# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 21 18:38:59 2022
#   Inital geometry file: a 75 line input string
#   Ligand name: 9-beta-D-arabinofuranosyl-9H-purin-6-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO)[C@@H](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
 RAB  RAB  9-beta-D-arabinofuranosyl-9H-purin-6-amine  ligand  32  19  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_RAB
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
 RAB  O5'   O  OH1   0  -0.665  -4.2721   1.8633  -1.2830
 RAB  C5'   C  CH2   0  -0.152  -3.8226   1.2629  -0.0954
 RAB  C4'   C  CH1   0  -0.020  -3.1114  -0.0247  -0.4238
 RAB  O4'   O  O2    0  -0.490  -1.9199   0.2459  -1.1658
 RAB  C1'   C  CH1   0   0.161  -0.8982  -0.6374  -0.8155
 RAB  N9    N  NR5   0  -0.518   0.2327   0.1161  -0.3105
 RAB  C4    C  CR56  0   0.495   1.5415  -0.2440  -0.4395
 RAB  N3    N  N     0  -0.456   2.0510  -1.2792  -1.1039
 RAB  C2    C  CR16  0   0.040   3.3699  -1.3043  -1.0314
 RAB  N1    N  N     0  -0.474   4.1811  -0.4586  -0.4002
 RAB  C6    C  CR6   0   0.454   3.6542   0.5767   0.2627
 RAB  N6    N  NH2   0  -0.816   4.4634   1.4205   0.9072
 RAB  C5    C  CR56  0  -0.010   2.2544   0.7178   0.2593
 RAB  N7    N  N     0  -0.451   1.4086   1.6453   0.8092
 RAB  C8    C  CR15  0   0.106   0.2217   1.2500   0.4534
 RAB  C2'   C  CH1   0  -0.010  -1.4830  -1.5966   0.2338
 RAB  O2'   O  OH1   0  -0.648  -0.5019  -1.9868   1.1428
 RAB  C3'   C  CH1   0  -0.025  -2.6417  -0.7953   0.8091
 RAB  O3'   O  OH1   0  -0.658  -3.6033  -1.6482   1.3630
 RAB  H5'   H  HOH1  0   0.460  -4.7023   2.6925  -1.0558
 RAB  H5'1  H  HCH2  0   0.204  -4.6541   1.0182   0.5800
 RAB  H5'2  H  HCH2  0   0.203  -3.1425   1.9176   0.4668
 RAB  H4'   H  HCH1  0   0.243  -3.7732  -0.6698  -1.0173
 RAB  H1'   H  HCH1  0   0.275  -0.5324  -1.1804  -1.6904
 RAB  H2    H  HCR6  0   0.251   3.8620  -2.1185  -1.5526
 RAB  HN61  H  HNH2  0   0.402   5.4606   1.3318   0.8134
 RAB  HN62  H  HNH2  0   0.410   4.1020   2.2525   1.3393
 RAB  H8    H  HCR5  0   0.290  -0.6930   1.7662   0.7008
 RAB  H2'   H  HCH1  0   0.250  -1.9018  -2.4578  -0.3050
 RAB  H1    H  HOH1  0   0.465  -0.8217  -2.7552   1.6256
 RAB  H3'   H  HCH1  0   0.225  -2.2550  -0.0928   1.5629
 RAB  H3    H  HOH1  0   0.460  -4.2124  -1.1288   1.8966

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
 RAB  O5'  C5'   single    1.405  0.020  1.405
 RAB  O5'  H5'   single    0.850  0.020  0.980
 RAB  C5'  C4'   single    1.507  0.020  1.507
 RAB  C5'  H5'1  single    0.970  0.020  1.090
 RAB  C5'  H5'2  single    0.970  0.020  1.090
 RAB  C4'  O4'   single    1.429  0.020  1.429
 RAB  C4'  C3'   single    1.528  0.020  1.528
 RAB  C4'  H4'   single    0.970  0.020  1.090
 RAB  O4'  C1'   single    1.395  0.020  1.395
 RAB  C1'  N9    single    1.450  0.020  1.450
 RAB  C1'  C2'   single    1.537  0.020  1.537
 RAB  C1'  H1'   single    0.970  0.020  1.090
 RAB  N9   C4    aromatic  1.364  0.020  1.364
 RAB  N9   C8    aromatic  1.367  0.020  1.367
 RAB  C4   N3    aromatic  1.331  0.020  1.331
 RAB  C4   C5    aromatic  1.386  0.020  1.386
 RAB  N3   C2    aromatic  1.321  0.020  1.321
 RAB  C2   N1    aromatic  1.331  0.020  1.331
 RAB  C2   H2    single    0.930  0.020  1.080
 RAB  N1   C6    aromatic  1.338  0.020  1.338
 RAB  C6   N6    single    1.335  0.020  1.335
 RAB  C6   C5    aromatic  1.407  0.020  1.407
 RAB  N6   HN61  single    0.860  0.020  1.020
 RAB  N6   HN62  single    0.860  0.020  1.020
 RAB  C5   N7    aromatic  1.370  0.020  1.370
 RAB  N7   C8    aromatic  1.301  0.020  1.301
 RAB  C8   H8    single    0.930  0.020  1.080
 RAB  C2'  O2'   single    1.393  0.020  1.393
 RAB  C2'  C3'   single    1.522  0.020  1.522
 RAB  C2'  H2'   single    0.970  0.020  1.090
 RAB  O2'  H1    single    0.850  0.020  0.980
 RAB  C3'  O3'   single    1.400  0.020  1.400
 RAB  C3'  H3'   single    0.970  0.020  1.090
 RAB  O3'  H3    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
 RAB  H5'   O5'  C5'   108.18  3.000
 RAB  H5'2  C5'  H5'1  106.66  3.000
 RAB  H5'2  C5'  C4'   109.17  3.000
 RAB  H5'1  C5'  C4'   107.50  3.000
 RAB  H5'2  C5'  O5'   112.09  3.000
 RAB  H5'1  C5'  O5'   111.88  3.000
 RAB  C4'   C5'  O5'   109.38  3.000
 RAB  H4'   C4'  C3'   108.97  3.000
 RAB  H4'   C4'  O4'   109.45  3.000
 RAB  C3'   C4'  O4'   104.95  3.000
 RAB  H4'   C4'  C5'   109.58  3.000
 RAB  C3'   C4'  C5'   113.58  3.000
 RAB  O4'   C4'  C5'   110.16  3.000
 RAB  C1'   O4'  C4'   111.11  3.000
 RAB  H1'   C1'  C2'   111.34  3.000
 RAB  H1'   C1'  N9    106.02  3.000
 RAB  C2'   C1'  N9    112.54  3.000
 RAB  H1'   C1'  O4'   111.02  3.000
 RAB  C2'   C1'  O4'   106.73  3.000
 RAB  N9    C1'  O4'   109.24  3.000
 RAB  C8    N9   C4    106.24  3.000
 RAB  C8    N9   C1'   128.27  3.000
 RAB  C4    N9   C1'   125.35  3.000
 RAB  C5    C4   N3    126.46  3.000
 RAB  C5    C4   N9    105.23  3.000
 RAB  N3    C4   N9    128.31  3.000
 RAB  C2    N3   C4    111.68  3.000
 RAB  H2    C2   N1    115.36  3.000
 RAB  H2    C2   N3    116.15  3.000
 RAB  N1    C2   N3    128.49  3.000
 RAB  C6    N1   C2    119.13  3.000
 RAB  C5    C6   N6    122.74  3.000
 RAB  C5    C6   N1    117.93  3.000
 RAB  N6    C6   N1    119.32  3.000
 RAB  HN62  N6   HN61  118.03  3.000
 RAB  HN62  N6   C6    120.86  3.000
 RAB  HN61  N6   C6    120.02  3.000
 RAB  N7    C5   C6    132.92  3.000
 RAB  N7    C5   C4    110.76  3.000
 RAB  C6    C5   C4    116.32  3.000
 RAB  C8    N7   C5    104.35  3.000
 RAB  H8    C8   N7    124.44  3.000
 RAB  H8    C8   N9    122.12  3.000
 RAB  N7    C8   N9    113.42  3.000
 RAB  H2'   C2'  C3'   107.93  3.000
 RAB  H2'   C2'  O2'   111.64  3.000
 RAB  C3'   C2'  O2'   115.91  3.000
 RAB  H2'   C2'  C1'   107.42  3.000
 RAB  C3'   C2'  C1'   102.66  3.000
 RAB  O2'   C2'  C1'   110.63  3.000
 RAB  H1    O2'  C2'   108.48  3.000
 RAB  H3'   C3'  O3'   111.06  3.000
 RAB  H3'   C3'  C2'   109.12  3.000
 RAB  O3'   C3'  C2'   110.60  3.000
 RAB  H3'   C3'  C4'   109.80  3.000
 RAB  O3'   C3'  C4'   114.54  3.000
 RAB  C2'   C3'  C4'   101.22  3.000
 RAB  H3    O3'  C3'   109.00  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
 RAB  CONST_01  C2    N3  C4  N9   180.00  0.0  0
 RAB  CONST_02  C6    C5  C4  N9   180.00  0.0  0
 RAB  CONST_03  N7    C5  C4  N9     0.00  0.0  0
 RAB  CONST_04  C5    N7  C8  N9     0.00  0.0  0
 RAB  CONST_05  N7    C8  N9  C4     0.00  0.0  0
 RAB  CONST_06  N1    C2  N3  C4     0.00  0.0  0
 RAB  CONST_07  N1    C6  C5  C4     0.00  0.0  0
 RAB  CONST_08  C8    N7  C5  C4     0.00  0.0  0
 RAB  CONST_09  C8    N9  C4  N3   180.00  0.0  0
 RAB  CONST_10  C6    C5  C4  N3     0.00  0.0  0
 RAB  CONST_11  N7    C5  C4  N3   180.00  0.0  0
 RAB  CONST_12  C6    N1  C2  N3     0.00  0.0  0
 RAB  CONST_13  C5    C4  N3  C2     0.00  0.0  0
 RAB  CONST_14  C5    C6  N1  C2     0.00  0.0  0
 RAB  CONST_15  N7    C5  C6  N1   180.00  0.0  0
 RAB  CONST_16  C8    N7  C5  C6   180.00  0.0  0
 RAB  CONST_17  C8    N9  C4  C5     0.00  0.0  0
 RAB  CONST_18  N3    C4  N9  C1'    0.00  0.0  0
 RAB  CONST_19  C5    C4  N9  C1'  180.00  0.0  0
 RAB  CONST_20  N7    C8  N9  C1'  180.00  0.0  0
 RAB  CONST_21  N6    C6  C5  C4   180.00  0.0  0
 RAB  CONST_22  N6    C6  N1  C2   180.00  0.0  0
 RAB  CONST_23  N7    C5  C6  N6     0.00  0.0  0
 RAB  CONST_24  H8    C8  N9  C1'    0.00  0.0  0
 RAB  CONST_25  H2    C2  N3  C4   180.00  0.0  0
 RAB  CONST_26  HN61  N6  C6  N1     0.00  0.0  0
 RAB  CONST_27  HN62  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
 RAB  chir_01  C4'  C5'  O4'  C3'  negativ
 RAB  chir_02  C1'  O4'  N9   C2'  negativ
 RAB  chir_03  C2'  O2'  C1'  C3'  positiv
 RAB  chir_04  C3'  O3'  C4'  C2'  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
 RAB  plan-1  C1'   0.020
 RAB  plan-1  N9    0.020
 RAB  plan-1  C4    0.020
 RAB  plan-1  N3    0.020
 RAB  plan-1  C2    0.020
 RAB  plan-1  N1    0.020
 RAB  plan-1  C6    0.020
 RAB  plan-1  N6    0.020
 RAB  plan-1  C5    0.020
 RAB  plan-1  N7    0.020
 RAB  plan-1  C8    0.020
 RAB  plan-1  H2    0.020
 RAB  plan-1  H8    0.020
 RAB  plan-2  C6    0.020
 RAB  plan-2  N6    0.020
 RAB  plan-2  HN61  0.020
 RAB  plan-2  HN62  0.020

