# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 07:38:25 2020
#   Inital geometry file: a 136 line input string
#   Ligand name: N~2~-[(R)-({[(benzyloxy)carbonyl]amino}methyl)(hydroxy)phosphoryl]-N-propyl-L-leucinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCNC(=O)[C@H](CC(C)C)N[P](O)(=O)CNC(=O)OCc1ccccc1
#
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
 2G8  2G8  N~2~-[(R)-({[(benzyloxy)carbonyl]amino}methyl)(hydroxy)phosphoryl]-N-propyl-L-leucinamide  peptide  57  27  .  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_2G8
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
 2G8  C7   C  CH2   0  -0.240  -4.8710   1.4289   0.3009
 2G8  C6   C  CR6   0   0.076  -6.1497   0.6760   0.5080
 2G8  C1   C  CR16  0  -0.292  -7.2252   0.8541  -0.3565
 2G8  C2   C  CR16  0  -0.242  -8.4006   0.1361  -0.1786
 2G8  C3   C  CR16  0  -0.261  -8.5084  -0.7713   0.8669
 2G8  C4   C  CR16  0  -0.242  -7.4387  -0.9560   1.7343
 2G8  C5   C  CR16  0  -0.288  -6.2662  -0.2359   1.5539
 2G8  C9   C  C     0   0.762  -2.7756   1.0272  -0.7109
 2G8  O10  O  O     0  -0.512  -2.3396   2.0829  -0.3043
 2G8  O8   O  O2    0  -0.478  -4.0161   0.5874  -0.4836
 2G8  N11  N  NH1   0  -0.655  -2.0934   0.1473  -1.4735
 2G8  C12  C  CH2   0  -0.567  -0.6880   0.2973  -1.7367
 2G8  P13  P  P     0   1.311   0.3002  -0.4939  -0.4234
 2G8  O14  O  O     0  -0.714   0.1064   0.0549   0.9440
 2G8  O15  O  OH1   0  -0.752  -0.1994  -2.0363  -0.4193
 2G8  N16  N  NH1   0  -0.783   1.8578  -0.3657  -0.9763
 2G8  C17  C  CH1   0  -0.201   3.0011  -0.5454  -0.0927
 2G8  C22  C  C     0   0.565   4.1622   0.2529  -0.6757
 2G8  O23  O  O     0  -0.497   4.4921   0.1151  -1.8462
 2G8  C18  C  CH2   0  -0.410   3.3992  -2.0169   0.0622
 2G8  C19  C  CH1   0  -0.254   4.5804  -2.2875   0.9958
 2G8  C20  C  CH3   0  -0.657   4.2792  -1.8737   2.4331
 2G8  C21  C  CH3   0  -0.648   4.9503  -3.7665   0.9364
 2G8  C29  C  CH3   0  -0.665   7.8324   3.2659   0.7249
 2G8  C26  C  CH2   0  -0.473   6.6330   2.3963   1.0690
 2G8  C25  C  CH2   0  -0.239   5.9429   1.8690  -0.1788
 2G8  N24  N  NH1   0  -0.638   4.7924   1.0636   0.1786
 2G8  H23  H  HCH2  0   0.249  -5.0533   2.3697  -0.2228
 2G8  H24  H  HCH2  0   0.249  -4.3974   1.6591   1.2571
 2G8  H25  H  HCR6  0   0.256  -7.1473   1.5634  -1.1718
 2G8  H26  H  HCR6  0   0.259  -9.2325   0.2876  -0.8541
 2G8  H27  H  HCR6  0   0.259  -9.4244  -1.3304   1.0085
 2G8  H28  H  HCR6  0   0.259  -7.5194  -1.6583   2.5536
 2G8  H29  H  HCR6  0   0.255  -5.4368  -0.3809   2.2363
 2G8  H30  H  HNH1  0   0.409  -2.5297  -0.7287  -1.7131
 2G8  H21  H  HCH2  0   0.303  -0.4503  -0.1417  -2.7074
 2G8  H22  H  HCH2  0   0.297  -0.4201   1.3517  -1.7908
 2G8  H20  H  HOH1  0   0.483   0.0218  -2.5442  -1.2097
 2G8  H1   H  HNH1  0   0.399   2.0370  -0.6302  -1.9376
 2G8  H2   H  HCH1  0   0.266   2.7220  -0.1359   0.8799
 2G8  H3   H  HCH2  0   0.233   2.5251  -2.5635   0.4318
 2G8  H4   H  HCH2  0   0.233   3.6178  -2.4190  -0.9323
 2G8  H5   H  HCH1  0   0.226   5.4482  -1.7164   0.6469
 2G8  H6   H  HCH3  0   0.233   5.1251  -2.0919   3.0863
 2G8  H7   H  HCH3  0   0.220   4.0653  -0.8083   2.5328
 2G8  H8   H  HCH3  0   0.220   3.4133  -2.4185   2.8164
 2G8  H9   H  HCH3  0   0.227   5.2085  -4.0721  -0.0788
 2G8  H10  H  HCH3  0   0.228   5.8044  -3.9859   1.5791
 2G8  H11  H  HCH3  0   0.215   4.1180  -4.3908   1.2707
 2G8  H17  H  HCH3  0   0.224   7.5366   4.1325   0.1315
 2G8  H18  H  HCH3  0   0.236   8.3204   3.6339   1.6270
 2G8  H19  H  HCH3  0   0.224   8.5743   2.7090   0.1504
 2G8  H15  H  HCH2  0   0.232   6.9498   1.5524   1.6878
 2G8  H16  H  HCH2  0   0.232   5.9192   2.9727   1.6649
 2G8  H13  H  HCH2  0   0.233   5.6384   2.7035  -0.8190
 2G8  H14  H  HCH2  0   0.237   6.6396   1.2601  -0.7582
 2G8  H12  H  HNH1  0   0.402   4.4094   1.1818   1.1026

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
 2G8  C2   C1   aromatic  1.389  0.020  1.389
 2G8  C2   C3   aromatic  1.389  0.020  1.389
 2G8  C1   C6   aromatic  1.391  0.020  1.391
 2G8  C3   C4   aromatic  1.389  0.020  1.389
 2G8  C6   C7   single    1.498  0.020  1.498
 2G8  C6   C5   aromatic  1.392  0.020  1.392
 2G8  C4   C5   aromatic  1.388  0.020  1.388
 2G8  C7   O8   single    1.433  0.020  1.433
 2G8  O8   C9   single    1.336  0.020  1.336
 2G8  C9   O10  double    1.212  0.020  1.212
 2G8  C9   N11  single    1.350  0.020  1.350
 2G8  N11  C12  single    1.438  0.020  1.438
 2G8  C12  P13  single    1.824  0.020  1.824
 2G8  O14  P13  double    1.486  0.020  1.486
 2G8  O15  P13  single    1.621  0.020  1.621
 2G8  P13  N16  single    1.658  0.020  1.658
 2G8  N16  C17  single    1.456  0.020  1.456
 2G8  C25  N24  single    1.449  0.020  1.449
 2G8  C25  C26  single    1.520  0.020  1.520
 2G8  N24  C22  single    1.336  0.020  1.336
 2G8  O23  C22  double    1.224  0.020  1.224
 2G8  C22  C17  single    1.525  0.020  1.525
 2G8  C17  C18  single    1.532  0.020  1.532
 2G8  C26  C29  single    1.521  0.020  1.521
 2G8  C18  C19  single    1.530  0.020  1.530
 2G8  C20  C19  single    1.526  0.020  1.526
 2G8  C19  C21  single    1.526  0.020  1.526
 2G8  N16  H1   single    0.890  0.020  1.040
 2G8  C17  H2   single    0.970  0.020  1.090
 2G8  C18  H3   single    0.970  0.020  1.090
 2G8  C18  H4   single    0.970  0.020  1.090
 2G8  C19  H5   single    0.970  0.020  1.090
 2G8  C20  H6   single    0.970  0.020  1.090
 2G8  C20  H7   single    0.970  0.020  1.090
 2G8  C20  H8   single    0.970  0.020  1.090
 2G8  C21  H9   single    0.970  0.020  1.090
 2G8  C21  H10  single    0.970  0.020  1.090
 2G8  C21  H11  single    0.970  0.020  1.090
 2G8  N24  H12  single    0.860  0.020  1.020
 2G8  C25  H13  single    0.970  0.020  1.090
 2G8  C25  H14  single    0.970  0.020  1.090
 2G8  C26  H15  single    0.970  0.020  1.090
 2G8  C26  H16  single    0.970  0.020  1.090
 2G8  C29  H17  single    0.970  0.020  1.090
 2G8  C29  H18  single    0.970  0.020  1.090
 2G8  C29  H19  single    0.970  0.020  1.090
 2G8  O15  H20  single    0.850  0.020  0.980
 2G8  C12  H21  single    0.970  0.020  1.090
 2G8  C12  H22  single    0.970  0.020  1.090
 2G8  C7   H23  single    0.970  0.020  1.090
 2G8  C7   H24  single    0.970  0.020  1.090
 2G8  C1   H25  single    0.930  0.020  1.080
 2G8  C2   H26  single    0.930  0.020  1.080
 2G8  C3   H27  single    0.930  0.020  1.080
 2G8  C4   H28  single    0.930  0.020  1.080
 2G8  C5   H29  single    0.930  0.020  1.080
 2G8  N11  H30  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
 2G8  H24  C7   H23  108.11  3.000
 2G8  H24  C7   O8   110.15  3.000
 2G8  H23  C7   O8   110.06  3.000
 2G8  H24  C7   C6   110.80  3.000
 2G8  H23  C7   C6   110.90  3.000
 2G8  O8   C7   C6   106.84  3.000
 2G8  C5   C6   C1   119.07  3.000
 2G8  C5   C6   C7   120.29  3.000
 2G8  C1   C6   C7   120.63  3.000
 2G8  H25  C1   C2   119.72  3.000
 2G8  H25  C1   C6   119.72  3.000
 2G8  C2   C1   C6   120.56  3.000
 2G8  H26  C2   C3   120.12  3.000
 2G8  H26  C2   C1   119.88  3.000
 2G8  C3   C2   C1   120.00  3.000
 2G8  H27  C3   C4   120.08  3.000
 2G8  H27  C3   C2   120.11  3.000
 2G8  C4   C3   C2   119.81  3.000
 2G8  H28  C4   C5   119.88  3.000
 2G8  H28  C4   C3   120.10  3.000
 2G8  C5   C4   C3   120.02  3.000
 2G8  H29  C5   C4   119.69  3.000
 2G8  H29  C5   C6   119.77  3.000
 2G8  C4   C5   C6   120.54  3.000
 2G8  N11  C9   O8   110.55  3.000
 2G8  N11  C9   O10  125.13  3.000
 2G8  O8   C9   O10  124.31  3.000
 2G8  C9   O8   C7   116.98  3.000
 2G8  H30  N11  C12  118.07  3.000
 2G8  H30  N11  C9   118.83  3.000
 2G8  C12  N11  C9   121.98  3.000
 2G8  H22  C12  H21  106.96  3.000
 2G8  H22  C12  P13  108.81  3.000
 2G8  H21  C12  P13  110.36  3.000
 2G8  H22  C12  N11  110.51  3.000
 2G8  H21  C12  N11  109.50  3.000
 2G8  P13  C12  N11  110.64  3.000
 2G8  N16  P13  O15  111.34  3.000
 2G8  N16  P13  O14  113.63  3.000
 2G8  O15  P13  O14  107.99  3.000
 2G8  N16  P13  C12  103.61  3.000
 2G8  O15  P13  C12  104.33  3.000
 2G8  O14  P13  C12  115.58  3.000
 2G8  H20  O15  P13  115.34  3.000
 2G8  H1   N16  C17  113.87  3.000
 2G8  H1   N16  P13  117.55  3.000
 2G8  C17  N16  P13  121.72  3.000
 2G8  H2   C17  C18  109.67  3.000
 2G8  H2   C17  C22  109.81  3.000
 2G8  C18  C17  C22  110.09  3.000
 2G8  H2   C17  N16  107.08  3.000
 2G8  C18  C17  N16  112.58  3.000
 2G8  C22  C17  N16  107.54  3.000
 2G8  N24  C22  O23  123.56  3.000
 2G8  O23  C22  C17  120.79  3.000
 2G8  N24  C22  C17  115.63  3.000
 2G8  H4   C18  H3   106.42  3.000
 2G8  H4   C18  C19  109.58  3.000
 2G8  H3   C18  C19  108.78  3.000
 2G8  H4   C18  C17  108.23  3.000
 2G8  H3   C18  C17  107.82  3.000
 2G8  C19  C18  C17  115.61  3.000
 2G8  H5   C19  C21  107.50  3.000
 2G8  H5   C19  C20  108.35  3.000
 2G8  C21  C19  C20  110.34  3.000
 2G8  H5   C19  C18  108.96  3.000
 2G8  C21  C19  C18  109.57  3.000
 2G8  C20  C19  C18  111.99  3.000
 2G8  H8   C20  H7   107.42  3.000
 2G8  H8   C20  H6   107.74  3.000
 2G8  H7   C20  H6   107.02  3.000
 2G8  H8   C20  C19  110.59  3.000
 2G8  H7   C20  C19  112.93  3.000
 2G8  H6   C20  C19  110.90  3.000
 2G8  H11  C21  H10  107.52  3.000
 2G8  H11  C21  H9   107.75  3.000
 2G8  H10  C21  H9   107.84  3.000
 2G8  H11  C21  C19  110.93  3.000
 2G8  H10  C21  C19  111.21  3.000
 2G8  H9   C21  C19  111.42  3.000
 2G8  H19  C29  H18  107.69  3.000
 2G8  H19  C29  H17  107.66  3.000
 2G8  H18  C29  H17  107.66  3.000
 2G8  H19  C29  C26  111.32  3.000
 2G8  H18  C29  C26  111.04  3.000
 2G8  H17  C29  C26  111.30  3.000
 2G8  H16  C26  H15  106.70  3.000
 2G8  H16  C26  C25  109.49  3.000
 2G8  H15  C26  C25  109.17  3.000
 2G8  H16  C26  C29  109.67  3.000
 2G8  H15  C26  C29  109.92  3.000
 2G8  C25  C26  C29  111.75  3.000
 2G8  H14  C25  H13  106.99  3.000
 2G8  H14  C25  N24  109.12  3.000
 2G8  H13  C25  N24  110.30  3.000
 2G8  H14  C25  C26  109.84  3.000
 2G8  H13  C25  C26  109.99  3.000
 2G8  N24  C25  C26  110.53  3.000
 2G8  H12  N24  C25  117.58  3.000
 2G8  H12  N24  C22  118.59  3.000
 2G8  C25  N24  C22  123.65  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
 2G8  CONST_01  C3   C2   C1   C6      0.00   0.0  0
 2G8  CONST_02  C3   C4   C5   C6      0.00   0.0  0
 2G8  CONST_03  C4   C3   C2   C1      0.00   0.0  0
 2G8  CONST_04  C4   C5   C6   C1      0.00   0.0  0
 2G8  CONST_05  C5   C6   C1   C2      0.00   0.0  0
 2G8  CONST_06  C5   C4   C3   C2      0.00   0.0  0
 2G8  CONST_07  C2   C1   C6   C7    180.00   0.0  0
 2G8  CONST_08  C4   C5   C6   C7    180.00   0.0  0
 2G8  CONST_09  H26  C2   C1   C6    180.00   0.0  0
 2G8  CONST_10  H28  C4   C5   C6    180.00   0.0  0
 2G8  CONST_11  H27  C3   C2   C1    180.00   0.0  0
 2G8  CONST_12  H29  C5   C6   C1    180.00   0.0  0
 2G8  CONST_13  H25  C1   C2   C3    180.00   0.0  0
 2G8  CONST_14  C25  N24  C22  C17   180.00   0.0  0
 2G8  CONST_15  C25  N24  C22  O23     0.00   0.0  0
 2G8  CONST_16  H12  N24  C22  C17     0.00   0.0  0
 2G8  Var_01    O8   C7   C6   C1    -93.38  30.0  2
 2G8  Var_02    O10  C9   O8   C7     -0.37  30.0  3
 2G8  Var_03    P13  C12  N11  C9     87.33  30.0  3
 2G8  Var_04    C12  N11  C9   O10     8.70  30.0  2
 2G8  Var_05    O14  P13  C12  N11   -60.97  30.0  3
 2G8  Var_06    C17  N16  P13  C12   163.36  30.0  3
 2G8  Var_07    C20  C19  C18  C17    63.09  30.0  3
 2G8  Var_08    C26  C25  N24  C22  -165.66  30.0  2
 2G8  Var_09    N24  C25  C26  C29  -179.04  30.0  1
 2G8  Var_10    H6   C20  C19  C18   178.91  30.0  3
 2G8  Var_11    H9   C21  C19  C18    58.54  30.0  3
 2G8  Var_12    H17  C29  C26  C25    60.31  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
 2G8  chir_02  C17  N16  C22  C18  positiv
 2G8  chir_03  P13  O14  O15  N16  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
 2G8  plan-1  C7   0.020
 2G8  plan-1  C6   0.020
 2G8  plan-1  C1   0.020
 2G8  plan-1  C2   0.020
 2G8  plan-1  C3   0.020
 2G8  plan-1  C4   0.020
 2G8  plan-1  C5   0.020
 2G8  plan-1  H25  0.020
 2G8  plan-1  H26  0.020
 2G8  plan-1  H27  0.020
 2G8  plan-1  H28  0.020
 2G8  plan-1  H29  0.020
 2G8  plan-2  C17  0.020
 2G8  plan-2  C22  0.020
 2G8  plan-2  O23  0.020
 2G8  plan-2  C25  0.020
 2G8  plan-2  N24  0.020
 2G8  plan-2  H12  0.020
 2G8  plan-3  C9   0.020
 2G8  plan-3  O10  0.020
 2G8  plan-3  O8   0.020
 2G8  plan-3  N11  0.020

