# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 16:51:56 2022
#   Inital geometry file: a 118 line input string
#   Ligand name: 4-methyl-N-(6-phenoxypyridine-3-carbonyl)-L-leucine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(C)C[C@H](NC(=O)c1ccc(Oc2ccccc2)nc1)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
 UOY  UOY  4-methyl-N-(6-phenoxypyridine-3-carbonyl)-L-leucine  ligand  46  25  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_UOY
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
 UOY  C2   C  C      0   0.528  -33.4587  39.5671  15.7524
 UOY  C3   C  CR6    0  -0.147  -33.6070  38.1516  16.2034
 UOY  C5   C  CR16   0  -0.407  -34.8953  36.4691  17.3390
 UOY  C7   C  CR6    0   0.304  -34.7738  33.8563  18.4057
 UOY  C9   C  CR16   0  -0.251  -36.6308  32.4262  18.8808
 UOY  C10  C  CR16   0  -0.253  -36.6096  32.8392  20.2056
 UOY  C11  C  CR16   0  -0.250  -35.6609  33.7635  20.6256
 UOY  C12  C  CR16   0  -0.295  -34.7344  34.2746  19.7284
 UOY  C13  C  CR16   0  -0.086  -32.6185  37.1889  16.0467
 UOY  C18  C  CH3    0  -0.636  -28.6746  41.0214  12.9339
 UOY  C    C  C      0   0.407  -33.5783  41.6031  13.3051
 UOY  O2   O  OC    -1  -0.593  -34.4015  40.7658  12.9001
 UOY  C1   C  CH1    0  -0.188  -32.3869  41.0842  14.1641
 UOY  C14  C  CH2    0  -0.431  -31.1132  41.0645  13.3125
 UOY  C17  C  CH3    0  -0.642  -29.5634  42.3079  14.8662
 UOY  C16  C  CH3    0  -0.644  -29.5602  39.8132  14.9150
 UOY  N    N  NH1    0  -0.628  -32.6334  39.7730  14.7209
 UOY  O1   O  O      0  -0.494  -34.0499  40.4683  16.3367
 UOY  N1   N  N      0  -0.423  -32.7232  35.9455  16.4950
 UOY  C6   C  CR6    0   0.496  -33.8280  35.5967  17.1201
 UOY  C4   C  CR16   0  -0.144  -34.7621  37.7627  16.8806
 UOY  O    O  O2     0  -0.477  -33.8312  34.3060  17.5097
 UOY  C8   C  CR16   0  -0.305  -35.7147  32.9374  17.9705
 UOY  H1   H  HCR6   0   0.293  -35.7966  36.1569  17.8473
 UOY  H2   H  HCR6   0   0.264  -37.3653  31.7047  18.5478
 UOY  H3   H  HCR6   0   0.260  -37.3268  32.4398  20.9103
 UOY  H4   H  HCR6   0   0.264  -35.6352  34.0860  21.6582
 UOY  H5   H  HCR6   0   0.280  -33.9876  34.9875  20.0555
 UOY  H6   H  HCR6   0   0.273  -31.6786  37.4275  15.5599
 UOY  H7   H  HCH3   0   0.221  -27.6723  41.0299  13.3673
 UOY  H8   H  HCH3   0   0.220  -28.7609  40.1266  12.3131
 UOY  H9   H  HCH3   0   0.219  -28.7611  41.8900  12.2773
 UOY  H11  H  HCH1   0   0.231  -32.2565  41.7857  14.9911
 UOY  H12  H  HCH2   0   0.232  -31.1326  41.9587  12.6849
 UOY  H13  H  HCH2   0   0.222  -31.1687  40.2115  12.6238
 UOY  H14  H  HCH3   0   0.224  -30.2864  42.3704  15.6817
 UOY  H15  H  HCH3   0   0.222  -28.5684  42.3305  15.3158
 UOY  H16  H  HCH3   0   0.219  -29.6726  43.2071  14.2556
 UOY  H17  H  HCH3   0   0.227  -30.2249  39.8229  15.7792
 UOY  H18  H  HCH3   0   0.218  -29.7451  38.8880  14.3635
 UOY  H19  H  HCH3   0   0.219  -28.5354  39.7734  15.2917
 UOY  H20  H  HNH1   0   0.392  -32.3348  38.9808  14.1753
 UOY  H21  H  HCR6   0   0.276  -35.5640  38.4713  17.0404
 UOY  H22  H  HCR6   0   0.273  -35.7259  32.6210  16.9352
 UOY  O3   O  O      0  -0.609  -33.5647  42.8302  13.0834
 UOY  C15  C  CT     0  -0.080  -29.7478  41.0435  14.0263

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
 UOY  C18  C15  single    1.531  0.020  1.531
 UOY  O3   C    deloc     1.247  0.020  1.247
 UOY  C14  C15  single    1.541  0.020  1.541
 UOY  C14  C1   single    1.532  0.020  1.532
 UOY  O2   C    deloc     1.242  0.020  1.242
 UOY  C    C1   single    1.558  0.020  1.558
 UOY  C15  C16  single    1.529  0.020  1.529
 UOY  C15  C17  single    1.529  0.020  1.529
 UOY  C1   N    single    1.446  0.020  1.446
 UOY  N    C2   single    1.337  0.020  1.337
 UOY  C2   O1   double    1.226  0.020  1.226
 UOY  C2   C3   single    1.493  0.020  1.493
 UOY  C3   C13  aromatic  1.389  0.020  1.389
 UOY  C3   C4   aromatic  1.394  0.020  1.394
 UOY  C13  N1   aromatic  1.326  0.020  1.326
 UOY  N1   C6   aromatic  1.316  0.020  1.316
 UOY  C4   C5   aromatic  1.379  0.020  1.379
 UOY  C6   C5   aromatic  1.396  0.020  1.396
 UOY  C6   O    single    1.348  0.020  1.348
 UOY  C8   C9   aromatic  1.389  0.020  1.389
 UOY  C8   C7   aromatic  1.385  0.020  1.385
 UOY  O    C7   single    1.376  0.020  1.376
 UOY  C9   C10  aromatic  1.388  0.020  1.388
 UOY  C7   C12  aromatic  1.388  0.020  1.388
 UOY  C10  C11  aromatic  1.389  0.020  1.389
 UOY  C12  C11  aromatic  1.387  0.020  1.387
 UOY  C5   H1   single    0.930  0.020  1.080
 UOY  C9   H2   single    0.930  0.020  1.080
 UOY  C10  H3   single    0.930  0.020  1.080
 UOY  C11  H4   single    0.930  0.020  1.080
 UOY  C12  H5   single    0.930  0.020  1.080
 UOY  C13  H6   single    0.930  0.020  1.080
 UOY  C18  H7   single    0.970  0.020  1.090
 UOY  C18  H8   single    0.970  0.020  1.090
 UOY  C18  H9   single    0.970  0.020  1.090
 UOY  C1   H11  single    0.970  0.020  1.090
 UOY  C14  H12  single    0.970  0.020  1.090
 UOY  C14  H13  single    0.970  0.020  1.090
 UOY  C17  H14  single    0.970  0.020  1.090
 UOY  C17  H15  single    0.970  0.020  1.090
 UOY  C17  H16  single    0.970  0.020  1.090
 UOY  C16  H17  single    0.970  0.020  1.090
 UOY  C16  H18  single    0.970  0.020  1.090
 UOY  C16  H19  single    0.970  0.020  1.090
 UOY  N    H20  single    0.860  0.020  1.020
 UOY  C4   H21  single    0.930  0.020  1.080
 UOY  C8   H22  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
 UOY  O1   C2   N    123.51  3.000
 UOY  O1   C2   C3   120.34  3.000
 UOY  N    C2   C3   116.13  3.000
 UOY  C4   C3   C13  116.82  3.000
 UOY  C4   C3   C2   119.57  3.000
 UOY  C13  C3   C2   123.53  3.000
 UOY  H1   C5   C4   120.53  3.000
 UOY  H1   C5   C6   122.06  3.000
 UOY  C4   C5   C6   117.41  3.000
 UOY  C8   C7   O    118.52  3.000
 UOY  O    C7   C12  120.17  3.000
 UOY  C8   C7   C12  121.24  3.000
 UOY  H2   C9   C8   119.43  3.000
 UOY  H2   C9   C10  120.17  3.000
 UOY  C8   C9   C10  120.40  3.000
 UOY  H3   C10  C11  120.09  3.000
 UOY  H3   C10  C9   120.11  3.000
 UOY  C11  C10  C9   119.80  3.000
 UOY  H4   C11  C12  119.44  3.000
 UOY  H4   C11  C10  120.19  3.000
 UOY  C12  C11  C10  120.37  3.000
 UOY  H5   C12  C11  120.51  3.000
 UOY  H5   C12  C7   120.38  3.000
 UOY  C11  C12  C7   119.10  3.000
 UOY  H6   C13  N1   115.23  3.000
 UOY  H6   C13  C3   120.99  3.000
 UOY  N1   C13  C3   123.76  3.000
 UOY  H9   C18  H8   107.67  3.000
 UOY  H9   C18  H7   107.76  3.000
 UOY  H8   C18  H7   107.72  3.000
 UOY  H9   C18  C15  111.21  3.000
 UOY  H8   C18  C15  111.21  3.000
 UOY  H7   C18  C15  111.10  3.000
 UOY  C1   C    O2   117.53  3.000
 UOY  C1   C    O3   114.67  3.000
 UOY  O2   C    O3   127.78  3.000
 UOY  H11  C1   N    108.13  3.000
 UOY  H11  C1   C14  109.26  3.000
 UOY  N    C1   C14  110.13  3.000
 UOY  H11  C1   C    107.15  3.000
 UOY  N    C1   C    112.59  3.000
 UOY  C14  C1   C    109.49  3.000
 UOY  H13  C14  H12  105.94  3.000
 UOY  H13  C14  C1   108.46  3.000
 UOY  H12  C14  C1   107.09  3.000
 UOY  H13  C14  C15  108.96  3.000
 UOY  H12  C14  C15  107.04  3.000
 UOY  C1   C14  C15  118.64  3.000
 UOY  H16  C17  H15  107.70  3.000
 UOY  H16  C17  H14  107.71  3.000
 UOY  H15  C17  H14  107.14  3.000
 UOY  H16  C17  C15  111.19  3.000
 UOY  H15  C17  C15  110.68  3.000
 UOY  H14  C17  C15  112.20  3.000
 UOY  H19  C16  H18  107.57  3.000
 UOY  H19  C16  H17  107.39  3.000
 UOY  H18  C16  H17  107.72  3.000
 UOY  H19  C16  C15  110.17  3.000
 UOY  H18  C16  C15  111.54  3.000
 UOY  H17  C16  C15  112.25  3.000
 UOY  H20  N    C1   117.01  3.000
 UOY  H20  N    C2   118.67  3.000
 UOY  C1   N    C2   122.83  3.000
 UOY  C6   N1   C13  118.38  3.000
 UOY  O    C6   N1   113.13  3.000
 UOY  O    C6   C5   123.45  3.000
 UOY  N1   C6   C5   123.41  3.000
 UOY  H21  C4   C5   119.58  3.000
 UOY  H21  C4   C3   120.20  3.000
 UOY  C5   C4   C3   120.21  3.000
 UOY  C6   O    C7   120.17  3.000
 UOY  H22  C8   C9   120.82  3.000
 UOY  H22  C8   C7   120.09  3.000
 UOY  C9   C8   C7   119.09  3.000
 UOY  C16  C15  C17  109.34  3.000
 UOY  C17  C15  C14  110.49  3.000
 UOY  C16  C15  C14  112.88  3.000
 UOY  C17  C15  C18  108.62  3.000
 UOY  C16  C15  C18  108.47  3.000
 UOY  C14  C15  C18  106.90  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
 UOY  CONST_01  C6   N1   C13  C3      0.00   0.0  0
 UOY  CONST_02  C6   C5   C4   C3      0.00   0.0  0
 UOY  CONST_03  C13  C3   C4   C5      0.00   0.0  0
 UOY  CONST_04  C13  N1   C6   C5      0.00   0.0  0
 UOY  CONST_05  C10  C9   C8   C7      0.00   0.0  0
 UOY  CONST_06  C10  C11  C12  C7      0.00   0.0  0
 UOY  CONST_07  C12  C7   C8   C9      0.00   0.0  0
 UOY  CONST_08  C12  C11  C10  C9      0.00   0.0  0
 UOY  CONST_09  C8   C9   C10  C11     0.00   0.0  0
 UOY  CONST_10  C8   C7   C12  C11     0.00   0.0  0
 UOY  CONST_11  C4   C3   C13  N1      0.00   0.0  0
 UOY  CONST_12  C4   C5   C6   N1      0.00   0.0  0
 UOY  CONST_13  N1   C13  C3   C2    180.00   0.0  0
 UOY  CONST_14  C5   C4   C3   C2    180.00   0.0  0
 UOY  CONST_15  O    C7   C8   C9    180.00   0.0  0
 UOY  CONST_16  O    C7   C12  C11   180.00   0.0  0
 UOY  CONST_17  O    C6   N1   C13   180.00   0.0  0
 UOY  CONST_18  O    C6   C5   C4    180.00   0.0  0
 UOY  CONST_19  H1   C5   C4   C3    180.00   0.0  0
 UOY  CONST_20  H2   C9   C8   C7    180.00   0.0  0
 UOY  CONST_21  H4   C11  C12  C7    180.00   0.0  0
 UOY  CONST_22  H22  C8   C9   C10   180.00   0.0  0
 UOY  CONST_23  H5   C12  C11  C10   180.00   0.0  0
 UOY  CONST_24  H3   C10  C11  C12   180.00   0.0  0
 UOY  CONST_25  H21  C4   C3   C13   180.00   0.0  0
 UOY  CONST_26  H6   C13  N1   C6    180.00   0.0  0
 UOY  CONST_27  C1   N    C2   C3    180.00   0.0  0
 UOY  CONST_28  H20  N    C2   C3      0.00   0.0  0
 UOY  CONST_29  O1   C2   N    C1      0.00   0.0  0
 UOY  Var_01    N1   C6   O    C7    166.56  30.0  2
 UOY  Var_02    C8   C7   O    C6    113.75  30.0  2
 UOY  Var_03    N    C2   C3   C13    27.64  30.0  2
 UOY  Var_04    C1   C14  C15  C18   179.79  30.0  2
 UOY  Var_05    H17  C16  C15  C18   173.80  30.0  3
 UOY  Var_06    H14  C17  C15  C18  -178.58  30.0  3
 UOY  Var_07    H7   C18  C15  C14   178.64  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
 UOY  chir_01  C1  C14  C  N  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
 UOY  plan-1  C2   0.020
 UOY  plan-1  C3   0.020
 UOY  plan-1  C5   0.020
 UOY  plan-1  C13  0.020
 UOY  plan-1  N1   0.020
 UOY  plan-1  C6   0.020
 UOY  plan-1  C4   0.020
 UOY  plan-1  O    0.020
 UOY  plan-1  H1   0.020
 UOY  plan-1  H6   0.020
 UOY  plan-1  H21  0.020
 UOY  plan-2  C7   0.020
 UOY  plan-2  C9   0.020
 UOY  plan-2  C10  0.020
 UOY  plan-2  C11  0.020
 UOY  plan-2  C12  0.020
 UOY  plan-2  O    0.020
 UOY  plan-2  C8   0.020
 UOY  plan-2  H2   0.020
 UOY  plan-2  H3   0.020
 UOY  plan-2  H4   0.020
 UOY  plan-2  H5   0.020
 UOY  plan-2  H22  0.020
 UOY  plan-3  C2   0.020
 UOY  plan-3  C3   0.020
 UOY  plan-3  C1   0.020
 UOY  plan-3  N    0.020
 UOY  plan-3  O1   0.020
 UOY  plan-3  H20  0.020
 UOY  plan-4  C    0.020
 UOY  plan-4  O2   0.020
 UOY  plan-4  C1   0.020
 UOY  plan-4  O3   0.020

