# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 16:21:25 2022
#   Inital geometry file: a 149 line input string
#   Ligand name: ~{N}-[(2~{S})-1-[[(2~{S},3~{R},4~{S})-2,6-dimethyl-1,2,3-tris(oxidanyl)heptan-4-yl]amino]-3-oxidanyl-1-oxidanylidene-propan-2-yl]-6-methyl-heptanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)CCCCC(=O)N[C@@H](CO)C(=O)N[C@@H](CC(C)C)[C@@H](O)[C@@](C)(O)CO
#
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
 6VC  6VC  ~{N}-[(2~{S})-1-[[(2~{S},3~{R},4~{S})-2,6-dimethyl-1,2,3-tris(oxidanyl)heptan-4-yl]amino]-3-oxidanyl-1-oxidanylidene-propan-2-yl]-6-methyl-heptanamide  ligand  68  28  .  2022-03-10  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_6VC
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
 6VC  C5   C  CH2   0  -0.586   -3.6045   0.0587  -0.1328
 6VC  C6   C  CH2   0  -0.410   -4.9472  -0.0494   0.5722
 6VC  C8   C  C     0   0.570   -2.4225   0.1200   0.8113
 6VC  O2   O  O     0  -0.500   -2.5269   0.4338   1.9887
 6VC  N2   N  NH1   0  -0.638   -1.2381  -0.1803   0.2459
 6VC  C9   C  CH1   0  -0.239    0.0092  -0.0861   0.9521
 6VC  C10  C  CH2   0  -0.164    0.3892  -1.3905   1.6478
 6VC  O3   O  OH1   0  -0.666    0.7923  -2.3167   0.6601
 6VC  C12  C  C     0   0.555    1.1124   0.3100  -0.0324
 6VC  O4   O  O     0  -0.480    0.9137   0.3342  -1.2368
 6VC  N3   N  NH1   0  -0.636    2.2936   0.5657   0.5470
 6VC  C13  C  CH1   0  -0.139    3.5066   0.9495  -0.1524
 6VC  C21  C  CH1   0   0.064    4.6709   0.0109   0.2120
 6VC  C22  C  CT    0   0.129    4.5614  -1.4683  -0.2600
 6VC  C23  C  CH3   0  -0.662    5.9499  -2.0990  -0.1559
 6VC  O6   O  OH1   0  -0.699    3.7361  -2.1997   0.6318
 6VC  C24  C  CH2   0  -0.181    4.0528  -1.5433  -1.6968
 6VC  O5   O  OH1   0  -0.674    4.9030   0.0359   1.6019
 6VC  C14  C  CH2   0  -0.397    3.8709   2.4037   0.1568
 6VC  C15  C  CH1   0  -0.238    2.8127   3.4399  -0.2246
 6VC  C16  C  CH3   0  -0.649    3.2295   4.8130   0.2953
 6VC  C20  C  CH3   0  -0.666    2.5727   3.4966  -1.7306
 6VC  C1   C  CH2   0  -0.425   -6.1120  -0.0677  -0.4103
 6VC  C2   C  CH2   0  -0.395   -7.4576  -0.2139   0.2901
 6VC  C3   C  CH1   0  -0.231   -8.6767  -0.1352  -0.6307
 6VC  C4   C  CH3   0  -0.659   -8.6807  -1.2467  -1.6759
 6VC  C7   C  CH3   0  -0.651   -9.9618  -0.1730   0.1911
 6VC  O8   O  OH1   0  -0.669    4.1342  -2.8695  -2.1591
 6VC  H1   H  HCH2  0   0.255   -3.4731  -0.7771  -0.8265
 6VC  H2   H  HCH2  0   0.270   -3.5776   0.9625  -0.7526
 6VC  H3   H  HCH2  0   0.220   -4.9717  -0.9597   1.1791
 6VC  H4   H  HCH2  0   0.222   -5.0708   0.7854   1.2656
 6VC  H5   H  HNH1  0   0.399   -1.2039  -0.4217  -0.7321
 6VC  H6   H  HCH1  0   0.297   -0.0789   0.6839   1.7234
 6VC  H7   H  HCH2  0   0.213    1.1896  -1.2024   2.3733
 6VC  H8   H  HCH2  0   0.251   -0.4755  -1.7523   2.2106
 6VC  H9   H  HOH1  0   0.474    0.7901  -3.1993   1.0448
 6VC  H10  H  HNH1  0   0.398    2.3232   0.6202   1.5543
 6VC  H11  H  HCH1  0   0.267    3.3111   0.8571  -1.2202
 6VC  H12  H  HCH1  0   0.230    5.5569   0.4361  -0.2742
 6VC  H13  H  HCH3  0   0.233    6.3369  -2.0159   0.8599
 6VC  H14  H  HCH3  0   0.242    5.9261  -3.1545  -0.4213
 6VC  H15  H  HCH3  0   0.224    6.6528  -1.5967  -0.8215
 6VC  H16  H  HOH1  0   0.453    2.7965  -2.0645   0.4371
 6VC  H17  H  HCH2  0   0.217    3.0184  -1.1826  -1.7530
 6VC  H18  H  HCH2  0   0.204    4.6568  -0.8603  -2.3119
 6VC  H19  H  HOH1  0   0.441    4.4240  -0.7147   1.9784
 6VC  H20  H  HCH2  0   0.230    4.0935   2.4945   1.2247
 6VC  H21  H  HCH2  0   0.222    4.8016   2.6433  -0.3700
 6VC  H22  H  HCH1  0   0.216    1.8702   3.1684   0.2641
 6VC  H23  H  HCH3  0   0.225    2.4783   5.5692   0.0615
 6VC  H24  H  HCH3  0   0.224    3.3696   4.8067   1.3777
 6VC  H25  H  HCH3  0   0.213    4.1705   5.1311  -0.1599
 6VC  H26  H  HCH3  0   0.233    2.1908   2.5557  -2.1263
 6VC  H27  H  HCH3  0   0.226    1.8430   4.2699  -1.9779
 6VC  H28  H  HCH3  0   0.211    3.4985   3.7348  -2.2608
 6VC  H29  H  HCH2  0   0.210   -6.1046   0.8543  -1.0030
 6VC  H30  H  HCH2  0   0.216   -5.9697  -0.8866  -1.1218
 6VC  H31  H  HCH2  0   0.203   -7.4810  -1.1695   0.8291
 6VC  H32  H  HCH2  0   0.213   -7.5440   0.5656   1.0555
 6VC  H33  H  HCH1  0   0.208   -8.6376   0.8261  -1.1582
 6VC  H34  H  HCH3  0   0.224   -9.5732  -1.1919  -2.3017
 6VC  H35  H  HCH3  0   0.228   -7.8151  -1.1937  -2.3366
 6VC  H36  H  HCH3  0   0.211   -8.6736  -2.2295  -1.1971
 6VC  H37  H  HCH3  0   0.222   -9.9996   0.6441   0.9140
 6VC  H38  H  HCH3  0   0.223  -10.8459  -0.0959  -0.4446
 6VC  H39  H  HCH3  0   0.211  -10.0371  -1.1110   0.7474
 6VC  H40  H  HOH1  0   0.457    3.6865  -2.9121  -3.0084

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
 6VC  C16  C15  single  1.526  0.020  1.526
 6VC  C7   C3   single  1.526  0.020  1.526
 6VC  C4   C3   single  1.526  0.020  1.526
 6VC  C15  C20  single  1.526  0.020  1.526
 6VC  C15  C14  single  1.529  0.020  1.529
 6VC  C3   C2   single  1.530  0.020  1.530
 6VC  O2   C8   double  1.223  0.020  1.223
 6VC  C6   C1   single  1.524  0.020  1.524
 6VC  C6   C5   single  1.520  0.020  1.520
 6VC  C14  C13  single  1.531  0.020  1.531
 6VC  C2   C1   single  1.524  0.020  1.524
 6VC  C8   C5   single  1.514  0.020  1.514
 6VC  C8   N2   single  1.346  0.020  1.346
 6VC  N3   C13  single  1.452  0.020  1.452
 6VC  N3   C12  single  1.340  0.020  1.340
 6VC  C13  C21  single  1.539  0.020  1.539
 6VC  N2   C9   single  1.436  0.020  1.436
 6VC  C9   C12  single  1.531  0.020  1.531
 6VC  C9   C10  single  1.526  0.020  1.526
 6VC  C12  O4   double  1.221  0.020  1.221
 6VC  O5   C21  single  1.409  0.020  1.409
 6VC  C21  C22  single  1.557  0.020  1.557
 6VC  O3   C10  single  1.413  0.020  1.413
 6VC  C22  O6   single  1.418  0.020  1.418
 6VC  C22  C24  single  1.526  0.020  1.526
 6VC  C22  C23  single  1.529  0.020  1.529
 6VC  C24  O8   single  1.407  0.020  1.407
 6VC  C5   H1   single  0.970  0.020  1.090
 6VC  C5   H2   single  0.970  0.020  1.090
 6VC  C6   H3   single  0.970  0.020  1.090
 6VC  C6   H4   single  0.970  0.020  1.090
 6VC  N2   H5   single  0.860  0.020  1.020
 6VC  C9   H6   single  0.970  0.020  1.090
 6VC  C10  H7   single  0.970  0.020  1.090
 6VC  C10  H8   single  0.970  0.020  1.090
 6VC  O3   H9   single  0.850  0.020  0.980
 6VC  N3   H10  single  0.860  0.020  1.020
 6VC  C13  H11  single  0.970  0.020  1.090
 6VC  C21  H12  single  0.970  0.020  1.090
 6VC  C23  H13  single  0.970  0.020  1.090
 6VC  C23  H14  single  0.970  0.020  1.090
 6VC  C23  H15  single  0.970  0.020  1.090
 6VC  O6   H16  single  0.850  0.020  0.980
 6VC  C24  H17  single  0.970  0.020  1.090
 6VC  C24  H18  single  0.970  0.020  1.090
 6VC  O5   H19  single  0.850  0.020  0.980
 6VC  C14  H20  single  0.970  0.020  1.090
 6VC  C14  H21  single  0.970  0.020  1.090
 6VC  C15  H22  single  0.970  0.020  1.090
 6VC  C16  H23  single  0.970  0.020  1.090
 6VC  C16  H24  single  0.970  0.020  1.090
 6VC  C16  H25  single  0.970  0.020  1.090
 6VC  C20  H26  single  0.970  0.020  1.090
 6VC  C20  H27  single  0.970  0.020  1.090
 6VC  C20  H28  single  0.970  0.020  1.090
 6VC  C1   H29  single  0.970  0.020  1.090
 6VC  C1   H30  single  0.970  0.020  1.090
 6VC  C2   H31  single  0.970  0.020  1.090
 6VC  C2   H32  single  0.970  0.020  1.090
 6VC  C3   H33  single  0.970  0.020  1.090
 6VC  C4   H34  single  0.970  0.020  1.090
 6VC  C4   H35  single  0.970  0.020  1.090
 6VC  C4   H36  single  0.970  0.020  1.090
 6VC  C7   H37  single  0.970  0.020  1.090
 6VC  C7   H38  single  0.970  0.020  1.090
 6VC  C7   H39  single  0.970  0.020  1.090
 6VC  O8   H40  single  0.850  0.020  0.980

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
 6VC  H2   C5   H1   105.58  3.000
 6VC  H2   C5   C8   107.46  3.000
 6VC  H1   C5   C8   109.43  3.000
 6VC  H2   C5   C6   110.03  3.000
 6VC  H1   C5   C6   110.22  3.000
 6VC  C8   C5   C6   113.77  3.000
 6VC  H4   C6   H3   106.33  3.000
 6VC  H4   C6   C1   109.39  3.000
 6VC  H3   C6   C1   109.30  3.000
 6VC  H4   C6   C5   109.88  3.000
 6VC  H3   C6   C5   109.64  3.000
 6VC  C1   C6   C5   112.14  3.000
 6VC  N2   C8   O2   122.45  3.000
 6VC  N2   C8   C5   114.57  3.000
 6VC  O2   C8   C5   122.97  3.000
 6VC  H5   N2   C9   117.60  3.000
 6VC  H5   N2   C8   119.39  3.000
 6VC  C9   N2   C8   122.88  3.000
 6VC  H6   C9   C12  109.24  3.000
 6VC  H6   C9   C10  107.48  3.000
 6VC  C12  C9   C10  109.57  3.000
 6VC  H6   C9   N2   108.84  3.000
 6VC  C10  C9   N2   112.60  3.000
 6VC  C12  C9   N2   109.06  3.000
 6VC  H8   C10  H7   107.07  3.000
 6VC  H8   C10  O3   111.63  3.000
 6VC  H7   C10  O3   111.52  3.000
 6VC  H8   C10  C9   108.69  3.000
 6VC  H7   C10  C9   109.68  3.000
 6VC  O3   C10  C9   108.21  3.000
 6VC  H9   O3   C10  108.72  3.000
 6VC  N3   C12  O4   124.48  3.000
 6VC  O4   C12  C9   121.48  3.000
 6VC  N3   C12  C9   113.99  3.000
 6VC  H10  N3   C13  116.23  3.000
 6VC  H10  N3   C12  117.88  3.000
 6VC  C13  N3   C12  125.35  3.000
 6VC  H11  C13  C14  108.74  3.000
 6VC  H11  C13  C21  108.42  3.000
 6VC  C14  C13  C21  110.58  3.000
 6VC  H11  C13  N3   107.44  3.000
 6VC  C21  C13  N3   110.90  3.000
 6VC  C14  C13  N3   110.65  3.000
 6VC  H12  C21  O5   107.30  3.000
 6VC  H12  C21  C22  106.91  3.000
 6VC  O5   C21  C22  109.12  3.000
 6VC  H12  C21  C13  105.65  3.000
 6VC  C22  C21  C13  117.03  3.000
 6VC  O5   C21  C13  110.32  3.000
 6VC  C24  C22  O6   111.89  3.000
 6VC  C24  C22  C23  110.28  3.000
 6VC  O6   C22  C23  105.84  3.000
 6VC  C23  C22  C21  107.91  3.000
 6VC  C24  C22  C21  110.83  3.000
 6VC  O6   C22  C21  109.90  3.000
 6VC  H15  C23  H14  108.17  3.000
 6VC  H15  C23  H13  107.75  3.000
 6VC  H14  C23  H13  107.99  3.000
 6VC  H15  C23  C22  110.72  3.000
 6VC  H14  C23  C22  111.32  3.000
 6VC  H13  C23  C22  110.76  3.000
 6VC  H16  O6   C22  111.47  3.000
 6VC  H18  C24  H17  106.56  3.000
 6VC  H18  C24  O8   111.71  3.000
 6VC  H17  C24  O8   110.35  3.000
 6VC  H18  C24  C22  108.24  3.000
 6VC  H17  C24  C22  110.26  3.000
 6VC  O8   C24  C22  109.66  3.000
 6VC  H19  O5   C21  106.78  3.000
 6VC  H21  C14  H20  106.15  3.000
 6VC  H21  C14  C15  108.64  3.000
 6VC  H20  C14  C15  109.14  3.000
 6VC  H21  C14  C13  108.22  3.000
 6VC  H20  C14  C13  108.92  3.000
 6VC  C15  C14  C13  115.38  3.000
 6VC  H22  C15  C20  108.30  3.000
 6VC  H22  C15  C16  107.81  3.000
 6VC  C20  C15  C16  110.23  3.000
 6VC  H22  C15  C14  108.42  3.000
 6VC  C20  C15  C14  112.34  3.000
 6VC  C16  C15  C14  109.61  3.000
 6VC  H25  C16  H24  107.72  3.000
 6VC  H25  C16  H23  107.57  3.000
 6VC  H24  C16  H23  107.75  3.000
 6VC  H25  C16  C15  110.80  3.000
 6VC  H24  C16  C15  111.58  3.000
 6VC  H23  C16  C15  111.25  3.000
 6VC  H28  C20  H27  107.57  3.000
 6VC  H28  C20  H26  107.99  3.000
 6VC  H27  C20  H26  107.17  3.000
 6VC  H28  C20  C15  110.70  3.000
 6VC  H27  C20  C15  110.79  3.000
 6VC  H26  C20  C15  112.42  3.000
 6VC  H30  C1   H29  106.09  3.000
 6VC  H30  C1   C2   109.99  3.000
 6VC  H29  C1   C2   109.58  3.000
 6VC  H30  C1   C6   109.20  3.000
 6VC  H29  C1   C6   109.47  3.000
 6VC  C2   C1   C6   112.31  3.000
 6VC  H32  C2   H31  105.95  3.000
 6VC  H32  C2   C3   108.72  3.000
 6VC  H31  C2   C3   108.87  3.000
 6VC  H32  C2   C1   108.81  3.000
 6VC  H31  C2   C1   109.15  3.000
 6VC  C3   C2   C1   114.96  3.000
 6VC  H33  C3   C7   108.10  3.000
 6VC  H33  C3   C4   107.99  3.000
 6VC  C7   C3   C4   110.41  3.000
 6VC  H33  C3   C2   107.83  3.000
 6VC  C4   C3   C2   112.15  3.000
 6VC  C7   C3   C2   110.23  3.000
 6VC  H36  C4   H35  107.69  3.000
 6VC  H36  C4   H34  107.55  3.000
 6VC  H35  C4   H34  107.42  3.000
 6VC  H36  C4   C3   110.78  3.000
 6VC  H35  C4   C3   112.19  3.000
 6VC  H34  C4   C3   111.00  3.000
 6VC  H39  C7   H38  107.52  3.000
 6VC  H39  C7   H37  107.63  3.000
 6VC  H38  C7   H37  107.74  3.000
 6VC  H39  C7   C3   110.69  3.000
 6VC  H38  C7   C3   111.52  3.000
 6VC  H37  C7   C3   111.55  3.000
 6VC  H40  O8   C24  107.77  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
 6VC  CONST_01  C9   N2   C8   C5    180.00   0.0  0
 6VC  CONST_02  C9   N2   C8   O2      0.00   0.0  0
 6VC  CONST_03  C13  N3   C12  C9    180.00   0.0  0
 6VC  CONST_04  C13  N3   C12  O4      0.00   0.0  0
 6VC  CONST_05  H5   N2   C8   C5      0.00   0.0  0
 6VC  CONST_06  H10  N3   C12  C9      0.00   0.0  0
 6VC  Var_01    C2   C1   C6   C5    178.46  30.0  3
 6VC  Var_02    C3   C2   C1   C6    175.67  30.0  1
 6VC  Var_03    O2   C8   C5   C6    -19.68  30.0  1
 6VC  Var_04    C1   C6   C5   C8    178.34  30.0  1
 6VC  Var_05    C16  C15  C14  C13   172.95  30.0  1
 6VC  Var_06    C7   C3   C2   C1   -175.14  30.0  3
 6VC  Var_07    H23  C16  C15  C14  -178.42  30.0  3
 6VC  Var_08    H26  C20  C15  C14    62.34  30.0  3
 6VC  Var_09    H37  C7   C3   C2     58.23  30.0  3
 6VC  Var_10    H34  C4   C3   C2    178.20  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
 6VC  chir_01  C9   N2   C12  C10  positiv
 6VC  chir_02  C13  N3   C14  C21  negativ
 6VC  chir_03  C21  O5   C13  C22  positiv
 6VC  chir_04  C22  C23  C24  C21  positiv

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
 6VC  plan-1  C5   0.020
 6VC  plan-1  C8   0.020
 6VC  plan-1  O2   0.020
 6VC  plan-1  N2   0.020
 6VC  plan-1  C9   0.020
 6VC  plan-1  H5   0.020
 6VC  plan-2  C9   0.020
 6VC  plan-2  C12  0.020
 6VC  plan-2  O4   0.020
 6VC  plan-2  N3   0.020
 6VC  plan-2  C13  0.020
 6VC  plan-2  H10  0.020

