# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 15:10:50 2022
#   Inital geometry file: a 157 line input string
#   Ligand name: N-[(S)-({[(benzyloxy)carbonyl]amino}methyl)(hydroxy)phosphoryl]-L-leucyl-3-methyl-L-valine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](N[P](O)(=O)CNC(=O)OCc1ccccc1)C(=O)N[C@H](C(O)=O)C(C)(C)C
#
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
 5H8  5H8  N-[(S)-({[(benzyloxy)carbonyl]amino}methyl)(hydroxy)phosphoryl]-L-leucyl-3-methyl-L-valine  ligand  64  32  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_5H8
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
 5H8  C1   C  CR16   0  -0.263   7.6661  -2.6840   2.1863
 5H8  C2   C  CR16   0  -0.242   6.3945  -3.1158   1.8259
 5H8  C3   C  CR16   0  -0.285   5.6959  -2.4583   0.8247
 5H8  C9   C  C      0   0.749   3.5485   0.6996  -1.0299
 5H8  C11  C  CH2    0  -0.552   1.4138   1.8723  -0.8371
 5H8  C14  C  CH1    0  -0.199  -2.4303   1.7898  -0.6654
 5H8  C15  C  C      0   0.556  -3.3992   0.6083  -0.5415
 5H8  O17  O  O      0  -0.526   3.5671   0.6370  -2.2428
 5H8  C20  C  CH2    0  -0.390  -3.0766   2.9906  -1.3443
 5H8  C21  C  CH1    0  -0.243  -4.3070   3.5629  -0.6350
 5H8  C22  C  CH3    0  -0.664  -4.0323   3.8966   0.8289
 5H8  C30  C  C      0   0.418  -4.4772  -1.2204   2.3138
 5H8  C4   C  CR6    0   0.076   6.2563  -1.3613   0.1731
 5H8  P12  P  P      0   1.259   0.0790   0.6219  -0.5803
 5H8  O19  O  OP    -1  -0.792   0.4850  -0.6270  -1.3213
 5H8  O18  O  O      0  -0.800  -0.2044   0.5838   0.9087
 5H8  N13  N  NH1    0  -0.789  -1.2372   1.3656  -1.3745
 5H8  C23  C  CH3    0  -0.651  -4.8070   4.7983  -1.3781
 5H8  O24  O  O      0  -0.528  -4.2613   0.3963  -1.3927
 5H8  N16  N  NH1    0  -0.621  -3.1925  -0.1633   0.5278
 5H8  C25  C  CH1    0  -0.155  -3.9538  -1.3454   0.8623
 5H8  C26  C  CT     0  -0.087  -3.1376  -2.6466   0.6254
 5H8  C29  C  CH3    0  -0.665  -2.6387  -2.6710  -0.8226
 5H8  C28  C  CH3    0  -0.634  -4.0351  -3.8652   0.8468
 5H8  C5   C  CR16   0  -0.300   7.5273  -0.9348   0.5411
 5H8  C6   C  CR16   0  -0.242   8.2324  -1.5939   1.5411
 5H8  O8   O  O2     0  -0.485   4.4583   0.1015  -0.2443
 5H8  N10  N  NH1    0  -0.650   2.6689   1.3975  -0.2909
 5H8  H1   H  HCR6   0   0.258   8.2142  -3.1987   2.9648
 5H8  H2   H  HCR6   0   0.258   5.9497  -3.9681   2.3231
 5H8  H3   H  HCR6   0   0.255   4.7083  -2.8046   0.5429
 5H8  H6   H  HCH2   0   0.247   1.5451   2.0859  -1.8970
 5H8  H7   H  HCH2   0   0.247   1.1500   2.8151  -0.3537
 5H8  H8   H  HCH1   0   0.240  -2.1081   2.0887   0.3331
 5H8  H9   H  HCH2   0   0.215  -2.3100   3.7699  -1.4152
 5H8  H10  H  HCH2   0   0.214  -3.3468   2.7253  -2.3707
 5H8  H11  H  HCH1   0   0.219  -5.1028   2.8125  -0.6668
 5H8  H12  H  HCH3   0   0.227  -4.9049   4.3583   1.2940
 5H8  H13  H  HCH3   0   0.224  -3.7887   3.0092   1.4151
 5H8  H14  H  HCH3   0   0.213  -3.1981   4.5972   0.9232
 5H8  H15  H  HCH3   0   0.232  -1.2735  -1.8625   1.4443
 5H8  H16  H  HCH3   0   0.218  -2.2229  -2.7949   2.6064
 5H8  H17  H  HCH3   0   0.209  -1.3360  -3.6170   1.3262
 5H8  H19  H  HNH1   0   0.358  -1.4272   1.0083  -2.3010
 5H8  H20  H  HCH3   0   0.211  -4.0568   5.5930  -1.3661
 5H8  H21  H  HCH3   0   0.222  -5.0328   4.5730  -2.4221
 5H8  H22  H  HCH3   0   0.223  -5.7155   5.1939  -0.9205
 5H8  H23  H  HNH1   0   0.387  -2.4119   0.0684   1.1268
 5H8  H24  H  HCH1   0   0.222  -4.8068  -1.3747   0.1812
 5H8  H26  H  HCH3   0   0.213  -2.1905  -3.6426  -1.0467
 5H8  H27  H  HCH3   0   0.212  -3.4566  -2.5145  -1.5292
 5H8  H28  H  HCH3   0   0.248  -1.8759  -1.9135  -1.0054
 5H8  H29  H  HCH3   0   0.225  -4.4123  -3.9227   1.8665
 5H8  H30  H  HCH3   0   0.212  -4.8971  -3.8502   0.1752
 5H8  H31  H  HCH3   0   0.210  -3.4775  -4.7823   0.6453
 5H8  H32  H  HCR6   0   0.254   7.9736  -0.0833   0.0411
 5H8  H33  H  HCR6   0   0.258   9.2230  -1.2549   1.8148
 5H8  H34  H  HNH1   0   0.391   2.7041   1.2720   0.7090
 5H8  C7   C  CH2    0  -0.233   5.4849  -0.6489  -0.8971
 5H8  O32  O  O      0  -0.603  -3.7482  -0.6154   3.1236
 5H8  C27  C  CH3    0  -0.663  -1.9281  -2.7286   1.5588
 5H8  H4   H  HCH2   0   0.244   6.1387   0.0143  -1.4682
 5H8  H5   H  HCH2   0   0.244   5.0420  -1.3659  -1.5915
 5H8  O31  O  OC    -1  -0.610  -5.5833  -1.7436   2.5550

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
 5H8  C23  C21  single    1.526  0.020  1.526
 5H8  C21  C22  single    1.526  0.020  1.526
 5H8  C21  C20  single    1.531  0.020  1.531
 5H8  C28  C26  single    1.530  0.020  1.530
 5H8  C20  C14  single    1.523  0.020  1.523
 5H8  C27  C26  single    1.530  0.020  1.530
 5H8  C26  C29  single    1.532  0.020  1.532
 5H8  C26  C25  single    1.554  0.020  1.554
 5H8  C14  C15  single    1.533  0.020  1.533
 5H8  C14  N13  single    1.451  0.020  1.451
 5H8  O24  C15  double    1.230  0.020  1.230
 5H8  C15  N16  single    1.335  0.020  1.335
 5H8  N16  C25  single    1.445  0.020  1.445
 5H8  C25  C30  single    1.548  0.020  1.548
 5H8  N13  P12  single    1.708  0.020  1.708
 5H8  C30  O32  deloc     1.246  0.020  1.246
 5H8  C30  O31  deloc     1.247  0.020  1.247
 5H8  P12  O18  deloc     1.516  0.020  1.516
 5H8  P12  O19  deloc     1.508  0.020  1.508
 5H8  P12  C11  single    1.847  0.020  1.847
 5H8  C11  N10  single    1.449  0.020  1.449
 5H8  N10  C9   single    1.344  0.020  1.344
 5H8  O17  C9   double    1.215  0.020  1.215
 5H8  C9   O8   single    1.343  0.020  1.343
 5H8  O8   C7   single    1.429  0.020  1.429
 5H8  C5   C6   aromatic  1.390  0.020  1.390
 5H8  C5   C4   aromatic  1.390  0.020  1.390
 5H8  C7   C4   single    1.499  0.020  1.499
 5H8  C6   C1   aromatic  1.388  0.020  1.388
 5H8  C4   C3   aromatic  1.394  0.020  1.394
 5H8  C1   C2   aromatic  1.390  0.020  1.390
 5H8  C3   C2   aromatic  1.387  0.020  1.387
 5H8  C1   H1   single    0.930  0.020  1.080
 5H8  C2   H2   single    0.930  0.020  1.080
 5H8  C3   H3   single    0.930  0.020  1.080
 5H8  C7   H4   single    0.970  0.020  1.090
 5H8  C7   H5   single    0.970  0.020  1.090
 5H8  C11  H6   single    0.970  0.020  1.090
 5H8  C11  H7   single    0.970  0.020  1.090
 5H8  C14  H8   single    0.970  0.020  1.090
 5H8  C20  H9   single    0.970  0.020  1.090
 5H8  C20  H10  single    0.970  0.020  1.090
 5H8  C21  H11  single    0.970  0.020  1.090
 5H8  C22  H12  single    0.970  0.020  1.090
 5H8  C22  H13  single    0.970  0.020  1.090
 5H8  C22  H14  single    0.970  0.020  1.090
 5H8  C27  H15  single    0.970  0.020  1.090
 5H8  C27  H16  single    0.970  0.020  1.090
 5H8  C27  H17  single    0.970  0.020  1.090
 5H8  N13  H19  single    0.890  0.020  1.040
 5H8  C23  H20  single    0.970  0.020  1.090
 5H8  C23  H21  single    0.970  0.020  1.090
 5H8  C23  H22  single    0.970  0.020  1.090
 5H8  N16  H23  single    0.860  0.020  1.020
 5H8  C25  H24  single    0.970  0.020  1.090
 5H8  C29  H26  single    0.970  0.020  1.090
 5H8  C29  H27  single    0.970  0.020  1.090
 5H8  C29  H28  single    0.970  0.020  1.090
 5H8  C28  H29  single    0.970  0.020  1.090
 5H8  C28  H30  single    0.970  0.020  1.090
 5H8  C28  H31  single    0.970  0.020  1.090
 5H8  C5   H32  single    0.930  0.020  1.080
 5H8  C6   H33  single    0.930  0.020  1.080
 5H8  N10  H34  single    0.890  0.020  1.040

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
 5H8  H1   C1   C6   120.09  3.000
 5H8  H1   C1   C2   120.13  3.000
 5H8  C6   C1   C2   119.78  3.000
 5H8  H2   C2   C3   119.87  3.000
 5H8  H2   C2   C1   120.08  3.000
 5H8  C3   C2   C1   120.04  3.000
 5H8  H3   C3   C4   119.76  3.000
 5H8  H3   C3   C2   119.69  3.000
 5H8  C4   C3   C2   120.55  3.000
 5H8  N10  C9   O8   110.67  3.000
 5H8  O8   C9   O17  123.43  3.000
 5H8  N10  C9   O17  125.86  3.000
 5H8  H7   C11  H6   106.89  3.000
 5H8  H7   C11  N10  108.99  3.000
 5H8  H6   C11  N10  109.07  3.000
 5H8  H7   C11  P12  110.39  3.000
 5H8  H6   C11  P12  110.81  3.000
 5H8  N10  C11  P12  110.60  3.000
 5H8  H8   C14  N13  106.53  3.000
 5H8  H8   C14  C20  108.49  3.000
 5H8  N13  C14  C20  111.19  3.000
 5H8  H8   C14  C15  108.90  3.000
 5H8  N13  C14  C15  109.50  3.000
 5H8  C20  C14  C15  112.05  3.000
 5H8  N16  C15  O24  124.28  3.000
 5H8  N16  C15  C14  114.36  3.000
 5H8  O24  C15  C14  121.33  3.000
 5H8  H10  C20  H9   106.54  3.000
 5H8  H10  C20  C21  109.07  3.000
 5H8  H9   C20  C21  109.05  3.000
 5H8  H10  C20  C14  109.37  3.000
 5H8  H9   C20  C14  107.03  3.000
 5H8  C21  C20  C14  115.41  3.000
 5H8  H11  C21  C23  107.62  3.000
 5H8  H11  C21  C22  107.98  3.000
 5H8  C23  C21  C22  110.43  3.000
 5H8  H11  C21  C20  108.34  3.000
 5H8  C22  C21  C20  112.42  3.000
 5H8  C23  C21  C20  109.90  3.000
 5H8  H14  C22  H13  107.73  3.000
 5H8  H14  C22  H12  107.59  3.000
 5H8  H13  C22  H12  107.07  3.000
 5H8  H14  C22  C21  111.11  3.000
 5H8  H13  C22  C21  112.19  3.000
 5H8  H12  C22  C21  110.94  3.000
 5H8  O31  C30  O32  126.64  3.000
 5H8  O31  C30  C25  116.58  3.000
 5H8  O32  C30  C25  116.78  3.000
 5H8  C5   C4   C7   120.89  3.000
 5H8  C7   C4   C3   120.06  3.000
 5H8  C5   C4   C3   119.04  3.000
 5H8  N13  P12  O18  108.88  3.000
 5H8  O18  P12  O19  120.81  3.000
 5H8  N13  P12  O19  109.86  3.000
 5H8  O19  P12  C11  107.33  3.000
 5H8  O18  P12  C11  106.78  3.000
 5H8  N13  P12  C11  101.39  3.000
 5H8  H19  N13  P12  114.65  3.000
 5H8  H19  N13  C14  113.36  3.000
 5H8  P12  N13  C14  122.25  3.000
 5H8  H22  C23  H21  107.67  3.000
 5H8  H22  C23  H20  107.64  3.000
 5H8  H21  C23  H20  107.61  3.000
 5H8  H22  C23  C21  111.23  3.000
 5H8  H21  C23  C21  111.50  3.000
 5H8  H20  C23  C21  111.00  3.000
 5H8  H23  N16  C25  117.20  3.000
 5H8  H23  N16  C15  117.50  3.000
 5H8  C25  N16  C15  125.22  3.000
 5H8  H24  C25  C26  107.02  3.000
 5H8  H24  C25  N16  106.80  3.000
 5H8  C26  C25  N16  111.89  3.000
 5H8  H24  C25  C30  108.83  3.000
 5H8  N16  C25  C30  109.22  3.000
 5H8  C26  C25  C30  112.84  3.000
 5H8  C28  C26  C29  108.38  3.000
 5H8  C29  C26  C25  109.18  3.000
 5H8  C28  C26  C25  109.68  3.000
 5H8  C25  C26  C27  111.53  3.000
 5H8  C29  C26  C27  108.57  3.000
 5H8  C28  C26  C27  109.44  3.000
 5H8  H28  C29  H27  108.42  3.000
 5H8  H28  C29  H26  107.23  3.000
 5H8  H27  C29  H26  107.56  3.000
 5H8  H28  C29  C26  112.04  3.000
 5H8  H27  C29  C26  111.43  3.000
 5H8  H26  C29  C26  109.97  3.000
 5H8  H31  C28  H30  107.51  3.000
 5H8  H31  C28  H29  107.78  3.000
 5H8  H30  C28  H29  107.64  3.000
 5H8  H31  C28  C26  110.05  3.000
 5H8  H30  C28  C26  111.28  3.000
 5H8  H29  C28  C26  112.39  3.000
 5H8  H32  C5   C6   119.72  3.000
 5H8  H32  C5   C4   119.71  3.000
 5H8  C6   C5   C4   120.58  3.000
 5H8  H33  C6   C5   119.85  3.000
 5H8  H33  C6   C1   120.14  3.000
 5H8  C5   C6   C1   120.01  3.000
 5H8  C9   O8   C7   116.96  3.000
 5H8  H34  N10  C11  116.41  3.000
 5H8  H34  N10  C9   117.24  3.000
 5H8  C11  N10  C9   121.99  3.000
 5H8  H5   C7   H4   107.99  3.000
 5H8  H5   C7   O8   110.11  3.000
 5H8  H4   C7   O8   110.48  3.000
 5H8  H5   C7   C4   110.52  3.000
 5H8  H4   C7   C4   110.72  3.000
 5H8  O8   C7   C4   107.04  3.000
 5H8  H17  C27  H16  107.55  3.000
 5H8  H17  C27  H15  107.33  3.000
 5H8  H16  C27  H15  108.12  3.000
 5H8  H17  C27  C26  110.00  3.000
 5H8  H16  C27  C26  112.07  3.000
 5H8  H15  C27  C26  111.57  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
 5H8  CONST_01  C4   C5   C6   C1      0.00   0.0  0
 5H8  CONST_02  C4   C3   C2   C1      0.00   0.0  0
 5H8  CONST_03  C5   C6   C1   C2      0.00   0.0  0
 5H8  CONST_04  C5   C4   C3   C2      0.00   0.0  0
 5H8  CONST_05  C6   C5   C4   C3      0.00   0.0  0
 5H8  CONST_06  C6   C1   C2   C3      0.00   0.0  0
 5H8  CONST_07  C7   C4   C3   C2    180.00   0.0  0
 5H8  CONST_08  C6   C5   C4   C7    180.00   0.0  0
 5H8  CONST_09  H32  C5   C6   C1    180.00   0.0  0
 5H8  CONST_10  H3   C3   C2   C1    180.00   0.0  0
 5H8  CONST_11  H33  C6   C1   C2    180.00   0.0  0
 5H8  CONST_12  H1   C1   C2   C3    180.00   0.0  0
 5H8  CONST_13  H2   C2   C3   C4    180.00   0.0  0
 5H8  CONST_14  C25  N16  C15  C14   180.00   0.0  0
 5H8  CONST_15  C25  N16  C15  O24     0.00   0.0  0
 5H8  CONST_16  H23  N16  C15  C14     0.00   0.0  0
 5H8  Var_01    O8   C7   C4   C3     73.43  30.0  3
 5H8  Var_02    C4   C7   O8   C9   -172.61  30.0  3
 5H8  Var_03    N10  C9   O8   C7   -178.28  30.0  1
 5H8  Var_04    P12  C11  N10  C9     90.83  30.0  1
 5H8  Var_05    C14  N13  P12  C11  -115.64  30.0  1
 5H8  Var_06    C23  C21  C20  C14   177.06  30.0  2
 5H8  Var_07    N10  C11  P12  O19   -61.66  30.0  3
 5H8  Var_08    H20  C23  C21  C20   -63.13  30.0  3
 5H8  Var_09    H12  C22  C21  C20   176.54  30.0  3
 5H8  Var_10    H29  C28  C26  C27    60.67  30.0  3
 5H8  Var_11    H26  C29  C26  C27    66.49  30.0  3
 5H8  Var_12    H15  C27  C26  C25   -57.23  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
 5H8  chir_01  C14  C20  C15  N13  negativ
 5H8  chir_03  C25  C26  N16  C30  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
 5H8  plan-1  C1   0.020
 5H8  plan-1  C2   0.020
 5H8  plan-1  C3   0.020
 5H8  plan-1  C4   0.020
 5H8  plan-1  C5   0.020
 5H8  plan-1  C6   0.020
 5H8  plan-1  H1   0.020
 5H8  plan-1  H2   0.020
 5H8  plan-1  H3   0.020
 5H8  plan-1  H32  0.020
 5H8  plan-1  H33  0.020
 5H8  plan-1  C7   0.020
 5H8  plan-2  C14  0.020
 5H8  plan-2  C15  0.020
 5H8  plan-2  O24  0.020
 5H8  plan-2  N16  0.020
 5H8  plan-2  C25  0.020
 5H8  plan-2  H23  0.020
 5H8  plan-3  C30  0.020
 5H8  plan-3  C25  0.020
 5H8  plan-3  O32  0.020
 5H8  plan-3  O31  0.020
 5H8  plan-4  C9   0.020
 5H8  plan-4  O17  0.020
 5H8  plan-4  O8   0.020
 5H8  plan-4  N10  0.020

