# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Jun  9 20:22:16 2020
#   Inital geometry file: a 134 line input string
#   Ligand name: benzyl [(2S)-5-[(diaminomethyl)amino]-1-{[(2S)-4-fluoro-3-oxobutan-2-yl]amino}-1-oxopentan-2-yl]carbamate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](NC(=O)[C@H](CCCNC(N)N)NC(=O)OCc1ccccc1)C(=O)CF
#
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
 ZRA  ZRA  'benzyl [(2S)-5-[(diaminomethyl)amino]-1-{[(2S)-4-fluoro-3-oxobutan-2-yl]amino}-1-oxopentan-2-yl]carbamate'  peptide  56  28  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_ZRA
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
 ZRA  C1    C  C     0   0.766   1.5427  -0.9120   0.6953
 ZRA  O1    O  O     0  -0.515   1.1537  -1.7477   1.4856
 ZRA  O2    O  O2    0  -0.478   2.8043  -0.8005   0.2732
 ZRA  C2    C  CH2   0  -0.241   3.7508  -1.7433   0.7927
 ZRA  C3    C  CR6   0   0.076   5.0928  -1.3540   0.2524
 ZRA  C4    C  CR16  0  -0.289   5.8657  -0.4010   0.9101
 ZRA  C5    C  CR16  0  -0.242   7.0975  -0.0175   0.3990
 ZRA  C6    C  CR16  0  -0.261   7.5687  -0.5846  -0.7787
 ZRA  C7    C  CR16  0  -0.242   6.8039  -1.5356  -1.4414
 ZRA  C8    C  CR16  0  -0.292   5.5715  -1.9161  -0.9273
 ZRA  CA1   C  CH1   0  -0.185  -0.6627   0.0191   0.3654
 ZRA  CB1   C  CH2   0  -0.462  -1.3150   1.2164  -0.3284
 ZRA  CG    C  CH2   0  -0.445  -0.8159   2.5612   0.1846
 ZRA  CD    C  CH2   0  -0.246  -1.5437   3.7222  -0.4760
 ZRA  NE    N  NH1   0  -0.602  -1.0279   4.9879   0.0045
 ZRA  CZ    C  CH1   0   0.179  -1.5545   6.1525  -0.6615
 ZRA  NH1   N  NH2   0  -0.791  -2.9912   6.2928  -0.5271
 ZRA  NH2   N  NH2   0  -0.808  -0.8524   7.2983  -0.1081
 ZRA  C     C  C     0   0.568  -1.2760  -1.2706  -0.1837
 ZRA  N1    N  NH1   0  -0.665   0.7582   0.0345   0.1465
 ZRA  O     O  O     0  -0.488  -0.8287  -1.8227  -1.1747
 ZRA  N2    N  NH1   0  -0.639  -2.3700  -1.6889   0.4712
 ZRA  CA2   C  CH1   0  -0.203  -3.1170  -2.8527   0.0718
 ZRA  CT    C  C     0   0.335  -4.5651  -2.6925   0.4905
 ZRA  OT    O  O     0  -0.373  -4.9055  -1.9754   1.3963
 ZRA  CB2   C  CH3   0  -0.654  -2.5483  -4.1412   0.6803
 ZRA  CM    C  CH2   0  -0.098  -5.5504  -3.5024  -0.3104
 ZRA  F1    F  F     0  -0.355  -6.7984  -3.4460   0.2617
 ZRA  H21   H  HCH2  0   0.249   3.4822  -2.7541   0.4786
 ZRA  H22   H  HCH2  0   0.248   3.7494  -1.7143   1.8839
 ZRA  H4    H  HCR6  0   0.255   5.5057   0.0418   1.8315
 ZRA  H5    H  HCR6  0   0.259   7.6914   0.7218   0.9205
 ZRA  H6    H  HCR6  0   0.259   8.5311  -0.2888  -1.1757
 ZRA  H7    H  HCR6  0   0.258   7.1670  -1.9837  -2.3572
 ZRA  H8    H  HCR6  0   0.256   4.9777  -2.6593  -1.4460
 ZRA  HA1   H  HCH1  0   0.270  -0.8658   0.0921   1.4389
 ZRA  HB11  H  HCH2  0   0.244  -1.1493   1.1407  -1.4080
 ZRA  HB12  H  HCH2  0   0.254  -2.3948   1.1475  -0.1761
 ZRA  HG1   H  HCH2  0   0.226  -0.9560   2.6095   1.2699
 ZRA  HG2   H  HCH2  0   0.226   0.2561   2.6678   0.0025
 ZRA  HD1   H  HCH2  0   0.213  -1.3836   3.6783  -1.5586
 ZRA  HD2   H  HCH2  0   0.196  -2.6262   3.6131  -0.3244
 ZRA  HE    H  HNH1  0   0.332  -1.1908   5.0749   1.0025
 ZRA  HZ    H  HCH1  0   0.198  -1.3676   6.0114  -1.7363
 ZRA  HH11  H  HNH2  0   0.330  -3.2105   6.6048   0.4134
 ZRA  HH12  H  HNH2  0   0.346  -3.3297   7.0148  -1.1519
 ZRA  HH21  H  HNH2  0   0.340   0.1403   7.2089  -0.2895
 ZRA  HH22  H  HNH2  0   0.341  -1.1553   8.1414  -0.5800
 ZRA  HN1   H  HNH1  0   0.405   1.1315   0.6099  -0.5926
 ZRA  HN2   H  HNH1  0   0.402  -2.6402  -1.2319   1.3294
 ZRA  HA2   H  HCH1  0   0.287  -3.0755  -2.9370  -1.0173
 ZRA  HB21  H  HCH3  0   0.243  -2.6036  -4.1166   1.7684
 ZRA  HB22  H  HCH3  0   0.241  -3.0808  -5.0237   0.3263
 ZRA  HB23  H  HCH3  0   0.262  -1.5045  -4.2460   0.3897
 ZRA  HM1   H  HCH2  0   0.262  -5.5928  -3.0913  -1.3237
 ZRA  HM2   H  HCH2  0   0.248  -5.2290  -4.5436  -0.3887

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
 ZRA  C1   N1    single    1.346  0.020  1.346
 ZRA  C1   O1    double    1.214  0.020  1.214
 ZRA  C1   O2    single    1.335  0.020  1.335
 ZRA  C2   C3    single    1.498  0.020  1.498
 ZRA  C2   O2    single    1.433  0.020  1.433
 ZRA  C2   H21   single    0.970  0.020  1.090
 ZRA  C2   H22   single    0.970  0.020  1.090
 ZRA  C3   C4    aromatic  1.392  0.020  1.392
 ZRA  C3   C8    aromatic  1.392  0.020  1.392
 ZRA  C4   C5    aromatic  1.388  0.020  1.388
 ZRA  C4   H4    single    0.930  0.020  1.080
 ZRA  C5   C6    aromatic  1.389  0.020  1.389
 ZRA  C5   H5    single    0.930  0.020  1.080
 ZRA  C6   C7    aromatic  1.389  0.020  1.389
 ZRA  C6   H6    single    0.930  0.020  1.080
 ZRA  C7   C8    aromatic  1.388  0.020  1.388
 ZRA  C7   H7    single    0.930  0.020  1.080
 ZRA  C8   H8    single    0.930  0.020  1.080
 ZRA  CA1  CB1   single    1.530  0.020  1.530
 ZRA  CA1  C     single    1.530  0.020  1.530
 ZRA  CA1  N1    single    1.438  0.020  1.438
 ZRA  CA1  HA1   single    0.970  0.020  1.090
 ZRA  CB1  CG    single    1.523  0.020  1.523
 ZRA  CB1  HB11  single    0.970  0.020  1.090
 ZRA  CB1  HB12  single    0.970  0.020  1.090
 ZRA  CG   CD    single    1.521  0.020  1.521
 ZRA  CG   HG1   single    0.970  0.020  1.090
 ZRA  CG   HG2   single    0.970  0.020  1.090
 ZRA  CD   NE    single    1.449  0.020  1.449
 ZRA  CD   HD1   single    0.970  0.020  1.090
 ZRA  CD   HD2   single    0.970  0.020  1.090
 ZRA  NE   CZ    single    1.441  0.020  1.441
 ZRA  NE   HE    single    0.890  0.020  1.040
 ZRA  CZ   NH1   single    1.450  0.020  1.450
 ZRA  CZ   NH2   single    1.453  0.020  1.453
 ZRA  CZ   HZ    single    0.970  0.020  1.090
 ZRA  NH1  HH11  single    0.890  0.020  1.040
 ZRA  NH1  HH12  single    0.890  0.020  1.040
 ZRA  NH2  HH21  single    0.890  0.020  1.040
 ZRA  NH2  HH22  single    0.890  0.020  1.040
 ZRA  C    N2    single    1.342  0.020  1.342
 ZRA  C    O     double    1.231  0.020  1.231
 ZRA  CA2  CB2   single    1.534  0.020  1.534
 ZRA  CA2  CT    single    1.516  0.020  1.516
 ZRA  CA2  N2    single    1.439  0.020  1.439
 ZRA  CA2  HA2   single    0.970  0.020  1.090
 ZRA  CB2  HB21  single    0.970  0.020  1.090
 ZRA  CB2  HB22  single    0.970  0.020  1.090
 ZRA  CB2  HB23  single    0.970  0.020  1.090
 ZRA  CT   CM    single    1.506  0.020  1.506
 ZRA  CT   OT    double    1.204  0.020  1.204
 ZRA  CM   HM1   single    0.970  0.020  1.090
 ZRA  CM   HM2   single    0.970  0.020  1.090
 ZRA  CM   F1    single    1.374  0.020  1.374
 ZRA  N1   HN1   single    0.860  0.020  1.020
 ZRA  N2   HN2   single    0.860  0.020  1.020

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
 ZRA  N1    C1   O2    111.29  3.000
 ZRA  O2    C1   O1    124.47  3.000
 ZRA  N1    C1   O1    124.23  3.000
 ZRA  C2    O2   C1    117.03  3.000
 ZRA  H22   C2   H21   108.17  3.000
 ZRA  H22   C2   C3    110.78  3.000
 ZRA  H21   C2   C3    110.92  3.000
 ZRA  H22   C2   O2    110.12  3.000
 ZRA  H21   C2   O2    110.01  3.000
 ZRA  C3    C2   O2    106.85  3.000
 ZRA  C8    C3   C4    119.07  3.000
 ZRA  C8    C3   C2    120.59  3.000
 ZRA  C4    C3   C2    120.32  3.000
 ZRA  H4    C4   C5    119.68  3.000
 ZRA  H4    C4   C3    119.79  3.000
 ZRA  C5    C4   C3    120.53  3.000
 ZRA  H5    C5   C6    120.08  3.000
 ZRA  H5    C5   C4    119.90  3.000
 ZRA  C6    C5   C4    120.03  3.000
 ZRA  H6    C6   C7    120.12  3.000
 ZRA  H6    C6   C5    120.06  3.000
 ZRA  C7    C6   C5    119.82  3.000
 ZRA  H7    C7   C8    119.85  3.000
 ZRA  H7    C7   C6    120.17  3.000
 ZRA  C8    C7   C6    119.98  3.000
 ZRA  H8    C8   C7    119.81  3.000
 ZRA  H8    C8   C3    119.62  3.000
 ZRA  C7    C8   C3    120.57  3.000
 ZRA  HA1   CA1  N1    109.38  3.000
 ZRA  HA1   CA1  C     109.50  3.000
 ZRA  N1    CA1  C     110.52  3.000
 ZRA  HA1   CA1  CB1   108.26  3.000
 ZRA  N1    CA1  CB1   110.12  3.000
 ZRA  C     CA1  CB1   109.03  3.000
 ZRA  HB12  CB1  HB11  106.42  3.000
 ZRA  HB12  CB1  CG    109.41  3.000
 ZRA  HB11  CB1  CG    110.08  3.000
 ZRA  HB12  CB1  CA1   107.99  3.000
 ZRA  HB11  CB1  CA1   109.18  3.000
 ZRA  CG    CB1  CA1   113.48  3.000
 ZRA  HG2   CG   HG1   106.64  3.000
 ZRA  HG2   CG   CD    108.82  3.000
 ZRA  HG1   CG   CD    109.60  3.000
 ZRA  HG2   CG   CB1   110.58  3.000
 ZRA  HG1   CG   CB1   109.31  3.000
 ZRA  CD    CG   CB1   111.76  3.000
 ZRA  HD2   CD   HD1   106.05  3.000
 ZRA  HD2   CD   NE    113.06  3.000
 ZRA  HD1   CD   NE    108.11  3.000
 ZRA  HD2   CD   CG    109.62  3.000
 ZRA  HD1   CD   CG    109.19  3.000
 ZRA  NE    CD   CG    110.64  3.000
 ZRA  HE    NE   CZ    109.06  3.000
 ZRA  HE    NE   CD    110.11  3.000
 ZRA  CZ    NE   CD    115.00  3.000
 ZRA  HZ    CZ   NH2   113.02  3.000
 ZRA  HZ    CZ   NH1   105.74  3.000
 ZRA  NH2   CZ   NH1   111.54  3.000
 ZRA  HZ    CZ   NE    106.61  3.000
 ZRA  NH2   CZ   NE    106.54  3.000
 ZRA  NH1   CZ   NE    113.42  3.000
 ZRA  HH12  NH1  HH11  106.27  3.000
 ZRA  HH12  NH1  CZ    110.05  3.000
 ZRA  HH11  NH1  CZ    109.25  3.000
 ZRA  HH22  NH2  HH21  106.45  3.000
 ZRA  HH22  NH2  CZ    109.55  3.000
 ZRA  HH21  NH2  CZ    109.61  3.000
 ZRA  N2    C    O     123.68  3.000
 ZRA  O     C    CA1   121.75  3.000
 ZRA  N2    C    CA1   114.48  3.000
 ZRA  HN1   N1   CA1   118.93  3.000
 ZRA  HN1   N1   C1    118.96  3.000
 ZRA  CA1   N1   C1    120.41  3.000
 ZRA  HN2   N2   CA2   117.59  3.000
 ZRA  HN2   N2   C     119.49  3.000
 ZRA  CA2   N2   C     122.66  3.000
 ZRA  HA2   CA2  CB2   108.44  3.000
 ZRA  HA2   CA2  CT    108.64  3.000
 ZRA  CB2   CA2  CT    109.47  3.000
 ZRA  HA2   CA2  N2    108.60  3.000
 ZRA  CT    CA2  N2    109.49  3.000
 ZRA  CB2   CA2  N2    112.12  3.000
 ZRA  CM    CT   OT    122.36  3.000
 ZRA  OT    CT   CA2   122.73  3.000
 ZRA  CM    CT   CA2   114.91  3.000
 ZRA  HB23  CB2  HB22  107.69  3.000
 ZRA  HB23  CB2  HB21  108.50  3.000
 ZRA  HB22  CB2  HB21  108.53  3.000
 ZRA  HB23  CB2  CA2   109.29  3.000
 ZRA  HB22  CB2  CA2   111.72  3.000
 ZRA  HB21  CB2  CA2   110.99  3.000
 ZRA  HM2   CM   HM1   107.64  3.000
 ZRA  HM2   CM   F1    109.64  3.000
 ZRA  HM1   CM   F1    109.57  3.000
 ZRA  F1    CM   CT    110.53  3.000
 ZRA  HM2   CM   CT    110.99  3.000
 ZRA  HM1   CM   CT    108.40  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
 ZRA  CONST_01  C6    C5   C4   C3      0.00   0.0  0
 ZRA  CONST_02  C6    C7   C8   C3      0.00   0.0  0
 ZRA  CONST_03  C7    C8   C3   C4      0.00   0.0  0
 ZRA  CONST_04  C7    C6   C5   C4      0.00   0.0  0
 ZRA  CONST_05  C8    C3   C4   C5      0.00   0.0  0
 ZRA  CONST_06  C8    C7   C6   C5      0.00   0.0  0
 ZRA  CONST_07  C5    C4   C3   C2    180.00   0.0  0
 ZRA  CONST_08  C7    C8   C3   C2    180.00   0.0  0
 ZRA  CONST_09  H5    C5   C4   C3    180.00   0.0  0
 ZRA  CONST_10  H7    C7   C8   C3    180.00   0.0  0
 ZRA  CONST_11  H8    C8   C3   C4    180.00   0.0  0
 ZRA  CONST_12  H6    C6   C5   C4    180.00   0.0  0
 ZRA  CONST_13  H4    C4   C5   C6    180.00   0.0  0
 ZRA  CONST_14  CA2   N2   C    CA1   180.00   0.0  0
 ZRA  CONST_15  CA2   N2   C    O       0.00   0.0  0
 ZRA  CONST_16  HN2   N2   C    CA1     0.00   0.0  0
 ZRA  Var_01    C4    C3   C2   O2     85.92  30.0  2
 ZRA  Var_02    C3    C2   O2   C1   -176.08  30.0  1
 ZRA  Var_03    CA1   N1   C1   O1     -6.86  30.0  2
 ZRA  Var_04    N1    C1   O2   C2    179.44  30.0  1
 ZRA  Var_05    CD    CG   CB1  CA1  -176.86  30.0  3
 ZRA  Var_06    NE    CD   CG   CB1  -178.59  30.0  3
 ZRA  Var_07    CZ    NE   CD   CG    173.85  30.0  3
 ZRA  Var_08    NH1   CZ   NE   CD     60.82  30.0  3
 ZRA  Var_09    F1    CM   CT   CA2   171.15  30.0  3
 ZRA  Var_10    HH11  NH1  CZ   NE     74.47  30.0  3
 ZRA  Var_11    HH21  NH2  CZ   NE     60.68  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
 ZRA  chir_01  CA1  CB1  C    N1  negativ
 ZRA  chir_02  CA2  N2   CB2  CT  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
 ZRA  plan-1  C2   0.020
 ZRA  plan-1  C3   0.020
 ZRA  plan-1  C4   0.020
 ZRA  plan-1  C5   0.020
 ZRA  plan-1  C6   0.020
 ZRA  plan-1  C7   0.020
 ZRA  plan-1  C8   0.020
 ZRA  plan-1  H4   0.020
 ZRA  plan-1  H5   0.020
 ZRA  plan-1  H6   0.020
 ZRA  plan-1  H7   0.020
 ZRA  plan-1  H8   0.020
 ZRA  plan-2  CA1  0.020
 ZRA  plan-2  C    0.020
 ZRA  plan-2  O    0.020
 ZRA  plan-2  N2   0.020
 ZRA  plan-2  CA2  0.020
 ZRA  plan-2  HN2  0.020
 ZRA  plan-3  CA2  0.020
 ZRA  plan-3  CT   0.020
 ZRA  plan-3  OT   0.020
 ZRA  plan-3  CM   0.020
 ZRA  plan-4  C1   0.020
 ZRA  plan-4  O1   0.020
 ZRA  plan-4  O2   0.020
 ZRA  plan-4  N1   0.020

