# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 10:50:05 2020
#   Inital geometry file: a 141 line input string
#   Ligand name: (2~{S})-4-methyl-2-[[(2~{S})-3-oxidanyl-2-[[oxidanyl(phenylmethoxycarbonylaminomethyl)phosphoryl]amino]propanoyl]amino]pentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](NC(=O)[C@H](CO)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
 79F  79F  '(2~{S})-4-methyl-2-[[(2~{S})-3-oxidanyl-2-[[oxidanyl(phenylmethoxycarbonylaminomethyl)phosphoryl]amino]propanoyl]amino]pentanoic acid'  ligand  56  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_79F
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
 79F  C2   C  CR16   0  -0.303   7.3321  -0.7962   1.4098
 79F  C3   C  CR16   0  -0.241   8.6742  -0.4733   1.2459
 79F  C8   C  CR6    0   0.075   6.5457  -1.1333   0.3144
 79F  C9   C  CH2    0  -0.230   5.0962  -1.4755   0.4889
 79F  C13  C  C      0   0.748   3.0078  -0.5831  -0.1665
 79F  C24  C  C      0   0.565  -3.3003   1.0069  -0.0114
 79F  N25  N  NH1    0  -0.622  -3.9425  -0.1192   0.3358
 79F  C27  C  CH2    0  -0.442  -5.5985  -1.8887   0.1682
 79F  C33  C  CH3    0  -0.649  -5.0456  -4.3142  -0.0708
 79F  C4   C  CR16   0  -0.264   9.2390  -0.4783  -0.0210
 79F  C5   C  CR16   0  -0.242   8.4587  -0.8122  -1.1228
 79F  C6   C  CR16   0  -0.283   7.1220  -1.1390  -0.9550
 79F  C17  C  CH2    0  -0.558   1.0144   0.6489  -0.8884
 79F  P18  P  P      0   1.229   0.5638   1.9861   0.3026
 79F  O19  O  O      0  -0.806   0.8933   1.4826   1.6873
 79F  O20  O  OP    -1  -0.814   1.1673   3.2750  -0.2030
 79F  N21  N  NH1    0  -0.783  -1.1164   2.0858   0.0609
 79F  C23  C  CH1    0  -0.245  -2.0546   1.3066   0.8219
 79F  C47  C  CH2    0  -0.136  -2.4672   1.9589   2.1420
 79F  O50  O  OH1    0  -0.669  -3.0279   3.2200   1.8662
 79F  O12  O  O2     0  -0.486   4.3415  -0.4288  -0.1232
 79F  O14  O  O      0  -0.527   2.4258  -1.5193   0.3453
 79F  N15  N  NH1    0  -0.648   2.4413   0.4063  -0.8735
 79F  C26  C  CH1    0  -0.198  -5.2848  -0.4172  -0.1037
 79F  C28  C  CH1    0  -0.226  -4.6447  -2.8983  -0.4751
 79F  C29  C  CH3    0  -0.659  -4.6008  -2.7676  -1.9935
 79F  C41  C  C      0   0.412  -6.3481   0.4852   0.5742
 79F  O42  O  OC    -1  -0.622  -7.4811   0.4473   0.0510
 79F  O43  O  O      0  -0.587  -6.0014   1.1363   1.5733
 79F  H1   H  HCR6   0   0.255   6.8953  -0.7879   2.4015
 79F  H2   H  HCR6   0   0.257   9.2748  -0.2158   2.1088
 79F  H3   H  HCH2   0   0.244   4.8655  -2.4325   0.0146
 79F  H4   H  HCH2   0   0.245   4.8481  -1.5595   1.5495
 79F  H5   H  HNH1   0   0.383  -3.6282  -0.5908   1.1700
 79F  H6   H  HCH2   0   0.221  -5.6096  -2.0539   1.2531
 79F  H7   H  HCH2   0   0.228  -6.6158  -2.0848  -0.1810
 79F  H8   H  HCH3   0   0.211  -6.0456  -4.5551  -0.4389
 79F  H9   H  HCH3   0   0.223  -4.3557  -5.0546  -0.4795
 79F  H10  H  HCH3   0   0.222  -5.0552  -4.4314   1.0145
 79F  H11  H  HCR6   0   0.258  10.2836  -0.2274  -0.1527
 79F  H12  H  HCR6   0   0.257   8.8948  -0.8198  -2.1135
 79F  H13  H  HCR6   0   0.254   6.5240  -1.4039  -1.8191
 79F  H14  H  HCH2   0   0.247   0.4958  -0.2781  -0.6448
 79F  H15  H  HCH2   0   0.244   0.7121   0.9273  -1.9001
 79F  H17  H  HNH1   0   0.360  -1.4619   2.9957  -0.2048
 79F  H18  H  HCH1   0   0.256  -1.5808   0.3565   1.0889
 79F  H19  H  HCH2   0   0.192  -3.1779   1.3082   2.6657
 79F  H20  H  HCH2   0   0.204  -1.5669   2.0375   2.7619
 79F  H21  H  HOH1   0   0.454  -3.3027   3.6131   2.6986
 79F  H22  H  HNH1   0   0.391   3.0321   1.1682  -1.1680
 79F  H23  H  HCH1   0   0.232  -5.3357  -0.2412  -1.1806
 79F  H24  H  HCH1   0   0.213  -3.6346  -2.7154  -0.0918
 79F  H25  H  HCH3   0   0.229  -4.2508  -1.7852  -2.3123
 79F  H26  H  HCH3   0   0.225  -3.9264  -3.5083  -2.4269
 79F  H27  H  HCH3   0   0.211  -5.5909  -2.9285  -2.4285
 79F  O45  O  O      0  -0.506  -3.6668   1.7346  -0.9227

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
 79F  C5   C6   aromatic  1.386  0.020  1.386
 79F  C5   C4   aromatic  1.391  0.020  1.391
 79F  C6   C8   aromatic  1.394  0.020  1.394
 79F  C4   C3   aromatic  1.387  0.020  1.387
 79F  C8   C9   single    1.499  0.020  1.499
 79F  C8   C2   aromatic  1.390  0.020  1.390
 79F  C3   C2   aromatic  1.390  0.020  1.390
 79F  C9   O12  single    1.428  0.020  1.428
 79F  O12  C13  single    1.343  0.020  1.343
 79F  O14  C13  double    1.215  0.020  1.215
 79F  C13  N15  single    1.341  0.020  1.341
 79F  N15  C17  single    1.448  0.020  1.448
 79F  C17  P18  single    1.847  0.020  1.847
 79F  O19  P18  deloc     1.510  0.020  1.510
 79F  O20  P18  deloc     1.510  0.020  1.510
 79F  P18  N21  single    1.700  0.020  1.700
 79F  O43  C41  deloc     1.242  0.020  1.242
 79F  O42  C41  deloc     1.249  0.020  1.249
 79F  C41  C26  single    1.551  0.020  1.551
 79F  C26  N25  single    1.444  0.020  1.444
 79F  C26  C27  single    1.529  0.020  1.529
 79F  N21  C23  single    1.438  0.020  1.438
 79F  N25  C24  single    1.342  0.020  1.342
 79F  C24  O45  double    1.222  0.020  1.222
 79F  C24  C23  single    1.528  0.020  1.528
 79F  C23  C47  single    1.529  0.020  1.529
 79F  C27  C28  single    1.531  0.020  1.531
 79F  C28  C29  single    1.525  0.020  1.525
 79F  C28  C33  single    1.526  0.020  1.526
 79F  C47  O50  single    1.407  0.020  1.407
 79F  C2   H1   single    0.930  0.020  1.080
 79F  C3   H2   single    0.930  0.020  1.080
 79F  C9   H3   single    0.970  0.020  1.090
 79F  C9   H4   single    0.970  0.020  1.090
 79F  N25  H5   single    0.890  0.020  1.040
 79F  C27  H6   single    0.970  0.020  1.090
 79F  C27  H7   single    0.970  0.020  1.090
 79F  C33  H8   single    0.970  0.020  1.090
 79F  C33  H9   single    0.970  0.020  1.090
 79F  C33  H10  single    0.970  0.020  1.090
 79F  C4   H11  single    0.930  0.020  1.080
 79F  C5   H12  single    0.930  0.020  1.080
 79F  C6   H13  single    0.930  0.020  1.080
 79F  C17  H14  single    0.970  0.020  1.090
 79F  C17  H15  single    0.970  0.020  1.090
 79F  N21  H17  single    0.890  0.020  1.040
 79F  C23  H18  single    0.970  0.020  1.090
 79F  C47  H19  single    0.970  0.020  1.090
 79F  C47  H20  single    0.970  0.020  1.090
 79F  O50  H21  single    0.850  0.020  0.980
 79F  N15  H22  single    0.860  0.020  1.020
 79F  C26  H23  single    0.970  0.020  1.090
 79F  C28  H24  single    0.970  0.020  1.090
 79F  C29  H25  single    0.970  0.020  1.090
 79F  C29  H26  single    0.970  0.020  1.090
 79F  C29  H27  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
 79F  H1   C2   C8   119.67  3.000
 79F  H1   C2   C3   119.69  3.000
 79F  C8   C2   C3   120.64  3.000
 79F  H2   C3   C4   120.20  3.000
 79F  H2   C3   C2   119.80  3.000
 79F  C4   C3   C2   119.99  3.000
 79F  C6   C8   C9   120.31  3.000
 79F  C9   C8   C2   120.70  3.000
 79F  C6   C8   C2   118.99  3.000
 79F  H4   C9   H3   107.82  3.000
 79F  H4   C9   O12  110.64  3.000
 79F  H3   C9   O12  110.13  3.000
 79F  H4   C9   C8   110.50  3.000
 79F  H3   C9   C8   110.70  3.000
 79F  O12  C9   C8   107.08  3.000
 79F  N15  C13  O14  126.00  3.000
 79F  N15  C13  O12  110.58  3.000
 79F  O14  C13  O12  123.39  3.000
 79F  O45  C24  C23  122.28  3.000
 79F  C23  C24  N25  114.42  3.000
 79F  O45  C24  N25  123.29  3.000
 79F  H5   N25  C26  116.43  3.000
 79F  H5   N25  C24  117.21  3.000
 79F  C26  N25  C24  122.64  3.000
 79F  H7   C27  H6   106.22  3.000
 79F  H7   C27  C28  109.11  3.000
 79F  H6   C27  C28  108.81  3.000
 79F  H7   C27  C26  107.86  3.000
 79F  H6   C27  C26  108.83  3.000
 79F  C28  C27  C26  115.61  3.000
 79F  H10  C33  H9   107.76  3.000
 79F  H10  C33  H8   107.66  3.000
 79F  H9   C33  H8   107.62  3.000
 79F  H10  C33  C28  111.43  3.000
 79F  H9   C33  C28  111.35  3.000
 79F  H8   C33  C28  110.84  3.000
 79F  H11  C4   C5   120.05  3.000
 79F  H11  C4   C3   120.22  3.000
 79F  C5   C4   C3   119.73  3.000
 79F  H12  C5   C6   119.84  3.000
 79F  H12  C5   C4   120.04  3.000
 79F  C6   C5   C4   120.12  3.000
 79F  H13  C6   C5   119.55  3.000
 79F  H13  C6   C8   119.93  3.000
 79F  C5   C6   C8   120.52  3.000
 79F  H15  C17  H14  106.99  3.000
 79F  H15  C17  N15  108.98  3.000
 79F  H14  C17  N15  108.92  3.000
 79F  H15  C17  P18  110.20  3.000
 79F  H14  C17  P18  110.84  3.000
 79F  N15  C17  P18  110.81  3.000
 79F  N21  P18  O20  107.29  3.000
 79F  N21  P18  O19  111.45  3.000
 79F  O20  P18  O19  120.29  3.000
 79F  N21  P18  C17  101.06  3.000
 79F  O20  P18  C17  107.73  3.000
 79F  O19  P18  C17  107.27  3.000
 79F  H17  N21  C23  113.88  3.000
 79F  H17  N21  P18  115.39  3.000
 79F  C23  N21  P18  122.53  3.000
 79F  H18  C23  C47  106.05  3.000
 79F  H18  C23  N21  108.49  3.000
 79F  C47  C23  N21  113.69  3.000
 79F  H18  C23  C24  108.39  3.000
 79F  C47  C23  C24  109.53  3.000
 79F  N21  C23  C24  110.46  3.000
 79F  H20  C47  H19  107.74  3.000
 79F  H20  C47  O50  111.95  3.000
 79F  H19  C47  O50  111.54  3.000
 79F  H20  C47  C23  107.29  3.000
 79F  H19  C47  C23  109.51  3.000
 79F  O50  C47  C23  108.70  3.000
 79F  H21  O50  C47  108.11  3.000
 79F  C13  O12  C9   117.02  3.000
 79F  H22  N15  C17  116.61  3.000
 79F  H22  N15  C13  117.64  3.000
 79F  C17  N15  C13  123.04  3.000
 79F  H23  C26  C41  107.78  3.000
 79F  H23  C26  C27  108.72  3.000
 79F  C41  C26  C27  109.98  3.000
 79F  H23  C26  N25  108.07  3.000
 79F  C27  C26  N25  109.59  3.000
 79F  C41  C26  N25  112.60  3.000
 79F  H24  C28  C29  107.91  3.000
 79F  H24  C28  C33  107.72  3.000
 79F  C29  C28  C33  110.54  3.000
 79F  H24  C28  C27  108.51  3.000
 79F  C33  C28  C27  109.69  3.000
 79F  C29  C28  C27  112.33  3.000
 79F  H27  C29  H26  107.56  3.000
 79F  H27  C29  H25  107.88  3.000
 79F  H26  C29  H25  107.27  3.000
 79F  H27  C29  C28  110.96  3.000
 79F  H26  C29  C28  110.79  3.000
 79F  H25  C29  C28  112.19  3.000
 79F  O43  C41  O42  127.32  3.000
 79F  O42  C41  C26  114.92  3.000
 79F  O43  C41  C26  117.74  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
 79F  CONST_01  C5   C6   C8   C2      0.00   0.0  0
 79F  CONST_02  C5   C4   C3   C2      0.00   0.0  0
 79F  CONST_03  C6   C5   C4   C3      0.00   0.0  0
 79F  CONST_04  C6   C8   C2   C3      0.00   0.0  0
 79F  CONST_05  C4   C5   C6   C8      0.00   0.0  0
 79F  CONST_06  C4   C3   C2   C8      0.00   0.0  0
 79F  CONST_07  C9   C8   C2   C3    180.00   0.0  0
 79F  CONST_08  C5   C6   C8   C9    180.00   0.0  0
 79F  CONST_09  H13  C6   C8   C2    180.00   0.0  0
 79F  CONST_10  H11  C4   C3   C2    180.00   0.0  0
 79F  CONST_11  H12  C5   C4   C3    180.00   0.0  0
 79F  CONST_12  H2   C3   C2   C8    180.00   0.0  0
 79F  CONST_13  H1   C2   C3   C4    180.00   0.0  0
 79F  CONST_14  C26  N25  C24  C23   180.00   0.0  0
 79F  CONST_16  H5   N25  C24  C23     0.00   0.0  0
 79F  Var_01    O12  C9   C8   C2    112.09  30.0  2
 79F  Var_02    O14  C13  O12  C9      4.02  30.0  3
 79F  Var_03    P18  C17  N15  C13    97.59  30.0  3
 79F  Var_04    C26  C27  C28  C33   177.65  30.0  1
 79F  Var_05    O12  C13  N15  C17  -168.20  30.0  1
 79F  Var_06    C23  N21  P18  C17    90.34  30.0  3
 79F  Var_07    N15  C17  P18  O19   -64.38  30.0  1
 79F  Var_08    H25  C29  C28  C27    61.04  30.0  3
 79F  Var_09    H8   C33  C28  C27    62.73  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
 79F  chir_02  C23  N21  C24  C47  positiv
 79F  chir_03  C26  N25  C27  C41  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
 79F  plan-1  C2   0.020
 79F  plan-1  C3   0.020
 79F  plan-1  C8   0.020
 79F  plan-1  C9   0.020
 79F  plan-1  C4   0.020
 79F  plan-1  C5   0.020
 79F  plan-1  C6   0.020
 79F  plan-1  H1   0.020
 79F  plan-1  H2   0.020
 79F  plan-1  H11  0.020
 79F  plan-1  H12  0.020
 79F  plan-1  H13  0.020
 79F  plan-2  C24  0.020
 79F  plan-2  N25  0.020
 79F  plan-2  C23  0.020
 79F  plan-2  C26  0.020
 79F  plan-2  H5   0.020
 79F  plan-2  O45  0.020
 79F  plan-3  C26  0.020
 79F  plan-3  C41  0.020
 79F  plan-3  O42  0.020
 79F  plan-3  O43  0.020
 79F  plan-4  C13  0.020
 79F  plan-4  O12  0.020
 79F  plan-4  O14  0.020
 79F  plan-4  N15  0.020

