# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 18:25:42 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  66  30  .  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_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  -0.237   5.5258  -0.3930  -1.1391
 2G6  C6   C  CR6   0   0.075   6.6765  -0.9240  -0.3398
 2G6  C1   C  CR16  0  -0.297   6.7544  -2.2755  -0.0221
 2G6  C2   C  CR16  0  -0.242   7.8143  -2.7641   0.7318
 2G6  C3   C  CR16  0  -0.261   8.8039  -1.8996   1.1786
 2G6  C4   C  CR16  0  -0.243   8.7320  -0.5467   0.8676
 2G6  C5   C  CR16  0  -0.284   7.6742  -0.0631   0.1120
 2G6  C9   C  C     0   0.768   3.5518   0.8342  -0.7340
 2G6  O10  O  O     0  -0.516   3.2856   0.8515  -1.9171
 2G6  O8   O  O2    0  -0.479   4.6292   0.2366  -0.2160
 2G6  N11  N  NH1   0  -0.661   2.8274   1.4280   0.2353
 2G6  C12  C  CH2   0  -0.552   1.5559   2.0476  -0.0245
 2G6  P13  P  P     0   1.296   0.1669   0.9277   0.3439
 2G6  O14  O  O     0  -0.726  -0.0584   0.6822   1.7971
 2G6  O15  O  OH1   0  -0.771   0.5653  -0.3837  -0.5022
 2G6  N16  N  NH1   0  -0.765  -1.1513   1.6445  -0.3793
 2G6  C17  C  CH1   0  -0.219  -2.5021   1.3397   0.0344
 2G6  C22  C  C     0   0.599  -2.9188  -0.0751  -0.4083
 2G6  O23  O  O     0  -0.526  -2.0891  -0.8884  -0.8172
 2G6  C18  C  CH2   0  -0.444  -3.4492   2.4397  -0.4537
 2G6  C19  C  CH1   0  -0.218  -3.0418   3.8506  -0.0248
 2G6  C20  C  CH3   0  -0.654  -4.0513   4.8575  -0.5670
 2G6  C21  C  CH3   0  -0.669  -2.9105   3.9715   1.4892
 2G6  N24  N  NH1   0  -0.632  -4.2089  -0.3781  -0.2711
 2G6  C25  C  CH2   0  -0.268  -4.7901  -1.6821  -0.5301
 2G6  C26  C  CH2   0  -0.421  -5.7129  -2.0893   0.6119
 2G6  C27  C  CT    0  -0.096  -6.3823  -3.4655   0.4611
 2G6  C28  C  CH3   0  -0.648  -7.2590  -3.5166  -0.7921
 2G6  C30  C  CH3   0  -0.648  -5.3297  -4.5748   0.4027
 2G6  C29  C  CH3   0  -0.636  -7.2652  -3.6882   1.6908
 2G6  H29  H  HCH2  0   0.248   5.8697   0.3310  -1.8808
 2G6  H30  H  HCH2  0   0.249   5.0159  -1.2015  -1.6668
 2G6  H31  H  HCR6  0   0.256   5.9836  -2.9534  -0.3696
 2G6  H32  H  HCR6  0   0.259   7.8657  -3.8186   0.9696
 2G6  H33  H  HCR6  0   0.259   9.6321  -2.2783   1.7634
 2G6  H34  H  HCR6  0   0.258   9.5035   0.1305   1.2107
 2G6  H35  H  HCR6  0   0.255   7.6273   0.9912  -0.1345
 2G6  H36  H  HNH1  0   0.409   3.1203   1.3285   1.1943
 2G6  H27  H  HCH2  0   0.297   1.4462   2.9343   0.6014
 2G6  H28  H  HCH2  0   0.288   1.5080   2.3802  -1.0611
 2G6  H26  H  HOH1  0   0.489  -0.2761  -0.8204  -0.7584
 2G6  H1   H  HNH1  0   0.396  -1.0618   1.8341  -1.3705
 2G6  H2   H  HCH1  0   0.291  -2.5226   1.3225   1.1288
 2G6  H3   H  HCH2  0   0.245  -3.5180   2.3943  -1.5456
 2G6  H4   H  HCH2  0   0.232  -4.4577   2.2553  -0.0728
 2G6  H5   H  HCH1  0   0.226  -2.0678   4.0773  -0.4676
 2G6  H6   H  HCH3  0   0.214  -5.0500   4.6741  -0.1629
 2G6  H7   H  HCH3  0   0.228  -3.7705   5.8776  -0.3004
 2G6  H8   H  HCH3  0   0.225  -4.1208   4.8052  -1.6552
 2G6  H9   H  HCH3  0   0.215  -3.8381   3.6834   1.9907
 2G6  H10  H  HCH3  0   0.231  -2.1088   3.3447   1.8825
 2G6  H11  H  HCH3  0   0.231  -2.6850   4.9997   1.7762
 2G6  H12  H  HNH1  0   0.407  -4.8394   0.3360   0.0571
 2G6  H13  H  HCH2  0   0.243  -5.3340  -1.6528  -1.4774
 2G6  H14  H  HCH2  0   0.248  -3.9784  -2.3968  -0.6466
 2G6  H15  H  HCH2  0   0.230  -5.1353  -2.0785   1.5424
 2G6  H16  H  HCH2  0   0.227  -6.4961  -1.3302   0.7232
 2G6  H23  H  HCH3  0   0.226  -6.6740  -3.4475  -1.7109
 2G6  H24  H  HCH3  0   0.227  -7.8113  -4.4580  -0.8343
 2G6  H25  H  HCH3  0   0.223  -7.9889  -2.7039  -0.7979
 2G6  H20  H  HCH3  0   0.223  -4.6701  -4.5360   1.2722
 2G6  H21  H  HCH3  0   0.227  -5.8062  -5.5572   0.3908
 2G6  H22  H  HCH3  0   0.226  -4.7066  -4.5088  -0.4907
 2G6  H17  H  HCH3  0   0.222  -8.0419  -2.9237   1.7669
 2G6  H18  H  HCH3  0   0.224  -7.7606  -4.6606   1.6463
 2G6  H19  H  HCH3  0   0.222  -6.6781  -3.6607   2.6118

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    1.524  0.020  1.524
 2G6  C19  C20  single    1.526  0.020  1.526
 2G6  C19  C18  single    1.530  0.020  1.530
 2G6  C28  C27  single    1.530  0.020  1.530
 2G6  C18  C17  single    1.531  0.020  1.531
 2G6  C26  C27  single    1.538  0.020  1.538
 2G6  C26  C25  single    1.524  0.020  1.524
 2G6  C27  C30  single    1.530  0.020  1.530
 2G6  C27  C29  single    1.530  0.020  1.530
 2G6  C17  C22  single    1.540  0.020  1.540
 2G6  C17  N16  single    1.445  0.020  1.445
 2G6  C22  O23  double    1.232  0.020  1.232
 2G6  C22  N24  single    1.332  0.020  1.332
 2G6  N24  C25  single    1.451  0.020  1.451
 2G6  N16  P13  single    1.666  0.020  1.666
 2G6  P13  O14  double    1.491  0.020  1.491
 2G6  P13  O15  single    1.611  0.020  1.611
 2G6  P13  C12  single    1.822  0.020  1.822
 2G6  C12  N11  single    1.438  0.020  1.438
 2G6  N11  C9   single    1.348  0.020  1.348
 2G6  O10  C9   double    1.213  0.020  1.213
 2G6  C9   O8   single    1.336  0.020  1.336
 2G6  O8   C7   single    1.433  0.020  1.433
 2G6  C5   C4   aromatic  1.387  0.020  1.387
 2G6  C5   C6   aromatic  1.393  0.020  1.393
 2G6  C7   C6   single    1.498  0.020  1.498
 2G6  C4   C3   aromatic  1.390  0.020  1.390
 2G6  C6   C1   aromatic  1.391  0.020  1.391
 2G6  C3   C2   aromatic  1.388  0.020  1.388
 2G6  C1   C2   aromatic  1.389  0.020  1.389
 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  O15  H26  single    0.850  0.020  0.980
 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    0.860  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
 2G6  H30  C7   H29  108.04  3.000
 2G6  H30  C7   O8   110.15  3.000
 2G6  H29  C7   O8   110.09  3.000
 2G6  H30  C7   C6   110.73  3.000
 2G6  H29  C7   C6   110.82  3.000
 2G6  O8   C7   C6   107.02  3.000
 2G6  C5   C6   C1   119.10  3.000
 2G6  C1   C6   C7   120.62  3.000
 2G6  C5   C6   C7   120.27  3.000
 2G6  H31  C1   C2   119.78  3.000
 2G6  H31  C1   C6   119.65  3.000
 2G6  C2   C1   C6   120.56  3.000
 2G6  H32  C2   C3   120.15  3.000
 2G6  H32  C2   C1   119.87  3.000
 2G6  C3   C2   C1   119.97  3.000
 2G6  H33  C3   C4   120.07  3.000
 2G6  H33  C3   C2   120.11  3.000
 2G6  C4   C3   C2   119.82  3.000
 2G6  H34  C4   C5   119.88  3.000
 2G6  H34  C4   C3   120.07  3.000
 2G6  C5   C4   C3   120.04  3.000
 2G6  H35  C5   C4   119.74  3.000
 2G6  H35  C5   C6   119.76  3.000
 2G6  C4   C5   C6   120.50  3.000
 2G6  N11  C9   O8   110.58  3.000
 2G6  O8   C9   O10  124.16  3.000
 2G6  N11  C9   O10  125.25  3.000
 2G6  C9   O8   C7   116.83  3.000
 2G6  H36  N11  C12  118.13  3.000
 2G6  H36  N11  C9   118.99  3.000
 2G6  C12  N11  C9   122.35  3.000
 2G6  H28  C12  H27  107.06  3.000
 2G6  H28  C12  P13  110.27  3.000
 2G6  H27  C12  P13  107.88  3.000
 2G6  H28  C12  N11  110.01  3.000
 2G6  H27  C12  N11  109.60  3.000
 2G6  P13  C12  N11  111.88  3.000
 2G6  N16  P13  O15  108.55  3.000
 2G6  O15  P13  O14  114.54  3.000
 2G6  N16  P13  O14  111.99  3.000
 2G6  O15  P13  C12  101.87  3.000
 2G6  O14  P13  C12  114.43  3.000
 2G6  N16  P13  C12  104.54  3.000
 2G6  H26  O15  P13  106.68  3.000
 2G6  H1   N16  C17  113.71  3.000
 2G6  H1   N16  P13  115.81  3.000
 2G6  C17  N16  P13  121.64  3.000
 2G6  H2   C17  C18  108.56  3.000
 2G6  H2   C17  C22  105.54  3.000
 2G6  C18  C17  C22  113.64  3.000
 2G6  H2   C17  N16  107.88  3.000
 2G6  C22  C17  N16  111.37  3.000
 2G6  C18  C17  N16  109.59  3.000
 2G6  N24  C22  O23  122.43  3.000
 2G6  N24  C22  C17  116.19  3.000
 2G6  O23  C22  C17  121.32  3.000
 2G6  H4   C18  H3   106.40  3.000
 2G6  H4   C18  C19  107.66  3.000
 2G6  H3   C18  C19  109.54  3.000
 2G6  H4   C18  C17  109.77  3.000
 2G6  H3   C18  C17  109.09  3.000
 2G6  C19  C18  C17  114.10  3.000
 2G6  H5   C19  C21  108.00  3.000
 2G6  H5   C19  C20  107.97  3.000
 2G6  C21  C19  C20  110.95  3.000
 2G6  H5   C19  C18  108.35  3.000
 2G6  C20  C19  C18  109.44  3.000
 2G6  C21  C19  C18  111.99  3.000
 2G6  H8   C20  H7   107.74  3.000
 2G6  H8   C20  H6   107.60  3.000
 2G6  H7   C20  H6   107.57  3.000
 2G6  H8   C20  C19  111.39  3.000
 2G6  H7   C20  C19  111.10  3.000
 2G6  H6   C20  C19  111.26  3.000
 2G6  H11  C21  H10  107.13  3.000
 2G6  H11  C21  H9   107.64  3.000
 2G6  H10  C21  H9   107.87  3.000
 2G6  H11  C21  C19  110.72  3.000
 2G6  H10  C21  C19  112.07  3.000
 2G6  H9   C21  C19  111.20  3.000
 2G6  H12  N24  C25  116.38  3.000
 2G6  H12  N24  C22  118.57  3.000
 2G6  C25  N24  C22  125.03  3.000
 2G6  H14  C25  H13  107.23  3.000
 2G6  H14  C25  C26  110.90  3.000
 2G6  H13  C25  C26  110.82  3.000
 2G6  H14  C25  N24  108.10  3.000
 2G6  H13  C25  N24  109.27  3.000
 2G6  C26  C25  N24  110.43  3.000
 2G6  H16  C26  H15  106.48  3.000
 2G6  H16  C26  C27  108.58  3.000
 2G6  H15  C26  C27  108.77  3.000
 2G6  H16  C26  C25  108.89  3.000
 2G6  H15  C26  C25  108.34  3.000
 2G6  C27  C26  C25  115.42  3.000
 2G6  C29  C27  C30  108.79  3.000
 2G6  C29  C27  C28  108.83  3.000
 2G6  C30  C27  C28  109.79  3.000
 2G6  C29  C27  C26  107.61  3.000
 2G6  C30  C27  C26  110.68  3.000
 2G6  C28  C27  C26  111.08  3.000
 2G6  H25  C28  H24  107.64  3.000
 2G6  H25  C28  H23  107.85  3.000
 2G6  H24  C28  H23  107.05  3.000
 2G6  H25  C28  C27  111.24  3.000
 2G6  H24  C28  C27  110.50  3.000
 2G6  H23  C28  C27  112.34  3.000
 2G6  H22  C30  H21  107.14  3.000
 2G6  H22  C30  H20  107.75  3.000
 2G6  H21  C30  H20  107.71  3.000
 2G6  H22  C30  C27  112.34  3.000
 2G6  H21  C30  C27  110.64  3.000
 2G6  H20  C30  C27  111.06  3.000
 2G6  H19  C29  H18  107.49  3.000
 2G6  H19  C29  H17  107.80  3.000
 2G6  H18  C29  H17  107.66  3.000
 2G6  H19  C29  C27  111.33  3.000
 2G6  H18  C29  C27  111.01  3.000
 2G6  H17  C29  C27  111.37  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    101.63  30.0  2
 2G6  Var_02    N11  C9   O8   C7   -177.54  30.0  1
 2G6  Var_03    P13  C12  N11  C9     96.22  30.0  1
 2G6  Var_04    C12  N11  C9   O10     6.58  30.0  2
 2G6  Var_05    N16  P13  C12  N11  -165.59  30.0  2
 2G6  Var_06    C17  N16  P13  C12  -158.82  30.0  1
 2G6  Var_07    C21  C19  C18  C17   -56.62  30.0  1
 2G6  Var_08    C26  C25  N24  C22   133.07  30.0  3
 2G6  Var_09    C27  C26  C25  N24  -179.42  30.0  1
 2G6  Var_10    C28  C27  C26  C25   -60.71  30.0  3
 2G6  Var_11    H9   C21  C19  C18   -56.60  30.0  3
 2G6  Var_12    H6   C20  C19  C18    61.81  30.0  3
 2G6  Var_13    H23  C28  C27  C26    66.50  30.0  3
 2G6  Var_14    H20  C30  C27  C26    55.09  30.0  3
 2G6  Var_15    H17  C29  C27  C26    60.74  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
 2G6  chir_02  C17  C18  C22  N16  negativ
 2G6  chir_03  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
 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

