# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 18:04:30 2020
#   Inital geometry file: a 75 line input string
#   Ligand name: 6-chloro-9-(beta-D-ribofuranosyl)-9H-purin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nc(Cl)c2ncn([C@@H]3O[C@H](CO)[C@@H](O)[C@H]3O)c2n1
#
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
 6CR  6CR  6-chloro-9-(beta-D-ribofuranosyl)-9H-purin-2-amine  ligand  32  20  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_6CR
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
 6CR  N1    N   N     0  -0.454  -3.4808   0.3527   0.0457
 6CR  C2    C   CR6   0   0.550  -2.6791   1.4267  -0.1288
 6CR  N3    N   N     0  -0.482  -1.3658   1.3916  -0.3584
 6CR  C4    C   CR56  0   0.528  -0.8784   0.1670  -0.3992
 6CR  C5    C   CR56  0   0.112  -1.5960  -1.0232  -0.2372
 6CR  C6    C   CR6   0   0.115  -2.9473  -0.8364  -0.0093
 6CR  N7    N   N     0  -0.434  -0.7712  -2.1091  -0.3596
 6CR  C8    C   CR15  0   0.107   0.3994  -1.5968  -0.5868
 6CR  N9    N   NR5   0  -0.550   0.4073  -0.2227  -0.6113
 6CR  C1'   C   CH1   0   0.175   1.5300   0.6697  -0.9051
 6CR  CL1   CL  CL    0  -0.079  -3.9802  -2.1978   0.2093
 6CR  C2'   C   CH1   0  -0.039   1.9028   1.5159   0.3094
 6CR  O2'   O   OH1   0  -0.664   2.5449   2.6670  -0.1643
 6CR  N20   N   NH2   0  -0.822  -3.2696   2.6303  -0.0318
 6CR  C3'   C   CH1   0  -0.046   2.8927   0.5843   1.0163
 6CR  O3'   O   OH1   0  -0.656   3.8108   1.2520   1.8349
 6CR  C4'   C   CH1   0   0.008   3.6123  -0.0665  -0.1616
 6CR  O4'   O   O2    0  -0.495   2.6484  -0.0980  -1.2177
 6CR  C5'   C   CH2   0  -0.154   4.1177  -1.4536   0.1506
 6CR  O5'   O   OH1   0  -0.669   4.7696  -1.9706  -0.9819
 6CR  H8    H   HCR5  0   0.302   1.2964  -2.1709  -0.7544
 6CR  H1'   H   HCH1  0   0.289   1.2424   1.2876  -1.7601
 6CR  H2'   H   HCH1  0   0.263   1.0344   1.7597   0.9322
 6CR  HO2'  H   HOH1  0   0.452   3.1877   2.9392   0.5024
 6CR  HN20  H   HNH2  0   0.402  -4.2729   2.6856  -0.0413
 6CR  HN2A  H   HNH2  0   0.402  -2.7593   3.4484  -0.3154
 6CR  H3'   H   HCH1  0   0.249   2.3309  -0.1744   1.5774
 6CR  HO3'  H   HOH1  0   0.469   3.4116   1.3921   2.6996
 6CR  H4'   H   HCH1  0   0.248   4.4553   0.5616  -0.4751
 6CR  H5'   H   HCH2  0   0.217   4.7929  -1.3657   1.0118
 6CR  H5'A  H   HCH2  0   0.196   3.2796  -2.0889   0.4699
 6CR  HO5'  H   HOH1  0   0.460   5.1153  -2.8397  -0.7596

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
 6CR  C2   N1    aromatic  1.352  0.020  1.352
 6CR  N1   C6    aromatic  1.305  0.020  1.305
 6CR  N3   C2    aromatic  1.334  0.020  1.334
 6CR  N20  C2    single    1.344  0.020  1.344
 6CR  N3   C4    aromatic  1.319  0.020  1.319
 6CR  N9   C4    aromatic  1.360  0.020  1.360
 6CR  C4   C5    aromatic  1.399  0.020  1.399
 6CR  C5   N7    aromatic  1.369  0.020  1.369
 6CR  C5   C6    aromatic  1.383  0.020  1.383
 6CR  C6   CL1   single    1.723  0.020  1.723
 6CR  C8   N7    aromatic  1.298  0.020  1.298
 6CR  N9   C8    aromatic  1.374  0.020  1.374
 6CR  C8   H8    single    0.930  0.020  1.080
 6CR  C1'  N9    single    1.464  0.020  1.464
 6CR  C2'  C1'   single    1.526  0.020  1.526
 6CR  C1'  O4'   single    1.392  0.020  1.392
 6CR  C1'  H1'   single    0.970  0.020  1.090
 6CR  O2'  C2'   single    1.401  0.020  1.401
 6CR  C3'  C2'   single    1.532  0.020  1.532
 6CR  C2'  H2'   single    0.970  0.020  1.090
 6CR  O2'  HO2'  single    0.850  0.020  0.980
 6CR  N20  HN20  single    0.890  0.020  1.040
 6CR  N20  HN2A  single    0.890  0.020  1.040
 6CR  O3'  C3'   single    1.400  0.020  1.400
 6CR  C3'  C4'   single    1.526  0.020  1.526
 6CR  C3'  H3'   single    0.970  0.020  1.090
 6CR  O3'  HO3'  single    0.850  0.020  0.980
 6CR  C4'  O4'   single    1.430  0.020  1.430
 6CR  C4'  C5'   single    1.509  0.020  1.509
 6CR  C4'  H4'   single    0.970  0.020  1.090
 6CR  C5'  O5'   single    1.405  0.020  1.405
 6CR  C5'  H5'   single    0.970  0.020  1.090
 6CR  C5'  H5'A  single    0.970  0.020  1.090
 6CR  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
 6CR  C6    N1   C2    118.44  3.000
 6CR  N20   C2   N3    117.94  3.000
 6CR  N20   C2   N1    116.21  3.000
 6CR  N3    C2   N1    125.84  3.000
 6CR  C4    N3   C2    113.18  3.000
 6CR  N9    C4   C5    105.02  3.000
 6CR  C5    C4   N3    126.64  3.000
 6CR  N9    C4   N3    128.34  3.000
 6CR  N7    C5   C6    135.28  3.000
 6CR  C6    C5   C4    113.91  3.000
 6CR  N7    C5   C4    110.81  3.000
 6CR  CL1   C6   C5    120.00  3.000
 6CR  CL1   C6   N1    118.02  3.000
 6CR  C5    C6   N1    121.98  3.000
 6CR  C8    N7   C5    104.24  3.000
 6CR  H8    C8   N9    121.66  3.000
 6CR  H8    C8   N7    124.58  3.000
 6CR  N9    C8   N7    113.76  3.000
 6CR  C1'   N9   C8    128.13  3.000
 6CR  C1'   N9   C4    125.57  3.000
 6CR  C8    N9   C4    106.16  3.000
 6CR  H1'   C1'  O4'   110.33  3.000
 6CR  H1'   C1'  C2'   111.91  3.000
 6CR  O4'   C1'  C2'   106.75  3.000
 6CR  H1'   C1'  N9    107.44  3.000
 6CR  O4'   C1'  N9    108.96  3.000
 6CR  C2'   C1'  N9    111.44  3.000
 6CR  H2'   C2'  C3'   112.64  3.000
 6CR  H2'   C2'  O2'   111.87  3.000
 6CR  C3'   C2'  O2'   111.07  3.000
 6CR  H2'   C2'  C1'   112.45  3.000
 6CR  C3'   C2'  C1'   100.83  3.000
 6CR  O2'   C2'  C1'   107.36  3.000
 6CR  HO2'  O2'  C2'   107.67  3.000
 6CR  HN2A  N20  HN20  117.35  3.000
 6CR  HN2A  N20  C2    119.05  3.000
 6CR  HN20  N20  C2    119.15  3.000
 6CR  H3'   C3'  C4'   109.93  3.000
 6CR  H3'   C3'  O3'   111.49  3.000
 6CR  C4'   C3'  O3'   110.22  3.000
 6CR  H3'   C3'  C2'   108.99  3.000
 6CR  C4'   C3'  C2'   102.00  3.000
 6CR  O3'   C3'  C2'   113.81  3.000
 6CR  HO3'  O3'  C3'   108.83  3.000
 6CR  H4'   C4'  C5'   109.15  3.000
 6CR  H4'   C4'  O4'   108.64  3.000
 6CR  C5'   C4'  O4'   111.00  3.000
 6CR  H4'   C4'  C3'   109.80  3.000
 6CR  C5'   C4'  C3'   112.97  3.000
 6CR  O4'   C4'  C3'   105.16  3.000
 6CR  C4'   O4'  C1'   111.32  3.000
 6CR  H5'A  C5'  H5'   106.70  3.000
 6CR  H5'A  C5'  O5'   112.04  3.000
 6CR  H5'   C5'  O5'   112.11  3.000
 6CR  H5'A  C5'  C4'   109.64  3.000
 6CR  H5'   C5'  C4'   107.14  3.000
 6CR  O5'   C5'  C4'   109.07  3.000
 6CR  HO5'  O5'  C5'   108.24  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
 6CR  CONST_01  C4    N3   C2  N1    0.00  0.0  0
 6CR  CONST_02  C4    C5   C6  N1    0.00  0.0  0
 6CR  CONST_03  N7    C5   C6  N1  180.00  0.0  0
 6CR  CONST_04  C5    C6   N1  C2    0.00  0.0  0
 6CR  CONST_05  N9    C4   N3  C2  180.00  0.0  0
 6CR  CONST_06  C5    C4   N3  C2    0.00  0.0  0
 6CR  CONST_07  C6    N1   C2  N3    0.00  0.0  0
 6CR  CONST_08  C8    N9   C4  N3  180.00  0.0  0
 6CR  CONST_09  N7    C5   C4  N3  180.00  0.0  0
 6CR  CONST_10  C6    C5   C4  N3    0.00  0.0  0
 6CR  CONST_11  N7    C8   N9  C4    0.00  0.0  0
 6CR  CONST_12  C8    N7   C5  C4    0.00  0.0  0
 6CR  CONST_13  C8    N9   C4  C5    0.00  0.0  0
 6CR  CONST_14  N9    C8   N7  C5    0.00  0.0  0
 6CR  CONST_15  N9    C4   C5  C6  180.00  0.0  0
 6CR  CONST_16  C8    N7   C5  C6  180.00  0.0  0
 6CR  CONST_17  N9    C4   C5  N7    0.00  0.0  0
 6CR  CONST_18  C1'   N9   C4  N3    0.00  0.0  0
 6CR  CONST_19  C1'   N9   C4  C5  180.00  0.0  0
 6CR  CONST_20  C1'   N9   C8  N7  180.00  0.0  0
 6CR  CONST_21  CL1   C6   N1  C2  180.00  0.0  0
 6CR  CONST_22  N20   C2   N3  C4  180.00  0.0  0
 6CR  CONST_23  CL1   C6   C5  C4  180.00  0.0  0
 6CR  CONST_24  N20   C2   N1  C6  180.00  0.0  0
 6CR  CONST_25  CL1   C6   C5  N7    0.00  0.0  0
 6CR  CONST_26  H8    C8   N9  C4  180.00  0.0  0
 6CR  CONST_27  HN20  N20  C2  N1    0.00  0.0  0
 6CR  CONST_28  HN2A  N20  C2  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
 6CR  chir_01  C1'  N9   C2'  O4'  negativ
 6CR  chir_02  C2'  O2'  C3'  C1'  positiv
 6CR  chir_03  C3'  O3'  C4'  C2'  positiv
 6CR  chir_04  C4'  O4'  C3'  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
 6CR  plan-1  N1    0.020
 6CR  plan-1  C2    0.020
 6CR  plan-1  N3    0.020
 6CR  plan-1  C4    0.020
 6CR  plan-1  C5    0.020
 6CR  plan-1  C6    0.020
 6CR  plan-1  N7    0.020
 6CR  plan-1  C8    0.020
 6CR  plan-1  N9    0.020
 6CR  plan-1  C1'   0.020
 6CR  plan-1  CL1   0.020
 6CR  plan-1  N20   0.020
 6CR  plan-1  H8    0.020
 6CR  plan-2  C2    0.020
 6CR  plan-2  N20   0.020
 6CR  plan-2  HN20  0.020
 6CR  plan-2  HN2A  0.020

