# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 08:22:08 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: 5'-[(S)-(3-aminopropyl)(methyl)-lambda~4~-sulfanyl]-5'-deoxyadenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[SH](CCCN)C[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
 S4M  S4M  5'-[(S)-(3-aminopropyl)(methyl)-lambda~4~-sulfanyl]-5'-deoxyadenosine  ligand  48  24  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_S4M
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
 S4M  CA    C  CH2   0  -0.281   7.5241   2.3385  -2.1406
 S4M  N     N  NH2   0  -0.788   7.5524   2.4037  -3.5911
 S4M  CB    C  CH2   0  -0.438   6.2582   2.8983  -1.4902
 S4M  CG    C  CH2   0  -0.528   6.3127   2.7818   0.0222
 S4M  SD    S  SH1   0   0.177   4.8321   3.4372   0.8468
 S4M  CE    C  CH3   0  -0.887   5.5852   5.2817   0.8085
 S4M  C5'   C  CH2   0  -0.717   3.9221   1.5391   0.5906
 S4M  C4'   C  CH1   0   0.068   2.4571   1.6990   0.8659
 S4M  O4'   O  O2    0  -0.508   1.8685   2.5904  -0.1068
 S4M  C1'   C  CH1   0   0.177   0.6283   2.1367  -0.5360
 S4M  C2'   C  CH1   0  -0.037   0.2162   1.0064   0.4055
 S4M  O2'   O  OH1   0  -0.667  -0.4201   1.5839   1.5129
 S4M  C3'   C  CH1   0  -0.026   1.5882   0.4407   0.7873
 S4M  O3'   O  OH1   0  -0.660   1.6006  -0.2230   2.0214
 S4M  N9    N  NR5   0  -0.535   0.7437   1.6606  -1.9145
 S4M  C8    C  CR15  0   0.105   1.8769   1.4312  -2.6438
 S4M  N7    N  N     0  -0.452   1.6375   1.0156  -3.8544
 S4M  C5    C  CR56  0  -0.004   0.2712   0.9683  -3.9331
 S4M  C6    C  CR6   0   0.456  -0.6201   0.6052  -4.9601
 S4M  N6    N  NH2   0  -0.817  -0.2098   0.2045  -6.1639
 S4M  C4    C  CR56  0   0.485  -0.3034   1.3682  -2.7366
 S4M  N3    N  N     0  -0.459  -1.6062   1.4438  -2.4670
 S4M  C2    C  CR16  0   0.038  -2.3393   1.0800  -3.5046
 S4M  N1    N  N     0  -0.474  -1.9315   0.6738  -4.7045
 S4M  HA1   H  HCH2  0   0.222   8.3949   2.8747  -1.7529
 S4M  HA2   H  HCH2  0   0.221   7.6522   1.2945  -1.8419
 S4M  HN1   H  HNH2  0   0.341   7.4397   3.3648  -3.8909
 S4M  HN2   H  HNH2  0   0.341   6.7555   1.9043  -3.9670
 S4M  HB1   H  HCH2  0   0.232   5.3879   2.3581  -1.8739
 S4M  HB2   H  HCH2  0   0.235   6.1379   3.9459  -1.7813
 S4M  HG1   H  HCH2  0   0.286   6.3945   1.7407   0.3350
 S4M  HG2   H  HCH2  0   0.284   7.1569   3.3419   0.4278
 S4M  HSD   H  HSH1  0   0.270   3.9507   3.8563  -0.0674
 S4M  HE1   H  HCH3  0   0.225   5.9506   5.5985  -0.1704
 S4M  HE2   H  HCH3  0   0.226   4.7714   5.9413   1.1153
 S4M  HE3   H  HCH3  0   0.229   6.3939   5.3562   1.5370
 S4M  H5'1  H  HCH2  0   0.196   4.0972   1.0659  -0.3828
 S4M  H5'2  H  HCH2  0   0.218   4.3691   0.9051   1.3618
 S4M  H4'   H  HCH1  0   0.218   2.3195   2.1475   1.8612
 S4M  H1'   H  HCH1  0   0.279  -0.1042   2.9493  -0.5374
 S4M  H2'   H  HCH1  0   0.252  -0.4269   0.2715  -0.0942
 S4M  HO2'  H  HOH1  0   0.450  -0.2190   1.0364   2.2821
 S4M  H3'   H  HCH1  0   0.231   1.9508  -0.2082  -0.0196
 S4M  HO3'  H  HOH1  0   0.466   1.2987  -1.1276   1.8919
 S4M  H8    H  HCR5  0   0.287   2.8613   1.5945  -2.2344
 S4M  HN61  H  HNH2  0   0.411   0.7677   0.1195  -6.3789
 S4M  HN62  H  HNH2  0   0.403  -0.8779  -0.0776  -6.8602
 S4M  H2    H  HCR6  0   0.251  -3.4147   1.1135  -3.3654

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
 S4M  CA   N     single    1.452  0.020  1.452
 S4M  CA   CB    single    1.529  0.020  1.529
 S4M  CA   HA1   single    0.970  0.020  1.090
 S4M  CA   HA2   single    0.970  0.020  1.090
 S4M  N    HN1   single    0.890  0.020  1.040
 S4M  N    HN2   single    0.890  0.020  1.040
 S4M  CB   CG    single    1.518  0.020  1.518
 S4M  CB   HB1   single    0.970  0.020  1.090
 S4M  CB   HB2   single    0.970  0.020  1.090
 S4M  CG   SD    single    1.817  0.020  1.817
 S4M  CG   HG1   single    0.970  0.020  1.090
 S4M  CG   HG2   single    0.970  0.020  1.090
 S4M  SD   CE    single    1.993  0.020  1.993
 S4M  SD   C5'   single    2.121  0.020  2.121
 S4M  SD   HSD   single    1.200  0.020  1.300
 S4M  CE   HE1   single    0.970  0.020  1.090
 S4M  CE   HE2   single    0.970  0.020  1.090
 S4M  CE   HE3   single    0.970  0.020  1.090
 S4M  C5'  C4'   single    1.499  0.020  1.499
 S4M  C5'  H5'1  single    0.970  0.020  1.090
 S4M  C5'  H5'2  single    0.970  0.020  1.090
 S4M  C4'  C3'   single    1.531  0.020  1.531
 S4M  C4'  O4'   single    1.445  0.020  1.445
 S4M  C4'  H4'   single    0.970  0.020  1.090
 S4M  O4'  C1'   single    1.388  0.020  1.388
 S4M  C1'  C2'   single    1.528  0.020  1.528
 S4M  C1'  N9    single    1.463  0.020  1.463
 S4M  C1'  H1'   single    0.970  0.020  1.090
 S4M  C2'  O2'   single    1.402  0.020  1.402
 S4M  C2'  C3'   single    1.532  0.020  1.532
 S4M  C2'  H2'   single    0.970  0.020  1.090
 S4M  O2'  HO2'  single    0.850  0.020  0.980
 S4M  C3'  O3'   single    1.401  0.020  1.401
 S4M  C3'  H3'   single    0.970  0.020  1.090
 S4M  O3'  HO3'  single    0.850  0.020  0.980
 S4M  N9   C4    aromatic  1.363  0.020  1.363
 S4M  N9   C8    aromatic  1.367  0.020  1.367
 S4M  C8   N7    aromatic  1.302  0.020  1.302
 S4M  C8   H8    single    0.930  0.020  1.080
 S4M  N7   C5    aromatic  1.369  0.020  1.369
 S4M  C5   C4    aromatic  1.386  0.020  1.386
 S4M  C5   C6    aromatic  1.407  0.020  1.407
 S4M  C6   N1    aromatic  1.338  0.020  1.338
 S4M  C6   N6    single    1.334  0.020  1.334
 S4M  N6   HN61  single    0.860  0.020  1.020
 S4M  N6   HN62  single    0.860  0.020  1.020
 S4M  C4   N3    aromatic  1.333  0.020  1.333
 S4M  N3   C2    aromatic  1.322  0.020  1.322
 S4M  C2   N1    aromatic  1.331  0.020  1.331
 S4M  C2   H2    single    0.930  0.020  1.080

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
 S4M  HA2   CA   HA1   106.14  3.000
 S4M  HA2   CA   CB    109.28  3.000
 S4M  HA1   CA   CB    109.20  3.000
 S4M  HA2   CA   N     108.27  3.000
 S4M  HA1   CA   N     108.46  3.000
 S4M  CB    CA   N     115.11  3.000
 S4M  HN2   N    HN1   105.69  3.000
 S4M  HN2   N    CA    109.47  3.000
 S4M  HN1   N    CA    109.64  3.000
 S4M  HB2   CB   HB1   106.99  3.000
 S4M  HB2   CB   CG    110.04  3.000
 S4M  HB1   CB   CG    109.89  3.000
 S4M  HB2   CB   CA    109.17  3.000
 S4M  HB1   CB   CA    109.19  3.000
 S4M  CG    CB   CA    111.46  3.000
 S4M  HG2   CG   HG1   108.99  3.000
 S4M  HG2   CG   SD    106.05  3.000
 S4M  HG1   CG   SD    105.98  3.000
 S4M  HG2   CG   CB    111.03  3.000
 S4M  HG1   CG   CB    111.22  3.000
 S4M  SD    CG   CB    113.28  3.000
 S4M  HSD   SD   C5'    85.13  3.000
 S4M  HSD   SD   CE     86.90  3.000
 S4M  C5'   SD   CE    171.27  3.000
 S4M  HSD   SD   CG    109.87  3.000
 S4M  C5'   SD   CG     88.39  3.000
 S4M  CE    SD   CG     90.98  3.000
 S4M  HE3   CE   HE2   108.88  3.000
 S4M  HE3   CE   HE1   109.32  3.000
 S4M  HE2   CE   HE1   109.04  3.000
 S4M  HE3   CE   SD    109.30  3.000
 S4M  HE2   CE   SD    105.79  3.000
 S4M  HE1   CE   SD    114.35  3.000
 S4M  H5'2  C5'  H5'1  108.09  3.000
 S4M  H5'2  C5'  C4'   109.37  3.000
 S4M  H5'1  C5'  C4'   111.42  3.000
 S4M  H5'2  C5'  SD    104.96  3.000
 S4M  H5'1  C5'  SD    115.16  3.000
 S4M  C4'   C5'  SD    107.56  3.000
 S4M  H4'   C4'  C3'   108.09  3.000
 S4M  H4'   C4'  O4'   107.85  3.000
 S4M  C3'   C4'  O4'   103.96  3.000
 S4M  H4'   C4'  C5'   109.38  3.000
 S4M  O4'   C4'  C5'   109.89  3.000
 S4M  C3'   C4'  C5'   117.22  3.000
 S4M  C1'   O4'  C4'   111.74  3.000
 S4M  H1'   C1'  N9    107.06  3.000
 S4M  H1'   C1'  C2'   111.70  3.000
 S4M  N9    C1'  C2'   111.17  3.000
 S4M  H1'   C1'  O4'   110.84  3.000
 S4M  N9    C1'  O4'   109.10  3.000
 S4M  C2'   C1'  O4'   106.99  3.000
 S4M  H2'   C2'  C3'   113.02  3.000
 S4M  H2'   C2'  O2'   111.70  3.000
 S4M  C3'   C2'  O2'   111.21  3.000
 S4M  H2'   C2'  C1'   111.90  3.000
 S4M  C3'   C2'  C1'   100.67  3.000
 S4M  O2'   C2'  C1'   107.73  3.000
 S4M  HO2'  O2'  C2'   107.53  3.000
 S4M  H3'   C3'  O3'   111.39  3.000
 S4M  H3'   C3'  C2'   109.33  3.000
 S4M  O3'   C3'  C2'   113.72  3.000
 S4M  H3'   C3'  C4'   109.65  3.000
 S4M  O3'   C3'  C4'   109.81  3.000
 S4M  C2'   C3'  C4'   102.56  3.000
 S4M  HO3'  O3'  C3'   108.90  3.000
 S4M  C4    N9   C8    106.20  3.000
 S4M  C8    N9   C1'   128.51  3.000
 S4M  C4    N9   C1'   125.28  3.000
 S4M  H8    C8   N7    124.68  3.000
 S4M  H8    C8   N9    121.92  3.000
 S4M  N7    C8   N9    113.40  3.000
 S4M  C5    N7   C8    104.35  3.000
 S4M  C4    C5   C6    116.22  3.000
 S4M  C6    C5   N7    133.05  3.000
 S4M  C4    C5   N7    110.73  3.000
 S4M  N1    C6   N6    119.30  3.000
 S4M  N6    C6   C5    122.78  3.000
 S4M  N1    C6   C5    117.91  3.000
 S4M  HN62  N6   HN61  118.34  3.000
 S4M  HN62  N6   C6    120.34  3.000
 S4M  HN61  N6   C6    121.20  3.000
 S4M  N3    C4   C5    126.60  3.000
 S4M  N3    C4   N9    128.09  3.000
 S4M  C5    C4   N9    105.31  3.000
 S4M  C2    N3   C4    111.59  3.000
 S4M  H2    C2   N1    115.39  3.000
 S4M  H2    C2   N3    116.15  3.000
 S4M  N1    C2   N3    128.46  3.000
 S4M  C2    N1   C6    119.23  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
 S4M  CONST_01  N7    C5  C4  N9     0.00   0.0  0
 S4M  CONST_02  C6    C5  C4  N9   180.00   0.0  0
 S4M  CONST_03  C2    N3  C4  N9   180.00   0.0  0
 S4M  CONST_04  C5    N7  C8  N9     0.00   0.0  0
 S4M  CONST_05  C5    C4  N9  C8     0.00   0.0  0
 S4M  CONST_06  N3    C4  N9  C8   180.00   0.0  0
 S4M  CONST_07  C4    C5  N7  C8     0.00   0.0  0
 S4M  CONST_08  C6    C5  N7  C8   180.00   0.0  0
 S4M  CONST_09  C4    N9  C8  N7     0.00   0.0  0
 S4M  CONST_10  N3    C4  C5  N7   180.00   0.0  0
 S4M  CONST_11  N1    C6  C5  N7   180.00   0.0  0
 S4M  CONST_12  C2    N3  C4  C5     0.00   0.0  0
 S4M  CONST_13  C2    N1  C6  C5     0.00   0.0  0
 S4M  CONST_14  N3    C4  C5  C6     0.00   0.0  0
 S4M  CONST_15  N3    C2  N1  C6     0.00   0.0  0
 S4M  CONST_16  N1    C6  C5  C4     0.00   0.0  0
 S4M  CONST_17  N1    C2  N3  C4     0.00   0.0  0
 S4M  CONST_18  C5    C4  N9  C1'  180.00   0.0  0
 S4M  CONST_19  N3    C4  N9  C1'    0.00   0.0  0
 S4M  CONST_20  N7    C8  N9  C1'  180.00   0.0  0
 S4M  CONST_21  N6    C6  C5  N7     0.00   0.0  0
 S4M  CONST_22  C4    C5  C6  N6   180.00   0.0  0
 S4M  CONST_23  C2    N1  C6  N6   180.00   0.0  0
 S4M  CONST_24  H8    C8  N9  C1'    0.00   0.0  0
 S4M  CONST_25  H2    C2  N1  C6   180.00   0.0  0
 S4M  CONST_26  HN61  N6  C6  C5     0.00   0.0  0
 S4M  CONST_27  HN62  N6  C6  C5   180.00   0.0  0
 S4M  Var_01    SD    CG  CB  CA   179.86  30.0  3
 S4M  Var_02    CG    CB  CA  N    179.67  30.0  3
 S4M  Var_03    HN1   N   CA  CB    57.67  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
 S4M  chir_01  SD   CG   CE   C5'  negativ
 S4M  chir_02  C4'  O4'  C3'  C5'  negativ
 S4M  chir_03  C1'  O4'  N9   C2'  negativ
 S4M  chir_04  C2'  O2'  C1'  C3'  negativ
 S4M  chir_05  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
 S4M  plan-1  C1'   0.020
 S4M  plan-1  N9    0.020
 S4M  plan-1  C8    0.020
 S4M  plan-1  N7    0.020
 S4M  plan-1  C5    0.020
 S4M  plan-1  C6    0.020
 S4M  plan-1  N6    0.020
 S4M  plan-1  C4    0.020
 S4M  plan-1  N3    0.020
 S4M  plan-1  C2    0.020
 S4M  plan-1  N1    0.020
 S4M  plan-1  H8    0.020
 S4M  plan-1  H2    0.020
 S4M  plan-2  C6    0.020
 S4M  plan-2  N6    0.020
 S4M  plan-2  HN61  0.020
 S4M  plan-2  HN62  0.020

