# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 01:51:31 2020
#   Inital geometry file: a 119 line input string
#   Ligand name: benzyl (2S)-2-{[2-(4-aminobutyl)hydrazinyl]carbonyl}pyrrolidine-1-carboxylate (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCCCNNC(=O)[C@@H]1CCCN1C(=O)OCc2ccccc2
#
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
 ALZ  ALZ  'benzyl (2S)-2-{[2-(4-aminobutyl)hydrazinyl]carbonyl}pyrrolidine-1-carboxylate (non-preferred name)'  peptide  50  24  .  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_ALZ
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
 ALZ  C14   C  C     0   0.776  -1.5591  -0.0095  -0.7211
 ALZ  O14   O  O     0  -0.530  -1.0413  -0.8239  -1.4632
 ALZ  O15   O  O2    0  -0.476  -2.8033  -0.1146  -0.2483
 ALZ  C16   C  CH2   0  -0.237  -3.5736  -1.2386  -0.6901
 ALZ  C17   C  CR6   0   0.076  -4.9497  -1.0753  -0.1204
 ALZ  C18   C  CR16  0  -0.284  -5.8545  -0.1970  -0.7122
 ALZ  C19   C  CR16  0  -0.243  -7.1226  -0.0258  -0.1769
 ALZ  C20   C  CR16  0  -0.262  -7.5005  -0.7339   0.9579
 ALZ  C21   C  CR16  0  -0.242  -6.6051  -1.6114   1.5535
 ALZ  C22   C  CR16  0  -0.297  -5.3348  -1.7781   1.0161
 ALZ  N8    N  NR5   0  -0.514  -0.9482   1.1025  -0.2858
 ALZ  C9    C  CR15  0  -0.171   0.4298   1.3549  -0.6445
 ALZ  C8    C  C     0   0.539   1.3435   0.2244  -0.1864
 ALZ  O8    O  O     0  -0.473   1.1453  -0.3847   0.8474
 ALZ  C10   C  CH2   0  -0.478   0.7631   2.6536   0.1093
 ALZ  C11   C  CH2   0  -0.475  -0.5957   3.3209   0.2964
 ALZ  C12   C  CH2   0  -0.263  -1.5299   2.1456   0.5487
 ALZ  N1    N  NH2   0  -0.800   9.4937  -0.6908   0.7027
 ALZ  C2    C  CH2   0  -0.268   8.2126  -1.3711   0.5729
 ALZ  C3    C  CH2   0  -0.432   7.1289  -0.4077   0.1144
 ALZ  C4    C  CH2   0  -0.455   5.7800  -1.0915  -0.0658
 ALZ  C5    C  CH2   0  -0.258   4.6893  -0.1134  -0.4679
 ALZ  N6    N  NH1   0  -0.455   3.4276  -0.8164  -0.6574
 ALZ  N7    N  NH1   0  -0.507   2.3966   0.0338  -1.0007
 ALZ  H161  H  HCH2  0   0.247  -3.6060  -1.2647  -1.7811
 ALZ  H162  H  HCH2  0   0.248  -3.1169  -2.1674  -0.3415
 ALZ  H18   H  HCR6  0   0.254  -5.5688   0.3507  -1.6027
 ALZ  H19   H  HCR6  0   0.258  -7.8179   0.6577  -0.6466
 ALZ  H20   H  HCR6  0   0.259  -8.4919  -0.6047   1.3724
 ALZ  H21   H  HCR6  0   0.258  -6.8940  -2.1666   2.4364
 ALZ  H22   H  HCR6  0   0.256  -4.6400  -2.4655   1.4838
 ALZ  H9    H  HCR5  0   0.276   0.5232   1.5103  -1.7251
 ALZ  H101  H  HCH2  0   0.252   1.2028   2.4268   1.0831
 ALZ  H102  H  HCH2  0   0.266   1.4729   3.2659  -0.4441
 ALZ  H111  H  HCH2  0   0.257  -0.6038   4.0391   1.1146
 ALZ  H112  H  HCH2  0   0.244  -0.8922   3.8434  -0.6151
 ALZ  H121  H  HCH2  0   0.256  -2.5575   2.3594   0.2596
 ALZ  H122  H  HCH2  0   0.239  -1.5254   1.8530   1.6026
 ALZ  HN11  H  HNH2  0   0.337   9.4278  -0.0018   1.4423
 ALZ  HN12  H  HNH2  0   0.345  10.1939  -1.3520   1.0142
 ALZ  H21A  H  HCH2  0   0.211   8.3208  -2.1666  -0.1699
 ALZ  H22A  H  HCH2  0   0.188   7.8811  -1.8606   1.5006
 ALZ  H31   H  HCH2  0   0.215   7.0320   0.4009   0.8476
 ALZ  H32   H  HCH2  0   0.217   7.4400   0.0588  -0.8250
 ALZ  H41   H  HCH2  0   0.222   5.8708  -1.8752  -0.8258
 ALZ  H42   H  HCH2  0   0.225   5.4863  -1.5892   0.8629
 ALZ  H51   H  HCH2  0   0.231   4.5475   0.6274   0.3228
 ALZ  H52   H  HCH2  0   0.204   4.9976   0.4350  -1.3703
 ALZ  HN6   H  HNH1  0   0.366   3.5240  -1.5136  -1.3862
 ALZ  HN7   H  HNH1  0   0.397   2.4877   0.6031  -1.8331

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
 ALZ  N1   C2    single    1.456  0.020  1.456
 ALZ  N1   HN11  single    0.890  0.020  1.040
 ALZ  N1   HN12  single    0.890  0.020  1.040
 ALZ  C2   C3    single    1.521  0.020  1.521
 ALZ  C2   H21A  single    0.970  0.020  1.090
 ALZ  C2   H22A  single    0.970  0.020  1.090
 ALZ  C3   C4    single    1.523  0.020  1.523
 ALZ  C3   H31   single    0.970  0.020  1.090
 ALZ  C3   H32   single    0.970  0.020  1.090
 ALZ  C4   C5    single    1.519  0.020  1.519
 ALZ  C4   H41   single    0.970  0.020  1.090
 ALZ  C4   H42   single    0.970  0.020  1.090
 ALZ  C5   N6    single    1.457  0.020  1.457
 ALZ  C5   H51   single    0.970  0.020  1.090
 ALZ  C5   H52   single    0.970  0.020  1.090
 ALZ  N6   N7    single    1.380  0.020  1.380
 ALZ  N6   HN6   single    0.890  0.020  1.040
 ALZ  N7   C8    single    1.345  0.020  1.345
 ALZ  N7   HN7   single    0.860  0.020  1.020
 ALZ  C8   O8    double    1.216  0.020  1.216
 ALZ  C8   C9    single    1.524  0.020  1.524
 ALZ  C9   N8    single    1.446  0.020  1.446
 ALZ  C9   C10   single    1.538  0.020  1.538
 ALZ  C9   H9    single    0.970  0.020  1.090
 ALZ  N8   C12   single    1.457  0.020  1.457
 ALZ  N8   C14   single    1.341  0.020  1.341
 ALZ  C10  C11   single    1.525  0.020  1.525
 ALZ  C10  H101  single    0.970  0.020  1.090
 ALZ  C10  H102  single    0.970  0.020  1.090
 ALZ  C11  C12   single    1.522  0.020  1.522
 ALZ  C11  H111  single    0.970  0.020  1.090
 ALZ  C11  H112  single    0.970  0.020  1.090
 ALZ  C12  H121  single    0.970  0.020  1.090
 ALZ  C12  H122  single    0.970  0.020  1.090
 ALZ  C14  O14   double    1.217  0.020  1.217
 ALZ  C14  O15   single    1.335  0.020  1.335
 ALZ  O15  C16   single    1.432  0.020  1.432
 ALZ  C16  C17   single    1.498  0.020  1.498
 ALZ  C16  H161  single    0.970  0.020  1.090
 ALZ  C16  H162  single    0.970  0.020  1.090
 ALZ  C17  C18   aromatic  1.393  0.020  1.393
 ALZ  C17  C22   aromatic  1.391  0.020  1.391
 ALZ  C18  C19   aromatic  1.387  0.020  1.387
 ALZ  C18  H18   single    0.930  0.020  1.080
 ALZ  C19  C20   aromatic  1.390  0.020  1.390
 ALZ  C19  H19   single    0.930  0.020  1.080
 ALZ  C20  C21   aromatic  1.388  0.020  1.388
 ALZ  C20  H20   single    0.930  0.020  1.080
 ALZ  C21  C22   aromatic  1.389  0.020  1.389
 ALZ  C21  H21   single    0.930  0.020  1.080
 ALZ  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
 ALZ  N8    C14  O15   112.01  3.000
 ALZ  O15   C14  O14   124.03  3.000
 ALZ  N8    C14  O14   123.97  3.000
 ALZ  C16   O15  C14   116.98  3.000
 ALZ  H162  C16  H161  108.12  3.000
 ALZ  H162  C16  C17   110.82  3.000
 ALZ  H161  C16  C17   110.81  3.000
 ALZ  H162  C16  O15   110.12  3.000
 ALZ  H161  C16  O15   110.05  3.000
 ALZ  C17   C16  O15   106.92  3.000
 ALZ  C22   C17  C18   119.08  3.000
 ALZ  C22   C17  C16   120.67  3.000
 ALZ  C18   C17  C16   120.25  3.000
 ALZ  H18   C18  C19   119.72  3.000
 ALZ  H18   C18  C17   119.77  3.000
 ALZ  C19   C18  C17   120.51  3.000
 ALZ  H19   C19  C20   120.09  3.000
 ALZ  H19   C19  C18   119.86  3.000
 ALZ  C20   C19  C18   120.05  3.000
 ALZ  H20   C20  C21   120.14  3.000
 ALZ  H20   C20  C19   120.06  3.000
 ALZ  C21   C20  C19   119.80  3.000
 ALZ  H21   C21  C22   119.87  3.000
 ALZ  H21   C21  C20   120.14  3.000
 ALZ  C22   C21  C20   119.99  3.000
 ALZ  H22   C22  C21   119.70  3.000
 ALZ  H22   C22  C17   119.72  3.000
 ALZ  C21   C22  C17   120.58  3.000
 ALZ  C12   N8   C9    113.42  3.000
 ALZ  C12   N8   C14   126.70  3.000
 ALZ  C9    N8   C14   119.88  3.000
 ALZ  H9    C9   C10   110.19  3.000
 ALZ  H9    C9   C8    110.52  3.000
 ALZ  C10   C9   C8    110.44  3.000
 ALZ  H9    C9   N8    110.52  3.000
 ALZ  C10   C9   N8    103.43  3.000
 ALZ  C8    C9   N8    111.55  3.000
 ALZ  N7    C8   O8    124.84  3.000
 ALZ  O8    C8   C9    121.96  3.000
 ALZ  N7    C8   C9    113.12  3.000
 ALZ  H102  C10  H101  107.91  3.000
 ALZ  H102  C10  C11   113.40  3.000
 ALZ  H101  C10  C11   109.89  3.000
 ALZ  H102  C10  C9    111.53  3.000
 ALZ  H101  C10  C9    110.41  3.000
 ALZ  C11   C10  C9    103.68  3.000
 ALZ  H112  C11  H111  108.05  3.000
 ALZ  H112  C11  C12   109.96  3.000
 ALZ  H111  C11  C12   112.34  3.000
 ALZ  H112  C11  C10   110.42  3.000
 ALZ  H111  C11  C10   112.79  3.000
 ALZ  C12   C11  C10   103.25  3.000
 ALZ  H122  C12  H121  108.20  3.000
 ALZ  H122  C12  C11   111.33  3.000
 ALZ  H121  C12  C11   112.56  3.000
 ALZ  H122  C12  N8    111.02  3.000
 ALZ  H121  C12  N8    111.43  3.000
 ALZ  C11   C12  N8    102.28  3.000
 ALZ  HN12  N1   HN11  105.34  3.000
 ALZ  HN12  N1   C2    109.32  3.000
 ALZ  HN11  N1   C2    109.00  3.000
 ALZ  H22A  C2   H21A  106.19  3.000
 ALZ  H22A  C2   C3    108.75  3.000
 ALZ  H21A  C2   C3    109.06  3.000
 ALZ  H22A  C2   N1    113.44  3.000
 ALZ  H21A  C2   N1    108.25  3.000
 ALZ  C3    C2   N1    110.97  3.000
 ALZ  H32   C3   H31   106.56  3.000
 ALZ  H32   C3   C4    109.98  3.000
 ALZ  H31   C3   C4    109.40  3.000
 ALZ  H32   C3   C2    109.05  3.000
 ALZ  H31   C3   C2    109.19  3.000
 ALZ  C4    C3   C2    112.48  3.000
 ALZ  H42   C4   H41   106.61  3.000
 ALZ  H42   C4   C5    108.96  3.000
 ALZ  H41   C4   C5    109.66  3.000
 ALZ  H42   C4   C3    109.98  3.000
 ALZ  H41   C4   C3    109.26  3.000
 ALZ  C5    C4   C3    112.22  3.000
 ALZ  H52   C5   H51   106.98  3.000
 ALZ  H52   C5   N6    112.13  3.000
 ALZ  H51   C5   N6    107.99  3.000
 ALZ  H52   C5   C4    109.69  3.000
 ALZ  H51   C5   C4    109.76  3.000
 ALZ  N6    C5   C4    110.22  3.000
 ALZ  HN6   N6   N7    108.43  3.000
 ALZ  HN6   N6   C5    110.08  3.000
 ALZ  N7    N6   C5    112.47  3.000
 ALZ  HN7   N7   N6    118.93  3.000
 ALZ  HN7   N7   C8    119.24  3.000
 ALZ  N6    N7   C8    121.46  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
 ALZ  CONST_01  C20   C19  C18  C17     0.00   0.0  0
 ALZ  CONST_02  C20   C21  C22  C17     0.00   0.0  0
 ALZ  CONST_03  C21   C22  C17  C18     0.00   0.0  0
 ALZ  CONST_04  C21   C20  C19  C18     0.00   0.0  0
 ALZ  CONST_05  C22   C17  C18  C19     0.00   0.0  0
 ALZ  CONST_06  C22   C21  C20  C19     0.00   0.0  0
 ALZ  CONST_07  C19   C18  C17  C16   180.00   0.0  0
 ALZ  CONST_08  C21   C22  C17  C16   180.00   0.0  0
 ALZ  CONST_09  H19   C19  C18  C17   180.00   0.0  0
 ALZ  CONST_10  H21   C21  C22  C17   180.00   0.0  0
 ALZ  CONST_11  H22   C22  C17  C18   180.00   0.0  0
 ALZ  CONST_12  H20   C20  C19  C18   180.00   0.0  0
 ALZ  CONST_13  H18   C18  C19  C20   180.00   0.0  0
 ALZ  CONST_14  N6    N7   C8   C9    180.00   0.0  0
 ALZ  CONST_15  HN7   N7   C8   C9      0.00   0.0  0
 ALZ  CONST_16  N6    N7   C8   O8      0.00   0.0  0
 ALZ  Var_01    C10   C11  C12  N8    -34.07  30.0  1
 ALZ  Var_02    C11   C12  N8   C9     19.50  30.0  1
 ALZ  Var_03    C12   C11  C10  C9     36.76  30.0  1
 ALZ  Var_04    C9    N8   C14  O14    -3.12  30.0  1
 ALZ  Var_05    C18   C17  C16  O15    78.76  30.0  2
 ALZ  Var_06    C17   C16  O15  C14  -175.45  30.0  3
 ALZ  Var_07    N8    C14  O15  C16   177.57  30.0  2
 ALZ  Var_08    C5    N6   N7   C8   -114.88  30.0  1
 ALZ  Var_09    C4    C3   C2   N1    178.59  30.0  3
 ALZ  Var_10    C5    C4   C3   C2    177.63  30.0  3
 ALZ  Var_11    N6    C5   C4   C3    178.73  30.0  3
 ALZ  Var_12    N7    N6   C5   C4    178.89  30.0  3
 ALZ  Var_13    HN11  N1   C2   C3     64.97  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
 ALZ  chir_01  C9  C8  N8  C10  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
 ALZ  plan-1  C16  0.020
 ALZ  plan-1  C17  0.020
 ALZ  plan-1  C18  0.020
 ALZ  plan-1  C19  0.020
 ALZ  plan-1  C20  0.020
 ALZ  plan-1  C21  0.020
 ALZ  plan-1  C22  0.020
 ALZ  plan-1  H18  0.020
 ALZ  plan-1  H19  0.020
 ALZ  plan-1  H20  0.020
 ALZ  plan-1  H21  0.020
 ALZ  plan-1  H22  0.020
 ALZ  plan-2  C9   0.020
 ALZ  plan-2  C8   0.020
 ALZ  plan-2  O8   0.020
 ALZ  plan-2  N6   0.020
 ALZ  plan-2  N7   0.020
 ALZ  plan-2  HN7  0.020
 ALZ  plan-3  C14  0.020
 ALZ  plan-3  O14  0.020
 ALZ  plan-3  O15  0.020
 ALZ  plan-3  N8   0.020

