# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sun Jun  7 20:22:31 2020
#   Inital geometry file: a 136 line input string
#   Ligand name: 5'-O-[(S)-{[(2S)-2-amino-4-(methylsulfanyl)butyl]oxy}(hydroxy)phosphoryl]adenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CSCC[C@H](N)CO[P@@](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N2C=NC3=C(N)NC=N[C@@H]23
#
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
 MOD  MOD  5'-O-[(S)-{[(2S)-2-amino-4-(methylsulfanyl)butyl]oxy}(hydroxy)phosphoryl]adenosine  L-peptide  56  30  .  2022-07-25  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_MOD
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
 MOD  N2    N  NH2    0  -0.788  -3.5089   0.6810   1.1947
 MOD  CA    C  CH1    0  -0.148  -2.6698  -0.0366   0.2470
 MOD  CB    C  CH2    0  -0.431  -3.1372  -1.4617  -0.0774
 MOD  CG    C  CH2    0  -0.556  -3.0839  -2.3578   1.1490
 MOD  SD    S  S2     0  -0.040  -3.5121  -4.0691   0.7194
 MOD  CE    C  CH3    0  -0.761  -3.1744  -4.8651   2.3052
 MOD  C9    C  CH2    0  -0.118  -2.5265   0.7660  -1.0352
 MOD  O1    O  O2     0  -0.608  -1.8083   1.9507  -0.7615
 MOD  P1    P  P      0   1.354  -1.5165   2.9900  -1.9910
 MOD  O1S   O  OP    -1  -0.801  -0.7802   2.2974  -3.0995
 MOD  O2S   O  O      0  -0.798  -2.7652   3.7645  -2.2834
 MOD  O5'   O  O2     0  -0.615  -0.5257   4.0192  -1.1842
 MOD  C5'   C  CH2    0  -0.158   0.8797   3.9545  -1.2727
 MOD  C4'   C  CH1    0  -0.029   1.5084   3.5537   0.0517
 MOD  O4'   O  O2     0  -0.485   1.0726   2.2653   0.4695
 MOD  C3'   C  CH1    0  -0.026   3.0261   3.4668  -0.0562
 MOD  O3'   O  OH1    0  -0.672   3.5902   3.7281   1.2043
 MOD  C2'   C  CH1    0  -0.061   3.2106   1.9983  -0.4457
 MOD  O2'   O  OH1    0  -0.657   4.4607   1.4602  -0.1231
 MOD  C1'   C  CH1    0   0.221   2.1208   1.3197   0.3846
 MOD  N9    N  NR5    0  -0.520   1.6664   0.0752  -0.1417
 MOD  C8    C  CR15   0   0.156   1.0192  -0.0416  -1.3502
 MOD  N7    N  N      0  -0.470   0.3175  -1.1039  -1.5163
 MOD  C5    C  CR5    0   0.060   0.4230  -1.7935  -0.3088
 MOD  C6    C  C      0   0.353   0.1730  -3.0790  -0.0420
 MOD  N6    N  NH2    0  -0.841  -0.3672  -4.0384  -0.8909
 MOD  N1    N  NH1    0  -0.663   0.6300  -3.5348   1.2035
 MOD  C2    C  C1     0   0.097   1.7070  -2.8859   1.7610
 MOD  N3    N  N      0  -0.418   2.0476  -1.6816   1.5308
 MOD  C4    C  CR15   0   0.070   1.0987  -0.9475   0.7282
 MOD  HN21  H  HNH2   0   0.334  -4.4725   0.6579   0.8792
 MOD  HN22  H  HNH2   0   0.346  -3.5008   0.2179   2.0945
 MOD  HA    H  HCH1   0   0.239  -1.6712  -0.1123   0.6900
 MOD  HB1   H  HCH2   0   0.229  -2.4917  -1.8821  -0.8534
 MOD  HB2   H  HCH2   0   0.232  -4.1539  -1.4351  -0.4844
 MOD  HG1   H  HCH2   0   0.259  -3.7730  -2.0140   1.9232
 MOD  HG2   H  HCH2   0   0.259  -2.0756  -2.3516   1.5708
 MOD  HE1   H  HCH3   0   0.263  -3.8221  -4.4716   3.0873
 MOD  HE2   H  HCH3   0   0.276  -3.3673  -5.9304   2.1942
 MOD  HE3   H  HCH3   0   0.257  -2.1336  -4.7249   2.5948
 MOD  H91   H  HCH2   0   0.213  -1.9969   0.1612  -1.7761
 MOD  H92   H  HCH2   0   0.192  -3.5246   0.9909  -1.4389
 MOD  H5'1  H  HCH2   0   0.211   1.1952   3.2809  -2.0746
 MOD  H5'2  H  HCH2   0   0.224   1.2508   4.9522  -1.5292
 MOD  H4'   H  HCH1   0   0.245   1.2212   4.2857   0.8148
 MOD  H3'   H  HCH1   0   0.242   3.4239   4.1459  -0.8228
 MOD  H2    H  HOH1   0   0.446   4.4626   3.3172   1.2247
 MOD  H1    H  HCH1   0   0.241   2.9972   1.8881  -1.5167
 MOD  H2'   H  HOH1   0   0.466   5.0900   1.7088  -0.8079
 MOD  H1'   H  HCH1   0   0.242   2.5203   1.1025   1.3828
 MOD  H8    H  HCR5   0   0.275   1.1221   0.7162  -2.1148
 MOD  HN61  H  HNH2   0   0.374  -0.6031  -3.6264  -1.7838
 MOD  HN62  H  HNH2   0   0.373  -1.2183  -4.4439  -0.5067
 MOD  HN1   H  HNH1   0   0.405   0.5798  -4.5281   1.3690
 MOD  H3    H  H      0   0.280   2.2967  -3.4966   2.4367
 MOD  H4    H  HCR5   0   0.231   0.3803  -0.4727   1.4218

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
 MOD  N2   CA    single  1.455  0.020  1.455
 MOD  N2   HN21  single  0.890  0.020  1.040
 MOD  N2   HN22  single  0.890  0.020  1.040
 MOD  CA   CB    single  1.521  0.033  1.521
 MOD  CA   C9    single  1.519  0.020  1.519
 MOD  CA   HA    single  0.970  0.020  0.970
 MOD  CB   CG    single  1.520  0.020  1.520
 MOD  CB   HB1   single  0.970  0.020  1.090
 MOD  CB   HB2   single  0.970  0.020  1.090
 MOD  CG   SD    single  1.816  0.020  1.816
 MOD  CG   HG1   single  0.970  0.020  1.090
 MOD  CG   HG2   single  0.970  0.020  1.090
 MOD  SD   CE    single  1.806  0.020  1.806
 MOD  CE   HE1   single  0.970  0.020  1.090
 MOD  CE   HE2   single  0.970  0.020  1.090
 MOD  CE   HE3   single  0.970  0.020  1.090
 MOD  C9   O1    single  1.412  0.020  1.412
 MOD  C9   H91   single  0.970  0.020  1.090
 MOD  C9   H92   single  0.970  0.020  1.090
 MOD  O1   P1    single  1.636  0.020  1.636
 MOD  P1   O1S   deloc   1.500  0.020  1.500
 MOD  P1   O2S   deloc   1.498  0.020  1.498
 MOD  P1   O5'   single  1.641  0.020  1.641
 MOD  O5'  C5'   single  1.410  0.020  1.410
 MOD  C5'  C4'   single  1.520  0.020  1.520
 MOD  C5'  H5'1  single  0.970  0.020  1.090
 MOD  C5'  H5'2  single  0.970  0.020  1.090
 MOD  C4'  O4'   single  1.423  0.020  1.423
 MOD  C4'  C3'   single  1.524  0.020  1.524
 MOD  C4'  H4'   single  0.970  0.020  1.090
 MOD  O4'  C1'   single  1.414  0.020  1.414
 MOD  C3'  O3'   single  1.405  0.020  1.405
 MOD  C3'  C2'   single  1.530  0.020  1.530
 MOD  C3'  H3'   single  0.970  0.020  1.090
 MOD  O3'  H2    single  0.850  0.020  0.980
 MOD  C2'  O2'   single  1.399  0.020  1.399
 MOD  C2'  C1'   single  1.529  0.020  1.529
 MOD  C2'  H1    single  0.970  0.020  1.090
 MOD  O2'  H2'   single  0.850  0.020  0.980
 MOD  C1'  N9    single  1.426  0.020  1.426
 MOD  C1'  H1'   single  0.970  0.020  1.090
 MOD  N9   C8    single  1.376  0.020  1.376
 MOD  N9   C4    single  1.458  0.020  1.458
 MOD  C8   N7    double  1.284  0.020  1.284
 MOD  C8   H8    single  0.930  0.020  1.080
 MOD  N7   C5    single  1.395  0.020  1.395
 MOD  C5   C6    double  1.336  0.020  1.336
 MOD  C5   C4    single  1.499  0.020  1.499
 MOD  C6   N6    single  1.390  0.020  1.390
 MOD  C6   N1    single  1.403  0.020  1.403
 MOD  N6   HN61  single  0.890  0.020  1.040
 MOD  N6   HN62  single  0.890  0.020  1.040
 MOD  N1   C2    single  1.375  0.020  1.375
 MOD  N1   HN1   single  0.890  0.020  1.040
 MOD  C2   N3    double  1.273  0.020  1.273
 MOD  C2   H3    single  0.930  0.020  1.080
 MOD  N3   C4    single  1.443  0.020  1.443
 MOD  C4   H4    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
 MOD  HN22  N2   HN21  105.89  3.000
 MOD  HN22  N2   CA    110.41  3.000
 MOD  HN21  N2   CA    109.51  3.000
 MOD  HA    CA   C9    106.97  3.000
 MOD  HA    CA   CB    109.00  3.000
 MOD  C9    CA   CB    109.93  3.000
 MOD  HA    CA   N2    107.25  3.000
 MOD  C9    CA   N2    110.09  3.000
 MOD  CB    CA   N2    114.84  3.000
 MOD  HB2   CB   HB1   107.07  3.000
 MOD  HB2   CB   CG    110.28  3.000
 MOD  HB1   CB   CG    108.98  3.000
 MOD  HB2   CB   CA    109.80  3.000
 MOD  HB1   CB   CA    109.10  3.000
 MOD  CG    CB   CA    111.49  3.000
 MOD  HG2   CG   HG1   107.86  3.000
 MOD  HG2   CG   SD    108.32  3.000
 MOD  HG1   CG   SD    108.40  3.000
 MOD  HG2   CG   CB    109.90  3.000
 MOD  HG1   CG   CB    111.37  3.000
 MOD  SD    CG   CB    110.89  3.000
 MOD  CE    SD   CG     99.41  3.000
 MOD  HE3   CE   HE2   108.81  3.000
 MOD  HE3   CE   HE1   109.31  3.000
 MOD  HE2   CE   HE1   108.76  3.000
 MOD  HE3   CE   SD    110.81  3.000
 MOD  HE2   CE   SD    107.98  3.000
 MOD  HE1   CE   SD    111.10  3.000
 MOD  H92   C9   H91   107.70  3.000
 MOD  H92   C9   O1    111.17  3.000
 MOD  H91   C9   O1    110.43  3.000
 MOD  H92   C9   CA    109.40  3.000
 MOD  H91   C9   CA    108.99  3.000
 MOD  O1    C9   CA    109.12  3.000
 MOD  P1    O1   C9    118.55  3.000
 MOD  O5'   P1   O2S   105.97  3.000
 MOD  O5'   P1   O1S   110.89  3.000
 MOD  O2S   P1   O1S   120.23  3.000
 MOD  O5'   P1   O1     97.85  3.000
 MOD  O2S   P1   O1    109.05  3.000
 MOD  O1S   P1   O1    110.46  3.000
 MOD  C5'   O5'  P1    122.85  3.000
 MOD  H5'2  C5'  H5'1  106.95  3.000
 MOD  H5'2  C5'  C4'   107.72  3.000
 MOD  H5'1  C5'  C4'   110.92  3.000
 MOD  H5'2  C5'  O5'   108.11  3.000
 MOD  H5'1  C5'  O5'   111.21  3.000
 MOD  C4'   C5'  O5'   111.70  3.000
 MOD  H4'   C4'  C3'   110.39  3.000
 MOD  H4'   C4'  O4'   108.67  3.000
 MOD  C3'   C4'  O4'   105.92  3.000
 MOD  H4'   C4'  C5'   108.80  3.000
 MOD  C3'   C4'  C5'   111.42  3.000
 MOD  O4'   C4'  C5'   111.59  3.000
 MOD  C1'   O4'  C4'   111.15  3.000
 MOD  H3'   C3'  C2'   111.83  3.000
 MOD  H3'   C3'  O3'   111.44  3.000
 MOD  C2'   C3'  O3'   110.99  3.000
 MOD  H3'   C3'  C4'   112.01  3.000
 MOD  C2'   C3'  C4'   101.11  3.000
 MOD  O3'   C3'  C4'   109.00  3.000
 MOD  H2    O3'  C3'   107.62  3.000
 MOD  H1    C2'  C1'   110.29  3.000
 MOD  H1    C2'  O2'   111.11  3.000
 MOD  C1'   C2'  O2'   109.94  3.000
 MOD  H1    C2'  C3'   108.74  3.000
 MOD  C1'   C2'  C3'   101.64  3.000
 MOD  O2'   C2'  C3'   114.72  3.000
 MOD  H2'   O2'  C2'   108.71  3.000
 MOD  H1'   C1'  N9    106.21  3.000
 MOD  H1'   C1'  C2'   108.81  3.000
 MOD  N9    C1'  C2'   114.47  3.000
 MOD  H1'   C1'  O4'   110.35  3.000
 MOD  N9    C1'  O4'   111.69  3.000
 MOD  C2'   C1'  O4'   105.31  3.000
 MOD  C4    N9   C8    106.34  3.000
 MOD  C4    N9   C1'   121.08  3.000
 MOD  C8    N9   C1'   123.25  3.000
 MOD  H8    C8   N7    122.70  3.000
 MOD  H8    C8   N9    121.12  3.000
 MOD  N7    C8   N9    116.17  3.000
 MOD  C5    N7   C8    104.82  3.000
 MOD  C4    C5   C6    119.27  3.000
 MOD  C4    C5   N7    110.73  3.000
 MOD  C6    C5   N7    129.37  3.000
 MOD  N1    C6   N6    116.39  3.000
 MOD  N1    C6   C5    115.39  3.000
 MOD  N6    C6   C5    127.92  3.000
 MOD  HN62  N6   HN61  107.49  3.000
 MOD  HN62  N6   C6    111.67  3.000
 MOD  HN61  N6   C6    110.41  3.000
 MOD  HN1   N1   C2    115.93  3.000
 MOD  HN1   N1   C6    116.72  3.000
 MOD  C2    N1   C6    117.50  3.000
 MOD  H3    C2   N3    119.99  3.000
 MOD  H3    C2   N1    114.36  3.000
 MOD  N3    C2   N1    125.64  3.000
 MOD  C4    N3   C2    113.95  3.000
 MOD  H4    C4   N3    107.26  3.000
 MOD  H4    C4   C5    112.54  3.000
 MOD  N3    C4   C5    113.20  3.000
 MOD  H4    C4   N9    109.03  3.000
 MOD  N3    C4   N9    115.63  3.000
 MOD  C5    C4   N9     99.13  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
 MOD  CONST_02  C5    N7   C8   N9     0.00   0.0  0
 MOD  CONST_03  C4    C5   N7   C8     0.00   0.0  0
 MOD  CONST_04  C4    N9   C8   N7     0.00   0.0  0
 MOD  CONST_07  C4    N3   C2   N1     0.00   0.0  0
 MOD  CONST_10  HN1   N1   C6   C5   180.00   0.0  0
 MOD  CONST_12  HN61  N6   C6   C5     0.00   0.0  0
 MOD  Var_01    C6    C5   N7   C8  -161.80  30.0  1
 MOD  Var_02    N1    C6   C5   N7   167.60  30.0  1
 MOD  Var_03    C4'   C5'  O5'  P1  -113.59  30.0  3
 MOD  Var_04    SD    CG   CB   CA  -175.47  30.0  3
 MOD  Var_05    O1S   P1   O1   C9   -57.02  30.0  3
 MOD  Var_06    HE1   CE   SD   CG    62.21  30.0  3
 MOD  Var_07    H91   C9   O1   P1    60.03  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
 MOD  chir_01  CA   N2   CB   C9   negativ
 MOD  chir_03  C4'  O4'  C5'  C3'  positiv
 MOD  chir_04  C3'  O3'  C4'  C2'  positiv
 MOD  chir_05  C2'  O2'  C3'  C1'  positiv
 MOD  chir_06  C1'  O4'  N9   C2'  negativ
 MOD  chir_07  C4   N9   N3   C5   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
 MOD  plan-1  C1'   0.020
 MOD  plan-1  N9    0.020
 MOD  plan-1  C8    0.020
 MOD  plan-1  N7    0.020
 MOD  plan-1  C5    0.020
 MOD  plan-1  C4    0.020
 MOD  plan-1  H8    0.020
 MOD  plan-2  C5    0.020
 MOD  plan-2  C6    0.020
 MOD  plan-2  N6    0.020
 MOD  plan-2  N1    0.020
 MOD  plan-2  C2    0.020
 MOD  plan-2  N3    0.020
 MOD  plan-2  C4    0.020
 MOD  plan-2  HN61  0.020
 MOD  plan-2  HN62  0.020
 MOD  plan-2  HN1   0.020
 MOD  plan-2  H3    0.020

