# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 15:04:46 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  67  32  .  2021-08-06  2021-08-06  
;
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  -0.509   2.7332   0.7339   1.7362
 79E  C4   C  CH1   0  -0.202  -4.4034   1.6833   0.4616
 79E  C5   C  C     0   0.594  -2.9562  -0.2606   0.4916
 79E  O4   O  O2    0  -0.479   4.5018  -0.0656   0.5894
 79E  C6   C  CH1   0  -0.247  -2.4402  -1.4448  -0.3190
 79E  N1   N  NH1   0  -0.777  -1.1949  -1.9445   0.2234
 79E  C7   C  CH2   0  -0.405  -3.5086  -2.5421  -0.3292
 79E  C8   C  CH1   0  -0.227  -3.1092  -3.8070  -1.0902
 79E  N2   N  NH1   0  -0.656   2.7270  -1.3513   0.8269
 79E  C9   C  CH3   0  -0.652  -4.2479  -4.8205  -1.0349
 79E  C10  C  CH3   0  -0.667  -2.7194  -3.5132  -2.5351
 79E  C11  C  CH2   0  -0.579   1.3689  -1.6756   1.1637
 79E  C12  C  C     0   0.762   3.2699  -0.1463   1.0992
 79E  C13  C  CH2   0  -0.237   5.2218   1.1518   0.8180
 79E  C14  C  CR6   0   0.075   6.5428   1.0124   0.1243
 79E  C15  C  CR16  0  -0.298   7.6959   0.7222   0.8454
 79E  C20  C  C     0   0.523  -5.5628   1.0695   1.2527
 79E  O    O  O     0  -0.491  -2.7757  -0.1821   1.6970
 79E  P    P  P     0   1.316   0.2450  -1.2356  -0.2059
 79E  O2   O  O     0  -0.707   0.2018   0.2040  -0.5720
 79E  O1   O  OH1   0  -0.749   0.7988  -2.0548  -1.4881
 79E  C19  C  CR16  0  -0.283   6.6255   1.1488  -1.2598
 79E  C18  C  CR16  0  -0.243   7.8410   0.9975  -1.9104
 79E  C17  C  CR16  0  -0.261   8.9894   0.7091  -1.1820
 79E  C16  C  CR16  0  -0.242   8.9159   0.5735   0.1972
 79E  C3   C  CH2   0  -0.447  -4.9509   2.6821  -0.5599
 79E  C1   C  CH1   0  -0.231  -3.8849   3.4283  -1.3655
 79E  C2   C  CH3   0  -0.654  -4.5701   4.3559  -2.3643
 79E  C    C  CH3   0  -0.665  -2.9308   4.2089  -0.4682
 79E  H1   H  HCH1  0   0.274  -3.7444   2.2088   1.1583
 79E  H2   H  HCH1  0   0.273  -2.2622  -1.1178  -1.3470
 79E  H3   H  HNH1  0   0.402  -1.2651  -2.3020   1.1674
 79E  H4   H  HCH2  0   0.238  -3.7523  -2.8044   0.7057
 79E  H5   H  HCH2  0   0.236  -4.4255  -2.1285  -0.7616
 79E  H6   H  HCH1  0   0.224  -2.2420  -4.2452  -0.5860
 79E  H7   H  HNH1  0   0.410   3.2373  -1.9947   0.2435
 79E  H8   H  HCH3  0   0.214  -5.1384  -4.4408  -1.5415
 79E  H9   H  HCH3  0   0.227  -3.9645  -5.7549  -1.5218
 79E  H10  H  HCH3  0   0.225  -4.5268  -5.0554  -0.0062
 79E  H11  H  HCH3  0   0.217  -3.5351  -3.0207  -3.0706
 79E  H12  H  HCH3  0   0.222  -1.8411  -2.8695  -2.6029
 79E  H13  H  HCH3  0   0.232  -2.4825  -4.4352  -3.0683
 79E  H14  H  HCH2  0   0.306   1.2931  -2.7412   1.3849
 79E  H15  H  HCH2  0   0.298   1.0623  -1.1400   2.0620
 79E  H16  H  HNH2  0   0.403  -6.7857   1.5397   2.8238
 79E  H17  H  HNH2  0   0.407  -5.5265   2.6740   2.5404
 79E  H18  H  HCH2  0   0.249   4.6597   1.9975   0.4164
 79E  H19  H  HCH2  0   0.250   5.3606   1.3128   1.8888
 79E  H20  H  HCR6  0   0.256   7.6426   0.6154   1.9223
 79E  H22  H  HOH1  0   0.482   0.6831  -3.0114  -1.4286
 79E  H23  H  HCR6  0   0.255   5.7344   1.3797  -1.8319
 79E  H24  H  HCR6  0   0.258   7.8945   1.1063  -2.9859
 79E  H25  H  HCR6  0   0.259   9.9386   0.5932  -1.6892
 79E  H26  H  HCR6  0   0.259   9.8068   0.3507   0.7699
 79E  H27  H  HCH2  0   0.248  -5.6231   2.1542  -1.2449
 79E  H28  H  HCH2  0   0.246  -5.5665   3.4140  -0.0288
 79E  H29  H  HCH1  0   0.225  -3.2981   2.6979  -1.9332
 79E  H30  H  HCH3  0   0.216  -5.1811   5.1018  -1.8496
 79E  H31  H  HCH3  0   0.230  -3.8394   4.8900  -2.9731
 79E  H32  H  HCH3  0   0.227  -5.2240   3.8026  -3.0410
 79E  H33  H  HCH3  0   0.231  -2.3340   3.5546   0.1678
 79E  H34  H  HCH3  0   0.234  -2.2333   4.7974  -1.0659
 79E  H35  H  HCH3  0   0.217  -3.4770   4.8993   0.1798
 79E  N    N  NH1   0  -0.631  -3.6528   0.6523  -0.2014
 79E  O5   O  O     0  -0.479  -6.0703   0.0079   0.9324
 79E  N3   N  NH2   0  -0.801  -5.9852   1.8178   2.2798
 79E  H21  H  HNH1  0   0.403  -3.8292   0.4907  -1.1809

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  1.391  0.020  1.391
 79E  C17  C18  aromatic  1.390  0.020  1.390
 79E  C14  C13  single    1.499  0.020  1.499
 79E  C14  C19  aromatic  1.393  0.020  1.393
 79E  C18  C19  aromatic  1.387  0.020  1.387
 79E  C13  O4   single    1.433  0.020  1.433
 79E  O4   C12  single    1.336  0.020  1.336
 79E  C12  O3   double    1.212  0.020  1.212
 79E  C12  N2   single    1.349  0.020  1.349
 79E  N2   C11  single    1.436  0.020  1.436
 79E  C11  P    single    1.826  0.020  1.826
 79E  O2   P    double    1.486  0.020  1.486
 79E  O1   P    single    1.619  0.020  1.619
 79E  N3   C20  single    1.339  0.020  1.339
 79E  P    N1   single    1.661  0.020  1.661
 79E  O5   C20  double    1.220  0.020  1.220
 79E  C20  C4   single    1.532  0.020  1.532
 79E  N1   C6   single    1.447  0.020  1.447
 79E  C4   N    single    1.437  0.020  1.437
 79E  C4   C3   single    1.530  0.020  1.530
 79E  N    C5   single    1.341  0.020  1.341
 79E  C5   O    double    1.221  0.020  1.221
 79E  C5   C6   single    1.525  0.020  1.525
 79E  C6   C7   single    1.532  0.020  1.532
 79E  C3   C1   single    1.530  0.020  1.530
 79E  C7   C8   single    1.529  0.020  1.529
 79E  C1   C    single    1.525  0.020  1.525
 79E  C1   C2   single    1.526  0.020  1.526
 79E  C10  C8   single    1.525  0.020  1.525
 79E  C8   C9   single    1.525  0.020  1.525
 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    0.860  0.020  1.020
 79E  O1   H22  single    0.850  0.020  0.980
 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    108.89  3.000
 79E  C3   C4   N    110.32  3.000
 79E  H1   C4   C20  108.64  3.000
 79E  C3   C4   C20  109.60  3.000
 79E  N    C4   C20  110.25  3.000
 79E  O    C5   N    122.88  3.000
 79E  O    C5   C6   121.64  3.000
 79E  N    C5   C6   115.45  3.000
 79E  C13  O4   C12  117.00  3.000
 79E  H2   C6   C7   108.76  3.000
 79E  H2   C6   N1   108.40  3.000
 79E  C7   C6   N1   110.82  3.000
 79E  H2   C6   C5   108.82  3.000
 79E  C7   C6   C5   108.90  3.000
 79E  N1   C6   C5   111.10  3.000
 79E  H3   N1   P    116.87  3.000
 79E  H3   N1   C6   114.33  3.000
 79E  P    N1   C6   120.10  3.000
 79E  H5   C7   H4   106.10  3.000
 79E  H5   C7   C8   109.55  3.000
 79E  H4   C7   C8   109.29  3.000
 79E  H5   C7   C6   108.43  3.000
 79E  H4   C7   C6   108.70  3.000
 79E  C8   C7   C6   114.44  3.000
 79E  H6   C8   C10  108.12  3.000
 79E  H6   C8   C9   107.98  3.000
 79E  C10  C8   C9   110.67  3.000
 79E  H6   C8   C7   107.99  3.000
 79E  C9   C8   C7   109.67  3.000
 79E  C10  C8   C7   112.26  3.000
 79E  H7   N2   C12  118.91  3.000
 79E  H7   N2   C11  118.07  3.000
 79E  C12  N2   C11  122.33  3.000
 79E  H10  C9   H9   107.62  3.000
 79E  H10  C9   H8   107.67  3.000
 79E  H9   C9   H8   107.60  3.000
 79E  H10  C9   C8   111.59  3.000
 79E  H9   C9   C8   111.03  3.000
 79E  H8   C9   C8   111.15  3.000
 79E  H13  C10  H12  107.06  3.000
 79E  H13  C10  H11  107.66  3.000
 79E  H12  C10  H11  107.73  3.000
 79E  H13  C10  C8   110.84  3.000
 79E  H12  C10  C8   112.22  3.000
 79E  H11  C10  C8   111.11  3.000
 79E  H15  C11  H14  107.06  3.000
 79E  H15  C11  P    109.07  3.000
 79E  H14  C11  P    110.17  3.000
 79E  H15  C11  N2   110.38  3.000
 79E  H14  C11  N2   109.50  3.000
 79E  P    C11  N2   110.60  3.000
 79E  N2   C12  O4   110.37  3.000
 79E  N2   C12  O3   125.20  3.000
 79E  O4   C12  O3   124.42  3.000
 79E  H19  C13  H18  108.17  3.000
 79E  H19  C13  C14  110.84  3.000
 79E  H18  C13  C14  110.83  3.000
 79E  H19  C13  O4   110.23  3.000
 79E  H18  C13  O4   109.92  3.000
 79E  C14  C13  O4   106.86  3.000
 79E  C19  C14  C15  119.11  3.000
 79E  C19  C14  C13  120.20  3.000
 79E  C15  C14  C13  120.68  3.000
 79E  H20  C15  C16  119.75  3.000
 79E  H20  C15  C14  119.68  3.000
 79E  C16  C15  C14  120.56  3.000
 79E  N3   C20  O5   123.82  3.000
 79E  O5   C20  C4   121.88  3.000
 79E  N3   C20  C4   114.26  3.000
 79E  O1   P    O2   107.76  3.000
 79E  O1   P    C11  105.17  3.000
 79E  O2   P    C11  115.87  3.000
 79E  O1   P    N1   106.57  3.000
 79E  O2   P    N1   116.86  3.000
 79E  C11  P    N1   103.70  3.000
 79E  H22  O1   P    114.30  3.000
 79E  H23  C19  C18  119.74  3.000
 79E  H23  C19  C14  119.77  3.000
 79E  C18  C19  C14  120.49  3.000
 79E  H24  C18  C17  120.04  3.000
 79E  H24  C18  C19  119.91  3.000
 79E  C17  C18  C19  120.05  3.000
 79E  H25  C17  C16  120.11  3.000
 79E  H25  C17  C18  120.08  3.000
 79E  C16  C17  C18  119.82  3.000
 79E  H26  C16  C17  120.16  3.000
 79E  H26  C16  C15  119.87  3.000
 79E  C17  C16  C15  119.98  3.000
 79E  H28  C3   H27  106.30  3.000
 79E  H28  C3   C1   108.74  3.000
 79E  H27  C3   C1   109.47  3.000
 79E  H28  C3   C4   108.30  3.000
 79E  H27  C3   C4   108.82  3.000
 79E  C1   C3   C4   114.87  3.000
 79E  H29  C1   C    108.12  3.000
 79E  H29  C1   C2   107.86  3.000
 79E  C    C1   C2   110.80  3.000
 79E  H29  C1   C3   108.71  3.000
 79E  C2   C1   C3   109.16  3.000
 79E  C    C1   C3   112.07  3.000
 79E  H32  C2   H31  107.67  3.000
 79E  H32  C2   H30  107.63  3.000
 79E  H31  C2   H30  107.64  3.000
 79E  H32  C2   C1   111.52  3.000
 79E  H31  C2   C1   111.24  3.000
 79E  H30  C2   C1   110.96  3.000
 79E  H35  C    H34  107.67  3.000
 79E  H35  C    H33  107.86  3.000
 79E  H34  C    H33  107.06  3.000
 79E  H35  C    C1   111.07  3.000
 79E  H34  C    C1   110.72  3.000
 79E  H33  C    C1   112.25  3.000
 79E  H21  N    C5   118.92  3.000
 79E  H21  N    C4   118.15  3.000
 79E  C5   N    C4   121.41  3.000
 79E  H17  N3   H16  117.25  3.000
 79E  H17  N3   C20  122.04  3.000
 79E  H16  N3   C20  120.71  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  CONST_18  H21  N    C5   C6      0.00   0.0  0
 79E  Var_01    C15  C14  C13  O4   -102.21  30.0  2
 79E  Var_02    C14  C13  O4   C12  -178.47  30.0  1
 79E  Var_03    C11  N2   C12  O3      6.32  30.0  2
 79E  Var_04    C    C1   C3   C4    -58.39  30.0  3
 79E  Var_05    C11  P    N1   C6    157.29  30.0  1
 79E  Var_06    C10  C8   C7   C6    -56.36  30.0  3
 79E  Var_07    N2   C11  P    N1    169.12  30.0  1
 79E  Var_08    P    C11  N2   C12    89.69  30.0  3
 79E  Var_09    H11  C10  C8   C7    -57.78  30.0  3
 79E  Var_10    H8   C9   C8   C7     63.57  30.0  3
 79E  Var_11    H33  C    C1   C3     65.13  30.0  3
 79E  Var_12    H30  C2   C1   C3     61.43  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
 79E  chir_03  P   O2   O1  N1  both

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  O    0.020
 79E  plan-2  N    0.020
 79E  plan-2  H21  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

