# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 18:30:49 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: Nalpha-[5-chloro-6-methyl-2-(pyridin-2-yl)pyrimidin-4-yl]-D-phenylalaninamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1nc(nc(N[C@H](Cc2ccccc2)C(N)=O)c1Cl)c3ccccn3
#
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
 SHX  SHX  Nalpha-[5-chloro-6-methyl-2-(pyridin-2-yl)pyrimidin-4-yl]-D-phenylalaninamide  ligand  44  26  .  2022-07-22  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_SHX
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
 SHX  CL   CL  CL    0  -0.109   1.0936   3.2471   0.1116
 SHX  C8   C   CR6   0  -0.254  -0.2327   2.1426   0.1272
 SHX  C7   C   CR6   0   0.331  -1.5170   2.5622   0.4073
 SHX  C19  C   CH3   0  -0.738  -1.8348   3.9891   0.7117
 SHX  N2   N   N     0  -0.480  -2.5249   1.6840   0.4140
 SHX  C6   C   CR6   0   0.360  -2.2399   0.4185   0.1528
 SHX  C5   C   CR6   0   0.141  -3.3759  -0.5426   0.1588
 SHX  C4   C   CR16  0  -0.296  -4.6829  -0.0877   0.3156
 SHX  C3   C   CR16  0  -0.153  -5.7151  -1.0119   0.3005
 SHX  C2   C   CR16  0  -0.312  -5.4092  -2.3530   0.1337
 SHX  C1   C   CR16  0  -0.086  -4.0734  -2.7057  -0.0087
 SHX  N1   N   N     0  -0.391  -3.0810  -1.8299   0.0013
 SHX  N3   N   N     0  -0.460  -1.0427  -0.0668  -0.1219
 SHX  C9   C   CR6   0   0.655  -0.0173   0.7790  -0.1493
 SHX  N4   N   NH1   0  -0.673   1.1897   0.2744  -0.4355
 SHX  C10  C   CH1   0  -0.163   1.3732  -1.1252  -0.7127
 SHX  C11  C   C     0   0.524   0.5830  -1.5412  -1.9574
 SHX  N5   N   NH2   0  -0.792   0.0391  -2.7636  -1.8892
 SHX  O    O   O     0  -0.483   0.5507  -0.8318  -2.9485
 SHX  C12  C   CH2   0  -0.563   2.8618  -1.4103  -0.9482
 SHX  C13  C   CR6   0   0.138   3.7007  -1.0580   0.2498
 SHX  C18  C   CR16  0  -0.299   3.6563  -1.8477   1.3979
 SHX  C17  C   CR16  0  -0.238   4.3986  -1.5109   2.5196
 SHX  C16  C   CR16  0  -0.269   5.2005  -0.3752   2.5111
 SHX  C15  C   CR16  0  -0.238   5.2542   0.4167   1.3733
 SHX  C14  C   CR16  0  -0.329   4.5088   0.0753   0.2508
 SHX  H1   H   HCH3  0   0.263  -1.5833   4.6362  -0.1299
 SHX  H2   H   HCH3  0   0.262  -2.8946   4.0965   0.9274
 SHX  H3   H   HCH3  0   0.262  -1.2647   4.3449   1.5707
 SHX  H4   H   HCR6  0   0.272  -4.8797   0.9666   0.4443
 SHX  H5   H   HCR6  0   0.275  -6.7408  -0.6881   0.4173
 SHX  H6   H   HCR6  0   0.274  -6.1800  -3.1108   0.1147
 SHX  H7   H   HCR6  0   0.261  -3.7962  -3.7465  -0.1364
 SHX  H8   H   HNH1  0   0.396   1.9752   0.8982  -0.5186
 SHX  H9   H   HCH1  0   0.278   1.0334  -1.7105   0.1477
 SHX  H10  H   HNH2  0   0.404  -0.1086  -3.2059  -0.9980
 SHX  H11  H   HNH2  0   0.399  -0.5387  -3.0899  -2.6472
 SHX  H12  H   HCH2  0   0.283   2.9679  -2.4706  -1.1858
 SHX  H13  H   HCH2  0   0.273   3.2009  -0.8524  -1.8246
 SHX  H14  H   HCR6  0   0.251   3.0343  -2.7357   1.4137
 SHX  H15  H   HCR6  0   0.257   4.3530  -2.1364   3.4019
 SHX  H16  H   HCR6  0   0.256   5.7817  -0.1125   3.3855
 SHX  H17  H   HCR6  0   0.257   5.8775   1.3014   1.3556
 SHX  H18  H   HCR6  0   0.256   4.5652   0.6958  -0.6369

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
 SHX  C1   C2   aromatic  1.389  0.020  1.389
 SHX  C1   N1   aromatic  1.324  0.020  1.324
 SHX  C2   C3   aromatic  1.386  0.020  1.386
 SHX  N1   C5   aromatic  1.330  0.020  1.330
 SHX  C3   C4   aromatic  1.386  0.020  1.386
 SHX  C5   C4   aromatic  1.393  0.020  1.393
 SHX  C5   C6   single    1.488  0.020  1.488
 SHX  N2   C6   aromatic  1.323  0.020  1.323
 SHX  N2   C7   aromatic  1.337  0.020  1.337
 SHX  C6   N3   aromatic  1.321  0.020  1.321
 SHX  C19  C7   single    1.493  0.020  1.493
 SHX  C7   C8   aromatic  1.380  0.020  1.380
 SHX  C16  C15  aromatic  1.387  0.020  1.387
 SHX  C16  C17  aromatic  1.390  0.020  1.390
 SHX  C15  C14  aromatic  1.390  0.020  1.390
 SHX  N3   C9   aromatic  1.329  0.020  1.329
 SHX  C17  C18  aromatic  1.387  0.020  1.387
 SHX  C8   C9   aromatic  1.408  0.020  1.408
 SHX  C8   CL   single    1.726  0.020  1.726
 SHX  C14  C13  aromatic  1.392  0.020  1.392
 SHX  C9   N4   single    1.339  0.020  1.339
 SHX  C18  C13  aromatic  1.394  0.020  1.394
 SHX  C13  C12  single    1.504  0.020  1.504
 SHX  N4   C10  single    1.439  0.020  1.439
 SHX  C10  C12  single    1.534  0.020  1.534
 SHX  C10  C11  single    1.532  0.020  1.532
 SHX  C11  O    double    1.219  0.020  1.219
 SHX  C11  N5   single    1.340  0.020  1.340
 SHX  C19  H1   single    0.970  0.020  1.090
 SHX  C19  H2   single    0.970  0.020  1.090
 SHX  C19  H3   single    0.970  0.020  1.090
 SHX  C4   H4   single    0.930  0.020  1.080
 SHX  C3   H5   single    0.930  0.020  1.080
 SHX  C2   H6   single    0.930  0.020  1.080
 SHX  C1   H7   single    0.930  0.020  1.080
 SHX  N4   H8   single    0.860  0.020  1.020
 SHX  C10  H9   single    0.970  0.020  1.090
 SHX  N5   H10  single    0.890  0.020  1.040
 SHX  N5   H11  single    0.890  0.020  1.040
 SHX  C12  H12  single    0.970  0.020  1.090
 SHX  C12  H13  single    0.970  0.020  1.090
 SHX  C18  H14  single    0.930  0.020  1.080
 SHX  C17  H15  single    0.930  0.020  1.080
 SHX  C16  H16  single    0.930  0.020  1.080
 SHX  C15  H17  single    0.930  0.020  1.080
 SHX  C14  H18  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
 SHX  C9   C8   C7   118.47  3.000
 SHX  C9   C8   CL   120.03  3.000
 SHX  C7   C8   CL   121.50  3.000
 SHX  N2   C7   C19  117.79  3.000
 SHX  C19  C7   C8   122.01  3.000
 SHX  N2   C7   C8   120.20  3.000
 SHX  H3   C19  H2   108.73  3.000
 SHX  H3   C19  H1   107.07  3.000
 SHX  H2   C19  H1   108.62  3.000
 SHX  H3   C19  C7   111.17  3.000
 SHX  H2   C19  C7   110.03  3.000
 SHX  H1   C19  C7   111.13  3.000
 SHX  C6   N2   C7   117.70  3.000
 SHX  N3   C6   C5   117.10  3.000
 SHX  N3   C6   N2   126.00  3.000
 SHX  C5   C6   N2   116.90  3.000
 SHX  N1   C5   C4   122.51  3.000
 SHX  C4   C5   C6   120.39  3.000
 SHX  N1   C5   C6   117.09  3.000
 SHX  H4   C4   C3   121.11  3.000
 SHX  H4   C4   C5   120.21  3.000
 SHX  C3   C4   C5   118.68  3.000
 SHX  H5   C3   C2   120.79  3.000
 SHX  H5   C3   C4   120.36  3.000
 SHX  C2   C3   C4   118.85  3.000
 SHX  H6   C2   C1   120.39  3.000
 SHX  H6   C2   C3   121.55  3.000
 SHX  C1   C2   C3   118.06  3.000
 SHX  H7   C1   N1   116.37  3.000
 SHX  H7   C1   C2   120.10  3.000
 SHX  N1   C1   C2   123.52  3.000
 SHX  C1   N1   C5   118.37  3.000
 SHX  C9   N3   C6   118.01  3.000
 SHX  N4   C9   N3   117.38  3.000
 SHX  N4   C9   C8   123.01  3.000
 SHX  N3   C9   C8   119.61  3.000
 SHX  H8   N4   C10  119.18  3.000
 SHX  H8   N4   C9   119.17  3.000
 SHX  C10  N4   C9   121.52  3.000
 SHX  H9   C10  C12  108.82  3.000
 SHX  H9   C10  C11  109.48  3.000
 SHX  C12  C10  C11  108.99  3.000
 SHX  H9   C10  N4   109.22  3.000
 SHX  C11  C10  N4   110.79  3.000
 SHX  C12  C10  N4   109.52  3.000
 SHX  O    C11  N5   124.16  3.000
 SHX  N5   C11  C10  114.57  3.000
 SHX  O    C11  C10  121.08  3.000
 SHX  H11  N5   H10  116.10  3.000
 SHX  H11  N5   C11  119.35  3.000
 SHX  H10  N5   C11  120.39  3.000
 SHX  H13  C12  H12  106.92  3.000
 SHX  H13  C12  C13  110.25  3.000
 SHX  H12  C12  C13  110.27  3.000
 SHX  H13  C12  C10  109.23  3.000
 SHX  H12  C12  C10  107.95  3.000
 SHX  C13  C12  C10  112.05  3.000
 SHX  C14  C13  C18  118.63  3.000
 SHX  C18  C13  C12  120.36  3.000
 SHX  C14  C13  C12  120.99  3.000
 SHX  H14  C18  C17  119.61  3.000
 SHX  H14  C18  C13  119.62  3.000
 SHX  C17  C18  C13  120.77  3.000
 SHX  H15  C17  C16  120.09  3.000
 SHX  H15  C17  C18  119.77  3.000
 SHX  C16  C17  C18  120.14  3.000
 SHX  H16  C16  C15  120.21  3.000
 SHX  H16  C16  C17  120.20  3.000
 SHX  C15  C16  C17  119.59  3.000
 SHX  H17  C15  C14  119.76  3.000
 SHX  H17  C15  C16  120.16  3.000
 SHX  C14  C15  C16  120.08  3.000
 SHX  H18  C14  C15  119.51  3.000
 SHX  H18  C14  C13  119.70  3.000
 SHX  C15  C14  C13  120.79  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
 SHX  CONST_01  C6   N2   C7   C8      0.00   0.0  0
 SHX  CONST_02  C6   N3   C9   C8      0.00   0.0  0
 SHX  CONST_03  C5   C6   N2   C7    180.00   0.0  0
 SHX  CONST_04  N3   C6   N2   C7      0.00   0.0  0
 SHX  CONST_05  N3   C9   C8   C7      0.00   0.0  0
 SHX  CONST_06  N1   C5   C6   N2    180.00   0.0  0
 SHX  CONST_07  C4   C5   C6   N2      0.00   0.0  0
 SHX  CONST_08  C9   N3   C6   N2      0.00   0.0  0
 SHX  CONST_09  C9   C8   C7   N2      0.00   0.0  0
 SHX  CONST_10  C1   N1   C5   C6    180.00   0.0  0
 SHX  CONST_11  C3   C4   C5   C6    180.00   0.0  0
 SHX  CONST_12  C2   C1   N1   C5      0.00   0.0  0
 SHX  CONST_13  C2   C3   C4   C5      0.00   0.0  0
 SHX  CONST_14  C9   N3   C6   C5    180.00   0.0  0
 SHX  CONST_15  C1   C2   C3   C4      0.00   0.0  0
 SHX  CONST_16  C1   N1   C5   C4      0.00   0.0  0
 SHX  CONST_17  N3   C6   C5   C4    180.00   0.0  0
 SHX  CONST_18  N1   C1   C2   C3      0.00   0.0  0
 SHX  CONST_19  N1   C5   C4   C3      0.00   0.0  0
 SHX  CONST_20  N3   C6   C5   N1      0.00   0.0  0
 SHX  CONST_21  C16  C15  C14  C13     0.00   0.0  0
 SHX  CONST_22  C16  C17  C18  C13     0.00   0.0  0
 SHX  CONST_23  C15  C16  C17  C18     0.00   0.0  0
 SHX  CONST_24  C15  C14  C13  C18     0.00   0.0  0
 SHX  CONST_25  C14  C15  C16  C17     0.00   0.0  0
 SHX  CONST_26  C14  C13  C18  C17     0.00   0.0  0
 SHX  CONST_27  N2   C7   C8   CL    180.00   0.0  0
 SHX  CONST_28  N3   C9   C8   CL    180.00   0.0  0
 SHX  CONST_29  N4   C9   C8   C7    180.00   0.0  0
 SHX  CONST_30  C6   N2   C7   C19   180.00   0.0  0
 SHX  CONST_31  C9   C8   C7   C19   180.00   0.0  0
 SHX  CONST_32  N4   C9   N3   C6    180.00   0.0  0
 SHX  CONST_33  C15  C14  C13  C12   180.00   0.0  0
 SHX  CONST_34  C17  C18  C13  C12   180.00   0.0  0
 SHX  CONST_35  H4   C4   C5   C6      0.00   0.0  0
 SHX  CONST_36  H7   C1   N1   C5    180.00   0.0  0
 SHX  CONST_37  H5   C3   C4   C5    180.00   0.0  0
 SHX  CONST_38  H6   C2   C3   C4    180.00   0.0  0
 SHX  CONST_39  H17  C15  C14  C13   180.00   0.0  0
 SHX  CONST_40  H15  C17  C18  C13   180.00   0.0  0
 SHX  CONST_41  H16  C16  C17  C18   180.00   0.0  0
 SHX  CONST_42  H18  C14  C13  C18   180.00   0.0  0
 SHX  CONST_43  H14  C18  C17  C16   180.00   0.0  0
 SHX  CONST_44  C10  N4   C9   C8    180.00   0.0  0
 SHX  CONST_45  C10  N4   C9   N3      0.00   0.0  0
 SHX  CONST_46  H8   N4   C9   C8      0.00   0.0  0
 SHX  CONST_48  H11  N5   C11  C10   180.00   0.0  0
 SHX  Var_01    C14  C13  C12  C10  -105.98  30.0  2
 SHX  Var_02    H1   C19  C7   C8     61.13  30.0  2

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
 SHX  chir_01  C10  N4  C12  C11  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
 SHX  plan-1  CL   0.020
 SHX  plan-1  C8   0.020
 SHX  plan-1  C7   0.020
 SHX  plan-1  C19  0.020
 SHX  plan-1  N2   0.020
 SHX  plan-1  C6   0.020
 SHX  plan-1  C5   0.020
 SHX  plan-1  N3   0.020
 SHX  plan-1  C9   0.020
 SHX  plan-1  N4   0.020
 SHX  plan-2  C6   0.020
 SHX  plan-2  C5   0.020
 SHX  plan-2  C4   0.020
 SHX  plan-2  C3   0.020
 SHX  plan-2  C2   0.020
 SHX  plan-2  C1   0.020
 SHX  plan-2  N1   0.020
 SHX  plan-2  H4   0.020
 SHX  plan-2  H5   0.020
 SHX  plan-2  H6   0.020
 SHX  plan-2  H7   0.020
 SHX  plan-3  C12  0.020
 SHX  plan-3  C13  0.020
 SHX  plan-3  C18  0.020
 SHX  plan-3  C17  0.020
 SHX  plan-3  C16  0.020
 SHX  plan-3  C15  0.020
 SHX  plan-3  C14  0.020
 SHX  plan-3  H14  0.020
 SHX  plan-3  H15  0.020
 SHX  plan-3  H16  0.020
 SHX  plan-3  H17  0.020
 SHX  plan-3  H18  0.020
 SHX  plan-4  C10  0.020
 SHX  plan-4  C11  0.020
 SHX  plan-4  N5   0.020
 SHX  plan-4  O    0.020
 SHX  plan-4  H10  0.020
 SHX  plan-4  H11  0.020
 SHX  plan-5  C9   0.020
 SHX  plan-5  N4   0.020
 SHX  plan-5  C10  0.020
 SHX  plan-5  H8   0.020

