# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr  3 13:25:51 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: (3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-{[(4-chlorophenyl)sulfanyl]methyl}pyrrolidin-3-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2c(CN3C[C@H](O)[C@@H](CSc4ccc(Cl)cc4)C3)c[nH]c12
#
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
 4CT  4CT  (3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-{[(4-chlorophenyl)sulfanyl]methyl}pyrrolidin-3-ol  ligand  46  26  .  2022-07-23  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_4CT
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
 4CT  N1    N   N     0  -0.470   7.0167  -1.3218   0.6300
 4CT  CL1   CL  CL    0  -0.126  -8.8202   0.5639  -0.3319
 4CT  C2    C   CR16  0   0.006   5.8491  -1.9707   0.5618
 4CT  N3    N   N     0  -0.445   4.7197  -1.5613   0.0349
 4CT  C4    C   CR56  0   0.159   4.7837  -0.3270  -0.5045
 4CT  C5    C   CR56  0   0.205   5.9578   0.4344  -0.4987
 4CT  C6    C   CR6   0   0.454   7.1058  -0.1042   0.1029
 4CT  N6    N   NH2   0  -0.826   8.2942   0.5325   0.1368
 4CT  N7    N   NR15  0  -0.676   5.6953   1.6153  -1.1329
 4CT  C8    C   CR15  0  -0.051   4.3972   1.6102  -1.5358
 4CT  C9    C   CR5   0  -0.040   3.7856   0.4363  -1.1740
 4CT  C1'   C   CH2   0  -0.263   0.2331  -0.4507  -0.3983
 4CT  N1'   N   NT    0  -0.414   1.5755   0.0581  -0.2074
 4CT  C10   C   CH2   0  -0.368   2.3702   0.0390  -1.4171
 4CT  C11   C   CR6   0  -0.050  -7.1591   0.0868  -0.2120
 4CT  C13   C   CR16  0  -0.199  -6.8356  -1.1183   0.3903
 4CT  C14   C   CR16  0  -0.265  -5.5023  -1.4855   0.4975
 4CT  C2'   C   CH2   0  -0.298   1.3763   1.3748   0.3615
 4CT  C3'   C   CH1   0   0.052   0.2998   1.1572   1.4246
 4CT  O3'   O   OH1   0  -0.674   0.8182   0.8313   2.6951
 4CT  C4'   C   CH1   0  -0.287  -0.4922  -0.0593   0.8943
 4CT  C5'   C   CH2   0  -0.569  -1.9620   0.2657   0.6928
 4CT  S6'   S   S2    0   0.014  -2.8232  -1.2225   0.0882
 4CT  C7'   C   CR6   0  -0.101  -4.4975  -0.6674  -0.0125
 4CT  C8'   C   CR16  0  -0.241  -4.8449   0.5317  -0.6311
 4CT  C9'   C   CR16  0  -0.198  -6.1724   0.9188  -0.7199
 4CT  H2    H   HCR6  0   0.237   5.8479  -2.9613   1.0067
 4CT  HN6   H   HNH2  0   0.397   9.0056   0.1534   0.7400
 4CT  HN6A  H   HNH2  0   0.400   8.3399   1.5263  -0.0091
 4CT  HN7   H   HNR5  0   0.416   6.3453   2.3613  -1.3162
 4CT  H8    H   HCR5  0   0.290   3.9853   2.4576  -2.0614
 4CT  H1'A  H   HCH2  0   0.244   0.2419  -1.5281  -0.5778
 4CT  H10   H   HCH2  0   0.206   1.9335   0.6923  -2.1925
 4CT  H10A  H   HCH2  0   0.240   2.3424  -0.9780  -1.8188
 4CT  H13   H   HCR6  0   0.284  -7.6083  -1.7625   0.7875
 4CT  H14   H   HCR6  0   0.277  -5.2477  -2.4151   0.9897
 4CT  H2'   H   HCH2  0   0.244   2.2988   1.7919   0.7707
 4CT  H2'A  H   HCH2  0   0.190   1.0000   2.0886  -0.3935
 4CT  H3'   H   HCH1  0   0.221  -0.3416   2.0452   1.4902
 4CT  HO3'  H   HOH1  0   0.450   1.2381   1.6178   3.0570
 4CT  H4'   H   HCH1  0   0.267  -0.4002  -0.8653   1.6273
 4CT  H5'   H   HCH2  0   0.289  -2.4250   0.5779   1.6296
 4CT  H5'A  H   HCH2  0   0.268  -2.0692   1.0725  -0.0340
 4CT  H8'   H   HCR6  0   0.275  -4.0849   1.1754  -1.0544
 4CT  H9'   H   HCR6  0   0.285  -6.4330   1.8548  -1.1946
 4CT  H1'   H   HCH2  0   0.194  -0.2648   0.0199  -1.2667

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
 4CT  N1   C2    aromatic  1.338  0.020  1.338
 4CT  N1   C6    aromatic  1.330  0.020  1.330
 4CT  CL1  C11   single    1.732  0.020  1.732
 4CT  C2   N3    aromatic  1.312  0.020  1.312
 4CT  N3   C4    aromatic  1.349  0.020  1.349
 4CT  C4   C5    aromatic  1.399  0.020  1.399
 4CT  C4   C9    aromatic  1.424  0.020  1.424
 4CT  C5   C6    aromatic  1.403  0.020  1.403
 4CT  C5   N7    aromatic  1.366  0.020  1.366
 4CT  C6   N6    single    1.349  0.020  1.349
 4CT  N7   C8    aromatic  1.359  0.020  1.359
 4CT  C8   C9    aromatic  1.372  0.020  1.372
 4CT  C9   C10   single    1.490  0.020  1.490
 4CT  C1'  N1'   single    1.448  0.020  1.448
 4CT  C1'  C4'   single    1.533  0.020  1.533
 4CT  N1'  C10   single    1.448  0.020  1.448
 4CT  N1'  C2'   single    1.448  0.020  1.448
 4CT  C11  C13   aromatic  1.385  0.020  1.385
 4CT  C11  C9'   aromatic  1.387  0.020  1.387
 4CT  C13  C14   aromatic  1.387  0.020  1.387
 4CT  C14  C7'   aromatic  1.392  0.020  1.392
 4CT  C2'  C3'   single    1.528  0.020  1.528
 4CT  C3'  O3'   single    1.410  0.020  1.410
 4CT  C3'  C4'   single    1.545  0.020  1.545
 4CT  C4'  C5'   single    1.519  0.020  1.519
 4CT  C5'  S6'   single    1.823  0.020  1.823
 4CT  S6'  C7'   single    1.767  0.020  1.767
 4CT  C7'  C8'   aromatic  1.393  0.020  1.393
 4CT  C8'  C9'   aromatic  1.386  0.020  1.386
 4CT  C2   H2    single    0.930  0.020  1.080
 4CT  N6   HN6   single    0.890  0.020  1.040
 4CT  N6   HN6A  single    0.890  0.020  1.040
 4CT  N7   HN7   single    0.860  0.020  1.020
 4CT  C8   H8    single    0.930  0.020  1.080
 4CT  C1'  H1'   single    0.970  0.020  1.090
 4CT  C1'  H1'A  single    0.970  0.020  1.090
 4CT  C10  H10   single    0.970  0.020  1.090
 4CT  C10  H10A  single    0.970  0.020  1.090
 4CT  C13  H13   single    0.930  0.020  1.080
 4CT  C14  H14   single    0.930  0.020  1.080
 4CT  C2'  H2'   single    0.970  0.020  1.090
 4CT  C2'  H2'A  single    0.970  0.020  1.090
 4CT  C3'  H3'   single    0.970  0.020  1.090
 4CT  O3'  HO3'  single    0.850  0.020  0.980
 4CT  C4'  H4'   single    0.970  0.020  1.090
 4CT  C5'  H5'   single    0.970  0.020  1.090
 4CT  C5'  H5'A  single    0.970  0.020  1.090
 4CT  C8'  H8'   single    0.930  0.020  1.080
 4CT  C9'  H9'   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
 4CT  C6    N1   C2   118.85  3.000
 4CT  H2    C2   N3   116.63  3.000
 4CT  H2    C2   N1   115.00  3.000
 4CT  N3    C2   N1   128.36  3.000
 4CT  C4    N3   C2   113.92  3.000
 4CT  C9    C4   C5   107.36  3.000
 4CT  C9    C4   N3   130.21  3.000
 4CT  C5    C4   N3   122.42  3.000
 4CT  N7    C5   C6   133.47  3.000
 4CT  N7    C5   C4   107.89  3.000
 4CT  C6    C5   C4   118.63  3.000
 4CT  N6    C6   C5   123.39  3.000
 4CT  N6    C6   N1   118.77  3.000
 4CT  C5    C6   N1   117.81  3.000
 4CT  HN6A  N6   HN6  115.27  3.000
 4CT  HN6A  N6   C6   120.20  3.000
 4CT  HN6   N6   C6   117.38  3.000
 4CT  HN7   N7   C8   124.45  3.000
 4CT  HN7   N7   C5   126.97  3.000
 4CT  C8    N7   C5   108.54  3.000
 4CT  H8    C8   C9   129.07  3.000
 4CT  H8    C8   N7   120.40  3.000
 4CT  C9    C8   N7   110.53  3.000
 4CT  C10   C9   C8   127.47  3.000
 4CT  C10   C9   C4   126.85  3.000
 4CT  C8    C9   C4   105.68  3.000
 4CT  H1'A  C1'  H1'  107.12  3.000
 4CT  H1'A  C1'  C4'  113.21  3.000
 4CT  H1'   C1'  C4'  109.90  3.000
 4CT  H1'A  C1'  N1'  111.14  3.000
 4CT  H1'   C1'  N1'  111.80  3.000
 4CT  C4'   C1'  N1'  103.75  3.000
 4CT  C2'   N1'  C10  114.57  3.000
 4CT  C2'   N1'  C1'  104.11  3.000
 4CT  C10   N1'  C1'  113.21  3.000
 4CT  H10A  C10  H10  106.39  3.000
 4CT  H10A  C10  N1'  107.77  3.000
 4CT  H10   C10  N1'  111.22  3.000
 4CT  H10A  C10  C9   109.39  3.000
 4CT  H10   C10  C9   109.43  3.000
 4CT  N1'   C10  C9   112.44  3.000
 4CT  C9'   C11  C13  120.99  3.000
 4CT  C9'   C11  CL1  119.44  3.000
 4CT  C13   C11  CL1  119.57  3.000
 4CT  H13   C13  C14  120.04  3.000
 4CT  H13   C13  C11  120.72  3.000
 4CT  C14   C13  C11  119.23  3.000
 4CT  H14   C14  C7'  120.10  3.000
 4CT  H14   C14  C13  119.25  3.000
 4CT  C7'   C14  C13  120.65  3.000
 4CT  H2'A  C2'  H2'  107.28  3.000
 4CT  H2'A  C2'  C3'  109.11  3.000
 4CT  H2'   C2'  C3'  112.88  3.000
 4CT  H2'A  C2'  N1'  111.45  3.000
 4CT  H2'   C2'  N1'  112.23  3.000
 4CT  C3'   C2'  N1'  103.92  3.000
 4CT  H3'   C3'  C4'  110.98  3.000
 4CT  H3'   C3'  O3'  110.36  3.000
 4CT  C4'   C3'  O3'  108.40  3.000
 4CT  H3'   C3'  C2'  109.76  3.000
 4CT  C4'   C3'  C2'  103.56  3.000
 4CT  O3'   C3'  C2'  113.61  3.000
 4CT  HO3'  O3'  C3'  108.08  3.000
 4CT  H4'   C4'  C5'  109.16  3.000
 4CT  H4'   C4'  C3'  107.88  3.000
 4CT  C5'   C4'  C3'  111.90  3.000
 4CT  H4'   C4'  C1'  109.72  3.000
 4CT  C5'   C4'  C1'  113.62  3.000
 4CT  C3'   C4'  C1'  104.35  3.000
 4CT  H5'A  C5'  H5'  108.59  3.000
 4CT  H5'A  C5'  S6'  109.66  3.000
 4CT  H5'   C5'  S6'  108.55  3.000
 4CT  H5'A  C5'  C4'  109.98  3.000
 4CT  H5'   C5'  C4'  110.98  3.000
 4CT  S6'   C5'  C4'  109.06  3.000
 4CT  C7'   S6'  C5'  102.13  3.000
 4CT  C8'   C7'  S6'  122.14  3.000
 4CT  C8'   C7'  C14  119.23  3.000
 4CT  S6'   C7'  C14  118.58  3.000
 4CT  H8'   C8'  C9'  118.79  3.000
 4CT  H8'   C8'  C7'  120.69  3.000
 4CT  C9'   C8'  C7'  120.51  3.000
 4CT  H9'   C9'  C8'  120.05  3.000
 4CT  H9'   C9'  C11  120.57  3.000
 4CT  C8'   C9'  C11  119.37  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
 4CT  CONST_01  C4   N3   C2   N1      0.00   0.0  0
 4CT  CONST_02  C4   C5   C6   N1      0.00   0.0  0
 4CT  CONST_03  N7   C5   C6   N1    180.00   0.0  0
 4CT  CONST_04  C5   C6   N1   C2      0.00   0.0  0
 4CT  CONST_05  C5   C4   N3   C2      0.00   0.0  0
 4CT  CONST_06  C9   C4   N3   C2    180.00   0.0  0
 4CT  CONST_07  C6   N1   C2   N3      0.00   0.0  0
 4CT  CONST_08  C6   C5   C4   N3      0.00   0.0  0
 4CT  CONST_09  N7   C5   C4   N3    180.00   0.0  0
 4CT  CONST_10  C8   C9   C4   N3    180.00   0.0  0
 4CT  CONST_11  C8   N7   C5   C4      0.00   0.0  0
 4CT  CONST_12  N7   C8   C9   C4      0.00   0.0  0
 4CT  CONST_13  C8   C9   C4   C5      0.00   0.0  0
 4CT  CONST_14  C9   C8   N7   C5      0.00   0.0  0
 4CT  CONST_15  C9   C4   C5   C6    180.00   0.0  0
 4CT  CONST_16  C8   N7   C5   C6    180.00   0.0  0
 4CT  CONST_17  C9   C4   C5   N7      0.00   0.0  0
 4CT  CONST_18  C7'  C14  C13  C11     0.00   0.0  0
 4CT  CONST_19  C7'  C8'  C9'  C11     0.00   0.0  0
 4CT  CONST_20  C8'  C9'  C11  C13     0.00   0.0  0
 4CT  CONST_21  C8'  C7'  C14  C13     0.00   0.0  0
 4CT  CONST_22  C9'  C11  C13  C14     0.00   0.0  0
 4CT  CONST_23  C9'  C8'  C7'  C14     0.00   0.0  0
 4CT  CONST_24  C14  C13  C11  CL1   180.00   0.0  0
 4CT  CONST_25  C8'  C9'  C11  CL1   180.00   0.0  0
 4CT  CONST_26  N6   C6   N1   C2    180.00   0.0  0
 4CT  CONST_27  C10  C9   C4   N3      0.00   0.0  0
 4CT  CONST_28  N6   C6   C5   C4    180.00   0.0  0
 4CT  CONST_29  C10  C9   C4   C5    180.00   0.0  0
 4CT  CONST_30  N7   C5   C6   N6      0.00   0.0  0
 4CT  CONST_31  C10  C9   C8   N7    180.00   0.0  0
 4CT  CONST_32  S6'  C7'  C14  C13   180.00   0.0  0
 4CT  CONST_33  C9'  C8'  C7'  S6'   180.00   0.0  0
 4CT  CONST_34  H2   C2   N3   C4    180.00   0.0  0
 4CT  CONST_35  HN7  N7   C5   C4    180.00   0.0  0
 4CT  CONST_36  H8   C8   C9   C4    180.00   0.0  0
 4CT  CONST_37  H14  C14  C13  C11   180.00   0.0  0
 4CT  CONST_38  H8'  C8'  C9'  C11   180.00   0.0  0
 4CT  CONST_39  H9'  C9'  C11  C13   180.00   0.0  0
 4CT  CONST_40  H13  C13  C14  C7'   180.00   0.0  0
 4CT  CONST_41  HN6  N6   C6   N1      0.00   0.0  0
 4CT  Var_01    C3'  C2'  N1'  C1'    44.64  30.0  1
 4CT  Var_02    C4'  C1'  N1'  C2'   -43.23  30.0  1
 4CT  Var_03    N1'  C10  C9   C4     71.89  30.0  2
 4CT  Var_04    C1'  N1'  C10  C9   -174.26  30.0  1
 4CT  Var_05    C8'  C7'  S6'  C5'    48.42  30.0  2
 4CT  Var_06    H5'  C5'  S6'  C7'    56.61  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
 4CT  chir_01  C3'  C2'  O3'  C4'  positiv
 4CT  chir_02  C4'  C1'  C3'  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
 4CT  plan-1  CL1   0.020
 4CT  plan-1  C11   0.020
 4CT  plan-1  C13   0.020
 4CT  plan-1  C14   0.020
 4CT  plan-1  S6'   0.020
 4CT  plan-1  C7'   0.020
 4CT  plan-1  C8'   0.020
 4CT  plan-1  C9'   0.020
 4CT  plan-1  H13   0.020
 4CT  plan-1  H14   0.020
 4CT  plan-1  H8'   0.020
 4CT  plan-1  H9'   0.020
 4CT  plan-2  N1    0.020
 4CT  plan-2  C2    0.020
 4CT  plan-2  N3    0.020
 4CT  plan-2  C4    0.020
 4CT  plan-2  C5    0.020
 4CT  plan-2  C6    0.020
 4CT  plan-2  N6    0.020
 4CT  plan-2  N7    0.020
 4CT  plan-2  C8    0.020
 4CT  plan-2  C9    0.020
 4CT  plan-2  C10   0.020
 4CT  plan-2  H2    0.020
 4CT  plan-2  HN7   0.020
 4CT  plan-2  H8    0.020
 4CT  plan-3  C6    0.020
 4CT  plan-3  N6    0.020
 4CT  plan-3  HN6   0.020
 4CT  plan-3  HN6A  0.020

