# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 10:53:02 2020
#   Inital geometry file: a 76 line input string
#   Ligand name: 9-(beta-D-ribofuranuronosyl)-9H-purin-6-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@@H]3O[C@@H]([C@@H](O)[C@H]3O)C(O)=O
#
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
 44A  44A  9-(beta-D-ribofuranuronosyl)-9H-purin-6-amine  ligand  30  20  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_44A
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
 44A  N1    N  N      0  -0.474  -4.3829  -0.4635  -0.1946
 44A  C2    C  C1     0   0.038  -3.6197  -1.5010   0.1406
 44A  N3    N  N      0  -0.459  -2.3263  -1.5159   0.4110
 44A  C4    C  CR5    0   0.484  -1.7906  -0.2995   0.3158
 44A  C5    C  CR5    0  -0.003  -2.4534   0.8707  -0.0218
 44A  C6    C  C      0   0.450  -3.8294   0.7508  -0.2872
 44A  N6    N  NH2    0  -0.817  -4.5909   1.7902  -0.6396
 44A  N7    N  N      0  -0.455  -1.5928   1.9361  -0.0125
 44A  C8    C  CR15   0   0.089  -0.4429   1.4225   0.3209
 44A  N9    N  NR5    0  -0.535  -0.4965   0.0705   0.5283
 44A  OAL   O  O      0  -0.571   2.9108   2.2888   0.5642
 44A  OAN   O  OH1    0  -0.669   2.9780  -1.4162  -1.7014
 44A  OAO   O  OH1    0  -0.666   1.6841  -2.8205   0.3134
 44A  OBV   O  O2     0  -0.490   1.6792  -0.0478   1.3284
 44A  CCC   C  C      0   0.416   3.3076   1.2677  -0.0138
 44A  CCK   C  CH1    0  -0.029   2.0684  -0.7451  -0.8819
 44A  CCL   C  CH1    0  -0.029   1.0633  -1.6899  -0.2349
 44A  CCM   C  CH1    0  -0.108   2.7107  -0.0929   0.3476
 44A  CCN   C  CH1    0   0.159   0.5906  -0.8188   0.9327
 44A  H2    H  H      0   0.251  -4.1312  -2.4561   0.1983
 44A  HN6   H  HNH2   0   0.402  -5.5876   1.6773  -0.7102
 44A  HN6A  H  HNH2   0   0.409  -4.2262   2.7262  -0.6087
 44A  H8    H  HCR5   0   0.299   0.4771   1.9773   0.4377
 44A  HOAN  H  HOH1   0   0.447   3.7192  -0.8039  -1.8200
 44A  HOAO  H  HOH1   0   0.454   2.3797  -3.1051  -0.2908
 44A  O5    O  OC    -1  -0.608   4.1669   1.1816  -0.9205
 44A  HCK   H  HCH1   0   0.227   1.5096   0.0116  -1.4538
 44A  HCL   H  HCH1   0   0.258   0.2383  -1.9612  -0.9046
 44A  HCM   H  HCH1   0   0.246   3.5199  -0.7388   0.7135
 44A  HCN   H  HCH1   0   0.283   0.2236  -1.4240   1.7662

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
 44A  N1   C2    aromatic  1.331  0.020  1.331
 44A  N1   C6    aromatic  1.338  0.020  1.338
 44A  C2   N3    aromatic  1.322  0.020  1.322
 44A  C2   H2    single    0.930  0.020  1.080
 44A  N3   C4    aromatic  1.332  0.020  1.332
 44A  C4   C5    aromatic  1.387  0.020  1.387
 44A  C4   N9    aromatic  1.363  0.020  1.363
 44A  C5   C6    aromatic  1.406  0.020  1.406
 44A  C5   N7    aromatic  1.370  0.020  1.370
 44A  C6   N6    single    1.336  0.020  1.336
 44A  N6   HN6   single    0.860  0.020  1.020
 44A  N6   HN6A  single    0.860  0.020  1.020
 44A  N7   C8    aromatic  1.303  0.020  1.303
 44A  C8   N9    aromatic  1.369  0.020  1.369
 44A  C8   H8    single    0.930  0.020  1.080
 44A  N9   CCN   single    1.462  0.020  1.462
 44A  OAL  CCC   deloc     1.239  0.020  1.239
 44A  OAN  CCK   single    1.396  0.020  1.396
 44A  OAN  HOAN  single    0.850  0.020  0.980
 44A  OAO  CCL   single    1.402  0.020  1.402
 44A  OAO  HOAO  single    0.850  0.020  0.980
 44A  OBV  CCM   single    1.424  0.020  1.424
 44A  OBV  CCN   single    1.391  0.020  1.391
 44A  CCC  CCM   single    1.529  0.020  1.529
 44A  CCC  O5    deloc     1.252  0.020  1.252
 44A  CCK  CCL   single    1.524  0.020  1.524
 44A  CCK  CCM   single    1.533  0.020  1.533
 44A  CCK  HCK   single    0.970  0.020  1.090
 44A  CCL  CCN   single    1.532  0.020  1.532
 44A  CCL  HCL   single    0.970  0.020  1.090
 44A  CCM  HCM   single    0.970  0.020  1.090
 44A  CCN  HCN   single    0.970  0.020  1.090

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
 44A  C6    N1   C2   119.19  3.000
 44A  H2    C2   N3   116.14  3.000
 44A  H2    C2   N1   115.43  3.000
 44A  N3    C2   N1   128.43  3.000
 44A  C4    N3   C2   111.63  3.000
 44A  N9    C4   C5   105.23  3.000
 44A  N9    C4   N3   128.21  3.000
 44A  C5    C4   N3   126.56  3.000
 44A  N7    C5   C6   133.02  3.000
 44A  N7    C5   C4   110.76  3.000
 44A  C6    C5   C4   116.21  3.000
 44A  N6    C6   C5   122.76  3.000
 44A  N6    C6   N1   119.25  3.000
 44A  C5    C6   N1   117.98  3.000
 44A  HN6A  N6   HN6  117.80  3.000
 44A  HN6A  N6   C6   120.64  3.000
 44A  HN6   N6   C6   119.75  3.000
 44A  C8    N7   C5   104.46  3.000
 44A  H8    C8   N9   121.60  3.000
 44A  H8    C8   N7   125.22  3.000
 44A  N9    C8   N7   113.18  3.000
 44A  CCN   N9   C8   127.86  3.000
 44A  CCN   N9   C4   125.75  3.000
 44A  C8    N9   C4   106.37  3.000
 44A  HOAN  OAN  CCK  105.46  3.000
 44A  HOAO  OAO  CCL  108.20  3.000
 44A  CCN   OBV  CCM  110.69  3.000
 44A  O5    CCC  CCM  112.20  3.000
 44A  O5    CCC  OAL  127.91  3.000
 44A  CCM   CCC  OAL  119.88  3.000
 44A  HCK   CCK  CCM  109.68  3.000
 44A  HCK   CCK  CCL  108.18  3.000
 44A  CCM   CCK  CCL  101.52  3.000
 44A  HCK   CCK  OAN  110.87  3.000
 44A  CCM   CCK  OAN  113.72  3.000
 44A  CCL   CCK  OAN  112.39  3.000
 44A  HCL   CCL  CCN  111.96  3.000
 44A  HCL   CCL  CCK  112.97  3.000
 44A  CCN   CCL  CCK  100.06  3.000
 44A  HCL   CCL  OAO  111.88  3.000
 44A  CCN   CCL  OAO  107.29  3.000
 44A  CCK   CCL  OAO  111.97  3.000
 44A  HCM   CCM  CCK  109.01  3.000
 44A  HCM   CCM  CCC  108.33  3.000
 44A  CCK   CCM  CCC  110.65  3.000
 44A  HCM   CCM  OBV  108.83  3.000
 44A  CCK   CCM  OBV  105.21  3.000
 44A  CCC   CCM  OBV  114.67  3.000
 44A  HCN   CCN  CCL  111.71  3.000
 44A  HCN   CCN  OBV  110.64  3.000
 44A  CCL   CCN  OBV  106.89  3.000
 44A  HCN   CCN  N9   107.34  3.000
 44A  CCL   CCN  N9   111.39  3.000
 44A  OBV   CCN  N9   108.87  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
 44A  CONST_01  C4    N3  C2  N1    0.00  0.0  0
 44A  CONST_02  C4    C5  C6  N1    0.00  0.0  0
 44A  CONST_03  N7    C5  C6  N1  180.00  0.0  0
 44A  CONST_04  C5    C6  N1  C2    0.00  0.0  0
 44A  CONST_05  C5    C4  N3  C2    0.00  0.0  0
 44A  CONST_06  N9    C4  N3  C2  180.00  0.0  0
 44A  CONST_07  C6    N1  C2  N3    0.00  0.0  0
 44A  CONST_08  C6    C5  C4  N3    0.00  0.0  0
 44A  CONST_09  N7    C5  C4  N3  180.00  0.0  0
 44A  CONST_10  C8    N9  C4  N3  180.00  0.0  0
 44A  CONST_11  C8    N7  C5  C4    0.00  0.0  0
 44A  CONST_12  N7    C8  N9  C4    0.00  0.0  0
 44A  CONST_13  C8    N9  C4  C5    0.00  0.0  0
 44A  CONST_14  N9    C8  N7  C5    0.00  0.0  0
 44A  CONST_15  N9    C4  C5  C6  180.00  0.0  0
 44A  CONST_16  C8    N7  C5  C6  180.00  0.0  0
 44A  CONST_17  N9    C4  C5  N7    0.00  0.0  0
 44A  CONST_18  CCN   N9  C4  N3    0.00  0.0  0
 44A  CONST_19  CCN   N9  C4  C5  180.00  0.0  0
 44A  CONST_20  CCN   N9  C8  N7  180.00  0.0  0
 44A  CONST_21  N6    C6  N1  C2  180.00  0.0  0
 44A  CONST_22  N6    C6  C5  C4  180.00  0.0  0
 44A  CONST_23  N7    C5  C6  N6    0.00  0.0  0
 44A  CONST_24  H2    C2  N3  C4  180.00  0.0  0
 44A  CONST_25  H8    C8  N9  C4  180.00  0.0  0
 44A  CONST_26  HN6   N6  C6  N1    0.00  0.0  0
 44A  CONST_27  HN6A  N6  C6  N1  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
 44A  chir_01  CCK  OAN  CCL  CCM  negativ
 44A  chir_02  CCL  OAO  CCN  CCK  negativ
 44A  chir_03  CCM  OBV  CCC  CCK  positiv
 44A  chir_04  CCN  OBV  N9   CCL  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
 44A  plan-1  N1    0.020
 44A  plan-1  C2    0.020
 44A  plan-1  N3    0.020
 44A  plan-1  C4    0.020
 44A  plan-1  C5    0.020
 44A  plan-1  C6    0.020
 44A  plan-1  N6    0.020
 44A  plan-1  N7    0.020
 44A  plan-1  C8    0.020
 44A  plan-1  N9    0.020
 44A  plan-1  CCN   0.020
 44A  plan-1  H2    0.020
 44A  plan-1  H8    0.020
 44A  plan-2  C6    0.020
 44A  plan-2  N6    0.020
 44A  plan-2  HN6   0.020
 44A  plan-2  HN6A  0.020
 44A  plan-3  OAL   0.020
 44A  plan-3  CCC   0.020
 44A  plan-3  CCM   0.020
 44A  plan-3  O5    0.020

