# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 18:18:40 2020
#   Inital geometry file: a 148 line input string
#   Ligand name: N~2~-[(S)-({[(benzyloxy)carbonyl]amino}methyl)(hydroxy)phosphoryl]-N-[(2S)-2-methylbutyl]-L-leucinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@H](C)CNC(=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
 2G9  2G9  N~2~-[(S)-({[(benzyloxy)carbonyl]amino}methyl)(hydroxy)phosphoryl]-N-[(2S)-2-methylbutyl]-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_2G9
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
 2G9  C7   C  CH2   0  -0.241   4.9600  -0.8149  -1.1842
 2G9  C6   C  CR6   0   0.075   6.2682  -0.9742  -0.4722
 2G9  C1   C  CR16  0  -0.286   7.3650  -0.1967  -0.8335
 2G9  C2   C  CR16  0  -0.243   8.5710  -0.3216  -0.1584
 2G9  C3   C  CR16  0  -0.261   8.6908  -1.2280   0.8878
 2G9  C4   C  CR16  0  -0.242   7.6016  -2.0075   1.2544
 2G9  C5   C  CR16  0  -0.293   6.3963  -1.8790   0.5772
 2G9  C9   C  C     0   0.768   3.0318   0.5288  -0.9748
 2G9  O10  O  O     0  -0.519   2.4684  -0.0856  -1.8580
 2G9  O8   O  O2    0  -0.476   4.2633   0.2602  -0.5390
 2G9  N11  N  NH1   0  -0.654   2.5071   1.5831  -0.3189
 2G9  C12  C  CH2   0  -0.578   1.1510   2.0051  -0.5360
 2G9  P13  P  P     0   1.313  -0.0157   1.1170   0.5547
 2G9  O14  O  O     0  -0.716   0.0493   1.4763   1.9967
 2G9  O15  O  OH1   0  -0.745   0.3645  -0.4512   0.4235
 2G9  N16  N  NH1   0  -0.760  -1.4849   1.4314  -0.1496
 2G9  C17  C  CH1   0  -0.245  -2.7047   0.9455   0.4614
 2G9  C22  C  C     0   0.560  -2.9902  -0.5013   0.0465
 2G9  O23  O  O     0  -0.493  -2.5693  -0.9512  -1.0097
 2G9  C18  C  CH2   0  -0.410  -3.8933   1.8325   0.0784
 2G9  C19  C  CH1   0  -0.221  -3.7146   3.3107   0.4253
 2G9  C20  C  CH3   0  -0.654  -4.9524   4.0891  -0.0093
 2G9  C21  C  CH3   0  -0.671  -3.4322   3.5203   1.9092
 2G9  N24  N  NH1   0  -0.629  -3.7462  -1.1893   0.9122
 2G9  C25  C  CH2   0  -0.263  -4.2352  -2.5326   0.6978
 2G9  C26  C  CH1   0  -0.237  -5.7346  -2.6023   0.3999
 2G9  C28  C  CH2   0  -0.414  -6.1456  -4.0723   0.2918
 2G9  C27  C  CH3   0  -0.666  -6.0914  -1.8078  -0.8500
 2G9  C29  C  CH3   0  -0.666  -7.6459  -4.2983   0.1620
 2G9  H27  H  HCH2  0   0.250   5.1175  -0.5753  -2.2380
 2G9  H28  H  HCH2  0   0.251   4.3716  -1.7326  -1.1277
 2G9  H29  H  HCR6  0   0.256   7.2771   0.5075  -1.6524
 2G9  H30  H  HCR6  0   0.259   9.4176   0.2864  -0.4501
 2G9  H31  H  HCR6  0   0.259   9.6317  -1.3287   1.4133
 2G9  H32  H  HCR6  0   0.259   7.6894  -2.7169   2.0668
 2G9  H33  H  HCR6  0   0.255   5.5507  -2.4931   0.8645
 2G9  H34  H  HNH1  0   0.413   3.0274   2.0055   0.4333
 2G9  H25  H  HCH2  0   0.311   1.0663   3.0708  -0.3230
 2G9  H26  H  HCH2  0   0.292   0.8754   1.8699  -1.5829
 2G9  H24  H  HOH1  0   0.476   0.2619  -0.8184  -0.4639
 2G9  H1   H  HNH1  0   0.394  -1.5092   1.4200  -1.1621
 2G9  H2   H  HCH1  0   0.275  -2.5731   0.9873   1.5460
 2G9  H3   H  HCH2  0   0.239  -4.0787   1.7325  -0.9967
 2G9  H4   H  HCH2  0   0.233  -4.7893   1.4516   0.5800
 2G9  H5   H  HCH1  0   0.224  -2.8576   3.6899  -0.1398
 2G9  H6   H  HCH3  0   0.214  -5.8421   3.7412   0.5218
 2G9  H7   H  HCH3  0   0.227  -4.8410   5.1549   0.1959
 2G9  H8   H  HCH3  0   0.225  -5.1404   3.9751  -1.0787
 2G9  H9   H  HCH3  0   0.231  -2.4896   3.0642   2.2148
 2G9  H10  H  HCH3  0   0.230  -3.3680   4.5837   2.1450
 2G9  H11  H  HCH3  0   0.214  -4.2282   3.0926   2.5247
 2G9  H12  H  HNH1  0   0.399  -4.0281  -0.7321   1.7650
 2G9  H13  H  HCH2  0   0.239  -3.6707  -2.9705  -0.1260
 2G9  H14  H  HCH2  0   0.247  -4.0121  -3.1247   1.5889
 2G9  H15  H  HCH1  0   0.217  -6.2680  -2.1653   1.2542
 2G9  H19  H  HCH2  0   0.213  -5.6311  -4.5240  -0.5636
 2G9  H20  H  HCH2  0   0.221  -5.7838  -4.6039   1.1775
 2G9  H16  H  HCH3  0   0.229  -5.8105  -0.7584  -0.7540
 2G9  H17  H  HCH3  0   0.215  -5.5810  -2.2118  -1.7273
 2G9  H18  H  HCH3  0   0.235  -7.1633  -1.8324  -1.0471
 2G9  H21  H  HCH3  0   0.217  -8.1887  -3.8296   0.9855
 2G9  H22  H  HCH3  0   0.222  -8.0444  -3.8954  -0.7694
 2G9  H23  H  HCH3  0   0.230  -7.8798  -5.3633   0.1791

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
 2G9  C21  C19  single    1.525  0.020  1.525
 2G9  C19  C20  single    1.525  0.020  1.525
 2G9  C19  C18  single    1.529  0.020  1.529
 2G9  C27  C26  single    1.523  0.020  1.523
 2G9  C18  C17  single    1.532  0.020  1.532
 2G9  C26  C28  single    1.530  0.020  1.530
 2G9  C26  C25  single    1.530  0.020  1.530
 2G9  C28  C29  single    1.523  0.020  1.523
 2G9  C17  C22  single    1.532  0.020  1.532
 2G9  C17  N16  single    1.448  0.020  1.448
 2G9  C22  O23  double    1.223  0.020  1.223
 2G9  C22  N24  single    1.340  0.020  1.340
 2G9  N24  C25  single    1.445  0.020  1.445
 2G9  N16  P13  single    1.659  0.020  1.659
 2G9  P13  O14  double    1.488  0.020  1.488
 2G9  P13  O15  single    1.619  0.020  1.619
 2G9  P13  C12  single    1.827  0.020  1.827
 2G9  C12  N11  single    1.437  0.020  1.437
 2G9  N11  C9   single    1.348  0.020  1.348
 2G9  O10  C9   double    1.214  0.020  1.214
 2G9  C9   O8   single    1.334  0.020  1.334
 2G9  O8   C7   single    1.434  0.020  1.434
 2G9  C1   C2   aromatic  1.388  0.020  1.388
 2G9  C1   C6   aromatic  1.392  0.020  1.392
 2G9  C7   C6   single    1.498  0.020  1.498
 2G9  C2   C3   aromatic  1.389  0.020  1.389
 2G9  C6   C5   aromatic  1.391  0.020  1.391
 2G9  C3   C4   aromatic  1.389  0.020  1.389
 2G9  C5   C4   aromatic  1.389  0.020  1.389
 2G9  N16  H1   single    0.890  0.020  1.040
 2G9  C17  H2   single    0.970  0.020  1.090
 2G9  C18  H3   single    0.970  0.020  1.090
 2G9  C18  H4   single    0.970  0.020  1.090
 2G9  C19  H5   single    0.970  0.020  1.090
 2G9  C20  H6   single    0.970  0.020  1.090
 2G9  C20  H7   single    0.970  0.020  1.090
 2G9  C20  H8   single    0.970  0.020  1.090
 2G9  C21  H9   single    0.970  0.020  1.090
 2G9  C21  H10  single    0.970  0.020  1.090
 2G9  C21  H11  single    0.970  0.020  1.090
 2G9  N24  H12  single    0.860  0.020  1.020
 2G9  C25  H13  single    0.970  0.020  1.090
 2G9  C25  H14  single    0.970  0.020  1.090
 2G9  C26  H15  single    0.970  0.020  1.090
 2G9  C27  H16  single    0.970  0.020  1.090
 2G9  C27  H17  single    0.970  0.020  1.090
 2G9  C27  H18  single    0.970  0.020  1.090
 2G9  C28  H19  single    0.970  0.020  1.090
 2G9  C28  H20  single    0.970  0.020  1.090
 2G9  C29  H21  single    0.970  0.020  1.090
 2G9  C29  H22  single    0.970  0.020  1.090
 2G9  C29  H23  single    0.970  0.020  1.090
 2G9  O15  H24  single    0.850  0.020  0.980
 2G9  C12  H25  single    0.970  0.020  1.090
 2G9  C12  H26  single    0.970  0.020  1.090
 2G9  C7   H27  single    0.970  0.020  1.090
 2G9  C7   H28  single    0.970  0.020  1.090
 2G9  C1   H29  single    0.930  0.020  1.080
 2G9  C2   H30  single    0.930  0.020  1.080
 2G9  C3   H31  single    0.930  0.020  1.080
 2G9  C4   H32  single    0.930  0.020  1.080
 2G9  C5   H33  single    0.930  0.020  1.080
 2G9  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
 2G9  H28  C7   H27  108.19  3.000
 2G9  H28  C7   O8   110.18  3.000
 2G9  H27  C7   O8   109.85  3.000
 2G9  H28  C7   C6   110.90  3.000
 2G9  H27  C7   C6   110.86  3.000
 2G9  O8   C7   C6   106.86  3.000
 2G9  C5   C6   C1   119.10  3.000
 2G9  C5   C6   C7   120.53  3.000
 2G9  C1   C6   C7   120.35  3.000
 2G9  H29  C1   C2   119.78  3.000
 2G9  H29  C1   C6   119.68  3.000
 2G9  C2   C1   C6   120.54  3.000
 2G9  H30  C2   C3   120.13  3.000
 2G9  H30  C2   C1   119.87  3.000
 2G9  C3   C2   C1   120.00  3.000
 2G9  H31  C3   C4   120.09  3.000
 2G9  H31  C3   C2   120.08  3.000
 2G9  C4   C3   C2   119.82  3.000
 2G9  H32  C4   C5   119.82  3.000
 2G9  H32  C4   C3   120.17  3.000
 2G9  C5   C4   C3   120.01  3.000
 2G9  H33  C5   C4   119.71  3.000
 2G9  H33  C5   C6   119.77  3.000
 2G9  C4   C5   C6   120.52  3.000
 2G9  N11  C9   O8   110.98  3.000
 2G9  O8   C9   O10  124.34  3.000
 2G9  N11  C9   O10  124.68  3.000
 2G9  C9   O8   C7   116.91  3.000
 2G9  H34  N11  C12  118.50  3.000
 2G9  H34  N11  C9   119.35  3.000
 2G9  C12  N11  C9   121.58  3.000
 2G9  H26  C12  H25  106.80  3.000
 2G9  H26  C12  P13  110.56  3.000
 2G9  H25  C12  P13  107.99  3.000
 2G9  H26  C12  N11  110.30  3.000
 2G9  H25  C12  N11  109.33  3.000
 2G9  P13  C12  N11  111.69  3.000
 2G9  N16  P13  O15  110.92  3.000
 2G9  O15  P13  O14  107.59  3.000
 2G9  N16  P13  O14  113.85  3.000
 2G9  O15  P13  C12  105.81  3.000
 2G9  O14  P13  C12  115.68  3.000
 2G9  N16  P13  C12  102.70  3.000
 2G9  H24  O15  P13  114.70  3.000
 2G9  H1   N16  C17  113.44  3.000
 2G9  H1   N16  P13  116.32  3.000
 2G9  C17  N16  P13  120.21  3.000
 2G9  H2   C17  C18  108.62  3.000
 2G9  H2   C17  C22  109.10  3.000
 2G9  C18  C17  C22  109.54  3.000
 2G9  H2   C17  N16  107.72  3.000
 2G9  C22  C17  N16  111.07  3.000
 2G9  C18  C17  N16  110.72  3.000
 2G9  N24  C22  O23  124.29  3.000
 2G9  N24  C22  C17  114.53  3.000
 2G9  O23  C22  C17  121.16  3.000
 2G9  H4   C18  H3   106.21  3.000
 2G9  H4   C18  C19  109.15  3.000
 2G9  H3   C18  C19  109.31  3.000
 2G9  H4   C18  C17  108.60  3.000
 2G9  H3   C18  C17  108.90  3.000
 2G9  C19  C18  C17  114.36  3.000
 2G9  H5   C19  C21  108.05  3.000
 2G9  H5   C19  C20  108.15  3.000
 2G9  C21  C19  C20  110.94  3.000
 2G9  H5   C19  C18  108.02  3.000
 2G9  C20  C19  C18  109.50  3.000
 2G9  C21  C19  C18  112.04  3.000
 2G9  H8   C20  H7   107.69  3.000
 2G9  H8   C20  H6   107.61  3.000
 2G9  H7   C20  H6   107.62  3.000
 2G9  H8   C20  C19  111.44  3.000
 2G9  H7   C20  C19  111.22  3.000
 2G9  H6   C20  C19  111.08  3.000
 2G9  H11  C21  H10  107.60  3.000
 2G9  H11  C21  H9   107.93  3.000
 2G9  H10  C21  H9   107.23  3.000
 2G9  H11  C21  C19  111.05  3.000
 2G9  H10  C21  C19  110.80  3.000
 2G9  H9   C21  C19  112.04  3.000
 2G9  H12  N24  C25  116.90  3.000
 2G9  H12  N24  C22  118.14  3.000
 2G9  C25  N24  C22  124.92  3.000
 2G9  H14  C25  H13  107.01  3.000
 2G9  H14  C25  C26  109.52  3.000
 2G9  H13  C25  C26  109.99  3.000
 2G9  H14  C25  N24  108.27  3.000
 2G9  H13  C25  N24  108.07  3.000
 2G9  C26  C25  N24  113.74  3.000
 2G9  H15  C26  C27  108.48  3.000
 2G9  H15  C26  C28  107.87  3.000
 2G9  C27  C26  C28  112.34  3.000
 2G9  H15  C26  C25  107.85  3.000
 2G9  C28  C26  C25  108.70  3.000
 2G9  C27  C26  C25  111.44  3.000
 2G9  H20  C28  H19  106.04  3.000
 2G9  H20  C28  C29  108.82  3.000
 2G9  H19  C28  C29  109.56  3.000
 2G9  H20  C28  C26  108.70  3.000
 2G9  H19  C28  C26  108.97  3.000
 2G9  C29  C28  C26  114.41  3.000
 2G9  H18  C27  H17  107.81  3.000
 2G9  H18  C27  H16  106.92  3.000
 2G9  H17  C27  H16  107.83  3.000
 2G9  H18  C27  C26  111.52  3.000
 2G9  H17  C27  C26  110.89  3.000
 2G9  H16  C27  C26  111.66  3.000
 2G9  H23  C29  H22  107.21  3.000
 2G9  H23  C29  H21  107.50  3.000
 2G9  H22  C29  H21  107.69  3.000
 2G9  H23  C29  C28  110.79  3.000
 2G9  H22  C29  C28  112.22  3.000
 2G9  H21  C29  C28  111.21  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
 2G9  CONST_01  C3   C2   C1   C6      0.00   0.0  0
 2G9  CONST_02  C3   C4   C5   C6      0.00   0.0  0
 2G9  CONST_03  C4   C3   C2   C1      0.00   0.0  0
 2G9  CONST_04  C4   C5   C6   C1      0.00   0.0  0
 2G9  CONST_05  C5   C6   C1   C2      0.00   0.0  0
 2G9  CONST_06  C5   C4   C3   C2      0.00   0.0  0
 2G9  CONST_07  C2   C1   C6   C7    180.00   0.0  0
 2G9  CONST_08  C4   C5   C6   C7    180.00   0.0  0
 2G9  CONST_09  H30  C2   C1   C6    180.00   0.0  0
 2G9  CONST_10  H32  C4   C5   C6    180.00   0.0  0
 2G9  CONST_11  H31  C3   C2   C1    180.00   0.0  0
 2G9  CONST_12  H33  C5   C6   C1    180.00   0.0  0
 2G9  CONST_13  H29  C1   C2   C3    180.00   0.0  0
 2G9  CONST_14  C25  N24  C22  C17   180.00   0.0  0
 2G9  CONST_15  C25  N24  C22  O23     0.00   0.0  0
 2G9  CONST_16  H12  N24  C22  C17     0.00   0.0  0
 2G9  Var_01    O8   C7   C6   C1    -85.43  30.0  3
 2G9  Var_02    N11  C9   O8   C7   -177.99  30.0  2
 2G9  Var_03    P13  C12  N11  C9     87.48  30.0  1
 2G9  Var_04    C12  N11  C9   O10     5.78  30.0  1
 2G9  Var_05    N16  P13  C12  N11  -164.68  30.0  1
 2G9  Var_06    C17  N16  P13  C12  -177.09  30.0  1
 2G9  Var_07    C21  C19  C18  C17   -56.81  30.0  1
 2G9  Var_08    C26  C25  N24  C22  -107.05  30.0  3
 2G9  Var_09    H9   C21  C19  C18    63.71  30.0  3
 2G9  Var_10    H6   C20  C19  C18    62.01  30.0  3
 2G9  Var_11    H21  C29  C28  C26   -55.44  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
 2G9  chir_02  C17  C18  C22  N16  negativ
 2G9  chir_03  C26  C27  C28  C25  negativ
 2G9  chir_04  P13  O14  O15  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
 2G9  plan-1  C7   0.020
 2G9  plan-1  C6   0.020
 2G9  plan-1  C1   0.020
 2G9  plan-1  C2   0.020
 2G9  plan-1  C3   0.020
 2G9  plan-1  C4   0.020
 2G9  plan-1  C5   0.020
 2G9  plan-1  H29  0.020
 2G9  plan-1  H30  0.020
 2G9  plan-1  H31  0.020
 2G9  plan-1  H32  0.020
 2G9  plan-1  H33  0.020
 2G9  plan-2  C17  0.020
 2G9  plan-2  C22  0.020
 2G9  plan-2  O23  0.020
 2G9  plan-2  N24  0.020
 2G9  plan-2  C25  0.020
 2G9  plan-2  H12  0.020
 2G9  plan-3  C9   0.020
 2G9  plan-3  O10  0.020
 2G9  plan-3  O8   0.020
 2G9  plan-3  N11  0.020

