# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 01:10:33 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: 2-(butylsulfanyl)adenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCSc1nc(N)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
 IVH  IVH  2-(butylsulfanyl)adenosine  ligand  45  24  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_IVH
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
 IVH  S     S  S2    0   0.029  -3.1373  -1.1348   0.3216
 IVH  C1    C  CH3   0  -0.663  -8.3613  -1.5558   0.5386
 IVH  N1    N  N     0  -0.470  -2.3809   1.3656  -0.1803
 IVH  O1    O  O2    0  -0.491   3.1511  -0.4590   0.9293
 IVH  C2    C  CH2   0  -0.418  -7.2101  -0.5618   0.4802
 IVH  N2    N  N     0  -0.475  -0.7081  -0.3295  -0.0279
 IVH  O2    O  OH1   0  -0.667   5.4781   0.7883   1.8436
 IVH  N3    N  NR5   0  -0.546   1.5209   0.5546  -0.3733
 IVH  O3    O  OH1   0  -0.667   3.8555  -3.0716  -0.4714
 IVH  C4    C  CH2   0  -0.546  -4.7165  -0.2416   0.3322
 IVH  N4    N  N     0  -0.446   1.0160   2.7040  -0.6987
 IVH  O4    O  OH1   0  -0.653   2.5156  -1.6099  -2.3472
 IVH  C5    C  CR6   0   0.230  -1.9529   0.1238   0.0018
 IVH  C6    C  CR6   0   0.474  -1.4914   2.3331  -0.4315
 IVH  C7    C  CR56  0  -0.029  -0.1309   1.9814  -0.4847
 IVH  C8    C  CR56  0   0.497   0.1621   0.6433  -0.2743
 IVH  C9    C  CR15  0   0.110   1.9696   1.8275  -0.6217
 IVH  C10   C  CH1   0   0.204   2.3137  -0.6315  -0.1792
 IVH  C11   C  CH1   0  -0.016   3.2362  -0.9598  -1.3519
 IVH  C12   C  CH1   0  -0.044   4.3302  -1.7642  -0.6512
 IVH  C13   C  CH1   0  -0.040   4.4515  -0.9970   0.6686
 IVH  C14   C  CH2   0  -0.153   5.4897   0.1049   0.6161
 IVH  H1    H  HCH3  0   0.219  -8.3632  -2.2065  -0.3374
 IVH  H1A   H  HCH3  0   0.219  -8.2885  -2.1912   1.4228
 IVH  H1B   H  HCH3  0   0.230  -9.3250  -1.0471   0.5753
 IVH  H2    H  HCH2  0   0.219  -7.3220   0.0819  -0.3973
 IVH  H2A   H  HCH2  0   0.220  -7.2485   0.0993   1.3509
 IVH  HO2   H  HOH1  0   0.459   6.1361   1.4879   1.8029
 IVH  H3    H  HCH2  0   0.230  -5.7274  -1.8739   1.3216
 IVH  H3A   H  HCH2  0   0.231  -5.8157  -1.9285  -0.4301
 IVH  HO3   H  HOH1  0   0.458   4.5365  -3.5824  -0.0223
 IVH  H4    H  HCH2  0   0.268  -4.7353   0.4462   1.1780
 IVH  H4A   H  HCH2  0   0.270  -4.7978   0.3451  -0.5820
 IVH  HO4   H  HOH1  0   0.464   3.0668  -1.6823  -3.1325
 IVH  HN5   H  HNH2  0   0.406  -2.9088   3.7832  -0.5945
 IVH  HN5A  H  HNH2  0   0.413  -1.2863   4.3228  -0.8361
 IVH  H9    H  HCR5  0   0.292   3.0206   2.0488  -0.7328
 IVH  H10   H  HCH1  0   0.261   1.5998  -1.4481  -0.0234
 IVH  H11   H  HCH1  0   0.241   3.6936  -0.0331  -1.7247
 IVH  H12   H  HCH1  0   0.255   5.2731  -1.7505  -1.2129
 IVH  H13   H  HCH1  0   0.257   4.7075  -1.6781   1.4874
 IVH  H14   H  HCH2  0   0.195   5.2904   0.7812  -0.2275
 IVH  H14A  H  HCH2  0   0.211   6.4619  -0.3645   0.4171
 IVH  N5    N  NH2   0  -0.815  -1.9244   3.5791  -0.6137
 IVH  C3    C  CH2   0  -0.423  -5.8509  -1.2522   0.4292

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
 IVH  S    C4    single    1.814  0.020  1.814
 IVH  S    C5    single    1.758  0.020  1.758
 IVH  C1   C2    single    1.522  0.020  1.522
 IVH  C1   H1    single    0.970  0.020  1.090
 IVH  C1   H1A   single    0.970  0.020  1.090
 IVH  C1   H1B   single    0.970  0.020  1.090
 IVH  N1   C5    aromatic  1.326  0.020  1.326
 IVH  N1   C6    aromatic  1.338  0.020  1.338
 IVH  C10  O1    single    1.400  0.020  1.400
 IVH  C13  O1    single    1.431  0.020  1.431
 IVH  C2   C3    single    1.525  0.020  1.525
 IVH  C2   H2    single    0.970  0.020  1.090
 IVH  C2   H2A   single    0.970  0.020  1.090
 IVH  C5   N2    aromatic  1.325  0.020  1.325
 IVH  N2   C8    aromatic  1.328  0.020  1.328
 IVH  C14  O2    single    1.405  0.020  1.405
 IVH  O2   HO2   single    0.850  0.020  0.980
 IVH  C3   C4    single    1.522  0.020  1.522
 IVH  C3   H3    single    0.970  0.020  1.090
 IVH  C3   H3A   single    0.970  0.020  1.090
 IVH  C8   N3    aromatic  1.365  0.020  1.365
 IVH  N3   C9    aromatic  1.372  0.020  1.372
 IVH  N3   C10   single    1.440  0.020  1.440
 IVH  C12  O3    single    1.403  0.020  1.403
 IVH  O3   HO3   single    0.850  0.020  0.980
 IVH  C4   H4    single    0.970  0.020  1.090
 IVH  C4   H4A   single    0.970  0.020  1.090
 IVH  C7   N4    aromatic  1.372  0.020  1.372
 IVH  N4   C9    aromatic  1.298  0.020  1.298
 IVH  C11  O4    single    1.390  0.020  1.390
 IVH  O4   HO4   single    0.850  0.020  0.980
 IVH  N5   C6    single    1.332  0.020  1.332
 IVH  N5   HN5   single    0.860  0.020  1.020
 IVH  N5   HN5A  single    0.860  0.020  1.020
 IVH  C6   C7    aromatic  1.406  0.020  1.406
 IVH  C7   C8    aromatic  1.386  0.020  1.386
 IVH  C9   H9    single    0.930  0.020  1.080
 IVH  C11  C10   single    1.528  0.020  1.528
 IVH  C10  H10   single    0.970  0.020  1.090
 IVH  C12  C11   single    1.528  0.020  1.528
 IVH  C11  H11   single    0.970  0.020  1.090
 IVH  C12  C13   single    1.531  0.020  1.531
 IVH  C12  H12   single    0.970  0.020  1.090
 IVH  C14  C13   single    1.515  0.020  1.515
 IVH  C13  H13   single    0.970  0.020  1.090
 IVH  C14  H14   single    0.970  0.020  1.090
 IVH  C14  H14A  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
 IVH  C5    S    C4   103.60  3.000
 IVH  H1B   C1   H1A  107.66  3.000
 IVH  H1B   C1   H1   107.68  3.000
 IVH  H1A   C1   H1   107.66  3.000
 IVH  H1B   C1   C2   111.41  3.000
 IVH  H1A   C1   C2   111.15  3.000
 IVH  H1    C1   C2   111.09  3.000
 IVH  C6    N1   C5   119.23  3.000
 IVH  C13   O1   C10  110.67  3.000
 IVH  H2A   C2   H2   106.22  3.000
 IVH  H2A   C2   C3   109.36  3.000
 IVH  H2    C2   C3   109.31  3.000
 IVH  H2A   C2   C1   109.73  3.000
 IVH  H2    C2   C1   109.73  3.000
 IVH  C3    C2   C1   112.31  3.000
 IVH  C8    N2   C5   111.66  3.000
 IVH  HO2   O2   C14  108.15  3.000
 IVH  C10   N3   C9   127.48  3.000
 IVH  C10   N3   C8   126.29  3.000
 IVH  C9    N3   C8   106.15  3.000
 IVH  HO3   O3   C12  108.37  3.000
 IVH  H4A   C4   H4   108.05  3.000
 IVH  H4A   C4   C3   110.82  3.000
 IVH  H4    C4   C3   110.89  3.000
 IVH  H4A   C4   S    108.98  3.000
 IVH  H4    C4   S    109.28  3.000
 IVH  C3    C4   S    108.80  3.000
 IVH  C9    N4   C7   104.43  3.000
 IVH  HO4   O4   C11  108.82  3.000
 IVH  N2    C5   N1   128.35  3.000
 IVH  N2    C5   S    113.09  3.000
 IVH  N1    C5   S    118.56  3.000
 IVH  C7    C6   N5   122.92  3.000
 IVH  C7    C6   N1   118.00  3.000
 IVH  N5    C6   N1   119.08  3.000
 IVH  C8    C7   C6   116.12  3.000
 IVH  C8    C7   N4   110.82  3.000
 IVH  C6    C7   N4   133.06  3.000
 IVH  C7    C8   N3   105.20  3.000
 IVH  C7    C8   N2   126.64  3.000
 IVH  N3    C8   N2   128.16  3.000
 IVH  H9    C9   N4   124.80  3.000
 IVH  H9    C9   N3   121.80  3.000
 IVH  N4    C9   N3   113.39  3.000
 IVH  H10   C10  C11  110.02  3.000
 IVH  H10   C10  N3   105.92  3.000
 IVH  C11   C10  N3   113.96  3.000
 IVH  H10   C10  O1   111.65  3.000
 IVH  C11   C10  O1   105.85  3.000
 IVH  N3    C10  O1   109.55  3.000
 IVH  H11   C11  C12  107.55  3.000
 IVH  H11   C11  C10  109.31  3.000
 IVH  C12   C11  C10  101.15  3.000
 IVH  H11   C11  O4   111.55  3.000
 IVH  C12   C11  O4   116.95  3.000
 IVH  C10   C11  O4   109.69  3.000
 IVH  H12   C12  C13  111.52  3.000
 IVH  H12   C12  C11  111.95  3.000
 IVH  C13   C12  C11  100.85  3.000
 IVH  H12   C12  O3   111.59  3.000
 IVH  C13   C12  O3   112.54  3.000
 IVH  C11   C12  O3   107.89  3.000
 IVH  H13   C13  C14  108.54  3.000
 IVH  H13   C13  C12  110.56  3.000
 IVH  C14   C13  C12  112.88  3.000
 IVH  H13   C13  O1   108.06  3.000
 IVH  C14   C13  O1   110.84  3.000
 IVH  C12   C13  O1   105.86  3.000
 IVH  H14A  C14  H14  106.53  3.000
 IVH  H14A  C14  C13  107.59  3.000
 IVH  H14   C14  C13  110.47  3.000
 IVH  H14A  C14  O2   111.95  3.000
 IVH  H14   C14  O2   111.69  3.000
 IVH  C13   C14  O2   108.53  3.000
 IVH  HN5A  N5   HN5  118.41  3.000
 IVH  HN5A  N5   C6   121.08  3.000
 IVH  HN5   N5   C6   120.38  3.000
 IVH  H3A   C3   H3   106.60  3.000
 IVH  H3A   C3   C4   109.65  3.000
 IVH  H3    C3   C4   110.17  3.000
 IVH  H3A   C3   C2   109.56  3.000
 IVH  H3    C3   C2   109.29  3.000
 IVH  C4    C3   C2   111.45  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
 IVH  CONST_01  C8    N2  C5  N1    0.00   0.0  0
 IVH  CONST_02  N4    C7  C6  N1  180.00   0.0  0
 IVH  CONST_03  C8    C7  C6  N1    0.00   0.0  0
 IVH  CONST_04  C6    N1  C5  N2    0.00   0.0  0
 IVH  CONST_05  C9    N3  C8  N2  180.00   0.0  0
 IVH  CONST_06  N4    C7  C8  N2  180.00   0.0  0
 IVH  CONST_07  C6    C7  C8  N2    0.00   0.0  0
 IVH  CONST_08  C5    N2  C8  N3  180.00   0.0  0
 IVH  CONST_09  N4    C7  C8  N3    0.00   0.0  0
 IVH  CONST_10  C6    C7  C8  N3  180.00   0.0  0
 IVH  CONST_11  C7    N4  C9  N3    0.00   0.0  0
 IVH  CONST_12  C8    N3  C9  N4    0.00   0.0  0
 IVH  CONST_13  C7    C6  N1  C5    0.00   0.0  0
 IVH  CONST_14  C7    C8  N2  C5    0.00   0.0  0
 IVH  CONST_15  C9    N4  C7  C6  180.00   0.0  0
 IVH  CONST_16  C9    N3  C8  C7    0.00   0.0  0
 IVH  CONST_17  C9    N4  C7  C8    0.00   0.0  0
 IVH  CONST_18  C10   N3  C8  N2    0.00   0.0  0
 IVH  CONST_19  C10   N3  C9  N4  180.00   0.0  0
 IVH  CONST_20  C10   N3  C8  C7  180.00   0.0  0
 IVH  CONST_21  C6    N1  C5  S   180.00   0.0  0
 IVH  CONST_22  C8    N2  C5  S   180.00   0.0  0
 IVH  CONST_23  N5    C6  C7  N4    0.00   0.0  0
 IVH  CONST_24  N5    C6  N1  C5  180.00   0.0  0
 IVH  CONST_25  C8    C7  C6  N5  180.00   0.0  0
 IVH  CONST_26  H9    C9  N4  C7  180.00   0.0  0
 IVH  CONST_27  HN5   N5  C6  N1    0.00   0.0  0
 IVH  CONST_28  HN5A  N5  C6  N1  180.00   0.0  0
 IVH  Var_01    H4    C4  S   C5  -65.76  30.0  3
 IVH  Var_02    C2    C3  C4  S   178.49  30.0  1
 IVH  Var_03    C4    C3  C2  C1  178.42  30.0  3
 IVH  Var_04    H1    C1  C2  C3  -59.98  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
 IVH  chir_01  C10  O1  N3   C11  negativ
 IVH  chir_02  C11  O4  C10  C12  negativ
 IVH  chir_03  C12  O3  C13  C11  positiv
 IVH  chir_04  C13  O1  C12  C14  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
 IVH  plan-1  S     0.020
 IVH  plan-1  N1    0.020
 IVH  plan-1  N2    0.020
 IVH  plan-1  N3    0.020
 IVH  plan-1  N4    0.020
 IVH  plan-1  C5    0.020
 IVH  plan-1  C6    0.020
 IVH  plan-1  C7    0.020
 IVH  plan-1  C8    0.020
 IVH  plan-1  C9    0.020
 IVH  plan-1  C10   0.020
 IVH  plan-1  H9    0.020
 IVH  plan-1  N5    0.020
 IVH  plan-2  C6    0.020
 IVH  plan-2  HN5   0.020
 IVH  plan-2  HN5A  0.020
 IVH  plan-2  N5    0.020

