# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 03:11:23 2020
#   Inital geometry file: a 154 line input string
#   Ligand name: N~2~-[(S)-({[(benzyloxy)carbonyl]amino}methyl)(hydroxy)phosphoryl]-N-(3,3-dimethylbutyl)-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)NCCC(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
 2G6  2G6  N~2~-[(S)-({[(benzyloxy)carbonyl]amino}methyl)(hydroxy)phosphoryl]-N-(3,3-dimethylbutyl)-L-leucinamide  peptide  65  30  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_2G6
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
 2G6  C7   C  CH2    0  -0.235   5.8189   0.2399  -1.1049
 2G6  C6   C  CR6    0   0.077   6.7793  -0.4683  -0.1981
 2G6  C1   C  CR16   0  -0.289   6.5825  -1.8078   0.1272
 2G6  C2   C  CR16   0  -0.242   7.4498  -2.4585   0.9933
 2G6  C3   C  CR16   0  -0.262   8.5256  -1.7735   1.5447
 2G6  C4   C  CR16   0  -0.242   8.7303  -0.4379   1.2249
 2G6  C5   C  CR16   0  -0.293   7.8593   0.2097   0.3587
 2G6  C9   C  C      0   0.749   3.7062   1.2815  -0.9155
 2G6  O10  O  O      0  -0.525   3.6476   1.4181  -2.1207
 2G6  O8   O  O2     0  -0.485   4.7414   0.7031  -0.2863
 2G6  N11  N  NH1    0  -0.649   2.7948   1.7205  -0.0288
 2G6  C12  C  CH2    0  -0.561   1.4391   2.0388  -0.4300
 2G6  P13  P  P      0   1.231   0.3684   0.5384  -0.3269
 2G6  O14  O  O      0  -0.814   0.1184   0.2386   1.1339
 2G6  O15  O  OP    -1  -0.799   0.9963  -0.5111  -1.2119
 2G6  N16  N  NH1    0  -0.773  -1.0821   1.1283  -1.0032
 2G6  C17  C  CH1    0  -0.217  -2.3563   0.9700  -0.3540
 2G6  C22  C  C      0   0.548  -3.1060  -0.2550  -0.8756
 2G6  O23  O  O      0  -0.506  -3.0366  -0.6057  -2.0474
 2G6  C18  C  CH2    0  -0.390  -3.2480   2.2048  -0.5353
 2G6  C19  C  CH1    0  -0.222  -2.6556   3.4954   0.0285
 2G6  C20  C  CH3    0  -0.653  -3.6065   4.6583  -0.2379
 2G6  C21  C  CH3    0  -0.673  -2.3479   3.3834   1.5190
 2G6  N24  N  NH1    0  -0.636  -3.8752  -0.8777   0.0289
 2G6  C25  C  CH2    0  -0.248  -4.6956  -2.0352  -0.2636
 2G6  C26  C  CH2    0  -0.436  -5.8350  -2.1386   0.7408
 2G6  C27  C  CT     0  -0.093  -6.7431  -3.3690   0.5865
 2G6  C28  C  CH3    0  -0.648  -7.3783  -3.4019  -0.8050
 2G6  C30  C  CH3    0  -0.646  -5.9574  -4.6609   0.8243
 2G6  C29  C  CH3    0  -0.636  -7.8485  -3.2691   1.6390
 2G6  H29  H  HCH2   0   0.243   6.3046   1.0820  -1.6035
 2G6  H30  H  HCH2   0   0.244   5.4431  -0.4365  -1.8751
 2G6  H31  H  HCR6   0   0.255   5.7480  -2.3488  -0.3035
 2G6  H32  H  HCR6   0   0.258   7.2875  -3.5005   1.2368
 2G6  H33  H  HCR6   0   0.258   9.2038  -2.2812   2.2184
 2G6  H34  H  HCR6   0   0.258   9.5683   0.1000   1.6486
 2G6  H35  H  HCR6   0   0.255   8.0247   1.2512   0.1094
 2G6  H36  H  HNH1   0   0.390   2.9222   1.4447   0.9329
 2G6  H27  H  HCH2   0   0.247   1.0524   2.8301   0.2153
 2G6  H28  H  HCH2   0   0.246   1.4543   2.4367  -1.4441
 2G6  H1   H  HNH1   0   0.354  -1.1458   1.0502  -2.0095
 2G6  H2   H  HCH1   0   0.253  -2.1643   0.8261   0.7104
 2G6  H3   H  HCH2   0   0.223  -3.4555   2.3385  -1.6028
 2G6  H4   H  HCH2   0   0.214  -4.2167   2.0190  -0.0561
 2G6  H5   H  HCH1   0   0.219  -1.7161   3.6936  -0.4972
 2G6  H6   H  HCH3   0   0.210  -4.5721   4.4946   0.2480
 2G6  H7   H  HCH3   0   0.223  -3.2009   5.5971   0.1432
 2G6  H8   H  HCH3   0   0.222  -3.7926   4.7880  -1.3057
 2G6  H9   H  HCH3   0   0.210  -3.2409   3.1038   2.0844
 2G6  H10  H  HCH3   0   0.232  -1.5776   2.6388   1.7243
 2G6  H11  H  HCH3   0   0.225  -1.9927   4.3365   1.9151
 2G6  H12  H  HNH1   0   0.394  -3.8202  -0.5786   0.9896
 2G6  H13  H  HCH2   0   0.237  -5.0851  -1.9334  -1.2767
 2G6  H14  H  HCH2   0   0.231  -4.0823  -2.9413  -0.2467
 2G6  H15  H  HCH2   0   0.226  -5.4171  -2.1434   1.7547
 2G6  H16  H  HCH2   0   0.231  -6.4491  -1.2346   0.6674
 2G6  H23  H  HCH3   0   0.226  -6.6347  -3.5476  -1.5908
 2G6  H24  H  HCH3   0   0.226  -8.0971  -4.2205  -0.8837
 2G6  H25  H  HCH3   0   0.222  -7.9114  -2.4727  -1.0199
 2G6  H20  H  HCH3   0   0.222  -5.4705  -4.6530   1.8023
 2G6  H21  H  HCH3   0   0.226  -6.6220  -5.5271   0.7951
 2G6  H22  H  HCH3   0   0.225  -5.1853  -4.8197   0.0698
 2G6  H17  H  HCH3   0   0.222  -8.4493  -2.3671   1.5036
 2G6  H18  H  HCH3   0   0.224  -8.5189  -4.1284   1.5793
 2G6  H19  H  HCH3   0   0.222  -7.4308  -3.2419   2.6481

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
 2G6  C21  C19  single    1.526  0.020  1.526
 2G6  C19  C20  single    1.526  0.020  1.526
 2G6  C19  C18  single    1.528  0.020  1.528
 2G6  C28  C27  single    1.530  0.020  1.530
 2G6  C18  C17  single    1.534  0.020  1.534
 2G6  C26  C27  single    1.537  0.020  1.537
 2G6  C26  C25  single    1.522  0.020  1.522
 2G6  C27  C30  single    1.531  0.020  1.531
 2G6  C27  C29  single    1.530  0.020  1.530
 2G6  C17  C22  single    1.528  0.020  1.528
 2G6  C17  N16  single    1.439  0.020  1.439
 2G6  C22  O23  double    1.225  0.020  1.225
 2G6  C22  N24  single    1.341  0.020  1.341
 2G6  N24  C25  single    1.449  0.020  1.449
 2G6  N16  P13  single    1.706  0.020  1.706
 2G6  P13  O14  deloc     1.512  0.020  1.512
 2G6  P13  O15  deloc     1.510  0.020  1.510
 2G6  P13  C12  single    1.846  0.020  1.846
 2G6  C12  N11  single    1.449  0.020  1.449
 2G6  N11  C9   single    1.345  0.020  1.345
 2G6  O10  C9   double    1.214  0.020  1.214
 2G6  C9   O8   single    1.342  0.020  1.342
 2G6  O8   C7   single    1.430  0.020  1.430
 2G6  C5   C4   aromatic  1.389  0.020  1.389
 2G6  C5   C6   aromatic  1.391  0.020  1.391
 2G6  C7   C6   single    1.499  0.020  1.499
 2G6  C4   C3   aromatic  1.389  0.020  1.389
 2G6  C6   C1   aromatic  1.392  0.020  1.392
 2G6  C3   C2   aromatic  1.389  0.020  1.389
 2G6  C1   C2   aromatic  1.388  0.020  1.388
 2G6  N16  H1   single    0.890  0.020  1.040
 2G6  C17  H2   single    0.970  0.020  1.090
 2G6  C18  H3   single    0.970  0.020  1.090
 2G6  C18  H4   single    0.970  0.020  1.090
 2G6  C19  H5   single    0.970  0.020  1.090
 2G6  C20  H6   single    0.970  0.020  1.090
 2G6  C20  H7   single    0.970  0.020  1.090
 2G6  C20  H8   single    0.970  0.020  1.090
 2G6  C21  H9   single    0.970  0.020  1.090
 2G6  C21  H10  single    0.970  0.020  1.090
 2G6  C21  H11  single    0.970  0.020  1.090
 2G6  N24  H12  single    0.860  0.020  1.020
 2G6  C25  H13  single    0.970  0.020  1.090
 2G6  C25  H14  single    0.970  0.020  1.090
 2G6  C26  H15  single    0.970  0.020  1.090
 2G6  C26  H16  single    0.970  0.020  1.090
 2G6  C29  H17  single    0.970  0.020  1.090
 2G6  C29  H18  single    0.970  0.020  1.090
 2G6  C29  H19  single    0.970  0.020  1.090
 2G6  C30  H20  single    0.970  0.020  1.090
 2G6  C30  H21  single    0.970  0.020  1.090
 2G6  C30  H22  single    0.970  0.020  1.090
 2G6  C28  H23  single    0.970  0.020  1.090
 2G6  C28  H24  single    0.970  0.020  1.090
 2G6  C28  H25  single    0.970  0.020  1.090
 2G6  C12  H27  single    0.970  0.020  1.090
 2G6  C12  H28  single    0.970  0.020  1.090
 2G6  C7   H29  single    0.970  0.020  1.090
 2G6  C7   H30  single    0.970  0.020  1.090
 2G6  C1   H31  single    0.930  0.020  1.080
 2G6  C2   H32  single    0.930  0.020  1.080
 2G6  C3   H33  single    0.930  0.020  1.080
 2G6  C4   H34  single    0.930  0.020  1.080
 2G6  C5   H35  single    0.930  0.020  1.080
 2G6  N11  H36  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
 2G6  H30  C7   H29  107.97  3.000
 2G6  H30  C7   O8   110.18  3.000
 2G6  H29  C7   O8   110.27  3.000
 2G6  H30  C7   C6   110.77  3.000
 2G6  H29  C7   C6   110.82  3.000
 2G6  O8   C7   C6   106.83  3.000
 2G6  C5   C6   C1   119.01  3.000
 2G6  C1   C6   C7   120.35  3.000
 2G6  C5   C6   C7   120.61  3.000
 2G6  H31  C1   C2   119.68  3.000
 2G6  H31  C1   C6   119.75  3.000
 2G6  C2   C1   C6   120.57  3.000
 2G6  H32  C2   C3   120.10  3.000
 2G6  H32  C2   C1   119.88  3.000
 2G6  C3   C2   C1   120.03  3.000
 2G6  H33  C3   C4   120.14  3.000
 2G6  H33  C3   C2   120.06  3.000
 2G6  C4   C3   C2   119.80  3.000
 2G6  H34  C4   C5   119.87  3.000
 2G6  H34  C4   C3   120.14  3.000
 2G6  C5   C4   C3   119.99  3.000
 2G6  H35  C5   C4   119.74  3.000
 2G6  H35  C5   C6   119.65  3.000
 2G6  C4   C5   C6   120.61  3.000
 2G6  N11  C9   O8   110.74  3.000
 2G6  O8   C9   O10  123.43  3.000
 2G6  N11  C9   O10  125.79  3.000
 2G6  C9   O8   C7   116.89  3.000
 2G6  H36  N11  C12  116.25  3.000
 2G6  H36  N11  C9   116.98  3.000
 2G6  C12  N11  C9   121.53  3.000
 2G6  H28  C12  H27  106.88  3.000
 2G6  H28  C12  P13  110.91  3.000
 2G6  H27  C12  P13  110.52  3.000
 2G6  H28  C12  N11  108.96  3.000
 2G6  H27  C12  N11  109.08  3.000
 2G6  P13  C12  N11  110.40  3.000
 2G6  N16  P13  O15  111.21  3.000
 2G6  O15  P13  O14  119.82  3.000
 2G6  N16  P13  O14  108.13  3.000
 2G6  O15  P13  C12  106.92  3.000
 2G6  O14  P13  C12  108.12  3.000
 2G6  N16  P13  C12  100.95  3.000
 2G6  H1   N16  C17  112.62  3.000
 2G6  H1   N16  P13  114.93  3.000
 2G6  C17  N16  P13  122.42  3.000
 2G6  H2   C17  C18  108.89  3.000
 2G6  H2   C17  C22  108.28  3.000
 2G6  C18  C17  C22  108.65  3.000
 2G6  H2   C17  N16  107.39  3.000
 2G6  C22  C17  N16  111.64  3.000
 2G6  C18  C17  N16  111.89  3.000
 2G6  N24  C22  O23  123.01  3.000
 2G6  N24  C22  C17  115.06  3.000
 2G6  O23  C22  C17  121.89  3.000
 2G6  H4   C18  H3   106.21  3.000
 2G6  H4   C18  C19  108.93  3.000
 2G6  H3   C18  C19  109.26  3.000
 2G6  H4   C18  C17  108.99  3.000
 2G6  H3   C18  C17  108.87  3.000
 2G6  C19  C18  C17  114.27  3.000
 2G6  H5   C19  C21  108.01  3.000
 2G6  H5   C19  C20  108.24  3.000
 2G6  C21  C19  C20  110.62  3.000
 2G6  H5   C19  C18  107.98  3.000
 2G6  C20  C19  C18  109.74  3.000
 2G6  C21  C19  C18  112.12  3.000
 2G6  H8   C20  H7   107.62  3.000
 2G6  H8   C20  H6   107.58  3.000
 2G6  H7   C20  H6   107.57  3.000
 2G6  H8   C20  C19  111.57  3.000
 2G6  H7   C20  C19  111.29  3.000
 2G6  H6   C20  C19  111.02  3.000
 2G6  H11  C21  H10  107.34  3.000
 2G6  H11  C21  H9   107.54  3.000
 2G6  H10  C21  H9   107.75  3.000
 2G6  H11  C21  C19  110.85  3.000
 2G6  H10  C21  C19  112.10  3.000
 2G6  H9   C21  C19  111.05  3.000
 2G6  H12  N24  C25  117.43  3.000
 2G6  H12  N24  C22  118.29  3.000
 2G6  C25  N24  C22  124.04  3.000
 2G6  H14  C25  H13  106.97  3.000
 2G6  H14  C25  C26  110.67  3.000
 2G6  H13  C25  C26  110.61  3.000
 2G6  H14  C25  N24  109.95  3.000
 2G6  H13  C25  N24  108.39  3.000
 2G6  C26  C25  N24  110.17  3.000
 2G6  H16  C26  H15  106.22  3.000
 2G6  H16  C26  C27  108.83  3.000
 2G6  H15  C26  C27  108.33  3.000
 2G6  H16  C26  C25  108.62  3.000
 2G6  H15  C26  C25  108.97  3.000
 2G6  C27  C26  C25  115.49  3.000
 2G6  C29  C27  C30  108.62  3.000
 2G6  C29  C27  C28  109.10  3.000
 2G6  C30  C27  C28  109.65  3.000
 2G6  C29  C27  C26  107.79  3.000
 2G6  C30  C27  C26  110.90  3.000
 2G6  C28  C27  C26  110.72  3.000
 2G6  H25  C28  H24  107.58  3.000
 2G6  H25  C28  H23  107.72  3.000
 2G6  H24  C28  H23  107.24  3.000
 2G6  H25  C28  C27  111.29  3.000
 2G6  H24  C28  C27  110.79  3.000
 2G6  H23  C28  C27  112.01  3.000
 2G6  H22  C30  H21  107.26  3.000
 2G6  H22  C30  H20  107.74  3.000
 2G6  H21  C30  H20  107.50  3.000
 2G6  H22  C30  C27  112.25  3.000
 2G6  H21  C30  C27  110.66  3.000
 2G6  H20  C30  C27  111.21  3.000
 2G6  H19  C29  H18  107.75  3.000
 2G6  H19  C29  H17  107.71  3.000
 2G6  H18  C29  H17  107.79  3.000
 2G6  H19  C29  C27  111.16  3.000
 2G6  H18  C29  C27  110.78  3.000
 2G6  H17  C29  C27  111.48  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
 2G6  CONST_01  C3   C4   C5   C6      0.00   0.0  0
 2G6  CONST_02  C3   C2   C1   C6      0.00   0.0  0
 2G6  CONST_03  C4   C5   C6   C1      0.00   0.0  0
 2G6  CONST_04  C4   C3   C2   C1      0.00   0.0  0
 2G6  CONST_05  C5   C4   C3   C2      0.00   0.0  0
 2G6  CONST_06  C5   C6   C1   C2      0.00   0.0  0
 2G6  CONST_07  C4   C5   C6   C7    180.00   0.0  0
 2G6  CONST_08  C2   C1   C6   C7    180.00   0.0  0
 2G6  CONST_09  H34  C4   C5   C6    180.00   0.0  0
 2G6  CONST_10  H32  C2   C1   C6    180.00   0.0  0
 2G6  CONST_11  H35  C5   C6   C1    180.00   0.0  0
 2G6  CONST_12  H33  C3   C2   C1    180.00   0.0  0
 2G6  CONST_13  H31  C1   C2   C3    180.00   0.0  0
 2G6  CONST_14  C25  N24  C22  C17   180.00   0.0  0
 2G6  CONST_15  C25  N24  C22  O23     0.00   0.0  0
 2G6  CONST_16  H12  N24  C22  C17     0.00   0.0  0
 2G6  Var_01    O8   C7   C6   C1     84.79  30.0  2
 2G6  Var_02    N11  C9   O8   C7   -177.34  30.0  1
 2G6  Var_03    P13  C12  N11  C9     88.72  30.0  1
 2G6  Var_04    C12  N11  C9   O10    19.82  30.0  2
 2G6  Var_05    N16  P13  C12  N11  -173.92  30.0  2
 2G6  Var_06    C17  N16  P13  C12  -129.43  30.0  1
 2G6  Var_07    C21  C19  C18  C17   -58.08  30.0  1
 2G6  Var_08    C26  C25  N24  C22  -156.44  30.0  3
 2G6  Var_09    C27  C26  C25  N24  -177.00  30.0  1
 2G6  Var_10    C28  C27  C26  C25   -58.58  30.0  3
 2G6  Var_11    H9   C21  C19  C18   -56.50  30.0  3
 2G6  Var_12    H6   C20  C19  C18    60.99  30.0  3
 2G6  Var_13    H23  C28  C27  C26    65.77  30.0  3
 2G6  Var_14    H20  C30  C27  C26    55.92  30.0  3
 2G6  Var_15    H17  C29  C27  C26    60.56  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
 2G6  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
 2G6  plan-1  C7   0.020
 2G6  plan-1  C6   0.020
 2G6  plan-1  C1   0.020
 2G6  plan-1  C2   0.020
 2G6  plan-1  C3   0.020
 2G6  plan-1  C4   0.020
 2G6  plan-1  C5   0.020
 2G6  plan-1  H31  0.020
 2G6  plan-1  H32  0.020
 2G6  plan-1  H33  0.020
 2G6  plan-1  H34  0.020
 2G6  plan-1  H35  0.020
 2G6  plan-2  C17  0.020
 2G6  plan-2  C22  0.020
 2G6  plan-2  O23  0.020
 2G6  plan-2  N24  0.020
 2G6  plan-2  C25  0.020
 2G6  plan-2  H12  0.020
 2G6  plan-3  C9   0.020
 2G6  plan-3  O10  0.020
 2G6  plan-3  O8   0.020
 2G6  plan-3  N11  0.020

