# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 18:18:42 2022
#   Inital geometry file: a 145 line input string
#   Ligand name: N-{(2S,3R)-3-amino-4-[4-(benzyloxy)phenyl]-2-hydroxybutanoyl}-L-leucine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](NC(=O)[C@@H](O)[C@H](N)Cc1ccc(OCc2ccccc2)cc1)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
 D50  D50  N-{(2S,3R)-3-amino-4-[4-(benzyloxy)phenyl]-2-hydroxybutanoyl}-L-leucine  ligand  59  30  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_D50
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
 D50  C1    C  CH3    0  -0.651    6.7604  -1.6727   3.1677
 D50  N1    N  NH1    0  -0.611    4.1865   0.0745   0.1123
 D50  O1    O  O      0  -0.511    4.5139   1.2300  -1.8085
 D50  C2    C  CH1    0  -0.224    6.3674  -0.8991   1.9125
 D50  N2    N  NH2    0  -0.782    1.1861   1.2119  -1.7788
 D50  O2    O  OH1    0  -0.676    3.0074   3.2520  -1.0393
 D50  C3    C  CH3    0  -0.660    7.6090  -0.4070   1.1771
 D50  O3    O  O2     0  -0.471   -4.6712  -0.0320   0.3981
 D50  C4    C  CH2    0  -0.439    5.4812  -1.7725   1.0232
 D50  C5    C  CH1    0  -0.209    4.9456  -1.1030  -0.2426
 D50  C7    C  CH1    0  -0.074    2.8913   2.0839  -0.2762
 D50  C8    C  CH1    0  -0.096    1.4859   1.4716  -0.3859
 D50  C9    C  CH2    0  -0.528    0.4614   2.3635   0.3389
 D50  C10   C  C      0   0.120   -0.9139   1.7639   0.3411
 D50  C11   C  C1     0  -0.289   -1.2695   0.7916   1.2779
 D50  C12   C  C1     0  -0.331   -2.5220   0.2069   1.2754
 D50  C13   C  C      0   0.367   -3.4695   0.5799   0.3194
 D50  C14   C  CH2    0  -0.268   -5.6738   0.3233  -0.5443
 D50  C15   C  CR6    0   0.101   -6.8965  -0.4776  -0.2141
 D50  C16   C  CR16   0  -0.295   -7.8840   0.0522   0.6107
 D50  C17   C  CR16   0  -0.242   -9.0004  -0.7008   0.9494
 D50  C18   C  CR16   0  -0.261   -9.1357  -1.9959   0.4670
 D50  C19   C  CR16   0  -0.243   -8.1540  -2.5327  -0.3568
 D50  C20   C  CR16   0  -0.289   -7.0403  -1.7763  -0.6941
 D50  C21   C  C1     0  -0.369   -3.1324   1.5408  -0.6280
 D50  C22   C  C1     0  -0.310   -1.8652   2.1161  -0.6065
 D50  C23   C  C      0   0.414    4.1073  -2.1195  -1.0598
 D50  H1    H  HCH3   0   0.224    7.3514  -1.0545   3.8459
 D50  H1A   H  HCH3   0   0.222    5.8819  -2.0203   3.7151
 D50  H1B   H  HCH3   0   0.212    7.3592  -2.5508   2.9136
 D50  HN1   H  HNH1   0   0.388    3.5842  -0.0036   0.9176
 D50  H2    H  HCH1   0   0.214    5.7899  -0.0230   2.2278
 D50  HN2   H  HNH2   0   0.350    0.3752   0.6123  -1.8514
 D50  HN2A  H  HNH2   0   0.334    0.9429   2.0757  -2.2489
 D50  HO2   H  HOH1   0   0.441    3.4745   2.9940  -1.8476
 D50  H3    H  HCH3   0   0.212    8.1951  -1.2479   0.7965
 D50  H3A   H  HCH3   0   0.228    7.3605   0.2326   0.3293
 D50  H3B   H  HCH3   0   0.226    8.2532   0.1696   1.8434
 D50  H4    H  HCH2   0   0.229    6.0434  -2.6593   0.7192
 D50  H4A   H  HCH2   0   0.222    4.6322  -2.1379   1.6143
 D50  H5    H  HCH1   0   0.238    5.7880  -0.7808  -0.8582
 D50  H7    H  HCH1   0   0.245    3.0804   2.3311   0.7761
 D50  H8    H  HCH1   0   0.241    1.5089   0.5039   0.1251
 D50  H9    H  HCH2   0   0.239    0.7954   2.5245   1.3682
 D50  H9A   H  HCH2   0   0.244    0.4363   3.3457  -0.1415
 D50  H11   H  H      0   0.246   -0.5527   0.4888   2.0330
 D50  H12   H  H      0   0.258   -2.7780  -0.5380   2.0191
 D50  H14   H  HCH2   0   0.240   -5.8927   1.3950  -0.4849
 D50  H14A  H  HCH2   0   0.240   -5.3320   0.1080  -1.5627
 D50  H16   H  HCR6   0   0.254   -7.7814   1.0630   0.9876
 D50  H17   H  HCR6   0   0.258   -9.7637  -0.2757   1.5881
 D50  H18   H  HCR6   0   0.258  -10.0048  -2.5849   0.7305
 D50  H19   H  HCR6   0   0.258   -8.2582  -3.5401  -0.7380
 D50  H20   H  HCR6   0   0.254   -6.2791  -2.1990  -1.3391
 D50  H21   H  H      0   0.277   -3.8350   1.8623  -1.3848
 D50  H22   H  H      0   0.248   -1.6302   2.8713  -1.3475
 D50  O5    O  O      0  -0.585    2.8744  -1.9729  -1.0661
 D50  O4    O  OC    -1  -0.620    4.7689  -3.0193  -1.6167
 D50  C6    C  C      0   0.532    3.9397   1.0737  -0.7361

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
 D50  C1   C2    single    1.526  0.020  1.526
 D50  C1   H1    single    0.970  0.020  1.090
 D50  C1   H1A   single    0.970  0.020  1.090
 D50  C1   H1B   single    0.970  0.020  1.090
 D50  N1   C5    single    1.445  0.020  1.445
 D50  N1   C6    single    1.334  0.020  1.334
 D50  N1   HN1   single    0.890  0.020  1.040
 D50  C6   O1    double    1.227  0.020  1.227
 D50  C2   C3    single    1.525  0.020  1.525
 D50  C2   C4    single    1.529  0.020  1.529
 D50  C2   H2    single    0.970  0.020  1.090
 D50  N2   C8    single    1.448  0.020  1.448
 D50  N2   HN2   single    0.890  0.020  1.040
 D50  N2   HN2A  single    0.890  0.020  1.040
 D50  O2   C7    single    1.400  0.020  1.400
 D50  O2   HO2   single    0.850  0.020  0.980
 D50  C3   H3    single    0.970  0.020  1.090
 D50  C3   H3A   single    0.970  0.020  1.090
 D50  C3   H3B   single    0.970  0.020  1.090
 D50  C13  O3    single    1.351  0.020  1.351
 D50  O3   C14   single    1.421  0.020  1.421
 D50  C4   C5    single    1.529  0.020  1.529
 D50  C4   H4    single    0.970  0.020  1.090
 D50  C4   H4A   single    0.970  0.020  1.090
 D50  C23  O4    deloc     1.248  0.020  1.248
 D50  C5   C23   single    1.550  0.020  1.550
 D50  C5   H5    single    0.970  0.020  1.090
 D50  C23  O5    deloc     1.242  0.020  1.242
 D50  C6   C7    single    1.527  0.020  1.527
 D50  C7   C8    single    1.537  0.020  1.537
 D50  C7   H7    single    0.970  0.020  1.090
 D50  C8   C9    single    1.540  0.020  1.540
 D50  C8   H8    single    0.970  0.020  1.090
 D50  C9   C10   single    1.500  0.020  1.500
 D50  C9   H9    single    0.970  0.020  1.090
 D50  C9   H9A   single    0.970  0.020  1.090
 D50  C10  C11   aromatic  1.396  0.020  1.396
 D50  C10  C22   aromatic  1.388  0.020  1.388
 D50  C11  C12   aromatic  1.382  0.020  1.382
 D50  C11  H11   single    0.930  0.020  1.080
 D50  C12  C13   aromatic  1.397  0.020  1.397
 D50  C12  H12   single    0.930  0.020  1.080
 D50  C21  C13   aromatic  1.391  0.020  1.391
 D50  C14  C15   single    1.498  0.020  1.498
 D50  C14  H14   single    0.970  0.020  1.090
 D50  C14  H14A  single    0.970  0.020  1.090
 D50  C20  C15   aromatic  1.392  0.020  1.392
 D50  C15  C16   aromatic  1.391  0.020  1.391
 D50  C16  C17   aromatic  1.389  0.020  1.389
 D50  C16  H16   single    0.930  0.020  1.080
 D50  C18  C17   aromatic  1.389  0.020  1.389
 D50  C17  H17   single    0.930  0.020  1.080
 D50  C19  C18   aromatic  1.389  0.020  1.389
 D50  C18  H18   single    0.930  0.020  1.080
 D50  C20  C19   aromatic  1.388  0.020  1.388
 D50  C19  H19   single    0.930  0.020  1.080
 D50  C20  H20   single    0.930  0.020  1.080
 D50  C22  C21   aromatic  1.392  0.020  1.392
 D50  C21  H21   single    0.930  0.020  1.080
 D50  C22  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
 D50  H1B   C1   H1A  107.55  3.000
 D50  H1B   C1   H1   107.63  3.000
 D50  H1A   C1   H1   107.73  3.000
 D50  H1B   C1   C2   110.93  3.000
 D50  H1A   C1   C2   111.50  3.000
 D50  H1    C1   C2   111.31  3.000
 D50  HN1   N1   C6   117.09  3.000
 D50  HN1   N1   C5   116.52  3.000
 D50  C6    N1   C5   123.46  3.000
 D50  H2    C2   C4   108.58  3.000
 D50  H2    C2   C3   108.05  3.000
 D50  C4    C2   C3   112.07  3.000
 D50  H2    C2   C1   107.72  3.000
 D50  C4    C2   C1   109.76  3.000
 D50  C3    C2   C1   110.53  3.000
 D50  HN2A  N2   HN2  106.25  3.000
 D50  HN2A  N2   C8   110.07  3.000
 D50  HN2   N2   C8   109.97  3.000
 D50  HO2   O2   C7   105.82  3.000
 D50  H3B   C3   H3A  107.41  3.000
 D50  H3B   C3   H3   107.60  3.000
 D50  H3A   C3   H3   107.61  3.000
 D50  H3B   C3   C2   110.90  3.000
 D50  H3A   C3   C2   112.25  3.000
 D50  H3    C3   C2   110.87  3.000
 D50  C14   O3   C13  118.41  3.000
 D50  H4A   C4   H4   106.12  3.000
 D50  H4A   C4   C5   108.71  3.000
 D50  H4    C4   C5   107.77  3.000
 D50  H4A   C4   C2   108.98  3.000
 D50  H4    C4   C2   109.09  3.000
 D50  C5    C4   C2   115.75  3.000
 D50  H5    C5   C23  108.27  3.000
 D50  H5    C5   C4   109.00  3.000
 D50  C23   C5   C4   109.80  3.000
 D50  H5    C5   N1   107.65  3.000
 D50  C23   C5   N1   112.31  3.000
 D50  C4    C5   N1   109.72  3.000
 D50  H7    C7   C8   108.41  3.000
 D50  H7    C7   C6   108.63  3.000
 D50  C8    C7   C6   110.05  3.000
 D50  H7    C7   O2   108.69  3.000
 D50  C8    C7   O2   111.68  3.000
 D50  C6    C7   O2   109.32  3.000
 D50  H8    C8   C9   107.84  3.000
 D50  H8    C8   C7   107.44  3.000
 D50  C9    C8   C7   110.13  3.000
 D50  H8    C8   N2   107.14  3.000
 D50  C9    C8   N2   114.76  3.000
 D50  C7    C8   N2   109.23  3.000
 D50  H9A   C9   H9   106.74  3.000
 D50  H9A   C9   C10  109.79  3.000
 D50  H9    C9   C10  109.71  3.000
 D50  H9A   C9   C8   109.19  3.000
 D50  H9    C9   C8   108.96  3.000
 D50  C10   C9   C8   112.28  3.000
 D50  C22   C10  C11  117.40  3.000
 D50  C22   C10  C9   121.72  3.000
 D50  C11   C10  C9   120.85  3.000
 D50  H11   C11  C12  118.83  3.000
 D50  H11   C11  C10  119.56  3.000
 D50  C12   C11  C10  121.61  3.000
 D50  H12   C12  C13  119.55  3.000
 D50  H12   C12  C11  120.25  3.000
 D50  C13   C12  C11  120.20  3.000
 D50  C21   C13  C12  119.10  3.000
 D50  C21   C13  O3   124.63  3.000
 D50  C12   C13  O3   116.27  3.000
 D50  H14A  C14  H14  107.76  3.000
 D50  H14A  C14  C15  110.76  3.000
 D50  H14   C14  C15  110.35  3.000
 D50  H14A  C14  O3   110.31  3.000
 D50  H14   C14  O3   110.46  3.000
 D50  C15   C14  O3   107.21  3.000
 D50  C20   C15  C16  119.10  3.000
 D50  C16   C15  C14  120.41  3.000
 D50  C20   C15  C14  120.46  3.000
 D50  H16   C16  C17  119.81  3.000
 D50  H16   C16  C15  119.61  3.000
 D50  C17   C16  C15  120.58  3.000
 D50  H17   C17  C18  120.17  3.000
 D50  H17   C17  C16  119.87  3.000
 D50  C18   C17  C16  119.96  3.000
 D50  H18   C18  C19  120.09  3.000
 D50  H18   C18  C17  120.08  3.000
 D50  C19   C18  C17  119.83  3.000
 D50  H19   C19  C20  119.93  3.000
 D50  H19   C19  C18  120.03  3.000
 D50  C20   C19  C18  120.03  3.000
 D50  H20   C20  C19  119.72  3.000
 D50  H20   C20  C15  119.78  3.000
 D50  C19   C20  C15  120.50  3.000
 D50  H21   C21  C22  118.64  3.000
 D50  H21   C21  C13  121.64  3.000
 D50  C22   C21  C13  119.71  3.000
 D50  H22   C22  C21  118.35  3.000
 D50  H22   C22  C10  119.66  3.000
 D50  C21   C22  C10  121.98  3.000
 D50  O5    C23  C5   117.53  3.000
 D50  O5    C23  O4   127.54  3.000
 D50  C5    C23  O4   114.92  3.000
 D50  C7    C6   O1   120.03  3.000
 D50  C7    C6   N1   115.54  3.000
 D50  O1    C6   N1   124.41  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
 D50  CONST_01  C13  C12  C11  C10     0.00   0.0  0
 D50  CONST_02  C13  C21  C22  C10     0.00   0.0  0
 D50  CONST_03  C21  C22  C10  C11     0.00   0.0  0
 D50  CONST_04  C21  C13  C12  C11     0.00   0.0  0
 D50  CONST_05  C22  C10  C11  C12     0.00   0.0  0
 D50  CONST_06  C22  C21  C13  C12     0.00   0.0  0
 D50  CONST_07  C18  C19  C20  C15     0.00   0.0  0
 D50  CONST_08  C18  C17  C16  C15     0.00   0.0  0
 D50  CONST_09  C19  C20  C15  C16     0.00   0.0  0
 D50  CONST_10  C19  C18  C17  C16     0.00   0.0  0
 D50  CONST_11  C20  C15  C16  C17     0.00   0.0  0
 D50  CONST_12  C20  C19  C18  C17     0.00   0.0  0
 D50  CONST_13  C11  C12  C13  O3    180.00   0.0  0
 D50  CONST_14  C22  C21  C13  O3    180.00   0.0  0
 D50  CONST_15  C12  C11  C10  C9    180.00   0.0  0
 D50  CONST_16  C21  C22  C10  C9    180.00   0.0  0
 D50  CONST_17  C19  C20  C15  C14   180.00   0.0  0
 D50  CONST_18  C17  C16  C15  C14   180.00   0.0  0
 D50  CONST_19  H12  C12  C11  C10   180.00   0.0  0
 D50  CONST_20  H21  C21  C22  C10   180.00   0.0  0
 D50  CONST_21  H22  C22  C10  C11   180.00   0.0  0
 D50  CONST_22  H11  C11  C12  C13   180.00   0.0  0
 D50  CONST_23  H19  C19  C20  C15   180.00   0.0  0
 D50  CONST_24  H17  C17  C16  C15   180.00   0.0  0
 D50  CONST_25  H20  C20  C15  C16   180.00   0.0  0
 D50  CONST_26  H18  C18  C17  C16   180.00   0.0  0
 D50  CONST_27  H16  C16  C17  C18   180.00   0.0  0
 D50  CONST_28  C5   N1   C6   O1      0.00   0.0  0
 D50  CONST_29  C7   C6   N1   C5    180.00   0.0  0
 D50  CONST_30  HN1  N1   C6   O1    180.00   0.0  0
 D50  Var_01    C20  C15  C14  O3    -84.30  30.0  2
 D50  Var_02    C11  C10  C9   C8     81.86  30.0  2
 D50  Var_03    C15  C14  O3   C13  -178.95  30.0  3
 D50  Var_04    C21  C13  O3   C14    -0.20  30.0  1
 D50  Var_05    C5   C4   C2   C1    176.89  30.0  3
 D50  Var_06    H3   C3   C2   C1     65.24  30.0  3
 D50  Var_07    H1   C1   C2   C3     58.83  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
 D50  chir_01  C5  N1  C4  C23  negativ
 D50  chir_02  C7  O2  C6  C8   positiv
 D50  chir_03  C8  N2  C9  C7   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
 D50  plan-1  O3   0.020
 D50  plan-1  C9   0.020
 D50  plan-1  C10  0.020
 D50  plan-1  C11  0.020
 D50  plan-1  C12  0.020
 D50  plan-1  C13  0.020
 D50  plan-1  C21  0.020
 D50  plan-1  C22  0.020
 D50  plan-1  H11  0.020
 D50  plan-1  H12  0.020
 D50  plan-1  H21  0.020
 D50  plan-1  H22  0.020
 D50  plan-2  C14  0.020
 D50  plan-2  C15  0.020
 D50  plan-2  C16  0.020
 D50  plan-2  C17  0.020
 D50  plan-2  C18  0.020
 D50  plan-2  C19  0.020
 D50  plan-2  C20  0.020
 D50  plan-2  H16  0.020
 D50  plan-2  H17  0.020
 D50  plan-2  H18  0.020
 D50  plan-2  H19  0.020
 D50  plan-2  H20  0.020
 D50  plan-3  N1   0.020
 D50  plan-3  O1   0.020
 D50  plan-3  C5   0.020
 D50  plan-3  C7   0.020
 D50  plan-3  HN1  0.020
 D50  plan-3  C6   0.020
 D50  plan-4  C5   0.020
 D50  plan-4  C23  0.020
 D50  plan-4  O5   0.020
 D50  plan-4  O4   0.020

