# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 19:45:49 2020
#   Inital geometry file: a 143 line input string
#   Ligand name: (2~{S})-3-azanyl-2-[[(2~{S})-4-methyl-2-[[oxidanyl(phenylmethoxycarbonylaminomethyl)phosphoryl]amino]pentanoyl]amino]propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](N[P](O)(=O)CNC(=O)OCc1ccccc1)C(=O)N[C@@H](CN)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
 8L2  8L2  '(2~{S})-3-azanyl-2-[[(2~{S})-4-methyl-2-[[oxidanyl(phenylmethoxycarbonylaminomethyl)phosphoryl]amino]pentanoyl]amino]propanoic acid'  ligand  57  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 GRAND
;

data_comp_8L2
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
 8L2  C3   C  CH2    0  -0.562   0.5609   0.2801   1.1898
 8L2  C8   C  CH2    0  -0.234   4.6449   0.8475  -1.2616
 8L2  C9   C  CR6    0   0.075   6.0884   0.6756  -0.8962
 8L2  C10  C  CR16   0  -0.298   6.9079   1.7814  -0.6970
 8L2  C11  C  CR16   0  -0.242   8.2385   1.6190  -0.3314
 8L2  C12  C  CR16   0  -0.263   8.7593   0.3445  -0.1569
 8L2  C13  C  CR16   0  -0.242   7.9468  -0.7664  -0.3531
 8L2  C14  C  CR16   0  -0.284   6.6200  -0.6003  -0.7212
 8L2  C16  C  CH1    0  -0.191  -2.3256  -1.4020   0.2192
 8L2  C19  C  CH3    0  -0.649  -3.1672  -1.9905  -2.6906
 8L2  C20  C  CH3    0  -0.650  -4.2932  -4.0631  -1.8462
 8L2  C21  C  C      0   0.575  -3.4779  -0.4772   0.5977
 8L2  N23  N  NH1    0  -0.620  -3.5055   0.7003  -0.0386
 8L2  C24  C  CH1    0  -0.223  -4.5522   1.6822   0.1097
 8L2  P2   P  P      0   1.227   0.2220  -1.5349   1.2718
 8L2  O1   O  OP    -1  -0.814   0.7489  -2.0589   2.5867
 8L2  N4   N  NH1    0  -0.648   1.9762   0.5378   1.0306
 8L2  C5   C  C      0   0.749   2.5510   0.6920  -0.1737
 8L2  O6   O  O      0  -0.526   1.9696   0.9037  -1.2190
 8L2  O7   O  O2     0  -0.485   3.8881   0.6280  -0.0689
 8L2  N15  N  NH1    0  -0.791  -1.4750  -1.5279   1.3828
 8L2  C17  C  CH2    0  -0.400  -2.8465  -2.7436  -0.2911
 8L2  C18  C  CH1    0  -0.255  -3.8055  -2.6644  -1.4808
 8L2  O27  O  O      0  -0.803   0.6930  -2.1361  -0.0290
 8L2  C28  C  C      0   0.413  -5.6843   1.5127  -0.9375
 8L2  O29  O  OC    -1  -0.617  -6.5800   2.3803  -0.8884
 8L2  O30  O  O      0  -0.577  -5.6122   0.5483  -1.7162
 8L2  C25  C  CH2    0  -0.291  -3.9471   3.0815   0.0639
 8L2  H1   H  HCH2   0   0.243   0.0229   0.7375   0.3589
 8L2  H2   H  HCH2   0   0.246   0.2123   0.7709   2.1008
 8L2  H3   H  HCH2   0   0.244   4.4622   1.8523  -1.6490
 8L2  H4   H  HCH2   0   0.243   4.3527   0.1305  -2.0321
 8L2  H5   H  HCR6   0   0.255   6.5056   2.7785  -0.8320
 8L2  H6   H  HCR6   0   0.258   8.8662   2.4880  -0.1822
 8L2  H7   H  HCR6   0   0.258   9.7957   0.2148   0.1271
 8L2  H8   H  HCR6   0   0.258   8.3490  -1.7624  -0.2211
 8L2  H9   H  HCR6   0   0.254   5.9934  -1.4704  -0.8779
 8L2  H10  H  HCH1   0   0.234  -1.7295  -0.9394  -0.5723
 8L2  H11  H  HCH3   0   0.222  -3.8502  -1.9901  -3.5418
 8L2  H12  H  HCH3   0   0.222  -2.9106  -0.9498  -2.4939
 8L2  H13  H  HCH3   0   0.208  -2.2550  -2.5113  -2.9920
 8L2  H14  H  HCH3   0   0.221  -4.7620  -4.5597  -0.9948
 8L2  H15  H  HCH3   0   0.223  -5.0248  -4.0293  -2.6551
 8L2  H16  H  HCH3   0   0.210  -3.4622  -4.6911  -2.1782
 8L2  H17  H  HNH1   0   0.386  -2.9006   0.8035  -0.8384
 8L2  H18  H  HCH1   0   0.242  -4.9873   1.5421   1.1026
 8L2  H19  H  HNH2   0   0.332  -2.1912   2.6414   0.9801
 8L2  H20  H  HNH2   0   0.346  -2.5931   4.1991   1.0793
 8L2  H23  H  HNH1   0   0.392   2.5719   0.2639   1.7963
 8L2  H24  H  HNH1   0   0.360  -1.8777  -2.0712   2.1329
 8L2  H25  H  HCH2   0   0.222  -1.9754  -3.3489  -0.5624
 8L2  H26  H  HCH2   0   0.212  -3.3426  -3.2599   0.5373
 8L2  H27  H  HCH1   0   0.230  -4.6744  -2.0641  -1.1903
 8L2  H29  H  HCH2   0   0.191  -3.5346   3.2601  -0.9419
 8L2  H30  H  HCH2   0   0.229  -4.7537   3.8008   0.1991
 8L2  N26  N  NH2    0  -0.796  -2.9755   3.2636   1.1317
 8L2  O22  O  O      0  -0.519  -4.2744  -0.7987   1.4731

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
 8L2  C11  C10  aromatic  1.389  0.020  1.389
 8L2  C11  C12  aromatic  1.388  0.020  1.388
 8L2  C10  C9   aromatic  1.391  0.020  1.391
 8L2  C12  C13  aromatic  1.390  0.020  1.390
 8L2  C9   C8   single    1.499  0.020  1.499
 8L2  C9   C14  aromatic  1.393  0.020  1.393
 8L2  C8   O7   single    1.430  0.020  1.430
 8L2  C13  C14  aromatic  1.387  0.020  1.387
 8L2  O7   C5   single    1.343  0.020  1.343
 8L2  O6   C5   double    1.215  0.020  1.215
 8L2  C5   N4   single    1.343  0.020  1.343
 8L2  N4   C3   single    1.447  0.020  1.447
 8L2  C3   P2   single    1.848  0.020  1.848
 8L2  O27  P2   deloc     1.508  0.020  1.508
 8L2  O30  C28  deloc     1.242  0.020  1.242
 8L2  O1   P2   deloc     1.510  0.020  1.510
 8L2  O29  C28  deloc     1.248  0.020  1.248
 8L2  P2   N15  single    1.701  0.020  1.701
 8L2  C28  C24  single    1.551  0.020  1.551
 8L2  N15  C16  single    1.447  0.020  1.447
 8L2  C24  N23  single    1.443  0.020  1.443
 8L2  C24  C25  single    1.525  0.020  1.525
 8L2  N23  C21  single    1.339  0.020  1.339
 8L2  C21  O22  double    1.226  0.020  1.226
 8L2  C21  C16  single    1.525  0.020  1.525
 8L2  C16  C17  single    1.527  0.020  1.527
 8L2  C25  N26  single    1.455  0.020  1.455
 8L2  C17  C18  single    1.530  0.020  1.530
 8L2  C20  C18  single    1.526  0.020  1.526
 8L2  C18  C19  single    1.525  0.020  1.525
 8L2  C3   H1   single    0.970  0.020  1.090
 8L2  C3   H2   single    0.970  0.020  1.090
 8L2  C8   H3   single    0.970  0.020  1.090
 8L2  C8   H4   single    0.970  0.020  1.090
 8L2  C10  H5   single    0.930  0.020  1.080
 8L2  C11  H6   single    0.930  0.020  1.080
 8L2  C12  H7   single    0.930  0.020  1.080
 8L2  C13  H8   single    0.930  0.020  1.080
 8L2  C14  H9   single    0.930  0.020  1.080
 8L2  C16  H10  single    0.970  0.020  1.090
 8L2  C19  H11  single    0.970  0.020  1.090
 8L2  C19  H12  single    0.970  0.020  1.090
 8L2  C19  H13  single    0.970  0.020  1.090
 8L2  C20  H14  single    0.970  0.020  1.090
 8L2  C20  H15  single    0.970  0.020  1.090
 8L2  C20  H16  single    0.970  0.020  1.090
 8L2  N23  H17  single    0.860  0.020  1.020
 8L2  C24  H18  single    0.970  0.020  1.090
 8L2  N26  H19  single    0.890  0.020  1.040
 8L2  N26  H20  single    0.890  0.020  1.040
 8L2  N4   H23  single    0.890  0.020  1.040
 8L2  N15  H24  single    0.890  0.020  1.040
 8L2  C17  H25  single    0.970  0.020  1.090
 8L2  C17  H26  single    0.970  0.020  1.090
 8L2  C18  H27  single    0.970  0.020  1.090
 8L2  C25  H29  single    0.970  0.020  1.090
 8L2  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
 8L2  H2   C3   H1   106.83  3.000
 8L2  H2   C3   N4   108.90  3.000
 8L2  H1   C3   N4   108.91  3.000
 8L2  H2   C3   P2   110.23  3.000
 8L2  H1   C3   P2   110.81  3.000
 8L2  N4   C3   P2   111.05  3.000
 8L2  H4   C8   H3   107.99  3.000
 8L2  H4   C8   O7   110.25  3.000
 8L2  H3   C8   O7   110.40  3.000
 8L2  H4   C8   C9   110.75  3.000
 8L2  H3   C8   C9   110.67  3.000
 8L2  O7   C8   C9   106.79  3.000
 8L2  C14  C9   C10  119.03  3.000
 8L2  C14  C9   C8   120.21  3.000
 8L2  C10  C9   C8   120.74  3.000
 8L2  H5   C10  C11  119.73  3.000
 8L2  H5   C10  C9   119.67  3.000
 8L2  C11  C10  C9   120.60  3.000
 8L2  H6   C11  C12  120.16  3.000
 8L2  H6   C11  C10  119.86  3.000
 8L2  C12  C11  C10  119.98  3.000
 8L2  H7   C12  C13  120.06  3.000
 8L2  H7   C12  C11  120.15  3.000
 8L2  C13  C12  C11  119.79  3.000
 8L2  H8   C13  C14  119.88  3.000
 8L2  H8   C13  C12  120.07  3.000
 8L2  C14  C13  C12  120.06  3.000
 8L2  H9   C14  C13  119.69  3.000
 8L2  H9   C14  C9   119.77  3.000
 8L2  C13  C14  C9   120.54  3.000
 8L2  H10  C16  C17  108.40  3.000
 8L2  H10  C16  N15  107.37  3.000
 8L2  C17  C16  N15  113.13  3.000
 8L2  H10  C16  C21  109.57  3.000
 8L2  C17  C16  C21  110.97  3.000
 8L2  N15  C16  C21  107.30  3.000
 8L2  H13  C19  H12  107.97  3.000
 8L2  H13  C19  H11  107.91  3.000
 8L2  H12  C19  H11  106.72  3.000
 8L2  H13  C19  C18  110.95  3.000
 8L2  H12  C19  C18  112.17  3.000
 8L2  H11  C19  C18  110.91  3.000
 8L2  H16  C20  H15  107.60  3.000
 8L2  H16  C20  H14  107.58  3.000
 8L2  H15  C20  H14  107.72  3.000
 8L2  H16  C20  C18  110.88  3.000
 8L2  H15  C20  C18  111.32  3.000
 8L2  H14  C20  C18  111.57  3.000
 8L2  O22  C21  N23  123.81  3.000
 8L2  O22  C21  C16  120.59  3.000
 8L2  N23  C21  C16  115.53  3.000
 8L2  H17  N23  C24  116.56  3.000
 8L2  H17  N23  C21  117.05  3.000
 8L2  C24  N23  C21  124.38  3.000
 8L2  H18  C24  C25  107.63  3.000
 8L2  H18  C24  C28  107.98  3.000
 8L2  C25  C24  C28  111.68  3.000
 8L2  H18  C24  N23  107.15  3.000
 8L2  C25  C24  N23  109.48  3.000
 8L2  C28  C24  N23  112.68  3.000
 8L2  O27  P2   N15  111.68  3.000
 8L2  N15  P2   O1   107.02  3.000
 8L2  O27  P2   O1   120.24  3.000
 8L2  N15  P2   C3   100.48  3.000
 8L2  O1   P2   C3   108.38  3.000
 8L2  O27  P2   C3   107.21  3.000
 8L2  H23  N4   C5   117.34  3.000
 8L2  H23  N4   C3   116.49  3.000
 8L2  C5   N4   C3   122.51  3.000
 8L2  O7   C5   O6   123.51  3.000
 8L2  O6   C5   N4   125.93  3.000
 8L2  O7   C5   N4   110.53  3.000
 8L2  C5   O7   C8   117.05  3.000
 8L2  H24  N15  P2   116.37  3.000
 8L2  H24  N15  C16  114.19  3.000
 8L2  P2   N15  C16  122.31  3.000
 8L2  H26  C17  H25  106.70  3.000
 8L2  H26  C17  C18  109.19  3.000
 8L2  H25  C17  C18  109.55  3.000
 8L2  H26  C17  C16  108.42  3.000
 8L2  H25  C17  C16  107.28  3.000
 8L2  C18  C17  C16  115.35  3.000
 8L2  H27  C18  C17  108.62  3.000
 8L2  H27  C18  C20  108.20  3.000
 8L2  C17  C18  C20  109.82  3.000
 8L2  H27  C18  C19  107.47  3.000
 8L2  C20  C18  C19  110.42  3.000
 8L2  C17  C18  C19  112.17  3.000
 8L2  O30  C28  O29  127.32  3.000
 8L2  O29  C28  C24  114.91  3.000
 8L2  O30  C28  C24  117.76  3.000
 8L2  H30  C25  H29  106.47  3.000
 8L2  H30  C25  N26  108.70  3.000
 8L2  H29  C25  N26  113.56  3.000
 8L2  H30  C25  C24  107.96  3.000
 8L2  H29  C25  C24  108.95  3.000
 8L2  N26  C25  C24  110.96  3.000
 8L2  H20  N26  H19  105.52  3.000
 8L2  H20  N26  C25  109.27  3.000
 8L2  H19  N26  C25  109.29  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
 8L2  CONST_01  C12  C11  C10  C9      0.00   0.0  0
 8L2  CONST_02  C12  C13  C14  C9      0.00   0.0  0
 8L2  CONST_03  C13  C12  C11  C10     0.00   0.0  0
 8L2  CONST_04  C13  C14  C9   C10     0.00   0.0  0
 8L2  CONST_05  C14  C9   C10  C11     0.00   0.0  0
 8L2  CONST_06  C14  C13  C12  C11     0.00   0.0  0
 8L2  CONST_07  C11  C10  C9   C8    180.00   0.0  0
 8L2  CONST_08  C13  C14  C9   C8    180.00   0.0  0
 8L2  CONST_09  H6   C11  C10  C9    180.00   0.0  0
 8L2  CONST_10  H8   C13  C14  C9    180.00   0.0  0
 8L2  CONST_11  H7   C12  C11  C10   180.00   0.0  0
 8L2  CONST_12  H9   C14  C9   C10   180.00   0.0  0
 8L2  CONST_13  H5   C10  C11  C12   180.00   0.0  0
 8L2  CONST_14  C24  N23  C21  C16   180.00   0.0  0
 8L2  CONST_15  O22  C21  N23  C24     0.00   0.0  0
 8L2  CONST_16  H17  N23  C21  C16     0.00   0.0  0
 8L2  Var_01    O7   C8   C9   C10  -101.70  30.0  2
 8L2  Var_02    O7   C5   N4   C3   -166.59  30.0  2
 8L2  Var_03    C16  N15  P2   C3     82.35  30.0  3
 8L2  Var_04    C20  C18  C17  C16  -177.53  30.0  3
 8L2  Var_05    C5   N4   C3   P2     92.77  30.0  2
 8L2  Var_06    N4   C3   P2   O1     70.41  30.0  1
 8L2  Var_07    H14  C20  C18  C19  -179.49  30.0  3
 8L2  Var_08    H11  C19  C18  C20    54.28  30.0  3
 8L2  Var_09    H19  N26  C25  C24    65.17  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
 8L2  chir_01  C16  N15  C21  C17  positiv
 8L2  chir_02  C24  N23  C28  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
 8L2  plan-1  C8   0.020
 8L2  plan-1  C9   0.020
 8L2  plan-1  C10  0.020
 8L2  plan-1  C11  0.020
 8L2  plan-1  C12  0.020
 8L2  plan-1  C13  0.020
 8L2  plan-1  C14  0.020
 8L2  plan-1  H5   0.020
 8L2  plan-1  H6   0.020
 8L2  plan-1  H7   0.020
 8L2  plan-1  H8   0.020
 8L2  plan-1  H9   0.020
 8L2  plan-2  C16  0.020
 8L2  plan-2  C21  0.020
 8L2  plan-2  N23  0.020
 8L2  plan-2  C24  0.020
 8L2  plan-2  H17  0.020
 8L2  plan-2  O22  0.020
 8L2  plan-3  C24  0.020
 8L2  plan-3  C28  0.020
 8L2  plan-3  O29  0.020
 8L2  plan-3  O30  0.020
 8L2  plan-4  N4   0.020
 8L2  plan-4  C5   0.020
 8L2  plan-4  O6   0.020
 8L2  plan-4  O7   0.020

