# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 11:02:08 2020
#   Inital geometry file: a 89 line input string
#   Ligand name: (2S,3R,4S,5S)-3,4-dihydroxy-2-[(methylsulfanyl)methyl]-5-(4-oxo-4,5-dihydro-3H-pyrrolo[3,2-d]pyrimidin-7-yl)pyrrolidinium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CSC[C@H]1[NH2+][C@H]([C@H](O)[C@@H]1O)c2c[nH]c3C(=O)NC=Nc23
#
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
 MTI  MTI  (2S,3R,4S,5S)-3,4-dihydroxy-2-[(methylsulfanyl)methyl]-5-(4-oxo-4,5-dihydro-3H-pyrrolo[3,2-d]pyrimidin-7-yl)pyrrolidinium  ligand  37  20  .  2022-07-25  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_MTI
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
 MTI  CS    C  CH3   0  -0.744   2.4523  -2.7763  -1.7233
 MTI  S5'   S  S2    0  -0.049   2.7042  -0.9873  -1.7417
 MTI  C5'   C  CH2   0  -0.571   2.3558  -0.5345  -0.0101
 MTI  C4'   C  CH1   0  -0.185   2.2558   0.9773   0.0943
 MTI  N4'   N  NT2   1  -0.644   1.1178   1.4724  -0.7243
 MTI  C2'   C  CH1   0   0.030   0.8969   2.6078   1.2976
 MTI  O2'   O  OH1   0  -0.612   1.4981   3.7665   0.7932
 MTI  C3'   C  CH1   0   0.054   1.9527   1.4951   1.5163
 MTI  O3'   O  OH1   0  -0.641   3.1394   1.9558   2.0940
 MTI  C1'   C  CH1   0  -0.261   0.0519   2.0082   0.1843
 MTI  C9    C  CR5   0   0.167  -0.8479   0.9023   0.6483
 MTI  C8    C  CR15  0  -0.077  -1.5527   0.7850   1.8321
 MTI  N7    N  NR15  0  -0.684  -2.3296  -0.3291   1.7885
 MTI  C5    C  CR56  0   0.077  -2.1208  -0.9771   0.6088
 MTI  C6    C  CR6   0   0.525  -2.6437  -2.2134   0.0862
 MTI  O6    O  OC    0  -0.511  -3.4584  -2.9679   0.5895
 MTI  N1    N  NR16  0  -0.717  -2.0545  -2.4600  -1.0716
 MTI  C2    C  CR16  0   0.088  -1.1395  -1.7130  -1.7276
 MTI  N3    N  N     0  -0.357  -0.6900  -0.5931  -1.3118
 MTI  C4    C  CR56  0   0.203  -1.2007  -0.2261  -0.1104
 MTI  HS1   H  HCH3  0   0.263   1.4506  -3.0260  -1.3795
 MTI  HS2   H  HCH3  0   0.312   2.5730  -3.1313  -2.7534
 MTI  HS3   H  HCH3  0   0.273   3.1878  -3.2683  -1.0941
 MTI  H5'1  H  HCH2  0   0.288   1.4239  -1.0042   0.3175
 MTI  H5'2  H  HCH2  0   0.298   3.1436  -0.8798   0.6583
 MTI  H4'   H  HCH1  0   0.350   3.1612   1.4579  -0.2820
 MTI  H4'1  H  HNT2  0   0.488   1.4244   2.2315  -1.3360
 MTI  H4'2  H  HNT2  0   0.458   0.7522   0.7530  -1.3630
 MTI  H1    H  HCH1  0   0.245   0.3105   2.8079   2.2020
 MTI  H2'   H  HOH1  0   0.461   2.2650   3.9739   1.3410
 MTI  H3'   H  HCH1  0   0.263   1.5037   0.6916   2.1090
 MTI  H2    H  HOH1  0   0.469   3.0710   1.8826   3.0504
 MTI  H1'   H  HCH1  0   0.322  -0.4919   2.7510  -0.4049
 MTI  H8    H  HCR5  0   0.308  -1.5750   1.4327   2.6917
 MTI  HN7   H  HNR5  0   0.425  -2.9567  -0.6223   2.5222
 MTI  HN1   H  HNR6  0   0.406  -2.3229  -3.3285  -1.5159
 MTI  H3    H  HCR6  0   0.279  -0.7962  -2.1248  -2.6666

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
 MTI  CS   S5'   single    1.807  0.020  1.807
 MTI  CS   HS1   single    0.970  0.020  1.090
 MTI  CS   HS2   single    0.970  0.020  1.090
 MTI  CS   HS3   single    0.970  0.020  1.090
 MTI  S5'  C5'   single    1.823  0.020  1.823
 MTI  C5'  C4'   single    1.519  0.020  1.519
 MTI  C5'  H5'1  single    0.970  0.020  1.090
 MTI  C5'  H5'2  single    0.970  0.020  1.090
 MTI  C4'  N4'   single    1.487  0.020  1.487
 MTI  C4'  C3'   single    1.543  0.020  1.543
 MTI  C4'  H4'   single    0.970  0.020  1.090
 MTI  N4'  C1'   single    1.500  0.020  1.500
 MTI  N4'  H4'1  single    0.890  0.020  1.040
 MTI  N4'  H4'2  single    0.890  0.020  1.040
 MTI  C2'  O2'   single    1.399  0.020  1.399
 MTI  C2'  C3'   single    1.549  0.020  1.549
 MTI  C2'  C1'   single    1.521  0.020  1.521
 MTI  C2'  H1    single    0.970  0.020  1.090
 MTI  O2'  H2'   single    0.850  0.020  0.980
 MTI  C3'  O3'   single    1.398  0.020  1.398
 MTI  C3'  H3'   single    0.970  0.020  1.090
 MTI  O3'  H2    single    0.850  0.020  0.980
 MTI  C1'  C9    single    1.499  0.020  1.499
 MTI  C1'  H1'   single    0.970  0.020  1.090
 MTI  C9   C8    aromatic  1.383  0.020  1.383
 MTI  C9   C4    aromatic  1.405  0.020  1.405
 MTI  C8   N7    aromatic  1.359  0.020  1.359
 MTI  C8   H8    single    0.930  0.020  1.080
 MTI  N7   C5    aromatic  1.362  0.020  1.362
 MTI  N7   HN7   single    0.860  0.020  1.020
 MTI  C5   C6    aromatic  1.440  0.020  1.440
 MTI  C5   C4    aromatic  1.389  0.020  1.389
 MTI  C6   O6    double    1.219  0.020  1.219
 MTI  C6   N1    aromatic  1.322  0.020  1.322
 MTI  N1   C2    aromatic  1.351  0.020  1.351
 MTI  N1   HN1   single    0.860  0.020  1.020
 MTI  C2   N3    aromatic  1.276  0.020  1.276
 MTI  C2   H3    single    0.930  0.020  1.080
 MTI  N3   C4    aromatic  1.356  0.020  1.356

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
 MTI  HS3   CS   HS2   108.85  3.000
 MTI  HS3   CS   HS1   109.66  3.000
 MTI  HS2   CS   HS1   108.90  3.000
 MTI  HS3   CS   S5'   111.11  3.000
 MTI  HS2   CS   S5'   107.20  3.000
 MTI  HS1   CS   S5'   111.03  3.000
 MTI  C5'   S5'  CS    102.09  3.000
 MTI  H5'2  C5'  H5'1  107.23  3.000
 MTI  H5'2  C5'  C4'   108.72  3.000
 MTI  H5'1  C5'  C4'   110.53  3.000
 MTI  H5'2  C5'  S5'   111.46  3.000
 MTI  H5'1  C5'  S5'   109.91  3.000
 MTI  C4'   C5'  S5'   108.97  3.000
 MTI  H4'   C4'  C3'   109.43  3.000
 MTI  H4'   C4'  N4'   107.36  3.000
 MTI  C3'   C4'  N4'   104.20  3.000
 MTI  H4'   C4'  C5'   111.09  3.000
 MTI  C3'   C4'  C5'   114.22  3.000
 MTI  N4'   C4'  C5'   110.13  3.000
 MTI  H4'2  N4'  H4'1  104.73  3.000
 MTI  H4'2  N4'  C1'   111.92  3.000
 MTI  H4'1  N4'  C1'   108.09  3.000
 MTI  H4'2  N4'  C4'   112.38  3.000
 MTI  H4'1  N4'  C4'   110.32  3.000
 MTI  C1'   N4'  C4'   109.23  3.000
 MTI  H1    C2'  C1'   112.25  3.000
 MTI  H1    C2'  C3'   112.28  3.000
 MTI  C1'   C2'  C3'   101.47  3.000
 MTI  H1    C2'  O2'   112.08  3.000
 MTI  C1'   C2'  O2'   107.54  3.000
 MTI  C3'   C2'  O2'   110.66  3.000
 MTI  H2'   O2'  C2'   108.34  3.000
 MTI  H3'   C3'  O3'   111.49  3.000
 MTI  H3'   C3'  C2'   108.91  3.000
 MTI  O3'   C3'  C2'   113.58  3.000
 MTI  H3'   C3'  C4'   109.46  3.000
 MTI  O3'   C3'  C4'   108.94  3.000
 MTI  C2'   C3'  C4'   104.16  3.000
 MTI  H2    O3'  C3'   109.00  3.000
 MTI  H1'   C1'  C9    111.69  3.000
 MTI  H1'   C1'  C2'   113.77  3.000
 MTI  C9    C1'  C2'   113.44  3.000
 MTI  H1'   C1'  N4'   105.65  3.000
 MTI  C9    C1'  N4'   110.52  3.000
 MTI  C2'   C1'  N4'   100.92  3.000
 MTI  C4    C9   C8    105.44  3.000
 MTI  C4    C9   C1'   125.17  3.000
 MTI  C8    C9   C1'   129.31  3.000
 MTI  H8    C8   N7    120.47  3.000
 MTI  H8    C8   C9    130.02  3.000
 MTI  N7    C8   C9    109.49  3.000
 MTI  HN7   N7   C5    125.94  3.000
 MTI  HN7   N7   C8    124.78  3.000
 MTI  C5    N7   C8    109.28  3.000
 MTI  C4    C5   C6    121.12  3.000
 MTI  C4    C5   N7    107.03  3.000
 MTI  C6    C5   N7    131.83  3.000
 MTI  N1    C6   O6    122.94  3.000
 MTI  N1    C6   C5    108.42  3.000
 MTI  O6    C6   C5    128.60  3.000
 MTI  HN1   N1   C2    116.16  3.000
 MTI  HN1   N1   C6    115.25  3.000
 MTI  C2    N1   C6    128.59  3.000
 MTI  H3    C2   N3    120.35  3.000
 MTI  H3    C2   N1    115.22  3.000
 MTI  N3    C2   N1    124.43  3.000
 MTI  C4    N3   C2    113.17  3.000
 MTI  N3    C4   C5    124.20  3.000
 MTI  N3    C4   C9    126.97  3.000
 MTI  C5    C4   C9    108.73  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
 MTI  CONST_01  C5   N7   C8   C9      0.00   0.0  0
 MTI  CONST_02  N7   C5   C4   C9      0.00   0.0  0
 MTI  CONST_03  C6   C5   C4   C9    180.00   0.0  0
 MTI  CONST_04  C2   N3   C4   C9    180.00   0.0  0
 MTI  CONST_05  C5   C4   C9   C8      0.00   0.0  0
 MTI  CONST_06  N3   C4   C9   C8    180.00   0.0  0
 MTI  CONST_07  C6   C5   N7   C8    180.00   0.0  0
 MTI  CONST_08  C4   C5   N7   C8      0.00   0.0  0
 MTI  CONST_09  C4   C9   C8   N7      0.00   0.0  0
 MTI  CONST_10  N1   C6   C5   N7    180.00   0.0  0
 MTI  CONST_11  N3   C4   C5   N7    180.00   0.0  0
 MTI  CONST_12  C2   N1   C6   C5      0.00   0.0  0
 MTI  CONST_13  C2   N3   C4   C5      0.00   0.0  0
 MTI  CONST_14  N3   C4   C5   C6      0.00   0.0  0
 MTI  CONST_15  N3   C2   N1   C6      0.00   0.0  0
 MTI  CONST_16  C4   C5   C6   N1      0.00   0.0  0
 MTI  CONST_17  C4   N3   C2   N1      0.00   0.0  0
 MTI  CONST_18  N7   C8   C9   C1'   180.00   0.0  0
 MTI  CONST_19  C5   C4   C9   C1'   180.00   0.0  0
 MTI  CONST_20  N3   C4   C9   C1'     0.00   0.0  0
 MTI  CONST_21  O6   C6   C5   N7      0.00   0.0  0
 MTI  CONST_22  C4   C5   C6   O6    180.00   0.0  0
 MTI  CONST_23  C2   N1   C6   O6    180.00   0.0  0
 MTI  CONST_24  H8   C8   C9   C1'     0.00   0.0  0
 MTI  CONST_25  HN7  N7   C8   C9    180.00   0.0  0
 MTI  CONST_26  HN1  N1   C6   C5    180.00   0.0  0
 MTI  CONST_27  H3   C2   N1   C6    180.00   0.0  0
 MTI  Var_01    C4'  C5'  S5'  CS   -168.99  30.0  3
 MTI  Var_02    HS1  CS   S5'  C5'    57.22  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
 MTI  chir_01  C4'  C5'  N4'  C3'  negativ
 MTI  chir_02  C2'  O2'  C3'  C1'  positiv
 MTI  chir_03  C3'  O3'  C4'  C2'  positiv
 MTI  chir_04  C1'  N4'  C9   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
 MTI  plan-1  C1'  0.020
 MTI  plan-1  C9   0.020
 MTI  plan-1  C8   0.020
 MTI  plan-1  N7   0.020
 MTI  plan-1  C5   0.020
 MTI  plan-1  C6   0.020
 MTI  plan-1  O6   0.020
 MTI  plan-1  N1   0.020
 MTI  plan-1  C2   0.020
 MTI  plan-1  N3   0.020
 MTI  plan-1  C4   0.020
 MTI  plan-1  H8   0.020
 MTI  plan-1  HN7  0.020
 MTI  plan-1  HN1  0.020
 MTI  plan-1  H3   0.020

