# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 31 12:44:55 2021
#   Inital geometry file: a 161 line input string
#   Ligand name: N-(tert-butoxycarbonyl)-L-alpha-glutamyl-N-[(1R)-1-(carboxycarbonyl)-3,3-difluoropropyl]-L-leucinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](NC(=O)[C@H](CCC(O)=O)NC(=O)OC(C)(C)C)C(=O)N[C@@H](CC(F)F)C(=O)C(O)=O
#
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
 2ZF  2ZF  N-(tert-butoxycarbonyl)-L-alpha-glutamyl-N-[(1R)-1-(carboxycarbonyl)-3,3-difluoropropyl]-L-leucinamide  peptide  68  35  .  2022-03-10  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_2ZF
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
 2ZF  O1    O  O     0  -0.501  56.4035   5.5804   5.1740
 2ZF  C     C  C     0   0.770  56.0315   6.4395   4.4022
 2ZF  O2    O  O2    0  -0.502  54.8153   6.9729   4.3458
 2ZF  CT    C  CT    0   0.188  53.7550   6.5878   5.2637
 2ZF  C1    C  CH3   0  -0.658  52.5892   7.4690   4.8312
 2ZF  C2    C  CH3   0  -0.671  53.3877   5.1202   5.0823
 2ZF  C3    C  CH3   0  -0.676  54.1384   6.9111   6.7028
 2ZF  N     N  NH1   0  -0.667  56.8324   6.9713   3.4488
 2ZF  CA    C  CH1   0  -0.164  58.2369   6.6568   3.4377
 2ZF  C4    C  C     0   0.557  58.9002   7.1637   4.7199
 2ZF  O     O  O     0  -0.485  58.6942   8.2953   5.1287
 2ZF  CB    C  CH2   0  -0.470  58.8860   7.3175   2.2209
 2ZF  CG    C  CH2   0  -0.583  60.3602   6.9546   2.0891
 2ZF  CD    C  C     0   0.549  61.0429   7.4595   0.8456
 2ZF  OE1   O  O     0  -0.452  61.9874   6.9124   0.3317
 2ZF  OE2   O  OH1   0  -0.588  60.5158   8.5827   0.3779
 2ZF  N1    N  NH1   0  -0.617  59.7384   6.2986   5.3104
 2ZF  CA1   C  CH1   0  -0.265  60.4626   6.5935   6.5292
 2ZF  C5    C  C     0   0.619  61.8920   6.9873   6.1554
 2ZF  O3    O  O     0  -0.477  62.8420   6.2260   6.2312
 2ZF  CB1   C  CH2   0  -0.414  60.4154   5.4243   7.5014
 2ZF  CG1   C  CH1   0  -0.240  58.9998   4.9893   7.8881
 2ZF  CD1   C  CH3   0  -0.652  59.0780   3.7990   8.8394
 2ZF  CD2   C  CH3   0  -0.661  58.1927   6.1207   8.5180
 2ZF  N2    N  NH1   0  -0.644  62.0213   8.2409   5.6815
 2ZF  CA2   C  CH1   0  -0.193  63.3076   8.7175   5.2507
 2ZF  C6    C  C     0   0.300  64.2676   8.7544   6.4347
 2ZF  O4    O  O     0  -0.322  63.9063   8.9098   7.5651
 2ZF  CB2   C  CH2   0  -0.594  63.2301  10.1350   4.6731
 2ZF  CG2   C  CH1   0   0.540  62.5024  10.2539   3.3566
 2ZF  F1    F  F     0  -0.341  61.1703   9.9909   3.4933
 2ZF  F2    F  F     0  -0.343  62.9812   9.3447   2.4595
 2ZF  CD3   C  C     0   0.487  65.7799   8.6228   6.1809
 2ZF  OE11  O  OH1   0  -0.575  66.0704   8.5584   4.8988
 2ZF  OE21  O  O     0  -0.398  66.5637   8.5877   7.0858
 2ZF  H11   H  HCH3  0   0.231  51.7239   7.2708   5.4636
 2ZF  H12   H  HCH3  0   0.237  52.8353   8.5281   4.9240
 2ZF  H13   H  HCH3  0   0.237  52.3005   7.2697   3.7978
 2ZF  H21   H  HCH3  0   0.235  53.1627   4.9034   4.0368
 2ZF  H22   H  HCH3  0   0.246  54.1742   4.4481   5.4173
 2ZF  H23   H  HCH3  0   0.234  52.4921   4.8976   5.6637
 2ZF  H31   H  HCH3  0   0.252  54.9381   6.2758   7.0764
 2ZF  H32   H  HCH3  0   0.234  54.4498   7.9528   6.7978
 2ZF  H33   H  HCH3  0   0.234  53.2688   6.7694   7.3452
 2ZF  H     H  HNH1  0   0.401  56.5184   7.7869   2.9458
 2ZF  HA    H  HCH1  0   0.272  58.3595   5.5727   3.3543
 2ZF  HB2   H  HCH2  0   0.269  58.3403   6.9875   1.3341
 2ZF  HB3   H  HCH2  0   0.256  58.7616   8.3993   2.2971
 2ZF  HG2   H  HCH2  0   0.280  60.9308   7.3503   2.9349
 2ZF  HG3   H  HCH2  0   0.275  60.4962   5.8722   2.1137
 2ZF  HE2   H  HOH1  0   0.482  61.0035   8.8749  -0.4071
 2ZF  H1    H  HNH1  0   0.405  59.8194   5.3661   4.9353
 2ZF  HA1   H  HCH1  0   0.287  59.9842   7.4612   6.9871
 2ZF  HB21  H  HCH2  0   0.238  60.9533   4.5718   7.0770
 2ZF  HB31  H  HCH2  0   0.238  60.9627   5.7146   8.4041
 2ZF  HG    H  HCH1  0   0.231  58.4755   4.6674   6.9829
 2ZF  HD11  H  HCH3  0   0.225  59.6313   2.9676   8.3992
 2ZF  HD12  H  HCH3  0   0.213  59.5801   4.0765   9.7695
 2ZF  HD13  H  HCH3  0   0.227  58.0821   3.4355   9.0972
 2ZF  HD21  H  HCH3  0   0.228  57.1970   5.7738   8.7991
 2ZF  HD22  H  HCH3  0   0.212  58.6833   6.4931   9.4208
 2ZF  HD23  H  HCH3  0   0.231  58.0558   6.9612   7.8376
 2ZF  H14   H  HNH1  0   0.408  61.2355   8.8712   5.7167
 2ZF  HA2   H  HCH1  0   0.303  63.7110   8.0433   4.4920
 2ZF  HB22  H  HCH2  0   0.294  62.7657  10.8165   5.3900
 2ZF  HB1   H  HCH2  0   0.299  64.2402  10.5145   4.5065
 2ZF  HG1   H  HCH1  0   0.230  62.6075  11.2497   2.9249
 2ZF  HE1   H  HOH1  0   0.500  67.0284   8.4842   4.7591

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
 2ZF  O1    C     double  1.213  0.020  1.213
 2ZF  C     O2    single  1.329  0.020  1.329
 2ZF  O2    CT    single  1.454  0.020  1.454
 2ZF  CT    C1    single  1.524  0.020  1.524
 2ZF  CT    C2    single  1.524  0.020  1.524
 2ZF  CT    C3    single  1.524  0.020  1.524
 2ZF  C1    H11   single  0.970  0.020  1.090
 2ZF  C1    H12   single  0.970  0.020  1.090
 2ZF  C1    H13   single  0.970  0.020  1.090
 2ZF  C2    H21   single  0.970  0.020  1.090
 2ZF  C2    H22   single  0.970  0.020  1.090
 2ZF  C2    H23   single  0.970  0.020  1.090
 2ZF  C3    H31   single  0.970  0.020  1.090
 2ZF  C3    H32   single  0.970  0.020  1.090
 2ZF  C3    H33   single  0.970  0.020  1.090
 2ZF  N     CA    single  1.458  0.019  1.458
 2ZF  N     H     single  0.860  0.020  0.860
 2ZF  CA    C4    single  1.530  0.020  1.530
 2ZF  CA    CB    single  1.521  0.033  1.521
 2ZF  CA    HA    single  0.970  0.020  0.970
 2ZF  C4    O     double  1.221  0.020  1.221
 2ZF  CB    CG    single  1.524  0.020  1.524
 2ZF  CB    HB2   single  0.970  0.020  1.090
 2ZF  CB    HB3   single  0.970  0.020  1.090
 2ZF  CG    CD    single  1.506  0.020  1.506
 2ZF  CG    HG2   single  0.970  0.020  1.090
 2ZF  CG    HG3   single  0.970  0.020  1.090
 2ZF  CD    OE1   double  1.206  0.020  1.206
 2ZF  CD    OE2   single  1.326  0.020  1.326
 2ZF  OE2   HE2   single  0.850  0.020  0.980
 2ZF  N1    CA1   single  1.448  0.020  1.448
 2ZF  N1    H1    single  0.860  0.020  1.020
 2ZF  CA1   C5    single  1.529  0.020  1.529
 2ZF  CA1   CB1   single  1.521  0.020  1.521
 2ZF  CA1   HA1   single  0.970  0.020  1.090
 2ZF  C5    O3    double  1.220  0.020  1.220
 2ZF  CB1   CG1   single  1.531  0.020  1.531
 2ZF  CB1   HB21  single  0.970  0.020  1.090
 2ZF  CB1   HB31  single  0.970  0.020  1.090
 2ZF  CG1   CD1   single  1.526  0.020  1.526
 2ZF  CG1   CD2   single  1.526  0.020  1.526
 2ZF  CG1   HG    single  0.970  0.020  1.090
 2ZF  CD1   HD11  single  0.970  0.020  1.090
 2ZF  CD1   HD12  single  0.970  0.020  1.090
 2ZF  CD1   HD13  single  0.970  0.020  1.090
 2ZF  CD2   HD21  single  0.970  0.020  1.090
 2ZF  CD2   HD22  single  0.970  0.020  1.090
 2ZF  CD2   HD23  single  0.970  0.020  1.090
 2ZF  N2    CA2   single  1.438  0.020  1.438
 2ZF  N2    H14   single  0.860  0.020  1.020
 2ZF  CA2   C6    single  1.525  0.020  1.525
 2ZF  CA2   CB2   single  1.533  0.020  1.533
 2ZF  CA2   HA2   single  0.970  0.020  1.090
 2ZF  C6    O4    double  1.197  0.020  1.197
 2ZF  C6    CD3   single  1.539  0.020  1.539
 2ZF  CB2   CG2   single  1.509  0.020  1.509
 2ZF  CB2   HB22  single  0.970  0.020  1.090
 2ZF  CB2   HB1   single  0.970  0.020  1.090
 2ZF  CG2   F1    single  1.365  0.020  1.365
 2ZF  CG2   F2    single  1.364  0.020  1.364
 2ZF  CG2   HG1   single  0.970  0.020  1.090
 2ZF  CD3   OE11  single  1.316  0.020  1.316
 2ZF  CD3   OE21  double  1.198  0.020  1.198
 2ZF  OE11  HE1   single  0.850  0.020  0.980
 2ZF  C     N     single  1.354  0.020  1.354
 2ZF  C4    N1    single  1.342  0.020  1.342
 2ZF  C5    N2    single  1.346  0.020  1.346

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
 2ZF  N     C     O2    110.72  3.000
 2ZF  N     C     O1    123.00  3.000
 2ZF  O2    C     O1    126.27  3.000
 2ZF  CT    O2    C     122.28  3.000
 2ZF  C3    CT    C2    112.17  3.000
 2ZF  C3    CT    C1    109.74  3.000
 2ZF  C2    CT    C1    109.80  3.000
 2ZF  C3    CT    O2    110.88  3.000
 2ZF  C2    CT    O2    110.83  3.000
 2ZF  C1    CT    O2    103.03  3.000
 2ZF  H13   C1    H12   108.51  3.000
 2ZF  H13   C1    H11   107.83  3.000
 2ZF  H12   C1    H11   107.83  3.000
 2ZF  H13   C1    CT    111.44  3.000
 2ZF  H12   C1    CT    111.37  3.000
 2ZF  H11   C1    CT    109.72  3.000
 2ZF  H23   C2    H22   107.67  3.000
 2ZF  H23   C2    H21   107.51  3.000
 2ZF  H22   C2    H21   108.75  3.000
 2ZF  H23   C2    CT    109.33  3.000
 2ZF  H22   C2    CT    112.60  3.000
 2ZF  H21   C2    CT    110.80  3.000
 2ZF  H33   C3    H32   107.48  3.000
 2ZF  H33   C3    H31   107.95  3.000
 2ZF  H32   C3    H31   108.53  3.000
 2ZF  H33   C3    CT    109.15  3.000
 2ZF  H32   C3    CT    110.88  3.000
 2ZF  H31   C3    CT    112.67  3.000
 2ZF  H     N     CA    114.00  3.000
 2ZF  H     N     C     119.00  3.000
 2ZF  CA    N     C     111.00  2.800
 2ZF  HA    CA    CB    109.00  3.000
 2ZF  HA    CA    C4    110.09  3.000
 2ZF  CB    CA    C4    109.86  3.000
 2ZF  HA    CA    N     110.00  3.000
 2ZF  CB    CA    N     110.40  1.500
 2ZF  C4    CA    N     110.13  3.000
 2ZF  N1    C4    O     123.77  3.000
 2ZF  N1    C4    CA    115.22  3.000
 2ZF  O     C4    CA    120.97  3.000
 2ZF  HB3   CB    HB2   107.41  3.000
 2ZF  HB3   CB    CG    110.62  3.000
 2ZF  HB2   CB    CG    109.95  3.000
 2ZF  HB3   CB    CA    108.92  3.000
 2ZF  HB2   CB    CA    107.67  3.000
 2ZF  CG    CB    CA    112.12  3.000
 2ZF  HG3   CG    HG2   106.04  3.000
 2ZF  HG3   CG    CD    107.14  3.000
 2ZF  HG2   CG    CD    106.30  3.000
 2ZF  HG3   CG    CB    110.78  3.000
 2ZF  HG2   CG    CB    110.58  3.000
 2ZF  CD    CG    CB    115.47  3.000
 2ZF  OE2   CD    OE1   123.03  3.000
 2ZF  OE2   CD    CG    113.27  3.000
 2ZF  OE1   CD    CG    123.69  3.000
 2ZF  HE2   OE2   CD    109.94  3.000
 2ZF  H1    N1    CA1   117.47  3.000
 2ZF  H1    N1    C4    118.86  3.000
 2ZF  CA1   N1    C4    123.48  3.000
 2ZF  HA1   CA1   CB1   109.23  3.000
 2ZF  HA1   CA1   C5    107.91  3.000
 2ZF  CB1   CA1   C5    112.53  3.000
 2ZF  HA1   CA1   N1    107.21  3.000
 2ZF  CB1   CA1   N1    111.46  3.000
 2ZF  C5    CA1   N1    108.31  3.000
 2ZF  N2    C5    O3    121.89  3.000
 2ZF  N2    C5    CA1   114.56  3.000
 2ZF  O3    C5    CA1   123.51  3.000
 2ZF  HB31  CB1   HB21  106.30  3.000
 2ZF  HB31  CB1   CG1   109.23  3.000
 2ZF  HB21  CB1   CG1   109.35  3.000
 2ZF  HB31  CB1   CA1   107.91  3.000
 2ZF  HB21  CB1   CA1   109.62  3.000
 2ZF  CG1   CB1   CA1   114.11  3.000
 2ZF  HG    CG1   CD2   107.83  3.000
 2ZF  HG    CG1   CD1   108.10  3.000
 2ZF  CD2   CG1   CD1   110.38  3.000
 2ZF  HG    CG1   CB1   108.52  3.000
 2ZF  CD2   CG1   CB1   112.51  3.000
 2ZF  CD1   CG1   CB1   109.38  3.000
 2ZF  HD13  CD1   HD12  107.63  3.000
 2ZF  HD13  CD1   HD11  107.71  3.000
 2ZF  HD12  CD1   HD11  107.68  3.000
 2ZF  HD13  CD1   CG1   111.13  3.000
 2ZF  HD12  CD1   CG1   110.86  3.000
 2ZF  HD11  CD1   CG1   111.65  3.000
 2ZF  HD23  CD2   HD22  108.02  3.000
 2ZF  HD23  CD2   HD21  106.94  3.000
 2ZF  HD22  CD2   HD21  107.77  3.000
 2ZF  HD23  CD2   CG1   112.36  3.000
 2ZF  HD22  CD2   CG1   110.87  3.000
 2ZF  HD21  CD2   CG1   110.68  3.000
 2ZF  H14   N2    CA2   120.03  3.000
 2ZF  H14   N2    C5    119.68  3.000
 2ZF  CA2   N2    C5    120.00  3.000
 2ZF  HA2   CA2   CB2   109.13  3.000
 2ZF  HA2   CA2   C6    108.77  3.000
 2ZF  CB2   CA2   C6    107.59  3.000
 2ZF  HA2   CA2   N2    109.51  3.000
 2ZF  CB2   CA2   N2    111.98  3.000
 2ZF  C6    CA2   N2    109.79  3.000
 2ZF  CD3   C6    O4    117.61  3.000
 2ZF  CD3   C6    CA2   119.25  3.000
 2ZF  O4    C6    CA2   123.13  3.000
 2ZF  HB1   CB2   HB22  106.05  3.000
 2ZF  HB1   CB2   CG2   106.60  3.000
 2ZF  HB22  CB2   CG2   108.56  3.000
 2ZF  HB1   CB2   CA2   109.40  3.000
 2ZF  HB22  CB2   CA2   110.55  3.000
 2ZF  CG2   CB2   CA2   115.22  3.000
 2ZF  HG1   CG2   F2    108.33  3.000
 2ZF  HG1   CG2   F1    108.04  3.000
 2ZF  F2    CG2   F1    106.26  3.000
 2ZF  HG1   CG2   CB2   111.77  3.000
 2ZF  F2    CG2   CB2   110.61  3.000
 2ZF  F1    CG2   CB2   111.60  3.000
 2ZF  OE21  CD3   OE11  126.17  3.000
 2ZF  OE21  CD3   C6    121.40  3.000
 2ZF  OE11  CD3   C6    112.44  3.000
 2ZF  HE1   OE11  CD3   111.20  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
 2ZF  CONST_01  CA1   N1    C4   CA    180.00   0.0  0
 2ZF  CONST_02  CA1   N1    C4   O       0.00   0.0  0
 2ZF  CONST_03  CA2   N2    C5   CA1   180.00   0.0  0
 2ZF  CONST_04  CA2   N2    C5   O3      0.00   0.0  0
 2ZF  CONST_05  H1    N1    C4   CA      0.00   0.0  0
 2ZF  CONST_06  H14   N2    C5   CA1     0.00   0.0  0
 2ZF  CONST_07  HE2   OE2   CD   CG    180.00   0.0  0
 2ZF  CONST_08  HE1   OE11  CD3  C6    180.00   0.0  0
 2ZF  Var_01    CA    N     C    O1     -8.62  30.0  2
 2ZF  Var_02    C1    CT    O2   C     178.97  30.0  3
 2ZF  Var_03    N     C     O2   CT   -179.60  30.0  1
 2ZF  Var_04    CD    CG    CB   CA    174.51  30.0  3
 2ZF  Var_05    OE1   CD    CG   CB   -152.06  30.0  3
 2ZF  Var_06    CD1   CG1   CB1  CA1   178.89  30.0  3
 2ZF  Var_07    OE11  CD3   C6   CA2     3.34  30.0  2
 2ZF  Var_08    F1    CG2   CB2  CA2    67.38  30.0  3
 2ZF  Var_09    H11   C1    CT   O2   -179.59  30.0  3
 2ZF  Var_10    H21   C2    CT   O2    -52.81  30.0  3
 2ZF  Var_11    H31   C3    CT   O2    -69.50  30.0  3
 2ZF  Var_12    HD11  CD1   CG1  CB1   -57.06  30.0  3
 2ZF  Var_13    HD21  CD2   CG1  CB1  -178.92  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
 2ZF  chir_01  CA   N   C4   CB   positiv
 2ZF  chir_02  CA1  N1  CB1  C5   negativ
 2ZF  chir_03  CA2  N2  C6   CB2  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
 2ZF  plan-1  CA    0.020
 2ZF  plan-1  C4    0.020
 2ZF  plan-1  O     0.020
 2ZF  plan-1  N1    0.020
 2ZF  plan-1  CA1   0.020
 2ZF  plan-1  H1    0.020
 2ZF  plan-2  CA1   0.020
 2ZF  plan-2  C5    0.020
 2ZF  plan-2  O3    0.020
 2ZF  plan-2  N2    0.020
 2ZF  plan-2  CA2   0.020
 2ZF  plan-2  H14   0.020
 2ZF  plan-3  CA2   0.020
 2ZF  plan-3  C6    0.020
 2ZF  plan-3  O4    0.020
 2ZF  plan-3  CD3   0.020
 2ZF  plan-4  CG    0.020
 2ZF  plan-4  CD    0.020
 2ZF  plan-4  OE1   0.020
 2ZF  plan-4  OE2   0.020
 2ZF  plan-4  HE2   0.020
 2ZF  plan-5  C6    0.020
 2ZF  plan-5  CD3   0.020
 2ZF  plan-5  OE11  0.020
 2ZF  plan-5  OE21  0.020
 2ZF  plan-5  HE1   0.020
 2ZF  plan-6  O1    0.020
 2ZF  plan-6  C     0.020
 2ZF  plan-6  O2    0.020
 2ZF  plan-6  N     0.020

