# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 16:15:09 2022
#   Inital geometry file: a 154 line input string
#   Ligand name: ~{N}-[(2~{S})-1-[[(2~{R})-2,3-dimethylbutyl]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](N[P](O)(=O)CNC(=O)OCc1ccccc1)C(=O)NC[C@H](C)C(C)C
#
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
 6QC  6QC  '~{N}-[(2~{S})-1-[[(2~{R})-2,3-dimethylbutyl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]-(phenylmethoxycarbonylaminomethyl)phosphonamidic acid'  ligand  65  30  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_6QC
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
 6QC  C1   C  C1     0  -0.296   4.9844  -1.5507   1.9033
 6QC  C2   C  C1     0  -0.242   6.3484  -1.5892   2.1631
 6QC  C3   C  C1     0  -0.263   7.2254  -2.0701   1.2003
 6QC  C9   C  C      0   0.754   1.5285  -0.4889  -0.7437
 6QC  C12  C  CH2    0  -0.576   0.2084   1.2908  -1.7494
 6QC  C20  C  CH3    0  -0.652  -4.6404   5.3728   1.6401
 6QC  C21  C  CH3    0  -0.675  -2.6776   4.1204   2.5844
 6QC  C22  C  C      0   0.581  -3.4120   0.9774  -0.4683
 6QC  C27  C  CH3    0  -0.670  -2.9769  -2.6266   1.1361
 6QC  P13  P  P      0   1.246  -0.1634   2.4883  -0.3830
 6QC  C6   C  C      0   0.075   4.4836  -1.9941   0.6836
 6QC  C4   C  C1     0  -0.242   6.7337  -2.5139  -0.0216
 6QC  C5   C  C1     0  -0.286   5.3705  -2.4754  -0.2764
 6QC  N16  N  NH1    0  -0.778  -1.8153   2.8341  -0.5459
 6QC  C17  C  CH1    0  -0.226  -2.8579   2.2162   0.2418
 6QC  C18  C  CH2    0  -0.404  -3.9614   3.2049   0.5980
 6QC  C25  C  CH2    0  -0.278  -2.8975  -1.3645  -1.0235
 6QC  C26  C  CH1    0  -0.215  -3.7034  -2.3595  -0.1799
 6QC  C28  C  CH1    0  -0.212  -3.9735  -3.6538  -0.9693
 6QC  C29  C  CH3    0  -0.665  -4.7281  -3.3960  -2.2742
 6QC  O14  O  OP    -1  -0.805   0.6395   3.7339  -0.6622
 6QC  N11  N  NH1    0  -0.647   1.4677   0.6151  -1.5108
 6QC  O10  O  O      0  -0.514   0.5936  -1.2107  -0.4594
 6QC  O8   O  O2     0  -0.485   2.7922  -0.7364  -0.3642
 6QC  H1   H  H      0   0.255   4.3037  -1.1766   2.6592
 6QC  H2   H  H      0   0.258   6.7249  -1.2435   3.1169
 6QC  H3   H  H      0   0.258   8.2883  -2.1027   1.4021
 6QC  H4   H  HCH2   0   0.242   2.6966  -2.8047  -0.1804
 6QC  H5   H  HCH2   0   0.244   2.4376  -1.9051   1.3180
 6QC  H6   H  HCH2   0   0.255  -0.5781   0.5429  -1.8341
 6QC  H7   H  HCH2   0   0.248   0.2612   1.8055  -2.7105
 6QC  H8   H  HCH1   0   0.214  -2.7902   4.9930   0.6434
 6QC  H9   H  HCH3   0   0.222  -4.3085   6.2973   2.1164
 6QC  H10  H  HCH3   0   0.220  -5.1901   5.6464   0.7371
 6QC  H11  H  HCH3   0   0.209  -5.3444   4.8870   2.3208
 6QC  H12  H  HCH3   0   0.234  -1.7662   3.5663   2.3572
 6QC  H13  H  HCH3   0   0.222  -2.3839   5.0280   3.1155
 6QC  H14  H  HCH3   0   0.208  -3.2770   3.5151   3.2700
 6QC  H16  H  HCH3   0   0.212  -2.0246  -3.1347   0.9599
 6QC  H17  H  HCH3   0   0.228  -2.7607  -1.6956   1.6611
 6QC  H18  H  H      0   0.257   7.4125  -2.8928  -0.7748
 6QC  H19  H  H      0   0.255   4.9917  -2.8294  -1.2280
 6QC  H20  H  HNH1   0   0.361  -2.1287   3.3568  -1.3506
 6QC  H21  H  HCH1   0   0.256  -2.3903   1.8762   1.1676
 6QC  H22  H  HCH2   0   0.215  -4.6949   2.6956   1.2336
 6QC  H23  H  HCH2   0   0.218  -4.4975   3.5022  -0.3088
 6QC  H25  H  HCH2   0   0.242  -3.4144  -1.1421  -1.9553
 6QC  H26  H  HCH2   0   0.239  -1.9336  -1.8061  -1.2860
 6QC  H27  H  HCH1   0   0.210  -4.6733  -1.8961   0.0455
 6QC  H28  H  HCH1   0   0.207  -3.0007  -4.0972  -1.2209
 6QC  H30  H  HCH3   0   0.229  -4.1617  -2.7967  -2.9865
 6QC  H31  H  HCH3   0   0.227  -4.9669  -4.3391  -2.7693
 6QC  H32  H  HCH3   0   0.214  -5.6728  -2.8809  -2.0814
 6QC  H34  H  HNH1   0   0.391   2.3032   1.1759  -1.5748
 6QC  C8   C  CH3    0  -0.662  -4.7540  -4.6724  -0.1404
 6QC  H29  H  HCH3   0   0.226  -4.9557  -5.5711  -0.7255
 6QC  H35  H  HCH3   0   0.230  -4.2189  -4.9840   0.7557
 6QC  H36  H  HCH3   0   0.213  -5.7169  -4.2601   0.1721
 6QC  C7   C  CH2    0  -0.233   3.0152  -1.9301   0.3915
 6QC  O23  O  O      0  -0.510  -4.4508   0.9888  -1.1178
 6QC  C19  C  CH1    0  -0.215  -3.4625   4.4572   1.3206
 6QC  O15  O  O      0  -0.804   0.0067   1.7392   0.9201
 6QC  N24  N  NH1    0  -0.646  -2.6350  -0.1128  -0.3492
 6QC  H15  H  HCH3   0   0.233  -3.5637  -3.2436   1.8151
 6QC  H24  H  HNH1   0   0.392  -1.7694  -0.0290   0.1638

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
 6QC  C4   C5   aromatic  1.387  0.020  1.387
 6QC  C4   C3   aromatic  1.390  0.020  1.390
 6QC  C5   C6   aromatic  1.393  0.020  1.393
 6QC  C3   C2   aromatic  1.388  0.020  1.388
 6QC  C6   C7   single    1.499  0.020  1.499
 6QC  C6   C1   aromatic  1.391  0.020  1.391
 6QC  C2   C1   aromatic  1.389  0.020  1.389
 6QC  C7   O8   single    1.430  0.020  1.430
 6QC  O8   C9   single    1.342  0.020  1.342
 6QC  C9   O10  double    1.215  0.020  1.215
 6QC  C9   N11  single    1.346  0.020  1.346
 6QC  N11  C12  single    1.449  0.020  1.449
 6QC  C12  P13  single    1.854  0.020  1.854
 6QC  O15  P13  deloc     1.513  0.020  1.513
 6QC  O14  P13  deloc     1.508  0.020  1.508
 6QC  P13  N16  single    1.696  0.020  1.696
 6QC  C25  N24  single    1.446  0.020  1.446
 6QC  C25  C26  single    1.533  0.020  1.533
 6QC  N16  C17  single    1.445  0.020  1.445
 6QC  N24  C22  single    1.344  0.020  1.344
 6QC  C22  O23  double    1.225  0.020  1.225
 6QC  C22  C17  single    1.532  0.020  1.532
 6QC  C28  C29  single    1.529  0.020  1.529
 6QC  C28  C26  single    1.540  0.020  1.540
 6QC  C17  C18  single    1.524  0.020  1.524
 6QC  C26  C27  single    1.527  0.020  1.527
 6QC  C18  C19  single    1.530  0.020  1.530
 6QC  C20  C19  single    1.526  0.020  1.526
 6QC  C19  C21  single    1.525  0.020  1.525
 6QC  C1   H1   single    0.930  0.020  1.080
 6QC  C2   H2   single    0.930  0.020  1.080
 6QC  C3   H3   single    0.930  0.020  1.080
 6QC  C7   H4   single    0.970  0.020  1.090
 6QC  C7   H5   single    0.970  0.020  1.090
 6QC  C12  H6   single    0.970  0.020  1.090
 6QC  C12  H7   single    0.970  0.020  1.090
 6QC  C19  H8   single    0.970  0.020  1.090
 6QC  C20  H9   single    0.970  0.020  1.090
 6QC  C20  H10  single    0.970  0.020  1.090
 6QC  C20  H11  single    0.970  0.020  1.090
 6QC  C21  H12  single    0.970  0.020  1.090
 6QC  C21  H13  single    0.970  0.020  1.090
 6QC  C21  H14  single    0.970  0.020  1.090
 6QC  C27  H15  single    0.970  0.020  1.090
 6QC  C27  H16  single    0.970  0.020  1.090
 6QC  C27  H17  single    0.970  0.020  1.090
 6QC  C4   H18  single    0.930  0.020  1.080
 6QC  C5   H19  single    0.930  0.020  1.080
 6QC  N16  H20  single    0.860  0.020  1.020
 6QC  C17  H21  single    0.970  0.020  1.090
 6QC  C18  H22  single    0.970  0.020  1.090
 6QC  C18  H23  single    0.970  0.020  1.090
 6QC  N24  H24  single    0.860  0.020  1.020
 6QC  C25  H25  single    0.970  0.020  1.090
 6QC  C25  H26  single    0.970  0.020  1.090
 6QC  C26  H27  single    0.970  0.020  1.090
 6QC  C28  H28  single    0.970  0.020  1.090
 6QC  C29  H30  single    0.970  0.020  1.090
 6QC  C29  H31  single    0.970  0.020  1.090
 6QC  C29  H32  single    0.970  0.020  1.090
 6QC  N11  H34  single    0.890  0.020  1.040
 6QC  C28  C8   single    1.528  0.020  1.528
 6QC  C8   H29  single    0.970  0.020  1.090
 6QC  C8   H35  single    0.970  0.020  1.090
 6QC  C8   H36  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
 6QC  H1   C1   C6   119.70  3.000
 6QC  H1   C1   C2   119.73  3.000
 6QC  C6   C1   C2   120.57  3.000
 6QC  H2   C2   C3   120.14  3.000
 6QC  H2   C2   C1   119.84  3.000
 6QC  C3   C2   C1   120.02  3.000
 6QC  H3   C3   C4   120.12  3.000
 6QC  H3   C3   C2   120.09  3.000
 6QC  C4   C3   C2   119.79  3.000
 6QC  O8   C9   O10  123.28  3.000
 6QC  O10  C9   N11  125.88  3.000
 6QC  O8   C9   N11  110.79  3.000
 6QC  H7   C12  H6   106.88  3.000
 6QC  H7   C12  N11  108.83  3.000
 6QC  H6   C12  N11  108.69  3.000
 6QC  H7   C12  P13  110.73  3.000
 6QC  H6   C12  P13  110.86  3.000
 6QC  N11  C12  P13  110.74  3.000
 6QC  H11  C20  H10  107.58  3.000
 6QC  H11  C20  H9   107.49  3.000
 6QC  H10  C20  H9   107.56  3.000
 6QC  H11  C20  C19  111.15  3.000
 6QC  H10  C20  C19  111.46  3.000
 6QC  H9   C20  C19  111.40  3.000
 6QC  H14  C21  H13  107.62  3.000
 6QC  H14  C21  H12  107.91  3.000
 6QC  H13  C21  H12  107.39  3.000
 6QC  H14  C21  C19  111.08  3.000
 6QC  H13  C21  C19  110.97  3.000
 6QC  H12  C21  C19  111.69  3.000
 6QC  N24  C22  O23  123.00  3.000
 6QC  O23  C22  C17  123.02  3.000
 6QC  N24  C22  C17  113.94  3.000
 6QC  H17  C27  H16  107.55  3.000
 6QC  H17  C27  H15  106.88  3.000
 6QC  H16  C27  H15  107.85  3.000
 6QC  H17  C27  C26  111.09  3.000
 6QC  H16  C27  C26  110.90  3.000
 6QC  H15  C27  C26  112.34  3.000
 6QC  O14  P13  N16  109.42  3.000
 6QC  N16  P13  O15  107.06  3.000
 6QC  O14  P13  O15  120.57  3.000
 6QC  N16  P13  C12  104.85  3.000
 6QC  O14  P13  C12  106.87  3.000
 6QC  O15  P13  C12  107.00  3.000
 6QC  C5   C6   C7   120.29  3.000
 6QC  C7   C6   C1   120.67  3.000
 6QC  C5   C6   C1   119.03  3.000
 6QC  H18  C4   C5   119.88  3.000
 6QC  H18  C4   C3   120.11  3.000
 6QC  C5   C4   C3   120.01  3.000
 6QC  H19  C5   C4   119.71  3.000
 6QC  H19  C5   C6   119.71  3.000
 6QC  C4   C5   C6   120.58  3.000
 6QC  H20  N16  C17  115.59  3.000
 6QC  H20  N16  P13  118.99  3.000
 6QC  C17  N16  P13  124.28  3.000
 6QC  H21  C17  C18  108.30  3.000
 6QC  H21  C17  N16  106.65  3.000
 6QC  C18  C17  N16  111.86  3.000
 6QC  H21  C17  C22  107.23  3.000
 6QC  C18  C17  C22  111.79  3.000
 6QC  N16  C17  C22  110.73  3.000
 6QC  H23  C18  H22  106.19  3.000
 6QC  H23  C18  C17  109.71  3.000
 6QC  H22  C18  C17  108.59  3.000
 6QC  H23  C18  C19  109.19  3.000
 6QC  H22  C18  C19  108.95  3.000
 6QC  C17  C18  C19  113.92  3.000
 6QC  H26  C25  H25  107.21  3.000
 6QC  H26  C25  C26  109.49  3.000
 6QC  H25  C25  C26  110.73  3.000
 6QC  H26  C25  N24  107.57  3.000
 6QC  H25  C25  N24  107.97  3.000
 6QC  C26  C25  N24  113.62  3.000
 6QC  H27  C26  C28  107.76  3.000
 6QC  H27  C26  C25  107.65  3.000
 6QC  C28  C26  C25  110.83  3.000
 6QC  H27  C26  C27  108.49  3.000
 6QC  C28  C26  C27  112.23  3.000
 6QC  C25  C26  C27  109.73  3.000
 6QC  C8   C28  H28  107.92  3.000
 6QC  C8   C28  C29  108.86  3.000
 6QC  H28  C28  C29  108.03  3.000
 6QC  C8   C28  C26  111.84  3.000
 6QC  H28  C28  C26  107.54  3.000
 6QC  C29  C28  C26  112.48  3.000
 6QC  H32  C29  H31  107.35  3.000
 6QC  H32  C29  H30  107.78  3.000
 6QC  H31  C29  H30  107.00  3.000
 6QC  H32  C29  C28  110.81  3.000
 6QC  H31  C29  C28  110.45  3.000
 6QC  H30  C29  C28  113.20  3.000
 6QC  H34  N11  C12  116.77  3.000
 6QC  H34  N11  C9   117.06  3.000
 6QC  C12  N11  C9   121.05  3.000
 6QC  C9   O8   C7   116.75  3.000
 6QC  H36  C8   H35  107.78  3.000
 6QC  H36  C8   H29  107.53  3.000
 6QC  H35  C8   H29  107.24  3.000
 6QC  H36  C8   C28  110.71  3.000
 6QC  H35  C8   C28  112.71  3.000
 6QC  H29  C8   C28  110.65  3.000
 6QC  H5   C7   H4   107.95  3.000
 6QC  H5   C7   O8   110.28  3.000
 6QC  H4   C7   O8   110.25  3.000
 6QC  H5   C7   C6   110.72  3.000
 6QC  H4   C7   C6   110.71  3.000
 6QC  O8   C7   C6   106.94  3.000
 6QC  H8   C19  C18  107.99  3.000
 6QC  H8   C19  C21  107.74  3.000
 6QC  C18  C19  C21  112.24  3.000
 6QC  H8   C19  C20  108.06  3.000
 6QC  C21  C19  C20  110.87  3.000
 6QC  C18  C19  C20  109.78  3.000
 6QC  H24  N24  C25  117.68  3.000
 6QC  H24  N24  C22  118.25  3.000
 6QC  C25  N24  C22  123.78  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
 6QC  CONST_01  C4   C5   C6   C1      0.00   0.0  0
 6QC  CONST_02  C4   C3   C2   C1      0.00   0.0  0
 6QC  CONST_03  C5   C4   C3   C2      0.00   0.0  0
 6QC  CONST_04  C5   C6   C1   C2      0.00   0.0  0
 6QC  CONST_05  C6   C5   C4   C3      0.00   0.0  0
 6QC  CONST_06  C6   C1   C2   C3      0.00   0.0  0
 6QC  CONST_07  C7   C6   C1   C2    180.00   0.0  0
 6QC  CONST_08  C4   C5   C6   C7    180.00   0.0  0
 6QC  CONST_09  H19  C5   C6   C1    180.00   0.0  0
 6QC  CONST_10  H3   C3   C2   C1    180.00   0.0  0
 6QC  CONST_11  H18  C4   C3   C2    180.00   0.0  0
 6QC  CONST_12  H1   C1   C2   C3    180.00   0.0  0
 6QC  CONST_13  H2   C2   C1   C6    180.00   0.0  0
 6QC  CONST_14  C25  N24  C22  C17   180.00   0.0  0
 6QC  CONST_15  C25  N24  C22  O23     0.00   0.0  0
 6QC  CONST_16  H24  N24  C22  C17     0.00   0.0  0
 6QC  Var_01    O8   C7   C6   C1     97.31  30.0  2
 6QC  Var_02    C6   C7   O8   C9    179.49  30.0  2
 6QC  Var_03    O10  C9   O8   C7      1.11  30.0  3
 6QC  Var_04    P13  C12  N11  C9     85.43  30.0  3
 6QC  Var_05    O8   C9   N11  C12  -163.41  30.0  1
 6QC  Var_06    C17  N16  P13  C12    99.06  30.0  3
 6QC  Var_07    C17  C18  C19  C20  -179.58  30.0  2
 6QC  Var_08    C26  C25  N24  C22   -93.65  30.0  2
 6QC  Var_09    N11  C12  P13  O15   -50.07  30.0  2
 6QC  Var_10    H12  C21  C19  C20  -173.17  30.0  3
 6QC  Var_11    H9   C20  C19  C21    58.01  30.0  3
 6QC  Var_12    H30  C29  C28  C26    64.25  30.0  3
 6QC  Var_13    H29  C8   C28  C26   178.62  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
 6QC  chir_02  C17  N16  C22  C18  positiv
 6QC  chir_03  C26  C25  C28  C27  negativ

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
 6QC  plan-1  C1   0.020
 6QC  plan-1  C2   0.020
 6QC  plan-1  C3   0.020
 6QC  plan-1  C6   0.020
 6QC  plan-1  C4   0.020
 6QC  plan-1  C5   0.020
 6QC  plan-1  H1   0.020
 6QC  plan-1  H2   0.020
 6QC  plan-1  H3   0.020
 6QC  plan-1  H18  0.020
 6QC  plan-1  H19  0.020
 6QC  plan-1  C7   0.020
 6QC  plan-2  C22  0.020
 6QC  plan-2  C17  0.020
 6QC  plan-2  C25  0.020
 6QC  plan-2  O23  0.020
 6QC  plan-2  N24  0.020
 6QC  plan-2  H24  0.020
 6QC  plan-3  C9   0.020
 6QC  plan-3  N11  0.020
 6QC  plan-3  O10  0.020
 6QC  plan-3  O8   0.020

