# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 08:27:44 2022
#   Inital geometry file: a 122 line input string
#   Ligand name: N-[(benzyloxy)carbonyl]-L-leucyl-N-hydroxy-L-alaninamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](NC(=O)OCc1ccccc1)C(=O)N[C@@H](C)C(=O)NO
#
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
 0Z9  0Z9  N-[(benzyloxy)carbonyl]-L-leucyl-N-hydroxy-L-alaninamide  peptide  50  25  .  2019-03-22  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_0Z9
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
 0Z9  O4    O  O2    0  -0.478  -14.1463  21.7805  31.4294
 0Z9  O5    O  O     0  -0.511  -12.4987  21.1390  32.8281
 0Z9  C11   C  CH2   0  -0.237  -13.2256  22.5945  30.6947
 0Z9  C12   C  CR6   0   0.075  -13.9836  23.1837  29.5441
 0Z9  C13   C  CR16  0  -0.260  -15.4403  24.2549  27.4186
 0Z9  C14   C  CR16  0  -0.240  -14.8939  22.9814  27.3176
 0Z9  C15   C  CR16  0  -0.285  -14.1704  22.4501  28.3756
 0Z9  C16   C  CR16  0  -0.292  -14.5345  24.4579  29.6371
 0Z9  C17   C  CR16  0  -0.239  -15.2576  24.9938  28.5797
 0Z9  C10   C  C     0   0.765  -13.6583  21.1006  32.4724
 0Z9  N     N  NH1   0  -0.655  -14.6191  20.3603  33.0558
 0Z9  CA    C  CH1   0  -0.220  -14.3789  19.6369  34.2772
 0Z9  C     C  C     0   0.583  -13.9707  20.6205  35.3852
 0Z9  O     O  O     0  -0.482  -14.2690  21.8019  35.3307
 0Z9  CB    C  CH2   0  -0.449  -13.4307  18.4411  34.1080
 0Z9  CG    C  CH1   0  -0.228  -13.7194  17.5579  32.8945
 0Z9  CD1   C  CH3   0  -0.649  -12.6926  16.4312  32.8394
 0Z9  CD2   C  CH3   0  -0.662  -15.1350  16.9917  32.9097
 0Z9  N1    N  NH1   0  -0.647  -13.3238  20.1046  36.4426
 0Z9  CA1   C  CH1   0  -0.199  -12.8750  20.9485  37.5207
 0Z9  CB1   C  CH3   0  -0.687  -12.2462  20.0970  38.6172
 0Z9  C1    C  C     0   0.521  -11.8358  21.9469  37.0059
 0Z9  O1    O  O     0  -0.462  -10.9867  21.6440  36.1915
 0Z9  N2    N  NH1   0  -0.373  -11.9455  23.1608  37.5726
 0Z9  OH    O  OH1   0  -0.539  -10.9424  24.0729  37.4368
 0Z9  H19   H  HCH2  0   0.246  -12.8228  23.3809  31.3369
 0Z9  H20   H  HCH2  0   0.245  -12.3906  21.9881  30.3373
 0Z9  H21   H  HCR6  0   0.257  -16.0024  24.6712  26.5926
 0Z9  H22   H  HCR6  0   0.256  -15.0288  22.4030  26.4127
 0Z9  H23   H  HCR6  0   0.253  -13.7408  21.4587  28.2892
 0Z9  H24   H  HCR6  0   0.254  -14.3929  25.0392  30.5408
 0Z9  H25   H  HCR6  0   0.256  -15.6779  25.9877  28.6627
 0Z9  H     H  HNH1  0   0.402  -15.5699  20.4662  32.7426
 0Z9  HA    H  HCH1  0   0.305  -15.3554  19.2483  34.5814
 0Z9  HB2   H  HCH2  0   0.245  -12.3971  18.7897  34.0611
 0Z9  HB3   H  HCH2  0   0.230  -13.5114  17.8103  34.9998
 0Z9  HG    H  HCH1  0   0.225  -13.6016  18.1632  31.9903
 0Z9  HD11  H  HCH3  0   0.227  -12.8408  15.8050  31.9582
 0Z9  HD12  H  HCH3  0   0.225  -11.6739  16.8212  32.8030
 0Z9  HD13  H  HCH3  0   0.213  -12.7711  15.7879  33.7190
 0Z9  HD21  H  HCH3  0   0.230  -15.2883  16.3118  32.0701
 0Z9  HD22  H  HCH3  0   0.215  -15.3204  16.4290  33.8280
 0Z9  HD23  H  HCH3  0   0.228  -15.8961  17.7696  32.8353
 0Z9  HN1   H  HNH1  0   0.414  -13.0253  19.1433  36.4418
 0Z9  HA1   H  HCH1  0   0.274  -13.7311  21.4853  37.9395
 0Z9  HB1   H  HCH3  0   0.256  -11.9186  20.7232  39.4458
 0Z9  HB21  H  HCH3  0   0.258  -12.9703  19.3806  39.0039
 0Z9  HB31  H  HCH3  0   0.244  -11.3814  19.5488  38.2419
 0Z9  HN2   H  HNH1  0   0.415  -12.5886  23.3488  38.3290
 0Z9  HO    H  HOH1  0   0.476  -11.2147  24.6684  36.7263

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
 0Z9  N    CA    single    1.458  0.019  1.458
 0Z9  N    H     single    0.860  0.020  0.860
 0Z9  N    C10   single    1.346  0.020  1.346
 0Z9  CA   C     single    1.525  0.021  1.525
 0Z9  CA   CB    single    1.521  0.033  1.521
 0Z9  CA   HA    single    0.970  0.020  0.970
 0Z9  C    O     double    1.231  0.020  1.231
 0Z9  C    N1    single    1.343  0.020  1.343
 0Z9  CB   CG    single    1.528  0.020  1.528
 0Z9  CB   HB2   single    0.970  0.020  1.090
 0Z9  CB   HB3   single    0.970  0.020  1.090
 0Z9  CG   CD1   single    1.525  0.020  1.525
 0Z9  CG   CD2   single    1.525  0.020  1.525
 0Z9  CG   HG    single    0.970  0.020  1.090
 0Z9  CD1  HD11  single    0.970  0.020  1.090
 0Z9  CD1  HD12  single    0.970  0.020  1.090
 0Z9  CD1  HD13  single    0.970  0.020  1.090
 0Z9  CD2  HD21  single    0.970  0.020  1.090
 0Z9  CD2  HD22  single    0.970  0.020  1.090
 0Z9  CD2  HD23  single    0.970  0.020  1.090
 0Z9  N1   CA1   single    1.441  0.020  1.441
 0Z9  N1   HN1   single    0.860  0.020  1.020
 0Z9  CA1  CB1   single    1.524  0.020  1.524
 0Z9  CA1  C1    single    1.530  0.020  1.530
 0Z9  CA1  HA1   single    0.970  0.020  1.090
 0Z9  CB1  HB1   single    0.970  0.020  1.090
 0Z9  CB1  HB21  single    0.970  0.020  1.090
 0Z9  CB1  HB31  single    0.970  0.020  1.090
 0Z9  C1   O1    double    1.215  0.020  1.215
 0Z9  C1   N2    single    1.344  0.020  1.344
 0Z9  N2   OH    single    1.363  0.020  1.363
 0Z9  N2   HN2   single    0.860  0.020  1.020
 0Z9  OH   HO    single    0.850  0.020  0.980
 0Z9  C10  O4    single    1.337  0.020  1.337
 0Z9  C10  O5    double    1.214  0.020  1.214
 0Z9  O4   C11   single    1.432  0.020  1.432
 0Z9  C11  C12   single    1.499  0.020  1.499
 0Z9  C15  C12   aromatic  1.392  0.020  1.392
 0Z9  C12  C16   aromatic  1.391  0.020  1.391
 0Z9  C13  C14   aromatic  1.389  0.020  1.389
 0Z9  C14  C15   aromatic  1.387  0.020  1.387
 0Z9  C16  C17   aromatic  1.389  0.020  1.389
 0Z9  C13  C17   aromatic  1.388  0.020  1.388
 0Z9  C11  H19   single    0.970  0.020  1.090
 0Z9  C11  H20   single    0.970  0.020  1.090
 0Z9  C13  H21   single    0.930  0.020  1.080
 0Z9  C14  H22   single    0.930  0.020  1.080
 0Z9  C15  H23   single    0.930  0.020  1.080
 0Z9  C16  H24   single    0.930  0.020  1.080
 0Z9  C17  H25   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
 0Z9  C10   O4   C11   117.04  3.000
 0Z9  H20   C11  H19   108.08  3.000
 0Z9  H20   C11  C12   110.72  3.000
 0Z9  H19   C11  C12   110.79  3.000
 0Z9  H20   C11  O4    110.11  3.000
 0Z9  H19   C11  O4    110.17  3.000
 0Z9  C12   C11  O4    106.99  3.000
 0Z9  C16   C12  C15   119.05  3.000
 0Z9  C16   C12  C11   120.60  3.000
 0Z9  C15   C12  C11   120.33  3.000
 0Z9  H21   C13  C17   120.12  3.000
 0Z9  H21   C13  C14   120.09  3.000
 0Z9  C17   C13  C14   119.80  3.000
 0Z9  H22   C14  C15   119.86  3.000
 0Z9  H22   C14  C13   120.10  3.000
 0Z9  C15   C14  C13   120.04  3.000
 0Z9  H23   C15  C14   119.74  3.000
 0Z9  H23   C15  C12   119.72  3.000
 0Z9  C14   C15  C12   120.54  3.000
 0Z9  H24   C16  C17   119.74  3.000
 0Z9  H24   C16  C12   119.69  3.000
 0Z9  C17   C16  C12   120.58  3.000
 0Z9  H25   C17  C16   119.88  3.000
 0Z9  H25   C17  C13   120.12  3.000
 0Z9  C16   C17  C13   120.00  3.000
 0Z9  N     C10  O5    124.92  3.000
 0Z9  O5    C10  O4    124.14  3.000
 0Z9  N     C10  O4    110.93  3.000
 0Z9  H     N    CA    114.00  3.000
 0Z9  H     N    C10   118.78  3.000
 0Z9  CA    N    C10   121.67  3.000
 0Z9  HA    CA   CB    109.00  3.000
 0Z9  HA    CA   C     110.00  3.000
 0Z9  CB    CA   C     110.50  1.500
 0Z9  HA    CA   N     110.00  3.000
 0Z9  CB    CA   N     110.40  1.500
 0Z9  C     CA   N     111.00  2.800
 0Z9  N1    C    O     121.68  3.000
 0Z9  N1    C    CA    116.74  3.000
 0Z9  O     C    CA    120.80  1.700
 0Z9  HB3   CB   HB2   106.77  3.000
 0Z9  HB3   CB   CG    107.44  3.000
 0Z9  HB2   CB   CG    109.22  3.000
 0Z9  HB3   CB   CA    108.26  3.000
 0Z9  HB2   CB   CA    109.92  3.000
 0Z9  CG    CB   CA    114.89  3.000
 0Z9  HG    CG   CD2   108.27  3.000
 0Z9  HG    CG   CD1   107.83  3.000
 0Z9  CD2   CG   CD1   110.55  3.000
 0Z9  HG    CG   CB    108.42  3.000
 0Z9  CD2   CG   CB    112.46  3.000
 0Z9  CD1   CG   CB    109.17  3.000
 0Z9  HD13  CD1  HD12  107.71  3.000
 0Z9  HD13  CD1  HD11  107.61  3.000
 0Z9  HD12  CD1  HD11  107.75  3.000
 0Z9  HD13  CD1  CG    110.95  3.000
 0Z9  HD12  CD1  CG    111.45  3.000
 0Z9  HD11  CD1  CG    111.20  3.000
 0Z9  HD23  CD2  HD22  107.83  3.000
 0Z9  HD23  CD2  HD21  107.09  3.000
 0Z9  HD22  CD2  HD21  107.57  3.000
 0Z9  HD23  CD2  CG    112.47  3.000
 0Z9  HD22  CD2  CG    110.92  3.000
 0Z9  HD21  CD2  CG    110.74  3.000
 0Z9  HN1   N1   CA1   117.88  3.000
 0Z9  HN1   N1   C     120.61  3.000
 0Z9  CA1   N1   C     120.95  3.000
 0Z9  HA1   CA1  C1    109.88  3.000
 0Z9  HA1   CA1  CB1   108.76  3.000
 0Z9  C1    CA1  CB1   109.05  3.000
 0Z9  HA1   CA1  N1    109.28  3.000
 0Z9  C1    CA1  N1    110.00  3.000
 0Z9  CB1   CA1  N1    109.86  3.000
 0Z9  HB31  CB1  HB21  108.58  3.000
 0Z9  HB31  CB1  HB1   108.20  3.000
 0Z9  HB21  CB1  HB1   107.94  3.000
 0Z9  HB31  CB1  CA1   111.13  3.000
 0Z9  HB21  CB1  CA1   110.40  3.000
 0Z9  HB1   CB1  CA1   110.51  3.000
 0Z9  N2    C1   O1    124.39  3.000
 0Z9  N2    C1   CA1   113.07  3.000
 0Z9  O1    C1   CA1   122.51  3.000
 0Z9  HN2   N2   OH    114.74  3.000
 0Z9  HN2   N2   C1    122.39  3.000
 0Z9  OH    N2   C1    120.16  3.000
 0Z9  HO    OH   N2    106.17  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
 0Z9  CONST_01  C13   C14  C15  C12     0.00   0.0  0
 0Z9  CONST_02  C13   C17  C16  C12     0.00   0.0  0
 0Z9  CONST_03  C16   C17  C13  C14     0.00   0.0  0
 0Z9  CONST_04  C16   C12  C15  C14     0.00   0.0  0
 0Z9  CONST_05  C17   C16  C12  C15     0.00   0.0  0
 0Z9  CONST_06  C17   C13  C14  C15     0.00   0.0  0
 0Z9  CONST_07  C14   C15  C12  C11   180.00   0.0  0
 0Z9  CONST_08  C17   C16  C12  C11   180.00   0.0  0
 0Z9  CONST_09  H22   C14  C15  C12   180.00   0.0  0
 0Z9  CONST_10  H25   C17  C16  C12   180.00   0.0  0
 0Z9  CONST_11  H23   C15  C14  C13   180.00   0.0  0
 0Z9  CONST_12  H24   C16  C17  C13   180.00   0.0  0
 0Z9  CONST_13  H21   C13  C14  C15   180.00   0.0  0
 0Z9  CONST_14  CA1   N1   C    CA    180.00   0.0  0
 0Z9  CONST_15  CA1   N1   C    O       0.00   0.0  0
 0Z9  CONST_16  OH    N2   C1   CA1   180.00   0.0  0
 0Z9  CONST_17  OH    N2   C1   O1      0.00   0.0  0
 0Z9  CONST_18  HN1   N1   C    CA      0.00   0.0  0
 0Z9  CONST_19  HN2   N2   C1   CA1     0.00   0.0  0
 0Z9  Var_01    C15   C12  C11  O4    -82.85  30.0  2
 0Z9  Var_02    CA    N    C10  O4   -173.93  30.0  1
 0Z9  Var_03    N     C10  O4   C11  -178.84  30.0  2
 0Z9  Var_04    CD1   CG   CB   CA    179.06  30.0  3
 0Z9  Var_05    HD11  CD1  CG   CB   -177.43  30.0  3
 0Z9  Var_06    HD21  CD2  CG   CB   -176.06  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
 0Z9  chir_01  CA   N   C    CB  positiv
 0Z9  chir_02  CA1  N1  CB1  C1  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
 0Z9  plan-1  C11  0.020
 0Z9  plan-1  C12  0.020
 0Z9  plan-1  C13  0.020
 0Z9  plan-1  C14  0.020
 0Z9  plan-1  C15  0.020
 0Z9  plan-1  C16  0.020
 0Z9  plan-1  C17  0.020
 0Z9  plan-1  H21  0.020
 0Z9  plan-1  H22  0.020
 0Z9  plan-1  H23  0.020
 0Z9  plan-1  H24  0.020
 0Z9  plan-1  H25  0.020
 0Z9  plan-2  CA   0.020
 0Z9  plan-2  C    0.020
 0Z9  plan-2  O    0.020
 0Z9  plan-2  N1   0.020
 0Z9  plan-2  CA1  0.020
 0Z9  plan-2  HN1  0.020
 0Z9  plan-3  CA1  0.020
 0Z9  plan-3  C1   0.020
 0Z9  plan-3  O1   0.020
 0Z9  plan-3  N2   0.020
 0Z9  plan-3  OH   0.020
 0Z9  plan-3  HN2  0.020
 0Z9  plan-4  O4   0.020
 0Z9  plan-4  O5   0.020
 0Z9  plan-4  C10  0.020
 0Z9  plan-4  N    0.020

