# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 16:05:39 2020
#   Inital geometry file: a 148 line input string
#   Ligand name: N~2~-[(S)-({[(benzyloxy)carbonyl]amino}methyl)(hydroxy)phosphoryl]-N-(2,2-dimethylpropyl)-L-leucinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](N[P](O)(=O)CNC(=O)OCc1ccccc1)C(=O)NCC(C)(C)C
#
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
 2GZ  2GZ  N~2~-[(S)-({[(benzyloxy)carbonyl]amino}methyl)(hydroxy)phosphoryl]-N-(2,2-dimethylpropyl)-L-leucinamide  peptide  62  29  .  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_2GZ
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
 2GZ  C7   C  CH2    0  -0.233  -5.1802   0.0262   0.6711
 2GZ  C6   C  C      0   0.076  -5.9931  -0.9254  -0.1540
 2GZ  C1   C  C1     0  -0.283  -5.6485  -2.2746  -0.2101
 2GZ  C2   C  C1     0  -0.243  -6.3907  -3.1599  -0.9769
 2GZ  C3   C  C1     0  -0.263  -7.4906  -2.7061  -1.6962
 2GZ  C4   C  C1     0  -0.241  -7.8417  -1.3646  -1.6444
 2GZ  C5   C  C1     0  -0.301  -7.0921  -0.4791  -0.8791
 2GZ  C9   C  C      0   0.749  -3.0122   0.9618   0.6208
 2GZ  O10  O  O      0  -0.524  -3.1958   1.4908   1.6988
 2GZ  O8   O  O2     0  -0.485  -3.9344   0.2140  -0.0046
 2GZ  N11  N  NH1    0  -0.648  -1.9011   1.0700  -0.1281
 2GZ  C12  C  CH2    0  -0.561  -0.6541   1.5720   0.4108
 2GZ  P13  P  P      0   1.246   0.3867   0.1908   1.0538
 2GZ  O15  O  O      0  -0.805   0.7271  -0.6752  -0.1495
 2GZ  O14  O  OP    -1  -0.791  -0.3016  -0.4071   2.2512
 2GZ  N16  N  NH1    0  -0.789   1.8152   0.9427   1.5525
 2GZ  C17  C  CH1    0  -0.202   2.9239   1.2346   0.6656
 2GZ  C22  C  C      0   0.574   3.9534   0.0972   0.7682
 2GZ  O23  O  O      0  -0.513   5.0196   0.2218   1.3608
 2GZ  C18  C  CH2    0  -0.408   3.5264   2.6027   0.9531
 2GZ  C19  C  CH1    0  -0.241   4.6094   3.0756  -0.0201
 2GZ  C20  C  CH3    0  -0.663   4.1141   3.1399  -1.4626
 2GZ  C21  C  CH3    0  -0.653   5.1249   4.4427   0.4200
 2GZ  N24  N  NH1    0  -0.660   3.5456  -1.0363   0.1798
 2GZ  C25  C  CH2    0  -0.255   4.2910  -2.2698   0.1749
 2GZ  C26  C  CT     0  -0.095   4.9473  -2.5934  -1.1781
 2GZ  C27  C  CH3    0  -0.641   5.6564  -3.9400  -1.0382
 2GZ  C28  C  CH3    0  -0.645   3.8788  -2.6853  -2.2670
 2GZ  C29  C  CH3    0  -0.638   5.9604  -1.5111  -1.5476
 2GZ  H27  H  HCH2   0   0.245  -5.7007   0.9797   0.7854
 2GZ  H28  H  HCH2   0   0.244  -5.0066  -0.3835   1.6688
 2GZ  H29  H  H      0   0.255  -4.7961  -2.6370   0.3525
 2GZ  H30  H  H      0   0.258  -6.1137  -4.2056  -1.0119
 2GZ  H31  H  H      0   0.258  -8.0710  -3.3969  -2.2937
 2GZ  H32  H  H      0   0.258  -8.6983  -1.0048  -2.1994
 2GZ  H33  H  H      0   0.255  -7.3686   0.5680  -0.8449
 2GZ  H34  H  HNH1   0   0.392  -1.8329   0.4840  -0.9459
 2GZ  H25  H  HCH2   0   0.249  -0.1230   2.1114  -0.3773
 2GZ  H26  H  HCH2   0   0.251  -0.8664   2.2935   1.1985
 2GZ  H1   H  HNH1   0   0.369   1.8913   1.2967   2.4934
 2GZ  H2   H  HCH1   0   0.240   2.5338   1.2349  -0.3563
 2GZ  H3   H  HCH2   0   0.221   2.7048   3.3278   0.9418
 2GZ  H4   H  HCH2   0   0.220   3.9303   2.6087   1.9707
 2GZ  H5   H  HCH1   0   0.224   5.4461   2.3729   0.0226
 2GZ  H6   H  HCH3   0   0.228   4.8882   3.5456  -2.1169
 2GZ  H7   H  HCH3   0   0.223   3.8432   2.1603  -1.8600
 2GZ  H8   H  HCH3   0   0.214   3.2381   3.7884  -1.5478
 2GZ  H9   H  HCH3   0   0.212   4.3305   5.1917   0.3762
 2GZ  H10  H  HCH3   0   0.223   5.4997   4.4168   1.4450
 2GZ  H11  H  HCH3   0   0.224   5.9375   4.7864  -0.2224
 2GZ  H12  H  HNH1   0   0.410   2.5733  -1.0553  -0.1351
 2GZ  H13  H  HCH2   0   0.234   5.0580  -2.2256   0.9502
 2GZ  H14  H  HCH2   0   0.232   3.6111  -3.0845   0.4421
 2GZ  H15  H  HCH3   0   0.222   6.4351  -3.9032  -0.2730
 2GZ  H16  H  HCH3   0   0.221   4.9543  -4.7308  -0.7623
 2GZ  H17  H  HCH3   0   0.225   6.1299  -4.2334  -1.9772
 2GZ  H18  H  HCH3   0   0.224   4.3280  -2.9203  -3.2340
 2GZ  H19  H  HCH3   0   0.220   3.1475  -3.4666  -2.0460
 2GZ  H20  H  HCH3   0   0.222   3.3403  -1.7421  -2.3770
 2GZ  H21  H  HCH3   0   0.219   6.7293  -1.4035  -0.7798
 2GZ  H22  H  HCH3   0   0.222   6.4578  -1.7553  -2.4885
 2GZ  H23  H  HCH3   0   0.223   5.4786  -0.5402  -1.6760

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
 2GZ  C21  C19  single    1.526  0.020  1.526
 2GZ  C19  C20  single    1.527  0.020  1.527
 2GZ  C19  C18  single    1.531  0.020  1.531
 2GZ  C18  C17  single    1.522  0.020  1.522
 2GZ  C27  C26  single    1.528  0.020  1.528
 2GZ  C28  C26  single    1.528  0.020  1.528
 2GZ  C26  C29  single    1.528  0.020  1.528
 2GZ  C26  C25  single    1.538  0.020  1.538
 2GZ  C17  C22  single    1.538  0.020  1.538
 2GZ  C17  N16  single    1.449  0.020  1.449
 2GZ  C22  O23  double    1.226  0.020  1.226
 2GZ  C22  N24  single    1.341  0.020  1.341
 2GZ  N24  C25  single    1.441  0.020  1.441
 2GZ  N16  P13  single    1.690  0.020  1.690
 2GZ  P13  O15  deloc     1.521  0.020  1.521
 2GZ  P13  O14  deloc     1.505  0.020  1.505
 2GZ  P13  C12  single    1.845  0.020  1.845
 2GZ  C12  N11  single    1.448  0.020  1.448
 2GZ  N11  C9   single    1.344  0.020  1.344
 2GZ  O10  C9   double    1.215  0.020  1.215
 2GZ  C9   O8   single    1.342  0.020  1.342
 2GZ  O8   C7   single    1.430  0.020  1.430
 2GZ  C5   C4   aromatic  1.390  0.020  1.390
 2GZ  C5   C6   aromatic  1.390  0.020  1.390
 2GZ  C7   C6   single    1.499  0.020  1.499
 2GZ  C4   C3   aromatic  1.388  0.020  1.388
 2GZ  C6   C1   aromatic  1.394  0.020  1.394
 2GZ  C3   C2   aromatic  1.390  0.020  1.390
 2GZ  C1   C2   aromatic  1.387  0.020  1.387
 2GZ  N16  H1   single    0.860  0.020  1.020
 2GZ  C17  H2   single    0.970  0.020  1.090
 2GZ  C18  H3   single    0.970  0.020  1.090
 2GZ  C18  H4   single    0.970  0.020  1.090
 2GZ  C19  H5   single    0.970  0.020  1.090
 2GZ  C20  H6   single    0.970  0.020  1.090
 2GZ  C20  H7   single    0.970  0.020  1.090
 2GZ  C20  H8   single    0.970  0.020  1.090
 2GZ  C21  H9   single    0.970  0.020  1.090
 2GZ  C21  H10  single    0.970  0.020  1.090
 2GZ  C21  H11  single    0.970  0.020  1.090
 2GZ  N24  H12  single    0.860  0.020  1.020
 2GZ  C25  H13  single    0.970  0.020  1.090
 2GZ  C25  H14  single    0.970  0.020  1.090
 2GZ  C27  H15  single    0.970  0.020  1.090
 2GZ  C27  H16  single    0.970  0.020  1.090
 2GZ  C27  H17  single    0.970  0.020  1.090
 2GZ  C28  H18  single    0.970  0.020  1.090
 2GZ  C28  H19  single    0.970  0.020  1.090
 2GZ  C28  H20  single    0.970  0.020  1.090
 2GZ  C29  H21  single    0.970  0.020  1.090
 2GZ  C29  H22  single    0.970  0.020  1.090
 2GZ  C29  H23  single    0.970  0.020  1.090
 2GZ  C12  H25  single    0.970  0.020  1.090
 2GZ  C12  H26  single    0.970  0.020  1.090
 2GZ  C7   H27  single    0.970  0.020  1.090
 2GZ  C7   H28  single    0.970  0.020  1.090
 2GZ  C1   H29  single    0.930  0.020  1.080
 2GZ  C2   H30  single    0.930  0.020  1.080
 2GZ  C3   H31  single    0.930  0.020  1.080
 2GZ  C4   H32  single    0.930  0.020  1.080
 2GZ  C5   H33  single    0.930  0.020  1.080
 2GZ  N11  H34  single    0.890  0.020  1.040

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
 2GZ  H28  C7   H27  107.91  3.000
 2GZ  H28  C7   O8   110.03  3.000
 2GZ  H27  C7   O8   110.49  3.000
 2GZ  H28  C7   C6   110.54  3.000
 2GZ  H27  C7   C6   110.69  3.000
 2GZ  O8   C7   C6   107.20  3.000
 2GZ  C5   C6   C1   119.03  3.000
 2GZ  C1   C6   C7   120.17  3.000
 2GZ  C5   C6   C7   120.80  3.000
 2GZ  H29  C1   C2   119.64  3.000
 2GZ  H29  C1   C6   119.82  3.000
 2GZ  C2   C1   C6   120.53  3.000
 2GZ  H30  C2   C3   120.07  3.000
 2GZ  H30  C2   C1   119.86  3.000
 2GZ  C3   C2   C1   120.07  3.000
 2GZ  H31  C3   C4   120.13  3.000
 2GZ  H31  C3   C2   120.10  3.000
 2GZ  C4   C3   C2   119.76  3.000
 2GZ  H32  C4   C5   119.83  3.000
 2GZ  H32  C4   C3   120.17  3.000
 2GZ  C5   C4   C3   120.00  3.000
 2GZ  H33  C5   C4   119.70  3.000
 2GZ  H33  C5   C6   119.70  3.000
 2GZ  C4   C5   C6   120.60  3.000
 2GZ  N11  C9   O8   110.68  3.000
 2GZ  O8   C9   O10  123.53  3.000
 2GZ  N11  C9   O10  125.75  3.000
 2GZ  C9   O8   C7   116.85  3.000
 2GZ  H34  N11  C12  116.42  3.000
 2GZ  H34  N11  C9   117.45  3.000
 2GZ  C12  N11  C9   122.16  3.000
 2GZ  H26  C12  H25  106.82  3.000
 2GZ  H26  C12  P13  110.72  3.000
 2GZ  H25  C12  P13  110.29  3.000
 2GZ  H26  C12  N11  109.32  3.000
 2GZ  H25  C12  N11  108.74  3.000
 2GZ  P13  C12  N11  110.84  3.000
 2GZ  N16  P13  O14  109.19  3.000
 2GZ  O14  P13  O15  120.37  3.000
 2GZ  N16  P13  O15  107.31  3.000
 2GZ  O14  P13  C12  108.47  3.000
 2GZ  O15  P13  C12  106.06  3.000
 2GZ  N16  P13  C12  104.28  3.000
 2GZ  H1   N16  C17  116.27  3.000
 2GZ  H1   N16  P13  119.70  3.000
 2GZ  C17  N16  P13  123.76  3.000
 2GZ  H2   C17  C18  108.50  3.000
 2GZ  H2   C17  C22  107.54  3.000
 2GZ  C18  C17  C22  112.78  3.000
 2GZ  H2   C17  N16  107.39  3.000
 2GZ  C22  C17  N16  108.80  3.000
 2GZ  C18  C17  N16  111.60  3.000
 2GZ  N24  C22  O23  124.23  3.000
 2GZ  N24  C22  C17  113.11  3.000
 2GZ  O23  C22  C17  122.64  3.000
 2GZ  H4   C18  H3   106.41  3.000
 2GZ  H4   C18  C19  109.16  3.000
 2GZ  H3   C18  C19  108.63  3.000
 2GZ  H4   C18  C17  109.05  3.000
 2GZ  H3   C18  C17  107.21  3.000
 2GZ  C19  C18  C17  115.95  3.000
 2GZ  H5   C19  C21  107.82  3.000
 2GZ  H5   C19  C20  108.19  3.000
 2GZ  C21  C19  C20  110.15  3.000
 2GZ  H5   C19  C18  108.54  3.000
 2GZ  C20  C19  C18  112.59  3.000
 2GZ  C21  C19  C18  109.42  3.000
 2GZ  H8   C20  H7   107.76  3.000
 2GZ  H8   C20  H6   107.52  3.000
 2GZ  H7   C20  H6   106.94  3.000
 2GZ  H8   C20  C19  111.02  3.000
 2GZ  H7   C20  C19  112.76  3.000
 2GZ  H6   C20  C19  110.61  3.000
 2GZ  H11  C21  H10  107.73  3.000
 2GZ  H11  C21  H9   107.56  3.000
 2GZ  H10  C21  H9   107.67  3.000
 2GZ  H11  C21  C19  111.34  3.000
 2GZ  H10  C21  C19  111.44  3.000
 2GZ  H9   C21  C19  110.91  3.000
 2GZ  H12  N24  C25  118.37  3.000
 2GZ  H12  N24  C22  116.12  3.000
 2GZ  C25  N24  C22  124.59  3.000
 2GZ  H14  C25  H13  107.05  3.000
 2GZ  H14  C25  C26  108.86  3.000
 2GZ  H13  C25  C26  109.48  3.000
 2GZ  H14  C25  N24  108.36  3.000
 2GZ  H13  C25  N24  109.05  3.000
 2GZ  C26  C25  N24  113.81  3.000
 2GZ  C29  C26  C28  109.50  3.000
 2GZ  C29  C26  C27  109.80  3.000
 2GZ  C28  C26  C27  109.67  3.000
 2GZ  C29  C26  C25  110.28  3.000
 2GZ  C28  C26  C25  109.94  3.000
 2GZ  C27  C26  C25  107.63  3.000
 2GZ  H17  C27  H16  107.54  3.000
 2GZ  H17  C27  H15  107.60  3.000
 2GZ  H16  C27  H15  107.79  3.000
 2GZ  H17  C27  C26  111.06  3.000
 2GZ  H16  C27  C26  111.26  3.000
 2GZ  H15  C27  C26  111.41  3.000
 2GZ  H20  C28  H19  107.94  3.000
 2GZ  H20  C28  H18  107.43  3.000
 2GZ  H19  C28  H18  107.49  3.000
 2GZ  H20  C28  C26  111.39  3.000
 2GZ  H19  C28  C26  111.52  3.000
 2GZ  H18  C28  C26  110.88  3.000
 2GZ  H23  C29  H22  107.38  3.000
 2GZ  H23  C29  H21  107.82  3.000
 2GZ  H22  C29  H21  107.89  3.000
 2GZ  H23  C29  C26  111.46  3.000
 2GZ  H22  C29  C26  110.61  3.000
 2GZ  H21  C29  C26  111.51  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
 2GZ  CONST_01  C3   C4   C5   C6      0.00   0.0  0
 2GZ  CONST_02  C3   C2   C1   C6      0.00   0.0  0
 2GZ  CONST_03  C4   C5   C6   C1      0.00   0.0  0
 2GZ  CONST_04  C4   C3   C2   C1      0.00   0.0  0
 2GZ  CONST_05  C5   C4   C3   C2      0.00   0.0  0
 2GZ  CONST_06  C5   C6   C1   C2      0.00   0.0  0
 2GZ  CONST_07  C4   C5   C6   C7    180.00   0.0  0
 2GZ  CONST_08  C2   C1   C6   C7    180.00   0.0  0
 2GZ  CONST_09  H32  C4   C5   C6    180.00   0.0  0
 2GZ  CONST_10  H30  C2   C1   C6    180.00   0.0  0
 2GZ  CONST_11  H33  C5   C6   C1    180.00   0.0  0
 2GZ  CONST_12  H31  C3   C2   C1    180.00   0.0  0
 2GZ  CONST_13  H29  C1   C2   C3    180.00   0.0  0
 2GZ  CONST_14  C25  N24  C22  C17   180.00   0.0  0
 2GZ  CONST_15  C25  N24  C22  O23     0.00   0.0  0
 2GZ  CONST_16  H12  N24  C22  C17     0.00   0.0  0
 2GZ  Var_01    O8   C7   C6   C1     71.95  30.0  2
 2GZ  Var_02    N11  C9   O8   C7   -179.27  30.0  2
 2GZ  Var_03    P13  C12  N11  C9     91.62  30.0  2
 2GZ  Var_04    C12  N11  C9   O10    15.51  30.0  1
 2GZ  Var_05    N16  P13  C12  N11   176.87  30.0  2
 2GZ  Var_06    C17  N16  P13  C12   -85.04  30.0  1
 2GZ  Var_07    C21  C19  C18  C17  -178.94  30.0  1
 2GZ  Var_08    C26  C25  N24  C22  -105.79  30.0  3
 2GZ  Var_09    C27  C26  C25  N24  -178.21  30.0  3
 2GZ  Var_10    H9   C21  C19  C18   -63.31  30.0  3
 2GZ  Var_11    H6   C20  C19  C18   176.08  30.0  3
 2GZ  Var_12    H15  C27  C26  C25   -61.04  30.0  3
 2GZ  Var_13    H18  C28  C26  C25  -179.68  30.0  3
 2GZ  Var_14    H21  C29  C26  C25    57.74  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
 2GZ  chir_02  C17  C18  C22  N16  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
 2GZ  plan-1  C7   0.020
 2GZ  plan-1  C6   0.020
 2GZ  plan-1  C1   0.020
 2GZ  plan-1  C2   0.020
 2GZ  plan-1  C3   0.020
 2GZ  plan-1  C4   0.020
 2GZ  plan-1  C5   0.020
 2GZ  plan-1  H29  0.020
 2GZ  plan-1  H30  0.020
 2GZ  plan-1  H31  0.020
 2GZ  plan-1  H32  0.020
 2GZ  plan-1  H33  0.020
 2GZ  plan-2  C17  0.020
 2GZ  plan-2  C22  0.020
 2GZ  plan-2  O23  0.020
 2GZ  plan-2  N24  0.020
 2GZ  plan-2  C25  0.020
 2GZ  plan-2  H12  0.020
 2GZ  plan-3  C9   0.020
 2GZ  plan-3  O10  0.020
 2GZ  plan-3  O8   0.020
 2GZ  plan-3  N11  0.020

