# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 13:46:33 2020
#   Inital geometry file: a 87 line input string
#   Ligand name: 5'-S-ethyl-5'-thioadenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCSC[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
 3DH  3DH  5'-S-ethyl-5'-thioadenosine  ligand  38  21  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3DH
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
 3DH  CB    C  CH3   0  -0.663   5.0515  -3.0969  -0.0216
 3DH  CG    C  CH2   0  -0.538   4.6690  -1.7436   0.5509
 3DH  SD    S  S2    0  -0.019   3.4198  -0.9584  -0.5091
 3DH  C5'   C  CH2   0  -0.583   3.1059   0.5376   0.4664
 3DH  C4'   C  CH1   0  -0.004   2.3254   1.5485  -0.3584
 3DH  O4'   O  O2    0  -0.492   1.2104   0.9339  -1.0130
 3DH  C3'   C  CH1   0  -0.014   1.7260   2.6513   0.5033
 3DH  O3'   O  OH1   0  -0.667   1.5205   3.7864  -0.2946
 3DH  C2'   C  CH1   0  -0.052   0.3916   2.0117   0.8985
 3DH  O2'   O  OH1   0  -0.651  -0.6109   2.9144   1.2549
 3DH  C1'   C  CH1   0   0.224   0.0088   1.2899  -0.3968
 3DH  N9    N  NR5   0  -0.540  -0.7857   0.1011  -0.1841
 3DH  C8    C  CR15  0   0.108  -0.3467  -1.1371   0.2024
 3DH  N7    N  N     0  -0.452  -1.3094  -1.9988   0.3525
 3DH  C5    C  CR56  0  -0.011  -2.4475  -1.2961   0.0541
 3DH  C4    C  CR56  0   0.488  -2.1438   0.0132  -0.2858
 3DH  N3    N  N     0  -0.453  -3.0098   0.9599  -0.6413
 3DH  C2    C  CR16  0   0.042  -4.2521   0.5103  -0.6389
 3DH  N1    N  N     0  -0.475  -4.6921  -0.7075  -0.3314
 3DH  C6    C  CR6   0   0.458  -3.8097  -1.6482   0.0235
 3DH  N6    N  NH2   0  -0.817  -4.2457  -2.8699   0.3334
 3DH  HB    H  HCH3  0   0.235   4.1942  -3.7684  -0.0621
 3DH  HBA   H  HCH3  0   0.234   5.4604  -3.0057  -1.0281
 3DH  HBB   H  HCH3  0   0.247   5.8116  -3.5620   0.6059
 3DH  HG    H  HCH2  0   0.262   4.2593  -1.8561   1.5558
 3DH  HGA   H  HCH2  0   0.262   5.5405  -1.0906   0.6165
 3DH  H5'   H  HCH2  0   0.266   2.5829   0.2661   1.3873
 3DH  H5'A  H  HCH2  0   0.290   4.0599   0.9861   0.7514
 3DH  H4'   H  HCH1  0   0.272   2.9792   1.9578  -1.1324
 3DH  H3'   H  HCH1  0   0.254   2.3523   2.8727   1.3776
 3DH  HO3'  H  HOH1  0   0.450   0.8415   4.3275   0.1258
 3DH  H2'   H  HCH1  0   0.251   0.5647   1.2706   1.6883
 3DH  HO2'  H  HOH1  0   0.470  -0.5112   3.1381   2.1859
 3DH  H1'   H  HCH1  0   0.265  -0.5900   1.9490  -1.0344
 3DH  H8    H  HCR5  0   0.291   0.7047  -1.3550   0.3288
 3DH  H2    H  HCR6  0   0.251  -5.0188   1.2236  -0.9226
 3DH  HN6   H  HNH2  0   0.411  -3.6067  -3.5982   0.5988
 3DH  HN6A  H  HNH2  0   0.403  -5.2270  -3.0846   0.2945

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
 3DH  CG   CB    single    1.518  0.020  1.518
 3DH  CB   HB    single    0.970  0.020  1.090
 3DH  CB   HBA   single    0.970  0.020  1.090
 3DH  CB   HBB   single    0.970  0.020  1.090
 3DH  CG   SD    single    1.817  0.020  1.817
 3DH  CG   HG    single    0.970  0.020  1.090
 3DH  CG   HGA   single    0.970  0.020  1.090
 3DH  C5'  SD    single    1.813  0.020  1.813
 3DH  C5'  C4'   single    1.520  0.020  1.520
 3DH  C5'  H5'   single    0.970  0.020  1.090
 3DH  C5'  H5'A  single    0.970  0.020  1.090
 3DH  C3'  C4'   single    1.522  0.020  1.522
 3DH  C4'  O4'   single    1.432  0.020  1.432
 3DH  C4'  H4'   single    0.970  0.020  1.090
 3DH  O4'  C1'   single    1.397  0.020  1.397
 3DH  O3'  C3'   single    1.403  0.020  1.403
 3DH  C3'  C2'   single    1.532  0.020  1.532
 3DH  C3'  H3'   single    0.970  0.020  1.090
 3DH  O3'  HO3'  single    0.850  0.020  0.980
 3DH  C2'  O2'   single    1.395  0.020  1.395
 3DH  C2'  C1'   single    1.531  0.020  1.531
 3DH  C2'  H2'   single    0.970  0.020  1.090
 3DH  O2'  HO2'  single    0.850  0.020  0.980
 3DH  C1'  N9    single    1.446  0.020  1.446
 3DH  C1'  H1'   single    0.970  0.020  1.090
 3DH  C8   N9    aromatic  1.369  0.020  1.369
 3DH  N9   C4    aromatic  1.365  0.020  1.365
 3DH  C8   N7    aromatic  1.301  0.020  1.301
 3DH  C8   H8    single    0.930  0.020  1.080
 3DH  N7   C5    aromatic  1.371  0.020  1.371
 3DH  C4   C5    aromatic  1.386  0.020  1.386
 3DH  C5   C6    aromatic  1.407  0.020  1.407
 3DH  C4   N3    aromatic  1.331  0.020  1.331
 3DH  N3   C2    aromatic  1.321  0.020  1.321
 3DH  C2   N1    aromatic  1.331  0.020  1.331
 3DH  C2   H2    single    0.930  0.020  1.080
 3DH  C6   N1    aromatic  1.338  0.020  1.338
 3DH  C6   N6    single    1.334  0.020  1.334
 3DH  N6   HN6   single    0.860  0.020  1.020
 3DH  N6   HN6A  single    0.860  0.020  1.020

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
 3DH  HBB   CB   HBA  107.80  3.000
 3DH  HBB   CB   HB   107.88  3.000
 3DH  HBA   CB   HB   108.20  3.000
 3DH  HBB   CB   CG   109.81  3.000
 3DH  HBA   CB   CG   111.59  3.000
 3DH  HB    CB   CG   111.41  3.000
 3DH  HGA   CG   HG   107.83  3.000
 3DH  HGA   CG   SD   109.01  3.000
 3DH  HG    CG   SD   108.89  3.000
 3DH  HGA   CG   CB   110.79  3.000
 3DH  HG    CG   CB   110.48  3.000
 3DH  SD    CG   CB   109.78  3.000
 3DH  C5'   SD   CG    99.31  3.000
 3DH  H5'A  C5'  H5'  107.47  3.000
 3DH  H5'A  C5'  C4'  108.48  3.000
 3DH  H5'   C5'  C4'  112.12  3.000
 3DH  H5'A  C5'  SD   109.15  3.000
 3DH  H5'   C5'  SD   109.33  3.000
 3DH  C4'   C5'  SD   110.21  3.000
 3DH  H4'   C4'  C3'  111.41  3.000
 3DH  H4'   C4'  O4'  107.64  3.000
 3DH  C3'   C4'  O4'  105.26  3.000
 3DH  H4'   C4'  C5'  109.04  3.000
 3DH  O4'   C4'  C5'  111.25  3.000
 3DH  C3'   C4'  C5'  112.12  3.000
 3DH  C1'   O4'  C4'  111.04  3.000
 3DH  H3'   C3'  C2'  112.07  3.000
 3DH  H3'   C3'  O3'  111.92  3.000
 3DH  C2'   C3'  O3'  110.92  3.000
 3DH  H3'   C3'  C4'  111.85  3.000
 3DH  C2'   C3'  C4'  100.75  3.000
 3DH  O3'   C3'  C4'  108.78  3.000
 3DH  HO3'  O3'  C3'  108.01  3.000
 3DH  H2'   C2'  C1'  109.27  3.000
 3DH  H2'   C2'  O2'  111.50  3.000
 3DH  C1'   C2'  O2'  109.96  3.000
 3DH  H2'   C2'  C3'  109.30  3.000
 3DH  C1'   C2'  C3'  101.33  3.000
 3DH  O2'   C2'  C3'  114.94  3.000
 3DH  HO2'  O2'  C2'  108.84  3.000
 3DH  H1'   C1'  N9   106.26  3.000
 3DH  H1'   C1'  C2'  110.21  3.000
 3DH  N9    C1'  C2'  113.62  3.000
 3DH  H1'   C1'  O4'  111.53  3.000
 3DH  N9    C1'  O4'  109.16  3.000
 3DH  C2'   C1'  O4'  106.16  3.000
 3DH  C4    N9   C8   106.37  3.000
 3DH  C4    N9   C1'  126.08  3.000
 3DH  C8    N9   C1'  127.51  3.000
 3DH  H8    C8   N7   124.94  3.000
 3DH  H8    C8   N9   121.80  3.000
 3DH  N7    C8   N9   113.22  3.000
 3DH  C5    N7   C8   104.46  3.000
 3DH  C6    C5   C4   116.30  3.000
 3DH  C6    C5   N7   132.87  3.000
 3DH  C4    C5   N7   110.84  3.000
 3DH  N3    C4   C5   126.48  3.000
 3DH  N3    C4   N9   128.42  3.000
 3DH  C5    C4   N9   105.10  3.000
 3DH  C2    N3   C4   111.66  3.000
 3DH  H2    C2   N1   115.37  3.000
 3DH  H2    C2   N3   116.12  3.000
 3DH  N1    C2   N3   128.51  3.000
 3DH  C6    N1   C2   119.13  3.000
 3DH  N6    C6   N1   119.35  3.000
 3DH  N6    C6   C5   122.72  3.000
 3DH  N1    C6   C5   117.92  3.000
 3DH  HN6A  N6   HN6  118.44  3.000
 3DH  HN6A  N6   C6   120.39  3.000
 3DH  HN6   N6   C6   121.17  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
 3DH  CONST_01  C5    N7   C8  N9     0.00   0.0  0
 3DH  CONST_02  N7    C5   C4  N9     0.00   0.0  0
 3DH  CONST_03  C6    C5   C4  N9   180.00   0.0  0
 3DH  CONST_04  C2    N3   C4  N9   180.00   0.0  0
 3DH  CONST_05  C5    C4   N9  C8     0.00   0.0  0
 3DH  CONST_06  N3    C4   N9  C8   180.00   0.0  0
 3DH  CONST_07  C4    C5   N7  C8     0.00   0.0  0
 3DH  CONST_08  C6    C5   N7  C8   180.00   0.0  0
 3DH  CONST_09  C4    N9   C8  N7     0.00   0.0  0
 3DH  CONST_10  N3    C4   C5  N7   180.00   0.0  0
 3DH  CONST_11  N1    C6   C5  N7   180.00   0.0  0
 3DH  CONST_12  C2    N3   C4  C5     0.00   0.0  0
 3DH  CONST_13  C2    N1   C6  C5     0.00   0.0  0
 3DH  CONST_14  N1    C6   C5  C4     0.00   0.0  0
 3DH  CONST_15  N1    C2   N3  C4     0.00   0.0  0
 3DH  CONST_16  C6    C5   C4  N3     0.00   0.0  0
 3DH  CONST_17  C6    N1   C2  N3     0.00   0.0  0
 3DH  CONST_18  N7    C8   N9  C1'  180.00   0.0  0
 3DH  CONST_19  C5    C4   N9  C1'  180.00   0.0  0
 3DH  CONST_20  N3    C4   N9  C1'    0.00   0.0  0
 3DH  CONST_21  N6    C6   C5  N7     0.00   0.0  0
 3DH  CONST_22  N6    C6   C5  C4   180.00   0.0  0
 3DH  CONST_23  N6    C6   N1  C2   180.00   0.0  0
 3DH  CONST_24  H8    C8   N9  C1'    0.00   0.0  0
 3DH  CONST_25  H2    C2   N3  C4   180.00   0.0  0
 3DH  CONST_26  HN6   N6   C6  C5     0.00   0.0  0
 3DH  CONST_27  HN6A  N6   C6  C5   180.00   0.0  0
 3DH  Var_01    C4'   C5'  SD  CG   166.65  30.0  2
 3DH  Var_02    HB    CB   CG  SD   -61.37  30.0  3
 3DH  Var_03    HG    CG   SD  C5'   55.58  30.0  1

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
 3DH  chir_01  C4'  C5'  C3'  O4'  positiv
 3DH  chir_02  C3'  O3'  C2'  C4'  negativ
 3DH  chir_03  C2'  O2'  C1'  C3'  negativ
 3DH  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
 3DH  plan-1  C1'   0.020
 3DH  plan-1  N9    0.020
 3DH  plan-1  C8    0.020
 3DH  plan-1  N7    0.020
 3DH  plan-1  C5    0.020
 3DH  plan-1  C4    0.020
 3DH  plan-1  N3    0.020
 3DH  plan-1  C2    0.020
 3DH  plan-1  N1    0.020
 3DH  plan-1  C6    0.020
 3DH  plan-1  N6    0.020
 3DH  plan-1  H8    0.020
 3DH  plan-1  H2    0.020
 3DH  plan-2  C6    0.020
 3DH  plan-2  N6    0.020
 3DH  plan-2  HN6   0.020
 3DH  plan-2  HN6A  0.020

