# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 17:50:08 2020
#   Inital geometry file: a 160 line input string
#   Ligand name: N~2~-[(R)-({[(benzyloxy)carbonyl]amino}methyl)(hydroxy)phosphoryl]-N-[(2R)-2,3,3-trimethylbutyl]-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)NC[C@H](C)C(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
 6NG  6NG  N~2~-[(R)-({[(benzyloxy)carbonyl]amino}methyl)(hydroxy)phosphoryl]-N-[(2R)-2,3,3-trimethylbutyl]-L-leucinamide  ligand  69  31  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_6NG
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
 6NG  C1   C  CR16  0  -0.293   6.9972  -1.2461   1.7530
 6NG  C2   C  CR16  0  -0.242   8.2479  -0.9156   2.2577
 6NG  C3   C  CR16  0  -0.261   9.3171  -0.7237   1.3926
 6NG  C9   C  C     0   0.763   3.5841  -0.5641  -1.0145
 6NG  C12  C  CH2   0  -0.569   1.7755   0.8746  -1.7781
 6NG  C20  C  CH3   0  -0.659  -3.3274   2.4990   2.4675
 6NG  C21  C  CH3   0  -0.649  -4.0504   4.5088   1.1624
 6NG  C22  C  C     0   0.574  -3.0921   0.7118  -0.8786
 6NG  C27  C  CH3   0  -0.678  -4.8187  -2.6729   1.2000
 6NG  N16  N  NH1   0  -0.776  -0.7889   1.4290  -0.9863
 6NG  C17  C  CH1   0  -0.213  -1.9836   1.4732  -0.1583
 6NG  C25  C  CH2   0  -0.242  -4.8886  -0.9463  -0.6189
 6NG  C26  C  CH1   0  -0.249  -5.6566  -1.5682   0.5517
 6NG  C28  C  CT    0  -0.079  -7.0798  -2.0349   0.1436
 6NG  C29  C  CH3   0  -0.649  -7.7654  -2.7009   1.3410
 6NG  C30  C  CH3   0  -0.647  -7.9315  -0.8266  -0.2614
 6NG  C31  C  CH3   0  -0.656  -7.0368  -3.0335  -1.0157
 6NG  O23  O  O     0  -0.498  -3.3466   0.9344  -2.0543
 6NG  C18  C  CH2   0  -0.406  -2.4320   2.9085   0.1339
 6NG  P13  P  P     0   1.305   0.7124   1.1887  -0.3291
 6NG  C6   C  CR6   0   0.074   6.8036  -1.3923   0.3829
 6NG  C5   C  CR16  0  -0.287   7.8809  -1.1980  -0.4775
 6NG  C4   C  CR16  0  -0.242   9.1317  -0.8656   0.0230
 6NG  O14  O  O     0  -0.714   0.7428   0.1433   0.7272
 6NG  O15  O  OH1   0  -0.752   1.2940   2.5574   0.3182
 6NG  N11  N  NH1   0  -0.656   3.1341   0.6607  -1.3593
 6NG  O8   O  O2    0  -0.479   4.8208  -0.4899  -0.5161
 6NG  O10  O  O     0  -0.512   2.9663  -1.5975  -1.1574
 6NG  H1   H  HCR6  0   0.256   6.1661  -1.3967   2.4319
 6NG  H2   H  HCR6  0   0.259   8.3876  -0.8104   3.3257
 6NG  H3   H  HCR6  0   0.259  10.2929  -0.4679   1.7844
 6NG  H4   H  HCH2  0   0.248   5.5333  -2.3695  -1.0426
 6NG  H5   H  HCH2  0   0.249   4.8506  -2.2540   0.5846
 6NG  H6   H  HCH2  0   0.298   1.4002   0.0006  -2.3086
 6NG  H7   H  HCH2  0   0.305   1.7332   1.7144  -2.4729
 6NG  H8   H  HCH1  0   0.226  -4.4751   2.4818   0.6602
 6NG  H9   H  HCH3  0   0.221  -2.4892   3.0368   2.9172
 6NG  H10  H  HCH3  0   0.235  -4.1887   2.6130   3.1266
 6NG  H11  H  HCH3  0   0.219  -3.0684   1.4392   2.4609
 6NG  H12  H  HCH3  0   0.216  -3.2380   5.1234   1.5583
 6NG  H13  H  HCH3  0   0.228  -4.3215   4.9068   0.1833
 6NG  H14  H  HCH3  0   0.228  -4.9101   4.6329   1.8228
 6NG  H16  H  HCH3  0   0.243  -5.2465  -3.0050   2.1442
 6NG  H17  H  HCH3  0   0.227  -4.7279  -3.5415   0.5456
 6NG  H18  H  HNH1  0   0.401  -0.8525   1.9560  -1.8486
 6NG  H19  H  HCH1  0   0.261  -1.7407   0.9706   0.7804
 6NG  H21  H  HCH2  0   0.248  -5.5308  -0.2891  -1.2053
 6NG  H22  H  HCH2  0   0.235  -4.5314  -1.7299  -1.2944
 6NG  H23  H  HCH1  0   0.228  -5.8009  -0.7754   1.2977
 6NG  H24  H  HCH3  0   0.223  -7.7723  -2.0441   2.2146
 6NG  H25  H  HCH3  0   0.227  -8.8030  -2.9362   1.0965
 6NG  H26  H  HCH3  0   0.229  -7.2806  -3.6342   1.6274
 6NG  H27  H  HCH3  0   0.226  -7.5740  -0.3400  -1.1700
 6NG  H28  H  HCH3  0   0.228  -8.9610  -1.1364  -0.4515
 6NG  H29  H  HCH3  0   0.224  -7.9548  -0.0742   0.5306
 6NG  H30  H  HCH3  0   0.226  -6.4616  -3.9251  -0.7606
 6NG  H31  H  HCH3  0   0.229  -8.0462  -3.3627  -1.2697
 6NG  H32  H  HCH3  0   0.228  -6.6027  -2.6016  -1.9190
 6NG  H33  H  HCH2  0   0.235  -2.6569   3.3993  -0.8184
 6NG  H34  H  HCH2  0   0.233  -1.5788   3.4420   0.5655
 6NG  H35  H  HCR6  0   0.255   7.7428  -1.3134  -1.5463
 6NG  H36  H  HCR6  0   0.259   9.9621  -0.7202  -0.6557
 6NG  H37  H  HOH1  0   0.483   1.2304   3.3367  -0.2481
 6NG  H38  H  HNH1  0   0.410   3.7050   1.4664  -1.1588
 6NG  C7   C  CH2   0  -0.238   5.4495  -1.7291  -0.1620
 6NG  N24  N  NH1   0  -0.643  -3.7667  -0.1674  -0.1306
 6NG  C19  C  CH1   0  -0.254  -3.6309   3.0444   1.0750
 6NG  H15  H  HCH3  0   0.229  -3.8044  -2.3369   1.4224
 6NG  H20  H  HNH1  0   0.396  -3.4547  -0.3313   0.8126

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
 6NG  C4   C5   aromatic  1.388  0.020  1.388
 6NG  C4   C3   aromatic  1.389  0.020  1.389
 6NG  C5   C6   aromatic  1.392  0.020  1.392
 6NG  C3   C2   aromatic  1.389  0.020  1.389
 6NG  C6   C7   single    1.498  0.020  1.498
 6NG  C6   C1   aromatic  1.391  0.020  1.391
 6NG  C2   C1   aromatic  1.389  0.020  1.389
 6NG  C7   O8   single    1.434  0.020  1.434
 6NG  O8   C9   single    1.335  0.020  1.335
 6NG  C9   O10  double    1.212  0.020  1.212
 6NG  C9   N11  single    1.350  0.020  1.350
 6NG  N11  C12  single    1.438  0.020  1.438
 6NG  C12  P13  single    1.824  0.020  1.824
 6NG  O14  P13  double    1.486  0.020  1.486
 6NG  O15  P13  single    1.622  0.020  1.622
 6NG  P13  N16  single    1.656  0.020  1.656
 6NG  C30  C28  single    1.533  0.020  1.533
 6NG  C25  N24  single    1.450  0.020  1.450
 6NG  C25  C26  single    1.532  0.020  1.532
 6NG  N16  C17  single    1.454  0.020  1.454
 6NG  N24  C22  single    1.337  0.020  1.337
 6NG  C28  C26  single    1.552  0.020  1.552
 6NG  C28  C31  single    1.531  0.020  1.531
 6NG  C28  C29  single    1.532  0.020  1.532
 6NG  O23  C22  double    1.223  0.020  1.223
 6NG  C22  C17  single    1.526  0.020  1.526
 6NG  C26  C27  single    1.531  0.020  1.531
 6NG  C17  C18  single    1.532  0.020  1.532
 6NG  C18  C19  single    1.530  0.020  1.530
 6NG  C21  C19  single    1.526  0.020  1.526
 6NG  C19  C20  single    1.526  0.020  1.526
 6NG  C1   H1   single    0.930  0.020  1.080
 6NG  C2   H2   single    0.930  0.020  1.080
 6NG  C3   H3   single    0.930  0.020  1.080
 6NG  C7   H4   single    0.970  0.020  1.090
 6NG  C7   H5   single    0.970  0.020  1.090
 6NG  C12  H6   single    0.970  0.020  1.090
 6NG  C12  H7   single    0.970  0.020  1.090
 6NG  C19  H8   single    0.970  0.020  1.090
 6NG  C20  H9   single    0.970  0.020  1.090
 6NG  C20  H10  single    0.970  0.020  1.090
 6NG  C20  H11  single    0.970  0.020  1.090
 6NG  C21  H12  single    0.970  0.020  1.090
 6NG  C21  H13  single    0.970  0.020  1.090
 6NG  C21  H14  single    0.970  0.020  1.090
 6NG  C27  H15  single    0.970  0.020  1.090
 6NG  C27  H16  single    0.970  0.020  1.090
 6NG  C27  H17  single    0.970  0.020  1.090
 6NG  N16  H18  single    0.890  0.020  1.040
 6NG  C17  H19  single    0.970  0.020  1.090
 6NG  N24  H20  single    0.860  0.020  1.020
 6NG  C25  H21  single    0.970  0.020  1.090
 6NG  C25  H22  single    0.970  0.020  1.090
 6NG  C26  H23  single    0.970  0.020  1.090
 6NG  C29  H24  single    0.970  0.020  1.090
 6NG  C29  H25  single    0.970  0.020  1.090
 6NG  C29  H26  single    0.970  0.020  1.090
 6NG  C30  H27  single    0.970  0.020  1.090
 6NG  C30  H28  single    0.970  0.020  1.090
 6NG  C30  H29  single    0.970  0.020  1.090
 6NG  C31  H30  single    0.970  0.020  1.090
 6NG  C31  H31  single    0.970  0.020  1.090
 6NG  C31  H32  single    0.970  0.020  1.090
 6NG  C18  H33  single    0.970  0.020  1.090
 6NG  C18  H34  single    0.970  0.020  1.090
 6NG  C5   H35  single    0.930  0.020  1.080
 6NG  C4   H36  single    0.930  0.020  1.080
 6NG  O15  H37  single    0.850  0.020  0.980
 6NG  N11  H38  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
 6NG  H1   C1   C6   119.71  3.000
 6NG  H1   C1   C2   119.75  3.000
 6NG  C6   C1   C2   120.55  3.000
 6NG  H2   C2   C3   120.13  3.000
 6NG  H2   C2   C1   119.87  3.000
 6NG  C3   C2   C1   119.99  3.000
 6NG  H3   C3   C4   120.08  3.000
 6NG  H3   C3   C2   120.09  3.000
 6NG  C4   C3   C2   119.82  3.000
 6NG  O10  C9   O8   124.29  3.000
 6NG  O10  C9   N11  124.99  3.000
 6NG  O8   C9   N11  110.72  3.000
 6NG  H7   C12  H6   107.11  3.000
 6NG  H7   C12  N11  109.68  3.000
 6NG  H6   C12  N11  110.38  3.000
 6NG  H7   C12  P13  110.53  3.000
 6NG  H6   C12  P13  108.92  3.000
 6NG  N11  C12  P13  110.18  3.000
 6NG  H11  C20  H10  107.02  3.000
 6NG  H11  C20  H9   107.36  3.000
 6NG  H10  C20  H9   107.80  3.000
 6NG  H11  C20  C19  112.88  3.000
 6NG  H10  C20  C19  110.92  3.000
 6NG  H9   C20  C19  110.62  3.000
 6NG  H14  C21  H13  107.81  3.000
 6NG  H14  C21  H12  107.61  3.000
 6NG  H13  C21  H12  107.74  3.000
 6NG  H14  C21  C19  111.13  3.000
 6NG  H13  C21  C19  111.53  3.000
 6NG  H12  C21  C19  110.86  3.000
 6NG  O23  C22  N24  123.53  3.000
 6NG  O23  C22  C17  120.93  3.000
 6NG  N24  C22  C17  115.51  3.000
 6NG  H17  C27  H16  108.07  3.000
 6NG  H17  C27  H15  106.85  3.000
 6NG  H16  C27  H15  106.41  3.000
 6NG  H17  C27  C26  111.46  3.000
 6NG  H16  C27  C26  111.87  3.000
 6NG  H15  C27  C26  111.89  3.000
 6NG  H18  N16  P13  118.05  3.000
 6NG  H18  N16  C17  114.67  3.000
 6NG  P13  N16  C17  121.54  3.000
 6NG  H19  C17  C18  109.42  3.000
 6NG  H19  C17  N16  107.02  3.000
 6NG  C18  C17  N16  112.18  3.000
 6NG  H19  C17  C22  109.73  3.000
 6NG  C18  C17  C22  110.18  3.000
 6NG  N16  C17  C22  108.24  3.000
 6NG  H22  C25  H21  106.98  3.000
 6NG  H22  C25  C26  110.15  3.000
 6NG  H21  C25  C26  111.13  3.000
 6NG  H22  C25  N24  109.87  3.000
 6NG  H21  C25  N24  108.24  3.000
 6NG  C26  C25  N24  110.40  3.000
 6NG  H23  C26  C28  105.98  3.000
 6NG  H23  C26  C25  106.97  3.000
 6NG  C28  C26  C25  112.38  3.000
 6NG  H23  C26  C27  107.77  3.000
 6NG  C28  C26  C27  113.34  3.000
 6NG  C25  C26  C27  110.01  3.000
 6NG  C31  C28  C30  109.26  3.000
 6NG  C31  C28  C29  108.72  3.000
 6NG  C30  C28  C29  107.49  3.000
 6NG  C29  C28  C26  109.60  3.000
 6NG  C31  C28  C26  111.68  3.000
 6NG  C30  C28  C26  109.99  3.000
 6NG  H26  C29  H25  107.27  3.000
 6NG  H26  C29  H24  107.90  3.000
 6NG  H25  C29  H24  107.61  3.000
 6NG  H26  C29  C28  112.24  3.000
 6NG  H25  C29  C28  110.12  3.000
 6NG  H24  C29  C28  111.49  3.000
 6NG  H29  C30  H28  107.55  3.000
 6NG  H29  C30  H27  107.67  3.000
 6NG  H28  C30  H27  106.89  3.000
 6NG  H29  C30  C28  111.30  3.000
 6NG  H28  C30  C28  110.26  3.000
 6NG  H27  C30  C28  112.93  3.000
 6NG  H32  C31  H31  107.13  3.000
 6NG  H32  C31  H30  107.89  3.000
 6NG  H31  C31  H30  107.19  3.000
 6NG  H32  C31  C28  112.32  3.000
 6NG  H31  C31  C28  110.30  3.000
 6NG  H30  C31  C28  111.76  3.000
 6NG  H34  C18  H33  106.54  3.000
 6NG  H34  C18  C17  107.67  3.000
 6NG  H33  C18  C17  108.32  3.000
 6NG  H34  C18  C19  108.95  3.000
 6NG  H33  C18  C19  109.53  3.000
 6NG  C17  C18  C19  115.46  3.000
 6NG  O15  P13  O14  107.61  3.000
 6NG  O15  P13  N16  111.16  3.000
 6NG  O14  P13  N16  113.74  3.000
 6NG  N16  P13  C12  103.77  3.000
 6NG  O15  P13  C12  104.68  3.000
 6NG  O14  P13  C12  115.56  3.000
 6NG  C5   C6   C7   120.39  3.000
 6NG  C7   C6   C1   120.51  3.000
 6NG  C5   C6   C1   119.09  3.000
 6NG  H35  C5   C4   119.74  3.000
 6NG  H35  C5   C6   119.74  3.000
 6NG  C4   C5   C6   120.53  3.000
 6NG  H36  C4   C5   119.84  3.000
 6NG  H36  C4   C3   120.14  3.000
 6NG  C5   C4   C3   120.02  3.000
 6NG  H37  O15  P13  115.05  3.000
 6NG  H38  N11  C12  118.33  3.000
 6NG  H38  N11  C9   119.07  3.000
 6NG  C12  N11  C9   121.64  3.000
 6NG  C9   O8   C7   116.75  3.000
 6NG  H5   C7   H4   108.16  3.000
 6NG  H5   C7   O8   110.11  3.000
 6NG  H4   C7   O8   109.95  3.000
 6NG  H5   C7   C6   110.80  3.000
 6NG  H4   C7   C6   110.85  3.000
 6NG  O8   C7   C6   106.97  3.000
 6NG  H20  N24  C25  117.88  3.000
 6NG  H20  N24  C22  118.34  3.000
 6NG  C25  N24  C22  123.72  3.000
 6NG  H8   C19  C18  108.98  3.000
 6NG  H8   C19  C21  107.61  3.000
 6NG  C18  C19  C21  109.62  3.000
 6NG  H8   C19  C20  108.37  3.000
 6NG  C21  C19  C20  110.20  3.000
 6NG  C18  C19  C20  111.94  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
 6NG  CONST_01  C4   C5   C6   C1      0.00   0.0  0
 6NG  CONST_02  C4   C3   C2   C1      0.00   0.0  0
 6NG  CONST_03  C5   C4   C3   C2      0.00   0.0  0
 6NG  CONST_04  C5   C6   C1   C2      0.00   0.0  0
 6NG  CONST_05  C6   C5   C4   C3      0.00   0.0  0
 6NG  CONST_06  C6   C1   C2   C3      0.00   0.0  0
 6NG  CONST_07  C7   C6   C1   C2    180.00   0.0  0
 6NG  CONST_08  C4   C5   C6   C7    180.00   0.0  0
 6NG  CONST_09  H35  C5   C6   C1    180.00   0.0  0
 6NG  CONST_10  H3   C3   C2   C1    180.00   0.0  0
 6NG  CONST_11  H36  C4   C3   C2    180.00   0.0  0
 6NG  CONST_12  H1   C1   C2   C3    180.00   0.0  0
 6NG  CONST_13  H2   C2   C1   C6    180.00   0.0  0
 6NG  CONST_14  C25  N24  C22  C17   180.00   0.0  0
 6NG  CONST_15  O23  C22  N24  C25     0.00   0.0  0
 6NG  CONST_16  H20  N24  C22  C17     0.00   0.0  0
 6NG  Var_01    O8   C7   C6   C1     94.54  30.0  2
 6NG  Var_02    C6   C7   O8   C9   -179.28  30.0  1
 6NG  Var_03    O10  C9   O8   C7      1.45  30.0  3
 6NG  Var_04    P13  C12  N11  C9     87.61  30.0  3
 6NG  Var_05    O8   C9   N11  C12  -172.79  30.0  1
 6NG  Var_06    C17  N16  P13  C12   168.67  30.0  3
 6NG  Var_07    C17  C18  C19  C20    63.05  30.0  2
 6NG  Var_08    C26  C25  N24  C22  -165.25  30.0  1
 6NG  Var_09    N11  C12  P13  N16   179.30  30.0  1
 6NG  Var_10    H12  C21  C19  C20    62.83  30.0  3
 6NG  Var_11    H9   C20  C19  C21   -62.41  30.0  3
 6NG  Var_12    H27  C30  C28  C26    66.23  30.0  3
 6NG  Var_13    H30  C31  C28  C26    59.65  30.0  3
 6NG  Var_14    H24  C29  C28  C26    54.59  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
 6NG  chir_01  C17  N16  C22  C18  positiv
 6NG  chir_02  C26  C25  C28  C27  negativ
 6NG  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
 6NG  plan-1  C1   0.020
 6NG  plan-1  C2   0.020
 6NG  plan-1  C3   0.020
 6NG  plan-1  C6   0.020
 6NG  plan-1  C5   0.020
 6NG  plan-1  C4   0.020
 6NG  plan-1  H1   0.020
 6NG  plan-1  H2   0.020
 6NG  plan-1  H3   0.020
 6NG  plan-1  H35  0.020
 6NG  plan-1  H36  0.020
 6NG  plan-1  C7   0.020
 6NG  plan-2  C22  0.020
 6NG  plan-2  C17  0.020
 6NG  plan-2  C25  0.020
 6NG  plan-2  O23  0.020
 6NG  plan-2  N24  0.020
 6NG  plan-2  H20  0.020
 6NG  plan-3  C9   0.020
 6NG  plan-3  N11  0.020
 6NG  plan-3  O8   0.020
 6NG  plan-3  O10  0.020

