# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 06:34:39 2021
#   Inital geometry file: a 89 line input string
#   Ligand name: (2R)-2-(3-chlorophenyl)-N-(4-methylpyridin-3-yl)propanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](C(=O)Nc1cnccc1C)c2cccc(Cl)c2
#
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
 UHA  UHA  (2R)-2-(3-chlorophenyl)-N-(4-methylpyridin-3-yl)propanamide  ligand  34  19  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_UHA
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
 UHA  N1   N   N     0  -0.409   7.5889   2.2525  18.2317
 UHA  C4   C   CR16  0  -0.082   8.1755   1.5531  19.1917
 UHA  C5   C   CR16  0  -0.068   6.3581   1.9022  17.8769
 UHA  C6   C   CR16  0  -0.372   5.6710   0.8514  18.4611
 UHA  C7   C   CR6   0   0.163   6.2667   0.1199  19.4817
 UHA  C8   C   CH3   0  -0.739   5.5606  -1.0129  20.1568
 UHA  C10  C   CR16  0  -0.284  11.8174   0.2490  22.5616
 UHA  C13  C   CR6   0  -0.020  12.6769  -2.2162  21.6733
 UHA  CL   CL  CL    0  -0.129  13.2059  -3.7724  21.1183
 UHA  C12  C   CR16  0  -0.230  13.5851  -1.1736  21.7423
 UHA  C11  C   CR16  0  -0.243  13.1396   0.0631  22.1899
 UHA  C14  C   CR16  0  -0.285  11.3501  -2.0471  22.0394
 UHA  C9   C   CR6   0   0.159  10.9110  -0.8076  22.4915
 UHA  C1   C   CH1   0  -0.484   9.4643  -0.6298  22.9017
 UHA  C    C   CH3   0  -0.642   9.3208  -0.1776  24.3508
 UHA  C2   C   C     0   0.564   8.8085   0.3605  21.9479
 UHA  O    O   O     0  -0.460   8.8282   1.5618  22.1333
 UHA  C3   C   CR6   0   0.206   7.5615   0.4924  19.8491
 UHA  H1   H   HCR6  0   0.269   9.1882   1.8382  19.4518
 UHA  H2   H   HCR6  0   0.265   5.8945   2.4820  17.0868
 UHA  H3   H   HCR6  0   0.269   4.6685   0.6123  18.1307
 UHA  H4   H   HCH3  0   0.262   6.0152  -1.9724  19.9009
 UHA  H5   H   HCH3  0   0.258   5.6034  -0.9164  21.2425
 UHA  H6   H   HCH3  0   0.263   4.5153  -1.0555  19.8582
 UHA  H7   H   HCR6  0   0.261  11.4931   1.2232  22.9036
 UHA  H8   H   HCR6  0   0.281  14.6178  -1.3186  21.4563
 UHA  H9   H   HCR6  0   0.269  13.8376   0.8876  22.2466
 UHA  H10  H   HCR6  0   0.279  10.6599  -2.8791  21.9795
 UHA  H11  H   HCH1  0   0.284   8.9680  -1.5982  22.7975
 UHA  H12  H   HCH3  0   0.244   9.7858  -0.9068  25.0131
 UHA  H13  H   HCH3  0   0.237   9.7915   0.7881  24.5263
 UHA  H14  H   HCH3  0   0.245   8.2695  -0.0962  24.6280
 UHA  H15  H   HNH1  0   0.413   8.1815  -1.2215  20.8327
 UHA  N    N   NH1   0  -0.741   8.2316  -0.2143  20.8625

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
 UHA  N1   C5   aromatic  1.328  0.020  1.328
 UHA  N1   C4   aromatic  1.325  0.020  1.325
 UHA  C5   C6   aromatic  1.385  0.020  1.385
 UHA  C4   C3   aromatic  1.391  0.020  1.391
 UHA  C6   C7   aromatic  1.390  0.020  1.390
 UHA  C3   C7   aromatic  1.397  0.020  1.397
 UHA  C3   N    single    1.405  0.020  1.405
 UHA  C7   C8   single    1.496  0.020  1.496
 UHA  N    C2   single    1.357  0.020  1.357
 UHA  CL   C13  single    1.735  0.020  1.735
 UHA  O    C2   double    1.216  0.020  1.216
 UHA  C2   C1   single    1.523  0.020  1.523
 UHA  C14  C13  aromatic  1.387  0.020  1.387
 UHA  C14  C9   aromatic  1.391  0.020  1.391
 UHA  C13  C12  aromatic  1.384  0.020  1.384
 UHA  C1   C9   single    1.514  0.020  1.514
 UHA  C1   C    single    1.525  0.020  1.525
 UHA  C9   C10  aromatic  1.394  0.020  1.394
 UHA  C12  C11  aromatic  1.389  0.020  1.389
 UHA  C10  C11  aromatic  1.386  0.020  1.386
 UHA  C4   H1   single    0.930  0.020  1.080
 UHA  C5   H2   single    0.930  0.020  1.080
 UHA  C6   H3   single    0.930  0.020  1.080
 UHA  C8   H4   single    0.970  0.020  1.090
 UHA  C8   H5   single    0.970  0.020  1.090
 UHA  C8   H6   single    0.970  0.020  1.090
 UHA  C10  H7   single    0.930  0.020  1.080
 UHA  C12  H8   single    0.930  0.020  1.080
 UHA  C11  H9   single    0.930  0.020  1.080
 UHA  C14  H10  single    0.930  0.020  1.080
 UHA  C1   H11  single    0.970  0.020  1.090
 UHA  C    H12  single    0.970  0.020  1.090
 UHA  C    H13  single    0.970  0.020  1.090
 UHA  C    H14  single    0.970  0.020  1.090
 UHA  N    H15  single    0.860  0.020  1.020

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
 UHA  C5   N1   C4   117.70  3.000
 UHA  H1   C4   C3   119.98  3.000
 UHA  H1   C4   N1   116.67  3.000
 UHA  C3   C4   N1   123.35  3.000
 UHA  H2   C5   C6   120.07  3.000
 UHA  H2   C5   N1   116.74  3.000
 UHA  C6   C5   N1   123.18  3.000
 UHA  H3   C6   C7   120.32  3.000
 UHA  H3   C6   C5   119.90  3.000
 UHA  C7   C6   C5   119.77  3.000
 UHA  C3   C7   C8   121.40  3.000
 UHA  C8   C7   C6   121.85  3.000
 UHA  C3   C7   C6   116.75  3.000
 UHA  H6   C8   H5   108.33  3.000
 UHA  H6   C8   H4   107.53  3.000
 UHA  H5   C8   H4   107.13  3.000
 UHA  H6   C8   C7   111.06  3.000
 UHA  H5   C8   C7   111.33  3.000
 UHA  H4   C8   C7   111.29  3.000
 UHA  H7   C10  C9   120.23  3.000
 UHA  H7   C10  C11  119.43  3.000
 UHA  C9   C10  C11  120.34  3.000
 UHA  C14  C13  C12  121.51  3.000
 UHA  C12  C13  CL   119.44  3.000
 UHA  C14  C13  CL   119.05  3.000
 UHA  H8   C12  C11  120.73  3.000
 UHA  H8   C12  C13  120.82  3.000
 UHA  C11  C12  C13  118.45  3.000
 UHA  H9   C11  C12  119.26  3.000
 UHA  H9   C11  C10  119.95  3.000
 UHA  C12  C11  C10  120.80  3.000
 UHA  H10  C14  C9   120.11  3.000
 UHA  H10  C14  C13  120.11  3.000
 UHA  C9   C14  C13  119.78  3.000
 UHA  C1   C9   C14  119.64  3.000
 UHA  C1   C9   C10  121.24  3.000
 UHA  C14  C9   C10  119.13  3.000
 UHA  H11  C1   C2   108.71  3.000
 UHA  H11  C1   C    108.10  3.000
 UHA  C2   C1   C    111.21  3.000
 UHA  H11  C1   C9   107.69  3.000
 UHA  C    C1   C9   112.47  3.000
 UHA  C2   C1   C9   108.55  3.000
 UHA  H14  C    H13  108.04  3.000
 UHA  H14  C    H12  107.88  3.000
 UHA  H13  C    H12  108.13  3.000
 UHA  H14  C    C1   110.77  3.000
 UHA  H13  C    C1   112.06  3.000
 UHA  H12  C    C1   109.82  3.000
 UHA  N    C2   O    123.19  3.000
 UHA  O    C2   C1   122.68  3.000
 UHA  N    C2   C1   114.12  3.000
 UHA  N    C3   C7   119.84  3.000
 UHA  N    C3   C4   120.92  3.000
 UHA  C7   C3   C4   119.24  3.000
 UHA  H15  N    C3   117.19  3.000
 UHA  H15  N    C2   117.88  3.000
 UHA  C3   N    C2   124.51  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
 UHA  CONST_01  C7   C6   C5   N1     0.00   0.0  0
 UHA  CONST_02  C7   C3   C4   N1     0.00   0.0  0
 UHA  CONST_03  C6   C5   N1   C4     0.00   0.0  0
 UHA  CONST_04  C6   C7   C3   C4     0.00   0.0  0
 UHA  CONST_05  C3   C4   N1   C5     0.00   0.0  0
 UHA  CONST_06  C3   C7   C6   C5     0.00   0.0  0
 UHA  CONST_07  C13  C14  C9   C10    0.00   0.0  0
 UHA  CONST_08  C13  C12  C11  C10    0.00   0.0  0
 UHA  CONST_09  C9   C14  C13  C12    0.00   0.0  0
 UHA  CONST_10  C9   C10  C11  C12    0.00   0.0  0
 UHA  CONST_11  C14  C13  C12  C11    0.00   0.0  0
 UHA  CONST_12  C14  C9   C10  C11    0.00   0.0  0
 UHA  CONST_13  N    C3   C4   N1   180.00   0.0  0
 UHA  CONST_14  C8   C7   C3   C4   180.00   0.0  0
 UHA  CONST_15  C8   C7   C6   C5   180.00   0.0  0
 UHA  CONST_16  N    C3   C7   C6   180.00   0.0  0
 UHA  CONST_17  C1   C9   C14  C13  180.00   0.0  0
 UHA  CONST_18  C9   C14  C13  CL   180.00   0.0  0
 UHA  CONST_19  C11  C12  C13  CL   180.00   0.0  0
 UHA  CONST_20  C1   C9   C10  C11  180.00   0.0  0
 UHA  CONST_21  H3   C6   C5   N1   180.00   0.0  0
 UHA  CONST_22  H2   C5   N1   C4   180.00   0.0  0
 UHA  CONST_23  H1   C4   N1   C5   180.00   0.0  0
 UHA  CONST_24  H10  C14  C9   C10  180.00   0.0  0
 UHA  CONST_25  H8   C12  C11  C10  180.00   0.0  0
 UHA  CONST_26  H9   C11  C12  C13  180.00   0.0  0
 UHA  CONST_27  H7   C10  C11  C12  180.00   0.0  0
 UHA  CONST_31  C3   N    C2   C1   180.00   0.0  0
 UHA  CONST_32  C3   N    C2   O      0.00   0.0  0
 UHA  Var_01    H4   C8   C7   C6   110.50  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
 UHA  chir_01  C1  C2  C9  C  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
 UHA  plan-1  N1   0.020
 UHA  plan-1  C4   0.020
 UHA  plan-1  C5   0.020
 UHA  plan-1  C6   0.020
 UHA  plan-1  C7   0.020
 UHA  plan-1  C8   0.020
 UHA  plan-1  C3   0.020
 UHA  plan-1  H1   0.020
 UHA  plan-1  H2   0.020
 UHA  plan-1  H3   0.020
 UHA  plan-1  N    0.020
 UHA  plan-2  C10  0.020
 UHA  plan-2  C13  0.020
 UHA  plan-2  CL   0.020
 UHA  plan-2  C12  0.020
 UHA  plan-2  C11  0.020
 UHA  plan-2  C14  0.020
 UHA  plan-2  C9   0.020
 UHA  plan-2  C1   0.020
 UHA  plan-2  H7   0.020
 UHA  plan-2  H8   0.020
 UHA  plan-2  H9   0.020
 UHA  plan-2  H10  0.020
 UHA  plan-3  C1   0.020
 UHA  plan-3  C2   0.020
 UHA  plan-3  O    0.020
 UHA  plan-3  C3   0.020
 UHA  plan-3  H15  0.020
 UHA  plan-3  N    0.020

