03  C6    C5  C4  N9   180.00  0.0  0
 NOC  CONST_04  C2    N3  C4  N9   180.00  0.0  0
 NOC  CONST_05  C5    C4  N9  C8     0.00  0.0  0
 NOC  CONST_06  N3    C4  N9  C8   180.00  0.0  0
 NOC  CONST_07  C6    C5  N7  C8   180.00  0.0  0
 NOC  CONST_08  C4    C5  N7  C8     0.00  0.0  0
 NOC  CONST_09  C4    N9  C8  N7     0.00  0.0  0
 NOC  CONST_10  N1    C6  C5  N7   180.00  0.0  0
 NOC  CONST_11  N3    C4  C5  N7   180.00  0.0  0
 NOC  CONST_12  C2    N1  C6  C5     0.00  0.0  0
 NOC  CONST_13  C2    N3  C4  C5     0.00  0.0  0
 NOC  CONST_14  N3    C4  C5  C6     0.00  0.0  0
 NOC  CONST_15  N3    C2  N1  C6     0.00  0.0  0
 NOC  CONST_16  C4    C5  C6  N1     0.00  0.0  0
 NOC  CONST_17  C4    N3  C2  N1     0.00  0.0  0
 NOC  CONST_18  N7    C8  N9  C1'  180.00  0.0  0
 NOC  CONST_19  C5    C4  N9  C1'  180.00  0.0  0
 NOC  CONST_20  N3    C4  N9  C1'    0.00  0.0  0
 NOC  CONST_21  N6    C6  C5  N7     0.00  0.0  0
 NOC  CONST_22  C4    C5  C6  N6   180.00  0.0  0
 NOC  CONST_23  C2    N1  C6  N6   180.00  0.0  0
 NOC  CONST_24  HC8   C8  N9  C1'    0.00  0.0  0
 NOC  CONST_25  HC2   C2  N1  C6   180.00  0.0  0
 NOC  CONST_26  HN61  N6  C6  C5   180.00  0.0  0
 NOC  CONST_27  HN62  N6  C6  C5     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
 NOC  chir_01  C4'  C6'  C5'  C3'  positiv
 NOC  chir_02  C3'  O3'  C4'  C2'  negativ
 NOC  chir_03  C2'  O2'  C3'  C1'  positiv
 NOC  chir_04  C1'  N9   C2'  C5'  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
 NOC  plan-1  C1'   0.020
 NOC  plan-1  N9    0.020
 NOC  plan-1  C8    0.020
 NOC  plan-1  N7    0.020
 NOC  plan-1  C5    0.020
 NOC  plan-1  C6    0.020
 NOC  plan-1  N6    0.020
 NOC  plan-1  N1    0.020
 NOC  plan-1  C2    0.020
 NOC  plan-1  N3    0.020
 NOC  plan-1  C4    0.020
 NOC  plan-1  HC8   0.020
 NOC  plan-1  HC2   0.020
 NOC  plan-2  C6    0.020
 NOC  plan-2  N6    0.020
 NOC  plan-2  HN61  0.020
 NOC  plan-2  HN62  0.020

