# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 14:31:03 2022
#   Inital geometry file: a 73 line input string
#   Ligand name: 9-(2-deoxy-beta-L-erythro-pentofuranosyl)-9H-purin-6-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@@H]3C[C@@H](O)[C@H](CO)O3
#
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
 3L1  3L1  9-(2-deoxy-beta-L-erythro-pentofuranosyl)-9H-purin-6-amine  ligand  31  18  .  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_3L1
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
 3L1  N6    N  NH2   0  -0.817   4.5610   1.5822  -0.2775
 3L1  C6    C  CR6   0   0.459   3.6981   0.6094   0.0192
 3L1  N1    N  N     0  -0.475   4.1519  -0.5282   0.5574
 3L1  C2    C  CR16  0   0.045   3.2864  -1.4937   0.8558
 3L1  N3    N  N     0  -0.458   1.9756  -1.5031   0.6887
 3L1  C4    C  CR56  0   0.490   1.5386  -0.3645   0.1553
 3L1  C5    C  CR56  0  -0.013   2.3137   0.7271  -0.2026
 3L1  N7    N  N     0  -0.450   1.5334   1.7316  -0.7153
 3L1  C8    C  CR15  0   0.112   0.3254   1.2546  -0.6715
 3L1  N9    N  NR5   0  -0.536   0.2577  -0.0134  -0.1617
 3L1  C1'   C  CH1   0   0.221  -0.9306  -0.8083   0.0449
 3L1  O4'   O  O2    0  -0.494  -1.8188  -0.1021   0.8745
 3L1  C2'   C  CH2   0  -0.560  -1.7010  -1.1189  -1.2329
 3L1  C3'   C  CH1   0  -0.010  -3.1242  -1.2547  -0.7110
 3L1  O3'   O  OH1   0  -0.670  -3.3422  -2.4981  -0.0860
 3L1  C4'   C  CH1   0  -0.021  -3.1524  -0.1802   0.3734
 3L1  C5'   C  CH2   0  -0.154  -3.6190   1.1595  -0.1586
 3L1  O5'   O  OH1   0  -0.667  -3.5307   2.1086   0.8735
 3L1  HN6   H  HNH2  0   0.403   5.5475   1.4429  -0.1439
 3L1  HN6A  H  HNH2  0   0.411   4.2568   2.4236  -0.7347
 3L1  H2    H  HCR6  0   0.252   3.7189  -2.3881   1.2913
 3L1  H8    H  HCR5  0   0.294  -0.5586   1.7876  -0.9888
 3L1  H1'   H  HCH1  0   0.260  -0.5907  -1.7255   0.5335
 3L1  H2'   H  HCH2  0   0.265  -1.6304  -0.2965  -1.9482
 3L1  H2'A  H  HCH2  0   0.286  -1.3313  -2.0153  -1.7310
 3L1  H3'   H  HCH1  0   0.251  -3.8679  -1.0629  -1.4936
 3L1  HO3'  H  HOH1  0   0.455  -3.2200  -3.1927  -0.7412
 3L1  H4'   H  HCH1  0   0.255  -3.8086  -0.4821   1.1966
 3L1  H5'   H  HCH2  0   0.195  -3.0194   1.4523  -1.0322
 3L1  H5'A  H  HCH2  0   0.212  -4.6503   1.0349  -0.5143
 3L1  HO5'  H  HOH1  0   0.458  -3.8534   2.9489   0.5361

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
 3L1  N6   C6    single    1.334  0.020  1.334
 3L1  C6   N1    aromatic  1.338  0.020  1.338
 3L1  C6   C5    aromatic  1.407  0.020  1.407
 3L1  N1   C2    aromatic  1.331  0.020  1.331
 3L1  C2   N3    aromatic  1.321  0.020  1.321
 3L1  N3   C4    aromatic  1.331  0.020  1.331
 3L1  C4   C5    aromatic  1.386  0.020  1.386
 3L1  C4   N9    aromatic  1.365  0.020  1.365
 3L1  C5   N7    aromatic  1.371  0.020  1.371
 3L1  N7   C8    aromatic  1.300  0.020  1.300
 3L1  C8   N9    aromatic  1.368  0.020  1.368
 3L1  N9   C1'   single    1.444  0.020  1.444
 3L1  C1'  O4'   single    1.406  0.020  1.406
 3L1  C1'  C2'   single    1.524  0.020  1.524
 3L1  O4'  C4'   single    1.427  0.020  1.427
 3L1  C2'  C3'   single    1.522  0.020  1.522
 3L1  C3'  O3'   single    1.409  0.020  1.409
 3L1  C3'  C4'   single    1.527  0.020  1.527
 3L1  C4'  C5'   single    1.515  0.020  1.515
 3L1  C5'  O5'   single    1.405  0.020  1.405
 3L1  N6   HN6   single    0.860  0.020  1.020
 3L1  N6   HN6A  single    0.860  0.020  1.020
 3L1  C2   H2    single    0.930  0.020  1.080
 3L1  C8   H8    single    0.930  0.020  1.080
 3L1  C1'  H1'   single    0.970  0.020  1.090
 3L1  C2'  H2'   single    0.970  0.020  1.090
 3L1  C2'  H2'A  single    0.970  0.020  1.090
 3L1  C3'  H3'   single    0.970  0.020  1.090
 3L1  O3'  HO3'  single    0.850  0.020  0.980
 3L1  C4'  H4'   single    0.970  0.020  1.090
 3L1  C5'  H5'   single    0.970  0.020  1.090
 3L1  C5'  H5'A  single    0.970  0.020  1.090
 3L1  O5'  HO5'  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
 3L1  HN6A  N6   HN6  118.27  3.000
 3L1  HN6A  N6   C6   121.07  3.000
 3L1  HN6   N6   C6   120.29  3.000
 3L1  C5    C6   N1   117.93  3.000
 3L1  C5    C6   N6   122.72  3.000
 3L1  N1    C6   N6   119.36  3.000
 3L1  C2    N1   C6   119.12  3.000
 3L1  H2    C2   N3   116.12  3.000
 3L1  H2    C2   N1   115.41  3.000
 3L1  N3    C2   N1   128.47  3.000
 3L1  C4    N3   C2   111.73  3.000
 3L1  N9    C4   C5   105.20  3.000
 3L1  N9    C4   N3   128.38  3.000
 3L1  C5    C4   N3   126.42  3.000
 3L1  N7    C5   C4   110.81  3.000
 3L1  N7    C5   C6   132.85  3.000
 3L1  C4    C5   C6   116.34  3.000
 3L1  C8    N7   C5   104.33  3.000
 3L1  H8    C8   N9   121.76  3.000
 3L1  H8    C8   N7   124.74  3.000
 3L1  N9    C8   N7   113.50  3.000
 3L1  C1'   N9   C8   127.15  3.000
 3L1  C1'   N9   C4   126.66  3.000
 3L1  C8    N9   C4   106.16  3.000
 3L1  H1'   C1'  C2'  111.15  3.000
 3L1  H1'   C1'  O4'  110.74  3.000
 3L1  C2'   C1'  O4'  106.13  3.000
 3L1  H1'   C1'  N9   105.65  3.000
 3L1  C2'   C1'  N9   114.09  3.000
 3L1  O4'   C1'  N9   109.13  3.000
 3L1  C4'   O4'  C1'  110.84  3.000
 3L1  H2'A  C2'  H2'  107.33  3.000
 3L1  H2'A  C2'  C3'  113.61  3.000
 3L1  H2'   C2'  C3'  110.62  3.000
 3L1  H2'A  C2'  C1'  112.29  3.000
 3L1  H2'   C2'  C1'  111.28  3.000
 3L1  C3'   C2'  C1'  101.74  3.000
 3L1  H3'   C3'  C4'  111.80  3.000
 3L1  H3'   C3'  O3'  111.48  3.000
 3L1  C4'   C3'  O3'  107.65  3.000
 3L1  H3'   C3'  C2'  111.95  3.000
 3L1  C4'   C3'  C2'  101.42  3.000
 3L1  O3'   C3'  C2'  112.06  3.000
 3L1  HO3'  O3'  C3'  108.38  3.000
 3L1  H4'   C4'  C5'  108.85  3.000
 3L1  H4'   C4'  C3'  110.55  3.000
 3L1  C5'   C4'  C3'  112.25  3.000
 3L1  H4'   C4'  O4'  108.13  3.000
 3L1  C5'   C4'  O4'  111.27  3.000
 3L1  C3'   C4'  O4'  105.71  3.000
 3L1  H5'A  C5'  H5'  106.56  3.000
 3L1  H5'A  C5'  O5'  111.95  3.000
 3L1  H5'   C5'  O5'  111.70  3.000
 3L1  H5'A  C5'  C4'  107.61  3.000
 3L1  H5'   C5'  C4'  110.27  3.000
 3L1  O5'   C5'  C4'  108.66  3.000
 3L1  HO5'  O5'  C5'  108.15  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
 3L1  CONST_01  N3    C2  N1  C6    0.00  0.0  0
 3L1  CONST_02  N3    C4  C5  C6    0.00  0.0  0
 3L1  CONST_03  N9    C4  C5  C6  180.00  0.0  0
 3L1  CONST_04  C8    N7  C5  C6  180.00  0.0  0
 3L1  CONST_05  C4    C5  C6  N1    0.00  0.0  0
 3L1  CONST_06  N7    C5  C6  N1  180.00  0.0  0
 3L1  CONST_07  C4    N3  C2  N1    0.00  0.0  0
 3L1  CONST_08  C5    C6  N1  C2    0.00  0.0  0
 3L1  CONST_09  C5    C4  N3  C2    0.00  0.0  0
 3L1  CONST_10  N9    C4  N3  C2  180.00  0.0  0
 3L1  CONST_11  N7    C5  C4  N3  180.00  0.0  0
 3L1  CONST_12  C8    N9  C4  N3  180.00  0.0  0
 3L1  CONST_13  C8    N7  C5  C4    0.00  0.0  0
 3L1  CONST_14  N7    C8  N9  C4    0.00  0.0  0
 3L1  CONST_15  C8    N9  C4  C5    0.00  0.0  0
 3L1  CONST_16  N9    C8  N7  C5    0.00  0.0  0
 3L1  CONST_17  N9    C4  C5  N7    0.00  0.0  0
 3L1  CONST_18  C1'   N9  C4  N3    0.00  0.0  0
 3L1  CONST_19  C1'   N9  C4  C5  180.00  0.0  0
 3L1  CONST_20  C1'   N9  C8  N7  180.00  0.0  0
 3L1  CONST_21  C2    N1  C6  N6  180.00  0.0  0
 3L1  CONST_22  C4    C5  C6  N6  180.00  0.0  0
 3L1  CONST_23  N7    C5  C6  N6    0.00  0.0  0
 3L1  CONST_24  H2    C2  N1  C6  180.00  0.0  0
 3L1  CONST_25  H8    C8  N9  C4  180.00  0.0  0
 3L1  CONST_26  HN6   N6  C6  N1    0.00  0.0  0
 3L1  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
 3L1  chir_01  C1'  N9   O4'  C2'  negativ
 3L1  chir_02  C3'  O3'  C4'  C2'  negativ
 3L1  chir_03  C4'  O4'  C3'  C5'  positiv

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
 3L1  plan-1  N6    0.020
 3L1  plan-1  C6    0.020
 3L1  plan-1  N1    0.020
 3L1  plan-1  C2    0.020
 3L1  plan-1  N3    0.020
 3L1  plan-1  C4    0.020
 3L1  plan-1  C5    0.020
 3L1  plan-1  N7    0.020
 3L1  plan-1  C8    0.020
 3L1  plan-1  N9    0.020
 3L1  plan-1  C1'   0.020
 3L1  plan-1  H2    0.020
 3L1  plan-1  H8    0.020
 3L1  plan-2  N6    0.020
 3L1  plan-2  C6    0.020
 3L1  plan-2  HN6   0.020
 3L1  plan-2  HN6A  0.020

