# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 18:13:15 2022
#   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  39  21  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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  -0.192  -32.8149  39.9112  14.0266
 UP4  C3   C   C      0   0.411  -34.0853  39.6909  13.1558
 UP4  C5   C   CH2    0  -0.379  -30.3383  40.5282  13.9345
 UP4  C7   C   CH3    0  -0.643  -28.6939  39.7765  12.1689
 UP4  C9   C   CH3    0  -0.634  -27.9533  41.2022  14.0692
 UP4  C10  C   CR16   0  -0.248  -31.5681  36.8078  16.7677
 UP4  C11  C   CR6    0  -0.028  -31.2914  35.6765  17.5182
 UP4  C12  C   CR16   0  -0.172  -32.2573  35.0682  18.3026
 UP4  C13  C   CR6    0  -0.029  -33.5232  35.6329  18.3296
 UP4  CL1  CL  CL     0  -0.105  -29.6964  35.0118  17.4889
 UP4  CL   CL  CL     0  -0.107  -34.7440  34.8968  19.3080
 UP4  C14  C   CR16   0  -0.225  -33.8290  36.7693  17.6023
 UP4  C    C   CR6    0  -0.053  -32.8481  37.3505  16.8059
 UP4  C1   C   C      0   0.536  -33.2064  38.5973  16.0487
 UP4  O2   O   O      0  -0.486  -34.0446  39.3683  16.4967
 UP4  N    N   NH1    0  -0.625  -32.5390  38.7979  14.9082
 UP4  O1   O   O      0  -0.607  -34.4540  40.6953  12.5163
 UP4  O    O   OC    -1  -0.590  -34.5954  38.5584  13.1586
 UP4  C4   C   CH2    0  -0.467  -31.5959  40.1819  13.1445
 UP4  C6   C   CT     0  -0.087  -29.1042  40.9176  13.1027
 UP4  C8   C   CH3    0  -0.643  -29.3749  42.1776  12.2781
 UP4  H1   H   HCH1   0   0.233  -32.9824  40.7924  14.6521
 UP4  H2   H   HCH2   0   0.216  -30.0646  39.6814  14.5735
 UP4  H3   H   HCH2   0   0.210  -30.5706  41.3555  14.6161
 UP4  H4   H   HCH3   0   0.218  -28.5348  38.8495  12.7246
 UP4  H5   H   HCH3   0   0.223  -29.4491  39.5823  11.4055
 UP4  H6   H   HCH3   0   0.221  -27.7627  40.0178  11.6518
 UP4  H7   H   HCH3   0   0.218  -27.7093  40.3204  14.6664
 UP4  H8   H   HCH3   0   0.219  -27.0509  41.4977  13.5294
 UP4  H9   H   HCH3   0   0.218  -28.2046  42.0108  14.7600
 UP4  H10  H   HCR6   0   0.292  -30.7806  37.2700  16.1869
 UP4  H11  H   HCR6   0   0.304  -32.0287  34.1845  18.8821
 UP4  H12  H   HCR6   0   0.285  -34.8203  37.1985  17.6470
 UP4  H13  H   HNH1   0   0.396  -32.0276  38.0247  14.5115
 UP4  H15  H   HCH2   0   0.237  -31.8584  41.0027  12.4769
 UP4  H16  H   HCH2   0   0.221  -31.4168  39.3108  12.5044
 UP4  H17  H   HCH3   0   0.218  -29.6933  43.0068  12.9143
 UP4  H18  H   HCH3   0   0.221  -28.4739  42.4943  11.7480
 UP4  H19  H   HCH3   0   0.223  -30.1512  42.0176  11.5281

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    1.530  0.020  1.530
 UP4  C7   C6   single    1.530  0.020  1.530
 UP4  O1   C3   deloc     1.246  0.020  1.246
 UP4  C6   C9   single    1.530  0.020  1.530
 UP4  C6   C5   single    1.538  0.020  1.538
 UP4  O    C3   deloc     1.242  0.020  1.242
 UP4  C3   C2   single    1.556  0.020  1.556
 UP4  C4   C5   single    1.525  0.020  1.525
 UP4  C4   C2   single    1.529  0.020  1.529
 UP4  C2   N    single    1.447  0.020  1.447
 UP4  N    C1   single    1.337  0.020  1.337
 UP4  C1   O2   double    1.224  0.020  1.224
 UP4  C1   C    single    1.502  0.020  1.502
 UP4  C14  C    aromatic  1.391  0.020  1.391
 UP4  C14  C13  aromatic  1.383  0.020  1.383
 UP4  C    C10  aromatic  1.391  0.020  1.391
 UP4  CL   C13  single    1.729  0.020  1.729
 UP4  C13  C12  aromatic  1.386  0.020  1.386
 UP4  C10  C11  aromatic  1.386  0.020  1.386
 UP4  C12  C11  aromatic  1.385  0.020  1.385
 UP4  C11  CL1  single    1.728  0.020  1.728
 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  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   108.03  3.000
 UP4  H1   C2   N    107.50  3.000
 UP4  C4   C2   N    109.62  3.000
 UP4  H1   C2   C3   108.01  3.000
 UP4  N    C2   C3   112.82  3.000
 UP4  C4   C2   C3   110.68  3.000
 UP4  O    C3   O1   127.90  3.000
 UP4  O    C3   C2   117.60  3.000
 UP4  O1   C3   C2   114.49  3.000
 UP4  H3   C5   H2   105.87  3.000
 UP4  H3   C5   C6   108.36  3.000
 UP4  H2   C5   C6   108.09  3.000
 UP4  H3   C5   C4   108.58  3.000
 UP4  H2   C5   C4   109.43  3.000
 UP4  C6   C5   C4   116.04  3.000
 UP4  H6   C7   H5   107.35  3.000
 UP4  H6   C7   H4   107.70  3.000
 UP4  H5   C7   H4   107.79  3.000
 UP4  H6   C7   C6   110.66  3.000
 UP4  H5   C7   C6   111.96  3.000
 UP4  H4   C7   C6   111.18  3.000
 UP4  H9   C9   H8   107.59  3.000
 UP4  H9   C9   H7   107.64  3.000
 UP4  H8   C9   H7   107.70  3.000
 UP4  H9   C9   C6   111.35  3.000
 UP4  H8   C9   C6   111.07  3.000
 UP4  H7   C9   C6   111.30  3.000
 UP4  H10  C10  C    121.18  3.000
 UP4  H10  C10  C11  119.62  3.000
 UP4  C    C10  C11  119.18  3.000
 UP4  CL1  C11  C12  118.97  3.000
 UP4  CL1  C11  C10  119.28  3.000
 UP4  C12  C11  C10  121.75  3.000
 UP4  H11  C12  C13  121.03  3.000
 UP4  H11  C12  C11  121.00  3.000
 UP4  C13  C12  C11  117.97  3.000
 UP4  C14  C13  CL   119.42  3.000
 UP4  CL   C13  C12  118.84  3.000
 UP4  C14  C13  C12  121.75  3.000
 UP4  H12  C14  C    120.30  3.000
 UP4  H12  C14  C13  120.46  3.000
 UP4  C    C14  C13  119.24  3.000
 UP4  C1   C    C14  117.86  3.000
 UP4  C14  C    C10  120.12  3.000
 UP4  C1   C    C10  121.98  3.000
 UP4  N    C1   O2   124.04  3.000
 UP4  O2   C1   C    120.12  3.000
 UP4  N    C1   C    115.83  3.000
 UP4  H13  N    C1   118.28  3.000
 UP4  H13  N    C2   116.56  3.000
 UP4  C1   N    C2   122.70  3.000
 UP4  H16  C4   H15  106.28  3.000
 UP4  H16  C4   C5   110.39  3.000
 UP4  H15  C4   C5   110.17  3.000
 UP4  H16  C4   C2   109.06  3.000
 UP4  H15  C4   C2   107.13  3.000
 UP4  C5   C4   C2   113.50  3.000
 UP4  C8   C6   C9   108.69  3.000
 UP4  C9   C6   C7   108.82  3.000
 UP4  C8   C6   C7   109.43  3.000
 UP4  C9   C6   C5   108.00  3.000
 UP4  C7   C6   C5   110.87  3.000
 UP4  C8   C6   C5   110.97  3.000
 UP4  H19  C8   H18  107.20  3.000
 UP4  H19  C8   H17  107.71  3.000
 UP4  H18  C8   H17  107.63  3.000
 UP4  H19  C8   C6   112.05  3.000
 UP4  H18  C8   C6   110.76  3.000
 UP4  H17  C8   C6   111.27  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  Var_01    N    C1   C    C10    30.91  30.0  3
 UP4  Var_02    C6   C5   C4   C2   -175.46  30.0  3
 UP4  Var_03    C4   C5   C6   C7    -59.93  30.0  3
 UP4  Var_04    H17  C8   C6   C5     56.02  30.0  3
 UP4  Var_05    H4   C7   C6   C5    -54.84  30.0  3
 UP4  Var_06    H7   C9   C6   C5     60.75  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

