# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 10:23:05 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: 6-ammonio-N-(trifluoroacetyl)-L-norleucyl-N-[4-(trifluoromethyl)phenyl]-L-alaninamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](NC(=O)[C@H](CCCC[NH3+])NC(=O)C(F)(F)F)C(=O)Nc1ccc(cc1)C(F)(F)F
#
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
 2Z5  2Z5  6-ammonio-N-(trifluoroacetyl)-L-norleucyl-N-[4-(trifluoromethyl)phenyl]-L-alaninamide  peptide  54  31  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_2Z5
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
 2Z5  C1    C  C     0   0.378  -4.7329  -0.9895   0.8117
 2Z5  C2    C  CT    0   0.951  -6.0934  -1.6767   1.0403
 2Z5  O     O  O     0  -0.445  -4.0206  -0.7395   1.7588
 2Z5  F1    F  F     0  -0.289  -6.3032  -1.8790   2.3312
 2Z5  F2    F  F     0  -0.306  -7.0964  -0.9304   0.5660
 2Z5  F3    F  F     0  -0.305  -6.1442  -2.8590   0.4196
 2Z5  N     N  NH1   0  -0.640  -4.4848  -0.7068  -0.4678
 2Z5  CA    C  CH1   0  -0.228  -3.2329  -0.1524  -0.9261
 2Z5  C     C  C     0   0.586  -2.1042  -1.1747  -0.7150
 2Z5  O1    O  O     0  -0.472  -2.3173  -2.2927  -0.2830
 2Z5  CB    C  CH2   0  -0.452  -2.9199   1.2329  -0.3431
 2Z5  CG    C  CH2   0  -0.426  -4.0789   2.2102  -0.4811
 2Z5  CD    C  CH2   0  -0.451  -3.6959   3.6014   0.0102
 2Z5  CE    C  CH2   0  -0.303  -4.8611   4.5589  -0.1274
 2Z5  NZ    N  NT3   1  -0.777  -4.5060   5.9160   0.3656
 2Z5  N1    N  NH1   0  -0.650  -0.8844  -0.7400  -1.0683
 2Z5  CA1   C  CH1   0  -0.213   0.2920  -1.5709  -0.9917
 2Z5  C3    C  C     0   0.554   1.5034  -0.6580  -0.8401
 2Z5  O2    O  O     0  -0.453   1.5108   0.4708  -1.2920
 2Z5  CB1   C  CH3   0  -0.650   0.4647  -2.4522  -2.2314
 2Z5  N2    N  NH1   0  -0.746   2.5475  -1.2454  -0.2079
 2Z5  C11   C  CR6   0   0.390   3.8248  -0.7439   0.0390
 2Z5  C21   C  CR16  0  -0.300   4.2861   0.4934  -0.4098
 2Z5  C31   C  CR16  0  -0.270   5.5775   0.8973  -0.1074
 2Z5  C4    C  CR6   0  -0.214   6.4259   0.0888   0.6343
 2Z5  C5    C  CR16  0  -0.257   5.9660  -1.1462   1.0818
 2Z5  C6    C  CR16  0  -0.338   4.6827  -1.5562   0.7862
 2Z5  C7    C  CT    0   1.052   7.7994   0.5425   1.0028
 2Z5  F11   F  F     0  -0.316   7.8478   1.0126   2.2608
 2Z5  F21   F  F     0  -0.311   8.6932  -0.4538   0.9388
 2Z5  F31   F  F     0  -0.305   8.2464   1.5220   0.2097
 2Z5  H     H  HNH1  0   0.424  -5.1330  -1.0025  -1.1809
 2Z5  HA    H  HCH1  0   0.315  -3.3497  -0.0341  -2.0072
 2Z5  HB2   H  HCH2  0   0.254  -2.6178   1.1510   0.7011
 2Z5  HB3   H  HCH2  0   0.245  -2.0630   1.6434  -0.8824
 2Z5  HG2   H  HCH2  0   0.236  -4.3914   2.2646  -1.5283
 2Z5  HG3   H  HCH2  0   0.238  -4.9444   1.8565   0.0845
 2Z5  HD2   H  HCH2  0   0.250  -3.3841   3.5489   1.0573
 2Z5  HD3   H  HCH2  0   0.251  -2.8407   3.9747  -0.5605
 2Z5  HE2   H  HCH2  0   0.292  -5.1672   4.6747  -1.1649
 2Z5  HE3   H  HCH2  0   0.292  -5.7216   4.2318   0.4526
 2Z5  HZ1   H  HNT3  0   0.478  -5.2869   6.5642   0.2712
 2Z5  HZ2   H  HNT3  0   0.469  -4.2438   5.9064   1.3509
 2Z5  HZ3   H  HNT3  0   0.469  -3.7235   6.3150  -0.1520
 2Z5  H1    H  HNH1  0   0.405  -0.7757   0.1654  -1.5000
 2Z5  HA1   H  HCH1  0   0.288   0.2017  -2.2100  -0.1110
 2Z5  HB1   H  HCH3  0   0.241   0.5477  -1.8435  -3.1316
 2Z5  HB21  H  HCH3  0   0.245   1.3556  -3.0749  -2.1531
 2Z5  HB31  H  HCH3  0   0.256  -0.3956  -3.1114  -2.3376
 2Z5  HN2   H  HNH1  0   0.426   2.3778  -2.1691   0.1630
 2Z5  H2    H  HCR6  0   0.292   3.6598   1.1466  -0.9931
 2Z5  H3    H  HCR6  0   0.275   5.9042   1.8625  -0.4697
 2Z5  H5    H  HCR6  0   0.279   6.5992  -1.8024   1.6643
 2Z5  H6    H  HCR6  0   0.284   4.3409  -2.5207   1.1408

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
 2Z5  C1   C2    single    1.541  0.020  1.541
 2Z5  C1   O     double    1.211  0.020  1.211
 2Z5  C2   F1    single    1.323  0.020  1.323
 2Z5  C2   F2    single    1.337  0.020  1.337
 2Z5  C2   F3    single    1.336  0.020  1.336
 2Z5  N    CA    single    1.458  0.019  1.458
 2Z5  N    H     single    0.860  0.020  0.860
 2Z5  CA   C     single    1.525  0.021  1.525
 2Z5  CA   CB    single    1.521  0.033  1.521
 2Z5  CA   HA    single    0.970  0.020  0.970
 2Z5  C    O1    double    1.217  0.020  1.217
 2Z5  CB   CG    single    1.522  0.020  1.522
 2Z5  CB   HB2   single    0.970  0.020  1.090
 2Z5  CB   HB3   single    0.970  0.020  1.090
 2Z5  CG   CD    single    1.524  0.020  1.524
 2Z5  CG   HG2   single    0.970  0.020  1.090
 2Z5  CG   HG3   single    0.970  0.020  1.090
 2Z5  CD   CE    single    1.514  0.020  1.514
 2Z5  CD   HD2   single    0.970  0.020  1.090
 2Z5  CD   HD3   single    0.970  0.020  1.090
 2Z5  CE   NZ    single    1.487  0.020  1.487
 2Z5  CE   HE2   single    0.970  0.020  1.090
 2Z5  CE   HE3   single    0.970  0.020  1.090
 2Z5  NZ   HZ1   single    0.890  0.020  1.040
 2Z5  NZ   HZ2   single    0.890  0.020  1.040
 2Z5  NZ   HZ3   single    0.890  0.020  1.040
 2Z5  N1   CA1   single    1.442  0.020  1.442
 2Z5  N1   H1    single    0.860  0.020  1.020
 2Z5  CA1  C3    single    1.524  0.020  1.524
 2Z5  CA1  CB1   single    1.531  0.020  1.531
 2Z5  CA1  HA1   single    0.970  0.020  1.090
 2Z5  C3   O2    double    1.216  0.020  1.216
 2Z5  CB1  HB1   single    0.970  0.020  1.090
 2Z5  CB1  HB21  single    0.970  0.020  1.090
 2Z5  CB1  HB31  single    0.970  0.020  1.090
 2Z5  N2   C11   single    1.394  0.020  1.394
 2Z5  N2   HN2   single    0.860  0.020  1.020
 2Z5  C11  C21   aromatic  1.395  0.020  1.395
 2Z5  C11  C6    aromatic  1.398  0.020  1.398
 2Z5  C21  C31   aromatic  1.387  0.020  1.387
 2Z5  C21  H2    single    0.930  0.020  1.080
 2Z5  C31  C4    aromatic  1.387  0.020  1.387
 2Z5  C31  H3    single    0.930  0.020  1.080
 2Z5  C4   C5    aromatic  1.392  0.020  1.392
 2Z5  C4   C7    single    1.493  0.020  1.493
 2Z5  C5   C6    aromatic  1.379  0.020  1.379
 2Z5  C5   H5    single    0.930  0.020  1.080
 2Z5  C6   H6    single    0.930  0.020  1.080
 2Z5  C7   F11   single    1.344  0.020  1.344
 2Z5  C7   F21   single    1.340  0.020  1.340
 2Z5  C7   F31   single    1.337  0.020  1.337
 2Z5  C1   N     single    1.334  0.020  1.334
 2Z5  C    N1    single    1.342  0.020  1.342
 2Z5  C3   N2    single    1.355  0.020  1.355

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
 2Z5  N     C1   O     126.66  3.000
 2Z5  N     C1   C2    113.64  3.000
 2Z5  O     C1   C2    119.68  3.000
 2Z5  F3    C2   F2    107.49  3.000
 2Z5  F3    C2   F1    108.17  3.000
 2Z5  F2    C2   F1    108.21  3.000
 2Z5  F3    C2   C1    111.05  3.000
 2Z5  F2    C2   C1    111.14  3.000
 2Z5  F1    C2   C1    110.66  3.000
 2Z5  H     N    CA    114.00  3.000
 2Z5  H     N    C1    119.79  3.000
 2Z5  CA    N    C1    123.18  3.000
 2Z5  HA    CA   CB    109.00  3.000
 2Z5  HA    CA   C     110.00  3.000
 2Z5  CB    CA   C     110.50  1.500
 2Z5  HA    CA   N     110.00  3.000
 2Z5  CB    CA   N     110.40  1.500
 2Z5  C     CA   N     111.00  2.800
 2Z5  N1    C    O1    123.36  3.000
 2Z5  N1    C    CA    114.56  3.000
 2Z5  O1    C    CA    122.07  3.000
 2Z5  HB3   CB   HB2   106.48  3.000
 2Z5  HB3   CB   CG    108.14  3.000
 2Z5  HB2   CB   CG    110.25  3.000
 2Z5  HB3   CB   CA    108.15  3.000
 2Z5  HB2   CB   CA    110.64  3.000
 2Z5  CG    CB   CA    112.93  3.000
 2Z5  HG3   CG   HG2   106.58  3.000
 2Z5  HG3   CG   CD    109.13  3.000
 2Z5  HG2   CG   CD    109.56  3.000
 2Z5  HG3   CG   CB    110.38  3.000
 2Z5  HG2   CG   CB    109.64  3.000
 2Z5  CD    CG   CB    111.43  3.000
 2Z5  HD3   CD   HD2   107.05  3.000
 2Z5  HD3   CD   CE    109.78  3.000
 2Z5  HD2   CD   CE    109.68  3.000
 2Z5  HD3   CD   CG    109.86  3.000
 2Z5  HD2   CD   CG    109.65  3.000
 2Z5  CE    CD   CG    110.76  3.000
 2Z5  HE3   CE   HE2   108.53  3.000
 2Z5  HE3   CE   NZ    106.65  3.000
 2Z5  HE2   CE   NZ    106.64  3.000
 2Z5  HE3   CE   CD    111.71  3.000
 2Z5  HE2   CE   CD    111.75  3.000
 2Z5  NZ    CE   CD    111.29  3.000
 2Z5  HZ3   NZ   HZ2   107.27  3.000
 2Z5  HZ3   NZ   HZ1   106.99  3.000
 2Z5  HZ2   NZ   HZ1   107.01  3.000
 2Z5  HZ3   NZ   CE    111.85  3.000
 2Z5  HZ2   NZ   CE    111.92  3.000
 2Z5  HZ1   NZ   CE    111.51  3.000
 2Z5  H1    N1   CA1   116.86  3.000
 2Z5  H1    N1   C     120.08  3.000
 2Z5  CA1   N1   C     122.73  3.000
 2Z5  HA1   CA1  CB1   109.00  3.000
 2Z5  HA1   CA1  C3    109.63  3.000
 2Z5  CB1   CA1  C3    109.61  3.000
 2Z5  HA1   CA1  N1    108.21  3.000
 2Z5  CB1   CA1  N1    112.38  3.000
 2Z5  C3    CA1  N1    107.96  3.000
 2Z5  N2    C3   O2    124.84  3.000
 2Z5  N2    C3   CA1   113.53  3.000
 2Z5  O2    C3   CA1   121.59  3.000
 2Z5  HB31  CB1  HB21  107.88  3.000
 2Z5  HB31  CB1  HB1   108.53  3.000
 2Z5  HB21  CB1  HB1   108.43  3.000
 2Z5  HB31  CB1  CA1   109.78  3.000
 2Z5  HB21  CB1  CA1   111.29  3.000
 2Z5  HB1   CB1  CA1   110.85  3.000
 2Z5  HN2   N2   C11   114.71  3.000
 2Z5  HN2   N2   C3    116.01  3.000
 2Z5  C11   N2   C3    129.26  3.000
 2Z5  C6    C11  C21   118.98  3.000
 2Z5  C6    C11  N2    116.61  3.000
 2Z5  C21   C11  N2    124.41  3.000
 2Z5  H2    C21  C31   118.90  3.000
 2Z5  H2    C21  C11   121.34  3.000
 2Z5  C31   C21  C11   119.76  3.000
 2Z5  H3    C31  C4    120.97  3.000
 2Z5  H3    C31  C21   117.92  3.000
 2Z5  C4    C31  C21   121.10  3.000
 2Z5  C7    C4   C5    119.63  3.000
 2Z5  C7    C4   C31   121.18  3.000
 2Z5  C5    C4   C31   119.15  3.000
 2Z5  H5    C5   C6    118.66  3.000
 2Z5  H5    C5   C4    121.19  3.000
 2Z5  C6    C5   C4    120.16  3.000
 2Z5  H6    C6   C5    119.22  3.000
 2Z5  H6    C6   C11   119.93  3.000
 2Z5  C5    C6   C11   120.85  3.000
 2Z5  F31   C7   F21   107.05  3.000
 2Z5  F31   C7   F11   106.68  3.000
 2Z5  F21   C7   F11   106.31  3.000
 2Z5  F31   C7   C4    112.57  3.000
 2Z5  F21   C7   C4    112.08  3.000
 2Z5  F11   C7   C4    111.75  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
 2Z5  CONST_01  C4   C31  C21  C11     0.00   0.0  0
 2Z5  CONST_02  C4   C5   C6   C11     0.00   0.0  0
 2Z5  CONST_03  C5   C6   C11  C21     0.00   0.0  0
 2Z5  CONST_04  C5   C4   C31  C21     0.00   0.0  0
 2Z5  CONST_05  C6   C11  C21  C31     0.00   0.0  0
 2Z5  CONST_06  C6   C5   C4   C31     0.00   0.0  0
 2Z5  CONST_07  C31  C21  C11  N2    180.00   0.0  0
 2Z5  CONST_08  C5   C6   C11  N2    180.00   0.0  0
 2Z5  CONST_09  C7   C4   C31  C21   180.00   0.0  0
 2Z5  CONST_10  C7   C4   C5   C6    180.00   0.0  0
 2Z5  CONST_11  H3   C31  C21  C11   180.00   0.0  0
 2Z5  CONST_12  H5   C5   C6   C11   180.00   0.0  0
 2Z5  CONST_13  H6   C6   C11  C21   180.00   0.0  0
 2Z5  CONST_14  H2   C21  C31  C4    180.00   0.0  0
 2Z5  CONST_15  C21  C11  N2   C3      0.00   0.0  0
 2Z5  CONST_16  C6   C11  N2   C3    180.00   0.0  0
 2Z5  CONST_17  HN2  N2   C11  C21   180.00   0.0  0
 2Z5  CONST_18  C11  N2   C3   CA1   180.00   0.0  0
 2Z5  CONST_19  C11  N2   C3   O2      0.00   0.0  0
 2Z5  CONST_20  CA   N    C1   C2    180.00   0.0  0
 2Z5  CONST_21  CA   N    C1   O       0.00   0.0  0
 2Z5  CONST_22  CA1  N1   C    CA    180.00   0.0  0
 2Z5  CONST_23  CA1  N1   C    O1      0.00   0.0  0
 2Z5  CONST_24  H    N    C1   C2      0.00   0.0  0
 2Z5  CONST_25  H1   N1   C    CA      0.00   0.0  0
 2Z5  Var_01    F11  C7   C4   C31    99.19  30.0  2
 2Z5  Var_02    F1   C2   C1   O       1.36  30.0  3
 2Z5  Var_03    CD   CG   CB   CA   -175.64  30.0  3
 2Z5  Var_04    CE   CD   CG   CB   -179.72  30.0  3
 2Z5  Var_05    NZ   CE   CD   CG    179.24  30.0  3
 2Z5  Var_06    HZ1  NZ   CE   CD    179.78  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
 2Z5  chir_01  CA   N   C   CB   positiv
 2Z5  chir_02  CA1  N1  C3  CB1  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
 2Z5  plan-1  N2   0.020
 2Z5  plan-1  C11  0.020
 2Z5  plan-1  C21  0.020
 2Z5  plan-1  C31  0.020
 2Z5  plan-1  C4   0.020
 2Z5  plan-1  C5   0.020
 2Z5  plan-1  C6   0.020
 2Z5  plan-1  C7   0.020
 2Z5  plan-1  H2   0.020
 2Z5  plan-1  H3   0.020
 2Z5  plan-1  H5   0.020
 2Z5  plan-1  H6   0.020
 2Z5  plan-2  C1   0.020
 2Z5  plan-2  C2   0.020
 2Z5  plan-2  O    0.020
 2Z5  plan-2  N    0.020
 2Z5  plan-2  CA   0.020
 2Z5  plan-2  H    0.020
 2Z5  plan-3  CA   0.020
 2Z5  plan-3  C    0.020
 2Z5  plan-3  O1   0.020
 2Z5  plan-3  N1   0.020
 2Z5  plan-3  CA1  0.020
 2Z5  plan-3  H1   0.020
 2Z5  plan-4  CA1  0.020
 2Z5  plan-4  C3   0.020
 2Z5  plan-4  O2   0.020
 2Z5  plan-4  N2   0.020
 2Z5  plan-4  C11  0.020
 2Z5  plan-4  HN2  0.020

