# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 23:13:07 2020
#   Inital geometry file: a 132 line input string
#   Ligand name: N-[(1S)-1-(3-chloro-4-fluorophenyl)-2-hydroxyethyl]-2-(tetrahydro-2H-pyran-4-ylamino)-5,8-dihydropyrido[3,4-d]pyrimidine-7(6H)-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H](NC(=O)N1CCc2cnc(NC3CCOCC3)nc2C1)c4ccc(F)c(Cl)c4
#
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
 2SH  2SH  N-[(1S)-1-(3-chloro-4-fluorophenyl)-2-hydroxyethyl]-2-(tetrahydro-2H-pyran-4-ylamino)-5,8-dihydropyrido[3,4-d]pyrimidine-7(6H)-carboxamide  ligand  56  31  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_2SH
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
 2SH  C4   C   CR6   0  -0.212  -6.2027  -1.1337  -0.5430
 2SH  C5   C   CR16  0  -0.271  -5.4872   0.0038  -0.2031
 2SH  C6   C   CR6   0   0.082  -4.1875  -0.0957   0.2793
 2SH  C7   C   CH1   0  -0.138  -3.4552   1.1648   0.6729
 2SH  C15  C   CH2   0  -0.330   0.5462   3.4250  -0.9627
 2SH  C17  C   CR6   0  -0.042   2.5046   2.3089   0.0252
 2SH  C20  C   CR6   0   0.587   3.9236   0.0247  -0.0268
 2SH  C22  C   CR6   0   0.244   1.9549   1.0981  -0.3857
 2SH  C26  C   CH2   0  -0.469   6.3805  -2.6753   0.6014
 2SH  C1   C   CR16  0  -0.269  -3.6143  -1.3596   0.4110
 2SH  C2   C   CR16  0  -0.403  -4.3210  -2.4996   0.0609
 2SH  C3   C   CR6   0   0.599  -5.6123  -2.3778  -0.4101
 2SH  C9   C   CH2   0  -0.146  -3.4235   1.3330   2.1905
 2SH  O10  O   OH1   0  -0.660  -2.7099   0.2734   2.7727
 2SH  N11  N   NH1   0  -0.704  -2.1224   1.1577   0.0928
 2SH  C12  C   C     0   0.754  -1.4271   2.3253  -0.0479
 2SH  O13  O   O     0  -0.538  -1.8789   3.3976   0.3398
 2SH  N14  N   NT    0  -0.509  -0.2038   2.2257  -0.6439
 2SH  C16  C   CH2   0  -0.487   1.7120   3.5825  -0.0014
 2SH  C18  C   CR16  0  -0.042   3.8370   2.2390   0.4057
 2SH  N19  N   N     0  -0.461   4.5524   1.1289   0.3908
 2SH  N21  N   N     0  -0.488   2.6481  -0.0280  -0.4213
 2SH  C23  C   CH2   0  -0.352   0.5170   0.9869  -0.8254
 2SH  C25  C   CH1   0  -0.060   6.0302  -1.2431   0.2150
 2SH  C27  C   CH2   0  -0.184   7.8826  -2.8150   0.7974
 2SH  O28  O   O2    0  -0.483   8.6078  -2.4142  -0.3437
 2SH  C29  C   CH2   0  -0.186   8.3572  -1.0667  -0.6810
 2SH  C30  C   CH2   0  -0.457   6.8866  -0.8202  -0.9795
 2SH  CL1  CL  CL    0  -0.093  -7.8153  -1.0186  -1.1393
 2SH  F32  F   F     0  -0.294  -6.3044  -3.4687  -0.7449
 2SH  H1   H   HCR6  0   0.286  -5.9520   0.9743  -0.3228
 2SH  H2   H   HCH1  0   0.267  -4.0234   2.0177   0.2873
 2SH  H3   H   HCH2  0   0.251   0.9210   3.3379  -1.9874
 2SH  H4   H   HCH2  0   0.270  -0.1118   4.2878  -0.9301
 2SH  H6   H   HCH2  0   0.230   6.0500  -3.3619  -0.1854
 2SH  H7   H   HCR6  0   0.273  -2.6076  -1.4730   0.7880
 2SH  H8   H   HCR6  0   0.291  -3.8762  -3.4810   0.1613
 2SH  H9   H   HCH2  0   0.215  -2.9744   2.3033   2.4270
 2SH  H10  H   HCH2  0   0.207  -4.4647   1.3700   2.5363
 2SH  H11  H   HOH1  0   0.458  -2.7562   0.3724   3.7276
 2SH  H12  H   HNH1  0   0.406  -1.9382   0.4217  -0.5693
 2SH  H13  H   HCH2  0   0.252   2.3434   4.4168  -0.3153
 2SH  H14  H   HCH2  0   0.251   1.3330   3.8295   0.9946
 2SH  H15  H   HCR6  0   0.262   4.3527   3.1385   0.7317
 2SH  H16  H   HCH2  0   0.271   0.4954   0.6553  -1.8704
 2SH  H17  H   HCH2  0   0.275   0.0661   0.1920  -0.2316
 2SH  H19  H   HCH1  0   0.240   6.2684  -0.5880   1.0579
 2SH  H20  H   HCH2  0   0.199   8.1939  -2.2268   1.6735
 2SH  H21  H   HCH2  0   0.240   8.1444  -3.8554   0.9948
 2SH  H22  H   HCH2  0   0.198   8.6808  -0.4033   0.1355
 2SH  H23  H   HCH2  0   0.238   8.9730  -0.8347  -1.5514
 2SH  H24  H   HCH2  0   0.224   6.5827  -1.3897  -1.8637
 2SH  H25  H   HCH2  0   0.242   6.7338   0.2380  -1.2030
 2SH  N24  N   NH1   0  -0.670   4.6115  -1.1357  -0.0369
 2SH  H5   H   HCH2  0   0.248   5.8666  -2.9623   1.5217
 2SH  H18  H   HNH1  0   0.385   4.1499  -1.9175  -0.4749

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
 2SH  O28  C29  single    1.411  0.020  1.411
 2SH  O28  C27  single    1.410  0.020  1.410
 2SH  C29  C30  single    1.521  0.020  1.521
 2SH  C27  C26  single    1.521  0.020  1.521
 2SH  O10  C9   single    1.404  0.020  1.404
 2SH  C30  C25  single    1.529  0.020  1.529
 2SH  C9   C7   single    1.527  0.020  1.527
 2SH  C26  C25  single    1.524  0.020  1.524
 2SH  C25  N24  single    1.445  0.020  1.445
 2SH  CL1  C4   single    1.723  0.020  1.723
 2SH  C7   C6   single    1.510  0.020  1.510
 2SH  C7   N11  single    1.454  0.020  1.454
 2SH  C5   C6   aromatic  1.390  0.020  1.390
 2SH  C5   C4   aromatic  1.386  0.020  1.386
 2SH  C6   C1   aromatic  1.394  0.020  1.394
 2SH  N24  C20  single    1.349  0.020  1.349
 2SH  C4   C3   aromatic  1.383  0.020  1.383
 2SH  N11  C12  single    1.366  0.020  1.366
 2SH  N21  C20  aromatic  1.336  0.020  1.336
 2SH  N21  C22  aromatic  1.323  0.020  1.323
 2SH  C20  N19  aromatic  1.338  0.020  1.338
 2SH  C1   C2   aromatic  1.386  0.020  1.386
 2SH  C23  C22  single    1.508  0.020  1.508
 2SH  C23  N14  single    1.445  0.020  1.445
 2SH  C3   C2   aromatic  1.380  0.020  1.380
 2SH  C3   F32  single    1.335  0.020  1.335
 2SH  C22  C17  aromatic  1.392  0.020  1.392
 2SH  C12  N14  single    1.364  0.020  1.364
 2SH  C12  O13  double    1.227  0.020  1.227
 2SH  N14  C15  single    1.450  0.020  1.450
 2SH  N19  C18  aromatic  1.321  0.020  1.321
 2SH  C17  C18  aromatic  1.387  0.020  1.387
 2SH  C17  C16  single    1.500  0.020  1.500
 2SH  C15  C16  single    1.519  0.020  1.519
 2SH  C5   H1   single    0.930  0.020  1.080
 2SH  C7   H2   single    0.970  0.020  1.090
 2SH  C15  H3   single    0.970  0.020  1.090
 2SH  C15  H4   single    0.970  0.020  1.090
 2SH  C26  H5   single    0.970  0.020  1.090
 2SH  C26  H6   single    0.970  0.020  1.090
 2SH  C1   H7   single    0.930  0.020  1.080
 2SH  C2   H8   single    0.930  0.020  1.080
 2SH  C9   H9   single    0.970  0.020  1.090
 2SH  C9   H10  single    0.970  0.020  1.090
 2SH  O10  H11  single    0.850  0.020  0.980
 2SH  N11  H12  single    0.890  0.020  1.040
 2SH  C16  H13  single    0.970  0.020  1.090
 2SH  C16  H14  single    0.970  0.020  1.090
 2SH  C18  H15  single    0.930  0.020  1.080
 2SH  C23  H16  single    0.970  0.020  1.090
 2SH  C23  H17  single    0.970  0.020  1.090
 2SH  N24  H18  single    0.860  0.020  1.020
 2SH  C25  H19  single    0.970  0.020  1.090
 2SH  C27  H20  single    0.970  0.020  1.090
 2SH  C27  H21  single    0.970  0.020  1.090
 2SH  C29  H22  single    0.970  0.020  1.090
 2SH  C29  H23  single    0.970  0.020  1.090
 2SH  C30  H24  single    0.970  0.020  1.090
 2SH  C30  H25  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
 2SH  CL1  C4   C3   119.52  3.000
 2SH  C3   C4   C5   119.61  3.000
 2SH  CL1  C4   C5   120.87  3.000
 2SH  H1   C5   C6   120.26  3.000
 2SH  H1   C5   C4   119.14  3.000
 2SH  C6   C5   C4   120.60  3.000
 2SH  C1   C6   C7   122.20  3.000
 2SH  C1   C6   C5   118.82  3.000
 2SH  C7   C6   C5   118.97  3.000
 2SH  H2   C7   N11  109.82  3.000
 2SH  H2   C7   C9   105.96  3.000
 2SH  N11  C7   C9   112.22  3.000
 2SH  H2   C7   C6   107.86  3.000
 2SH  N11  C7   C6   109.67  3.000
 2SH  C9   C7   C6   111.16  3.000
 2SH  H4   C15  H3   107.39  3.000
 2SH  H4   C15  C16  111.33  3.000
 2SH  H3   C15  C16  109.75  3.000
 2SH  H4   C15  N14  109.71  3.000
 2SH  H3   C15  N14  108.49  3.000
 2SH  C16  C15  N14  110.09  3.000
 2SH  C18  C17  C16  123.71  3.000
 2SH  C16  C17  C22  121.64  3.000
 2SH  C18  C17  C22  114.61  3.000
 2SH  N24  C20  N21  116.79  3.000
 2SH  N21  C20  N19  125.00  3.000
 2SH  N24  C20  N19  118.21  3.000
 2SH  C23  C22  N21  115.41  3.000
 2SH  C23  C22  C17  121.80  3.000
 2SH  N21  C22  C17  122.79  3.000
 2SH  H6   C26  H5   107.37  3.000
 2SH  H6   C26  C27  109.44  3.000
 2SH  H5   C26  C27  109.38  3.000
 2SH  H6   C26  C25  109.73  3.000
 2SH  H5   C26  C25  110.63  3.000
 2SH  C27  C26  C25  110.23  3.000
 2SH  H7   C1   C2   118.46  3.000
 2SH  H7   C1   C6   120.73  3.000
 2SH  C2   C1   C6   120.81  3.000
 2SH  H8   C2   C3   119.76  3.000
 2SH  H8   C2   C1   120.85  3.000
 2SH  C3   C2   C1   119.38  3.000
 2SH  F32  C3   C2   119.92  3.000
 2SH  F32  C3   C4   119.31  3.000
 2SH  C2   C3   C4   120.77  3.000
 2SH  H10  C9   H9   106.92  3.000
 2SH  H10  C9   O10  112.14  3.000
 2SH  H9   C9   O10  111.76  3.000
 2SH  H10  C9   C7   107.28  3.000
 2SH  H9   C9   C7   108.71  3.000
 2SH  O10  C9   C7   109.85  3.000
 2SH  H11  O10  C9   108.05  3.000
 2SH  H12  N11  C12  117.64  3.000
 2SH  H12  N11  C7   115.70  3.000
 2SH  C12  N11  C7   120.23  3.000
 2SH  N14  C12  O13  122.15  3.000
 2SH  O13  C12  N11  121.81  3.000
 2SH  N14  C12  N11  116.04  3.000
 2SH  C23  N14  C12  124.39  3.000
 2SH  C12  N14  C15  119.97  3.000
 2SH  C23  N14  C15  115.06  3.000
 2SH  H14  C16  H13  106.82  3.000
 2SH  H14  C16  C17  111.01  3.000
 2SH  H13  C16  C17  110.37  3.000
 2SH  H14  C16  C15  109.49  3.000
 2SH  H13  C16  C15  109.93  3.000
 2SH  C17  C16  C15  109.18  3.000
 2SH  H15  C18  N19  116.23  3.000
 2SH  H15  C18  C17  119.75  3.000
 2SH  N19  C18  C17  124.01  3.000
 2SH  C18  N19  C20  116.28  3.000
 2SH  C22  N21  C20  117.30  3.000
 2SH  H17  C23  H16  106.89  3.000
 2SH  H17  C23  N14  110.52  3.000
 2SH  H16  C23  N14  111.67  3.000
 2SH  H17  C23  C22  106.83  3.000
 2SH  H16  C23  C22  108.61  3.000
 2SH  N14  C23  C22  112.08  3.000
 2SH  H19  C25  C30  108.32  3.000
 2SH  H19  C25  N24  107.67  3.000
 2SH  C30  C25  N24  113.15  3.000
 2SH  H19  C25  C26  108.50  3.000
 2SH  N24  C25  C26  109.86  3.000
 2SH  C30  C25  C26  109.22  3.000
 2SH  H21  C27  H20  107.33  3.000
 2SH  H21  C27  O28  107.10  3.000
 2SH  H20  C27  O28  110.29  3.000
 2SH  H21  C27  C26  110.36  3.000
 2SH  H20  C27  C26  109.45  3.000
 2SH  O28  C27  C26  112.18  3.000
 2SH  C29  O28  C27  111.92  3.000
 2SH  H23  C29  H22  107.31  3.000
 2SH  H23  C29  C30  110.78  3.000
 2SH  H22  C29  C30  109.41  3.000
 2SH  H23  C29  O28  107.06  3.000
 2SH  H22  C29  O28  110.24  3.000
 2SH  C30  C29  O28  111.93  3.000
 2SH  H25  C30  H24  107.45  3.000
 2SH  H25  C30  C29  109.42  3.000
 2SH  H24  C30  C29  110.04  3.000
 2SH  H25  C30  C25  110.45  3.000
 2SH  H24  C30  C25  109.36  3.000
 2SH  C29  C30  C25  110.08  3.000
 2SH  H18  N24  C25  117.89  3.000
 2SH  H18  N24  C20  115.90  3.000
 2SH  C25  N24  C20  124.29  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
 2SH  CONST_01  C1   C6   C5   C4     0.00   0.0  0
 2SH  CONST_02  C1   C2   C3   C4     0.00   0.0  0
 2SH  CONST_03  C2   C1   C6   C5     0.00   0.0  0
 2SH  CONST_04  C2   C3   C4   C5     0.00   0.0  0
 2SH  CONST_05  C3   C4   C5   C6     0.00   0.0  0
 2SH  CONST_06  C3   C2   C1   C6     0.00   0.0  0
 2SH  CONST_07  C20  N21  C22  C17    0.00   0.0  0
 2SH  CONST_08  C20  N19  C18  C17    0.00   0.0  0
 2SH  CONST_09  N19  C20  N21  C22    0.00   0.0  0
 2SH  CONST_10  N19  C18  C17  C22    0.00   0.0  0
 2SH  CONST_11  N21  C20  N19  C18    0.00   0.0  0
 2SH  CONST_12  N21  C22  C17  C18    0.00   0.0  0
 2SH  CONST_13  C7   C6   C5   C4   180.00   0.0  0
 2SH  CONST_14  F32  C3   C4   C5   180.00   0.0  0
 2SH  CONST_15  CL1  C4   C5   C6   180.00   0.0  0
 2SH  CONST_16  C2   C1   C6   C7   180.00   0.0  0
 2SH  CONST_17  N24  C20  N21  C22  180.00   0.0  0
 2SH  CONST_18  F32  C3   C2   C1   180.00   0.0  0
 2SH  CONST_19  CL1  C4   C3   C2   180.00   0.0  0
 2SH  CONST_20  N24  C20  N19  C18  180.00   0.0  0
 2SH  CONST_21  C25  N24  C20  N19    0.00   0.0  0
 2SH  CONST_22  C25  N24  C20  N21  180.00   0.0  0
 2SH  CONST_23  H8   C2   C3   C4   180.00   0.0  0
 2SH  CONST_24  H7   C1   C6   C5   180.00   0.0  0
 2SH  CONST_25  H15  C18  N19  C20  180.00   0.0  0
 2SH  CONST_26  H1   C5   C6   C1   180.00   0.0  0
 2SH  CONST_27  O13  C12  N14  C15    0.00   0.0  0
 2SH  CONST_29  N11  C12  N14  C15  180.00   0.0  0
 2SH  CONST_31  H18  N24  C20  N19  180.00   0.0  0
 2SH  CONST_32  N14  C12  N11  C7   180.00   0.0  0
 2SH  CONST_34  O13  C12  N11  C7     0.00   0.0  0
 2SH  Var_01    C22  C23  N14  C15   39.32  30.0  1
 2SH  Var_02    C22  C17  C16  C15  -20.63  30.0  1
 2SH  Var_03    N14  C23  C22  C17   -5.37  30.0  1
 2SH  Var_04    N14  C15  C16  C17   52.04  30.0  1
 2SH  Var_05    C23  N14  C15  C16  -64.97  30.0  1
 2SH  Var_06    O28  C29  C30  C25   56.62  30.0  1
 2SH  Var_07    O28  C27  C26  C25  -56.10  30.0  1
 2SH  Var_08    C30  C29  O28  C27  -59.88  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
 2SH  chir_01  C7   C9   C6   N11  positiv
 2SH  chir_02  C25  C30  C26  N24  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
 2SH  plan-1  C4   0.020
 2SH  plan-1  C5   0.020
 2SH  plan-1  C6   0.020
 2SH  plan-1  C7   0.020
 2SH  plan-1  C1   0.020
 2SH  plan-1  C2   0.020
 2SH  plan-1  C3   0.020
 2SH  plan-1  CL1  0.020
 2SH  plan-1  F32  0.020
 2SH  plan-1  H1   0.020
 2SH  plan-1  H7   0.020
 2SH  plan-1  H8   0.020
 2SH  plan-2  C7   0.020
 2SH  plan-2  C15  0.020
 2SH  plan-2  N11  0.020
 2SH  plan-2  C12  0.020
 2SH  plan-2  O13  0.020
 2SH  plan-2  N14  0.020
 2SH  plan-2  C23  0.020
 2SH  plan-2  H12  0.020
 2SH  plan-3  C20  0.020
 2SH  plan-3  C25  0.020
 2SH  plan-3  N24  0.020
 2SH  plan-3  H18  0.020
 2SH  plan-4  C17  0.020
 2SH  plan-4  C20  0.020
 2SH  plan-4  C22  0.020
 2SH  plan-4  C16  0.020
 2SH  plan-4  C18  0.020
 2SH  plan-4  N19  0.020
 2SH  plan-4  N21  0.020
 2SH  plan-4  C23  0.020
 2SH  plan-4  H15  0.020
 2SH  plan-4  N24  0.020

