# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 00:13:55 2020
#   Inital geometry file: a 118 line input string
#   Ligand name: 2-(4-{[2-(3-chlorophenyl)-6-ethylpyrimidin-4-yl]methyl}phenyl)acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1cc(Cc2ccc(CC(N)=O)cc2)nc(n1)c3cccc(Cl)c3
#
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
 E31  E31  2-(4-{[2-(3-chlorophenyl)-6-ethylpyrimidin-4-yl]methyl}phenyl)acetamide  ligand  46  26  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_E31
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
 E31  C    C   CH3   0  -0.664   3.6857  -4.0022   1.3685
 E31  N    N   N     0  -0.442   2.2453  -1.4241   0.5661
 E31  O    O   O     0  -0.482  -3.9746   2.5599   1.1474
 E31  C12  C   C     0   0.527  -5.0604   2.0128   1.2592
 E31  N4   N   NH2   0  -0.798  -5.9165   2.2744   2.2566
 E31  C8   C   CR6   0   0.131  -4.4581   0.0899  -0.2316
 E31  C9   C   CR16  0  -0.283  -3.5847   0.4850  -1.2413
 E31  C10  C   CR16  0  -0.287  -2.5623  -0.3505  -1.6641
 E31  C7   C   CR16  0  -0.281  -4.2779  -1.1631   0.3446
 E31  C6   C   CR16  0  -0.286  -3.2528  -1.9993  -0.0762
 E31  C5   C   CR6   0   0.120  -2.3830  -1.6050  -1.0872
 E31  C4   C   CR6   0   0.333   0.0072  -2.1683  -0.7701
 E31  C20  C   CR16  0  -0.414   0.5358  -3.0129   0.1951
 E31  C2   C   CR6   0   0.320   1.6851  -2.5946   0.8547
 E31  C1   C   CH2   0  -0.498   2.3651  -3.4374   1.8890
 E31  N1   N   N     0  -0.431   0.5855  -1.0070  -1.0533
 E31  C3   C   CR6   0   0.374   1.6753  -0.6815  -0.3731
 E31  C13  C   CR6   0  -0.020   2.3062   0.6210  -0.6894
 E31  C18  C   CR16  0  -0.244   3.5013   0.9846  -0.0709
 E31  C17  C   CR6   0  -0.019   4.0811   2.2035  -0.3735
 E31  CL   CL  CL    0  -0.127   5.5700   2.6432   0.4003
 E31  C14  C   CR16  0  -0.275   1.7155   1.4939  -1.6016
 E31  C15  C   CR16  0  -0.245   2.3117   2.7112  -1.8897
 E31  C16  C   CR16  0  -0.216   3.5021   3.0796  -1.2789
 E31  H1   H   HCH3  0   0.240   4.1885  -4.5753   2.1469
 E31  H2   H   HCH3  0   0.231   3.5247  -4.6637   0.5168
 E31  H3   H   HCH3  0   0.232   4.3551  -3.2018   1.0539
 E31  H4   H   HNH2  0   0.401  -5.6863   2.9528   2.9645
 E31  H5   H   HNH2  0   0.408  -6.7965   1.7967   2.3419
 E31  H6   H   HCH2  0   0.272  -6.3832   0.4120   0.6498
 E31  H7   H   HCH2  0   0.294  -5.9649   1.5646  -0.5995
 E31  H8   H   HCR6  0   0.246  -3.7103   1.4527  -1.7111
 E31  H9   H   HCR6  0   0.246  -1.8978  -0.0239  -2.4544
 E31  H10  H   HCR6  0   0.249  -4.9496  -1.4968   1.1272
 E31  H11  H   HCR6  0   0.248  -3.1354  -2.9734   0.3843
 E31  H12  H   HCH2  0   0.273  -1.5138  -3.5484  -1.3524
 E31  H13  H   HCH2  0   0.283  -1.0642  -2.3807  -2.5896
 E31  H14  H   HCR6  0   0.273   0.0724  -3.9623   0.4266
 E31  H15  H   HCH2  0   0.247   1.7063  -4.2500   2.1989
 E31  H16  H   HCH2  0   0.255   2.5546  -2.8224   2.7714
 E31  H17  H   HCR6  0   0.277   3.9686   0.3150   0.6375
 E31  H18  H   HCR6  0   0.264   0.7867   1.2180  -2.0806
 E31  H19  H   HCR6  0   0.271   1.8471   3.3845  -2.5973
 E31  H20  H   HCR6  0   0.284   3.9671   4.0297  -1.5045
 E31  C19  C   CH2   0  -0.606  -1.2518  -2.5029  -1.5206
 E31  C11  C   CH2   0  -0.674  -5.5567   0.9961   0.2412

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
 E31  C15  C16  aromatic  1.388  0.020  1.388
 E31  C15  C14  aromatic  1.386  0.020  1.386
 E31  C16  C17  aromatic  1.387  0.020  1.387
 E31  C14  C13  aromatic  1.394  0.020  1.394
 E31  C17  CL   single    1.735  0.020  1.735
 E31  C17  C18  aromatic  1.383  0.020  1.383
 E31  C13  C18  aromatic  1.394  0.020  1.394
 E31  C13  C3   single    1.481  0.020  1.481
 E31  C    C1   single    1.528  0.020  1.528
 E31  N    C3   aromatic  1.326  0.020  1.326
 E31  N    C2   aromatic  1.329  0.020  1.329
 E31  C3   N1   aromatic  1.325  0.020  1.325
 E31  C1   C2   single    1.497  0.020  1.497
 E31  C2   C20  aromatic  1.390  0.020  1.390
 E31  N1   C4   aromatic  1.328  0.020  1.328
 E31  C20  C4   aromatic  1.387  0.020  1.387
 E31  C4   C19  single    1.503  0.020  1.503
 E31  N4   C12  single    1.340  0.020  1.340
 E31  C10  C9   aromatic  1.386  0.020  1.386
 E31  C10  C5   aromatic  1.392  0.020  1.392
 E31  C19  C5   single    1.508  0.020  1.508
 E31  C9   C8   aromatic  1.392  0.020  1.392
 E31  C5   C6   aromatic  1.391  0.020  1.391
 E31  C12  O    double    1.221  0.020  1.221
 E31  C12  C11  single    1.522  0.020  1.522
 E31  C8   C11  single    1.501  0.020  1.501
 E31  C8   C7   aromatic  1.391  0.020  1.391
 E31  C6   C7   aromatic  1.388  0.020  1.388
 E31  C    H1   single    0.970  0.020  1.090
 E31  C    H2   single    0.970  0.020  1.090
 E31  C    H3   single    0.970  0.020  1.090
 E31  N4   H4   single    0.860  0.020  1.020
 E31  N4   H5   single    0.860  0.020  1.020
 E31  C11  H6   single    0.970  0.020  1.090
 E31  C11  H7   single    0.970  0.020  1.090
 E31  C9   H8   single    0.930  0.020  1.080
 E31  C10  H9   single    0.930  0.020  1.080
 E31  C7   H10  single    0.930  0.020  1.080
 E31  C6   H11  single    0.930  0.020  1.080
 E31  C19  H12  single    0.970  0.020  1.090
 E31  C19  H13  single    0.970  0.020  1.090
 E31  C20  H14  single    0.930  0.020  1.080
 E31  C1   H15  single    0.970  0.020  1.090
 E31  C1   H16  single    0.970  0.020  1.090
 E31  C18  H17  single    0.930  0.020  1.080
 E31  C14  H18  single    0.930  0.020  1.080
 E31  C15  H19  single    0.930  0.020  1.080
 E31  C16  H20  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
 E31  H3   C    H2   108.11  3.000
 E31  H3   C    H1   108.00  3.000
 E31  H2   C    H1   107.89  3.000
 E31  H3   C    C1   110.96  3.000
 E31  H2   C    C1   111.27  3.000
 E31  H1   C    C1   110.49  3.000
 E31  C3   N    C2   117.75  3.000
 E31  C11  C12  N4   114.82  3.000
 E31  C11  C12  O    121.88  3.000
 E31  N4   C12  O    123.28  3.000
 E31  H5   N4   H4   117.44  3.000
 E31  H5   N4   C12  121.99  3.000
 E31  H4   N4   C12  120.56  3.000
 E31  C7   C8   C9   118.35  3.000
 E31  C7   C8   C11  120.56  3.000
 E31  C9   C8   C11  121.09  3.000
 E31  H8   C9   C10  119.45  3.000
 E31  H8   C9   C8   119.70  3.000
 E31  C10  C9   C8   120.85  3.000
 E31  H9   C10  C5   119.68  3.000
 E31  H9   C10  C9   119.55  3.000
 E31  C5   C10  C9   120.77  3.000
 E31  H10  C7   C6   119.41  3.000
 E31  H10  C7   C8   119.75  3.000
 E31  C6   C7   C8   120.85  3.000
 E31  H11  C6   C5   119.74  3.000
 E31  H11  C6   C7   119.50  3.000
 E31  C5   C6   C7   120.76  3.000
 E31  C19  C5   C6   120.62  3.000
 E31  C6   C5   C10  118.43  3.000
 E31  C19  C5   C10  120.93  3.000
 E31  N1   C4   C20  120.99  3.000
 E31  C20  C4   C19  122.07  3.000
 E31  N1   C4   C19  116.93  3.000
 E31  H14  C20  C2   121.13  3.000
 E31  H14  C20  C4   121.34  3.000
 E31  C2   C20  C4   117.53  3.000
 E31  C1   C2   C20  122.28  3.000
 E31  C20  C2   N    120.70  3.000
 E31  C1   C2   N    117.01  3.000
 E31  H16  C1   H15  107.13  3.000
 E31  H16  C1   C2   108.66  3.000
 E31  H15  C1   C2   109.95  3.000
 E31  H16  C1   C    109.48  3.000
 E31  H15  C1   C    110.08  3.000
 E31  C2   C1   C    111.43  3.000
 E31  C3   N1   C4   117.61  3.000
 E31  C13  C3   N1   117.17  3.000
 E31  N1   C3   N    125.41  3.000
 E31  C13  C3   N    117.42  3.000
 E31  C14  C13  C18  119.36  3.000
 E31  C18  C13  C3   119.98  3.000
 E31  C14  C13  C3   120.65  3.000
 E31  H17  C18  C17  120.52  3.000
 E31  H17  C18  C13  119.99  3.000
 E31  C17  C18  C13  119.48  3.000
 E31  C16  C17  CL   119.31  3.000
 E31  CL   C17  C18  119.05  3.000
 E31  C16  C17  C18  121.64  3.000
 E31  H18  C14  C15  120.13  3.000
 E31  H18  C14  C13  119.62  3.000
 E31  C15  C14  C13  120.25  3.000
 E31  H19  C15  C16  119.41  3.000
 E31  H19  C15  C14  119.87  3.000
 E31  C16  C15  C14  120.72  3.000
 E31  H20  C16  C15  120.68  3.000
 E31  H20  C16  C17  120.78  3.000
 E31  C15  C16  C17  118.54  3.000
 E31  H13  C19  H12  107.42  3.000
 E31  H13  C19  C4   108.65  3.000
 E31  H12  C19  C4   109.72  3.000
 E31  H13  C19  C5   110.09  3.000
 E31  H12  C19  C5   110.26  3.000
 E31  C4   C19  C5   110.62  3.000
 E31  H7   C11  H6   106.46  3.000
 E31  H7   C11  C8   110.18  3.000
 E31  H6   C11  C8   110.44  3.000
 E31  H7   C11  C12  106.77  3.000
 E31  H6   C11  C12  110.73  3.000
 E31  C8   C11  C12  112.05  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
 E31  CONST_01  C14  C13  C3   N    180.00   0.0  0
 E31  CONST_02  C18  C13  C3   N      0.00   0.0  0
 E31  CONST_03  C4   N1   C3   N      0.00   0.0  0
 E31  CONST_04  C4   C20  C2   N      0.00   0.0  0
 E31  CONST_05  C5   C10  C9   C8     0.00   0.0  0
 E31  CONST_06  C5   C6   C7   C8     0.00   0.0  0
 E31  CONST_07  C6   C5   C10  C9     0.00   0.0  0
 E31  CONST_08  C6   C7   C8   C9     0.00   0.0  0
 E31  CONST_09  C7   C8   C9   C10    0.00   0.0  0
 E31  CONST_10  C7   C6   C5   C10    0.00   0.0  0
 E31  CONST_11  C13  C3   N1   C4   180.00   0.0  0
 E31  CONST_12  C3   N    C2   C20    0.00   0.0  0
 E31  CONST_13  C3   N1   C4   C20    0.00   0.0  0
 E31  CONST_14  C13  C3   N    C2   180.00   0.0  0
 E31  CONST_15  N1   C3   N    C2     0.00   0.0  0
 E31  CONST_16  N1   C4   C20  C2     0.00   0.0  0
 E31  CONST_17  C14  C13  C3   N1     0.00   0.0  0
 E31  CONST_18  C18  C13  C3   N1   180.00   0.0  0
 E31  CONST_19  C15  C14  C13  C3   180.00   0.0  0
 E31  CONST_20  C17  C18  C13  C3   180.00   0.0  0
 E31  CONST_21  C16  C15  C14  C13    0.00   0.0  0
 E31  CONST_22  C16  C17  C18  C13    0.00   0.0  0
 E31  CONST_23  C15  C16  C17  C18    0.00   0.0  0
 E31  CONST_24  C15  C14  C13  C18    0.00   0.0  0
 E31  CONST_25  C14  C15  C16  C17    0.00   0.0  0
 E31  CONST_26  C14  C13  C18  C17    0.00   0.0  0
 E31  CONST_27  C10  C9   C8   C11  180.00   0.0  0
 E31  CONST_28  C6   C7   C8   C11  180.00   0.0  0
 E31  CONST_29  C19  C5   C10  C9   180.00   0.0  0
 E31  CONST_30  C19  C5   C6   C7   180.00   0.0  0
 E31  CONST_31  C3   N1   C4   C19  180.00   0.0  0
 E31  CONST_32  C2   C20  C4   C19  180.00   0.0  0
 E31  CONST_33  C1   C2   C20  C4   180.00   0.0  0
 E31  CONST_34  C3   N    C2   C1   180.00   0.0  0
 E31  CONST_35  CL   C17  C18  C13  180.00   0.0  0
 E31  CONST_36  C15  C16  C17  CL   180.00   0.0  0
 E31  CONST_37  H14  C20  C2   N    180.00   0.0  0
 E31  CONST_38  H9   C10  C9   C8   180.00   0.0  0
 E31  CONST_39  H11  C6   C7   C8   180.00   0.0  0
 E31  CONST_40  H10  C7   C8   C9   180.00   0.0  0
 E31  CONST_41  H8   C9   C8   C7   180.00   0.0  0
 E31  CONST_42  H18  C14  C13  C3     0.00   0.0  0
 E31  CONST_43  H17  C18  C13  C3     0.00   0.0  0
 E31  CONST_44  H19  C15  C14  C13  180.00   0.0  0
 E31  CONST_45  H20  C16  C17  C18  180.00   0.0  0
 E31  CONST_46  H4   N4   C12  O      0.00   0.0  0
 E31  CONST_47  H5   N4   C12  O    180.00   0.0  0
 E31  Var_01    C4   C19  C5   C10   85.22  30.0  2
 E31  Var_02    N1   C4   C19  C5   -69.50  30.0  3
 E31  Var_03    N    C2   C1   C    -70.37  30.0  2
 E31  Var_04    C9   C8   C11  C12  -82.55  30.0  2
 E31  Var_05    C8   C11  C12  O     39.47  30.0  3
 E31  Var_06    H1   C    C1   C2   177.46  30.0  3

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
 E31  plan-1  N    0.020
 E31  plan-1  C4   0.020
 E31  plan-1  C20  0.020
 E31  plan-1  C2   0.020
 E31  plan-1  C1   0.020
 E31  plan-1  N1   0.020
 E31  plan-1  C3   0.020
 E31  plan-1  C13  0.020
 E31  plan-1  H14  0.020
 E31  plan-1  C19  0.020
 E31  plan-2  C8   0.020
 E31  plan-2  C9   0.020
 E31  plan-2  C10  0.020
 E31  plan-2  C7   0.020
 E31  plan-2  C6   0.020
 E31  plan-2  C5   0.020
 E31  plan-2  H8   0.020
 E31  plan-2  H9   0.020
 E31  plan-2  H10  0.020
 E31  plan-2  H11  0.020
 E31  plan-2  C19  0.020
 E31  plan-2  C11  0.020
 E31  plan-3  C3   0.020
 E31  plan-3  C13  0.020
 E31  plan-3  C18  0.020
 E31  plan-3  C17  0.020
 E31  plan-3  CL   0.020
 E31  plan-3  C14  0.020
 E31  plan-3  C15  0.020
 E31  plan-3  C16  0.020
 E31  plan-3  H17  0.020
 E31  plan-3  H18  0.020
 E31  plan-3  H19  0.020
 E31  plan-3  H20  0.020
 E31  plan-4  O    0.020
 E31  plan-4  C12  0.020
 E31  plan-4  N4   0.020
 E31  plan-4  H4   0.020
 E31  plan-4  H5   0.020
 E31  plan-4  C11  0.020

