# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 22:30:14 2020
#   Inital geometry file: a 133 line input string
#   Ligand name: (2~{S})-4-methyl-2-[2-[[oxidanyl(phenylmethoxycarbonylaminomethyl)phosphoryl]amino]ethanoylamino]pentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](NC(=O)CN[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
 7GR  7GR  '(2~{S})-4-methyl-2-[2-[[oxidanyl(phenylmethoxycarbonylaminomethyl)phosphoryl]amino]ethanoylamino]pentanoic acid'  ligand  54  28  .  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_7GR
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
 7GR  C2   C  CH2   0  -0.369    2.2476  -0.4342  -0.3574
 7GR  C9   C  CH1   0  -0.203    5.8703   0.5697  -0.0395
 7GR  C10  C  C     0   0.557    5.8633   2.0818  -0.2159
 7GR  C14  C  CH2   0  -0.450    7.0190  -0.0616  -0.8345
 7GR  C19  C  CH3   0  -0.653    8.2686  -2.0928  -1.5595
 7GR  C31  C  CH2   0  -0.571   -1.4577  -0.3773   1.4305
 7GR  N1   N  NH1   0  -0.792    1.1216  -0.3270   0.5436
 7GR  C5   C  C     0   0.537    3.4974   0.1426   0.2862
 7GR  O6   O  O     0  -0.484    3.4832   0.6549   1.3937
 7GR  N7   N  NH1   0  -0.631    4.6110   0.0131  -0.4506
 7GR  O11  O  O     0  -0.430    5.0270   2.6952  -0.8247
 7GR  O12  O  OH1   0  -0.591    6.9090   2.6394   0.3772
 7GR  C17  C  CH1   0  -0.232    7.1372  -1.5794  -0.6742
 7GR  C23  C  CH3   0  -0.663    7.3665  -1.9863   0.7774
 7GR  P28  P  P     0   1.308   -0.4064  -0.0343  -0.0196
 7GR  O29  O  OH1   0  -0.751   -0.6221   1.5445  -0.3179
 7GR  O30  O  O     0  -0.716   -0.7351  -0.7816  -1.2611
 7GR  C39  C  CH2   0  -0.240   -5.9047  -1.2308  -0.1306
 7GR  C42  C  CR6   0   0.075   -7.1174  -0.3704  -0.3152
 7GR  C43  C  CR16  0  -0.289   -7.3237   0.3101  -1.5118
 7GR  C45  C  CR16  0  -0.242   -8.4297   1.1330  -1.6739
 7GR  C47  C  CR16  0  -0.261   -9.3408   1.2837  -0.6362
 7GR  C49  C  CR16  0  -0.242   -9.1424   0.6082   0.5611
 7GR  C51  C  CR16  0  -0.290   -8.0353  -0.2143   0.7192
 7GR  N34  N  NH1   0  -0.655   -2.8311  -0.0532   1.1593
 7GR  C36  C  C     0   0.763   -3.6893  -0.9521   0.6354
 7GR  O37  O  O     0  -0.513   -3.4388  -2.1222   0.4383
 7GR  O38  O  O2    0  -0.478   -4.8702  -0.3816   0.3832
 7GR  H1   H  HCH2  0   0.277    2.4444  -1.4763  -0.6254
 7GR  H2   H  HCH2  0   0.276    2.0756   0.0985  -1.2976
 7GR  H3   H  HCH1  0   0.293    6.0169   0.3648   1.0243
 7GR  H4   H  HCH2  0   0.250    6.8922   0.1836  -1.8944
 7GR  H5   H  HCH2  0   0.255    7.9571   0.4015  -0.5187
 7GR  H6   H  HCH3  0   0.230    8.3453  -3.1797  -1.5034
 7GR  H7   H  HCH3  0   0.228    8.1143  -1.8234  -2.6057
 7GR  H8   H  HCH3  0   0.217    9.2290  -1.6763  -1.2466
 7GR  H9   H  HCH2  0   0.297   -1.3592  -1.4295   1.6945
 7GR  H10  H  HCH2  0   0.303   -1.1104   0.1997   2.2900
 7GR  H11  H  HNH1  0   0.402    1.3696   0.0295   1.4595
 7GR  H12  H  HNH1  0   0.410    4.5298  -0.3240  -1.3981
 7GR  H13  H  HOH1  0   0.485    6.9069   3.5978   0.2328
 7GR  H14  H  HCH1  0   0.225    6.2068  -2.0435  -1.0183
 7GR  H15  H  HCH3  0   0.230    6.5221  -1.7351   1.4207
 7GR  H16  H  HCH3  0   0.234    7.5203  -3.0636   0.8565
 7GR  H17  H  HCH3  0   0.218    8.2543  -1.4951   1.1833
 7GR  H18  H  HOH1  0   0.483   -0.3425   2.1381   0.3906
 7GR  H19  H  HCH2  0   0.249   -6.1070  -2.0416   0.5720
 7GR  H20  H  HCH2  0   0.249   -5.5917  -1.6716  -1.0793
 7GR  H21  H  HCR6  0   0.256   -6.6167   0.1926  -2.3246
 7GR  H22  H  HCR6  0   0.258   -8.5814   1.6547  -2.6101
 7GR  H23  H  HCR6  0   0.259  -10.2050   1.9232  -0.7616
 7GR  H24  H  HCR6  0   0.259   -9.8507   0.7206   1.3716
 7GR  H25  H  HCR6  0   0.255   -7.8878  -0.7433   1.6536
 7GR  H26  H  HNH1  0   0.410   -3.1225   0.9070   1.2486

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
 7GR  C49  C51  aromatic  1.388  0.020  1.388
 7GR  C49  C47  aromatic  1.389  0.020  1.389
 7GR  C51  C42  aromatic  1.392  0.020  1.392
 7GR  C47  C45  aromatic  1.389  0.020  1.389
 7GR  C42  C39  single    1.498  0.020  1.498
 7GR  C42  C43  aromatic  1.392  0.020  1.392
 7GR  C45  C43  aromatic  1.388  0.020  1.388
 7GR  C39  O38  single    1.434  0.020  1.434
 7GR  O38  C36  single    1.336  0.020  1.336
 7GR  C36  O37  double    1.213  0.020  1.213
 7GR  C36  N34  single    1.349  0.020  1.349
 7GR  N34  C31  single    1.437  0.020  1.437
 7GR  C31  P28  single    1.824  0.020  1.824
 7GR  O30  P28  double    1.486  0.020  1.486
 7GR  O29  P28  single    1.621  0.020  1.621
 7GR  P28  N1   single    1.655  0.020  1.655
 7GR  O11  C10  double    1.203  0.020  1.203
 7GR  O12  C10  single    1.325  0.020  1.325
 7GR  C10  C9   single    1.522  0.020  1.522
 7GR  N1   C2   single    1.446  0.020  1.446
 7GR  C9   N7   single    1.437  0.020  1.437
 7GR  C9   C14  single    1.533  0.020  1.533
 7GR  N7   C5   single    1.342  0.020  1.342
 7GR  C5   C2   single    1.519  0.020  1.519
 7GR  C5   O6   double    1.220  0.020  1.220
 7GR  C14  C17  single    1.531  0.020  1.531
 7GR  C17  C19  single    1.526  0.020  1.526
 7GR  C17  C23  single    1.525  0.020  1.525
 7GR  C2   H1   single    0.970  0.020  1.090
 7GR  C2   H2   single    0.970  0.020  1.090
 7GR  C9   H3   single    0.970  0.020  1.090
 7GR  C14  H4   single    0.970  0.020  1.090
 7GR  C14  H5   single    0.970  0.020  1.090
 7GR  C19  H6   single    0.970  0.020  1.090
 7GR  C19  H7   single    0.970  0.020  1.090
 7GR  C19  H8   single    0.970  0.020  1.090
 7GR  C31  H9   single    0.970  0.020  1.090
 7GR  C31  H10  single    0.970  0.020  1.090
 7GR  N1   H11  single    0.890  0.020  1.040
 7GR  N7   H12  single    0.860  0.020  1.020
 7GR  O12  H13  single    0.850  0.020  0.980
 7GR  C17  H14  single    0.970  0.020  1.090
 7GR  C23  H15  single    0.970  0.020  1.090
 7GR  C23  H16  single    0.970  0.020  1.090
 7GR  C23  H17  single    0.970  0.020  1.090
 7GR  O29  H18  single    0.850  0.020  0.980
 7GR  C39  H19  single    0.970  0.020  1.090
 7GR  C39  H20  single    0.970  0.020  1.090
 7GR  C43  H21  single    0.930  0.020  1.080
 7GR  C45  H22  single    0.930  0.020  1.080
 7GR  C47  H23  single    0.930  0.020  1.080
 7GR  C49  H24  single    0.930  0.020  1.080
 7GR  C51  H25  single    0.930  0.020  1.080
 7GR  N34  H26  single    0.860  0.020  1.020

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
 7GR  H2   C2   H1   106.35  3.000
 7GR  H2   C2   C5   107.97  3.000
 7GR  H1   C2   C5   108.51  3.000
 7GR  H2   C2   N1   112.14  3.000
 7GR  H1   C2   N1   111.31  3.000
 7GR  C5   C2   N1   110.39  3.000
 7GR  H3   C9   N7   108.86  3.000
 7GR  H3   C9   C14  109.09  3.000
 7GR  N7   C9   C14  110.42  3.000
 7GR  H3   C9   C10  107.43  3.000
 7GR  C14  C9   C10  110.63  3.000
 7GR  N7   C9   C10  110.34  3.000
 7GR  O12  C10  O11  124.10  3.000
 7GR  O12  C10  C9   111.25  3.000
 7GR  O11  C10  C9   124.64  3.000
 7GR  H5   C14  H4   106.51  3.000
 7GR  H5   C14  C17  108.88  3.000
 7GR  H4   C14  C17  109.41  3.000
 7GR  H5   C14  C9   108.59  3.000
 7GR  H4   C14  C9   108.84  3.000
 7GR  C17  C14  C9   114.32  3.000
 7GR  H8   C19  H7   107.74  3.000
 7GR  H8   C19  H6   107.65  3.000
 7GR  H7   C19  H6   107.77  3.000
 7GR  H8   C19  C17  110.94  3.000
 7GR  H7   C19  C17  111.62  3.000
 7GR  H6   C19  C17  110.95  3.000
 7GR  H10  C31  H9   106.91  3.000
 7GR  H10  C31  N34  109.48  3.000
 7GR  H9   C31  N34  110.49  3.000
 7GR  H10  C31  P28  110.07  3.000
 7GR  H9   C31  P28  108.80  3.000
 7GR  N34  C31  P28  111.01  3.000
 7GR  H11  N1   P28  118.12  3.000
 7GR  H11  N1   C2   113.49  3.000
 7GR  P28  N1   C2   121.34  3.000
 7GR  N7   C5   O6   123.27  3.000
 7GR  O6   C5   C2   122.29  3.000
 7GR  N7   C5   C2   114.42  3.000
 7GR  H12  N7   C5   118.77  3.000
 7GR  H12  N7   C9   117.94  3.000
 7GR  C5   N7   C9   122.20  3.000
 7GR  H13  O12  C10  110.35  3.000
 7GR  H14  C17  C23  108.28  3.000
 7GR  H14  C17  C19  107.76  3.000
 7GR  C23  C17  C19  110.55  3.000
 7GR  H14  C17  C14  108.77  3.000
 7GR  C23  C17  C14  112.08  3.000
 7GR  C19  C17  C14  109.28  3.000
 7GR  H17  C23  H16  107.60  3.000
 7GR  H17  C23  H15  107.84  3.000
 7GR  H16  C23  H15  107.08  3.000
 7GR  H17  C23  C17  110.85  3.000
 7GR  H16  C23  C17  110.72  3.000
 7GR  H15  C23  C17  112.55  3.000
 7GR  O30  P28  O29  107.86  3.000
 7GR  O29  P28  N1   110.97  3.000
 7GR  O30  P28  N1   113.56  3.000
 7GR  N1   P28  C31  103.20  3.000
 7GR  O29  P28  C31  104.64  3.000
 7GR  O30  P28  C31  116.25  3.000
 7GR  H18  O29  P28  115.15  3.000
 7GR  H20  C39  H19  108.20  3.000
 7GR  H20  C39  O38  110.10  3.000
 7GR  H19  C39  O38  110.06  3.000
 7GR  H20  C39  C42  110.90  3.000
 7GR  H19  C39  C42  110.84  3.000
 7GR  O38  C39  C42  106.74  3.000
 7GR  C51  C42  C43  119.10  3.000
 7GR  C43  C42  C39  120.44  3.000
 7GR  C51  C42  C39  120.44  3.000
 7GR  H21  C43  C45  119.77  3.000
 7GR  H21  C43  C42  119.68  3.000
 7GR  C45  C43  C42  120.55  3.000
 7GR  H22  C45  C47  120.13  3.000
 7GR  H22  C45  C43  119.89  3.000
 7GR  C47  C45  C43  119.98  3.000
 7GR  H23  C47  C49  120.08  3.000
 7GR  H23  C47  C45  120.08  3.000
 7GR  C49  C47  C45  119.83  3.000
 7GR  H24  C49  C51  119.88  3.000
 7GR  H24  C49  C47  120.11  3.000
 7GR  C51  C49  C47  120.02  3.000
 7GR  H25  C51  C49  119.73  3.000
 7GR  H25  C51  C42  119.75  3.000
 7GR  C49  C51  C42  120.52  3.000
 7GR  H26  N34  C36  119.06  3.000
 7GR  H26  N34  C31  118.34  3.000
 7GR  C36  N34  C31  122.08  3.000
 7GR  O38  C36  O37  124.34  3.000
 7GR  O37  C36  N34  125.09  3.000
 7GR  O38  C36  N34  110.56  3.000
 7GR  C36  O38  C39  116.92  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
 7GR  CONST_01  C47  C49  C51  C42     0.00   0.0  0
 7GR  CONST_02  C47  C45  C43  C42     0.00   0.0  0
 7GR  CONST_03  C49  C51  C42  C43     0.00   0.0  0
 7GR  CONST_04  C49  C47  C45  C43     0.00   0.0  0
 7GR  CONST_05  C51  C49  C47  C45     0.00   0.0  0
 7GR  CONST_06  C51  C42  C43  C45     0.00   0.0  0
 7GR  CONST_07  C49  C51  C42  C39   180.00   0.0  0
 7GR  CONST_08  C45  C43  C42  C39   180.00   0.0  0
 7GR  CONST_09  H24  C49  C51  C42   180.00   0.0  0
 7GR  CONST_10  H22  C45  C43  C42   180.00   0.0  0
 7GR  CONST_11  H25  C51  C42  C43   180.00   0.0  0
 7GR  CONST_12  H23  C47  C45  C43   180.00   0.0  0
 7GR  CONST_13  H21  C43  C45  C47   180.00   0.0  0
 7GR  CONST_14  C9   N7   C5   C2    180.00   0.0  0
 7GR  CONST_15  O6   C5   N7   C9      0.00   0.0  0
 7GR  CONST_16  H12  N7   C5   C2      0.00   0.0  0
 7GR  CONST_17  H13  O12  C10  C9    180.00   0.0  0
 7GR  Var_01    O38  C39  C42  C43    88.58  30.0  2
 7GR  Var_02    C31  P28  N1   C2    167.42  30.0  1
 7GR  Var_03    C19  C17  C14  C9    177.38  30.0  3
 7GR  Var_04    O38  C36  N34  C31  -175.22  30.0  2
 7GR  Var_05    N34  C31  P28  N1    174.66  30.0  1
 7GR  Var_06    N7   C5   C2   N1    176.26  30.0  1
 7GR  Var_07    P28  N1   C2   C5    144.95  30.0  1
 7GR  Var_08    C36  N34  C31  P28    89.49  30.0  1
 7GR  Var_09    H6   C19  C17  C14  -177.23  30.0  3
 7GR  Var_10    H15  C23  C17  C14    64.35  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
 7GR  chir_01  C9   C10  N7   C14  negativ
 7GR  chir_02  P28  O30  O29  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
 7GR  plan-1  C39  0.020
 7GR  plan-1  C42  0.020
 7GR  plan-1  C43  0.020
 7GR  plan-1  C45  0.020
 7GR  plan-1  C47  0.020
 7GR  plan-1  C49  0.020
 7GR  plan-1  C51  0.020
 7GR  plan-1  H21  0.020
 7GR  plan-1  H22  0.020
 7GR  plan-1  H23  0.020
 7GR  plan-1  H24  0.020
 7GR  plan-1  H25  0.020
 7GR  plan-2  C2   0.020
 7GR  plan-2  C9   0.020
 7GR  plan-2  C5   0.020
 7GR  plan-2  O6   0.020
 7GR  plan-2  N7   0.020
 7GR  plan-2  H12  0.020
 7GR  plan-3  C9   0.020
 7GR  plan-3  C10  0.020
 7GR  plan-3  O11  0.020
 7GR  plan-3  O12  0.020
 7GR  plan-3  H13  0.020
 7GR  plan-4  N34  0.020
 7GR  plan-4  C36  0.020
 7GR  plan-4  O37  0.020
 7GR  plan-4  O38  0.020

