# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 13:40:50 2022
#   Inital geometry file: a 90 line input string
#   Ligand name: (3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-[(methylsulfanyl)methyl]pyrrolidin-3-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CSC[C@H]1CN(C[C@@H]1O)Cc2c[nH]c3c(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
 TDI  TDI  (3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-[(methylsulfanyl)methyl]pyrrolidin-3-ol  ligand  39  20  .  2022-09-15  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_TDI
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
 TDI  C2    C  CR16  0   0.004   3.9716   1.4011   1.0923
 TDI  C4    C  CR56  0   0.165   2.5203  -0.2063   0.5578
 TDI  C5    C  CR56  0   0.204   3.4530  -0.7482  -0.3341
 TDI  C6    C  CR6   0   0.455   4.7035  -0.1243  -0.4610
 TDI  CS5   C  CH3   0  -0.763  -6.1385  -1.4446  -1.1627
 TDI  S     S  S2    0  -0.047  -5.2984  -0.6154   0.2039
 TDI  C5'   C  CH2   0  -0.553  -3.9297   0.1595  -0.7033
 TDI  C4'   C  CH1   0  -0.278  -3.0103   0.9163   0.2454
 TDI  C1'   C  CH2   0  -0.274  -2.2007  -0.0079   1.1619
 TDI  N1'   N  NT    0  -0.416  -0.9371  -0.1589   0.4651
 TDI  C9    C  CR5   0  -0.048   1.3541  -1.0196   0.5029
 TDI  C8    C  CR15  0  -0.044   1.6323  -2.0034  -0.4140
 TDI  N7    N  NR15  0  -0.675   2.8844  -1.8450  -0.9163
 TDI  N6    N  NH2   0  -0.827   5.6607  -0.5457  -1.3121
 TDI  N1    N  N     0  -0.472   4.9332   0.9606   0.2731
 TDI  N3    N  N     0  -0.446   2.7781   0.8952   1.2922
 TDI  C2'   C  CH2   0  -0.306  -0.6084   1.1842   0.0390
 TDI  C3'   C  CH1   0   0.060  -1.9294   1.6895  -0.5463
 TDI  O3'   O  OH1   0  -0.672  -2.1260   3.0770  -0.4186
 TDI  H2    H  HCR6  0   0.237   4.2250   2.2905   1.6615
 TDI  HS51  H  HCH3  0   0.260  -5.4787  -2.1584  -1.6540
 TDI  HS52  H  HCH3  0   0.272  -6.9894  -1.9840  -0.7504
 TDI  HS53  H  HCH3  0   0.260  -6.5037  -0.7266  -1.8958
 TDI  H5'1  H  HCH2  0   0.259  -3.3668  -0.6132  -1.2342
 TDI  H5'2  H  HCH2  0   0.270  -4.3470   0.8413  -1.4485
 TDI  H4'   H  HCH1  0   0.257  -3.6006   1.6236   0.8339
 TDI  H1'1  H  HCH2  0   0.203  -2.0680   0.4636   2.1506
 TDI  H1'2  H  HCH2  0   0.235  -2.6771  -0.9772   1.3298
 TDI  H101  H  HCH2  0   0.205   0.2997  -0.2585   2.1799
 TDI  H102  H  HCH2  0   0.242  -0.3190  -1.7880   1.5693
 TDI  H8    H  HCR5  0   0.289   1.0118  -2.8203  -0.7478
 TDI  HN7   H  HNR5  0   0.416   3.3042  -2.4538  -1.5988
 TDI  HN61  H  HNH2  0   0.400   5.6293  -1.4757  -1.6926
 TDI  HN62  H  HNH2  0   0.397   6.5810  -0.1516  -1.2081
 TDI  H2'1  H  HCH2  0   0.191  -0.3103   1.8278   0.8856
 TDI  H2'2  H  HCH2  0   0.239   0.2071   1.1890  -0.6863
 TDI  H3'   H  HCH1  0   0.215  -1.9796   1.3951  -1.6035
 TDI  H1    H  HOH1  0   0.450  -1.4811   3.5237  -0.9758
 TDI  C10   C  CH2   0  -0.365   0.0813  -0.8199   1.2559

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
 TDI  C2   N1    aromatic  1.338  0.020  1.338
 TDI  C2   N3    aromatic  1.312  0.020  1.312
 TDI  C2   H2    single    0.930  0.020  1.080
 TDI  C4   C5    aromatic  1.400  0.020  1.400
 TDI  C4   C9    aromatic  1.423  0.020  1.423
 TDI  C4   N3    aromatic  1.349  0.020  1.349
 TDI  C5   C6    aromatic  1.403  0.020  1.403
 TDI  C5   N7    aromatic  1.366  0.020  1.366
 TDI  C6   N6    single    1.348  0.020  1.348
 TDI  C6   N1    aromatic  1.330  0.020  1.330
 TDI  CS5  S     single    1.806  0.020  1.806
 TDI  CS5  HS51  single    0.970  0.020  1.090
 TDI  CS5  HS52  single    0.970  0.020  1.090
 TDI  CS5  HS53  single    0.970  0.020  1.090
 TDI  S    C5'   single    1.816  0.020  1.816
 TDI  C5'  C4'   single    1.522  0.020  1.522
 TDI  C5'  H5'1  single    0.970  0.020  1.090
 TDI  C5'  H5'2  single    0.970  0.020  1.090
 TDI  C4'  C1'   single    1.533  0.020  1.533
 TDI  C4'  C3'   single    1.547  0.020  1.547
 TDI  C4'  H4'   single    0.970  0.020  1.090
 TDI  C1'  N1'   single    1.451  0.020  1.451
 TDI  C1'  H1'1  single    0.970  0.020  1.090
 TDI  C1'  H1'2  single    0.970  0.020  1.090
 TDI  N1'  C10   single    1.449  0.020  1.449
 TDI  N1'  C2'   single    1.447  0.020  1.447
 TDI  C10  C9    single    1.492  0.020  1.492
 TDI  C10  H101  single    0.970  0.020  1.090
 TDI  C10  H102  single    0.970  0.020  1.090
 TDI  C9   C8    aromatic  1.373  0.020  1.373
 TDI  C8   N7    aromatic  1.358  0.020  1.358
 TDI  C8   H8    single    0.930  0.020  1.080
 TDI  N7   HN7   single    0.860  0.020  1.020
 TDI  N6   HN61  single    0.890  0.020  1.040
 TDI  N6   HN62  single    0.890  0.020  1.040
 TDI  C2'  C3'   single    1.531  0.020  1.531
 TDI  C2'  H2'1  single    0.970  0.020  1.090
 TDI  C2'  H2'2  single    0.970  0.020  1.090
 TDI  C3'  O3'   single    1.407  0.020  1.407
 TDI  C3'  H3'   single    0.970  0.020  1.090
 TDI  O3'  H1    single    0.850  0.020  0.980

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
 TDI  H2    C2   N3    116.63  3.000
 TDI  H2    C2   N1    115.02  3.000
 TDI  N3    C2   N1    128.35  3.000
 TDI  N3    C4   C9    130.13  3.000
 TDI  N3    C4   C5    122.40  3.000
 TDI  C9    C4   C5    107.47  3.000
 TDI  N7    C5   C6    133.59  3.000
 TDI  N7    C5   C4    107.77  3.000
 TDI  C6    C5   C4    118.64  3.000
 TDI  N1    C6   N6    118.74  3.000
 TDI  N1    C6   C5    117.82  3.000
 TDI  N6    C6   C5    123.41  3.000
 TDI  HS53  CS5  HS52  108.63  3.000
 TDI  HS53  CS5  HS51  109.36  3.000
 TDI  HS52  CS5  HS51  108.64  3.000
 TDI  HS53  CS5  S     111.27  3.000
 TDI  HS52  CS5  S     107.73  3.000
 TDI  HS51  CS5  S     111.13  3.000
 TDI  C5'   S    CS5    99.71  3.000
 TDI  H5'2  C5'  H5'1  107.83  3.000
 TDI  H5'2  C5'  C4'   110.21  3.000
 TDI  H5'1  C5'  C4'   110.05  3.000
 TDI  H5'2  C5'  S     108.61  3.000
 TDI  H5'1  C5'  S     109.21  3.000
 TDI  C4'   C5'  S     110.86  3.000
 TDI  H4'   C4'  C3'   109.24  3.000
 TDI  H4'   C4'  C1'   110.69  3.000
 TDI  C3'   C4'  C1'   103.79  3.000
 TDI  H4'   C4'  C5'   109.33  3.000
 TDI  C3'   C4'  C5'   110.58  3.000
 TDI  C1'   C4'  C5'   113.07  3.000
 TDI  H1'2  C1'  H1'1  107.08  3.000
 TDI  H1'2  C1'  N1'   111.16  3.000
 TDI  H1'1  C1'  N1'   111.72  3.000
 TDI  H1'2  C1'  C4'   113.35  3.000
 TDI  H1'1  C1'  C4'   109.98  3.000
 TDI  N1'   C1'  C4'   103.63  3.000
 TDI  C2'   N1'  C10   115.12  3.000
 TDI  C2'   N1'  C1'   104.04  3.000
 TDI  C10   N1'  C1'   113.42  3.000
 TDI  C8    C9   C10   127.27  3.000
 TDI  C8    C9   C4    105.62  3.000
 TDI  C10   C9   C4    127.10  3.000
 TDI  H8    C8   N7    120.27  3.000
 TDI  H8    C8   C9    129.24  3.000
 TDI  N7    C8   C9    110.49  3.000
 TDI  HN7   N7   C8    124.38  3.000
 TDI  HN7   N7   C5    126.97  3.000
 TDI  C8    N7   C5    108.65  3.000
 TDI  HN62  N6   HN61  115.46  3.000
 TDI  HN62  N6   C6    117.48  3.000
 TDI  HN61  N6   C6    120.39  3.000
 TDI  C6    N1   C2    118.85  3.000
 TDI  C4    N3   C2    113.95  3.000
 TDI  H2'2  C2'  H2'1  107.77  3.000
 TDI  H2'2  C2'  C3'   112.91  3.000
 TDI  H2'1  C2'  C3'   109.49  3.000
 TDI  H2'2  C2'  N1'   111.69  3.000
 TDI  H2'1  C2'  N1'   112.12  3.000
 TDI  C3'   C2'  N1'   102.88  3.000
 TDI  H3'   C3'  O3'   110.19  3.000
 TDI  H3'   C3'  C2'   108.60  3.000
 TDI  O3'   C3'  C2'   114.29  3.000
 TDI  H3'   C3'  C4'   109.07  3.000
 TDI  O3'   C3'  C4'   110.41  3.000
 TDI  C2'   C3'  C4'   104.03  3.000
 TDI  H1    O3'  C3'   108.15  3.000
 TDI  H102  C10  H101  106.44  3.000
 TDI  H102  C10  C9    109.78  3.000
 TDI  H101  C10  C9    108.78  3.000
 TDI  H102  C10  N1'   107.64  3.000
 TDI  H101  C10  N1'   111.36  3.000
 TDI  C9    C10  N1'   112.65  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
 TDI  CONST_01  C5    C6   N1   C2      0.00   0.0  0
 TDI  CONST_02  C5    C4   N3   C2      0.00   0.0  0
 TDI  CONST_03  C9    C4   N3   C2    180.00   0.0  0
 TDI  CONST_04  N1    C6   C5   C4      0.00   0.0  0
 TDI  CONST_05  C8    N7   C5   C4      0.00   0.0  0
 TDI  CONST_06  N7    C8   C9   C4      0.00   0.0  0
 TDI  CONST_07  N1    C2   N3   C4      0.00   0.0  0
 TDI  CONST_08  C8    C9   C4   C5      0.00   0.0  0
 TDI  CONST_09  C9    C8   N7   C5      0.00   0.0  0
 TDI  CONST_10  C9    C4   C5   C6    180.00   0.0  0
 TDI  CONST_11  N3    C4   C5   C6      0.00   0.0  0
 TDI  CONST_12  C8    N7   C5   C6    180.00   0.0  0
 TDI  CONST_13  N3    C2   N1   C6      0.00   0.0  0
 TDI  CONST_14  N7    C5   C4   C9      0.00   0.0  0
 TDI  CONST_15  N3    C4   C9   C8    180.00   0.0  0
 TDI  CONST_16  N3    C4   C5   N7    180.00   0.0  0
 TDI  CONST_17  N1    C6   C5   N7    180.00   0.0  0
 TDI  CONST_18  N6    C6   N1   C2    180.00   0.0  0
 TDI  CONST_19  N6    C6   C5   C4    180.00   0.0  0
 TDI  CONST_20  C10   C9   C4   C5    180.00   0.0  0
 TDI  CONST_21  N3    C4   C9   C10     0.00   0.0  0
 TDI  CONST_22  N7    C8   C9   C10   180.00   0.0  0
 TDI  CONST_23  N6    C6   C5   N7      0.00   0.0  0
 TDI  CONST_24  HN7   N7   C5   C4    180.00   0.0  0
 TDI  CONST_25  H8    C8   C9   C4    180.00   0.0  0
 TDI  CONST_26  H2    C2   N3   C4    180.00   0.0  0
 TDI  CONST_28  HN62  N6   C6   C5    180.00   0.0  0
 TDI  Var_01    C2'   N1'  C1'  C4'    44.46  30.0  1
 TDI  Var_02    C3'   C2'  N1'  C1'   -46.04  30.0  1
 TDI  Var_03    N1'   C10  C9   C4     98.13  30.0  1
 TDI  Var_04    C9    C10  N1'  C1'   177.50  30.0  3
 TDI  Var_05    C4'   C5'  S    CS5  -178.35  30.0  3
 TDI  Var_06    HS51  CS5  S    C5'    59.76  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
 TDI  chir_01  C4'  C5'  C1'  C3'  negativ
 TDI  chir_02  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
 TDI  plan-1  C2    0.020
 TDI  plan-1  C4    0.020
 TDI  plan-1  C5    0.020
 TDI  plan-1  C6    0.020
 TDI  plan-1  C9    0.020
 TDI  plan-1  C8    0.020
 TDI  plan-1  N7    0.020
 TDI  plan-1  N6    0.020
 TDI  plan-1  N1    0.020
 TDI  plan-1  N3    0.020
 TDI  plan-1  H2    0.020
 TDI  plan-1  H8    0.020
 TDI  plan-1  HN7   0.020
 TDI  plan-1  C10   0.020
 TDI  plan-2  C6    0.020
 TDI  plan-2  N6    0.020
 TDI  plan-2  HN61  0.020
 TDI  plan-2  HN62  0.020

