# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 05:21:46 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  31  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  -4.3379  -0.5154  -0.3276
 44A  C2    C  CR16  0   0.040  -3.5679  -1.5286   0.0601
 44A  N3    N  N     0  -0.460  -2.2887  -1.5077   0.3925
 44A  C4    C  CR56  0   0.487  -1.7796  -0.2801   0.3040
 44A  C5    C  CR56  0  -0.001  -2.4521   0.8688  -0.0790
 44A  C6    C  CR6   0   0.457  -3.8105   0.7113  -0.4115
 44A  N6    N  NH2   0  -0.816  -4.5783   1.7259  -0.8115
 44A  N7    N  N     0  -0.451  -1.6180   1.9543  -0.0453
 44A  C8    C  CR15  0   0.096  -0.4732   1.4740   0.3454
 44A  N9    N  NR5   0  -0.541  -0.5026   0.1227   0.5669
 44A  OAL   O  O     0  -0.420   2.9086   2.2704   0.4773
 44A  OAN   O  OH1   0  -0.652   2.9686  -1.6355  -1.4925
 44A  OAO   O  OH1   0  -0.659   1.6119  -2.8030   0.5815
 44A  OBV   O  O     0  -0.483   1.6738   0.0293   1.3902
 44A  CCC   C  C     0   0.527   3.3269   1.2022   0.1179
 44A  CCK   C  CR15  0  -0.022   2.0944  -0.8419  -0.7581
 44A  CCL   C  CR15  0  -0.048   1.0393  -1.7003  -0.0625
 44A  CCM   C  CR15  0  -0.072   2.7246  -0.1368   0.4635
 44A  CCN   C  CR15  0   0.173   0.5680  -0.7492   1.0354
 44A  H2    H  HCR6  0   0.252  -4.0583  -2.4952   0.1084
 44A  HN6   H  HNH2  0   0.403  -5.5592   1.5815  -0.9789
 44A  HN6A  H  HNH2  0   0.411  -4.2280   2.6676  -0.8244
 44A  H8    H  HCR5  0   0.299   0.4203   2.0582   0.4977
 44A  HOAN  H  HOH1  0   0.467   3.5043  -1.0787  -2.0662
 44A  HOAO  H  HOH1  0   0.462   2.0937  -3.3263  -0.0683
 44A  O5    O  OH1   0  -0.591   4.3824   1.0312  -0.6634
 44A  HCK   H  HCR5  0   0.256   1.5851  -0.1038  -1.3928
 44A  HCL   H  HCR5  0   0.277   0.2280  -1.9881  -0.7398
 44A  HCM   H  HCR5  0   0.293   3.5100  -0.7756   0.8851
 44A  HCN   H  HCR5  0   0.296   0.1967  -1.2924   1.9079
 44A  H11   H  HOH1  0   0.493   4.7651   1.8861  -0.9146

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  1.330  0.020  1.330
 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  1.385  0.020  1.385
 44A  C4   N9    aromatic  1.365  0.020  1.365
 44A  C5   C6    aromatic  1.407  0.020  1.407
 44A  C5   N7    aromatic  1.369  0.020  1.369
 44A  C6   N6    single    1.334  0.020  1.334
 44A  N6   HN6   single    0.860  0.020  1.020
 44A  N6   HN6A  single    0.860  0.020  1.020
 44A  N7   C8    aromatic  1.302  0.020  1.302
 44A  C8   N9    aromatic  1.370  0.020  1.370
 44A  C8   H8    single    0.930  0.020  1.080
 44A  N9   CCN   single    1.458  0.020  1.458
 44A  OAL  CCC   double    1.202  0.020  1.202
 44A  OAN  CCK   single    1.390  0.020  1.390
 44A  OAN  HOAN  single    0.850  0.020  0.980
 44A  OAO  CCL   single    1.399  0.020  1.399
 44A  OAO  HOAO  single    0.850  0.020  0.980
 44A  OBV  CCM   single    1.411  0.020  1.411
 44A  OBV  CCN   single    1.398  0.020  1.398
 44A  CCC  CCM   single    1.508  0.020  1.508
 44A  CCC  O5    single    1.324  0.020  1.324
 44A  CCK  CCL   single    1.528  0.020  1.528
 44A  CCK  CCM   single    1.545  0.020  1.545
 44A  CCK  HCK   single    0.970  0.020  1.090
 44A  CCL  CCN   single    1.527  0.020  1.527
 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
 44A  O5   H11   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
 44A  C6    N1   C2   119.24  3.000
 44A  H2    C2   N3   116.13  3.000
 44A  H2    C2   N1   115.46  3.000
 44A  N3    C2   N1   128.41  3.000
 44A  C4    N3   C2   111.58  3.000
 44A  N9    C4   C5   105.24  3.000
 44A  N9    C4   N3   128.09  3.000
 44A  C5    C4   N3   126.67  3.000
 44A  N7    C5   C6   133.04  3.000
 44A  N7    C5   C4   110.79  3.000
 44A  C6    C5   C4   116.18  3.000
 44A  N6    C6   C5   122.78  3.000
 44A  N6    C6   N1   119.30  3.000
 44A  C5    C6   N1   117.92  3.000
 44A  HN6A  N6   HN6  118.20  3.000
 44A  HN6A  N6   C6   121.07  3.000
 44A  HN6   N6   C6   120.15  3.000
 44A  C8    N7   C5   104.52  3.000
 44A  H8    C8   N9   121.97  3.000
 44A  H8    C8   N7   124.84  3.000
 44A  N9    C8   N7   113.18  3.000
 44A  CCN   N9   C8   128.77  3.000
 44A  CCN   N9   C4   124.93  3.000
 44A  C8    N9   C4   106.27  3.000
 44A  HOAN  OAN  CCK  109.55  3.000
 44A  HOAO  OAO  CCL  108.80  3.000
 44A  CCN   OBV  CCM  110.91  3.000
 44A  O5    CCC  CCM  109.80  3.000
 44A  O5    CCC  OAL  124.64  3.000
 44A  CCM   CCC  OAL  125.55  3.000
 44A  HCK   CCK  CCM  109.83  3.000
 44A  HCK   CCK  CCL  108.69  3.000
 44A  CCM   CCK  CCL  100.26  3.000
 44A  HCK   CCK  OAN  111.70  3.000
 44A  CCM   CCK  OAN  114.94  3.000
 44A  CCL   CCK  OAN  110.74  3.000
 44A  HCL   CCL  CCN  112.31  3.000
 44A  HCL   CCL  CCK  112.18  3.000
 44A  CCN   CCL  CCK  100.98  3.000
 44A  HCL   CCL  OAO  112.37  3.000
 44A  CCN   CCL  OAO  106.63  3.000
 44A  CCK   CCL  OAO  111.70  3.000
 44A  HCM   CCM  CCK  109.28  3.000
 44A  HCM   CCM  CCC  108.62  3.000
 44A  CCK   CCM  CCC  112.76  3.000
 44A  HCM   CCM  OBV  110.46  3.000
 44A  CCK   CCM  OBV  105.62  3.000
 44A  CCC   CCM  OBV  110.08  3.000
 44A  HCN   CCN  CCL  111.67  3.000
 44A  HCN   CCN  OBV  110.05  3.000
 44A  CCL   CCN  OBV  106.57  3.000
 44A  HCN   CCN  N9   107.71  3.000
 44A  CCL   CCN  N9   111.60  3.000
 44A  OBV   CCN  N9   109.23  3.000
 44A  H11   O5   CCC  110.70  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
 44A  CONST_28  H11   O5  CCC  CCM  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
 44A  plan-3  H11   0.020

