# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Aug  1 01:22:45 2021
#   Inital geometry file: a 167 line input string
#   Ligand name: [6-[[(2~{R})-1-azanyl-1-oxidanylidene-propan-2-yl]amino]-6-oxidanylidene-5-[[(4~{R})-5-oxidanyl-5-oxidanylidene-4-[[(2~{S})-2-[[(2~{R})-2-oxidanylpropanoyl]amino]propanoyl]amino]pentanoyl]amino]hexyl]azanium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](O)C(=O)N[C@@H](C)C(=O)N[C@H](CCC(=O)N[C@H](CCCC[NH3+])C(=O)N[C@H](C)C(N)=O)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
 6X4  6X4  '[6-[[(2~{R})-1-azanyl-1-oxidanylidene-propan-2-yl]amino]-6-oxidanylidene-5-[[(4~{R})-5-oxidanyl-5-oxidanylidene-4-[[(2~{S})-2-[[(2~{R})-2-oxidanylpropanoyl]amino]propanoyl]amino]pentanoyl]amino]hexyl]azanium'  ligand  71  34  .  2021-08-05  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_6X4
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
 6X4  C18   C  C     0   0.503  10.2259   -3.4575  72.4345
 6X4  C19   C  CH1   0  -0.076  11.3204   -3.3064  73.4919
 6X4  C2    C  CH3   0  -0.697  11.9012   -4.6806  73.8192
 6X4  O6    O  O     0  -0.492  10.5134   -3.2883  71.2572
 6X4  O7    O  OH1   0  -0.660  12.2967   -2.4178  73.0221
 6X4  N6    N  NH1   0  -0.609   8.9840   -3.8170  72.8072
 6X4  C16   C  CH1   0  -0.248   8.4406   -3.9937  74.1403
 6X4  C15   C  C     0   0.604   8.0485   -5.4649  74.3021
 6X4  O5    O  O     0  -0.482   8.8311   -6.2807  74.7706
 6X4  C17   C  CH3   0  -0.669   7.3132   -3.0068  74.4080
 6X4  N5    N  NH1   0  -0.649   6.8377   -5.8165  73.8490
 6X4  C14   C  CH1   0  -0.156   6.4023   -7.1913  73.8975
 6X4  C20   C  C     0   0.549   6.1683   -7.6539  75.3294
 6X4  O2    O  O     0  -0.418   6.3635   -8.7777  75.7109
 6X4  C11   C  CH2   0  -0.488   5.1428   -7.3806  73.0374
 6X4  C10   C  CH2   0  -0.581   5.0000   -8.7925  72.4798
 6X4  C9    C  C     0   0.571   4.6903   -9.8339  73.5336
 6X4  O4    O  O     0  -0.495   3.7664   -9.6882  74.3182
 6X4  O8    O  OH1   0  -0.586   5.6880   -6.6850  76.0956
 6X4  N4    N  NH1   0  -0.643   5.4828  -10.9251  73.5031
 6X4  C4    C  CH1   0  -0.244   5.3404  -12.0337  74.4127
 6X4  C3    C  C     0   0.576   6.3452  -12.0586  75.5704
 6X4  O3    O  O     0  -0.484   5.9286  -12.2264  76.7062
 6X4  C5    C  CH2   0  -0.458   5.3116  -13.3834  73.6830
 6X4  C6    C  CH2   0  -0.431   4.2129  -13.4762  72.6298
 6X4  C7    C  CH2   0  -0.464   2.8063  -13.3062  73.1935
 6X4  C8    C  CH2   0  -0.299   1.7719  -13.5322  72.1099
 6X4  N2    N  NT3   1  -0.777   0.3936  -13.3506  72.6367
 6X4  N1    N  NH1   0  -0.625   7.6729  -11.9834  75.3327
 6X4  C1    C  CH1   0  -0.240   8.3912  -11.8274  74.0880
 6X4  C13   C  CH3   0  -0.660   9.7157  -12.5820  74.1681
 6X4  C12   C  C     0   0.555   8.6539  -10.3667  73.7079
 6X4  O1    O  O     0  -0.497   8.4608   -9.9837  72.5606
 6X4  N3    N  NH2   0  -0.798   9.1725   -9.5975  74.6699
 6X4  H32   H  HCH1  0   0.253  10.9199   -2.8597  74.4050
 6X4  H4    H  HCH3  0   0.250  12.7251   -4.5730  74.5241
 6X4  H3    H  HCH3  0   0.241  11.1575   -5.3373  74.2682
 6X4  H5    H  HCH3  0   0.234  12.2802   -5.1684  72.9194
 6X4  H14   H  HOH1  0   0.441  12.4391   -2.6098  72.0866
 6X4  H35   H  HNH1  0   0.399   8.3250   -3.9133  72.0448
 6X4  H28   H  HCH1  0   0.294   9.2272   -3.8230  74.8724
 6X4  H30   H  HCH3  0   0.255   6.8490   -3.1985  75.3748
 6X4  H29   H  HCH3  0   0.266   7.7114   -1.9934  74.4166
 6X4  H31   H  HCH3  0   0.235   6.5378   -3.0439  73.6414
 6X4  H34   H  HNH1  0   0.416   6.1769   -5.1118  73.5606
 6X4  H27   H  HCH1  0   0.294   7.1933   -7.8159  73.4802
 6X4  H18   H  HCH2  0   0.276   5.2234   -6.7047  72.1838
 6X4  H17   H  HCH2  0   0.264   4.2445   -7.0846  73.5825
 6X4  H15   H  HCH2  0   0.289   4.1668   -8.7987  71.7725
 6X4  H16   H  HCH2  0   0.261   5.8959   -9.0478  71.9110
 6X4  H21   H  HOH1  0   0.483   5.5238   -7.0224  76.9891
 6X4  H33   H  HNH1  0   0.401   6.1904  -10.9620  72.7877
 6X4  H6    H  HCH1  0   0.289   4.3801  -11.9019  74.9102
 6X4  H7    H  HCH2  0   0.256   5.1730  -14.1686  74.4303
 6X4  H8    H  HCH2  0   0.253   6.2699  -13.5885  73.2003
 6X4  H9    H  HCH2  0   0.237   4.3876  -12.7353  71.8455
 6X4  H10   H  HCH2  0   0.249   4.2904  -14.4544  72.1484
 6X4  H11   H  HCH2  0   0.252   2.6461  -14.0173  74.0093
 6X4  H12   H  HCH2  0   0.249   2.6762  -12.3040  73.6108
 6X4  H13   H  HCH2  0   0.292   1.8223  -14.5420  71.7084
 6X4  H23   H  HCH2  0   0.291   1.8871  -12.8267  71.2898
 6X4  HAO1  H  HNT3  0   0.478  -0.3083  -13.5246  71.9183
 6X4  H19   H  HNT3  0   0.469   0.1933  -13.9872  73.4074
 6X4  H20   H  HNT3  0   0.469   0.2394  -12.4031  72.9799
 6X4  H1    H  HNH1  0   0.398   8.2400  -12.0808  76.1646
 6X4  H2    H  HCH1  0   0.271   7.8198  -12.2635  73.2701
 6X4  H25   H  HCH3  0   0.257  10.2813  -12.4634  73.2449
 6X4  H26   H  HCH3  0   0.242  10.3322  -12.2158  74.9896
 6X4  H24   H  HCH3  0   0.259   9.5324  -13.6448  74.3205
 6X4  H22   H  HNH2  0   0.403   9.2442   -8.6002  74.5265
 6X4  H36   H  HNH2  0   0.401   9.1431   -9.8933  75.6311

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
 6X4  O6   C18   double  1.224  0.020  1.224
 6X4  C10  C11   single  1.525  0.020  1.525
 6X4  C10  C9    single  1.514  0.020  1.514
 6X4  C11  C14   single  1.537  0.020  1.537
 6X4  C2   C19   single  1.527  0.020  1.527
 6X4  C18  N6    single  1.346  0.020  1.346
 6X4  C18  C19   single  1.529  0.020  1.529
 6X4  N6   C16   single  1.450  0.020  1.450
 6X4  N2   C8    single  1.487  0.020  1.487
 6X4  C6   C5    single  1.525  0.020  1.525
 6X4  C6   C7    single  1.525  0.020  1.525
 6X4  C9   N4    single  1.349  0.020  1.349
 6X4  C9   O4    double  1.221  0.020  1.221
 6X4  C8   C7    single  1.515  0.020  1.515
 6X4  C5   C4    single  1.535  0.020  1.535
 6X4  C19  O7    single  1.401  0.020  1.401
 6X4  N4   C4    single  1.441  0.020  1.441
 6X4  C16  C15   single  1.531  0.020  1.531
 6X4  C16  C17   single  1.522  0.020  1.522
 6X4  N5   C14   single  1.443  0.020  1.443
 6X4  N5   C15   single  1.340  0.020  1.340
 6X4  C14  C20   single  1.523  0.020  1.523
 6X4  C15  O5    double  1.224  0.020  1.224
 6X4  C4   C3    single  1.533  0.020  1.533
 6X4  C20  O2    double  1.203  0.020  1.203
 6X4  C20  O8    single  1.325  0.020  1.325
 6X4  C13  C1    single  1.527  0.020  1.527
 6X4  C3   O3    double  1.221  0.020  1.221
 6X4  C3   N1    single  1.351  0.020  1.351
 6X4  C1   N1    single  1.445  0.020  1.445
 6X4  C1   C12   single  1.532  0.020  1.532
 6X4  O1   C12   double  1.225  0.020  1.225
 6X4  C12  N3    single  1.336  0.020  1.336
 6X4  C19  H32   single  0.970  0.020  1.090
 6X4  C2   H4    single  0.970  0.020  1.090
 6X4  C2   H3    single  0.970  0.020  1.090
 6X4  C2   H5    single  0.970  0.020  1.090
 6X4  O7   H14   single  0.850  0.020  0.980
 6X4  N6   H35   single  0.860  0.020  1.020
 6X4  C16  H28   single  0.970  0.020  1.090
 6X4  C17  H30   single  0.970  0.020  1.090
 6X4  C17  H29   single  0.970  0.020  1.090
 6X4  C17  H31   single  0.970  0.020  1.090
 6X4  N5   H34   single  0.860  0.020  1.020
 6X4  C14  H27   single  0.970  0.020  1.090
 6X4  C11  H18   single  0.970  0.020  1.090
 6X4  C11  H17   single  0.970  0.020  1.090
 6X4  C10  H15   single  0.970  0.020  1.090
 6X4  C10  H16   single  0.970  0.020  1.090
 6X4  O8   H21   single  0.850  0.020  0.980
 6X4  N4   H33   single  0.860  0.020  1.020
 6X4  C4   H6    single  0.970  0.020  1.090
 6X4  C5   H7    single  0.970  0.020  1.090
 6X4  C5   H8    single  0.970  0.020  1.090
 6X4  C6   H9    single  0.970  0.020  1.090
 6X4  C6   H10   single  0.970  0.020  1.090
 6X4  C7   H11   single  0.970  0.020  1.090
 6X4  C7   H12   single  0.970  0.020  1.090
 6X4  C8   H13   single  0.970  0.020  1.090
 6X4  C8   H23   single  0.970  0.020  1.090
 6X4  N2   HAO1  single  0.890  0.020  1.040
 6X4  N2   H19   single  0.890  0.020  1.040
 6X4  N2   H20   single  0.890  0.020  1.040
 6X4  N1   H1    single  0.860  0.020  1.020
 6X4  C1   H2    single  0.970  0.020  1.090
 6X4  C13  H25   single  0.970  0.020  1.090
 6X4  C13  H26   single  0.970  0.020  1.090
 6X4  C13  H24   single  0.970  0.020  1.090
 6X4  N3   H22   single  0.890  0.020  1.040
 6X4  N3   H36   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
 6X4  N6    C18  O6    121.35  3.000
 6X4  N6    C18  C19   119.70  3.000
 6X4  O6    C18  C19   118.91  3.000
 6X4  H32   C19  O7    106.04  3.000
 6X4  H32   C19  C2    109.15  3.000
 6X4  O7    C19  C2    112.18  3.000
 6X4  H32   C19  C18   110.84  3.000
 6X4  O7    C19  C18   109.24  3.000
 6X4  C2    C19  C18   109.35  3.000
 6X4  H5    C2   H3    107.91  3.000
 6X4  H5    C2   H4    108.35  3.000
 6X4  H3    C2   H4    108.01  3.000
 6X4  H5    C2   C19   110.95  3.000
 6X4  H3    C2   C19   111.79  3.000
 6X4  H4    C2   C19   109.72  3.000
 6X4  H14   O7   C19   107.54  3.000
 6X4  H35   N6   C16   115.90  3.000
 6X4  H35   N6   C18   114.69  3.000
 6X4  C16   N6   C18   129.26  3.000
 6X4  H28   C16  C17   108.39  3.000
 6X4  H28   C16  C15   105.36  3.000
 6X4  C17   C16  C15   114.51  3.000
 6X4  H28   C16  N6    109.17  3.000
 6X4  C17   C16  N6    111.11  3.000
 6X4  C15   C16  N6    108.06  3.000
 6X4  N5    C15  O5    122.18  3.000
 6X4  O5    C15  C16   121.14  3.000
 6X4  N5    C15  C16   116.61  3.000
 6X4  H31   C17  H29   107.28  3.000
 6X4  H31   C17  H30   108.34  3.000
 6X4  H29   C17  H30   108.21  3.000
 6X4  H31   C17  C16   112.39  3.000
 6X4  H29   C17  C16   109.51  3.000
 6X4  H30   C17  C16   110.95  3.000
 6X4  H34   N5   C14   118.54  3.000
 6X4  H34   N5   C15   120.37  3.000
 6X4  C14   N5   C15   120.76  3.000
 6X4  H27   C14  C11   108.04  3.000
 6X4  H27   C14  C20   107.29  3.000
 6X4  C11   C14  C20   111.27  3.000
 6X4  H27   C14  N5    108.30  3.000
 6X4  C20   C14  N5    111.55  3.000
 6X4  C11   C14  N5    110.24  3.000
 6X4  O8    C20  O2    123.95  3.000
 6X4  O8    C20  C14   112.16  3.000
 6X4  O2    C20  C14   123.86  3.000
 6X4  H17   C11  H18   106.46  3.000
 6X4  H17   C11  C10   110.89  3.000
 6X4  H18   C11  C10   107.11  3.000
 6X4  H17   C11  C14   111.19  3.000
 6X4  H18   C11  C14   107.50  3.000
 6X4  C10   C11  C14   113.30  3.000
 6X4  H16   C10  H15   106.69  3.000
 6X4  H16   C10  C9    111.70  3.000
 6X4  H15   C10  C9    106.90  3.000
 6X4  H16   C10  C11   109.29  3.000
 6X4  H15   C10  C11   108.26  3.000
 6X4  C9    C10  C11   113.68  3.000
 6X4  N4    C9   O4    123.76  3.000
 6X4  O4    C9   C10   121.34  3.000
 6X4  N4    C9   C10   114.88  3.000
 6X4  H21   O8   C20   109.87  3.000
 6X4  H33   N4   C4    119.32  3.000
 6X4  H33   N4   C9    117.29  3.000
 6X4  C4    N4   C9    123.37  3.000
 6X4  H6    C4   C5    107.88  3.000
 6X4  H6    C4   C3    103.58  3.000
 6X4  C5    C4   C3    110.92  3.000
 6X4  H6    C4   N4    106.39  3.000
 6X4  C3    C4   N4    115.11  3.000
 6X4  C5    C4   N4    112.23  3.000
 6X4  N1    C3   O3    120.43  3.000
 6X4  N1    C3   C4    120.69  3.000
 6X4  O3    C3   C4    118.74  3.000
 6X4  H8    C5   H7    106.17  3.000
 6X4  H8    C5   C6    108.39  3.000
 6X4  H7    C5   C6    109.71  3.000
 6X4  H8    C5   C4    111.03  3.000
 6X4  H7    C5   C4    108.01  3.000
 6X4  C6    C5   C4    113.29  3.000
 6X4  H10   C6   H9    106.22  3.000
 6X4  H10   C6   C7    109.15  3.000
 6X4  H9    C6   C7    109.70  3.000
 6X4  H10   C6   C5    107.91  3.000
 6X4  H9    C6   C5    109.83  3.000
 6X4  C7    C6   C5    113.74  3.000
 6X4  H12   C7   H11   107.08  3.000
 6X4  H12   C7   C8    109.18  3.000
 6X4  H11   C7   C8    109.66  3.000
 6X4  H12   C7   C6    110.68  3.000
 6X4  H11   C7   C6    109.77  3.000
 6X4  C8    C7   C6    110.41  3.000
 6X4  H23   C8   H13   108.59  3.000
 6X4  H23   C8   N2    106.62  3.000
 6X4  H13   C8   N2    106.68  3.000
 6X4  H23   C8   C7    111.72  3.000
 6X4  H13   C8   C7    111.77  3.000
 6X4  N2    C8   C7    111.18  3.000
 6X4  H20   N2   H19   107.22  3.000
 6X4  H20   N2   HAO1  106.96  3.000
 6X4  H19   N2   HAO1  106.92  3.000
 6X4  H20   N2   C8    111.90  3.000
 6X4  H19   N2   C8    111.95  3.000
 6X4  HAO1  N2   C8    111.58  3.000
 6X4  H1    N1   C1    116.10  3.000
 6X4  H1    N1   C3    113.64  3.000
 6X4  C1    N1   C3    130.24  3.000
 6X4  H2    C1   C12   106.59  3.000
 6X4  H2    C1   C13   107.26  3.000
 6X4  C12   C1   C13   109.61  3.000
 6X4  H2    C1   N1    110.05  3.000
 6X4  C12   C1   N1    113.68  3.000
 6X4  C13   C1   N1    109.43  3.000
 6X4  H24   C13  H26   108.51  3.000
 6X4  H24   C13  H25   108.20  3.000
 6X4  H26   C13  H25   107.97  3.000
 6X4  H24   C13  C1    110.10  3.000
 6X4  H26   C13  C1    111.35  3.000
 6X4  H25   C13  C1    110.63  3.000
 6X4  N3    C12  O1    123.74  3.000
 6X4  N3    C12  C1    115.90  3.000
 6X4  O1    C12  C1    120.23  3.000
 6X4  H36   N3   H22   115.34  3.000
 6X4  H36   N3   C12   120.47  3.000
 6X4  H22   N3   C12   119.58  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
 6X4  CONST_01  C16   N6   C18  C19     0.00   0.0  0
 6X4  CONST_02  C16   N6   C18  O6    180.00   0.0  0
 6X4  CONST_03  C14   N5   C15  C16   180.00   0.0  0
 6X4  CONST_04  C14   N5   C15  O5      0.00   0.0  0
 6X4  CONST_05  C4    N4   C9   C10   180.00   0.0  0
 6X4  CONST_06  C4    N4   C9   O4      0.00   0.0  0
 6X4  CONST_07  C1    N1   C3   C4      0.00   0.0  0
 6X4  CONST_08  C1    N1   C3   O3    180.00   0.0  0
 6X4  CONST_09  H35   N6   C18  C19   180.00   0.0  0
 6X4  CONST_10  H34   N5   C15  C16     0.00   0.0  0
 6X4  CONST_11  H33   N4   C9   C10     0.00   0.0  0
 6X4  CONST_12  H1    N1   C3   C4    180.00   0.0  0
 6X4  CONST_13  H22   N3   C12  C1    180.00   0.0  0
 6X4  CONST_15  H21   O8   C20  C14   180.00   0.0  0
 6X4  Var_01    C9    C10  C11  C14    69.39  30.0  1
 6X4  Var_02    N4    C9   C10  C11  -129.94  30.0  3
 6X4  Var_03    C7    C6   C5   C4    -60.36  30.0  1
 6X4  Var_04    C8    C7   C6   C5   -175.02  30.0  3
 6X4  Var_05    N2    C8   C7   C6   -179.16  30.0  1
 6X4  Var_06    HAO1  N2   C8   C7   -178.55  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
 6X4  chir_01  C19  C2  C18  O7   positiv
 6X4  chir_02  C16  N6  C15  C17  positiv
 6X4  chir_03  C14  N5  C20  C11  negativ
 6X4  chir_04  C4   N4  C5   C3   negativ
 6X4  chir_05  C1   N1  C13  C12  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
 6X4  plan-1  C18  0.020
 6X4  plan-1  C19  0.020
 6X4  plan-1  O6   0.020
 6X4  plan-1  N6   0.020
 6X4  plan-1  C16  0.020
 6X4  plan-1  H35  0.020
 6X4  plan-2  C14  0.020
 6X4  plan-2  C20  0.020
 6X4  plan-2  O2   0.020
 6X4  plan-2  O8   0.020
 6X4  plan-2  H21  0.020
 6X4  plan-3  C16  0.020
 6X4  plan-3  C15  0.020
 6X4  plan-3  O5   0.020
 6X4  plan-3  N5   0.020
 6X4  plan-3  C14  0.020
 6X4  plan-3  H34  0.020
 6X4  plan-4  C10  0.020
 6X4  plan-4  C9   0.020
 6X4  plan-4  O4   0.020
 6X4  plan-4  N4   0.020
 6X4  plan-4  C4   0.020
 6X4  plan-4  H33  0.020
 6X4  plan-5  C4   0.020
 6X4  plan-5  C3   0.020
 6X4  plan-5  O3   0.020
 6X4  plan-5  N1   0.020
 6X4  plan-5  C1   0.020
 6X4  plan-5  H1   0.020
 6X4  plan-6  C1   0.020
 6X4  plan-6  C12  0.020
 6X4  plan-6  O1   0.020
 6X4  plan-6  N3   0.020
 6X4  plan-6  H22  0.020
 6X4  plan-6  H36  0.020

