# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 09:11:24 2022
#   Inital geometry file: a 78 line input string
#   Ligand name: (2S,3R,5R)-3-(6-amino-9H-purin-9-yl)-2-hydroxy-5-(hydroxymethyl)cyclopentanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@@H]3C[C@H](CO)C(=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
 ARJ  ARJ  (2S,3R,5R)-3-(6-amino-9H-purin-9-yl)-2-hydroxy-5-(hydroxymethyl)cyclopentanone  ligand  32  19  .  2022-03-11  2022-03-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_ARJ
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
 ARJ  C2    C  CR16  0   0.044   3.2392  -1.4996  -1.1886
 ARJ  C4    C  CR56  0   0.486   1.7405  -0.1769  -0.2814
 ARJ  C5    C  CR56  0  -0.011   2.7111   0.6141   0.3133
 ARJ  C6    C  CR6   0   0.458   4.0480   0.2395   0.0828
 ARJ  O2'   O  OH1   0  -0.648  -1.0418  -1.8960   1.3234
 ARJ  C2'   C  CH1   0  -0.022  -1.5526  -0.6833   0.8809
 ARJ  C3D   C  C     0   0.388  -2.9616  -0.7441   0.3041
 ARJ  O3D   O  O     0  -0.372  -3.8063  -1.5138   0.6806
 ARJ  C4'   C  CH1   0  -0.405  -3.0799   0.2762  -0.8131
 ARJ  C6'   C  CH2   0  -0.137  -4.2214   1.2689  -0.6598
 ARJ  O6'   O  OH1   0  -0.661  -5.4482   0.5996  -0.7921
 ARJ  C5'   C  CH2   0  -0.462  -1.7064   0.9563  -0.8473
 ARJ  C1'   C  CH1   0  -0.152  -0.7603  -0.1031  -0.2815
 ARJ  N9    N  NR5   0  -0.511   0.5500   0.3849   0.0762
 ARJ  C8    C  CR15  0   0.103   0.8588   1.4621   0.8599
 ARJ  N7    N  N     0  -0.450   2.1376   1.6350   1.0249
 ARJ  N3    N  N     0  -0.456   1.9505  -1.2468  -1.0452
 ARJ  N1    N  N     0  -0.476   4.2747  -0.8355  -0.6804
 ARJ  N6    N  NH2   0  -0.817   5.0827   0.9083   0.5932
 ARJ  H2    H  HCR6  0   0.251   3.4925  -2.3600  -1.7992
 ARJ  HO2'  H  HOH1  0   0.461  -1.5910  -2.2200   2.0456
 ARJ  H2'   H  HCH1  0   0.255  -1.5895   0.0764   1.6831
 ARJ  H4'   H  HCH1  0   0.306  -3.2256  -0.2885  -1.7423
 ARJ  H6'   H  HCH2  0   0.204  -4.1303   1.7727   0.3117
 ARJ  H6A'  H  HCH2  0   0.218  -4.0938   2.0422  -1.4287
 ARJ  HO6'  H  HOH1  0   0.457  -6.1528   1.2371  -0.6442
 ARJ  H5'   H  HCH2  0   0.286  -1.4163   1.2743  -1.8468
 ARJ  H5A'  H  HCH2  0   0.253  -1.7097   1.8417  -0.2042
 ARJ  H1'   H  HCH1  0   0.299  -0.6044  -0.8856  -1.0286
 ARJ  H8    H  HCR5  0   0.297   0.0926   2.0925   1.2861
 ARJ  HN6   H  HNH2  0   0.411   4.9455   1.7314   1.1525
 ARJ  HN6A  H  HNH2  0   0.403   6.0240   0.6165   0.3948

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
 ARJ  C2   N3    aromatic  1.321  0.020  1.321
 ARJ  C2   N1    aromatic  1.331  0.020  1.331
 ARJ  C4   C5    aromatic  1.386  0.020  1.386
 ARJ  C4   N9    aromatic  1.364  0.020  1.364
 ARJ  C4   N3    aromatic  1.331  0.020  1.331
 ARJ  C5   C6    aromatic  1.407  0.020  1.407
 ARJ  C5   N7    aromatic  1.370  0.020  1.370
 ARJ  C6   N1    aromatic  1.338  0.020  1.338
 ARJ  C6   N6    single    1.334  0.020  1.334
 ARJ  O2'  C2'   single    1.388  0.020  1.388
 ARJ  C2'  C3D   single    1.524  0.020  1.524
 ARJ  C2'  C1'   single    1.522  0.020  1.522
 ARJ  C3D  O3D   double    1.203  0.020  1.203
 ARJ  C3D  C4'   single    1.518  0.020  1.518
 ARJ  C4'  C6'   single    1.520  0.020  1.520
 ARJ  C4'  C5'   single    1.533  0.020  1.533
 ARJ  C6'  O6'   single    1.404  0.020  1.404
 ARJ  C5'  C1'   single    1.529  0.020  1.529
 ARJ  C1'  N9    single    1.443  0.020  1.443
 ARJ  N9   C8    aromatic  1.367  0.020  1.367
 ARJ  C8   N7    aromatic  1.301  0.020  1.301
 ARJ  C2   H2    single    0.930  0.020  1.080
 ARJ  O2'  HO2'  single    0.850  0.020  0.980
 ARJ  C2'  H2'   single    0.970  0.020  1.090
 ARJ  C4'  H4'   single    0.970  0.020  1.090
 ARJ  C6'  H6'   single    0.970  0.020  1.090
 ARJ  C6'  H6A'  single    0.970  0.020  1.090
 ARJ  O6'  HO6'  single    0.850  0.020  0.980
 ARJ  C5'  H5'   single    0.970  0.020  1.090
 ARJ  C5'  H5A'  single    0.970  0.020  1.090
 ARJ  C1'  H1'   single    0.970  0.020  1.090
 ARJ  C8   H8    single    0.930  0.020  1.080
 ARJ  N6   HN6   single    0.860  0.020  1.020
 ARJ  N6   HN6A  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
 ARJ  H2    C2   N1   115.40  3.000
 ARJ  H2    C2   N3   116.14  3.000
 ARJ  N1    C2   N3   128.47  3.000
 ARJ  N3    C4   N9   128.25  3.000
 ARJ  N3    C4   C5   126.46  3.000
 ARJ  N9    C4   C5   105.28  3.000
 ARJ  N7    C5   C6   132.92  3.000
 ARJ  N7    C5   C4   110.79  3.000
 ARJ  C6    C5   C4   116.30  3.000
 ARJ  N6    C6   N1   119.33  3.000
 ARJ  N6    C6   C5   122.74  3.000
 ARJ  N1    C6   C5   117.92  3.000
 ARJ  HO2'  O2'  C2'  108.84  3.000
 ARJ  H2'   C2'  C1'  108.04  3.000
 ARJ  H2'   C2'  C3D  105.74  3.000
 ARJ  C1'   C2'  C3D  101.98  3.000
 ARJ  H2'   C2'  O2'  112.41  3.000
 ARJ  C1'   C2'  O2'  112.64  3.000
 ARJ  C3D   C2'  O2'  115.22  3.000
 ARJ  C4'   C3D  O3D  127.28  3.000
 ARJ  C4'   C3D  C2'  108.90  3.000
 ARJ  O3D   C3D  C2'  123.80  3.000
 ARJ  H4'   C4'  C5'  109.17  3.000
 ARJ  H4'   C4'  C6'  108.77  3.000
 ARJ  C5'   C4'  C6'  112.66  3.000
 ARJ  H4'   C4'  C3D  106.72  3.000
 ARJ  C5'   C4'  C3D  104.17  3.000
 ARJ  C6'   C4'  C3D  115.04  3.000
 ARJ  H6A'  C6'  H6'  106.66  3.000
 ARJ  H6A'  C6'  O6'  111.80  3.000
 ARJ  H6'   C6'  O6'  112.00  3.000
 ARJ  H6A'  C6'  C4'  107.58  3.000
 ARJ  H6'   C6'  C4'  109.05  3.000
 ARJ  O6'   C6'  C4'  109.59  3.000
 ARJ  HO6'  O6'  C6'  108.05  3.000
 ARJ  H5A'  C5'  H5'  107.71  3.000
 ARJ  H5A'  C5'  C1'  110.18  3.000
 ARJ  H5'   C5'  C1'  112.17  3.000
 ARJ  H5A'  C5'  C4'  110.07  3.000
 ARJ  H5'   C5'  C4'  112.89  3.000
 ARJ  C1'   C5'  C4'  103.81  3.000
 ARJ  H1'   C1'  N9   106.38  3.000
 ARJ  H1'   C1'  C5'  109.35  3.000
 ARJ  N9    C1'  C5'  114.79  3.000
 ARJ  H1'   C1'  C2'  108.86  3.000
 ARJ  N9    C1'  C2'  114.35  3.000
 ARJ  C5'   C1'  C2'  102.98  3.000
 ARJ  C8    N9   C1'  127.84  3.000
 ARJ  C8    N9   C4   106.12  3.000
 ARJ  C1'   N9   C4   126.02  3.000
 ARJ  H8    C8   N7   124.74  3.000
 ARJ  H8    C8   N9   121.72  3.000
 ARJ  N7    C8   N9   113.54  3.000
 ARJ  C8    N7   C5   104.27  3.000
 ARJ  C4    N3   C2   111.71  3.000
 ARJ  C6    N1   C2   119.14  3.000
 ARJ  HN6A  N6   HN6  118.40  3.000
 ARJ  HN6A  N6   C6   120.36  3.000
 ARJ  HN6   N6   C6   121.20  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
 ARJ  CONST_01  C5    C4  N3  C2     0.00  0.0  0
 ARJ  CONST_02  N9    C4  N3  C2   180.00  0.0  0
 ARJ  CONST_03  C5    C6  N1  C2     0.00  0.0  0
 ARJ  CONST_04  N1    C6  C5  C4     0.00  0.0  0
 ARJ  CONST_05  C8    N7  C5  C4     0.00  0.0  0
 ARJ  CONST_06  N7    C8  N9  C4     0.00  0.0  0
 ARJ  CONST_07  N1    C2  N3  C4     0.00  0.0  0
 ARJ  CONST_08  C8    N9  C4  C5     0.00  0.0  0
 ARJ  CONST_09  N9    C8  N7  C5     0.00  0.0  0
 ARJ  CONST_10  N9    C4  C5  C6   180.00  0.0  0
 ARJ  CONST_11  N3    C4  C5  C6     0.00  0.0  0
 ARJ  CONST_12  C8    N7  C5  C6   180.00  0.0  0
 ARJ  CONST_13  N3    C2  N1  C6     0.00  0.0  0
 ARJ  CONST_14  N7    C5  C4  N9     0.00  0.0  0
 ARJ  CONST_15  N3    C4  N9  C8   180.00  0.0  0
 ARJ  CONST_16  N3    C4  C5  N7   180.00  0.0  0
 ARJ  CONST_17  N1    C6  C5  N7   180.00  0.0  0
 ARJ  CONST_18  C1'   N9  C4  C5   180.00  0.0  0
 ARJ  CONST_19  N3    C4  N9  C1'    0.00  0.0  0
 ARJ  CONST_20  N7    C8  N9  C1'  180.00  0.0  0
 ARJ  CONST_21  N6    C6  N1  C2   180.00  0.0  0
 ARJ  CONST_22  N6    C6  C5  C4   180.00  0.0  0
 ARJ  CONST_23  N6    C6  C5  N7     0.00  0.0  0
 ARJ  CONST_24  H8    C8  N9  C4   180.00  0.0  0
 ARJ  CONST_25  H2    C2  N3  C4   180.00  0.0  0
 ARJ  CONST_26  HN6   N6  C6  C5     0.00  0.0  0
 ARJ  CONST_27  HN6A  N6  C6  C5   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
 ARJ  chir_01  C2'  O2'  C3D  C1'  positiv
 ARJ  chir_02  C4'  C5'  C6'  C3D  positiv
 ARJ  chir_03  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
 ARJ  plan-1  C2    0.020
 ARJ  plan-1  C4    0.020
 ARJ  plan-1  C5    0.020
 ARJ  plan-1  C6    0.020
 ARJ  plan-1  C1'   0.020
 ARJ  plan-1  N9    0.020
 ARJ  plan-1  C8    0.020
 ARJ  plan-1  N7    0.020
 ARJ  plan-1  N3    0.020
 ARJ  plan-1  N1    0.020
 ARJ  plan-1  N6    0.020
 ARJ  plan-1  H2    0.020
 ARJ  plan-1  H8    0.020
 ARJ  plan-2  C6    0.020
 ARJ  plan-2  N6    0.020
 ARJ  plan-2  HN6   0.020
 ARJ  plan-2  HN6A  0.020
 ARJ  plan-3  C2'   0.020
 ARJ  plan-3  C3D   0.020
 ARJ  plan-3  O3D   0.020
 ARJ  plan-3  C4'   0.020

