# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 12:10:19 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  68  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 GRAND
;

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  -0.288   5.7206  -0.8633   1.3175
 6NG  C2   C  CR16   0  -0.242   7.0915  -1.0639   1.2451
 6NG  C3   C  CR16   0  -0.262   7.5932  -2.2920   0.8311
 6NG  C9   C  C      0   0.753   1.7010  -0.6621  -0.3285
 6NG  C12  C  CH2    0  -0.580   0.2841   0.6365  -1.8181
 6NG  C20  C  CH3    0  -0.656  -3.1381   3.1374   2.5149
 6NG  C21  C  CH3    0  -0.649  -4.3939   5.1123   1.6305
 6NG  C22  C  C      0   0.552  -2.9982   1.7440  -0.8701
 6NG  C27  C  CH3    0  -0.687  -2.5060  -2.3252  -0.1430
 6NG  N16  N  NH1    0  -0.773  -1.0215   3.0939  -1.3649
 6NG  C17  C  CH1    0  -0.194  -1.9795   2.7479  -0.3375
 6NG  C25  C  CH2    0  -0.238  -4.0890  -0.4263  -0.5227
 6NG  C26  C  CH1    0  -0.253  -3.8346  -1.7012   0.2844
 6NG  C28  C  CT     0  -0.076  -5.0376  -2.6818   0.2201
 6NG  C29  C  CH3    0  -0.650  -4.6974  -3.9743   0.9684
 6NG  C30  C  CH3    0  -0.647  -6.2591  -2.0578   0.9054
 6NG  C31  C  CH3    0  -0.658  -5.4097  -3.0317  -1.2232
 6NG  C18  C  CH2    0  -0.394  -2.6999   4.0000   0.1701
 6NG  P13  P  P      0   1.218   0.5427   2.4232  -1.3984
 6NG  C6   C  CR6    0   0.076   4.8362  -1.8842   0.9785
 6NG  C5   C  CR16   0  -0.295   5.3470  -3.1099   0.5636
 6NG  C4   C  CR16   0  -0.242   6.7187  -3.3154   0.4911
 6NG  O14  O  O      0  -0.801   1.0994   2.4656   0.0018
 6NG  O15  O  OP    -1  -0.812   1.2798   3.0733  -2.5428
 6NG  N11  N  NH1    0  -0.647   1.4753  -0.1411  -1.5489
 6NG  O8   O  O2     0  -0.486   2.9886  -1.0204  -0.1953
 6NG  O10  O  O      0  -0.514   0.8654  -0.8395   0.5335
 6NG  H1   H  HCR6   0   0.255   5.3343   0.0937   1.6483
 6NG  H2   H  HCR6   0   0.258   7.7687  -0.2638   1.5151
 6NG  H3   H  HCR6   0   0.258   8.6624  -2.4513   0.7777
 6NG  H4   H  HCH2   0   0.243   2.8205  -2.5951   1.1527
 6NG  H5   H  HCH2   0   0.243   3.1002  -1.0084   1.8792
 6NG  H6   H  HCH2   0   0.251  -0.5370   0.2202  -1.2356
 6NG  H7   H  HCH2   0   0.248   0.0135   0.5211  -2.8696
 6NG  H8   H  HCH1   0   0.220  -4.5278   3.1205   0.8863
 6NG  H9   H  HCH3   0   0.218  -2.3034   3.7328   2.8923
 6NG  H10  H  HCH3   0   0.231  -3.8787   3.0606   3.3129
 6NG  H11  H  HCH3   0   0.215  -2.7652   2.1293   2.3307
 6NG  H12  H  HCH3   0   0.214  -3.6594   5.8045   2.0498
 6NG  H13  H  HCH3   0   0.225  -4.8401   5.5907   0.7572
 6NG  H14  H  HCH3   0   0.226  -5.1807   4.9762   2.3740
 6NG  H17  H  HCH3   0   0.219  -2.5487  -2.6917  -1.1706
 6NG  H18  H  HNH1   0   0.358  -1.4468   3.2939  -2.2599
 6NG  H19  H  HCH1   0   0.239  -1.4201   2.3053   0.4910
 6NG  H21  H  HCH2   0   0.243  -5.0982  -0.0457  -0.3479
 6NG  H22  H  HCH2   0   0.234  -4.0086  -0.6396  -1.5912
 6NG  H23  H  HCH1   0   0.223  -3.7413  -1.4070   1.3391
 6NG  H24  H  HCH3   0   0.222  -4.3679  -3.7730   1.9907
 6NG  H25  H  HCH3   0   0.226  -5.5784  -4.6167   1.0253
 6NG  H26  H  HCH3   0   0.229  -3.9130  -4.5476   0.4725
 6NG  H27  H  HCH3   0   0.226  -6.6306  -1.1806   0.3753
 6NG  H28  H  HCH3   0   0.227  -7.0797  -2.7769   0.9467
 6NG  H29  H  HCH3   0   0.223  -6.0302  -1.7576   1.9306
 6NG  H30  H  HCH3   0   0.227  -4.5719  -3.4663  -1.7710
 6NG  H31  H  HCH3   0   0.228  -6.2206  -3.7630  -1.2369
 6NG  H32  H  HCH3   0   0.227  -5.7569  -2.1594  -1.7803
 6NG  H33  H  HCH2   0   0.222  -3.1750   4.4935  -0.6836
 6NG  H34  H  HCH2   0   0.224  -1.9298   4.6865   0.5366
 6NG  H35  H  HCR6   0   0.254   4.6684  -3.9130   0.3007
 6NG  H36  H  HCR6   0   0.258   7.1034  -4.2746   0.1703
 6NG  H38  H  HNH1   0   0.390   2.2821   0.0556  -2.1210
 6NG  C7   C  CH2    0  -0.233   3.3569  -1.6509   1.0342
 6NG  N24  N  NH1    0  -0.644  -3.1275   0.6035  -0.1786
 6NG  C19  C  CH1    0  -0.254  -3.7403   3.7813   1.2695
 6NG  H15  H  HCH3   0   0.247  -1.6902  -1.6037  -0.0931
 6NG  H20  H  HNH1   0   0.392  -2.5763   0.4792   0.6553
 6NG  O23  O  O      0  -0.505  -3.6536   1.9820  -1.8783
 6NG  H16  H  HCH3   0   0.237  -2.2201  -3.1584   0.4966

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  1.389  0.020  1.389
 6NG  C4   C3   aromatic  1.388  0.020  1.388
 6NG  C5   C6   aromatic  1.391  0.020  1.391
 6NG  C3   C2   aromatic  1.390  0.020  1.390
 6NG  C6   C7   single    1.499  0.020  1.499
 6NG  C6   C1   aromatic  1.393  0.020  1.393
 6NG  C2   C1   aromatic  1.387  0.020  1.387
 6NG  C7   O8   single    1.430  0.020  1.430
 6NG  O8   C9   single    1.343  0.020  1.343
 6NG  C9   O10  double    1.214  0.020  1.214
 6NG  C9   N11  single    1.346  0.020  1.346
 6NG  N11  C12  single    1.448  0.020  1.448
 6NG  C12  P13  single    1.853  0.020  1.853
 6NG  O14  P13  deloc     1.507  0.020  1.507
 6NG  O15  P13  deloc     1.509  0.020  1.509
 6NG  P13  N16  single    1.702  0.020  1.702
 6NG  C30  C28  single    1.533  0.020  1.533
 6NG  C25  N24  single    1.450  0.020  1.450
 6NG  C25  C26  single    1.530  0.020  1.530
 6NG  N16  C17  single    1.447  0.020  1.447
 6NG  N24  C22  single    1.340  0.020  1.340
 6NG  C28  C26  single    1.553  0.020  1.553
 6NG  C28  C31  single    1.531  0.020  1.531
 6NG  C28  C29  single    1.532  0.020  1.532
 6NG  O23  C22  double    1.226  0.020  1.226
 6NG  C22  C17  single    1.526  0.020  1.526
 6NG  C26  C27  single    1.529  0.020  1.529
 6NG  C17  C18  single    1.531  0.020  1.531
 6NG  C18  C19  single    1.529  0.020  1.529
 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  N11  H38  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
 6NG  H1   C1   C6   119.69  3.000
 6NG  H1   C1   C2   119.73  3.000
 6NG  C6   C1   C2   120.58  3.000
 6NG  H2   C2   C3   120.11  3.000
 6NG  H2   C2   C1   119.89  3.000
 6NG  C3   C2   C1   120.01  3.000
 6NG  H3   C3   C4   120.11  3.000
 6NG  H3   C3   C2   120.10  3.000
 6NG  C4   C3   C2   119.79  3.000
 6NG  O10  C9   O8   123.42  3.000
 6NG  O10  C9   N11  125.81  3.000
 6NG  O8   C9   N11  110.72  3.000
 6NG  H7   C12  H6   106.72  3.000
 6NG  H7   C12  N11  109.04  3.000
 6NG  H6   C12  N11  108.39  3.000
 6NG  H7   C12  P13  110.76  3.000
 6NG  H6   C12  P13  110.64  3.000
 6NG  N11  C12  P13  111.15  3.000
 6NG  H11  C20  H10  106.89  3.000
 6NG  H11  C20  H9   107.51  3.000
 6NG  H10  C20  H9   107.71  3.000
 6NG  H11  C20  C19  112.78  3.000
 6NG  H10  C20  C19  111.01  3.000
 6NG  H9   C20  C19  110.70  3.000
 6NG  H14  C21  H13  107.77  3.000
 6NG  H14  C21  H12  107.59  3.000
 6NG  H13  C21  H12  107.71  3.000
 6NG  H14  C21  C19  111.17  3.000
 6NG  H13  C21  C19  111.60  3.000
 6NG  H12  C21  C19  110.81  3.000
 6NG  O23  C22  N24  122.56  3.000
 6NG  O23  C22  C17  121.07  3.000
 6NG  N24  C22  C17  116.37  3.000
 6NG  H17  C27  H16  107.83  3.000
 6NG  H17  C27  H15  107.13  3.000
 6NG  H16  C27  H15  106.44  3.000
 6NG  H17  C27  C26  111.48  3.000
 6NG  H16  C27  C26  112.11  3.000
 6NG  H15  C27  C26  111.56  3.000
 6NG  H18  N16  P13  116.56  3.000
 6NG  H18  N16  C17  113.42  3.000
 6NG  P13  N16  C17  121.89  3.000
 6NG  H19  C17  C18  108.69  3.000
 6NG  H19  C17  N16  107.23  3.000
 6NG  C18  C17  N16  110.57  3.000
 6NG  H19  C17  C22  109.86  3.000
 6NG  C18  C17  C22  109.85  3.000
 6NG  N16  C17  C22  110.58  3.000
 6NG  H22  C25  H21  107.00  3.000
 6NG  H22  C25  C26  109.93  3.000
 6NG  H21  C25  C26  111.07  3.000
 6NG  H22  C25  N24  108.77  3.000
 6NG  H21  C25  N24  109.09  3.000
 6NG  C26  C25  N24  110.87  3.000
 6NG  H23  C26  C28  105.92  3.000
 6NG  H23  C26  C25  107.29  3.000
 6NG  C28  C26  C25  112.05  3.000
 6NG  H23  C26  C27  107.69  3.000
 6NG  C28  C26  C27  113.82  3.000
 6NG  C25  C26  C27  109.70  3.000
 6NG  C31  C28  C30  108.71  3.000
 6NG  C31  C28  C29  108.76  3.000
 6NG  C30  C28  C29  107.58  3.000
 6NG  C29  C28  C26  109.91  3.000
 6NG  C31  C28  C26  111.81  3.000
 6NG  C30  C28  C26  109.97  3.000
 6NG  H26  C29  H25  107.14  3.000
 6NG  H26  C29  H24  107.78  3.000
 6NG  H25  C29  H24  107.63  3.000
 6NG  H26  C29  C28  112.41  3.000
 6NG  H25  C29  C28  110.04  3.000
 6NG  H24  C29  C28  111.62  3.000
 6NG  H29  C30  H28  107.64  3.000
 6NG  H29  C30  H27  107.85  3.000
 6NG  H28  C30  H27  106.99  3.000
 6NG  H29  C30  C28  111.37  3.000
 6NG  H28  C30  C28  110.34  3.000
 6NG  H27  C30  C28  112.43  3.000
 6NG  H32  C31  H31  107.01  3.000
 6NG  H32  C31  H30  107.83  3.000
 6NG  H31  C31  H30  107.28  3.000
 6NG  H32  C31  C28  112.07  3.000
 6NG  H31  C31  C28  110.21  3.000
 6NG  H30  C31  C28  112.19  3.000
 6NG  H34  C18  H33  106.49  3.000
 6NG  H34  C18  C17  107.03  3.000
 6NG  H33  C18  C17  108.32  3.000
 6NG  H34  C18  C19  109.12  3.000
 6NG  H33  C18  C19  109.26  3.000
 6NG  C17  C18  C19  116.19  3.000
 6NG  O15  P13  O14  120.80  3.000
 6NG  O15  P13  N16  107.10  3.000
 6NG  O14  P13  N16  108.06  3.000
 6NG  N16  P13  C12  104.84  3.000
 6NG  O15  P13  C12  108.17  3.000
 6NG  O14  P13  C12  106.80  3.000
 6NG  C5   C6   C7   120.71  3.000
 6NG  C7   C6   C1   120.25  3.000
 6NG  C5   C6   C1   119.04  3.000
 6NG  H35  C5   C4   119.74  3.000
 6NG  H35  C5   C6   119.70  3.000
 6NG  C4   C5   C6   120.56  3.000
 6NG  H36  C4   C5   119.85  3.000
 6NG  H36  C4   C3   120.14  3.000
 6NG  C5   C4   C3   120.02  3.000
 6NG  H38  N11  C12  116.62  3.000
 6NG  H38  N11  C9   117.11  3.000
 6NG  C12  N11  C9   120.96  3.000
 6NG  C9   O8   C7   116.73  3.000
 6NG  H5   C7   H4   108.00  3.000
 6NG  H5   C7   O8   110.20  3.000
 6NG  H4   C7   O8   110.36  3.000
 6NG  H5   C7   C6   110.63  3.000
 6NG  H4   C7   C6   110.74  3.000
 6NG  O8   C7   C6   106.92  3.000
 6NG  H20  N24  C25  118.13  3.000
 6NG  H20  N24  C22  118.66  3.000
 6NG  C25  N24  C22  123.08  3.000
 6NG  H8   C19  C18  108.86  3.000
 6NG  H8   C19  C21  107.48  3.000
 6NG  C18  C19  C21  109.67  3.000
 6NG  H8   C19  C20  108.32  3.000
 6NG  C21  C19  C20  110.12  3.000
 6NG  C18  C19  C20  112.25  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     83.26  30.0  2
 6NG  Var_02    C6   C7   O8   C9   -176.93  30.0  1
 6NG  Var_03    O10  C9   O8   C7      0.53  30.0  3
 6NG  Var_04    P13  C12  N11  C9     87.05  30.0  3
 6NG  Var_05    O8   C9   N11  C12  -163.35  30.0  1
 6NG  Var_06    C17  N16  P13  C12    68.75  30.0  3
 6NG  Var_07    C17  C18  C19  C20    59.03  30.0  2
 6NG  Var_08    C26  C25  N24  C22   169.91  30.0  1
 6NG  Var_09    N11  C12  P13  N16  -165.20  30.0  1
 6NG  Var_10    H12  C21  C19  C20    60.41  30.0  3
 6NG  Var_11    H9   C20  C19  C21   -66.42  30.0  3
 6NG  Var_12    H27  C30  C28  C26    65.93  30.0  3
 6NG  Var_13    H30  C31  C28  C26    57.44  30.0  3
 6NG  Var_14    H24  C29  C28  C26    53.99  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

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  N24  0.020
 6NG  plan-2  H20  0.020
 6NG  plan-2  O23  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

