# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Mon Jun  8 02:20:18 2020
#   Inital geometry file: a 138 line input string
#   Ligand name: 5'-O-(L-methionylsulfamoyl)adenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CSCC[C@H](N)C(=O)N[S](=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
 MSP  MSP  5'-O-(L-methionylsulfamoyl)adenosine  L-peptide  56  31  .  2022-09-22  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_MSP
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
 MSP  N2    N  NH2   0  -0.773   1.7398   1.6065  -0.9816
 MSP  CA    C  CH1   0  -0.223   2.7792   0.6971  -0.5536
 MSP  CB    C  CH2   0  -0.431   4.0014   1.3237   0.1422
 MSP  CG    C  CH2   0  -0.559   4.7341   2.2889  -0.7762
 MSP  SD    S  S2    0  -0.036   6.2400   2.8790   0.0454
 MSP  CE    C  CH3   0  -0.764   6.8103   4.0792  -1.1774
 MSP  C9    C  C     0   0.599   2.1630  -0.2969   0.4140
 MSP  N8    N  NC1   0  -0.837   2.5558  -1.6028   0.2110
 MSP  S1    S  S     0   1.629   2.1034  -2.8716   1.1897
 MSP  O1S   O  OS    0  -0.631   2.6617  -4.0400   0.5580
 MSP  O2S   O  OS    0  -0.610   2.3707  -2.5678   2.5669
 MSP  O5'   O  OC2   0  -0.565   0.5262  -2.8723   1.0816
 MSP  C5'   C  CH2   0  -0.198  -0.0958  -3.1104  -0.1957
 MSP  C4'   C  CH1   0  -0.022  -1.5879  -2.9886   0.0181
 MSP  O4'   O  O2    0  -0.494  -1.9044  -1.7099   0.5505
 MSP  C3'   C  CH1   0  -0.044  -2.3476  -3.1264  -1.3044
 MSP  O3'   O  OH1   0  -0.667  -3.5554  -3.7964  -1.0579
 MSP  C2'   C  CH1   0  -0.041  -2.5899  -1.6582  -1.6635
 MSP  O2'   O  OH1   0  -0.656  -3.6950  -1.4328  -2.4884
 MSP  C1'   C  CH1   0   0.237  -2.8332  -1.0466  -0.2854
 MSP  N9    N  NR5   0  -0.529  -2.6680   0.3588  -0.1732
 MSP  C8    C  CR15  0   0.138  -1.5699   1.0838  -0.5522
 MSP  N7    N  N     0  -0.470  -1.7105   2.3615  -0.5362
 MSP  C5    C  CR56  0   0.020  -3.0233   2.5719  -0.1089
 MSP  C6    C  CR6   0   0.392  -3.5743   3.6725   0.4227
 MSP  N6    N  NH2   0  -0.837  -3.0938   4.9677   0.3872
 MSP  N1    N  NR16  0  -0.668  -4.7709   3.4716   1.1109
 MSP  C2    C  CR16  0   0.105  -5.0068   2.2339   1.6516
 MSP  N3    N  N     0  -0.422  -4.5114   1.1421   1.2219
 MSP  C4    C  C     0   0.077  -3.7847   1.2784  -0.0210
 MSP  O1    O  O     0  -0.411   1.4133   0.0179   1.3043
 MSP  HN21  H  HNH2  0   0.354   1.4097   2.1711  -0.2089
 MSP  HN22  H  HNH2  0   0.367   2.1012   2.2431  -1.6794
 MSP  HA    H  HCH1  0   0.275   3.1341   0.1633  -1.4402
 MSP  HB1   H  HCH2  0   0.250   4.6828   0.5253   0.4512
 MSP  HB2   H  HCH2  0   0.253   3.6801   1.8428   1.0490
 MSP  HG1   H  HCH2  0   0.261   4.1070   3.1502  -1.0143
 MSP  HG2   H  HCH2  0   0.265   5.0040   1.7973  -1.7141
 MSP  HE1   H  HCH3  0   0.262   6.9872   3.6043  -2.1413
 MSP  HE2   H  HCH3  0   0.262   6.0935   4.8899  -1.3000
 MSP  HE3   H  HCH3  0   0.274   7.7494   4.4955  -0.8173
 MSP  HN8   H  HNC1  0   0.458   3.1336  -1.8466  -0.5852
 MSP  H5'1  H  HCH2  0   0.252   0.2672  -2.3833  -0.9274
 MSP  H5'2  H  HCH2  0   0.277   0.1434  -4.1151  -0.5482
 MSP  H4'   H  HCH1  0   0.269  -1.9077  -3.7694   0.7166
 MSP  H3'   H  HCH1  0   0.252  -1.7512  -3.6438  -2.0680
 MSP  H2    H  HOH1  0   0.449  -4.1717  -3.5666  -1.7637
 MSP  H1    H  HCH1  0   0.242  -1.6713  -1.2392  -2.0957
 MSP  H2'   H  HOH1  0   0.469  -3.4258  -1.5349  -3.4067
 MSP  H1'   H  HCH1  0   0.242  -3.8624  -1.2619   0.0289
 MSP  H8    H  HCR5  0   0.274  -0.6307   0.6057  -0.7984
 MSP  HN61  H  HNH2  0   0.382  -2.2040   5.0298  -0.0855
 MSP  HN62  H  HNH2  0   0.382  -3.0280   5.4070   1.2963
 MSP  HN1   H  HNR6  0   0.410  -5.2303   4.2671   1.5254
 MSP  H3    H  HCR6  0   0.280  -5.6562   2.2330   2.5208
 MSP  H4    H  H     0   0.232  -4.5038   1.1313  -0.8456

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
 MSP  N2   CA    single  1.446  0.020  1.446
 MSP  N2   HN21  single  0.890  0.020  1.040
 MSP  N2   HN22  single  0.890  0.020  1.040
 MSP  CA   CB    single  1.521  0.033  1.521
 MSP  CA   C9    single  1.518  0.020  1.518
 MSP  CA   HA    single  0.970  0.020  0.970
 MSP  CB   CG    single  1.521  0.020  1.521
 MSP  CB   HB1   single  0.970  0.020  1.090
 MSP  CB   HB2   single  0.970  0.020  1.090
 MSP  CG   SD    single  1.814  0.020  1.814
 MSP  CG   HG1   single  0.970  0.020  1.090
 MSP  CG   HG2   single  0.970  0.020  1.090
 MSP  SD   CE    single  1.806  0.020  1.806
 MSP  CE   HE1   single  0.970  0.020  1.090
 MSP  CE   HE2   single  0.970  0.020  1.090
 MSP  CE   HE3   single  0.970  0.020  1.090
 MSP  C9   N8    single  1.379  0.020  1.379
 MSP  C9   O1    double  1.206  0.020  1.206
 MSP  N8   S1    single  1.665  0.020  1.665
 MSP  N8   HN8   single  0.860  0.020  1.020
 MSP  S1   O1S   deloc   1.441  0.020  1.441
 MSP  S1   O2S   deloc   1.435  0.020  1.435
 MSP  S1   O5'   single  1.581  0.020  1.581
 MSP  O5'  C5'   single  1.440  0.020  1.440
 MSP  C5'  C4'   single  1.512  0.020  1.512
 MSP  C5'  H5'1  single  0.970  0.020  1.090
 MSP  C5'  H5'2  single  0.970  0.020  1.090
 MSP  C4'  O4'   single  1.421  0.020  1.421
 MSP  C4'  C3'   single  1.531  0.020  1.531
 MSP  C4'  H4'   single  0.970  0.020  1.090
 MSP  O4'  C1'   single  1.415  0.020  1.415
 MSP  C3'  O3'   single  1.403  0.020  1.403
 MSP  C3'  C2'   single  1.531  0.020  1.531
 MSP  C3'  H3'   single  0.970  0.020  1.090
 MSP  O3'  H2    single  0.850  0.020  0.980
 MSP  C2'  O2'   single  1.397  0.020  1.397
 MSP  C2'  C1'   single  1.527  0.020  1.527
 MSP  C2'  H1    single  0.970  0.020  1.090
 MSP  O2'  H2'   single  0.850  0.020  0.980
 MSP  C1'  N9    single  1.420  0.020  1.420
 MSP  C1'  H1'   single  0.970  0.020  1.090
 MSP  N9   C8    single  1.369  0.020  1.369
 MSP  N9   C4    single  1.455  0.020  1.455
 MSP  C8   N7    double  1.285  0.020  1.285
 MSP  C8   H8    single  0.930  0.020  1.080
 MSP  N7   C5    single  1.397  0.020  1.397
 MSP  C5   C6    double  1.341  0.020  1.341
 MSP  C5   C4    single  1.504  0.020  1.504
 MSP  C6   N6    single  1.382  0.020  1.382
 MSP  C6   N1    single  1.395  0.020  1.395
 MSP  N6   HN61  single  0.890  0.020  1.040
 MSP  N6   HN62  single  0.890  0.020  1.040
 MSP  N1   C2    single  1.371  0.020  1.371
 MSP  N1   HN1   single  0.890  0.020  1.040
 MSP  C2   N3    double  1.274  0.020  1.274
 MSP  C2   H3    single  0.930  0.020  1.080
 MSP  N3   C4    single  1.446  0.020  1.446
 MSP  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
 MSP  HN22  N2   HN21  106.98  3.000
 MSP  HN22  N2   CA    110.08  3.000
 MSP  HN21  N2   CA    111.05  3.000
 MSP  HA    CA   C9    109.19  3.000
 MSP  HA    CA   CB    109.00  3.000
 MSP  C9    CA   CB    107.50  3.000
 MSP  HA    CA   N2    107.47  3.000
 MSP  C9    CA   N2    107.99  3.000
 MSP  CB    CA   N2    116.65  3.000
 MSP  HB2   CB   HB1   107.17  3.000
 MSP  HB2   CB   CG    109.95  3.000
 MSP  HB1   CB   CG    109.49  3.000
 MSP  HB2   CB   CA    109.56  3.000
 MSP  HB1   CB   CA    108.97  3.000
 MSP  CG    CB   CA    111.59  3.000
 MSP  HG2   CG   HG1   108.04  3.000
 MSP  HG2   CG   SD    109.27  3.000
 MSP  HG1   CG   SD    108.60  3.000
 MSP  HG2   CG   CB    110.60  3.000
 MSP  HG1   CG   CB    110.84  3.000
 MSP  SD    CG   CB    109.45  3.000
 MSP  CE    SD   CG     99.89  3.000
 MSP  HE3   CE   HE2   108.69  3.000
 MSP  HE3   CE   HE1   108.63  3.000
 MSP  HE2   CE   HE1   109.38  3.000
 MSP  HE3   CE   SD    107.61  3.000
 MSP  HE2   CE   SD    111.29  3.000
 MSP  HE1   CE   SD    111.15  3.000
 MSP  O1    C9   N8    122.22  3.000
 MSP  O1    C9   CA    123.51  3.000
 MSP  N8    C9   CA    114.25  3.000
 MSP  HN8   N8   S1    115.68  3.000
 MSP  HN8   N8   C9    120.39  3.000
 MSP  S1    N8   C9    123.91  3.000
 MSP  O5'   S1   O2S   104.57  3.000
 MSP  O5'   S1   O1S   110.87  3.000
 MSP  O2S   S1   O1S   121.35  3.000
 MSP  O5'   S1   N8    103.37  3.000
 MSP  O2S   S1   N8    110.61  3.000
 MSP  O1S   S1   N8    104.77  3.000
 MSP  C5'   O5'  S1    119.44  3.000
 MSP  H5'2  C5'  H5'1  108.86  3.000
 MSP  H5'2  C5'  C4'   109.64  3.000
 MSP  H5'1  C5'  C4'   111.62  3.000
 MSP  H5'2  C5'  O5'   110.12  3.000
 MSP  H5'1  C5'  O5'   109.88  3.000
 MSP  C4'   C5'  O5'   106.70  3.000
 MSP  H4'   C4'  C3'   109.98  3.000
 MSP  H4'   C4'  O4'   109.72  3.000
 MSP  C3'   C4'  O4'   107.11  3.000
 MSP  H4'   C4'  C5'   108.71  3.000
 MSP  C3'   C4'  C5'   111.11  3.000
 MSP  O4'   C4'  C5'   110.20  3.000
 MSP  C1'   O4'  C4'   110.29  3.000
 MSP  H3'   C3'  C2'   112.00  3.000
 MSP  H3'   C3'  O3'   111.38  3.000
 MSP  C2'   C3'  O3'   111.28  3.000
 MSP  H3'   C3'  C4'   111.93  3.000
 MSP  C2'   C3'  C4'   101.23  3.000
 MSP  O3'   C3'  C4'   108.56  3.000
 MSP  H2    O3'  C3'   107.92  3.000
 MSP  H1    C2'  C1'   109.61  3.000
 MSP  H1    C2'  O2'   111.57  3.000
 MSP  C1'   C2'  O2'   110.01  3.000
 MSP  H1    C2'  C3'   109.01  3.000
 MSP  C1'   C2'  C3'   101.40  3.000
 MSP  O2'   C2'  C3'   114.74  3.000
 MSP  H2'   O2'  C2'   108.97  3.000
 MSP  H1'   C1'  N9    106.31  3.000
 MSP  H1'   C1'  C2'   109.22  3.000
 MSP  N9    C1'  C2'   116.70  3.000
 MSP  H1'   C1'  O4'   110.76  3.000
 MSP  N9    C1'  O4'   109.94  3.000
 MSP  C2'   C1'  O4'   103.94  3.000
 MSP  C4    N9   C8    108.05  3.000
 MSP  C4    N9   C1'   123.01  3.000
 MSP  C8    N9   C1'   126.56  3.000
 MSP  H8    C8   N7    122.47  3.000
 MSP  H8    C8   N9    121.67  3.000
 MSP  N7    C8   N9    115.79  3.000
 MSP  C5    N7   C8    104.86  3.000
 MSP  C4    C5   C6    118.36  3.000
 MSP  C4    C5   N7    111.36  3.000
 MSP  C6    C5   N7    129.15  3.000
 MSP  N1    C6   N6    116.48  3.000
 MSP  N1    C6   C5    115.46  3.000
 MSP  N6    C6   C5    128.05  3.000
 MSP  HN62  N6   HN61  109.67  3.000
 MSP  HN62  N6   C6    113.98  3.000
 MSP  HN61  N6   C6    112.10  3.000
 MSP  HN1   N1   C2    118.16  3.000
 MSP  HN1   N1   C6    118.70  3.000
 MSP  C2    N1   C6    118.17  3.000
 MSP  H3    C2   N3    120.16  3.000
 MSP  H3    C2   N1    114.81  3.000
 MSP  N3    C2   N1    125.02  3.000
 MSP  C4    N3   C2    113.87  3.000
 MSP  H4    C4   N3    107.58  3.000
 MSP  H4    C4   C5    113.63  3.000
 MSP  N3    C4   C5    112.69  3.000
 MSP  H4    C4   N9    109.74  3.000
 MSP  N3    C4   N9    114.59  3.000
 MSP  C5    C4   N9     98.57  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
 MSP  CONST_01  N7    C8   N9   C1'   180.00   0.0  0
 MSP  CONST_02  C5    N7   C8   N9      0.00   0.0  0
 MSP  CONST_03  C4    C5   N7   C8      0.00   0.0  0
 MSP  CONST_04  C4    N9   C8   N7      0.00   0.0  0
 MSP  CONST_07  C4    N3   C2   N1      0.00   0.0  0
 MSP  CONST_09  H8    C8   N9   C1'     0.00   0.0  0
 MSP  CONST_10  HN1   N1   C6   C5    180.00   0.0  0
 MSP  CONST_12  HN61  N6   C6   C5      0.00   0.0  0
 MSP  CONST_14  S1    N8   C9   CA    180.00   0.0  0
 MSP  CONST_15  O1    C9   N8   S1      0.00   0.0  0
 MSP  CONST_16  HN8   N8   C9   CA      0.00   0.0  0
 MSP  Var_01    C6    C5   N7   C8    159.90  30.0  1
 MSP  Var_02    N1    C6   C5   N7   -161.56  30.0  1
 MSP  Var_03    C4'   C5'  O5'  S1   -177.61  30.0  3
 MSP  Var_04    SD    CG   CB   CA   -175.03  30.0  3
 MSP  Var_05    O1S   S1   N8   C9    176.27  30.0  3
 MSP  Var_06    HE1   CE   SD   CG    -59.25  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
 MSP  chir_01  CA   N2   CB   C9   negativ
 MSP  chir_02  C4'  O4'  C5'  C3'  positiv
 MSP  chir_03  C3'  O3'  C4'  C2'  positiv
 MSP  chir_04  C2'  O2'  C3'  C1'  positiv
 MSP  chir_05  C1'  O4'  N9   C2'  negativ
 MSP  chir_06  C4   N9   N3   C5   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
 MSP  plan-1  CA    0.020
 MSP  plan-1  C9    0.020
 MSP  plan-1  N8    0.020
 MSP  plan-1  S1    0.020
 MSP  plan-1  O1    0.020
 MSP  plan-1  HN8   0.020
 MSP  plan-2  C1'   0.020
 MSP  plan-2  N9    0.020
 MSP  plan-2  C8    0.020
 MSP  plan-2  N7    0.020
 MSP  plan-2  C5    0.020
 MSP  plan-2  C4    0.020
 MSP  plan-2  H8    0.020
 MSP  plan-3  C5    0.020
 MSP  plan-3  C6    0.020
 MSP  plan-3  N6    0.020
 MSP  plan-3  N1    0.020
 MSP  plan-3  C2    0.020
 MSP  plan-3  N3    0.020
 MSP  plan-3  C4    0.020
 MSP  plan-3  HN61  0.020
 MSP  plan-3  HN62  0.020
 MSP  plan-3  HN1   0.020
 MSP  plan-3  H3    0.020

