# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 05:03:13 2020
#   Inital geometry file: a 148 line input string
#   Ligand name: ethyl {(2R)-1-[(2S)-2-{[2-(4-aminobutyl)hydrazinyl]carbonyl}pyrrolidin-1-yl]-1-oxo-3-phenylpropan-2-yl}carbamate (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCOC(=O)N[C@H](Cc1ccccc1)C(=O)N2CCC[C@H]2C(=O)NNCCCCN
#
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
 AZL  AZL  'ethyl {(2R)-1-[(2S)-2-{[2-(4-aminobutyl)hydrazinyl]carbonyl}pyrrolidin-1-yl]-1-oxo-3-phenylpropan-2-yl}carbamate (non-preferred name)'  peptide  63  30  .  2022-03-11  2022-07-24
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_AZL
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
 AZL  C23   C  C     0   0.762  -3.0036   1.5234  -0.6818
 AZL  O23   O  O     0  -0.511  -3.3524   1.0609  -1.7472
 AZL  O24   O  O2    0  -0.483  -3.3078   2.7538  -0.2636
 AZL  C24   C  CH2   0  -0.170  -4.1168   3.5610  -1.1248
 AZL  C25   C  CH3   0  -0.689  -4.3662   4.8735  -0.4211
 AZL  N9    N  NH1   0  -0.655  -2.2398   0.8905   0.2334
 AZL  C15   C  CH1   0  -0.212  -1.9272  -0.5084   0.1439
 AZL  C14   C  C     0   0.580  -0.4675  -0.7161   0.5322
 AZL  O14   O  O     0  -0.497   0.0614  -0.0030   1.3753
 AZL  C16   C  CH2   0  -0.529  -2.8241  -1.3479   1.0791
 AZL  C17   C  CR6   0   0.143  -4.2761  -1.1670   0.7458
 AZL  C18   C  CR16  0  -0.297  -4.8818  -1.9485  -0.2347
 AZL  C22   C  CR16  0  -0.306  -5.0289  -0.1755   1.3695
 AZL  C19   C  CR16  0  -0.242  -6.2079  -1.7439  -0.5873
 AZL  C21   C  CR16  0  -0.237  -6.3548   0.0370   1.0161
 AZL  C20   C  CR16  0  -0.270  -6.9478  -0.7463   0.0357
 AZL  N8    N  NR5   0  -0.482   0.1839  -1.7295  -0.0501
 AZL  C9    C  CR15  0  -0.171   1.5846  -1.9624   0.2556
 AZL  C8    C  C     0   0.546   2.4168  -0.7137  -0.0158
 AZL  O8    O  O     0  -0.474   2.1943   0.0065  -0.9699
 AZL  C10   C  CH2   0  -0.481   1.9809  -3.0984  -0.7003
 AZL  C11   C  CH2   0  -0.470   0.6608  -3.8059  -0.9817
 AZL  C12   C  CH2   0  -0.288  -0.3338  -2.6577  -1.0502
 AZL  N1    N  NH2   0  -0.801  10.3246   1.5993  -0.5513
 AZL  C2    C  CH2   0  -0.270   8.9482   2.0079  -0.3081
 AZL  C3    C  CH2   0  -0.430   8.0543   0.8021  -0.0587
 AZL  C4    C  CH2   0  -0.456   6.6135   1.2037   0.2259
 AZL  C5    C  CH2   0  -0.254   5.6961   0.0072   0.4197
 AZL  N6    N  NH1   0  -0.456   4.3443   0.4706   0.6988
 AZL  N7    N  NH1   0  -0.508   3.4341  -0.5535   0.8477
 AZL  H241  H  HCH2  0   0.229  -3.6041   3.7257  -2.0751
 AZL  H242  H  HCH2  0   0.228  -5.0591   3.0517  -1.3372
 AZL  H251  H  HCH3  0   0.234  -4.8985   4.7305   0.5194
 AZL  H252  H  HCH3  0   0.235  -3.4355   5.4028  -0.2162
 AZL  H253  H  HCH3  0   0.238  -4.9789   5.5104  -1.0585
 AZL  HN9   H  HNH1  0   0.395  -2.0423   1.3577   1.1050
 AZL  H15   H  HCH1  0   0.293  -2.0954  -0.8161  -0.8884
 AZL  H161  H  HCH2  0   0.265  -2.5421  -2.4014   1.0059
 AZL  H162  H  HCH2  0   0.268  -2.6309  -1.0428   2.1106
 AZL  H18   H  HCR6  0   0.244  -4.3092  -2.7266  -0.7273
 AZL  H22   H  HCR6  0   0.247  -4.5750   0.4362   2.1404
 AZL  H19   H  HCR6  0   0.252  -6.6657  -2.3629  -1.3484
 AZL  H21   H  HCR6  0   0.251  -6.9260   0.8128   1.5097
 AZL  H20   H  HCR6  0   0.253  -7.9820  -0.5841  -0.2394
 AZL  H9    H  HCR5  0   0.280   1.6945  -2.2837   1.2968
 AZL  H101  H  HCH2  0   0.253   2.3870  -2.6900  -1.6280
 AZL  H102  H  HCH2  0   0.268   2.7353  -3.7476  -0.2598
 AZL  H111  H  HCH2  0   0.261   0.6791  -4.3907  -1.9001
 AZL  H112  H  HCH2  0   0.247   0.4034  -4.4766  -0.1596
 AZL  H121  H  HCH2  0   0.257  -1.3479  -2.9804  -0.8168
 AZL  H122  H  HCH2  0   0.254  -0.3409  -2.1972  -2.0421
 AZL  HN11  H  HNH2  0   0.345  10.8840   2.4146  -0.7672
 AZL  HN12  H  HNH2  0   0.337  10.7160   1.2238   0.3040
 AZL  H21A  H  HCH2  0   0.188   8.8402   2.7085   0.5328
 AZL  H22A  H  HCH2  0   0.213   8.5893   2.5379  -1.1946
 AZL  H31   H  HCH2  0   0.216   8.0955   0.1400  -0.9291
 AZL  H32   H  HCH2  0   0.215   8.4486   0.2295   0.7879
 AZL  H41   H  HCH2  0   0.221   6.5818   1.8356   1.1202
 AZL  H42   H  HCH2  0   0.224   6.2271   1.8107  -0.5977
 AZL  H51   H  HCH2  0   0.229   5.6688  -0.5886  -0.4956
 AZL  H52   H  HCH2  0   0.203   6.0915  -0.6412   1.2149
 AZL  HN6   H  HNH1  0   0.366   4.3341   1.0332   1.5412
 AZL  HN7   H  HNH1  0   0.397   3.5444  -1.2064   1.6132

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
 AZL  N1   C2    single    1.456  0.020  1.456
 AZL  N1   HN11  single    0.890  0.020  1.040
 AZL  N1   HN12  single    0.890  0.020  1.040
 AZL  C2   C3    single    1.522  0.020  1.522
 AZL  C2   H21A  single    0.970  0.020  1.090
 AZL  C2   H22A  single    0.970  0.020  1.090
 AZL  C3   C4    single    1.523  0.020  1.523
 AZL  C3   H31   single    0.970  0.020  1.090
 AZL  C3   H32   single    0.970  0.020  1.090
 AZL  C4   C5    single    1.520  0.020  1.520
 AZL  C4   H41   single    0.970  0.020  1.090
 AZL  C4   H42   single    0.970  0.020  1.090
 AZL  C5   N6    single    1.456  0.020  1.456
 AZL  C5   H51   single    0.970  0.020  1.090
 AZL  C5   H52   single    0.970  0.020  1.090
 AZL  N6   N7    single    1.378  0.020  1.378
 AZL  N6   HN6   single    0.890  0.020  1.040
 AZL  N7   C8    single    1.344  0.020  1.344
 AZL  N7   HN7   single    0.860  0.020  1.020
 AZL  C8   O8    double    1.216  0.020  1.216
 AZL  C8   C9    single    1.525  0.020  1.525
 AZL  C9   N8    single    1.452  0.020  1.452
 AZL  C9   C10   single    1.537  0.020  1.537
 AZL  C9   H9    single    0.970  0.020  1.090
 AZL  N8   C12   single    1.459  0.020  1.459
 AZL  N8   C14   single    1.338  0.020  1.338
 AZL  C10  C11   single    1.524  0.020  1.524
 AZL  C10  H101  single    0.970  0.020  1.090
 AZL  C10  H102  single    0.970  0.020  1.090
 AZL  C11  C12   single    1.521  0.020  1.521
 AZL  C11  H111  single    0.970  0.020  1.090
 AZL  C11  H112  single    0.970  0.020  1.090
 AZL  C12  H121  single    0.970  0.020  1.090
 AZL  C12  H122  single    0.970  0.020  1.090
 AZL  C14  O14   double    1.224  0.020  1.224
 AZL  C14  C15   single    1.525  0.020  1.525
 AZL  C15  N9    single    1.436  0.020  1.436
 AZL  C15  C16   single    1.544  0.020  1.544
 AZL  C15  H15   single    0.970  0.020  1.090
 AZL  N9   C23   single    1.350  0.020  1.350
 AZL  N9   HN9   single    0.860  0.020  1.020
 AZL  C16  C17   single    1.501  0.020  1.501
 AZL  C16  H161  single    0.970  0.020  1.090
 AZL  C16  H162  single    0.970  0.020  1.090
 AZL  C17  C18   aromatic  1.393  0.020  1.393
 AZL  C17  C22   aromatic  1.392  0.020  1.392
 AZL  C18  C19   aromatic  1.387  0.020  1.387
 AZL  C18  H18   single    0.930  0.020  1.080
 AZL  C19  C20   aromatic  1.390  0.020  1.390
 AZL  C19  H19   single    0.930  0.020  1.080
 AZL  C20  C21   aromatic  1.388  0.020  1.388
 AZL  C20  H20   single    0.930  0.020  1.080
 AZL  C21  C22   aromatic  1.388  0.020  1.388
 AZL  C21  H21   single    0.930  0.020  1.080
 AZL  C22  H22   single    0.930  0.020  1.080
 AZL  C23  O23   double    1.213  0.020  1.213
 AZL  C23  O24   single    1.335  0.020  1.335
 AZL  O24  C24   single    1.431  0.020  1.431
 AZL  C24  C25   single    1.510  0.020  1.510
 AZL  C24  H241  single    0.970  0.020  1.090
 AZL  C24  H242  single    0.970  0.020  1.090
 AZL  C25  H251  single    0.970  0.020  1.090
 AZL  C25  H252  single    0.970  0.020  1.090
 AZL  C25  H253  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
 AZL  N9    C23  O24   110.42  3.000
 AZL  O24   C23  O23   124.15  3.000
 AZL  N9    C23  O23   125.42  3.000
 AZL  C24   O24  C23   117.41  3.000
 AZL  H242  C24  H241  107.83  3.000
 AZL  H242  C24  C25   110.70  3.000
 AZL  H241  C24  C25   110.60  3.000
 AZL  H242  C24  O24   109.99  3.000
 AZL  H241  C24  O24   110.08  3.000
 AZL  C25   C24  O24   107.65  3.000
 AZL  H253  C25  H252  107.83  3.000
 AZL  H253  C25  H251  107.87  3.000
 AZL  H252  C25  H251  108.56  3.000
 AZL  H253  C25  C24   109.17  3.000
 AZL  H252  C25  C24   111.63  3.000
 AZL  H251  C25  C24   111.64  3.000
 AZL  HN9   N9   C15   117.54  3.000
 AZL  HN9   N9   C23   118.66  3.000
 AZL  C15   N9   C23   122.53  3.000
 AZL  H15   C15  C16   109.30  3.000
 AZL  H15   C15  C14   110.51  3.000
 AZL  C16   C15  C14   109.14  3.000
 AZL  H15   C15  N9    107.47  3.000
 AZL  C16   C15  N9    111.43  3.000
 AZL  C14   C15  N9    108.98  3.000
 AZL  N8    C14  O14   122.04  3.000
 AZL  O14   C14  C15   120.63  3.000
 AZL  N8    C14  C15   117.29  3.000
 AZL  H162  C16  H161  106.66  3.000
 AZL  H162  C16  C17   110.31  3.000
 AZL  H161  C16  C17   110.55  3.000
 AZL  H162  C16  C15   108.49  3.000
 AZL  H161  C16  C15   109.49  3.000
 AZL  C17   C16  C15   111.22  3.000
 AZL  C22   C17  C18   118.68  3.000
 AZL  C22   C17  C16   120.63  3.000
 AZL  C18   C17  C16   120.63  3.000
 AZL  H18   C18  C19   119.68  3.000
 AZL  H18   C18  C17   119.53  3.000
 AZL  C19   C18  C17   120.79  3.000
 AZL  H22   C22  C21   119.64  3.000
 AZL  H22   C22  C17   119.61  3.000
 AZL  C21   C22  C17   120.75  3.000
 AZL  H19   C19  C20   120.04  3.000
 AZL  H19   C19  C18   119.90  3.000
 AZL  C20   C19  C18   120.07  3.000
 AZL  H21   C21  C20   120.07  3.000
 AZL  H21   C21  C22   119.84  3.000
 AZL  C20   C21  C22   120.09  3.000
 AZL  H20   C20  C21   120.21  3.000
 AZL  H20   C20  C19   120.16  3.000
 AZL  C21   C20  C19   119.63  3.000
 AZL  C12   N8   C9    112.60  3.000
 AZL  C12   N8   C14   127.39  3.000
 AZL  C9    N8   C14   119.96  3.000
 AZL  H9    C9   C10   110.41  3.000
 AZL  H9    C9   C8    110.77  3.000
 AZL  C10   C9   C8    110.72  3.000
 AZL  H9    C9   N8    110.12  3.000
 AZL  C10   C9   N8    103.67  3.000
 AZL  C8    C9   N8    110.95  3.000
 AZL  N7    C8   O8    124.89  3.000
 AZL  O8    C8   C9    121.66  3.000
 AZL  N7    C8   C9    113.35  3.000
 AZL  H102  C10  H101  108.01  3.000
 AZL  H102  C10  C11   113.47  3.000
 AZL  H101  C10  C11   109.81  3.000
 AZL  H102  C10  C9    111.59  3.000
 AZL  H101  C10  C9    110.36  3.000
 AZL  C11   C10  C9    103.57  3.000
 AZL  H112  C11  H111  108.01  3.000
 AZL  H112  C11  C12   110.09  3.000
 AZL  H111  C11  C12   112.24  3.000
 AZL  H112  C11  C10   110.51  3.000
 AZL  H111  C11  C10   112.99  3.000
 AZL  C12   C11  C10   102.96  3.000
 AZL  H122  C12  H121  108.24  3.000
 AZL  H122  C12  C11   111.28  3.000
 AZL  H121  C12  C11   112.05  3.000
 AZL  H122  C12  N8    110.86  3.000
 AZL  H121  C12  N8    111.83  3.000
 AZL  C11   C12  N8    102.56  3.000
 AZL  HN12  N1   HN11  105.38  3.000
 AZL  HN12  N1   C2    109.16  3.000
 AZL  HN11  N1   C2    109.39  3.000
 AZL  H22A  C2   H21A  106.19  3.000
 AZL  H22A  C2   C3    108.92  3.000
 AZL  H21A  C2   C3    108.77  3.000
 AZL  H22A  C2   N1    108.11  3.000
 AZL  H21A  C2   N1    113.53  3.000
 AZL  C3    C2   N1    111.12  3.000
 AZL  H32   C3   H31   106.56  3.000
 AZL  H32   C3   C4    109.51  3.000
 AZL  H31   C3   C4    110.11  3.000
 AZL  H32   C3   C2    109.23  3.000
 AZL  H31   C3   C2    109.08  3.000
 AZL  C4    C3   C2    112.18  3.000
 AZL  H42   C4   H41   106.52  3.000
 AZL  H42   C4   C5    108.64  3.000
 AZL  H41   C4   C5    109.42  3.000
 AZL  H42   C4   C3    109.88  3.000
 AZL  H41   C4   C3    109.40  3.000
 AZL  C5    C4   C3    112.79  3.000
 AZL  H52   C5   H51   107.06  3.000
 AZL  H52   C5   N6    112.51  3.000
 AZL  H51   C5   N6    108.11  3.000
 AZL  H52   C5   C4    109.84  3.000
 AZL  H51   C5   C4    109.72  3.000
 AZL  N6    C5   C4    109.53  3.000
 AZL  HN6   N6   N7    108.44  3.000
 AZL  HN6   N6   C5    110.21  3.000
 AZL  N7    N6   C5    113.41  3.000
 AZL  HN7   N7   N6    119.28  3.000
 AZL  HN7   N7   C8    119.44  3.000
 AZL  N6    N7   C8    121.27  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
 AZL  CONST_01  C20   C19  C18  C17     0.00   0.0  0
 AZL  CONST_02  C20   C21  C22  C17     0.00   0.0  0
 AZL  CONST_03  C21   C22  C17  C18     0.00   0.0  0
 AZL  CONST_04  C21   C20  C19  C18     0.00   0.0  0
 AZL  CONST_05  C19   C18  C17  C22     0.00   0.0  0
 AZL  CONST_06  C19   C20  C21  C22     0.00   0.0  0
 AZL  CONST_07  C19   C18  C17  C16   180.00   0.0  0
 AZL  CONST_08  C21   C22  C17  C16   180.00   0.0  0
 AZL  CONST_09  H19   C19  C18  C17   180.00   0.0  0
 AZL  CONST_10  H21   C21  C22  C17   180.00   0.0  0
 AZL  CONST_11  H22   C22  C17  C18   180.00   0.0  0
 AZL  CONST_12  H20   C20  C19  C18   180.00   0.0  0
 AZL  CONST_13  H18   C18  C17  C22   180.00   0.0  0
 AZL  CONST_14  C9    N8   C14  C15   180.00   0.0  0
 AZL  CONST_15  C12   N8   C14  C15     0.00   0.0  0
 AZL  CONST_16  C9    N8   C14  O14     0.00   0.0  0
 AZL  CONST_17  C12   N8   C14  O14   180.00   0.0  0
 AZL  CONST_18  N6    N7   C8   C9    180.00   0.0  0
 AZL  CONST_19  HN7   N7   C8   C9      0.00   0.0  0
 AZL  CONST_20  N6    N7   C8   O8      0.00   0.0  0
 AZL  Var_01    C10   C11  C12  N8    -35.14  30.0  1
 AZL  Var_02    C11   C12  N8   C9     20.35  30.0  1
 AZL  Var_03    C12   C11  C10  C9     37.50  30.0  1
 AZL  Var_04    C18   C17  C16  C15    86.21  30.0  2
 AZL  Var_05    C25   C24  O24  C23   177.93  30.0  3
 AZL  Var_06    C15   N9   C23  O23   -10.60  30.0  2
 AZL  Var_07    N9    C23  O24  C24   179.97  30.0  1
 AZL  Var_08    C5    N6   N7   C8   -115.32  30.0  1
 AZL  Var_09    C4    C3   C2   N1    178.87  30.0  3
 AZL  Var_10    C5    C4   C3   C2    177.60  30.0  3
 AZL  Var_11    N6    C5   C4   C3    179.48  30.0  3
 AZL  Var_12    N7    N6   C5   C4    178.10  30.0  3
 AZL  Var_13    H251  C25  C24  O24   -61.03  30.0  3
 AZL  Var_14    HN11  N1   C2   C3    176.71  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
 AZL  chir_01  C15  C14  N9   C16  positiv
 AZL  chir_02  C9   N8   C10  C8   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
 AZL  plan-1  C16  0.020
 AZL  plan-1  C17  0.020
 AZL  plan-1  C18  0.020
 AZL  plan-1  C22  0.020
 AZL  plan-1  C19  0.020
 AZL  plan-1  C21  0.020
 AZL  plan-1  C20  0.020
 AZL  plan-1  H18  0.020
 AZL  plan-1  H22  0.020
 AZL  plan-1  H19  0.020
 AZL  plan-1  H21  0.020
 AZL  plan-1  H20  0.020
 AZL  plan-2  C9   0.020
 AZL  plan-2  C8   0.020
 AZL  plan-2  O8   0.020
 AZL  plan-2  N6   0.020
 AZL  plan-2  N7   0.020
 AZL  plan-2  HN7  0.020
 AZL  plan-3  C15  0.020
 AZL  plan-3  C14  0.020
 AZL  plan-3  O14  0.020
 AZL  plan-3  N8   0.020
 AZL  plan-3  C9   0.020
 AZL  plan-3  C12  0.020
 AZL  plan-4  C23  0.020
 AZL  plan-4  O23  0.020
 AZL  plan-4  O24  0.020
 AZL  plan-4  N9   0.020

