# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Mon Jun  8 21:01:06 2020
#   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  70  34  .  2021-08-05  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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   0.507   7.3687   0.4648  -0.8883
 6X4  C19   C  CH1    0  -0.058   8.7472   0.3283  -0.2425
 6X4  C2    C  CH3    0  -0.684   9.0156  -1.1390   0.0864
 6X4  O6    O  O      0  -0.501   7.2675   0.6410  -2.0967
 6X4  O7    O  OH1    0  -0.666   9.7226   0.8608  -1.0953
 6X4  N6    N  NH1    0  -0.635   6.3279   0.3430  -0.0623
 6X4  C16   C  CH1    0  -0.199   4.9524   0.3438  -0.5000
 6X4  C15   C  C      0   0.555   4.0787   0.6577   0.7133
 6X4  O5    O  O      0  -0.501   4.4729   0.4331   1.8505
 6X4  C17   C  CH3    0  -0.651   4.5346  -1.0032  -1.0941
 6X4  N5    N  NH1    0  -0.618   2.8556   1.1001   0.4178
 6X4  C14   C  CH1    0  -0.205   1.9014   1.5146   1.4199
 6X4  C20   C  C      0   0.419   2.1889   2.9399   1.9682
 6X4  O2    O  O      0  -0.590   3.1118   3.5833   1.4449
 6X4  C11   C  CH2    0  -0.459   0.4871   1.4234   0.8520
 6X4  C10   C  CH2    0  -0.564   0.0980   0.0021   0.4557
 6X4  C9    C  C      0   0.565  -1.2960  -0.0557  -0.1225
 6X4  O4    O  O      0  -0.501  -1.6541   0.6682  -1.0420
 6X4  O8    O  OC    -1  -0.613   1.4397   3.2997   2.8974
 6X4  N4    N  NH1    0  -0.640  -2.1198  -0.9690   0.4206
 6X4  C4    C  CH1    0  -0.192  -3.4913  -1.0850   0.0053
 6X4  C3    C  C      0   0.563  -4.2688   0.1922   0.3295
 6X4  O3    O  O      0  -0.490  -4.0269   0.8650   1.3181
 6X4  C5    C  CH2    0  -0.462  -4.1579  -2.2696   0.7064
 6X4  C6    C  CH2    0  -0.429  -3.6052  -3.6166   0.2576
 6X4  C7    C  CH2    0  -0.453  -4.3076  -4.7728   0.9580
 6X4  C8    C  CH2    0  -0.303  -3.7794  -6.1047   0.4666
 6X4  N2    N  NT3    1  -0.777  -4.4619  -7.2351   1.1494
 6X4  N1    N  NH1    0  -0.643  -5.2639   0.4543  -0.5287
 6X4  C1    C  CH1    0  -0.189  -6.2219   1.5135  -0.3380
 6X4  C13   C  CH3    0  -0.654  -7.2999   1.1364   0.6826
 6X4  C12   C  C      0   0.518  -6.8709   1.8176  -1.6854
 6X4  O1    O  O      0  -0.484  -6.8585   1.0069  -2.6003
 6X4  N3    N  NH2    0  -0.797  -7.4728   3.0080  -1.7561
 6X4  H32   H  HCH1   0   0.250   8.7634   0.9089   0.6856
 6X4  H4    H  HCH3   0   0.234   8.9296  -1.7644  -0.8038
 6X4  H3    H  HCH3   0   0.248  10.0227  -1.2514   0.4875
 6X4  H5    H  HCH3   0   0.230   8.3186  -1.5174   0.8342
 6X4  H14   H  HOH1   0   0.441   9.4028   0.7472  -2.0003
 6X4  H35   H  HNH1   0   0.401   6.4829   0.1962   0.9252
 6X4  H28   H  HCH1   0   0.275   4.8218   1.1254  -1.2527
 6X4  H30   H  HCH3   0   0.250   5.1702  -1.2599  -1.9400
 6X4  H29   H  HCH3   0   0.236   4.6157  -1.7946  -0.3488
 6X4  H31   H  HCH3   0   0.239   3.5048  -0.9698  -1.4492
 6X4  H34   H  HNH1   0   0.394   2.6847   1.4018  -0.5292
 6X4  H27   H  HCH1   0   0.245   1.9754   0.8171   2.2592
 6X4  H18   H  HCH2   0   0.251  -0.2000   1.7938   1.6133
 6X4  H17   H  HCH2   0   0.236   0.3901   2.0895  -0.0099
 6X4  H15   H  HCH2   0   0.266   0.7806  -0.3791  -0.3095
 6X4  H16   H  HCH2   0   0.250   0.1949  -0.6629   1.3170
 6X4  H33   H  HNH1   0   0.403  -1.8254  -1.4588   1.2503
 6X4  H6    H  HCH1   0   0.270  -3.5267  -1.2588  -1.0756
 6X4  H7    H  HCH2   0   0.248  -4.0530  -2.1558   1.7899
 6X4  H8    H  HCH2   0   0.258  -5.2295  -2.2364   0.4949
 6X4  H9    H  HCH2   0   0.238  -3.7303  -3.7109  -0.8252
 6X4  H10   H  HCH2   0   0.239  -2.5309  -3.6744   0.4521
 6X4  H11   H  HCH2   0   0.251  -4.1609  -4.6932   2.0390
 6X4  H12   H  HCH2   0   0.250  -5.3847  -4.7142   0.7763
 6X4  H13   H  HCH2   0   0.292  -3.9484  -6.2351  -0.6001
 6X4  H23   H  HCH2   0   0.292  -2.7155  -6.2156   0.6652
 6X4  HAO1  H  HNT3   0   0.478  -4.1169  -8.1365   0.8223
 6X4  H19   H  HNT3   0   0.469  -4.3196  -7.2108   2.1585
 6X4  H20   H  HNT3   0   0.469  -5.4683  -7.2252   0.9864
 6X4  H1    H  HNH1   0   0.398  -5.3964  -0.1422  -1.3325
 6X4  H2    H  HCH1   0   0.279  -5.6978   2.4063   0.0121
 6X4  H25   H  HCH3   0   0.252  -6.8427   0.9310   1.6491
 6X4  H26   H  HCH3   0   0.241  -8.0181   1.9449   0.8190
 6X4  H24   H  HCH3   0   0.236  -7.8400   0.2462   0.3596
 6X4  H22   H  HNH2   0   0.414  -7.4596   3.6585  -0.9893
 6X4  H36   H  HNH2   0   0.407  -7.9970   3.2678  -2.5759

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  1.225  0.020  1.225
 6X4  C10  C11   single  1.526  0.020  1.526
 6X4  C10  C9    single  1.510  0.020  1.510
 6X4  C11  C14   single  1.527  0.020  1.527
 6X4  C2   C19   single  1.527  0.020  1.527
 6X4  C18  N6    single  1.334  0.020  1.334
 6X4  C18  C19   single  1.528  0.020  1.528
 6X4  N6   C16   single  1.443  0.020  1.443
 6X4  N2   C8    single  1.487  0.020  1.487
 6X4  C6   C5    single  1.524  0.020  1.524
 6X4  C6   C7    single  1.523  0.020  1.523
 6X4  C9   N4    single  1.344  0.020  1.344
 6X4  C9   O4    double  1.224  0.020  1.224
 6X4  C8   C7    single  1.515  0.020  1.515
 6X4  C5   C4    single  1.529  0.020  1.529
 6X4  C19  O7    single  1.401  0.020  1.401
 6X4  N4   C4    single  1.438  0.020  1.438
 6X4  C16  C15   single  1.528  0.020  1.528
 6X4  C16  C17   single  1.530  0.020  1.530
 6X4  N5   C14   single  1.444  0.020  1.444
 6X4  N5   C15   single  1.334  0.020  1.334
 6X4  C14  C20   single  1.554  0.020  1.554
 6X4  C15  O5    double  1.224  0.020  1.224
 6X4  C4   C3    single  1.530  0.020  1.530
 6X4  C20  O2    deloc   1.241  0.020  1.241
 6X4  C20  O8    deloc   1.247  0.020  1.247
 6X4  C13  C1    single  1.532  0.020  1.532
 6X4  C3   O3    double  1.220  0.020  1.220
 6X4  C3   N1    single  1.340  0.020  1.340
 6X4  C1   N1    single  1.441  0.020  1.441
 6X4  C1   C12   single  1.526  0.020  1.526
 6X4  O1   C12   double  1.223  0.020  1.223
 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  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  0.860  0.020  1.020
 6X4  N3   H36   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
 6X4  N6    C18  O6    124.00  3.000
 6X4  N6    C18  C19   115.71  3.000
 6X4  O6    C18  C19   120.27  3.000
 6X4  H32   C19  O7    107.71  3.000
 6X4  H32   C19  C2    108.93  3.000
 6X4  O7    C19  C2    111.96  3.000
 6X4  H32   C19  C18   108.91  3.000
 6X4  O7    C19  C18   109.68  3.000
 6X4  C2    C19  C18   109.59  3.000
 6X4  H5    C2   H3    107.61  3.000
 6X4  H5    C2   H4    108.08  3.000
 6X4  H3    C2   H4    108.30  3.000
 6X4  H5    C2   C19   111.64  3.000
 6X4  H3    C2   C19   109.92  3.000
 6X4  H4    C2   C19   111.17  3.000
 6X4  H14   O7   C19   107.16  3.000
 6X4  H35   N6   C16   116.27  3.000
 6X4  H35   N6   C18   119.91  3.000
 6X4  C16   N6   C18   123.75  3.000
 6X4  H28   C16  C17   109.23  3.000
 6X4  H28   C16  C15   109.37  3.000
 6X4  C17   C16  C15   109.46  3.000
 6X4  H28   C16  N6    108.85  3.000
 6X4  C17   C16  N6    112.17  3.000
 6X4  C15   C16  N6    107.71  3.000
 6X4  N5    C15  O5    124.18  3.000
 6X4  O5    C15  C16   121.05  3.000
 6X4  N5    C15  C16   114.62  3.000
 6X4  H31   C17  H29   108.38  3.000
 6X4  H31   C17  H30   107.80  3.000
 6X4  H29   C17  H30   108.46  3.000
 6X4  H31   C17  C16   110.95  3.000
 6X4  H29   C17  C16   110.68  3.000
 6X4  H30   C17  C16   110.47  3.000
 6X4  H34   N5   C14   116.98  3.000
 6X4  H34   N5   C15   117.56  3.000
 6X4  C14   N5   C15   123.18  3.000
 6X4  H27   C14  C11   108.06  3.000
 6X4  H27   C14  C20   107.55  3.000
 6X4  C11   C14  C20   110.94  3.000
 6X4  H27   C14  N5    107.74  3.000
 6X4  C20   C14  N5    112.69  3.000
 6X4  C11   C14  N5    109.68  3.000
 6X4  O8    C20  O2    127.71  3.000
 6X4  O8    C20  C14   114.62  3.000
 6X4  O2    C20  C14   117.68  3.000
 6X4  H17   C11  H18   106.70  3.000
 6X4  H17   C11  C10   109.88  3.000
 6X4  H18   C11  C10   109.70  3.000
 6X4  H17   C11  C14   109.81  3.000
 6X4  H18   C11  C14   107.68  3.000
 6X4  C10   C11  C14   112.86  3.000
 6X4  H16   C10  H15   106.50  3.000
 6X4  H16   C10  C9    111.13  3.000
 6X4  H15   C10  C9    107.15  3.000
 6X4  H16   C10  C11   109.85  3.000
 6X4  H15   C10  C11   110.31  3.000
 6X4  C9    C10  C11   111.74  3.000
 6X4  N4    C9   O4    121.73  3.000
 6X4  O4    C9   C10   122.35  3.000
 6X4  N4    C9   C10   115.91  3.000
 6X4  H33   N4   C4    118.52  3.000
 6X4  H33   N4   C9    118.94  3.000
 6X4  C4    N4   C9    121.51  3.000
 6X4  H6    C4   C5    108.39  3.000
 6X4  H6    C4   C3    108.97  3.000
 6X4  C5    C4   C3    109.15  3.000
 6X4  H6    C4   N4    109.19  3.000
 6X4  C3    C4   N4    110.86  3.000
 6X4  C5    C4   N4    110.24  3.000
 6X4  N1    C3   O3    123.95  3.000
 6X4  N1    C3   C4    113.89  3.000
 6X4  O3    C3   C4    122.09  3.000
 6X4  H8    C5   H7    106.40  3.000
 6X4  H8    C5   C6    109.00  3.000
 6X4  H7    C5   C6    110.41  3.000
 6X4  H8    C5   C4    108.37  3.000
 6X4  H7    C5   C4    109.36  3.000
 6X4  C6    C5   C4    113.06  3.000
 6X4  H10   C6   H9    106.49  3.000
 6X4  H10   C6   C7    109.34  3.000
 6X4  H9    C6   C7    109.69  3.000
 6X4  H10   C6   C5    110.54  3.000
 6X4  H9    C6   C5    109.04  3.000
 6X4  C7    C6   C5    111.61  3.000
 6X4  H12   C7   H11   107.00  3.000
 6X4  H12   C7   C8    109.67  3.000
 6X4  H11   C7   C8    109.74  3.000
 6X4  H12   C7   C6    109.69  3.000
 6X4  H11   C7   C6    109.71  3.000
 6X4  C8    C7   C6    110.94  3.000
 6X4  H23   C8   H13   108.58  3.000
 6X4  H23   C8   N2    106.71  3.000
 6X4  H13   C8   N2    106.73  3.000
 6X4  H23   C8   C7    111.81  3.000
 6X4  H13   C8   C7    111.68  3.000
 6X4  N2    C8   C7    111.07  3.000
 6X4  H20   N2   H19   107.21  3.000
 6X4  H20   N2   HAO1  106.95  3.000
 6X4  H19   N2   HAO1  106.95  3.000
 6X4  H20   N2   C8    111.86  3.000
 6X4  H19   N2   C8    111.86  3.000
 6X4  HAO1  N2   C8    111.70  3.000
 6X4  H1    N1   C1    116.90  3.000
 6X4  H1    N1   C3    119.46  3.000
 6X4  C1    N1   C3    123.55  3.000
 6X4  H2    C1   C12   108.90  3.000
 6X4  H2    C1   C13   108.98  3.000
 6X4  C12   C1   C13   109.76  3.000
 6X4  H2    C1   N1    108.91  3.000
 6X4  C12   C1   N1    108.20  3.000
 6X4  C13   C1   N1    112.03  3.000
 6X4  H24   C13  H26   108.44  3.000
 6X4  H24   C13  H25   108.48  3.000
 6X4  H26   C13  H25   107.79  3.000
 6X4  H24   C13  C1    110.63  3.000
 6X4  H26   C13  C1    111.38  3.000
 6X4  H25   C13  C1    110.02  3.000
 6X4  N3    C12  O1    123.78  3.000
 6X4  N3    C12  C1    114.57  3.000
 6X4  O1    C12  C1    121.62  3.000
 6X4  H36   N3   H22   117.43  3.000
 6X4  H36   N3   C12   120.50  3.000
 6X4  H22   N3   C12   122.02  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   180.00   0.0  0
 6X4  CONST_02  C16   N6   C18  O6      0.00   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    180.00   0.0  0
 6X4  CONST_08  C1    N1   C3   O3      0.00   0.0  0
 6X4  CONST_09  H35   N6   C18  C19     0.00   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      0.00   0.0  0
 6X4  CONST_13  H22   N3   C12  C1      0.00   0.0  0
 6X4  CONST_14  H36   N3   C12  C1    180.00   0.0  0
 6X4  Var_01    C9    C10  C11  C14  -179.10  30.0  1
 6X4  Var_02    N4    C9   C10  C11  -128.68  30.0  3
 6X4  Var_03    C7    C6   C5   C4   -179.03  30.0  1
 6X4  Var_04    C8    C7   C6   C5    178.08  30.0  3
 6X4  Var_05    N2    C8   C7   C6    179.94  30.0  2
 6X4  Var_06    HAO1  N2   C8   C7    179.71  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-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

