# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 09:31:19 2021
#   Inital geometry file: a 99 line input string
#   Ligand name: N-(3,5-dichlorobenzene-1-carbonyl)-5,5-dimethyl-L-norleucine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(C)CC[C@H](NC(=O)c1cc(Cl)cc(Cl)c1)C(O)=O
#
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
 UP4  UP4  N-(3,5-dichlorobenzene-1-carbonyl)-5,5-dimethyl-L-norleucine  ligand  40  21  .  2022-03-29  2022-11-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_UP4
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
 UP4  C2   C   CH1   0  -0.163  -32.8360  40.0602  14.1881
 UP4  C3   C   C     0   0.541  -34.1421  39.9528  13.4179
 UP4  C5   C   CH2   0  -0.393  -30.3777  40.6311  13.9404
 UP4  C7   C   CH3   0  -0.647  -28.8613  39.5272  12.2551
 UP4  C9   C   CH3   0  -0.636  -27.9484  41.1059  13.9504
 UP4  C10  C   CR16  0  -0.237  -31.5331  37.0180  16.9138
 UP4  C11  C   CR6   0  -0.030  -31.1692  35.9112  17.6631
 UP4  C12  C   CR16  0  -0.166  -32.1157  35.0940  18.2585
 UP4  C13  C   CR6   0  -0.030  -33.4542  35.4189  18.0974
 UP4  CL1  CL  CL    0  -0.101  -29.4944  35.5438  17.8704
 UP4  CL   CL  CL    0  -0.102  -34.6504  34.4140  18.8338
 UP4  C14  C   CR16  0  -0.220  -33.8517  36.5254  17.3686
 UP4  C    C   CR6   0  -0.048  -32.8826  37.3171  16.7630
 UP4  C1   C   C     0   0.557  -33.3305  38.5187  15.9945
 UP4  O2   O   O     0  -0.470  -34.3390  39.1344  16.3005
 UP4  N    N   NH1   0  -0.656  -32.5459  38.8821  14.9660
 UP4  O1   O   O     0  -0.440  -34.8075  40.9128  13.1219
 UP4  O    O   OH1   0  -0.584  -34.4297  38.7123  13.0611
 UP4  C4   C   CH2   0  -0.496  -31.6873  40.3402  13.2129
 UP4  C6   C   CT    0  -0.092  -29.1432  40.8089  13.0422
 UP4  C8   C   CH3   0  -0.646  -29.3360  41.9748  12.0718
 UP4  H1   H   HCH1  0   0.292  -32.9405  40.9161  14.8599
 UP4  H2   H   HCH2  0   0.221  -30.1626  39.8251  14.6504
 UP4  H3   H   HCH2  0   0.231  -30.5106  41.5344  14.5463
 UP4  H4   H   HCH3  0   0.221  -28.7767  38.6635  12.9193
 UP4  H5   H   HCH3  0   0.224  -29.6449  39.3115  11.5267
 UP4  H6   H   HCH3  0   0.228  -27.9236  39.6122  11.7020
 UP4  H7   H   HCH3  0   0.221  -27.7863  40.2966  14.6666
 UP4  H8   H   HCH3  0   0.224  -27.0315  41.2231  13.3691
 UP4  H9   H   HCH3  0   0.222  -28.1012  42.0253  14.5201
 UP4  H10  H   HCR6  0   0.290  -30.7663  37.6483  16.4838
 UP4  H11  H   HCR6  0   0.309  -31.8193  34.2286  18.8345
 UP4  H12  H   HCR6  0   0.291  -34.9004  36.7659  17.2628
 UP4  H13  H   HNH1  0   0.412  -31.8650  38.2308  14.6064
 UP4  H14  H   HOH1  0   0.486  -35.2490  38.6957  12.5431
 UP4  H15  H   HCH2  0   0.265  -31.9698  41.1965  12.5984
 UP4  H16  H   HCH2  0   0.251  -31.5789  39.4892  12.5342
 UP4  H17  H   HCH3  0   0.222  -29.5581  42.9024  12.6044
 UP4  H18  H   HCH3  0   0.226  -28.4306  42.1395  11.4834
 UP4  H19  H   HCH3  0   0.226  -30.1497  41.7921  11.3675

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
 UP4  C8   C6   single    1.529  0.020  1.529
 UP4  C7   C6   single    1.530  0.020  1.530
 UP4  O1   C3   double    1.205  0.020  1.205
 UP4  C6   C9   single    1.530  0.020  1.530
 UP4  C6   C5   single    1.537  0.020  1.537
 UP4  O    C3   single    1.322  0.020  1.322
 UP4  C3   C2   single    1.520  0.020  1.520
 UP4  C4   C5   single    1.526  0.020  1.526
 UP4  C4   C2   single    1.533  0.020  1.533
 UP4  C2   N    single    1.441  0.020  1.441
 UP4  N    C1   single    1.344  0.020  1.344
 UP4  C1   O2   double    1.221  0.020  1.221
 UP4  C1   C    single    1.495  0.020  1.495
 UP4  C14  C    aromatic  1.390  0.020  1.390
 UP4  C14  C13  aromatic  1.383  0.020  1.383
 UP4  C    C10  aromatic  1.390  0.020  1.390
 UP4  CL   C13  single    1.727  0.020  1.727
 UP4  C13  C12  aromatic  1.387  0.020  1.387
 UP4  C10  C11  aromatic  1.385  0.020  1.385
 UP4  C12  C11  aromatic  1.385  0.020  1.385
 UP4  C11  CL1  single    1.727  0.020  1.727
 UP4  C2   H1   single    0.970  0.020  1.090
 UP4  C5   H2   single    0.970  0.020  1.090
 UP4  C5   H3   single    0.970  0.020  1.090
 UP4  C7   H4   single    0.970  0.020  1.090
 UP4  C7   H5   single    0.970  0.020  1.090
 UP4  C7   H6   single    0.970  0.020  1.090
 UP4  C9   H7   single    0.970  0.020  1.090
 UP4  C9   H8   single    0.970  0.020  1.090
 UP4  C9   H9   single    0.970  0.020  1.090
 UP4  C10  H10  single    0.930  0.020  1.080
 UP4  C12  H11  single    0.930  0.020  1.080
 UP4  C14  H12  single    0.930  0.020  1.080
 UP4  N    H13  single    0.860  0.020  1.020
 UP4  O    H14  single    0.850  0.020  0.980
 UP4  C4   H15  single    0.970  0.020  1.090
 UP4  C4   H16  single    0.970  0.020  1.090
 UP4  C8   H17  single    0.970  0.020  1.090
 UP4  C8   H18  single    0.970  0.020  1.090
 UP4  C8   H19  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
 UP4  H1   C2   C4   108.64  3.000
 UP4  H1   C2   N    109.12  3.000
 UP4  C4   C2   N    110.00  3.000
 UP4  H1   C2   C3   106.53  3.000
 UP4  N    C2   C3   112.87  3.000
 UP4  C4   C2   C3   109.54  3.000
 UP4  O    C3   O1   124.12  3.000
 UP4  O    C3   C2   112.94  3.000
 UP4  O1   C3   C2   122.87  3.000
 UP4  H3   C5   H2   105.78  3.000
 UP4  H3   C5   C6   108.98  3.000
 UP4  H2   C5   C6   107.82  3.000
 UP4  H3   C5   C4   108.46  3.000
 UP4  H2   C5   C4   109.71  3.000
 UP4  C6   C5   C4   115.64  3.000
 UP4  H6   C7   H5   107.09  3.000
 UP4  H6   C7   H4   107.64  3.000
 UP4  H5   C7   H4   107.76  3.000
 UP4  H6   C7   C6   110.70  3.000
 UP4  H5   C7   C6   112.12  3.000
 UP4  H4   C7   C6   111.32  3.000
 UP4  H9   C9   H8   107.74  3.000
 UP4  H9   C9   H7   107.60  3.000
 UP4  H8   C9   H7   107.69  3.000
 UP4  H9   C9   C6   111.33  3.000
 UP4  H8   C9   C6   111.14  3.000
 UP4  H7   C9   C6   111.17  3.000
 UP4  H10  C10  C    121.30  3.000
 UP4  H10  C10  C11  119.63  3.000
 UP4  C    C10  C11  119.04  3.000
 UP4  CL1  C11  C12  119.05  3.000
 UP4  CL1  C11  C10  119.32  3.000
 UP4  C12  C11  C10  121.63  3.000
 UP4  H11  C12  C13  120.94  3.000
 UP4  H11  C12  C11  120.93  3.000
 UP4  C13  C12  C11  118.13  3.000
 UP4  C14  C13  CL   119.41  3.000
 UP4  CL   C13  C12  118.86  3.000
 UP4  C14  C13  C12  121.73  3.000
 UP4  H12  C14  C    120.46  3.000
 UP4  H12  C14  C13  120.55  3.000
 UP4  C    C14  C13  118.99  3.000
 UP4  C1   C    C14  118.21  3.000
 UP4  C14  C    C10  120.46  3.000
 UP4  C1   C    C10  121.29  3.000
 UP4  N    C1   O2   122.54  3.000
 UP4  O2   C1   C    121.61  3.000
 UP4  N    C1   C    115.85  3.000
 UP4  H13  N    C1   119.51  3.000
 UP4  H13  N    C2   118.11  3.000
 UP4  C1   N    C2   121.11  3.000
 UP4  H14  O    C3   110.12  3.000
 UP4  H16  C4   H15  106.66  3.000
 UP4  H16  C4   C5   111.04  3.000
 UP4  H15  C4   C5   109.94  3.000
 UP4  H16  C4   C2   109.08  3.000
 UP4  H15  C4   C2   107.92  3.000
 UP4  C5   C4   C2   112.01  3.000
 UP4  C8   C6   C9   109.10  3.000
 UP4  C9   C6   C7   108.91  3.000
 UP4  C8   C6   C7   109.60  3.000
 UP4  C9   C6   C5   107.63  3.000
 UP4  C7   C6   C5   110.59  3.000
 UP4  C8   C6   C5   110.96  3.000
 UP4  H19  C8   H18  107.19  3.000
 UP4  H19  C8   H17  107.77  3.000
 UP4  H18  C8   H17  107.65  3.000
 UP4  H19  C8   C6   112.07  3.000
 UP4  H18  C8   C6   110.63  3.000
 UP4  H17  C8   C6   111.33  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
 UP4  CONST_01  C13  C14  C    C10    0.00   0.0  0
 UP4  CONST_02  C13  C12  C11  C10    0.00   0.0  0
 UP4  CONST_03  C14  C    C10  C11    0.00   0.0  0
 UP4  CONST_04  C14  C13  C12  C11    0.00   0.0  0
 UP4  CONST_05  C    C14  C13  C12    0.00   0.0  0
 UP4  CONST_06  C    C10  C11  C12    0.00   0.0  0
 UP4  CONST_07  C1   C    C10  C11  180.00   0.0  0
 UP4  CONST_08  CL   C13  C12  C11  180.00   0.0  0
 UP4  CONST_09  C1   C    C14  C13  180.00   0.0  0
 UP4  CONST_10  CL1  C11  C12  C13  180.00   0.0  0
 UP4  CONST_11  C    C10  C11  CL1  180.00   0.0  0
 UP4  CONST_12  C    C14  C13  CL   180.00   0.0  0
 UP4  CONST_13  H12  C14  C    C10  180.00   0.0  0
 UP4  CONST_14  H11  C12  C11  C10  180.00   0.0  0
 UP4  CONST_15  H10  C10  C11  C12  180.00   0.0  0
 UP4  CONST_16  C    C1   N    C2   180.00   0.0  0
 UP4  CONST_18  O2   C1   N    C2     0.00   0.0  0
 UP4  CONST_19  H14  O    C3   C2   180.00   0.0  0
 UP4  Var_01    N    C1   C    C10   32.03  30.0  2
 UP4  Var_02    C6   C5   C4   C2   175.12  30.0  3
 UP4  Var_03    C4   C5   C6   C7   -61.79  30.0  3
 UP4  Var_04    H17  C8   C6   C5    56.50  30.0  3
 UP4  Var_05    H4   C7   C6   C5   -54.02  30.0  3
 UP4  Var_06    H7   C9   C6   C5    58.92  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
 UP4  chir_01  C2  C3  C4  N  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
 UP4  plan-1  C10  0.020
 UP4  plan-1  C11  0.020
 UP4  plan-1  C12  0.020
 UP4  plan-1  C13  0.020
 UP4  plan-1  CL1  0.020
 UP4  plan-1  CL   0.020
 UP4  plan-1  C14  0.020
 UP4  plan-1  C    0.020
 UP4  plan-1  C1   0.020
 UP4  plan-1  H10  0.020
 UP4  plan-1  H11  0.020
 UP4  plan-1  H12  0.020
 UP4  plan-2  C2   0.020
 UP4  plan-2  C    0.020
 UP4  plan-2  C1   0.020
 UP4  plan-2  O2   0.020
 UP4  plan-2  N    0.020
 UP4  plan-2  H13  0.020
 UP4  plan-3  C2   0.020
 UP4  plan-3  C3   0.020
 UP4  plan-3  O1   0.020
 UP4  plan-3  O    0.020
 UP4  plan-3  H14  0.020

