# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 08:29:01 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  52  28  .  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_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  -0.384    2.1767   1.3098  -0.1434
 7GR  C9   C  CH1    0  -0.201    5.8317   0.4057  -0.3132
 7GR  C10  C  C      0   0.416    6.4475   1.6830  -0.9430
 7GR  C14  C  CH2    0  -0.442    6.4144  -0.8457  -0.9675
 7GR  C19  C  CH3    0  -0.653    6.5650  -3.3321  -1.1634
 7GR  C31  C  CH2    0  -0.562   -0.8624   0.1372   1.2204
 7GR  N1   N  NH1    0  -0.793    1.3238   1.7537   0.9280
 7GR  C5   C  C      0   0.531    3.6221   1.2140   0.3160
 7GR  O6   O  O      0  -0.511    4.0401   1.8643   1.2653
 7GR  N7   N  NH1    0  -0.622    4.3899   0.3818  -0.4010
 7GR  O11  O  O      0  -0.595    5.6993   2.4204  -1.6063
 7GR  O12  O  OC    -1  -0.618    7.6671   1.8374  -0.7301
 7GR  C17  C  CH1    0  -0.224    5.9218  -2.1786  -0.3996
 7GR  C23  C  CH3    0  -0.660    6.2009  -2.3038   1.0944
 7GR  P28  P  P      0   1.232   -0.3664   1.8390   0.7057
 7GR  O29  O  OP    -1  -0.814   -0.9019   2.8134   1.7280
 7GR  O30  O  O      0  -0.808   -0.7253   1.9961  -0.7517
 7GR  C39  C  CH2    0  -0.233   -4.9443  -1.0089  -1.0318
 7GR  C42  C  CR6    0   0.075   -6.3890  -0.7191  -0.7543
 7GR  C43  C  CR16   0  -0.299   -7.0619   0.2755  -1.4556
 7GR  C45  C  CR16   0  -0.241   -8.3949   0.5556  -1.1813
 7GR  C47  C  CR16   0  -0.263   -9.0649  -0.1560  -0.1961
 7GR  C49  C  CR16   0  -0.242   -8.3994  -1.1507   0.5111
 7GR  C51  C  CR16   0  -0.284   -7.0699  -1.4299   0.2319
 7GR  N34  N  NH1    0  -0.648   -2.2925  -0.0404   1.0873
 7GR  C36  C  C      0   0.749   -2.8600  -0.5840  -0.0008
 7GR  O37  O  O      0  -0.526   -2.2815  -1.1981  -0.8752
 7GR  O38  O  O2     0  -0.485   -4.1898  -0.3967   0.0167
 7GR  H1   H  HCH2   0   0.241    1.8453   0.3336  -0.5069
 7GR  H2   H  HCH2   0   0.239    2.1706   1.9746  -1.0205
 7GR  H3   H  HCH1   0   0.235    6.1021   0.3989   0.7456
 7GR  H4   H  HCH2   0   0.222    6.2052  -0.8192  -2.0441
 7GR  H5   H  HCH2   0   0.228    7.5018  -0.7959  -0.8685
 7GR  H6   H  HCH3   0   0.225    6.1906  -4.2965  -0.8162
 7GR  H7   H  HCH3   0   0.223    6.3638  -3.2633  -2.2342
 7GR  H8   H  HCH3   0   0.212    7.6501  -3.3307  -1.0314
 7GR  H9   H  HCH2   0   0.248   -0.3549  -0.6182   0.6210
 7GR  H10  H  HCH2   0   0.247   -0.5801  -0.0398   2.2600
 7GR  H11  H  HNH1   0   0.361    1.7079   2.5485   1.4202
 7GR  H12  H  HNH1   0   0.386    3.9882  -0.0069  -1.2407
 7GR  H14  H  HCH1   0   0.213    4.8377  -2.2422  -0.5475
 7GR  H15  H  HCH3   0   0.228    5.6653  -1.5537   1.6776
 7GR  H16  H  HCH3   0   0.225    5.8960  -3.2831   1.4679
 7GR  H17  H  HCH3   0   0.212    7.2678  -2.1882   1.3025
 7GR  H19  H  HCH2   0   0.243   -4.7640  -2.0863  -1.0475
 7GR  H20  H  HCH2   0   0.245   -4.6495  -0.6023  -2.0015
 7GR  H21  H  HCR6   0   0.255   -6.5429   0.8348  -2.2252
 7GR  H22  H  HCR6   0   0.258   -8.9090   1.3296  -1.7362
 7GR  H23  H  HCR6   0   0.259  -10.1034   0.0600   0.0189
 7GR  H24  H  HCR6   0   0.258   -8.9196  -1.7103   1.2777
 7GR  H25  H  HCR6   0   0.254   -6.5583  -2.2118   0.7811
 7GR  H26  H  HNH1   0   0.392   -2.8758   0.5225   1.6864

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  1.387  0.020  1.387
 7GR  C49  C47  aromatic  1.390  0.020  1.390
 7GR  C51  C42  aromatic  1.393  0.020  1.393
 7GR  C47  C45  aromatic  1.388  0.020  1.388
 7GR  C42  C39  single    1.499  0.020  1.499
 7GR  C42  C43  aromatic  1.391  0.020  1.391
 7GR  C45  C43  aromatic  1.389  0.020  1.389
 7GR  C39  O38  single    1.429  0.020  1.429
 7GR  O38  C36  single    1.343  0.020  1.343
 7GR  C36  O37  double    1.215  0.020  1.215
 7GR  C36  N34  single    1.342  0.020  1.342
 7GR  N34  C31  single    1.447  0.020  1.447
 7GR  C31  P28  single    1.846  0.020  1.846
 7GR  O30  P28  deloc     1.509  0.020  1.509
 7GR  O29  P28  deloc     1.510  0.020  1.510
 7GR  P28  N1   single    1.707  0.020  1.707
 7GR  O11  C10  deloc     1.242  0.020  1.242
 7GR  O12  C10  deloc     1.248  0.020  1.248
 7GR  C10  C9   single    1.551  0.020  1.551
 7GR  N1   C2   single    1.440  0.020  1.440
 7GR  C9   N7   single    1.445  0.020  1.445
 7GR  C9   C14  single    1.528  0.020  1.528
 7GR  N7   C5   single    1.340  0.020  1.340
 7GR  C5   C2   single    1.520  0.020  1.520
 7GR  C5   O6   double    1.224  0.020  1.224
 7GR  C14  C17  single    1.530  0.020  1.530
 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    0.890  0.020  1.040
 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  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    0.890  0.020  1.040

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   105.83  3.000
 7GR  H2   C2   C5   106.52  3.000
 7GR  H1   C2   C5   109.43  3.000
 7GR  H2   C2   N1   113.80  3.000
 7GR  H1   C2   N1   110.07  3.000
 7GR  C5   C2   N1   110.98  3.000
 7GR  H3   C9   N7   107.80  3.000
 7GR  H3   C9   C14  108.39  3.000
 7GR  N7   C9   C14  109.94  3.000
 7GR  H3   C9   C10  107.48  3.000
 7GR  C14  C9   C10  110.43  3.000
 7GR  N7   C9   C10  112.65  3.000
 7GR  O12  C10  O11  127.32  3.000
 7GR  O12  C10  C9   114.87  3.000
 7GR  O11  C10  C9   117.80  3.000
 7GR  H5   C14  H4   106.11  3.000
 7GR  H5   C14  C17  109.05  3.000
 7GR  H4   C14  C17  108.89  3.000
 7GR  H5   C14  C9   107.66  3.000
 7GR  H4   C14  C9   109.13  3.000
 7GR  C17  C14  C9   115.58  3.000
 7GR  H8   C19  H7   107.53  3.000
 7GR  H8   C19  H6   107.65  3.000
 7GR  H7   C19  H6   107.73  3.000
 7GR  H8   C19  C17  110.92  3.000
 7GR  H7   C19  C17  111.45  3.000
 7GR  H6   C19  C17  111.36  3.000
 7GR  H10  C31  H9   106.92  3.000
 7GR  H10  C31  N34  108.86  3.000
 7GR  H9   C31  N34  108.93  3.000
 7GR  H10  C31  P28  110.22  3.000
 7GR  H9   C31  P28  111.14  3.000
 7GR  N34  C31  P28  110.67  3.000
 7GR  H11  N1   P28  113.60  3.000
 7GR  H11  N1   C2   112.32  3.000
 7GR  P28  N1   C2   120.35  3.000
 7GR  N7   C5   O6   123.31  3.000
 7GR  O6   C5   C2   121.71  3.000
 7GR  N7   C5   C2   114.98  3.000
 7GR  H12  N7   C5   117.16  3.000
 7GR  H12  N7   C9   117.03  3.000
 7GR  C5   N7   C9   121.93  3.000
 7GR  H14  C17  C23  107.97  3.000
 7GR  H14  C17  C19  107.79  3.000
 7GR  C23  C17  C19  110.56  3.000
 7GR  H14  C17  C14  108.60  3.000
 7GR  C23  C17  C14  112.09  3.000
 7GR  C19  C17  C14  109.70  3.000
 7GR  H17  C23  H16  107.60  3.000
 7GR  H17  C23  H15  107.75  3.000
 7GR  H16  C23  H15  107.27  3.000
 7GR  H17  C23  C17  110.88  3.000
 7GR  H16  C23  C17  110.96  3.000
 7GR  H15  C23  C17  112.18  3.000
 7GR  O30  P28  O29  120.14  3.000
 7GR  O29  P28  N1   107.17  3.000
 7GR  O30  P28  N1   111.49  3.000
 7GR  N1   P28  C31  100.59  3.000
 7GR  O29  P28  C31  108.11  3.000
 7GR  O30  P28  C31  107.54  3.000
 7GR  H20  C39  H19  108.04  3.000
 7GR  H20  C39  O38  110.45  3.000
 7GR  H19  C39  O38  110.23  3.000
 7GR  H20  C39  C42  110.64  3.000
 7GR  H19  C39  C42  110.63  3.000
 7GR  O38  C39  C42  106.87  3.000
 7GR  C51  C42  C43  119.03  3.000
 7GR  C43  C42  C39  120.74  3.000
 7GR  C51  C42  C39  120.22  3.000
 7GR  H21  C43  C45  119.71  3.000
 7GR  H21  C43  C42  119.70  3.000
 7GR  C45  C43  C42  120.59  3.000
 7GR  H22  C45  C47  120.09  3.000
 7GR  H22  C45  C43  119.92  3.000
 7GR  C47  C45  C43  119.99  3.000
 7GR  H23  C47  C49  120.07  3.000
 7GR  H23  C47  C45  120.13  3.000
 7GR  C49  C47  C45  119.80  3.000
 7GR  H24  C49  C51  119.95  3.000
 7GR  H24  C49  C47  120.01  3.000
 7GR  C51  C49  C47  120.03  3.000
 7GR  H25  C51  C49  119.72  3.000
 7GR  H25  C51  C42  119.73  3.000
 7GR  C49  C51  C42  120.55  3.000
 7GR  H26  N34  C36  117.61  3.000
 7GR  H26  N34  C31  116.65  3.000
 7GR  C36  N34  C31  122.83  3.000
 7GR  O38  C36  O37  123.46  3.000
 7GR  O37  C36  N34  125.93  3.000
 7GR  O38  C36  N34  110.58  3.000
 7GR  C36  O38  C39  116.96  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  Var_01    O38  C39  C42  C43   101.98  30.0  2
 7GR  Var_02    C31  P28  N1   C2     89.30  30.0  1
 7GR  Var_03    C19  C17  C14  C9    178.94  30.0  3
 7GR  Var_04    O38  C36  N34  C31  -168.01  30.0  1
 7GR  Var_05    N34  C31  P28  N1   -178.84  30.0  2
 7GR  Var_06    N7   C5   C2   N1    156.79  30.0  1
 7GR  Var_07    P28  N1   C2   C5   -175.65  30.0  1
 7GR  Var_08    C36  N34  C31  P28    95.08  30.0  1
 7GR  Var_09    H6   C19  C17  C14  -176.90  30.0  3
 7GR  Var_10    H15  C23  C17  C14    63.38  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

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-4  N34  0.020
 7GR  plan-4  C36  0.020
 7GR  plan-4  O37  0.020
 7GR  plan-4  O38  0.020

