# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 00:39:19 2020
#   Inital geometry file: a 125 line input string
#   Ligand name: 7-({4-[(3R)-3-aminopyrrolidin-1-yl]-5-chloro-6-ethyl-7H-pyrrolo[2,3-d]pyrimidin-2-yl}sulfanyl)-1,5-naphthyridin-1(4H)-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1[nH]c2nc(Sc3cnc4CC=CN(O)c4c3)nc(N5CC[C@@H](N)C5)c2c1Cl
#
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
 HTT  HTT  7-({4-[(3R)-3-aminopyrrolidin-1-yl]-5-chloro-6-ethyl-7H-pyrrolo[2,3-d]pyrimidin-2-yl}sulfanyl)-1,5-naphthyridin-1(4H)-ol  ligand  52  30  .  2021-08-11  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_HTT
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
 HTT  CL8  CL  CL    0  -0.153   4.2169   2.3615   0.6288
 HTT  C4   C   CR5   0  -0.316   2.6152   1.9243   0.1815
 HTT  C5   C   CR5   0   0.426   1.7040   2.8751  -0.1807
 HTT  C6   C   CH2   0  -0.511   1.8670   4.3407  -0.3757
 HTT  C7   C   CH3   0  -0.654   2.2358   4.7004  -1.8158
 HTT  N1   N   NR15  0  -0.710   0.5110   2.2404  -0.4076
 HTT  C3   C   CR56  0   0.061   1.9693   0.6392   0.1778
 HTT  C9   C   CR6   0   0.491   2.2238  -0.7416   0.4291
 HTT  N13  N   NT    0  -0.493   3.4155  -1.3101   0.6612
 HTT  C17  C   CH2   0  -0.277   3.5101  -2.7401   0.9653
 HTT  C16  C   CH2   0  -0.488   5.0104  -2.9778   1.0640
 HTT  C15  C   CH1   0  -0.144   5.5860  -1.9732   0.0616
 HTT  N18  N   NH2   0  -0.788   5.4827  -2.3601  -1.3370
 HTT  C14  C   CH2   0  -0.277   4.7229  -0.7465   0.3440
 HTT  N10  N   N     0  -0.501   1.1821  -1.5851   0.4377
 HTT  C11  C   CR6   0   0.213  -0.0243  -1.1503   0.1186
 HTT  N12  N   N     0  -0.433  -0.3853   0.0572  -0.2303
 HTT  C2   C   CR56  0   0.457   0.6329   0.9184  -0.1728
 HTT  S19  S   S2    0   0.059  -1.2294  -2.4490   0.1742
 HTT  C20  C   CR6   0  -0.200  -2.7228  -1.5796  -0.1854
 HTT  C25  C   CR16  0  -0.082  -3.1956  -1.5105  -1.4860
 HTT  N24  N   N     0  -0.414  -4.3308  -0.8986  -1.7923
 HTT  C23  C   CR66  0   0.166  -5.0550  -0.3347  -0.8390
 HTT  C26  C   C     0  -0.481  -6.3582   0.3053  -1.2328
 HTT  C27  C   CR16  0  -0.359  -6.7875   1.3075  -0.2052
 HTT  C28  C   CR16  0  -0.037  -6.3418   1.2502   1.0458
 HTT  N29  N   NR6   0  -0.301  -5.4441   0.2672   1.4618
 HTT  O30  O   OH1   0  -0.543  -4.8189   0.5332   2.6582
 HTT  C22  C   CR66  0   0.295  -4.6458  -0.3483   0.5060
 HTT  C21  C   CR16  0  -0.184  -3.4561  -0.9867   0.8309
 HTT  H1   H   HCH2  0   0.259   0.9426   4.8484  -0.0915
 HTT  H2   H   HCH2  0   0.254   2.6391   4.7063   0.3021
 HTT  H3   H   HCH3  0   0.238   2.3421   5.7797  -1.9244
 HTT  H4   H   HCH3  0   0.230   3.1795   4.2373  -2.1032
 HTT  H5   H   HCH3  0   0.230   1.4701   4.3671  -2.5166
 HTT  H6   H   HNR5  0   0.416  -0.3512   2.6974  -0.6612
 HTT  H7   H   HCH2  0   0.255   2.9768  -2.9844   1.8842
 HTT  H8   H   HCH2  0   0.235   3.0601  -3.3351   0.1660
 HTT  H9   H   HCH2  0   0.240   5.3694  -2.7502   2.0707
 HTT  H10  H   HCH2  0   0.255   5.2802  -4.0091   0.8366
 HTT  H11  H   HCH1  0   0.255   6.6333  -1.7512   0.2728
 HTT  H12  H   HNH2  0   0.350   6.0227  -3.2023  -1.4940
 HTT  H13  H   HNH2  0   0.344   4.5257  -2.6002  -1.5706
 HTT  H15  H   HCH2  0   0.251   4.6732  -0.0873  -0.5216
 HTT  H16  H   HCH2  0   0.248   5.1278  -0.1863   1.1881
 HTT  H17  H   HCR6  0   0.270  -2.6398  -1.9604  -2.3008
 HTT  H18  H   H     0   0.263  -6.2490   0.7687  -2.2152
 HTT  H19  H   HCR6  0   0.261  -7.5028   2.0721  -0.4725
 HTT  H20  H   HCR6  0   0.289  -6.6587   1.9323   1.8218
 HTT  H21  H   HOH1  0   0.483  -5.1932  -0.0957   3.2885
 HTT  H22  H   HCR6  0   0.288  -3.1009  -1.0256   1.8508
 HTT  H14  H   H     0   0.266  -7.1230  -0.4729  -1.3549

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
 HTT  C27  C26  single    1.498  0.020  1.498
 HTT  C27  C28  double    1.329  0.020  1.329
 HTT  C26  C23  single    1.504  0.020  1.504
 HTT  C28  N29  single    1.395  0.020  1.395
 HTT  C23  N24  aromatic  1.323  0.020  1.323
 HTT  C23  C22  aromatic  1.406  0.020  1.406
 HTT  N24  C25  aromatic  1.326  0.020  1.326
 HTT  N29  C22  single    1.389  0.020  1.389
 HTT  N29  O30  single    1.376  0.020  1.376
 HTT  C22  C21  aromatic  1.389  0.020  1.389
 HTT  C25  C20  aromatic  1.386  0.020  1.386
 HTT  C21  C20  aromatic  1.386  0.020  1.386
 HTT  C20  S19  single    1.765  0.020  1.765
 HTT  N18  C15  single    1.455  0.020  1.455
 HTT  S19  C11  single    1.773  0.020  1.773
 HTT  C16  C15  single    1.531  0.020  1.531
 HTT  C16  C17  single    1.522  0.020  1.522
 HTT  C15  C14  single    1.526  0.020  1.526
 HTT  C17  N13  single    1.465  0.020  1.465
 HTT  C11  N10  aromatic  1.322  0.020  1.322
 HTT  C11  N12  aromatic  1.308  0.020  1.308
 HTT  N10  C9   aromatic  1.340  0.020  1.340
 HTT  N13  C9   single    1.341  0.020  1.341
 HTT  N13  C14  single    1.459  0.020  1.459
 HTT  N12  C2   aromatic  1.335  0.020  1.335
 HTT  C9   C3   aromatic  1.426  0.020  1.426
 HTT  C2   C3   aromatic  1.410  0.020  1.410
 HTT  C2   N1   aromatic  1.348  0.020  1.348
 HTT  C3   C4   aromatic  1.438  0.020  1.438
 HTT  N1   C5   aromatic  1.370  0.020  1.370
 HTT  C4   C5   aromatic  1.366  0.020  1.366
 HTT  C4   CL8  single    1.719  0.020  1.719
 HTT  C5   C6   single    1.487  0.020  1.487
 HTT  C6   C7   single    1.530  0.020  1.530
 HTT  C6   H1   single    0.970  0.020  1.090
 HTT  C6   H2   single    0.970  0.020  1.090
 HTT  C7   H3   single    0.970  0.020  1.090
 HTT  C7   H4   single    0.970  0.020  1.090
 HTT  C7   H5   single    0.970  0.020  1.090
 HTT  N1   H6   single    0.860  0.020  1.020
 HTT  C17  H7   single    0.970  0.020  1.090
 HTT  C17  H8   single    0.970  0.020  1.090
 HTT  C16  H9   single    0.970  0.020  1.090
 HTT  C16  H10  single    0.970  0.020  1.090
 HTT  C15  H11  single    0.970  0.020  1.090
 HTT  N18  H12  single    0.890  0.020  1.040
 HTT  N18  H13  single    0.890  0.020  1.040
 HTT  C14  H15  single    0.970  0.020  1.090
 HTT  C14  H16  single    0.970  0.020  1.090
 HTT  C25  H17  single    0.930  0.020  1.080
 HTT  C26  H18  single    0.970  0.020  1.090
 HTT  C27  H19  single    0.930  0.020  1.080
 HTT  C28  H20  single    0.930  0.020  1.080
 HTT  O30  H21  single    0.850  0.020  0.980
 HTT  C21  H22  single    0.930  0.020  1.080
 HTT  C26  H14  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
 HTT  C3   C4   C5   108.77  3.000
 HTT  C5   C4   CL8  120.89  3.000
 HTT  C3   C4   CL8  130.25  3.000
 HTT  N1   C5   C6   122.01  3.000
 HTT  C6   C5   C4   130.36  3.000
 HTT  N1   C5   C4   107.60  3.000
 HTT  H2   C6   H1   106.36  3.000
 HTT  H2   C6   C7   109.61  3.000
 HTT  H1   C6   C7   109.86  3.000
 HTT  H2   C6   C5   109.06  3.000
 HTT  H1   C6   C5   109.34  3.000
 HTT  C7   C6   C5   112.43  3.000
 HTT  H5   C7   H4   107.99  3.000
 HTT  H5   C7   H3   107.89  3.000
 HTT  H4   C7   H3   108.07  3.000
 HTT  H5   C7   C6   111.35  3.000
 HTT  H4   C7   C6   110.92  3.000
 HTT  H3   C7   C6   110.50  3.000
 HTT  H6   N1   C2   124.44  3.000
 HTT  H6   N1   C5   125.19  3.000
 HTT  C2   N1   C5   110.28  3.000
 HTT  C2   C3   C9   113.87  3.000
 HTT  C2   C3   C4   104.44  3.000
 HTT  C9   C3   C4   141.66  3.000
 HTT  N10  C9   N13  115.02  3.000
 HTT  N13  C9   C3   126.84  3.000
 HTT  N10  C9   C3   118.14  3.000
 HTT  C14  N13  C17  111.37  3.000
 HTT  C14  N13  C9   126.54  3.000
 HTT  C17  N13  C9   120.48  3.000
 HTT  H8   C17  H7   107.04  3.000
 HTT  H8   C17  C16  111.59  3.000
 HTT  H7   C17  C16  113.11  3.000
 HTT  H8   C17  N13  110.66  3.000
 HTT  H7   C17  N13  111.23  3.000
 HTT  C16  C17  N13  103.27  3.000
 HTT  H10  C16  H9   107.93  3.000
 HTT  H10  C16  C15  113.03  3.000
 HTT  H9   C16  C15  110.05  3.000
 HTT  H10  C16  C17  112.22  3.000
 HTT  H9   C16  C17  110.54  3.000
 HTT  C15  C16  C17  103.04  3.000
 HTT  H11  C15  C14  110.09  3.000
 HTT  H11  C15  N18  107.96  3.000
 HTT  C14  C15  N18  110.58  3.000
 HTT  H11  C15  C16  111.56  3.000
 HTT  C14  C15  C16  101.17  3.000
 HTT  N18  C15  C16  115.35  3.000
 HTT  H13  N18  H12  105.70  3.000
 HTT  H13  N18  C15  110.57  3.000
 HTT  H12  N18  C15  109.41  3.000
 HTT  H16  C14  H15  108.72  3.000
 HTT  H16  C14  C15  110.24  3.000
 HTT  H15  C14  C15  111.42  3.000
 HTT  H16  C14  N13  111.28  3.000
 HTT  H15  C14  N13  111.45  3.000
 HTT  C15  C14  N13  103.68  3.000
 HTT  C11  N10  C9   120.05  3.000
 HTT  S19  C11  N12  119.82  3.000
 HTT  N12  C11  N10  128.34  3.000
 HTT  S19  C11  N10  111.84  3.000
 HTT  C2   N12  C11  111.95  3.000
 HTT  N12  C2   C3   127.31  3.000
 HTT  C3   C2   N1   108.86  3.000
 HTT  N12  C2   N1   123.79  3.000
 HTT  C20  S19  C11  102.00  3.000
 HTT  C21  C20  C25  119.10  3.000
 HTT  C21  C20  S19  120.59  3.000
 HTT  C25  C20  S19  120.29  3.000
 HTT  H17  C25  N24  117.19  3.000
 HTT  H17  C25  C20  120.66  3.000
 HTT  N24  C25  C20  122.15  3.000
 HTT  C23  N24  C25  119.93  3.000
 HTT  C22  C23  C26  120.44  3.000
 HTT  C22  C23  N24  121.72  3.000
 HTT  C26  C23  N24  117.83  3.000
 HTT  H14  C26  H18  105.69  3.000
 HTT  H14  C26  C27  110.54  3.000
 HTT  H18  C26  C27  111.22  3.000
 HTT  H14  C26  C23  109.33  3.000
 HTT  H18  C26  C23  109.24  3.000
 HTT  C27  C26  C23  110.69  3.000
 HTT  H19  C27  C28  119.03  3.000
 HTT  H19  C27  C26  119.56  3.000
 HTT  C28  C27  C26  121.37  3.000
 HTT  H20  C28  N29  114.80  3.000
 HTT  H20  C28  C27  123.38  3.000
 HTT  N29  C28  C27  121.80  3.000
 HTT  C22  N29  O30  115.01  3.000
 HTT  O30  N29  C28  114.55  3.000
 HTT  C22  N29  C28  118.49  3.000
 HTT  H21  O30  N29  105.39  3.000
 HTT  C21  C22  N29  122.35  3.000
 HTT  C21  C22  C23  118.53  3.000
 HTT  N29  C22  C23  119.12  3.000
 HTT  H22  C21  C22  121.26  3.000
 HTT  H22  C21  C20  120.17  3.000
 HTT  C22  C21  C20  118.57  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
 HTT  CONST_01  N10  C9   C3   C4    180.00   0.0  0
 HTT  CONST_02  N12  C2   C3   C4    180.00   0.0  0
 HTT  CONST_03  N1   C2   C3   C4      0.00   0.0  0
 HTT  CONST_04  C2   N1   C5   C4      0.00   0.0  0
 HTT  CONST_05  N12  C2   N1   C5    180.00   0.0  0
 HTT  CONST_06  C3   C2   N1   C5      0.00   0.0  0
 HTT  CONST_07  C9   C3   C4   C5    180.00   0.0  0
 HTT  CONST_08  C2   C3   C4   C5      0.00   0.0  0
 HTT  CONST_09  C11  N12  C2   N1    180.00   0.0  0
 HTT  CONST_10  C9   C3   C2   N1    180.00   0.0  0
 HTT  CONST_11  C3   C4   C5   N1      0.00   0.0  0
 HTT  CONST_12  C11  N10  C9   C3      0.00   0.0  0
 HTT  CONST_13  C11  N12  C2   C3      0.00   0.0  0
 HTT  CONST_14  N12  C11  N10  C9      0.00   0.0  0
 HTT  CONST_15  N12  C2   C3   C9      0.00   0.0  0
 HTT  CONST_16  C2   N12  C11  N10     0.00   0.0  0
 HTT  CONST_17  C2   C3   C9   N10     0.00   0.0  0
 HTT  CONST_18  C23  N24  C25  C20     0.00   0.0  0
 HTT  CONST_19  C23  C22  C21  C20     0.00   0.0  0
 HTT  CONST_20  C22  C23  N24  C25     0.00   0.0  0
 HTT  CONST_21  C22  C21  C20  C25     0.00   0.0  0
 HTT  CONST_22  C21  C22  C23  N24     0.00   0.0  0
 HTT  CONST_23  C21  C20  C25  N24     0.00   0.0  0
 HTT  CONST_24  N13  C9   C3   C4      0.00   0.0  0
 HTT  CONST_25  C11  N10  C9   N13   180.00   0.0  0
 HTT  CONST_26  C2   C3   C9   N13   180.00   0.0  0
 HTT  CONST_27  C9   C3   C4   CL8     0.00   0.0  0
 HTT  CONST_28  C2   C3   C4   CL8   180.00   0.0  0
 HTT  CONST_29  N1   C5   C4   CL8   180.00   0.0  0
 HTT  CONST_30  C2   N1   C5   C6    180.00   0.0  0
 HTT  CONST_31  C3   C4   C5   C6    180.00   0.0  0
 HTT  CONST_32  S19  C11  N10  C9    180.00   0.0  0
 HTT  CONST_33  S19  C11  N12  C2    180.00   0.0  0
 HTT  CONST_34  N24  C25  C20  S19   180.00   0.0  0
 HTT  CONST_35  C22  C21  C20  S19   180.00   0.0  0
 HTT  CONST_36  H6   N1   C5   C4    180.00   0.0  0
 HTT  CONST_37  H22  C21  C20  C25   180.00   0.0  0
 HTT  CONST_38  H17  C25  N24  C23   180.00   0.0  0
 HTT  Var_01    C17  N13  C9   C3    177.15  30.0  1
 HTT  Var_02    C16  C17  N13  C9    176.42  30.0  1
 HTT  Var_03    C15  C14  N13  C9   -149.21  30.0  1
 HTT  Var_04    C15  C16  C17  N13   -32.05  30.0  1
 HTT  Var_05    C27  C26  C23  N24  -158.74  30.0  1
 HTT  Var_06    C28  C27  C26  C23   -22.29  30.0  1
 HTT  Var_07    C28  N29  C22  C23   -22.06  30.0  1
 HTT  Var_08    N29  C28  C27  C26     0.70  30.0  1
 HTT  Var_09    C22  N29  C28  C27    23.12  30.0  1
 HTT  Var_10    C25  C20  S19  C11    94.15  30.0  3
 HTT  Var_11    C7   C6   C5   C4     90.45  30.0  2
 HTT  Var_12    H3   C7   C6   C5    179.70  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
 HTT  chir_01  C15  N18  C16  C14  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
 HTT  plan-1  CL8  0.020
 HTT  plan-1  C4   0.020
 HTT  plan-1  C5   0.020
 HTT  plan-1  C6   0.020
 HTT  plan-1  N1   0.020
 HTT  plan-1  C3   0.020
 HTT  plan-1  C9   0.020
 HTT  plan-1  N13  0.020
 HTT  plan-1  N10  0.020
 HTT  plan-1  C11  0.020
 HTT  plan-1  N12  0.020
 HTT  plan-1  C2   0.020
 HTT  plan-1  S19  0.020
 HTT  plan-1  H6   0.020
 HTT  plan-2  S19  0.020
 HTT  plan-2  C20  0.020
 HTT  plan-2  C25  0.020
 HTT  plan-2  N24  0.020
 HTT  plan-2  C23  0.020
 HTT  plan-2  C26  0.020
 HTT  plan-2  N29  0.020
 HTT  plan-2  C22  0.020
 HTT  plan-2  C21  0.020
 HTT  plan-2  H17  0.020
 HTT  plan-2  H22  0.020
 HTT  plan-3  C28  0.020
 HTT  plan-3  N29  0.020
 HTT  plan-3  O30  0.020
 HTT  plan-3  C22  0.020

