# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 06:31:29 2020
#   Inital geometry file: a 103 line input string
#   Ligand name: 5'-S-[(3R)-3,4-dihydroxybutyl]-5'-thioadenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CSCC[C@@H](O)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
 A7D  A7D  5'-S-[(3R)-3,4-dihydroxybutyl]-5'-thioadenosine  ligand  46  25  .  2022-07-24  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_A7D
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
 A7D  N1    N  N     0  -0.474  -5.6858   1.6090  -0.2065
 A7D  C2    C  CR16  0   0.039  -5.6290   0.3450   0.2059
 A7D  N3    N  N     0  -0.459  -4.5610  -0.3845   0.4769
 A7D  C4    C  CR56  0   0.488  -3.4354   0.3046   0.2926
 A7D  C5    C  CR56  0  -0.003  -3.3348   1.6227  -0.1238
 A7D  C6    C  CR6   0   0.457  -4.5473   2.2879  -0.3863
 A7D  N6    N  NH2   0  -0.817  -4.5987   3.5540  -0.8009
 A7D  N7    N  N     0  -0.450  -2.0245   2.0154  -0.1833
 A7D  C8    C  CR15  0   0.105  -1.3537   0.9630   0.1864
 A7D  N9    N  NR5   0  -0.541  -2.1495  -0.1131   0.4752
 A7D  OAC   O  OH1   0  -0.662   5.9244   1.5652  -1.4330
 A7D  OAD   O  OH1   0  -0.657  -0.5924  -3.7335  -1.5536
 A7D  OAE   O  OH1   0  -0.664  -2.1511  -3.7326   0.7142
 A7D  CAH   C  CH2   0  -0.155   7.1235   1.6675   0.6786
 A7D  CAI   C  CH2   0  -0.542   3.9053  -0.2361  -0.2980
 A7D  CAJ   C  CH2   0  -0.466   4.8863   0.5693   0.5393
 A7D  OAO   O  O     0  -0.492  -0.3540  -1.4416   1.1116
 A7D  SAP   S  S2    0  -0.018   2.4513  -0.6496   0.7085
 A7D  CAT   C  CH1   0   0.003   6.1730   0.8915  -0.2182
 A7D  CAU   C  CR15  0  -0.031  -0.8574  -2.5105  -0.9266
 A7D  CAV   C  CR15  0  -0.038  -2.0870  -2.5366  -0.0112
 A7D  CAW   C  CR15  0   0.047   0.2700  -2.1651   0.0500
 A7D  CAX   C  CR15  0   0.172  -1.7377  -1.4250   0.9744
 A7D  H2    H  HCR6  0   0.252  -6.5879  -0.1458   0.3349
 A7D  HN6   H  HNH2  0   0.404  -5.4839   3.9976  -0.9747
 A7D  HN6A  H  HNH2  0   0.412  -3.7599   4.0861  -0.9508
 A7D  H8    H  HCR5  0   0.290  -0.2796   0.9225   0.2835
 A7D  HOAB  H  HOH1  0   0.455   8.9157   2.3893   0.5676
 A7D  HOAD  H  HOH1  0   0.470  -1.1257  -3.7937  -2.3528
 A7D  HOAE  H  HOH1  0   0.452  -1.8877  -4.4487   0.1229
 A7D  HAH   H  HCH2  0   0.197   7.2580   1.1068   1.6130
 A7D  HAHA  H  HCH2  0   0.192   6.6529   2.6242   0.9507
 A7D  HAI   H  HCH2  0   0.265   3.5815   0.3340  -1.1693
 A7D  HAIA  H  HCH2  0   0.261   4.3697  -1.1591  -0.6522
 A7D  HAJ   H  HCH2  0   0.237   4.4118   1.4982   0.8741
 A7D  HAJA  H  HCH2  0   0.242   5.1465   0.0109   1.4429
 A7D  HAT   H  HCH1  0   0.228   6.6549  -0.0510  -0.5011
 A7D  HAU   H  HCR5  0   0.249  -0.9768  -1.7040  -1.6609
 A7D  HAV   H  HCR5  0   0.262  -3.0189  -2.3355  -0.5516
 A7D  HAW   H  HCR5  0   0.256   0.6990  -3.0826   0.4668
 A7D  HAX   H  HCR5  0   0.291  -2.2124  -1.5770   1.9473
 A7D  CAK   C  CH2   0  -0.581   1.3739  -1.3395  -0.5777
 A7D  HOAC  H  HOH1  0   0.442   5.4822   2.3976  -1.2324
 A7D  OAB   O  OH1   0  -0.670   8.3439   1.8596   0.0053
 A7D  HAK   H  HCH2  0   0.262   0.9640  -0.5320  -1.1892
 A7D  HAKA  H  HCH2  0   0.292   1.9602  -1.9887  -1.2312

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
 A7D  N1   C2    aromatic  1.331  0.020  1.331
 A7D  N1   C6    aromatic  1.338  0.020  1.338
 A7D  C2   N3    aromatic  1.321  0.020  1.321
 A7D  N3   C4    aromatic  1.333  0.020  1.333
 A7D  C4   C5    aromatic  1.386  0.020  1.386
 A7D  C4   N9    aromatic  1.364  0.020  1.364
 A7D  C5   C6    aromatic  1.408  0.020  1.408
 A7D  C5   N7    aromatic  1.369  0.020  1.369
 A7D  C6   N6    single    1.333  0.020  1.333
 A7D  N7   C8    aromatic  1.302  0.020  1.302
 A7D  C8   N9    aromatic  1.369  0.020  1.369
 A7D  N9   CAX   single    1.463  0.020  1.463
 A7D  OAB  CAH   single    1.407  0.020  1.407
 A7D  OAC  CAT   single    1.411  0.020  1.411
 A7D  OAD  CAU   single    1.400  0.020  1.400
 A7D  OAE  CAV   single    1.400  0.020  1.400
 A7D  CAH  CAT   single    1.520  0.020  1.520
 A7D  CAI  CAJ   single    1.521  0.020  1.521
 A7D  CAI  SAP   single    1.816  0.020  1.816
 A7D  CAJ  CAT   single    1.528  0.020  1.528
 A7D  CAK  SAP   single    1.814  0.020  1.814
 A7D  CAK  CAW   single    1.515  0.020  1.515
 A7D  OAO  CAW   single    1.428  0.020  1.428
 A7D  OAO  CAX   single    1.391  0.020  1.391
 A7D  CAU  CAV   single    1.533  0.020  1.533
 A7D  CAU  CAW   single    1.531  0.020  1.531
 A7D  CAV  CAX   single    1.526  0.020  1.526
 A7D  C2   H2    single    0.930  0.020  1.080
 A7D  N6   HN6   single    0.860  0.020  1.020
 A7D  N6   HN6A  single    0.860  0.020  1.020
 A7D  C8   H8    single    0.930  0.020  1.080
 A7D  OAB  HOAB  single    0.850  0.020  0.980
 A7D  OAC  HOAC  single    0.850  0.020  0.980
 A7D  OAD  HOAD  single    0.850  0.020  0.980
 A7D  OAE  HOAE  single    0.850  0.020  0.980
 A7D  CAH  HAH   single    0.970  0.020  1.090
 A7D  CAH  HAHA  single    0.970  0.020  1.090
 A7D  CAI  HAI   single    0.970  0.020  1.090
 A7D  CAI  HAIA  single    0.970  0.020  1.090
 A7D  CAJ  HAJ   single    0.970  0.020  1.090
 A7D  CAJ  HAJA  single    0.970  0.020  1.090
 A7D  CAK  HAK   single    0.970  0.020  1.090
 A7D  CAK  HAKA  single    0.970  0.020  1.090
 A7D  CAT  HAT   single    0.970  0.020  1.090
 A7D  CAU  HAU   single    0.970  0.020  1.090
 A7D  CAV  HAV   single    0.970  0.020  1.090
 A7D  CAW  HAW   single    0.970  0.020  1.090
 A7D  CAX  HAX   single    0.970  0.020  1.090

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
 A7D  C6    N1   C2   119.17  3.000
 A7D  H2    C2   N3   116.12  3.000
 A7D  H2    C2   N1   115.39  3.000
 A7D  N3    C2   N1   128.49  3.000
 A7D  C4    N3   C2   111.64  3.000
 A7D  N9    C4   C5   105.24  3.000
 A7D  N9    C4   N3   128.27  3.000
 A7D  C5    C4   N3   126.49  3.000
 A7D  N7    C5   C6   132.90  3.000
 A7D  N7    C5   C4   110.81  3.000
 A7D  C6    C5   C4   116.28  3.000
 A7D  N6    C6   C5   122.68  3.000
 A7D  N6    C6   N1   119.40  3.000
 A7D  C5    C6   N1   117.92  3.000
 A7D  HN6A  N6   HN6  118.40  3.000
 A7D  HN6A  N6   C6   121.15  3.000
 A7D  HN6   N6   C6   120.45  3.000
 A7D  C8    N7   C5   104.42  3.000
 A7D  H8    C8   N9   122.00  3.000
 A7D  H8    C8   N7   124.67  3.000
 A7D  N9    C8   N7   113.32  3.000
 A7D  CAX   N9   C8   127.83  3.000
 A7D  CAX   N9   C4   125.84  3.000
 A7D  C8    N9   C4   106.20  3.000
 A7D  HOAC  OAC  CAT  108.30  3.000
 A7D  HOAD  OAD  CAU  108.76  3.000
 A7D  HOAE  OAE  CAV  107.69  3.000
 A7D  HAHA  CAH  HAH  106.62  3.000
 A7D  HAHA  CAH  CAT  108.81  3.000
 A7D  HAH   CAH  CAT  108.55  3.000
 A7D  HAHA  CAH  OAB  111.75  3.000
 A7D  HAH   CAH  OAB  111.76  3.000
 A7D  CAT   CAH  OAB  109.25  3.000
 A7D  HAIA  CAI  HAI  108.00  3.000
 A7D  HAIA  CAI  SAP  109.13  3.000
 A7D  HAI   CAI  SAP  108.91  3.000
 A7D  HAIA  CAI  CAJ  110.60  3.000
 A7D  HAI   CAI  CAJ  110.78  3.000
 A7D  SAP   CAI  CAJ  109.38  3.000
 A7D  HAJA  CAJ  HAJ  106.47  3.000
 A7D  HAJA  CAJ  CAT  108.48  3.000
 A7D  HAJ   CAJ  CAT  109.73  3.000
 A7D  HAJA  CAJ  CAI  109.76  3.000
 A7D  HAJ   CAJ  CAI  109.76  3.000
 A7D  CAT   CAJ  CAI  112.46  3.000
 A7D  CAX   OAO  CAW  111.56  3.000
 A7D  CAK   SAP  CAI   99.74  3.000
 A7D  HAT   CAT  CAJ  108.49  3.000
 A7D  HAT   CAT  CAH  108.45  3.000
 A7D  CAJ   CAT  CAH  109.99  3.000
 A7D  HAT   CAT  OAC  105.42  3.000
 A7D  CAJ   CAT  OAC  112.29  3.000
 A7D  CAH   CAT  OAC  111.99  3.000
 A7D  HAU   CAU  CAW  109.95  3.000
 A7D  HAU   CAU  CAV  108.95  3.000
 A7D  CAW   CAU  CAV  102.33  3.000
 A7D  HAU   CAU  OAD  111.29  3.000
 A7D  CAW   CAU  OAD  110.09  3.000
 A7D  CAV   CAU  OAD  113.86  3.000
 A7D  HAV   CAV  CAX  112.30  3.000
 A7D  HAV   CAV  CAU  112.61  3.000
 A7D  CAX   CAV  CAU  100.93  3.000
 A7D  HAV   CAV  OAE  111.91  3.000
 A7D  CAX   CAV  OAE  107.34  3.000
 A7D  CAU   CAV  OAE  111.13  3.000
 A7D  HAW   CAW  CAU  110.01  3.000
 A7D  HAW   CAW  OAO  108.22  3.000
 A7D  CAU   CAW  OAO  105.47  3.000
 A7D  HAW   CAW  CAK  109.20  3.000
 A7D  CAU   CAW  CAK  113.29  3.000
 A7D  OAO   CAW  CAK  110.51  3.000
 A7D  HAX   CAX  CAV  111.97  3.000
 A7D  HAX   CAX  OAO  110.04  3.000
 A7D  CAV   CAX  OAO  106.43  3.000
 A7D  HAX   CAX  N9   107.83  3.000
 A7D  CAV   CAX  N9   111.62  3.000
 A7D  OAO   CAX  N9   108.93  3.000
 A7D  HAKA  CAK  HAK  107.81  3.000
 A7D  HAKA  CAK  CAW  108.38  3.000
 A7D  HAK   CAK  CAW  111.18  3.000
 A7D  HAKA  CAK  SAP  109.36  3.000
 A7D  HAK   CAK  SAP  109.79  3.000
 A7D  CAW   CAK  SAP  110.26  3.000
 A7D  HOAB  OAB  CAH  108.14  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
 A7D  CONST_01  C4    N3   C2   N1     0.00   0.0  0
 A7D  CONST_02  C4    C5   C6   N1     0.00   0.0  0
 A7D  CONST_03  N7    C5   C6   N1   180.00   0.0  0
 A7D  CONST_04  C5    C6   N1   C2     0.00   0.0  0
 A7D  CONST_05  C5    C4   N3   C2     0.00   0.0  0
 A7D  CONST_06  N9    C4   N3   C2   180.00   0.0  0
 A7D  CONST_07  C6    N1   C2   N3     0.00   0.0  0
 A7D  CONST_08  C6    C5   C4   N3     0.00   0.0  0
 A7D  CONST_09  N7    C5   C4   N3   180.00   0.0  0
 A7D  CONST_10  C8    N9   C4   N3   180.00   0.0  0
 A7D  CONST_11  C8    N7   C5   C4     0.00   0.0  0
 A7D  CONST_12  N7    C8   N9   C4     0.00   0.0  0
 A7D  CONST_13  C8    N9   C4   C5     0.00   0.0  0
 A7D  CONST_14  N9    C8   N7   C5     0.00   0.0  0
 A7D  CONST_15  N9    C4   C5   C6   180.00   0.0  0
 A7D  CONST_16  C8    N7   C5   C6   180.00   0.0  0
 A7D  CONST_17  N9    C4   C5   N7     0.00   0.0  0
 A7D  CONST_18  CAX   N9   C4   N3     0.00   0.0  0
 A7D  CONST_19  CAX   N9   C4   C5   180.00   0.0  0
 A7D  CONST_20  CAX   N9   C8   N7   180.00   0.0  0
 A7D  CONST_21  N6    C6   N1   C2   180.00   0.0  0
 A7D  CONST_22  N6    C6   C5   C4   180.00   0.0  0
 A7D  CONST_23  N7    C5   C6   N6     0.00   0.0  0
 A7D  CONST_24  H2    C2   N3   C4   180.00   0.0  0
 A7D  CONST_25  H8    C8   N9   C4   180.00   0.0  0
 A7D  CONST_26  HN6   N6   C6   N1     0.00   0.0  0
 A7D  CONST_27  HN6A  N6   C6   N1   180.00   0.0  0
 A7D  Var_01    CAW   CAK  SAP  CAI  161.87  30.0  1
 A7D  Var_02    CAT   CAJ  CAI  SAP  176.91  30.0  3
 A7D  Var_03    HAI   CAI  SAP  CAK   50.03  30.0  2

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
 A7D  chir_01  CAT  OAC  CAH  CAJ  negativ
 A7D  chir_02  CAU  OAD  CAV  CAW  negativ
 A7D  chir_03  CAV  OAE  CAX  CAU  negativ
 A7D  chir_04  CAW  OAO  CAK  CAU  positiv
 A7D  chir_05  CAX  OAO  N9   CAV  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
 A7D  plan-1  N1    0.020
 A7D  plan-1  C2    0.020
 A7D  plan-1  N3    0.020
 A7D  plan-1  C4    0.020
 A7D  plan-1  C5    0.020
 A7D  plan-1  C6    0.020
 A7D  plan-1  N6    0.020
 A7D  plan-1  N7    0.020
 A7D  plan-1  C8    0.020
 A7D  plan-1  N9    0.020
 A7D  plan-1  CAX   0.020
 A7D  plan-1  H2    0.020
 A7D  plan-1  H8    0.020
 A7D  plan-2  C6    0.020
 A7D  plan-2  N6    0.020
 A7D  plan-2  HN6   0.020
 A7D  plan-2  HN6A  0.020

