# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 00:56:36 2020
#   Inital geometry file: a 159 line input string
#   Ligand name: ~{N}-[(2~{S})-1-[[(2~{S})-1-azanyl-4-methyl-1-oxidanylidene-pentan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]-(phenylmethoxycarbonylaminomethyl)phosphonamidic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](NC(=O)[C@H](CC(C)C)N[P](O)(=O)CNC(=O)OCc1ccccc1)C(N)=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
 79E  79E  '~{N}-[(2~{S})-1-[[(2~{S})-1-azanyl-4-methyl-1-oxidanylidene-pentan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]-(phenylmethoxycarbonylaminomethyl)phosphonamidic acid'  ligand  66  32  .  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_79E
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
 79E  O3   O  O      0  -0.523   1.0625   0.6994   2.0989
 79E  C4   C  CH1    0  -0.194  -2.1979   1.3505   0.2909
 79E  C5   C  C      0   0.562  -2.8327  -0.9997   0.3630
 79E  O4   O  O2     0  -0.485   2.9279   0.7825   0.8351
 79E  C6   C  CH1    0  -0.185  -2.9245  -2.2847  -0.4627
 79E  N1   N  NH1    0  -0.808  -1.7382  -3.0827  -0.1989
 79E  C7   C  CH2    0  -0.417  -4.1976  -3.0388  -0.0888
 79E  C8   C  CH1    0  -0.254  -4.4675  -4.3094  -0.8993
 79E  N2   N  NH1    0  -0.656   1.5954  -0.9682   0.6437
 79E  C9   C  CH3    0  -0.647  -5.7748  -4.9374  -0.4251
 79E  C10  C  CH3    0  -0.662  -4.5136  -4.0431  -2.4003
 79E  C11  C  CH2    0  -0.562   0.4122  -1.7688   0.8478
 79E  C12  C  C      0   0.767   1.7954   0.2045   1.2627
 79E  C13  C  CH2    0  -0.243   3.2557   2.0599   1.3890
 79E  C14  C  CR6    0   0.079   4.4248   2.5850   0.6128
 79E  C15  C  CR16   0  -0.297   5.7155   2.4982   1.1227
 79E  C20  C  C      0   0.531  -3.2605   1.7456   1.3141
 79E  P    P  P      0   1.234  -0.2020  -2.5324  -0.7216
 79E  O2   O  O      0  -0.784  -0.3689  -1.4452  -1.7588
 79E  O1   O  OP    -1  -0.800   0.6482  -3.7412  -1.0197
 79E  C19  C  CR16   0  -0.284   4.2324   3.1473  -0.6473
 79E  C18  C  CR16   0  -0.242   5.3108   3.6135  -1.3842
 79E  C17  C  CR16   0  -0.262   6.5980   3.5225  -0.8669
 79E  C16  C  CR16   0  -0.242   6.7984   2.9664   0.3888
 79E  C3   C  CH2    0  -0.430  -2.1140   2.4848  -0.7359
 79E  C1   C  CH1    0  -0.244  -1.1044   2.3081  -1.8745
 79E  C2   C  CH3    0  -0.649  -1.1085   3.5658  -2.7385
 79E  C    C  CH3    0  -0.688   0.2998   1.9910  -1.3740
 79E  H1   H  HCH1   0   0.270  -1.2286   1.2500   0.7952
 79E  H2   H  HCH1   0   0.233  -2.9935  -2.0010  -1.5203
 79E  H3   H  HNH1   0   0.372  -1.8790  -4.0674  -0.3771
 79E  H4   H  HCH2   0   0.231  -4.1669  -3.2859   0.9755
 79E  H5   H  HCH2   0   0.226  -5.0467  -2.3604  -0.2273
 79E  H6   H  HCH1   0   0.217  -3.6696  -5.0371  -0.7071
 79E  H7   H  HNH1   0   0.394   2.2898  -1.2855  -0.0139
 79E  H8   H  HCH3   0   0.214  -6.6147  -4.2594  -0.5964
 79E  H9   H  HCH3   0   0.227  -5.9864  -5.8663  -0.9570
 79E  H10  H  HCH3   0   0.225  -5.7447  -5.1648   0.6419
 79E  H11  H  HCH3   0   0.216  -5.2523  -3.2729  -2.6361
 79E  H12  H  HCH3   0   0.230  -3.5516  -3.7124  -2.7940
 79E  H13  H  HCH3   0   0.230  -4.7917  -4.9464  -2.9456
 79E  H14  H  HCH2   0   0.241   0.5936  -2.5675   1.5752
 79E  H15  H  HCH2   0   0.256  -0.3605  -1.1348   1.2781
 79E  H16  H  HNH2   0   0.400  -3.3830   2.5698   3.1806
 79E  H17  H  HNH2   0   0.399  -1.7856   2.1869   2.6765
 79E  H18  H  HCH2   0   0.244   2.4036   2.7379   1.3061
 79E  H19  H  HCH2   0   0.248   3.5039   1.9608   2.4484
 79E  H20  H  HCR6   0   0.255   5.8794   2.0654   2.1024
 79E  H23  H  HCR6   0   0.253   3.2304   3.2303  -1.0530
 79E  H24  H  HCR6   0   0.258   5.1468   4.0521  -2.3599
 79E  H25  H  HCR6   0   0.258   7.4407   3.8872  -1.4399
 79E  H26  H  HCR6   0   0.258   7.7976   2.8948   0.7982
 79E  H27  H  HCH2   0   0.242  -3.1085   2.6413  -1.1634
 79E  H28  H  HCH2   0   0.234  -1.8603   3.3999  -0.1911
 79E  H29  H  HCH1   0   0.219  -1.4288   1.4771  -2.5111
 79E  H30  H  HCH3   0   0.215  -0.7470   4.4278  -2.1730
 79E  H31  H  HCH3   0   0.228  -0.4602   3.4447  -3.6076
 79E  H32  H  HCH3   0   0.225  -2.1107   3.8020  -3.1007
 79E  H33  H  HCH3   0   0.255   0.3592   0.9830  -0.9671
 79E  H34  H  HCH3   0   0.227   1.0226   2.0498  -2.1903
 79E  H35  H  HCH3   0   0.208   0.6156   2.6988  -0.6030
 79E  N    N  NH1    0  -0.646  -2.5496   0.1065  -0.3487
 79E  O5   O  O      0  -0.493  -4.4520   1.7079   1.0530
 79E  N3   N  NH2    0  -0.801  -2.7657   2.2359   2.4586
 79E  H21  H  HNH1   0   0.410  -2.1525  -0.0594  -1.2632
 79E  O    O  O      0  -0.494  -2.9990  -0.9843   1.5739

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
 79E  C16  C15  aromatic  1.389  0.020  1.389
 79E  C16  C17  aromatic  1.388  0.020  1.388
 79E  C15  C14  aromatic  1.390  0.020  1.390
 79E  C17  C18  aromatic  1.390  0.020  1.390
 79E  C14  C13  single    1.498  0.020  1.498
 79E  C14  C19  aromatic  1.393  0.020  1.393
 79E  C18  C19  aromatic  1.387  0.020  1.387
 79E  C13  O4   single    1.430  0.020  1.430
 79E  O4   C12  single    1.342  0.020  1.342
 79E  C12  O3   double    1.217  0.020  1.217
 79E  C12  N2   single    1.341  0.020  1.341
 79E  N2   C11  single    1.443  0.020  1.443
 79E  C11  P    single    1.850  0.020  1.850
 79E  O2   P    deloc     1.512  0.020  1.512
 79E  O1   P    deloc     1.508  0.020  1.508
 79E  N3   C20  single    1.340  0.020  1.340
 79E  P    N1   single    1.713  0.020  1.713
 79E  O5   C20  double    1.220  0.020  1.220
 79E  C20  C4   single    1.527  0.020  1.527
 79E  N1   C6   single    1.454  0.020  1.454
 79E  C4   N    single    1.442  0.020  1.442
 79E  C4   C3   single    1.532  0.020  1.532
 79E  N    C5   single    1.345  0.020  1.345
 79E  C5   O    double    1.222  0.020  1.222
 79E  C5   C6   single    1.530  0.020  1.530
 79E  C6   C7   single    1.526  0.020  1.526
 79E  C3   C1   single    1.532  0.020  1.532
 79E  C7   C8   single    1.531  0.020  1.531
 79E  C1   C    single    1.524  0.020  1.524
 79E  C1   C2   single    1.526  0.020  1.526
 79E  C10  C8   single    1.525  0.020  1.525
 79E  C8   C9   single    1.526  0.020  1.526
 79E  C4   H1   single    0.970  0.020  1.090
 79E  C6   H2   single    0.970  0.020  1.090
 79E  N1   H3   single    0.890  0.020  1.040
 79E  C7   H4   single    0.970  0.020  1.090
 79E  C7   H5   single    0.970  0.020  1.090
 79E  C8   H6   single    0.970  0.020  1.090
 79E  N2   H7   single    0.860  0.020  1.020
 79E  C9   H8   single    0.970  0.020  1.090
 79E  C9   H9   single    0.970  0.020  1.090
 79E  C9   H10  single    0.970  0.020  1.090
 79E  C10  H11  single    0.970  0.020  1.090
 79E  C10  H12  single    0.970  0.020  1.090
 79E  C10  H13  single    0.970  0.020  1.090
 79E  C11  H14  single    0.970  0.020  1.090
 79E  C11  H15  single    0.970  0.020  1.090
 79E  N3   H16  single    0.860  0.020  1.020
 79E  N3   H17  single    0.860  0.020  1.020
 79E  C13  H18  single    0.970  0.020  1.090
 79E  C13  H19  single    0.970  0.020  1.090
 79E  C15  H20  single    0.930  0.020  1.080
 79E  N    H21  single    0.890  0.020  1.040
 79E  C19  H23  single    0.930  0.020  1.080
 79E  C18  H24  single    0.930  0.020  1.080
 79E  C17  H25  single    0.930  0.020  1.080
 79E  C16  H26  single    0.930  0.020  1.080
 79E  C3   H27  single    0.970  0.020  1.090
 79E  C3   H28  single    0.970  0.020  1.090
 79E  C1   H29  single    0.970  0.020  1.090
 79E  C2   H30  single    0.970  0.020  1.090
 79E  C2   H31  single    0.970  0.020  1.090
 79E  C2   H32  single    0.970  0.020  1.090
 79E  C    H33  single    0.970  0.020  1.090
 79E  C    H34  single    0.970  0.020  1.090
 79E  C    H35  single    0.970  0.020  1.090

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
 79E  H1   C4   C3   109.11  3.000
 79E  H1   C4   N    109.89  3.000
 79E  C3   C4   N    110.77  3.000
 79E  H1   C4   C20  109.30  3.000
 79E  C3   C4   C20  107.19  3.000
 79E  N    C4   C20  110.53  3.000
 79E  O    C5   N    122.84  3.000
 79E  O    C5   C6   122.48  3.000
 79E  N    C5   C6   114.69  3.000
 79E  C13  O4   C12  117.05  3.000
 79E  H2   C6   C7   108.14  3.000
 79E  H2   C6   N1   111.61  3.000
 79E  C7   C6   N1   111.41  3.000
 79E  H2   C6   C5   107.86  3.000
 79E  C7   C6   C5   109.44  3.000
 79E  N1   C6   C5   108.30  3.000
 79E  H3   N1   P    112.58  3.000
 79E  H3   N1   C6   112.91  3.000
 79E  P    N1   C6   119.99  3.000
 79E  H5   C7   H4   106.55  3.000
 79E  H5   C7   C8   108.08  3.000
 79E  H4   C7   C8   109.43  3.000
 79E  H5   C7   C6   108.04  3.000
 79E  H4   C7   C6   109.08  3.000
 79E  C8   C7   C6   115.30  3.000
 79E  H6   C8   C10  108.08  3.000
 79E  H6   C8   C9   107.20  3.000
 79E  C10  C8   C9   110.60  3.000
 79E  H6   C8   C7   109.25  3.000
 79E  C9   C8   C7   109.15  3.000
 79E  C10  C8   C7   112.42  3.000
 79E  H7   N2   C12  118.29  3.000
 79E  H7   N2   C11  118.86  3.000
 79E  C12  N2   C11  122.82  3.000
 79E  H10  C9   H9   107.73  3.000
 79E  H10  C9   H8   107.68  3.000
 79E  H9   C9   H8   107.62  3.000
 79E  H10  C9   C8   111.46  3.000
 79E  H9   C9   C8   111.41  3.000
 79E  H8   C9   C8   110.75  3.000
 79E  H13  C10  H12  107.17  3.000
 79E  H13  C10  H11  107.66  3.000
 79E  H12  C10  H11  107.73  3.000
 79E  H13  C10  C8   110.79  3.000
 79E  H12  C10  C8   112.43  3.000
 79E  H11  C10  C8   110.85  3.000
 79E  H15  C11  H14  106.25  3.000
 79E  H15  C11  P    109.88  3.000
 79E  H14  C11  P    108.50  3.000
 79E  H15  C11  N2   108.36  3.000
 79E  H14  C11  N2   111.27  3.000
 79E  P    C11  N2   112.41  3.000
 79E  N2   C12  O4   110.83  3.000
 79E  N2   C12  O3   125.66  3.000
 79E  O4   C12  O3   123.51  3.000
 79E  H19  C13  H18  107.89  3.000
 79E  H19  C13  C14  110.90  3.000
 79E  H18  C13  C14  110.60  3.000
 79E  H19  C13  O4   110.28  3.000
 79E  H18  C13  O4   110.26  3.000
 79E  C14  C13  O4   106.93  3.000
 79E  C19  C14  C15  119.02  3.000
 79E  C19  C14  C13  120.14  3.000
 79E  C15  C14  C13  120.82  3.000
 79E  H20  C15  C16  119.63  3.000
 79E  H20  C15  C14  119.80  3.000
 79E  C16  C15  C14  120.58  3.000
 79E  N3   C20  O5   123.69  3.000
 79E  O5   C20  C4   121.87  3.000
 79E  N3   C20  C4   114.20  3.000
 79E  O1   P    O2   120.21  3.000
 79E  O1   P    C11  108.14  3.000
 79E  O2   P    C11  108.77  3.000
 79E  O1   P    N1   107.96  3.000
 79E  O2   P    N1   109.96  3.000
 79E  C11  P    N1    99.87  3.000
 79E  H23  C19  C18  119.61  3.000
 79E  H23  C19  C14  119.80  3.000
 79E  C18  C19  C14  120.58  3.000
 79E  H24  C18  C17  120.16  3.000
 79E  H24  C18  C19  119.82  3.000
 79E  C17  C18  C19  120.02  3.000
 79E  H25  C17  C16  120.10  3.000
 79E  H25  C17  C18  120.12  3.000
 79E  C16  C17  C18  119.77  3.000
 79E  H26  C16  C17  120.14  3.000
 79E  H26  C16  C15  119.83  3.000
 79E  C17  C16  C15  120.03  3.000
 79E  H28  C3   H27  106.60  3.000
 79E  H28  C3   C1   108.27  3.000
 79E  H27  C3   C1   108.98  3.000
 79E  H28  C3   C4   107.33  3.000
 79E  H27  C3   C4   108.54  3.000
 79E  C1   C3   C4   116.66  3.000
 79E  H29  C1   C    107.80  3.000
 79E  H29  C1   C2   107.17  3.000
 79E  C    C1   C2   111.09  3.000
 79E  H29  C1   C3   108.91  3.000
 79E  C2   C1   C3   108.91  3.000
 79E  C    C1   C3   112.78  3.000
 79E  H32  C2   H31  107.78  3.000
 79E  H32  C2   H30  107.75  3.000
 79E  H31  C2   H30  107.66  3.000
 79E  H32  C2   C1   111.63  3.000
 79E  H31  C2   C1   110.98  3.000
 79E  H30  C2   C1   110.87  3.000
 79E  H35  C    H34  107.53  3.000
 79E  H35  C    H33  108.67  3.000
 79E  H34  C    H33  107.05  3.000
 79E  H35  C    C1   111.28  3.000
 79E  H34  C    C1   110.68  3.000
 79E  H33  C    C1   111.45  3.000
 79E  H21  N    C5   115.23  3.000
 79E  H21  N    C4   116.55  3.000
 79E  C5   N    C4   121.73  3.000
 79E  H17  N3   H16  117.29  3.000
 79E  H17  N3   C20  121.83  3.000
 79E  H16  N3   C20  120.49  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
 79E  CONST_01  C17  C16  C15  C14     0.00   0.0  0
 79E  CONST_02  C17  C18  C19  C14     0.00   0.0  0
 79E  CONST_03  C18  C17  C16  C15     0.00   0.0  0
 79E  CONST_04  C18  C19  C14  C15     0.00   0.0  0
 79E  CONST_05  C16  C15  C14  C19     0.00   0.0  0
 79E  CONST_06  C16  C17  C18  C19     0.00   0.0  0
 79E  CONST_07  C16  C15  C14  C13   180.00   0.0  0
 79E  CONST_08  C18  C19  C14  C13   180.00   0.0  0
 79E  CONST_09  H26  C16  C15  C14   180.00   0.0  0
 79E  CONST_10  H24  C18  C19  C14   180.00   0.0  0
 79E  CONST_11  H25  C17  C16  C15   180.00   0.0  0
 79E  CONST_12  H23  C19  C14  C15   180.00   0.0  0
 79E  CONST_13  H20  C15  C14  C19   180.00   0.0  0
 79E  CONST_14  O    C5   N    C4      0.00   0.0  0
 79E  CONST_15  C6   C5   N    C4    180.00   0.0  0
 79E  CONST_16  H16  N3   C20  C4    180.00   0.0  0
 79E  CONST_17  H17  N3   C20  C4      0.00   0.0  0
 79E  Var_01    C15  C14  C13  O4   -100.50  30.0  3
 79E  Var_02    C14  C13  O4   C12  -171.41  30.0  1
 79E  Var_03    C11  N2   C12  O3      3.75  30.0  2
 79E  Var_04    C    C1   C3   C4    -52.87  30.0  3
 79E  Var_05    C11  P    N1   C6     97.58  30.0  2
 79E  Var_06    C10  C8   C7   C6    -56.18  30.0  3
 79E  Var_07    N2   C11  P    N1   -168.04  30.0  1
 79E  Var_08    P    C11  N2   C12   140.02  30.0  3
 79E  Var_09    H11  C10  C8   C7    -55.67  30.0  3
 79E  Var_10    H8   C9   C8   C7     62.15  30.0  3
 79E  Var_11    H33  C    C1   C3     71.19  30.0  3
 79E  Var_12    H30  C2   C1   C3     65.03  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
 79E  chir_01  C4  C20  N   C3  negativ
 79E  chir_02  C6  N1   C5  C7  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
 79E  plan-1  C13  0.020
 79E  plan-1  C14  0.020
 79E  plan-1  C15  0.020
 79E  plan-1  C19  0.020
 79E  plan-1  C18  0.020
 79E  plan-1  C17  0.020
 79E  plan-1  C16  0.020
 79E  plan-1  H20  0.020
 79E  plan-1  H23  0.020
 79E  plan-1  H24  0.020
 79E  plan-1  H25  0.020
 79E  plan-1  H26  0.020
 79E  plan-2  C4   0.020
 79E  plan-2  C5   0.020
 79E  plan-2  C6   0.020
 79E  plan-2  N    0.020
 79E  plan-2  H21  0.020
 79E  plan-2  O    0.020
 79E  plan-3  C4   0.020
 79E  plan-3  C20  0.020
 79E  plan-3  H16  0.020
 79E  plan-3  H17  0.020
 79E  plan-3  O5   0.020
 79E  plan-3  N3   0.020
 79E  plan-4  O3   0.020
 79E  plan-4  O4   0.020
 79E  plan-4  N2   0.020
 79E  plan-4  C12  0.020

