# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 10:13:26 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  63  29  .  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_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  -0.246  -4.8488  -0.9771   0.9468
 2GZ  C6   C  CR6   0   0.075  -6.0199  -1.2478   0.0540
 2GZ  C1   C  CR16  0  -0.286  -5.9660  -2.2728  -0.8868
 2GZ  C2   C  CR16  0  -0.242  -7.0405  -2.5099  -1.7322
 2GZ  C3   C  CR16  0  -0.260  -8.1810  -1.7214  -1.6442
 2GZ  C4   C  CR16  0  -0.242  -8.2426  -0.6969  -0.7086
 2GZ  C5   C  CR16  0  -0.290  -7.1651  -0.4614   0.1345
 2GZ  C9   C  C     0   0.802  -2.8471   0.2690   0.8242
 2GZ  O10  O  O     0  -0.554  -2.5373  -0.0822   1.9581
 2GZ  O8   O  O2    0  -0.465  -3.9759  -0.0862   0.2297
 2GZ  N11  N  NH1   0  -0.650  -2.0873   1.0524   0.0500
 2GZ  C12  C  CH2   0  -0.571  -0.8597   1.6465   0.5219
 2GZ  P13  P  P     0   1.309   0.4858   0.4405   0.8366
 2GZ  O15  O  O     0  -0.716   0.6769  -0.4747  -0.3280
 2GZ  O14  O  OH1   0  -0.770   0.1096  -0.2318   2.2398
 2GZ  N16  N  NH1   0  -0.771   1.8481   1.3059   1.1964
 2GZ  C17  C  CH1   0  -0.223   2.9824   1.4192   0.2912
 2GZ  C22  C  C     0   0.578   4.0110   0.3374   0.6526
 2GZ  O23  O  O     0  -0.494   4.9801   0.5721   1.3603
 2GZ  C18  C  CH2   0  -0.396   3.5633   2.8246   0.3261
 2GZ  C19  C  CH1   0  -0.246   4.6974   3.0900  -0.6675
 2GZ  C20  C  CH3   0  -0.664   4.2968   2.7766  -2.1062
 2GZ  C21  C  CH3   0  -0.651   5.1510   4.5415  -0.5429
 2GZ  N24  N  NH1   0  -0.647   3.7150  -0.8725   0.1536
 2GZ  C25  C  CH2   0  -0.255   4.4591  -2.0817   0.4143
 2GZ  C26  C  CT    0  -0.100   5.1172  -2.6817  -0.8371
 2GZ  C27  C  CH3   0  -0.642   5.7752  -3.9963  -0.4192
 2GZ  C28  C  CH3   0  -0.656   4.0615  -2.9568  -1.9087
 2GZ  C29  C  CH3   0  -0.639   6.1740  -1.7257  -1.3875
 2GZ  H27  H  HCH2  0   0.257  -5.1673  -0.5107   1.8802
 2GZ  H28  H  HCH2  0   0.256  -4.3183  -1.9003   1.1869
 2GZ  H29  H  HCR6  0   0.256  -5.0806  -2.8938  -0.9543
 2GZ  H30  H  HCR6  0   0.260  -6.9898  -3.3120  -2.4568
 2GZ  H31  H  HCR6  0   0.260  -9.0214  -1.9087  -2.3001
 2GZ  H32  H  HCR6  0   0.259  -9.1305  -0.0828  -0.6334
 2GZ  H33  H  HCR6  0   0.257  -7.2183   0.3381   0.8640
 2GZ  H34  H  HNH1  0   0.421  -2.3912   1.2645  -0.8864
 2GZ  H25  H  HCH2  0   0.305  -0.5040   2.3199  -0.2566
 2GZ  H26  H  HCH2  0   0.289  -1.0226   2.2578   1.4138
 2GZ  H24  H  HOH1  0   0.492  -0.8703  -0.2582   2.3536
 2GZ  H1   H  HNH1  0   0.403   1.9904   1.6397   2.1391
 2GZ  H2   H  HCH1  0   0.264   2.6099   1.2190  -0.7154
 2GZ  H3   H  HCH2  0   0.230   2.7421   3.5191   0.1196
 2GZ  H4   H  HCH2  0   0.229   3.9113   3.0471   1.3393
 2GZ  H5   H  HCH1  0   0.226   5.5466   2.4535  -0.4030
 2GZ  H6   H  HCH3  0   0.232   5.0991   3.0420  -2.7964
 2GZ  H7   H  HCH3  0   0.222   4.0811   1.7177  -2.2601
 2GZ  H8   H  HCH3  0   0.217   3.4085   3.3416  -2.4000
 2GZ  H9   H  HCH3  0   0.213   4.3431   5.2292  -0.8051
 2GZ  H10  H  HCH3  0   0.225   5.4661   4.7741   0.4758
 2GZ  H11  H  HCH3  0   0.227   5.9901   4.7520  -1.2080
 2GZ  H12  H  HNH1  0   0.396   2.8226  -0.9694  -0.3125
 2GZ  H13  H  HCH2  0   0.245   5.2208  -1.8653   1.1636
 2GZ  H14  H  HCH2  0   0.241   3.7822  -2.8213   0.8539
 2GZ  H15  H  HCH3  0   0.225   6.5328  -3.8313   0.3499
 2GZ  H16  H  HCH3  0   0.224   5.0402  -4.6975  -0.0172
 2GZ  H17  H  HCH3  0   0.229   6.2632  -4.4777  -1.2684
 2GZ  H18  H  HCH3  0   0.232   4.5032  -3.4761  -2.7612
 2GZ  H19  H  HCH3  0   0.225   3.2538  -3.5845  -1.5240
 2GZ  H20  H  HCH3  0   0.223   3.6186  -2.0334  -2.2881
 2GZ  H21  H  HCH3  0   0.222   6.9673  -1.5491  -0.6580
 2GZ  H22  H  HCH3  0   0.225   6.6377  -2.1358  -2.2875
 2GZ  H23  H  HCH3  0   0.223   5.7409  -0.7598  -1.6541

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    1.526  0.020  1.526
 2GZ  C19  C18  single    1.531  0.020  1.531
 2GZ  C18  C17  single    1.521  0.020  1.521
 2GZ  C27  C26  single    1.528  0.020  1.528
 2GZ  C28  C26  single    1.529  0.020  1.529
 2GZ  C26  C29  single    1.528  0.020  1.528
 2GZ  C26  C25  single    1.536  0.020  1.536
 2GZ  C17  C22  single    1.536  0.020  1.536
 2GZ  C17  N16  single    1.456  0.020  1.456
 2GZ  C22  O23  double    1.223  0.020  1.223
 2GZ  C22  N24  single    1.342  0.020  1.342
 2GZ  N24  C25  single    1.443  0.020  1.443
 2GZ  N16  P13  single    1.654  0.020  1.654
 2GZ  P13  O15  double    1.493  0.020  1.493
 2GZ  P13  O14  single    1.601  0.020  1.601
 2GZ  P13  C12  single    1.834  0.020  1.834
 2GZ  C12  N11  single    1.443  0.020  1.443
 2GZ  N11  C9   single    1.338  0.020  1.338
 2GZ  O10  C9   double    1.227  0.020  1.227
 2GZ  C9   O8   single    1.324  0.020  1.324
 2GZ  O8   C7   single    1.439  0.020  1.439
 2GZ  C5   C4   aromatic  1.388  0.020  1.388
 2GZ  C5   C6   aromatic  1.391  0.020  1.391
 2GZ  C7   C6   single    1.497  0.020  1.497
 2GZ  C4   C3   aromatic  1.389  0.020  1.389
 2GZ  C6   C1   aromatic  1.392  0.020  1.392
 2GZ  C3   C2   aromatic  1.389  0.020  1.389
 2GZ  C1   C2   aromatic  1.388  0.020  1.388
 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  O14  H24  single    0.850  0.020  0.980
 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    0.860  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
 2GZ  H28  C7   H27  108.38  3.000
 2GZ  H28  C7   O8   109.78  3.000
 2GZ  H27  C7   O8   109.80  3.000
 2GZ  H28  C7   C6   111.00  3.000
 2GZ  H27  C7   C6   111.04  3.000
 2GZ  O8   C7   C6   106.82  3.000
 2GZ  C5   C6   C1   119.15  3.000
 2GZ  C1   C6   C7   120.38  3.000
 2GZ  C5   C6   C7   120.47  3.000
 2GZ  H29  C1   C2   119.79  3.000
 2GZ  H29  C1   C6   119.71  3.000
 2GZ  C2   C1   C6   120.50  3.000
 2GZ  H30  C2   C3   120.11  3.000
 2GZ  H30  C2   C1   119.89  3.000
 2GZ  C3   C2   C1   120.00  3.000
 2GZ  H31  C3   C4   120.10  3.000
 2GZ  H31  C3   C2   120.05  3.000
 2GZ  C4   C3   C2   119.85  3.000
 2GZ  H32  C4   C5   119.89  3.000
 2GZ  H32  C4   C3   120.12  3.000
 2GZ  C5   C4   C3   119.99  3.000
 2GZ  H33  C5   C4   119.73  3.000
 2GZ  H33  C5   C6   119.76  3.000
 2GZ  C4   C5   C6   120.51  3.000
 2GZ  N11  C9   O8   112.42  3.000
 2GZ  O8   C9   O10  123.60  3.000
 2GZ  N11  C9   O10  123.98  3.000
 2GZ  C9   O8   C7   117.36  3.000
 2GZ  H34  N11  C12  118.30  3.000
 2GZ  H34  N11  C9   119.34  3.000
 2GZ  C12  N11  C9   122.33  3.000
 2GZ  H26  C12  H25  106.62  3.000
 2GZ  H26  C12  P13  109.69  3.000
 2GZ  H25  C12  P13  106.84  3.000
 2GZ  H26  C12  N11  111.72  3.000
 2GZ  H25  C12  N11  107.37  3.000
 2GZ  P13  C12  N11  114.17  3.000
 2GZ  N16  P13  O14  102.87  3.000
 2GZ  O14  P13  O15  117.15  3.000
 2GZ  N16  P13  O15  112.64  3.000
 2GZ  O14  P13  C12  104.72  3.000
 2GZ  O15  P13  C12  111.29  3.000
 2GZ  N16  P13  C12  107.31  3.000
 2GZ  H24  O14  P13  110.23  3.000
 2GZ  H1   N16  C17  116.41  3.000
 2GZ  H1   N16  P13  119.48  3.000
 2GZ  C17  N16  P13  123.19  3.000
 2GZ  H2   C17  C18  108.72  3.000
 2GZ  H2   C17  C22  108.44  3.000
 2GZ  C18  C17  C22  112.93  3.000
 2GZ  H2   C17  N16  107.04  3.000
 2GZ  C22  C17  N16  108.70  3.000
 2GZ  C18  C17  N16  110.81  3.000
 2GZ  N24  C22  O23  124.27  3.000
 2GZ  N24  C22  C17  113.57  3.000
 2GZ  O23  C22  C17  122.13  3.000
 2GZ  H4   C18  H3   106.51  3.000
 2GZ  H4   C18  C19  109.28  3.000
 2GZ  H3   C18  C19  108.86  3.000
 2GZ  H4   C18  C17  109.30  3.000
 2GZ  H3   C18  C17  107.17  3.000
 2GZ  C19  C18  C17  115.35  3.000
 2GZ  H5   C19  C21  107.64  3.000
 2GZ  H5   C19  C20  108.20  3.000
 2GZ  C21  C19  C20  110.52  3.000
 2GZ  H5   C19  C18  108.50  3.000
 2GZ  C20  C19  C18  112.44  3.000
 2GZ  C21  C19  C18  109.40  3.000
 2GZ  H8   C20  H7   107.64  3.000
 2GZ  H8   C20  H6   107.57  3.000
 2GZ  H7   C20  H6   106.98  3.000
 2GZ  H8   C20  C19  111.14  3.000
 2GZ  H7   C20  C19  112.59  3.000
 2GZ  H6   C20  C19  110.69  3.000
 2GZ  H11  C21  H10  107.81  3.000
 2GZ  H11  C21  H9   107.51  3.000
 2GZ  H10  C21  H9   107.65  3.000
 2GZ  H11  C21  C19  111.24  3.000
 2GZ  H10  C21  C19  111.39  3.000
 2GZ  H9   C21  C19  111.05  3.000
 2GZ  H12  N24  C25  117.24  3.000
 2GZ  H12  N24  C22  116.90  3.000
 2GZ  C25  N24  C22  125.06  3.000
 2GZ  H14  C25  H13  106.86  3.000
 2GZ  H14  C25  C26  109.16  3.000
 2GZ  H13  C25  C26  109.76  3.000
 2GZ  H14  C25  N24  108.64  3.000
 2GZ  H13  C25  N24  108.54  3.000
 2GZ  C26  C25  N24  113.64  3.000
 2GZ  C29  C26  C28  109.74  3.000
 2GZ  C29  C26  C27  109.81  3.000
 2GZ  C28  C26  C27  109.52  3.000
 2GZ  C29  C26  C25  110.21  3.000
 2GZ  C28  C26  C25  110.20  3.000
 2GZ  C27  C26  C25  107.32  3.000
 2GZ  H17  C27  H16  107.70  3.000
 2GZ  H17  C27  H15  107.73  3.000
 2GZ  H16  C27  H15  107.73  3.000
 2GZ  H17  C27  C26  111.05  3.000
 2GZ  H16  C27  C26  111.28  3.000
 2GZ  H15  C27  C26  111.18  3.000
 2GZ  H20  C28  H19  107.95  3.000
 2GZ  H20  C28  H18  107.16  3.000
 2GZ  H19  C28  H18  107.50  3.000
 2GZ  H20  C28  C26  111.80  3.000
 2GZ  H19  C28  C26  111.53  3.000
 2GZ  H18  C28  C26  110.70  3.000
 2GZ  H23  C29  H22  107.42  3.000
 2GZ  H23  C29  H21  107.95  3.000
 2GZ  H22  C29  H21  107.62  3.000
 2GZ  H23  C29  C26  111.55  3.000
 2GZ  H22  C29  C26  110.83  3.000
 2GZ  H21  C29  C26  111.29  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     86.48  30.0  2
 2GZ  Var_02    N11  C9   O8   C7    177.43  30.0  1
 2GZ  Var_03    P13  C12  N11  C9     68.17  30.0  1
 2GZ  Var_04    C12  N11  C9   O10    -4.77  30.0  2
 2GZ  Var_05    N16  P13  C12  N11   173.60  30.0  1
 2GZ  Var_06    C17  N16  P13  C12  -108.30  30.0  1
 2GZ  Var_07    C21  C19  C18  C17   178.52  30.0  2
 2GZ  Var_08    C26  C25  N24  C22  -116.14  30.0  3
 2GZ  Var_09    C27  C26  C25  N24  -176.03  30.0  3
 2GZ  Var_10    H9   C21  C19  C18   -62.81  30.0  3
 2GZ  Var_11    H6   C20  C19  C18   175.98  30.0  3
 2GZ  Var_12    H15  C27  C26  C25   -60.14  30.0  3
 2GZ  Var_13    H18  C28  C26  C25  -174.24  30.0  3
 2GZ  Var_14    H21  C29  C26  C25    61.17  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
 2GZ  chir_03  P13  O15  O14  C12  both

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

