# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 10:50:40 2020
#   Inital geometry file: a 143 line input string
#   Ligand name: (2~{S})-2-[[(2~{S})-3-azanyl-2-[[oxidanyl(phenylmethoxycarbonylaminomethyl)phosphoryl]amino]propanoyl]amino]-4-methyl-pentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](NC(=O)[C@H](CN)N[P](O)(=O)CNC(=O)OCc1ccccc1)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
 7K0  7K0  '(2~{S})-2-[[(2~{S})-3-azanyl-2-[[oxidanyl(phenylmethoxycarbonylaminomethyl)phosphoryl]amino]propanoyl]amino]-4-methyl-pentanoic acid'  ligand  59  30  .  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_7K0
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
 7K0  C1   C  CR6   0   0.212   4.1449  -1.9727  -0.6978
 7K0  C2   C  CH2   0  -0.238   2.8905  -1.3041  -1.1721
 7K0  C8   C  CR16  0  -0.368   4.0833  -3.0998   0.1135
 7K0  C9   C  CR16  0  -0.269   5.2470  -3.7215   0.5504
 7K0  C10  C  CR16  0  -0.272   6.4843  -3.2124   0.1833
 7K0  C11  C  CR16  0  -0.294   6.5548  -2.0820  -0.6234
 7K0  C12  C  CR16  0  -0.240   5.3919  -1.4681  -1.0626
 7K0  C20  C  CH1   0  -0.175  -2.9099  -0.9496  -0.7130
 7K0  C21  C  CH2   0  -0.454  -3.0650  -2.3526  -0.1169
 7K0  C22  C  CH1   0  -0.267  -2.0633  -2.6927   0.9920
 7K0  C24  C  CH3   0  -0.663  -2.3534  -4.0969   1.5117
 7K0  N26  N  NH2   0  -0.823  -4.2195   4.1723   2.1185
 7K0  C6   C  CH2   0  -0.546   0.6413   2.7400  -0.0143
 7K0  P13  P  P     0   1.224  -0.2680   2.3670   1.5302
 7K0  O14  O  OH1   0  -0.729   0.5160   3.1744   2.6886
 7K0  O15  O  O     0  -0.721  -0.3189   0.9096   1.8171
 7K0  N16  N  NH1   0  -0.675  -1.7662   3.0772   1.4004
 7K0  C17  C  CH1   0  -0.288  -2.9614   2.2694   1.2600
 7K0  C18  C  C     0   0.554  -2.8226   1.3363   0.0633
 7K0  N19  N  NH1   0  -0.624  -3.1101   0.0511   0.2978
 7K0  C23  C  CH3   0  -0.678  -0.6177  -2.5687   0.5240
 7K0  O27  O  O     0  -0.307  -2.4919   1.7456  -1.0390
 7K0  C28  C  C     0   0.567  -3.9146  -0.7658  -1.8372
 7K0  O29  O  OH1   0  -0.566  -3.4643  -1.2851  -2.9715
 7K0  O30  O  O     0  -0.564  -4.9964  -0.2541  -1.7141
 7K0  O3   O  O2    0  -0.565   2.7974  -0.0455  -0.4979
 7K0  C4   C  C     0   0.728   1.7119   0.6926  -0.7554
 7K0  N5   N  NH1   0  -0.658   1.7993   1.8978  -0.1507
 7K0  O7   O  O     0  -0.371   0.7992   0.3307  -1.4653
 7K0  C25  C  CH2   0  -0.319  -4.1534   3.2030   1.0406
 7K0  H1   H  HCH2  0   0.264   2.9221  -1.1428  -2.2536
 7K0  H2   H  HCH2  0   0.274   2.0175  -1.9217  -0.9508
 7K0  H3   H  HCR6  0   0.239   3.1189  -3.5009   0.4030
 7K0  H4   H  HCR6  0   0.273   5.1850  -4.6010   1.1779
 7K0  H5   H  HCR6  0   0.274   7.3926  -3.6957   0.5192
 7K0  H6   H  HCR6  0   0.238   7.5180  -1.6819  -0.9121
 7K0  H7   H  HCR6  0   0.255   5.4539  -0.5938  -1.6999
 7K0  H8   H  HCH1  0   0.272  -1.9050  -0.8455  -1.1336
 7K0  H9   H  HCH2  0   0.236  -4.0851  -2.4646   0.2651
 7K0  H10  H  HCH2  0   0.247  -2.9533  -3.0823  -0.9237
 7K0  H11  H  HCH1  0   0.217  -2.2027  -1.9973   1.8268
 7K0  H12  H  HCH3  0   0.245  -2.2193  -4.8411   0.7232
 7K0  H13  H  HCH3  0   0.245  -1.6820  -4.3590   2.3306
 7K0  H14  H  HCH3  0   0.226  -3.3773  -4.1833   1.8794
 7K0  H15  H  HNH2  0   0.361  -4.8362   4.9313   1.8624
 7K0  H16  H  HNH2  0   0.359  -4.6185   3.7469   2.9457
 7K0  H18  H  HCH2  0   0.337  -0.0401   2.5674  -0.8451
 7K0  H19  H  HCH2  0   0.281   0.9302   3.7919  -0.0556
 7K0  H20  H  HOH1  0   0.479   0.8577   4.0429   2.4421
 7K0  H21  H  HNH1  0   0.381  -1.9518   3.9384   1.9022
 7K0  H22  H  HCH1  0   0.228  -3.1519   1.6735   2.1621
 7K0  H23  H  HNH1  0   0.381  -3.3247  -0.2395   1.2375
 7K0  H24  H  HCH3  0   0.219   0.0661  -2.8874   1.3133
 7K0  H25  H  HCH3  0   0.229  -0.4312  -3.2032  -0.3466
 7K0  H26  H  HCH3  0   0.243  -0.3567  -1.5430   0.2641
 7K0  H27  H  HOH1  0   0.449  -4.1347  -1.2050  -3.6666
 7K0  H28  H  HNH1  0   0.423   2.5782   2.0638   0.4678
 7K0  H29  H  HCH2  0   0.239  -5.0578   2.5922   0.9301
 7K0  H30  H  HCH2  0   0.275  -4.0065   3.7391   0.1016

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
 7K0  C11  C12  aromatic  1.386  0.020  1.386
 7K0  C11  C10  aromatic  1.391  0.020  1.391
 7K0  C12  C1   aromatic  1.394  0.020  1.394
 7K0  C10  C9   aromatic  1.387  0.020  1.387
 7K0  C1   C2   single    1.499  0.020  1.499
 7K0  C1   C8   aromatic  1.390  0.020  1.390
 7K0  C9   C8   aromatic  1.390  0.020  1.390
 7K0  C2   O3   single    1.431  0.020  1.431
 7K0  O3   C4   single    1.338  0.020  1.338
 7K0  O7   C4   double    1.212  0.020  1.212
 7K0  C4   N5   single    1.351  0.020  1.351
 7K0  N5   C6   single    1.438  0.020  1.438
 7K0  C6   P13  single    1.831  0.020  1.831
 7K0  O15  P13  double    1.486  0.020  1.486
 7K0  O14  P13  single    1.615  0.020  1.615
 7K0  P13  N16  single    1.663  0.020  1.663
 7K0  O30  C28  double    1.203  0.020  1.203
 7K0  O29  C28  single    1.326  0.020  1.326
 7K0  C28  C20  single    1.519  0.020  1.519
 7K0  C20  N19  single    1.436  0.020  1.436
 7K0  C20  C21  single    1.532  0.020  1.532
 7K0  N16  C17  single    1.449  0.020  1.449
 7K0  N19  C18  single    1.338  0.020  1.338
 7K0  C18  O27  double    1.221  0.020  1.221
 7K0  C18  C17  single    1.524  0.020  1.524
 7K0  C17  C25  single    1.530  0.020  1.530
 7K0  C21  C22  single    1.533  0.020  1.533
 7K0  C22  C24  single    1.525  0.020  1.525
 7K0  C22  C23  single    1.524  0.020  1.524
 7K0  C25  N26  single    1.451  0.020  1.451
 7K0  C2   H1   single    0.970  0.020  1.090
 7K0  C2   H2   single    0.970  0.020  1.090
 7K0  C8   H3   single    0.930  0.020  1.080
 7K0  C9   H4   single    0.930  0.020  1.080
 7K0  C10  H5   single    0.930  0.020  1.080
 7K0  C11  H6   single    0.930  0.020  1.080
 7K0  C12  H7   single    0.930  0.020  1.080
 7K0  C20  H8   single    0.970  0.020  1.090
 7K0  C21  H9   single    0.970  0.020  1.090
 7K0  C21  H10  single    0.970  0.020  1.090
 7K0  C22  H11  single    0.970  0.020  1.090
 7K0  C24  H12  single    0.970  0.020  1.090
 7K0  C24  H13  single    0.970  0.020  1.090
 7K0  C24  H14  single    0.970  0.020  1.090
 7K0  N26  H15  single    0.890  0.020  1.040
 7K0  N26  H16  single    0.890  0.020  1.040
 7K0  C6   H18  single    0.970  0.020  1.090
 7K0  C6   H19  single    0.970  0.020  1.090
 7K0  O14  H20  single    0.850  0.020  0.980
 7K0  N16  H21  single    0.890  0.020  1.040
 7K0  C17  H22  single    0.970  0.020  1.090
 7K0  N19  H23  single    0.860  0.020  1.020
 7K0  C23  H24  single    0.970  0.020  1.090
 7K0  C23  H25  single    0.970  0.020  1.090
 7K0  C23  H26  single    0.970  0.020  1.090
 7K0  O29  H27  single    0.850  0.020  0.980
 7K0  N5   H28  single    0.890  0.020  1.040
 7K0  C25  H29  single    0.970  0.020  1.090
 7K0  C25  H30  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
 7K0  C12  C1   C8   119.08  3.000
 7K0  C8   C1   C2   120.62  3.000
 7K0  C12  C1   C2   120.30  3.000
 7K0  H2   C2   H1   107.87  3.000
 7K0  H2   C2   O3   110.49  3.000
 7K0  H1   C2   O3   109.75  3.000
 7K0  H2   C2   C1   110.65  3.000
 7K0  H1   C2   C1   110.76  3.000
 7K0  O3   C2   C1   107.32  3.000
 7K0  H3   C8   C9   119.70  3.000
 7K0  H3   C8   C1   119.70  3.000
 7K0  C9   C8   C1   120.60  3.000
 7K0  H4   C9   C10  120.18  3.000
 7K0  H4   C9   C8   119.86  3.000
 7K0  C10  C9   C8   119.96  3.000
 7K0  H5   C10  C11  120.04  3.000
 7K0  H5   C10  C9   120.16  3.000
 7K0  C11  C10  C9   119.80  3.000
 7K0  H6   C11  C12  119.90  3.000
 7K0  H6   C11  C10  120.02  3.000
 7K0  C12  C11  C10  120.08  3.000
 7K0  H7   C12  C11  119.70  3.000
 7K0  H7   C12  C1   119.82  3.000
 7K0  C11  C12  C1   120.48  3.000
 7K0  H8   C20  C28  108.15  3.000
 7K0  H8   C20  N19  109.40  3.000
 7K0  C28  C20  N19  110.14  3.000
 7K0  H8   C20  C21  109.24  3.000
 7K0  N19  C20  C21  110.49  3.000
 7K0  C28  C20  C21  109.38  3.000
 7K0  H10  C21  H9   106.51  3.000
 7K0  H10  C21  C22  108.61  3.000
 7K0  H9   C21  C22  109.50  3.000
 7K0  H10  C21  C20  108.28  3.000
 7K0  H9   C21  C20  108.88  3.000
 7K0  C22  C21  C20  114.74  3.000
 7K0  H11  C22  C23  107.64  3.000
 7K0  H11  C22  C24  107.49  3.000
 7K0  C23  C22  C24  111.09  3.000
 7K0  H11  C22  C21  109.11  3.000
 7K0  C23  C22  C21  112.31  3.000
 7K0  C24  C22  C21  109.06  3.000
 7K0  H14  C24  H13  107.79  3.000
 7K0  H14  C24  H12  107.72  3.000
 7K0  H13  C24  H12  107.62  3.000
 7K0  H14  C24  C22  111.48  3.000
 7K0  H13  C24  C22  111.09  3.000
 7K0  H12  C24  C22  110.97  3.000
 7K0  H16  N26  H15  106.39  3.000
 7K0  H16  N26  C25  110.14  3.000
 7K0  H15  N26  C25  109.95  3.000
 7K0  H19  C6   H18  106.84  3.000
 7K0  H19  C6   N5   110.34  3.000
 7K0  H18  C6   N5   109.80  3.000
 7K0  H19  C6   P13  111.08  3.000
 7K0  H18  C6   P13  107.50  3.000
 7K0  N5   C6   P13  111.13  3.000
 7K0  N16  P13  O15  113.77  3.000
 7K0  N16  P13  O14  106.25  3.000
 7K0  O15  P13  O14  111.62  3.000
 7K0  N16  P13  C6   107.13  3.000
 7K0  O14  P13  C6   105.20  3.000
 7K0  O15  P13  C6   112.32  3.000
 7K0  H20  O14  P13  116.01  3.000
 7K0  H21  N16  C17  111.74  3.000
 7K0  H21  N16  P13  119.28  3.000
 7K0  C17  N16  P13  120.82  3.000
 7K0  H22  C17  C25  108.29  3.000
 7K0  H22  C17  C18  109.20  3.000
 7K0  C25  C17  C18  109.39  3.000
 7K0  H22  C17  N16  111.47  3.000
 7K0  C25  C17  N16  108.43  3.000
 7K0  C18  C17  N16  110.01  3.000
 7K0  O27  C18  N19  122.57  3.000
 7K0  O27  C18  C17  121.88  3.000
 7K0  N19  C18  C17  115.53  3.000
 7K0  H23  N19  C18  119.13  3.000
 7K0  H23  N19  C20  119.04  3.000
 7K0  C18  N19  C20  121.07  3.000
 7K0  H26  C23  H25  108.38  3.000
 7K0  H26  C23  H24  107.29  3.000
 7K0  H25  C23  H24  107.42  3.000
 7K0  H26  C23  C22  112.14  3.000
 7K0  H25  C23  C22  111.04  3.000
 7K0  H24  C23  C22  110.38  3.000
 7K0  O30  C28  O29  124.01  3.000
 7K0  O29  C28  C20  111.16  3.000
 7K0  O30  C28  C20  124.79  3.000
 7K0  H27  O29  C28  110.25  3.000
 7K0  C4   O3   C2   116.58  3.000
 7K0  O7   C4   N5   125.26  3.000
 7K0  N5   C4   O3   110.70  3.000
 7K0  O7   C4   O3   124.01  3.000
 7K0  H28  N5   C4   118.12  3.000
 7K0  H28  N5   C6   117.86  3.000
 7K0  C4   N5   C6   120.84  3.000
 7K0  H30  C25  H29  107.33  3.000
 7K0  H30  C25  C17  108.56  3.000
 7K0  H29  C25  C17  108.48  3.000
 7K0  H30  C25  N26  108.49  3.000
 7K0  H29  C25  N26  114.16  3.000
 7K0  C17  C25  N26  109.67  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
 7K0  CONST_01  C10  C11  C12  C1      0.00   0.0  0
 7K0  CONST_02  C10  C9   C8   C1      0.00   0.0  0
 7K0  CONST_03  C11  C12  C1   C8      0.00   0.0  0
 7K0  CONST_04  C11  C10  C9   C8      0.00   0.0  0
 7K0  CONST_05  C12  C11  C10  C9      0.00   0.0  0
 7K0  CONST_06  C12  C1   C8   C9      0.00   0.0  0
 7K0  CONST_07  C11  C12  C1   C2    180.00   0.0  0
 7K0  CONST_08  C9   C8   C1   C2    180.00   0.0  0
 7K0  CONST_09  H6   C11  C12  C1    180.00   0.0  0
 7K0  CONST_10  H4   C9   C8   C1    180.00   0.0  0
 7K0  CONST_11  H7   C12  C1   C8    180.00   0.0  0
 7K0  CONST_12  H5   C10  C9   C8    180.00   0.0  0
 7K0  CONST_13  H3   C8   C9   C10   180.00   0.0  0
 7K0  CONST_14  O27  C18  N19  C20     0.00   0.0  0
 7K0  CONST_15  C17  C18  N19  C20   180.00   0.0  0
 7K0  CONST_16  H23  N19  C18  C17     0.00   0.0  0
 7K0  CONST_17  H27  O29  C28  C20   180.00   0.0  0
 7K0  Var_01    O3   C2   C1   C8    110.20  30.0  2
 7K0  Var_02    O7   C4   O3   C2      3.41  30.0  3
 7K0  Var_03    C24  C22  C21  C20   178.69  30.0  3
 7K0  Var_04    O3   C4   N5   C6   -165.31  30.0  1
 7K0  Var_05    C17  N16  P13  C6    110.73  30.0  3
 7K0  Var_06    C4   N5   C6   P13    88.48  30.0  2
 7K0  Var_07    N5   C6   P13  O14    82.05  30.0  1
 7K0  Var_08    H12  C24  C22  C21    62.49  30.0  3
 7K0  Var_09    H24  C23  C22  C21  -175.87  30.0  3
 7K0  Var_10    H15  N26  C25  C17   164.99  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
 7K0  chir_01  C20  C28  N19  C21  negativ
 7K0  chir_03  C17  N16  C18  C25  positiv
 7K0  chir_04  P13  O15  O14  N16  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
 7K0  plan-1  C1   0.020
 7K0  plan-1  C2   0.020
 7K0  plan-1  C8   0.020
 7K0  plan-1  C9   0.020
 7K0  plan-1  C10  0.020
 7K0  plan-1  C11  0.020
 7K0  plan-1  C12  0.020
 7K0  plan-1  H3   0.020
 7K0  plan-1  H4   0.020
 7K0  plan-1  H5   0.020
 7K0  plan-1  H6   0.020
 7K0  plan-1  H7   0.020
 7K0  plan-2  C20  0.020
 7K0  plan-2  C17  0.020
 7K0  plan-2  C18  0.020
 7K0  plan-2  N19  0.020
 7K0  plan-2  O27  0.020
 7K0  plan-2  H23  0.020
 7K0  plan-3  C20  0.020
 7K0  plan-3  C28  0.020
 7K0  plan-3  O29  0.020
 7K0  plan-3  O30  0.020
 7K0  plan-3  H27  0.020
 7K0  plan-4  O3   0.020
 7K0  plan-4  C4   0.020
 7K0  plan-4  N5   0.020
 7K0  plan-4  O7   0.020

