# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 10:35:06 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: (2S,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxy-N-propyltetrahydrofuran-2-carboxamide (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCNC(=O)[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
#
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
 PA7  PA7  '(2S,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxy-N-propyltetrahydrofuran-2-carboxamide (non-preferred name)'  ligand  41  23  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_PA7
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
 PA7  C5'   C  C     0   0.536   2.6739   0.4127   0.3295
 PA7  O5'   O  O     0  -0.485   2.2209   1.5415   0.2009
 PA7  N5'   N  NH1   0  -0.637   3.9738   0.1215   0.2526
 PA7  C51   C  CH2   0  -0.235   4.9978   1.1182   0.0062
 PA7  C52   C  CH2   0  -0.476   6.3605   0.4590  -0.1336
 PA7  C53   C  CH3   0  -0.665   7.4666   1.4863  -0.3204
 PA7  C4'   C  CR15  0  -0.080   1.7764  -0.7984   0.5136
 PA7  O4'   O  O     0  -0.486   0.6688  -0.4529   1.3200
 PA7  C3'   C  CR15  0  -0.014   1.1675  -1.2717  -0.8167
 PA7  O3'   O  OH1   0  -0.658   1.9882  -2.1458  -1.5269
 PA7  C2'   C  CR15  0  -0.052  -0.1016  -1.9613  -0.3155
 PA7  O2'   O  OH1   0  -0.660   0.1800  -3.2162   0.2384
 PA7  C1'   C  CR15  0   0.171  -0.5058  -1.0401   0.8346
 PA7  N9    N  NR5   0  -0.536  -1.4207   0.0046   0.4043
 PA7  C8    C  CR15  0   0.087  -1.1423   1.2954   0.0412
 PA7  N7    N  N     0  -0.454  -2.2025   1.9703  -0.2993
 PA7  C5    C  CR56  0  -0.003  -3.2361   1.0826  -0.1560
 PA7  C6    C  CR6   0   0.456  -4.6255   1.1834  -0.3556
 PA7  N6    N  NH2   0  -0.817  -5.2157   2.3033  -0.7746
 PA7  N1    N  N     0  -0.474  -5.3739   0.1014  -0.1111
 PA7  C2    C  CR16  0   0.041  -4.7846  -1.0159   0.3064
 PA7  N3    N  N     0  -0.459  -3.4995  -1.2338   0.5272
 PA7  C4    C  CR56  0   0.486  -2.7705  -0.1467   0.2817
 PA7  H5'   H  HNH1  0   0.406   4.2720  -0.8204   0.4519
 PA7  H511  H  HCH2  0   0.235   5.0173   1.8431   0.8258
 PA7  H512  H  HCH2  0   0.238   4.7562   1.6720  -0.9042
 PA7  H521  H  HCH2  0   0.235   6.3468  -0.2316  -0.9810
 PA7  H522  H  HCH2  0   0.232   6.5645  -0.1407   0.7582
 PA7  H531  H  HCH3  0   0.224   7.5198   2.1692   0.5290
 PA7  H532  H  HCH3  0   0.237   8.4375   1.0009  -0.4151
 PA7  H533  H  HCH3  0   0.224   7.3076   2.0844  -1.2189
 PA7  H4'   H  HCR5  0   0.266   2.3320  -1.6262   0.9704
 PA7  H3'   H  HCR5  0   0.258   0.8807  -0.4012  -1.4190
 PA7  H2    H  HOH1  0   0.472   2.4118  -1.6751  -2.2493
 PA7  H2'   H  HCR5  0   0.270  -0.8777  -2.0161  -1.0879
 PA7  H1    H  HOH1  0   0.460   0.6027  -3.7589  -0.4362
 PA7  H1'   H  HCR5  0   0.285  -1.0113  -1.5993   1.6267
 PA7  H8    H  HCR5  0   0.306  -0.1336   1.6808   0.0542
 PA7  HN61  H  HNH2  0   0.411  -4.6833   3.1356  -0.9572
 PA7  HN62  H  HNH2  0   0.403  -6.2137   2.3397  -0.8880
 PA7  H3    H  HCR6  0   0.252  -5.4501  -1.8534   0.4873

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
 PA7  C5'  O5'   double    1.223  0.020  1.223
 PA7  C5'  N5'   single    1.334  0.020  1.334
 PA7  C5'  C4'   single    1.519  0.020  1.519
 PA7  N5'  C51   single    1.450  0.020  1.450
 PA7  N5'  H5'   single    0.860  0.020  1.020
 PA7  C51  C52   single    1.520  0.020  1.520
 PA7  C51  H511  single    0.970  0.020  1.090
 PA7  C51  H512  single    0.970  0.020  1.090
 PA7  C52  C53   single    1.521  0.020  1.521
 PA7  C52  H521  single    0.970  0.020  1.090
 PA7  C52  H522  single    0.970  0.020  1.090
 PA7  C53  H531  single    0.970  0.020  1.090
 PA7  C53  H532  single    0.970  0.020  1.090
 PA7  C53  H533  single    0.970  0.020  1.090
 PA7  C4'  O4'   single    1.413  0.020  1.413
 PA7  C4'  C3'   single    1.538  0.020  1.538
 PA7  C4'  H4'   single    0.970  0.020  1.090
 PA7  O4'  C1'   single    1.400  0.020  1.400
 PA7  C3'  O3'   single    1.394  0.020  1.394
 PA7  C3'  C2'   single    1.529  0.020  1.529
 PA7  C3'  H3'   single    0.970  0.020  1.090
 PA7  O3'  H2    single    0.850  0.020  0.980
 PA7  C2'  O2'   single    1.400  0.020  1.400
 PA7  C2'  C1'   single    1.528  0.020  1.528
 PA7  C2'  H2'   single    0.970  0.020  1.090
 PA7  O2'  H1    single    0.850  0.020  0.980
 PA7  C1'  N9    single    1.454  0.020  1.454
 PA7  C1'  H1'   single    0.970  0.020  1.090
 PA7  N9   C8    aromatic  1.370  0.020  1.370
 PA7  N9   C4    aromatic  1.364  0.020  1.364
 PA7  C8   N7    aromatic  1.302  0.020  1.302
 PA7  C8   H8    single    0.930  0.020  1.080
 PA7  N7   C5    aromatic  1.370  0.020  1.370
 PA7  C5   C6    aromatic  1.407  0.020  1.407
 PA7  C5   C4    aromatic  1.386  0.020  1.386
 PA7  C6   N6    single    1.333  0.020  1.333
 PA7  C6   N1    aromatic  1.338  0.020  1.338
 PA7  N6   HN61  single    0.860  0.020  1.020
 PA7  N6   HN62  single    0.860  0.020  1.020
 PA7  N1   C2    aromatic  1.330  0.020  1.330
 PA7  C2   N3    aromatic  1.322  0.020  1.322
 PA7  C2   H3    single    0.930  0.020  1.080
 PA7  N3   C4    aromatic  1.332  0.020  1.332

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
 PA7  C4'   C5'  N5'   114.13  3.000
 PA7  C4'   C5'  O5'   121.99  3.000
 PA7  N5'   C5'  O5'   123.79  3.000
 PA7  H5'   N5'  C51   117.84  3.000
 PA7  H5'   N5'  C5'   118.74  3.000
 PA7  C51   N5'  C5'   123.22  3.000
 PA7  H512  C51  H511  106.99  3.000
 PA7  H512  C51  C52   109.96  3.000
 PA7  H511  C51  C52   109.89  3.000
 PA7  H512  C51  N5'   109.50  3.000
 PA7  H511  C51  N5'   109.91  3.000
 PA7  C52   C51  N5'   110.52  3.000
 PA7  H522  C52  H521  106.74  3.000
 PA7  H522  C52  C53   109.56  3.000
 PA7  H521  C52  C53   109.91  3.000
 PA7  H522  C52  C51   109.27  3.000
 PA7  H521  C52  C51   109.51  3.000
 PA7  C53   C52  C51   111.73  3.000
 PA7  H533  C53  H532  107.61  3.000
 PA7  H533  C53  H531  107.77  3.000
 PA7  H532  C53  H531  107.64  3.000
 PA7  H533  C53  C52   111.43  3.000
 PA7  H532  C53  C52   110.96  3.000
 PA7  H531  C53  C52   111.26  3.000
 PA7  H4'   C4'  C3'   109.19  3.000
 PA7  H4'   C4'  O4'   110.12  3.000
 PA7  C3'   C4'  O4'   104.99  3.000
 PA7  H4'   C4'  C5'   110.67  3.000
 PA7  C3'   C4'  C5'   112.00  3.000
 PA7  O4'   C4'  C5'   109.73  3.000
 PA7  C1'   O4'  C4'   110.93  3.000
 PA7  H3'   C3'  C2'   108.72  3.000
 PA7  H3'   C3'  O3'   111.84  3.000
 PA7  C2'   C3'  O3'   111.90  3.000
 PA7  H3'   C3'  C4'   109.54  3.000
 PA7  C2'   C3'  C4'   100.60  3.000
 PA7  O3'   C3'  C4'   113.63  3.000
 PA7  H2    O3'  C3'   109.61  3.000
 PA7  H2'   C2'  C1'   111.91  3.000
 PA7  H2'   C2'  O2'   112.10  3.000
 PA7  C1'   C2'  O2'   107.20  3.000
 PA7  H2'   C2'  C3'   112.29  3.000
 PA7  C1'   C2'  C3'   101.21  3.000
 PA7  O2'   C2'  C3'   111.53  3.000
 PA7  H1    O2'  C2'   108.42  3.000
 PA7  H1'   C1'  N9    106.92  3.000
 PA7  H1'   C1'  C2'   111.05  3.000
 PA7  N9    C1'  C2'   112.14  3.000
 PA7  H1'   C1'  O4'   110.56  3.000
 PA7  N9    C1'  O4'   109.22  3.000
 PA7  C2'   C1'  O4'   106.97  3.000
 PA7  C4    N9   C8    106.37  3.000
 PA7  C4    N9   C1'   124.73  3.000
 PA7  C8    N9   C1'   128.89  3.000
 PA7  H8    C8   N7    125.36  3.000
 PA7  H8    C8   N9    121.53  3.000
 PA7  N7    C8   N9    113.10  3.000
 PA7  C5    N7   C8    104.54  3.000
 PA7  C4    C5   C6    116.12  3.000
 PA7  C4    C5   N7    110.76  3.000
 PA7  C6    C5   N7    133.13  3.000
 PA7  N1    C6   N6    119.28  3.000
 PA7  N1    C6   C5    117.93  3.000
 PA7  N6    C6   C5    122.80  3.000
 PA7  HN62  N6   HN61  118.40  3.000
 PA7  HN62  N6   C6    120.35  3.000
 PA7  HN61  N6   C6    121.22  3.000
 PA7  C2    N1   C6    119.25  3.000
 PA7  H3    C2   N3    116.18  3.000
 PA7  H3    C2   N1    115.40  3.000
 PA7  N3    C2   N1    128.42  3.000
 PA7  C4    N3   C2    111.52  3.000
 PA7  N3    C4   C5    126.76  3.000
 PA7  N3    C4   N9    128.01  3.000
 PA7  C5    C4   N9    105.23  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
 PA7  CONST_01  C5    N7   C8   N9      0.00   0.0  0
 PA7  CONST_02  N7    C5   C4   N9      0.00   0.0  0
 PA7  CONST_03  C6    C5   C4   N9    180.00   0.0  0
 PA7  CONST_04  C2    N3   C4   N9    180.00   0.0  0
 PA7  CONST_05  C5    C4   N9   C8      0.00   0.0  0
 PA7  CONST_06  N3    C4   N9   C8    180.00   0.0  0
 PA7  CONST_07  C6    C5   N7   C8    180.00   0.0  0
 PA7  CONST_08  C4    C5   N7   C8      0.00   0.0  0
 PA7  CONST_09  C4    N9   C8   N7      0.00   0.0  0
 PA7  CONST_10  N1    C6   C5   N7    180.00   0.0  0
 PA7  CONST_11  N3    C4   C5   N7    180.00   0.0  0
 PA7  CONST_12  C2    N1   C6   C5      0.00   0.0  0
 PA7  CONST_13  C2    N3   C4   C5      0.00   0.0  0
 PA7  CONST_14  N3    C4   C5   C6      0.00   0.0  0
 PA7  CONST_15  N3    C2   N1   C6      0.00   0.0  0
 PA7  CONST_16  C4    C5   C6   N1      0.00   0.0  0
 PA7  CONST_17  C4    N3   C2   N1      0.00   0.0  0
 PA7  CONST_18  N7    C8   N9   C1'   180.00   0.0  0
 PA7  CONST_19  C5    C4   N9   C1'   180.00   0.0  0
 PA7  CONST_20  N3    C4   N9   C1'     0.00   0.0  0
 PA7  CONST_21  N6    C6   C5   N7      0.00   0.0  0
 PA7  CONST_22  C4    C5   C6   N6    180.00   0.0  0
 PA7  CONST_23  C2    N1   C6   N6    180.00   0.0  0
 PA7  CONST_24  H8    C8   N9   C1'     0.00   0.0  0
 PA7  CONST_25  H3    C2   N1   C6    180.00   0.0  0
 PA7  CONST_26  HN61  N6   C6   C5      0.00   0.0  0
 PA7  CONST_27  HN62  N6   C6   C5    180.00   0.0  0
 PA7  CONST_28  C4'   C5'  N5'  C51   180.00   0.0  0
 PA7  CONST_29  H5'   N5'  C5'  C4'     0.00   0.0  0
 PA7  CONST_30  C51   N5'  C5'  O5'     0.00   0.0  0
 PA7  Var_01    C52   C51  N5'  C5'  -175.52  30.0  3
 PA7  Var_02    C53   C52  C51  N5'  -177.02  30.0  3
 PA7  Var_03    H531  C53  C52  C51    59.95  30.0  3

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
 PA7  chir_01  C4'  C5'  O4'  C3'  negativ
 PA7  chir_02  C3'  O3'  C4'  C2'  positiv
 PA7  chir_03  C2'  O2'  C3'  C1'  positiv
 PA7  chir_04  C1'  O4'  N9   C2'  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
 PA7  plan-1  C1'   0.020
 PA7  plan-1  N9    0.020
 PA7  plan-1  C8    0.020
 PA7  plan-1  N7    0.020
 PA7  plan-1  C5    0.020
 PA7  plan-1  C6    0.020
 PA7  plan-1  N6    0.020
 PA7  plan-1  N1    0.020
 PA7  plan-1  C2    0.020
 PA7  plan-1  N3    0.020
 PA7  plan-1  C4    0.020
 PA7  plan-1  H8    0.020
 PA7  plan-1  H3    0.020
 PA7  plan-2  C6    0.020
 PA7  plan-2  N6    0.020
 PA7  plan-2  HN61  0.020
 PA7  plan-2  HN62  0.020
 PA7  plan-3  C5'   0.020
 PA7  plan-3  O5'   0.020
 PA7  plan-3  N5'   0.020
 PA7  plan-3  C51   0.020
 PA7  plan-3  C4'   0.020
 PA7  plan-3  H5'   0.020

