# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 02:54:45 2020
#   Inital geometry file: a 171 line input string
#   Ligand name: (2~{S})-3-cyclohexyl-2-[[(2~{S})-4-methyl-2-[[oxidanyl(phenylmethoxycarbonylaminomethyl)phosphoryl]amino]pentanoyl]amino]propanoic acid
#   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)N[C@@H](CC2CCCCC2)C(O)=O
#
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
 6XO  6XO  '(2~{S})-3-cyclohexyl-2-[[(2~{S})-4-methyl-2-[[oxidanyl(phenylmethoxycarbonylaminomethyl)phosphoryl]amino]pentanoyl]amino]propanoic acid'  ligand  71  35  .  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_6XO
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
 6XO  C1   C  CR16   0  -0.264   7.4327  -3.5072  -0.2007
 6XO  C2   C  CR16   0  -0.240   7.3654  -2.6691   0.9026
 6XO  C3   C  CR16   0  -0.305   6.1417  -2.1464   1.3051
 6XO  C9   C  C      0   0.762   1.9313  -0.5802   0.1459
 6XO  C11  C  CH2    0  -0.583   0.3329   0.8508  -1.0223
 6XO  C14  C  CH1    0  -0.195  -2.0195   2.7911   0.5276
 6XO  C15  C  C      0   0.564  -2.9996   1.8008  -0.0997
 6XO  C21  C  CH2    0  -0.393  -2.7720   3.9938   1.1018
 6XO  C22  C  CH1    0  -0.264  -3.8149   3.6826   2.1762
 6XO  C24  C  CH3    0  -0.659  -3.1999   2.9924   3.3899
 6XO  C27  C  CH1    0  -0.233  -2.1617  -2.2103  -0.0393
 6XO  C30  C  CH2    0  -0.425  -0.3772  -4.0338  -1.5640
 6XO  C31  C  CH2    0  -0.438  -0.4452  -4.0791  -0.0420
 6XO  C32  C  CH2    0  -0.407  -1.8060  -3.6116   0.4630
 6XO  C33  C  C      0   0.417  -5.4664  -0.1678   0.5865
 6XO  C4   C  CR6    0   0.080   4.9763  -2.4626   0.6168
 6XO  P12  P  P      0   1.226   0.5371   2.6131  -0.5035
 6XO  O20  O  O      0  -0.805   1.0800   2.6094   0.9025
 6XO  O19  O  OP    -1  -0.815   1.2629   3.3412  -1.6087
 6XO  N13  N  NH1    0  -0.774  -1.0504   3.2242  -0.4593
 6XO  C23  C  CH3    0  -0.651  -4.5142   4.9708   2.5995
 6XO  C17  C  CH1    0  -0.207  -4.0274  -0.4142   0.0609
 6XO  C26  C  CH2    0  -0.443  -3.5385  -1.8003   0.4836
 6XO  C29  C  CH2    0  -0.442  -0.7267  -2.6444  -2.0856
 6XO  C28  C  CH2    0  -0.425  -2.0773  -2.1621  -1.5642
 6XO  C5   C  CR16   0  -0.280   5.0527  -3.3068  -0.4899
 6XO  C6   C  CR16   0  -0.242   6.2721  -3.8246  -0.8980
 6XO  O8   O  O2     0  -0.487   3.1919  -1.0350   0.0287
 6XO  O18  O  O      0  -0.515   1.2258  -0.8143   1.1060
 6XO  N10  N  NH1    0  -0.651   1.5747   0.1149  -0.9441
 6XO  H1   H  HCR6   0   0.258   8.3844  -3.9148  -0.5162
 6XO  H2   H  HCR6   0   0.258   8.2644  -2.4193   1.4511
 6XO  H3   H  HCR6   0   0.255   6.0966  -1.4874   2.1640
 6XO  H6   H  HCH2   0   0.260  -0.4055   0.3508  -0.3969
 6XO  H7   H  HCH2   0   0.244  -0.0421   0.7948  -2.0467
 6XO  H8   H  HCH1   0   0.235  -1.4664   2.3058   1.3362
 6XO  H9   H  HCH2   0   0.218  -2.0223   4.6768   1.5152
 6XO  H10  H  HCH2   0   0.215  -3.2530   4.5262   0.2747
 6XO  H11  H  HCH1   0   0.242  -4.5659   3.0061   1.7565
 6XO  H12  H  HCH3   0   0.212  -2.3715   3.5785   3.7955
 6XO  H13  H  HCH3   0   0.225  -3.9385   2.8688   4.1843
 6XO  H14  H  HCH3   0   0.219  -2.8194   1.9983   3.1536
 6XO  H15  H  HCH1   0   0.223  -1.4075  -1.5227   0.3619
 6XO  H16  H  HCH2   0   0.219   0.6173  -4.3284  -1.9100
 6XO  H17  H  HCH2   0   0.203  -1.0787  -4.7664  -1.9792
 6XO  H18  H  HCH2   0   0.219  -0.2385  -5.0910   0.3166
 6XO  H19  H  HCH2   0   0.214   0.3353  -3.4352   0.3773
 6XO  H20  H  HCH2   0   0.218  -1.8260  -3.6273   1.5570
 6XO  H21  H  HCH2   0   0.199  -2.5783  -4.3172   0.1308
 6XO  H23  H  HNH1   0   0.354  -1.4694   3.4500  -1.3512
 6XO  H24  H  HCH3   0   0.222  -4.9671   5.4808   1.7473
 6XO  H25  H  HCH3   0   0.223  -5.3048   4.7717   3.3252
 6XO  H26  H  HCH3   0   0.210  -3.8090   5.6650   3.0643
 6XO  H28  H  HCH1   0   0.237  -4.0771  -0.3788  -1.0294
 6XO  H30  H  HCH2   0   0.225  -4.2796  -2.5265   0.1408
 6XO  H31  H  HCH2   0   0.220  -3.5341  -1.8616   1.5792
 6XO  H32  H  HCH2   0   0.226   0.0501  -1.9377  -1.7763
 6XO  H33  H  HCH2   0   0.219  -0.7283  -2.6399  -3.1789
 6XO  H34  H  HCH2   0   0.201  -2.8783  -2.7840  -1.9843
 6XO  H35  H  HCH2   0   0.225  -2.2560  -1.1443  -1.9217
 6XO  H36  H  HCR6   0   0.247   4.1521  -3.5666  -1.0343
 6XO  H37  H  HCR6   0   0.258   6.3183  -4.4805  -1.7577
 6XO  H38  H  HNH1   0   0.393   2.2802   0.3083  -1.6367
 6XO  C7   C  CH2    0  -0.236   3.6515  -1.9142   1.0551
 6XO  O25  O  O      0  -0.518  -3.6288   2.1047  -1.1084
 6XO  O35  O  OC    -1  -0.618  -6.3335  -0.9249   0.1045
 6XO  H4   H  HCH2   0   0.244   2.9341  -2.7256   1.2034
 6XO  H5   H  HCH2   0   0.245   3.7491  -1.3797   2.0028
 6XO  N16  N  NH1    0  -0.620  -3.0848   0.5973   0.4797
 6XO  O34  O  O      0  -0.580  -5.6384   0.7256   1.4326
 6XO  H27  H  HNH1   0   0.384  -2.6251   0.4670   1.3670

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
 6XO  C6   C5   aromatic  1.386  0.020  1.386
 6XO  C6   C1   aromatic  1.391  0.020  1.391
 6XO  C5   C4   aromatic  1.394  0.020  1.394
 6XO  C1   C2   aromatic  1.387  0.020  1.387
 6XO  C4   C7   single    1.499  0.020  1.499
 6XO  C4   C3   aromatic  1.390  0.020  1.390
 6XO  C2   C3   aromatic  1.390  0.020  1.390
 6XO  C7   O8   single    1.427  0.020  1.427
 6XO  O8   C9   single    1.345  0.020  1.345
 6XO  C9   O18  double    1.214  0.020  1.214
 6XO  C9   N10  single    1.341  0.020  1.341
 6XO  N10  C11  single    1.446  0.020  1.446
 6XO  C11  P12  single    1.848  0.020  1.848
 6XO  O20  P12  deloc     1.507  0.020  1.507
 6XO  O19  P12  deloc     1.510  0.020  1.510
 6XO  P12  N13  single    1.702  0.020  1.702
 6XO  O34  C33  deloc     1.242  0.020  1.242
 6XO  O35  C33  deloc     1.248  0.020  1.248
 6XO  C33  C17  single    1.552  0.020  1.552
 6XO  N13  C14  single    1.449  0.020  1.449
 6XO  C17  N16  single    1.445  0.020  1.445
 6XO  C17  C26  single    1.529  0.020  1.529
 6XO  N16  C15  single    1.338  0.020  1.338
 6XO  C15  O25  double    1.227  0.020  1.227
 6XO  C15  C14  single    1.528  0.020  1.528
 6XO  C14  C21  single    1.530  0.020  1.530
 6XO  C28  C29  single    1.526  0.020  1.526
 6XO  C28  C27  single    1.528  0.020  1.528
 6XO  C29  C30  single    1.525  0.020  1.525
 6XO  C26  C27  single    1.529  0.020  1.529
 6XO  C27  C32  single    1.530  0.020  1.530
 6XO  C21  C22  single    1.529  0.020  1.529
 6XO  C30  C31  single    1.524  0.020  1.524
 6XO  C23  C22  single    1.526  0.020  1.526
 6XO  C22  C24  single    1.526  0.020  1.526
 6XO  C32  C31  single    1.525  0.020  1.525
 6XO  C1   H1   single    0.930  0.020  1.080
 6XO  C2   H2   single    0.930  0.020  1.080
 6XO  C3   H3   single    0.930  0.020  1.080
 6XO  C7   H4   single    0.970  0.020  1.090
 6XO  C7   H5   single    0.970  0.020  1.090
 6XO  C11  H6   single    0.970  0.020  1.090
 6XO  C11  H7   single    0.970  0.020  1.090
 6XO  C14  H8   single    0.970  0.020  1.090
 6XO  C21  H9   single    0.970  0.020  1.090
 6XO  C21  H10  single    0.970  0.020  1.090
 6XO  C22  H11  single    0.970  0.020  1.090
 6XO  C24  H12  single    0.970  0.020  1.090
 6XO  C24  H13  single    0.970  0.020  1.090
 6XO  C24  H14  single    0.970  0.020  1.090
 6XO  C27  H15  single    0.970  0.020  1.090
 6XO  C30  H16  single    0.970  0.020  1.090
 6XO  C30  H17  single    0.970  0.020  1.090
 6XO  C31  H18  single    0.970  0.020  1.090
 6XO  C31  H19  single    0.970  0.020  1.090
 6XO  C32  H20  single    0.970  0.020  1.090
 6XO  C32  H21  single    0.970  0.020  1.090
 6XO  N13  H23  single    0.890  0.020  1.040
 6XO  C23  H24  single    0.970  0.020  1.090
 6XO  C23  H25  single    0.970  0.020  1.090
 6XO  C23  H26  single    0.970  0.020  1.090
 6XO  N16  H27  single    0.860  0.020  1.020
 6XO  C17  H28  single    0.970  0.020  1.090
 6XO  C26  H30  single    0.970  0.020  1.090
 6XO  C26  H31  single    0.970  0.020  1.090
 6XO  C29  H32  single    0.970  0.020  1.090
 6XO  C29  H33  single    0.970  0.020  1.090
 6XO  C28  H34  single    0.970  0.020  1.090
 6XO  C28  H35  single    0.970  0.020  1.090
 6XO  C5   H36  single    0.930  0.020  1.080
 6XO  C6   H37  single    0.930  0.020  1.080
 6XO  N10  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
 6XO  H1   C1   C6   120.11  3.000
 6XO  H1   C1   C2   120.14  3.000
 6XO  C6   C1   C2   119.75  3.000
 6XO  H2   C2   C3   119.84  3.000
 6XO  H2   C2   C1   120.14  3.000
 6XO  C3   C2   C1   120.01  3.000
 6XO  H3   C3   C4   119.74  3.000
 6XO  H3   C3   C2   119.66  3.000
 6XO  C4   C3   C2   120.60  3.000
 6XO  N10  C9   O18  126.02  3.000
 6XO  N10  C9   O8   110.71  3.000
 6XO  O18  C9   O8   123.24  3.000
 6XO  H7   C11  H6   106.39  3.000
 6XO  H7   C11  N10  108.63  3.000
 6XO  H6   C11  N10  108.52  3.000
 6XO  H7   C11  P12  110.49  3.000
 6XO  H6   C11  P12  110.57  3.000
 6XO  N10  C11  P12  112.05  3.000
 6XO  H8   C14  N13  107.33  3.000
 6XO  H8   C14  C21  108.67  3.000
 6XO  N13  C14  C21  110.45  3.000
 6XO  H8   C14  C15  109.91  3.000
 6XO  C21  C14  C15  110.37  3.000
 6XO  N13  C14  C15  110.06  3.000
 6XO  N16  C15  O25  123.09  3.000
 6XO  O25  C15  C14  120.39  3.000
 6XO  N16  C15  C14  116.48  3.000
 6XO  H10  C21  H9   106.42  3.000
 6XO  H10  C21  C22  109.27  3.000
 6XO  H9   C21  C22  109.18  3.000
 6XO  H10  C21  C14  108.34  3.000
 6XO  H9   C21  C14  107.17  3.000
 6XO  C22  C21  C14  116.04  3.000
 6XO  H11  C22  C23  108.28  3.000
 6XO  H11  C22  C24  107.58  3.000
 6XO  C23  C22  C24  110.24  3.000
 6XO  H11  C22  C21  108.93  3.000
 6XO  C24  C22  C21  112.09  3.000
 6XO  C23  C22  C21  109.61  3.000
 6XO  H14  C24  H13  106.90  3.000
 6XO  H14  C24  H12  107.75  3.000
 6XO  H13  C24  H12  107.67  3.000
 6XO  H14  C24  C22  112.38  3.000
 6XO  H13  C24  C22  110.94  3.000
 6XO  H12  C24  C22  110.99  3.000
 6XO  H15  C27  C28  107.90  3.000
 6XO  H15  C27  C26  109.03  3.000
 6XO  C28  C27  C26  112.50  3.000
 6XO  H15  C27  C32  107.11  3.000
 6XO  C26  C27  C32  110.04  3.000
 6XO  C28  C27  C32  110.09  3.000
 6XO  H17  C30  H16  106.39  3.000
 6XO  H17  C30  C29  109.44  3.000
 6XO  H16  C30  C29  110.23  3.000
 6XO  H17  C30  C31  109.26  3.000
 6XO  H16  C30  C31  110.40  3.000
 6XO  C29  C30  C31  111.01  3.000
 6XO  H19  C31  H18  106.49  3.000
 6XO  H19  C31  C32  109.20  3.000
 6XO  H18  C31  C32  110.11  3.000
 6XO  H19  C31  C30  109.45  3.000
 6XO  H18  C31  C30  110.28  3.000
 6XO  C32  C31  C30  111.18  3.000
 6XO  H21  C32  H20  106.29  3.000
 6XO  H21  C32  C31  109.30  3.000
 6XO  H20  C32  C31  110.06  3.000
 6XO  H21  C32  C27  109.01  3.000
 6XO  H20  C32  C27  109.69  3.000
 6XO  C31  C32  C27  112.30  3.000
 6XO  O34  C33  O35  127.10  3.000
 6XO  O35  C33  C17  114.65  3.000
 6XO  O34  C33  C17  118.24  3.000
 6XO  C5   C4   C7   120.13  3.000
 6XO  C7   C4   C3   120.86  3.000
 6XO  C5   C4   C3   119.01  3.000
 6XO  N13  P12  O19  107.12  3.000
 6XO  N13  P12  O20  108.22  3.000
 6XO  O19  P12  O20  120.73  3.000
 6XO  N13  P12  C11  104.28  3.000
 6XO  O19  P12  C11  107.91  3.000
 6XO  O20  P12  C11  107.41  3.000
 6XO  H23  N13  P12  116.36  3.000
 6XO  H23  N13  C14  112.97  3.000
 6XO  P12  N13  C14  122.29  3.000
 6XO  H26  C23  H25  107.49  3.000
 6XO  H26  C23  H24  107.63  3.000
 6XO  H25  C23  H24  107.69  3.000
 6XO  H26  C23  C22  111.00  3.000
 6XO  H25  C23  C22  111.25  3.000
 6XO  H24  C23  C22  111.59  3.000
 6XO  H28  C17  C26  108.66  3.000
 6XO  H28  C17  N16  107.24  3.000
 6XO  C26  C17  N16  110.23  3.000
 6XO  H28  C17  C33  106.90  3.000
 6XO  C26  C17  C33  110.29  3.000
 6XO  N16  C17  C33  113.31  3.000
 6XO  H31  C26  H30  106.19  3.000
 6XO  H31  C26  C17  109.14  3.000
 6XO  H30  C26  C17  107.38  3.000
 6XO  H31  C26  C27  108.84  3.000
 6XO  H30  C26  C27  108.99  3.000
 6XO  C17  C26  C27  115.88  3.000
 6XO  H33  C29  H32  106.31  3.000
 6XO  H33  C29  C28  109.83  3.000
 6XO  H32  C29  C28  109.12  3.000
 6XO  H33  C29  C30  110.25  3.000
 6XO  H32  C29  C30  109.20  3.000
 6XO  C28  C29  C30  111.96  3.000
 6XO  H35  C28  H34  106.44  3.000
 6XO  H35  C28  C29  109.10  3.000
 6XO  H34  C28  C29  109.64  3.000
 6XO  H35  C28  C27  110.28  3.000
 6XO  H34  C28  C27  108.89  3.000
 6XO  C29  C28  C27  112.33  3.000
 6XO  H36  C5   C6   119.57  3.000
 6XO  H36  C5   C4   119.89  3.000
 6XO  C6   C5   C4   120.54  3.000
 6XO  H37  C6   C5   119.86  3.000
 6XO  H37  C6   C1   120.06  3.000
 6XO  C5   C6   C1   120.08  3.000
 6XO  C9   O8   C7   116.57  3.000
 6XO  H38  N10  C11  117.82  3.000
 6XO  H38  N10  C9   118.17  3.000
 6XO  C11  N10  C9   122.43  3.000
 6XO  H5   C7   H4   107.70  3.000
 6XO  H5   C7   O8   110.56  3.000
 6XO  H4   C7   O8   110.09  3.000
 6XO  H5   C7   C4   110.70  3.000
 6XO  H4   C7   C4   110.37  3.000
 6XO  O8   C7   C4   107.43  3.000
 6XO  H27  N16  C17  117.54  3.000
 6XO  H27  N16  C15  117.93  3.000
 6XO  C17  N16  C15  123.06  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
 6XO  CONST_01  C4   C5   C6   C1      0.00   0.0  0
 6XO  CONST_02  C4   C3   C2   C1      0.00   0.0  0
 6XO  CONST_03  C5   C6   C1   C2      0.00   0.0  0
 6XO  CONST_04  C5   C4   C3   C2      0.00   0.0  0
 6XO  CONST_05  C6   C5   C4   C3      0.00   0.0  0
 6XO  CONST_06  C6   C1   C2   C3      0.00   0.0  0
 6XO  CONST_07  C7   C4   C3   C2    180.00   0.0  0
 6XO  CONST_08  C6   C5   C4   C7    180.00   0.0  0
 6XO  CONST_09  H36  C5   C6   C1    180.00   0.0  0
 6XO  CONST_10  H3   C3   C2   C1    180.00   0.0  0
 6XO  CONST_11  H37  C6   C1   C2    180.00   0.0  0
 6XO  CONST_12  H1   C1   C2   C3    180.00   0.0  0
 6XO  CONST_13  H2   C2   C3   C4    180.00   0.0  0
 6XO  CONST_14  C17  N16  C15  C14   180.00   0.0  0
 6XO  CONST_15  C17  N16  C15  O25     0.00   0.0  0
 6XO  CONST_16  H27  N16  C15  C14     0.00   0.0  0
 6XO  Var_01    C30  C29  C28  C27    54.39  30.0  1
 6XO  Var_02    C30  C31  C32  C27   -56.06  30.0  1
 6XO  Var_03    C28  C29  C30  C31   -54.29  30.0  1
 6XO  Var_04    C29  C30  C31  C32    54.92  30.0  1
 6XO  Var_05    O8   C7   C4   C3    113.93  30.0  2
 6XO  Var_06    C4   C7   O8   C9    171.14  30.0  1
 6XO  Var_07    O18  C9   O8   C7      4.80  30.0  3
 6XO  Var_08    P12  C11  N10  C9     92.59  30.0  3
 6XO  Var_09    O8   C9   N10  C11  -172.48  30.0  1
 6XO  Var_10    C14  N13  P12  C11    68.57  30.0  3
 6XO  Var_11    C23  C22  C21  C14  -177.56  30.0  3
 6XO  Var_12    N10  C11  P12  O20   -57.63  30.0  2
 6XO  Var_13    H24  C23  C22  C21    56.44  30.0  3
 6XO  Var_14    H12  C24  C22  C21    54.69  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
 6XO  chir_01  C14  N13  C15  C21  positiv
 6XO  chir_02  C27  C28  C26  C32  negativ
 6XO  chir_04  C17  C33  N16  C26  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
 6XO  plan-1  C1   0.020
 6XO  plan-1  C2   0.020
 6XO  plan-1  C3   0.020
 6XO  plan-1  C4   0.020
 6XO  plan-1  C5   0.020
 6XO  plan-1  C6   0.020
 6XO  plan-1  H1   0.020
 6XO  plan-1  H2   0.020
 6XO  plan-1  H3   0.020
 6XO  plan-1  H36  0.020
 6XO  plan-1  H37  0.020
 6XO  plan-1  C7   0.020
 6XO  plan-2  C14  0.020
 6XO  plan-2  C15  0.020
 6XO  plan-2  C17  0.020
 6XO  plan-2  O25  0.020
 6XO  plan-2  N16  0.020
 6XO  plan-2  H27  0.020
 6XO  plan-3  C33  0.020
 6XO  plan-3  C17  0.020
 6XO  plan-3  O35  0.020
 6XO  plan-3  O34  0.020
 6XO  plan-4  C9   0.020
 6XO  plan-4  O8   0.020
 6XO  plan-4  O18  0.020
 6XO  plan-4  N10  0.020

