# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 22:31:20 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  57  30  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

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   0.080   4.5270  -1.9294  -0.4973
 7K0  C2   C  CH2    0  -0.244   4.0043  -0.7056  -1.1873
 7K0  C8   C  CR16   0  -0.284   3.8072  -3.1208  -0.5553
 7K0  C9   C  CR16   0  -0.242   4.2601  -4.2520   0.1066
 7K0  C10  C  CR16   0  -0.262   5.4435  -4.2037   0.8347
 7K0  C11  C  CR16   0  -0.242   6.1690  -3.0221   0.8945
 7K0  C12  C  CR16   0  -0.296   5.7095  -1.8898   0.2327
 7K0  C20  C  CH1    0  -0.162  -3.1935  -1.1927  -0.0721
 7K0  C21  C  CH2    0  -0.454  -2.2297  -2.2075   0.5426
 7K0  C22  C  CH1    0  -0.242  -0.7411  -1.9264   0.3236
 7K0  C24  C  CH3    0  -0.653   0.1010  -2.9396   1.0922
 7K0  N26  N  NH2    0  -0.803  -4.3740   4.6103   1.5969
 7K0  C6   C  CH2    0  -0.553   0.0400   1.8743  -0.3511
 7K0  P13  P  P      0   1.235  -0.6934   2.6044   1.1752
 7K0  O14  O  OP    -1  -0.795   0.1049   3.8198   1.5703
 7K0  O15  O  O      0  -0.798  -0.8591   1.4562   2.1568
 7K0  N16  N  NH1    0  -0.799  -2.2203   3.1232   0.6085
 7K0  C17  C  CH1    0  -0.206  -3.4413   2.4310   1.0019
 7K0  C18  C  C      0   0.580  -3.6632   1.1839   0.1412
 7K0  N19  N  NH1    0  -0.649  -3.0028   0.0974   0.5463
 7K0  C23  C  CH3    0  -0.668  -0.3754  -1.9366  -1.1557
 7K0  O27  O  O      0  -0.525  -4.3911   1.1924  -0.8469
 7K0  C28  C  C      0   0.406  -4.6435  -1.7167   0.0926
 7K0  O29  O  OC    -1  -0.622  -4.9957  -2.5667  -0.7513
 7K0  O30  O  O      0  -0.601  -5.3053  -1.2968   1.0563
 7K0  O3   O  O2     0  -0.485   2.9782  -0.1663  -0.3504
 7K0  C4   C  C      0   0.760   2.1173   0.7038  -0.9005
 7K0  N5   N  NH1    0  -0.665   1.2144   1.1112   0.0054
 7K0  O7   O  O      0  -0.522   2.1715   1.0707  -2.0573
 7K0  C25  C  CH2    0  -0.289  -4.6250   3.3841   0.8576
 7K0  H1   H  HCH2   0   0.247   4.7967   0.0336  -1.3292
 7K0  H2   H  HCH2   0   0.247   3.6014  -0.9608  -2.1689
 7K0  H3   H  HCR6   0   0.253   2.8885  -3.1665  -1.1290
 7K0  H4   H  HCR6   0   0.258   3.6936  -5.1725   0.0504
 7K0  H5   H  HCR6   0   0.258   5.7990  -5.0860   1.3510
 7K0  H6   H  HCR6   0   0.258   7.0921  -2.9793   1.4580
 7K0  H7   H  HCR6   0   0.255   6.2775  -0.9685   0.2844
 7K0  H8   H  HCH1   0   0.218  -2.9887  -1.1162  -1.1444
 7K0  H9   H  HCH2   0   0.224  -2.4302  -2.2761   1.6187
 7K0  H10  H  HCH2   0   0.227  -2.4661  -3.1897   0.1231
 7K0  H11  H  HCH1   0   0.219  -0.5150  -0.9359   0.7293
 7K0  H12  H  HCH3   0   0.211  -0.0869  -3.9570   0.7397
 7K0  H13  H  HCH3   0   0.226   1.1674  -2.7401   0.9704
 7K0  H14  H  HCH3   0   0.223  -0.1212  -2.9131   2.1605
 7K0  H15  H  HNH2   0   0.357  -5.0782   5.2979   1.3652
 7K0  H16  H  HNH2   0   0.345  -4.4610   4.4416   2.5915
 7K0  H18  H  HCH2   0   0.239  -0.7044   1.2420  -0.8484
 7K0  H19  H  HCH2   0   0.251   0.3060   2.6710  -1.0463
 7K0  H21  H  HNH1   0   0.367  -2.3484   4.1168   0.7753
 7K0  H22  H  HCH1   0   0.226  -3.3971   2.1064   2.0508
 7K0  H23  H  HNH1   0   0.396  -2.3570   0.2052   1.3197
 7K0  H24  H  HCH3   0   0.224   0.6981  -1.7989  -1.2947
 7K0  H25  H  HCH3   0   0.217  -0.6455  -2.8907  -1.6162
 7K0  H26  H  HCH3   0   0.230  -0.8794  -1.1448  -1.7116
 7K0  H28  H  HNH1   0   0.391   1.2009   0.6480   0.9018
 7K0  H29  H  HCH2   0   0.212  -5.5362   2.8591   1.1703
 7K0  H30  H  HCH2   0   0.224  -4.7528   3.6416  -0.1947

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  1.390  0.020  1.390
 7K0  C11  C10  aromatic  1.388  0.020  1.388
 7K0  C12  C1   aromatic  1.390  0.020  1.390
 7K0  C10  C9   aromatic  1.390  0.020  1.390
 7K0  C1   C2   single    1.499  0.020  1.499
 7K0  C1   C8   aromatic  1.393  0.020  1.393
 7K0  C9   C8   aromatic  1.387  0.020  1.387
 7K0  C2   O3   single    1.430  0.020  1.430
 7K0  O3   C4   single    1.342  0.020  1.342
 7K0  O7   C4   double    1.215  0.020  1.215
 7K0  C4   N5   single    1.342  0.020  1.342
 7K0  N5   C6   single    1.445  0.020  1.445
 7K0  C6   P13  single    1.844  0.020  1.844
 7K0  O15  P13  deloc     1.520  0.020  1.520
 7K0  O14  P13  deloc     1.507  0.020  1.507
 7K0  P13  N16  single    1.709  0.020  1.709
 7K0  O30  C28  deloc     1.242  0.020  1.242
 7K0  O29  C28  deloc     1.248  0.020  1.248
 7K0  C28  C20  single    1.551  0.020  1.551
 7K0  C20  N19  single    1.443  0.020  1.443
 7K0  C20  C21  single    1.529  0.020  1.529
 7K0  N16  C17  single    1.458  0.020  1.458
 7K0  N19  C18  single    1.334  0.020  1.334
 7K0  C18  O27  double    1.227  0.020  1.227
 7K0  C18  C17  single    1.531  0.020  1.531
 7K0  C17  C25  single    1.527  0.020  1.527
 7K0  C21  C22  single    1.531  0.020  1.531
 7K0  C22  C24  single    1.525  0.020  1.525
 7K0  C22  C23  single    1.524  0.020  1.524
 7K0  C25  N26  single    1.454  0.020  1.454
 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  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  N5   H28  single    0.860  0.020  1.020
 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   119.06  3.000
 7K0  C8   C1   C2   119.92  3.000
 7K0  C12  C1   C2   121.00  3.000
 7K0  H2   C2   H1   108.00  3.000
 7K0  H2   C2   O3   110.47  3.000
 7K0  H1   C2   O3   109.95  3.000
 7K0  H2   C2   C1   110.60  3.000
 7K0  H1   C2   C1   111.05  3.000
 7K0  O3   C2   C1   106.78  3.000
 7K0  H3   C8   C9   119.67  3.000
 7K0  H3   C8   C1   119.73  3.000
 7K0  C9   C8   C1   120.60  3.000
 7K0  H4   C9   C10  120.15  3.000
 7K0  H4   C9   C8   119.87  3.000
 7K0  C10  C9   C8   119.98  3.000
 7K0  H5   C10  C11  120.11  3.000
 7K0  H5   C10  C9   120.08  3.000
 7K0  C11  C10  C9   119.81  3.000
 7K0  H6   C11  C12  119.86  3.000
 7K0  H6   C11  C10  120.13  3.000
 7K0  C12  C11  C10  120.02  3.000
 7K0  H7   C12  C11  119.78  3.000
 7K0  H7   C12  C1   119.68  3.000
 7K0  C11  C12  C1   120.54  3.000
 7K0  H8   C20  C28  107.62  3.000
 7K0  H8   C20  N19  109.43  3.000
 7K0  C28  C20  N19  112.35  3.000
 7K0  H8   C20  C21  108.81  3.000
 7K0  N19  C20  C21  109.74  3.000
 7K0  C28  C20  C21  108.81  3.000
 7K0  H10  C21  H9   106.30  3.000
 7K0  H10  C21  C22  108.67  3.000
 7K0  H9   C21  C22  109.25  3.000
 7K0  H10  C21  C20  107.80  3.000
 7K0  H9   C21  C20  108.71  3.000
 7K0  C22  C21  C20  115.70  3.000
 7K0  H11  C22  C23  108.45  3.000
 7K0  H11  C22  C24  107.48  3.000
 7K0  C23  C22  C24  110.62  3.000
 7K0  H11  C22  C21  108.31  3.000
 7K0  C23  C22  C21  111.79  3.000
 7K0  C24  C22  C21  110.05  3.000
 7K0  H14  C24  H13  107.67  3.000
 7K0  H14  C24  H12  107.65  3.000
 7K0  H13  C24  H12  107.58  3.000
 7K0  H14  C24  C22  111.39  3.000
 7K0  H13  C24  C22  111.21  3.000
 7K0  H12  C24  C22  111.16  3.000
 7K0  H16  N26  H15  106.17  3.000
 7K0  H16  N26  C25  110.13  3.000
 7K0  H15  N26  C25  109.68  3.000
 7K0  H19  C6   H18  107.33  3.000
 7K0  H19  C6   N5   110.17  3.000
 7K0  H18  C6   N5   111.05  3.000
 7K0  H19  C6   P13  109.60  3.000
 7K0  H18  C6   P13  109.51  3.000
 7K0  N5   C6   P13  109.15  3.000
 7K0  N16  P13  O15  110.25  3.000
 7K0  N16  P13  O14  108.38  3.000
 7K0  O15  P13  O14  119.86  3.000
 7K0  N16  P13  C6   101.60  3.000
 7K0  O14  P13  C6   109.01  3.000
 7K0  O15  P13  C6   106.19  3.000
 7K0  H21  N16  C17  108.34  3.000
 7K0  H21  N16  P13  110.80  3.000
 7K0  C17  N16  P13  120.97  3.000
 7K0  H22  C17  C25  107.81  3.000
 7K0  H22  C17  C18  107.56  3.000
 7K0  C25  C17  C18  110.06  3.000
 7K0  H22  C17  N16  111.35  3.000
 7K0  C25  C17  N16  109.12  3.000
 7K0  C18  C17  N16  110.88  3.000
 7K0  O27  C18  N19  122.93  3.000
 7K0  O27  C18  C17  122.19  3.000
 7K0  N19  C18  C17  114.88  3.000
 7K0  H23  N19  C18  117.42  3.000
 7K0  H23  N19  C20  120.42  3.000
 7K0  C18  N19  C20  122.16  3.000
 7K0  H26  C23  H25  107.73  3.000
 7K0  H26  C23  H24  107.34  3.000
 7K0  H25  C23  H24  107.43  3.000
 7K0  H26  C23  C22  112.27  3.000
 7K0  H25  C23  C22  110.82  3.000
 7K0  H24  C23  C22  111.04  3.000
 7K0  O30  C28  O29  127.18  3.000
 7K0  O29  C28  C20  114.97  3.000
 7K0  O30  C28  C20  117.80  3.000
 7K0  C4   O3   C2   117.71  3.000
 7K0  O7   C4   N5   125.52  3.000
 7K0  N5   C4   O3   110.59  3.000
 7K0  O7   C4   O3   123.89  3.000
 7K0  H28  N5   C4   117.98  3.000
 7K0  H28  N5   C6   116.78  3.000
 7K0  C4   N5   C6   122.71  3.000
 7K0  H30  C25  H29  106.90  3.000
 7K0  H30  C25  C17  109.24  3.000
 7K0  H29  C25  C17  108.56  3.000
 7K0  H30  C25  N26  108.16  3.000
 7K0  H29  C25  N26  113.71  3.000
 7K0  C17  C25  N26  110.16  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  Var_01    O3   C2   C1   C8     78.32  30.0  2
 7K0  Var_02    O7   C4   O3   C2     -1.05  30.0  3
 7K0  Var_03    C24  C22  C21  C20   174.87  30.0  3
 7K0  Var_04    O3   C4   N5   C6   -169.61  30.0  1
 7K0  Var_05    C17  N16  P13  C6    108.39  30.0  3
 7K0  Var_06    C4   N5   C6   P13  -165.34  30.0  2
 7K0  Var_07    N5   C6   P13  O14    78.62  30.0  1
 7K0  Var_08    H12  C24  C22  C21    61.67  30.0  3
 7K0  Var_09    H24  C23  C22  C21  -176.36  30.0  3
 7K0  Var_10    H15  N26  C25  C17   169.90  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

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-4  O3   0.020
 7K0  plan-4  C4   0.020
 7K0  plan-4  N5   0.020
 7K0  plan-4  O7   0.020

