# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 22:51:13 2020
#   Inital geometry file: a 160 line input string
#   Ligand name: N~2~-[(R)-({[(benzyloxy)carbonyl]amino}methyl)(hydroxy)phosphoryl]-N-[(2S)-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
 6MG  6MG  N~2~-[(R)-({[(benzyloxy)carbonyl]amino}methyl)(hydroxy)phosphoryl]-N-[(2S)-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_6MG
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
 6MG  C2   C  CH1   0  -0.202  -1.9338  -1.2559   0.1810
 6MG  C3   C  C     0   0.561  -3.1330  -0.6048   0.8618
 6MG  C7   C  CT    0  -0.076  -7.1314   2.1508  -0.2283
 6MG  C8   C  CH3   0  -0.651  -8.1740   2.1867  -1.3501
 6MG  C12  C  CH3   0  -0.645  -6.5596   3.5653  -0.0831
 6MG  C16  C  CH3   0  -0.658  -7.8330   1.7611   1.0764
 6MG  C20  C  CH3   0  -0.683  -6.4989  -0.1981  -1.0883
 6MG  O28  O  O     0  -0.498  -3.4324  -0.9116   2.0086
 6MG  C30  C  CH1   0  -0.263  -3.4192  -3.0231  -0.9920
 6MG  C31  C  CH3   0  -0.662  -3.2240  -2.4593  -2.3962
 6MG  C35  C  CH3   0  -0.646  -3.6685  -4.5266  -1.0540
 6MG  N1   N  NH1   0  -0.783  -0.7821  -1.0582   1.0503
 6MG  N4   N  NH1   0  -0.637  -3.8182   0.2703   0.1190
 6MG  C5   C  CH2   0  -0.256  -5.0142   0.9585   0.5621
 6MG  C6   C  CH1   0  -0.234  -5.9962   1.1573  -0.5959
 6MG  C29  C  CH2   0  -0.406  -2.2216  -2.7369  -0.0848
 6MG  P44  P  P     0   1.310   0.7642  -1.0121   0.4553
 6MG  O45  O  O     0  -0.714   0.8753  -0.3206  -0.8554
 6MG  C46  C  CH2   0  -0.566   1.7266  -0.2732   1.8180
 6MG  C50  C  CH2   0  -0.240   5.5986   1.6928  -0.1991
 6MG  C51  C  CR6   0   0.075   6.9667   1.1762  -0.5244
 6MG  C52  C  CR16  0  -0.293   8.0424   1.4368   0.3183
 6MG  C54  C  CR16  0  -0.242   9.3040   0.9332   0.0289
 6MG  C56  C  CR16  0  -0.261   9.4986   0.1595  -1.1075
 6MG  C58  C  CR16  0  -0.242   8.4295  -0.1055  -1.9546
 6MG  C60  C  CR16  0  -0.286   7.1710   0.4004  -1.6628
 6MG  O68  O  OH1   0  -0.751   1.3799  -2.5021   0.2858
 6MG  N47  N  NH1   0  -0.656   3.1185  -0.1976   1.4671
 6MG  C48  C  C     0   0.763   3.6317   0.8610   0.8067
 6MG  O49  O  O2    0  -0.478   4.9055   0.6346   0.4749
 6MG  O64  O  O     0  -0.513   3.0346   1.8886   0.5659
 6MG  H1   H  HCH1  0   0.265  -1.7139  -0.7479  -0.7598
 6MG  H2   H  HCH3  0   0.229  -8.7407   1.2573  -1.4148
 6MG  H3   H  HCH3  0   0.227  -8.8902   2.9912  -1.1720
 6MG  H4   H  HCH3  0   0.222  -7.7111   2.3660  -2.3236
 6MG  H5   H  HCH3  0   0.223  -6.0783   3.8923  -1.0075
 6MG  H6   H  HCH3  0   0.226  -7.3583   4.2756   0.1417
 6MG  H7   H  HCH3  0   0.225  -5.8262   3.6460   0.7206
 6MG  H8   H  HCH3  0   0.227  -7.1690   1.8238   1.9405
 6MG  H9   H  HCH3  0   0.229  -8.6706   2.4352   1.2667
 6MG  H10  H  HCH3  0   0.226  -8.2351   0.7467   1.0391
 6MG  H11  H  HCH3  0   0.240  -7.0581  -0.1120  -2.0187
 6MG  H12  H  HCH3  0   0.243  -5.6657  -0.8745  -1.2851
 6MG  H13  H  HCH3  0   0.220  -7.1436  -0.6854  -0.3540
 6MG  H14  H  HCH1  0   0.228  -4.3117  -2.5594  -0.5555
 6MG  H15  H  HCH3  0   0.224  -2.3449  -2.9013  -2.8720
 6MG  H16  H  HCH3  0   0.233  -4.0883  -2.6754  -3.0260
 6MG  H17  H  HCH3  0   0.221  -3.0876  -1.3766  -2.4031
 6MG  H18  H  HCH3  0   0.216  -2.8023  -5.0494  -1.4670
 6MG  H19  H  HCH3  0   0.227  -3.8638  -4.9395  -0.0629
 6MG  H20  H  HCH3  0   0.228  -4.5264  -4.7586  -1.6871
 6MG  H21  H  HNH1  0   0.398  -0.9143  -1.4062   1.9921
 6MG  H22  H  HNH1  0   0.400  -3.4509   0.5202  -0.7857
 6MG  H23  H  HCH2  0   0.243  -5.4733   0.3583   1.3475
 6MG  H24  H  HCH2  0   0.248  -4.7338   1.9150   1.0098
 6MG  H25  H  HCH1  0   0.225  -5.4408   1.6230  -1.4216
 6MG  H26  H  HCH2  0   0.233  -1.3253  -3.1796  -0.5313
 6MG  H27  H  HCH2  0   0.232  -2.3660  -3.2338   0.8795
 6MG  H28  H  HCH2  0   0.296   1.3324   0.7202   2.0287
 6MG  H29  H  HCH2  0   0.304   1.6141  -0.8629   2.7297
 6MG  H30  H  HCH2  0   0.249   5.6565   2.5726   0.4450
 6MG  H31  H  HCH2  0   0.249   5.0629   1.9721  -1.1085
 6MG  H32  H  HCR6  0   0.255   7.8954   2.0429   1.2044
 6MG  H33  H  HCR6  0   0.258  10.1343   1.1464   0.6896
 6MG  H34  H  HCR6  0   0.259  10.4815  -0.2325  -1.3353
 6MG  H35  H  HCR6  0   0.258   8.5775  -0.7042  -2.8440
 6MG  H36  H  HCR6  0   0.255   6.3416   0.1949  -2.3296
 6MG  H37  H  HOH1  0   0.483   1.2806  -3.0829   1.0506
 6MG  H38  H  HNH1  0   0.410   3.6864  -1.0213   1.5850

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
 6MG  C54  C52  aromatic  1.389  0.020  1.389
 6MG  C54  C56  aromatic  1.388  0.020  1.388
 6MG  C52  C51  aromatic  1.391  0.020  1.391
 6MG  C56  C58  aromatic  1.390  0.020  1.390
 6MG  C51  C50  single    1.498  0.020  1.498
 6MG  C51  C60  aromatic  1.393  0.020  1.393
 6MG  C58  C60  aromatic  1.387  0.020  1.387
 6MG  C50  O49  single    1.433  0.020  1.433
 6MG  O49  C48  single    1.336  0.020  1.336
 6MG  C48  O64  double    1.213  0.020  1.213
 6MG  C48  N47  single    1.349  0.020  1.349
 6MG  N47  C46  single    1.437  0.020  1.437
 6MG  C46  P44  single    1.825  0.020  1.825
 6MG  O45  P44  double    1.486  0.020  1.486
 6MG  O68  P44  single    1.621  0.020  1.621
 6MG  P44  N1   single    1.657  0.020  1.657
 6MG  C16  C7   single    1.532  0.020  1.532
 6MG  C5   N4   single    1.449  0.020  1.449
 6MG  C5   C6   single    1.531  0.020  1.531
 6MG  N1   C2   single    1.456  0.020  1.456
 6MG  C8   C7   single    1.532  0.020  1.532
 6MG  N4   C3   single    1.337  0.020  1.337
 6MG  O28  C3   double    1.224  0.020  1.224
 6MG  C3   C2   single    1.525  0.020  1.525
 6MG  C7   C6   single    1.553  0.020  1.553
 6MG  C7   C12  single    1.533  0.020  1.533
 6MG  C2   C29  single    1.532  0.020  1.532
 6MG  C6   C20  single    1.527  0.020  1.527
 6MG  C29  C30  single    1.529  0.020  1.529
 6MG  C31  C30  single    1.526  0.020  1.526
 6MG  C30  C35  single    1.525  0.020  1.525
 6MG  C2   H1   single    0.970  0.020  1.090
 6MG  C8   H2   single    0.970  0.020  1.090
 6MG  C8   H3   single    0.970  0.020  1.090
 6MG  C8   H4   single    0.970  0.020  1.090
 6MG  C12  H5   single    0.970  0.020  1.090
 6MG  C12  H6   single    0.970  0.020  1.090
 6MG  C12  H7   single    0.970  0.020  1.090
 6MG  C16  H8   single    0.970  0.020  1.090
 6MG  C16  H9   single    0.970  0.020  1.090
 6MG  C16  H10  single    0.970  0.020  1.090
 6MG  C20  H11  single    0.970  0.020  1.090
 6MG  C20  H12  single    0.970  0.020  1.090
 6MG  C20  H13  single    0.970  0.020  1.090
 6MG  C30  H14  single    0.970  0.020  1.090
 6MG  C31  H15  single    0.970  0.020  1.090
 6MG  C31  H16  single    0.970  0.020  1.090
 6MG  C31  H17  single    0.970  0.020  1.090
 6MG  C35  H18  single    0.970  0.020  1.090
 6MG  C35  H19  single    0.970  0.020  1.090
 6MG  C35  H20  single    0.970  0.020  1.090
 6MG  N1   H21  single    0.890  0.020  1.040
 6MG  N4   H22  single    0.860  0.020  1.020
 6MG  C5   H23  single    0.970  0.020  1.090
 6MG  C5   H24  single    0.970  0.020  1.090
 6MG  C6   H25  single    0.970  0.020  1.090
 6MG  C29  H26  single    0.970  0.020  1.090
 6MG  C29  H27  single    0.970  0.020  1.090
 6MG  C46  H28  single    0.970  0.020  1.090
 6MG  C46  H29  single    0.970  0.020  1.090
 6MG  C50  H30  single    0.970  0.020  1.090
 6MG  C50  H31  single    0.970  0.020  1.090
 6MG  C52  H32  single    0.930  0.020  1.080
 6MG  C54  H33  single    0.930  0.020  1.080
 6MG  C56  H34  single    0.930  0.020  1.080
 6MG  C58  H35  single    0.930  0.020  1.080
 6MG  C60  H36  single    0.930  0.020  1.080
 6MG  O68  H37  single    0.850  0.020  0.980
 6MG  N47  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
 6MG  H1   C2   C29  109.77  3.000
 6MG  H1   C2   N1   106.97  3.000
 6MG  C29  C2   N1   112.54  3.000
 6MG  H1   C2   C3   110.15  3.000
 6MG  C29  C2   C3   110.03  3.000
 6MG  N1   C2   C3   107.30  3.000
 6MG  N4   C3   O28  124.00  3.000
 6MG  O28  C3   C2   120.23  3.000
 6MG  N4   C3   C2   115.75  3.000
 6MG  C6   C7   C16  111.94  3.000
 6MG  C6   C7   C12  109.89  3.000
 6MG  C16  C7   C12  108.96  3.000
 6MG  C12  C7   C8   107.56  3.000
 6MG  C6   C7   C8   109.83  3.000
 6MG  C16  C7   C8   108.54  3.000
 6MG  H4   C8   H3   107.60  3.000
 6MG  H4   C8   H2   107.89  3.000
 6MG  H3   C8   H2   107.26  3.000
 6MG  H4   C8   C7   111.59  3.000
 6MG  H3   C8   C7   110.14  3.000
 6MG  H2   C8   C7   112.16  3.000
 6MG  H7   C12  H6   106.97  3.000
 6MG  H7   C12  H5   107.77  3.000
 6MG  H6   C12  H5   107.55  3.000
 6MG  H7   C12  C7   112.89  3.000
 6MG  H6   C12  C7   110.30  3.000
 6MG  H5   C12  C7   111.13  3.000
 6MG  H10  C16  H9   107.28  3.000
 6MG  H10  C16  H8   107.72  3.000
 6MG  H9   C16  H8   107.05  3.000
 6MG  H10  C16  C7   112.08  3.000
 6MG  H9   C16  C7   110.05  3.000
 6MG  H8   C16  C7   112.40  3.000
 6MG  H13  C20  H12  107.19  3.000
 6MG  H13  C20  H11  107.86  3.000
 6MG  H12  C20  H11  106.68  3.000
 6MG  H13  C20  C6   111.94  3.000
 6MG  H12  C20  C6   110.92  3.000
 6MG  H11  C20  C6   111.99  3.000
 6MG  H14  C30  C29  108.79  3.000
 6MG  H14  C30  C35  107.46  3.000
 6MG  C29  C30  C35  109.67  3.000
 6MG  H14  C30  C31  108.31  3.000
 6MG  C35  C30  C31  110.35  3.000
 6MG  C29  C30  C31  112.12  3.000
 6MG  H17  C31  H16  106.97  3.000
 6MG  H17  C31  H15  107.34  3.000
 6MG  H16  C31  H15  107.81  3.000
 6MG  H17  C31  C30  112.85  3.000
 6MG  H16  C31  C30  110.90  3.000
 6MG  H15  C31  C30  110.74  3.000
 6MG  H20  C35  H19  107.80  3.000
 6MG  H20  C35  H18  107.58  3.000
 6MG  H19  C35  H18  107.70  3.000
 6MG  H20  C35  C30  111.21  3.000
 6MG  H19  C35  C30  111.43  3.000
 6MG  H18  C35  C30  110.94  3.000
 6MG  H21  N1   P44  117.72  3.000
 6MG  H21  N1   C2   113.90  3.000
 6MG  P44  N1   C2   121.82  3.000
 6MG  H22  N4   C5   117.22  3.000
 6MG  H22  N4   C3   118.31  3.000
 6MG  C5   N4   C3   124.33  3.000
 6MG  H24  C5   H23  107.15  3.000
 6MG  H24  C5   C6   111.15  3.000
 6MG  H23  C5   C6   110.26  3.000
 6MG  H24  C5   N4   109.21  3.000
 6MG  H23  C5   N4   107.84  3.000
 6MG  C6   C5   N4   111.08  3.000
 6MG  H25  C6   C5   107.41  3.000
 6MG  H25  C6   C20  107.47  3.000
 6MG  C5   C6   C20  109.86  3.000
 6MG  H25  C6   C7   106.04  3.000
 6MG  C20  C6   C7   113.80  3.000
 6MG  C5   C6   C7   111.90  3.000
 6MG  H27  C29  H26  106.48  3.000
 6MG  H27  C29  C30  109.53  3.000
 6MG  H26  C29  C30  108.87  3.000
 6MG  H27  C29  C2   108.11  3.000
 6MG  H26  C29  C2   107.93  3.000
 6MG  C30  C29  C2   115.53  3.000
 6MG  O68  P44  C46  104.48  3.000
 6MG  O68  P44  O45  107.88  3.000
 6MG  C46  P44  O45  115.52  3.000
 6MG  O68  P44  N1   111.49  3.000
 6MG  O45  P44  N1   113.53  3.000
 6MG  C46  P44  N1   103.60  3.000
 6MG  H29  C46  H28  107.09  3.000
 6MG  H29  C46  N47  109.40  3.000
 6MG  H28  C46  N47  110.47  3.000
 6MG  H29  C46  P44  110.53  3.000
 6MG  H28  C46  P44  108.84  3.000
 6MG  N47  C46  P44  110.47  3.000
 6MG  H31  C50  H30  108.13  3.000
 6MG  H31  C50  O49  110.08  3.000
 6MG  H30  C50  O49  110.07  3.000
 6MG  H31  C50  C51  110.82  3.000
 6MG  H30  C50  C51  110.95  3.000
 6MG  O49  C50  C51  106.81  3.000
 6MG  C60  C51  C52  119.09  3.000
 6MG  C60  C51  C50  120.23  3.000
 6MG  C52  C51  C50  120.66  3.000
 6MG  H32  C52  C54  119.76  3.000
 6MG  H32  C52  C51  119.69  3.000
 6MG  C54  C52  C51  120.54  3.000
 6MG  H33  C54  C56  120.12  3.000
 6MG  H33  C54  C52  119.89  3.000
 6MG  C56  C54  C52  120.00  3.000
 6MG  H34  C56  C58  120.08  3.000
 6MG  H34  C56  C54  120.09  3.000
 6MG  C58  C56  C54  119.82  3.000
 6MG  H35  C58  C60  119.90  3.000
 6MG  H35  C58  C56  120.09  3.000
 6MG  C60  C58  C56  120.01  3.000
 6MG  H36  C60  C58  119.71  3.000
 6MG  H36  C60  C51  119.75  3.000
 6MG  C58  C60  C51  120.53  3.000
 6MG  H37  O68  P44  115.54  3.000
 6MG  H38  N47  C48  118.98  3.000
 6MG  H38  N47  C46  118.31  3.000
 6MG  C48  N47  C46  121.94  3.000
 6MG  O64  C48  O49  124.33  3.000
 6MG  O64  C48  N47  125.09  3.000
 6MG  O49  C48  N47  110.57  3.000
 6MG  C48  O49  C50  116.93  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
 6MG  CONST_01  C56  C54  C52  C51     0.00   0.0  0
 6MG  CONST_02  C56  C58  C60  C51     0.00   0.0  0
 6MG  CONST_03  C58  C56  C54  C52     0.00   0.0  0
 6MG  CONST_04  C58  C60  C51  C52     0.00   0.0  0
 6MG  CONST_05  C60  C51  C52  C54     0.00   0.0  0
 6MG  CONST_06  C60  C58  C56  C54     0.00   0.0  0
 6MG  CONST_07  C54  C52  C51  C50   180.00   0.0  0
 6MG  CONST_08  C58  C60  C51  C50   180.00   0.0  0
 6MG  CONST_09  H33  C54  C52  C51   180.00   0.0  0
 6MG  CONST_10  H35  C58  C60  C51   180.00   0.0  0
 6MG  CONST_11  H34  C56  C54  C52   180.00   0.0  0
 6MG  CONST_12  H36  C60  C51  C52   180.00   0.0  0
 6MG  CONST_13  H32  C52  C54  C56   180.00   0.0  0
 6MG  CONST_14  C5   N4   C3   C2    180.00   0.0  0
 6MG  CONST_15  C5   N4   C3   O28     0.00   0.0  0
 6MG  CONST_16  H22  N4   C3   C2      0.00   0.0  0
 6MG  Var_01    O49  C50  C51  C52   -95.57  30.0  2
 6MG  Var_02    C46  P44  N1   C2    163.98  30.0  1
 6MG  Var_03    C31  C30  C29  C2     62.67  30.0  3
 6MG  Var_04    C6   C5   N4   C3   -144.98  30.0  1
 6MG  Var_05    N47  C46  P44  N1    178.39  30.0  1
 6MG  Var_06    C48  N47  C46  P44    87.68  30.0  2
 6MG  Var_07    O49  C48  N47  C46  -173.48  30.0  1
 6MG  Var_08    H8   C16  C7   C8   -173.65  30.0  3
 6MG  Var_09    H5   C12  C7   C8    -60.66  30.0  3
 6MG  Var_10    H2   C8   C7   C12  -171.09  30.0  3
 6MG  Var_11    H18  C35  C30  C31    63.06  30.0  3
 6MG  Var_12    H15  C31  C30  C35   -62.27  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
 6MG  chir_01  C2   N1   C3   C29  positiv
 6MG  chir_02  C6   C5   C7   C20  positiv
 6MG  chir_03  P44  O45  O68  N1   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
 6MG  plan-1  C50  0.020
 6MG  plan-1  C51  0.020
 6MG  plan-1  C52  0.020
 6MG  plan-1  C54  0.020
 6MG  plan-1  C56  0.020
 6MG  plan-1  C58  0.020
 6MG  plan-1  C60  0.020
 6MG  plan-1  H32  0.020
 6MG  plan-1  H33  0.020
 6MG  plan-1  H34  0.020
 6MG  plan-1  H35  0.020
 6MG  plan-1  H36  0.020
 6MG  plan-2  C2   0.020
 6MG  plan-2  C3   0.020
 6MG  plan-2  O28  0.020
 6MG  plan-2  N4   0.020
 6MG  plan-2  C5   0.020
 6MG  plan-2  H22  0.020
 6MG  plan-3  N47  0.020
 6MG  plan-3  C48  0.020
 6MG  plan-3  O49  0.020
 6MG  plan-3  O64  0.020

