# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 06:36:49 2020
#   Inital geometry file: a 145 line input string
#   Ligand name: N-acetyl-L-phenylalanyl-4-[difluoro(phosphono)methyl]-L-phenylalaninamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@@H](Cc1ccccc1)C(=O)N[C@@H](Cc2ccc(cc2)C(F)(F)[P](O)(O)=O)C(N)=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
 DFM  DFM  N-acetyl-L-phenylalanyl-4-[difluoro(phosphono)methyl]-L-phenylalaninamide  ligand  57  33  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DFM
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
 DFM  C1    C  CT    0   0.538  -1.9836   4.3447  -3.8585
 DFM  O6    O  OH1   0  -0.735  -3.5692   4.1323  -6.0740
 DFM  O7    O  OH1   0  -0.734  -1.4408   2.8824  -6.0163
 DFM  O9    O  O     0  -0.667  -3.4176   2.0464  -4.4879
 DFM  C11   C  CR6   0  -0.118  -1.0691   3.6722  -2.8862
 DFM  C12   C  CR16  0  -0.259   0.2573   3.4340  -3.2348
 DFM  C13   C  CR16  0  -0.298   1.1041   2.7986  -2.3420
 DFM  C14   C  CR6   0   0.151   0.6563   2.3988  -1.0858
 DFM  C15   C  CR16  0  -0.278  -0.6713   2.6450  -0.7484
 DFM  C16   C  CR16  0  -0.263  -1.5328   3.2611  -1.6421
 DFM  C21   C  CH2   0  -0.527   1.5828   1.6944  -0.1391
 DFM  C22   C  CH1   0  -0.209   1.4187   0.1612  -0.1997
 DFM  C25   C  C     0   0.528   2.4731  -0.4796   0.7013
 DFM  O26   O  O     0  -0.481   2.2526  -0.6811   1.8850
 DFM  N27   N  NH2   0  -0.796   3.6385  -0.7391   0.1008
 DFM  N45   N  NH1   0  -0.630   0.1078  -0.2384   0.2321
 DFM  C47   C  C     0   0.578  -0.8320  -0.7591  -0.5740
 DFM  C48   C  CH1   0  -0.212  -2.1516  -1.0888   0.1247
 DFM  O49   O  O     0  -0.477  -0.6695  -0.9955  -1.7584
 DFM  N51   N  NH1   0  -0.610  -3.2611  -0.6554  -0.6788
 DFM  C4    C  CH2   0  -0.540  -2.2265  -2.6003   0.3832
 DFM  C5    C  CR6   0   0.157  -3.4637  -2.9732   1.1490
 DFM  C30   C  CR16  0  -0.306  -3.4967  -2.8550   2.5367
 DFM  C31   C  CR16  0  -0.240  -4.6460  -3.1665   3.2497
 DFM  C6    C  CR16  0  -0.271  -5.7835  -3.6018   2.5812
 DFM  C33   C  CR16  0  -0.241  -5.7614  -3.7241   1.1983
 DFM  C34   C  CR16  0  -0.313  -4.6090  -3.4104   0.4894
 DFM  C67   C  C     0   0.535  -3.9006   0.5183  -0.5027
 DFM  O70   O  O     0  -0.499  -3.6269   1.2956   0.4011
 DFM  C71   C  CH3   0  -0.801  -4.9697   0.8103  -1.5228
 DFM  F66   F  F     0  -0.335  -3.0373   4.9236  -3.2157
 DFM  F67   F  F     0  -0.332  -1.3342   5.3435  -4.5190
 DFM  P68   P  P     0   1.320  -2.7142   3.1858  -5.1105
 DFM  H12   H  HCR6  0   0.265   0.6442   3.7445  -4.1960
 DFM  H16   H  HCR6  0   0.256  -2.5605   3.4213  -1.3474
 DFM  H13   H  HCR6  0   0.255   2.1349   2.6227  -2.6259
 DFM  H15   H  HCR6  0   0.251  -1.0502   2.3553   0.2224
 DFM  H211  H  HCH2  0   0.273   2.6177   1.9452  -0.3801
 DFM  H212  H  HCH2  0   0.271   1.4053   2.0255   0.8876
 DFM  H22   H  HCH1  0   0.295   1.5479  -0.1721  -1.2303
 DFM  H45   H  HNH1  0   0.401  -0.1182  -0.0754   1.2012
 DFM  H271  H  HNH2  0   0.407   4.4200  -1.0933   0.6287
 DFM  H272  H  HNH2  0   0.412   3.7776  -0.5872  -0.8835
 DFM  H48   H  HCH1  0   0.280  -2.2132  -0.5644   1.0798
 DFM  H51   H  HNH1  0   0.399  -3.4927  -1.2090  -1.4879
 DFM  H4C1  H  HCH2  0   0.273  -1.3347  -2.9007   0.9381
 DFM  H4C2  H  HCH2  0   0.267  -2.1964  -3.1328  -0.5707
 DFM  H30   H  HCR6  0   0.247  -2.6112  -2.5207   3.0659
 DFM  H34   H  HCR6  0   0.247  -4.5993  -3.5169  -0.5892
 DFM  H31   H  HCR6  0   0.254  -4.6524  -3.0742   4.3282
 DFM  H6    H  HCR6  0   0.255  -6.6796  -3.8500   3.1353
 DFM  H33   H  HCR6  0   0.254  -6.6420  -4.0670   0.6702
 DFM  H711  H  HCH3  0   0.260  -5.7507   1.4244  -1.0803
 DFM  H712  H  HCH3  0   0.284  -4.5300   1.3675  -2.3521
 DFM  H713  H  HCH3  0   0.249  -5.4180  -0.0936  -1.9330
 DFM  HO6   H  HOH1  0   0.504  -4.4918   4.2503  -5.8094
 DFM  HO7   H  HOH1  0   0.508  -1.3494   1.9577  -6.2850

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
 DFM  C1   C11   single    1.495  0.020  1.495
 DFM  C1   F66   single    1.363  0.020  1.363
 DFM  C1   F67   single    1.362  0.020  1.362
 DFM  C1   P68   single    1.856  0.020  1.856
 DFM  O6   P68   single    1.598  0.020  1.598
 DFM  O6   HO6   single    0.850  0.020  0.980
 DFM  O7   P68   single    1.592  0.020  1.592
 DFM  O7   HO7   single    0.850  0.020  0.980
 DFM  O9   P68   double    1.477  0.020  1.477
 DFM  C11  C12   aromatic  1.392  0.020  1.392
 DFM  C11  C16   aromatic  1.390  0.020  1.390
 DFM  C12  C13   aromatic  1.385  0.020  1.385
 DFM  C12  H12   single    0.930  0.020  1.080
 DFM  C13  C14   aromatic  1.392  0.020  1.392
 DFM  C13  H13   single    0.930  0.020  1.080
 DFM  C14  C15   aromatic  1.392  0.020  1.392
 DFM  C14  C21   single    1.500  0.020  1.500
 DFM  C15  C16   aromatic  1.386  0.020  1.386
 DFM  C15  H15   single    0.930  0.020  1.080
 DFM  C16  H16   single    0.930  0.020  1.080
 DFM  C21  C22   single    1.543  0.020  1.543
 DFM  C21  H211  single    0.970  0.020  1.090
 DFM  C21  H212  single    0.970  0.020  1.090
 DFM  C22  C25   single    1.528  0.020  1.528
 DFM  C22  N45   single    1.437  0.020  1.437
 DFM  C22  H22   single    0.970  0.020  1.090
 DFM  C25  O26   double    1.221  0.020  1.221
 DFM  C25  N27   single    1.336  0.020  1.336
 DFM  N27  H271  single    0.860  0.020  1.020
 DFM  N27  H272  single    0.860  0.020  1.020
 DFM  N45  C47   single    1.343  0.020  1.343
 DFM  N45  H45   single    0.860  0.020  1.020
 DFM  C47  C48   single    1.529  0.020  1.529
 DFM  C47  O49   double    1.219  0.020  1.219
 DFM  C48  N51   single    1.437  0.020  1.437
 DFM  C48  C4    single    1.535  0.020  1.535
 DFM  C48  H48   single    0.970  0.020  1.090
 DFM  N51  C67   single    1.348  0.020  1.348
 DFM  N51  H51   single    0.860  0.020  1.020
 DFM  C4   C5    single    1.502  0.020  1.502
 DFM  C4   H4C1  single    0.970  0.020  1.090
 DFM  C4   H4C2  single    0.970  0.020  1.090
 DFM  C5   C30   aromatic  1.393  0.020  1.393
 DFM  C5   C34   aromatic  1.392  0.020  1.392
 DFM  C30  C31   aromatic  1.388  0.020  1.388
 DFM  C30  H30   single    0.930  0.020  1.080
 DFM  C31  C6    aromatic  1.389  0.020  1.389
 DFM  C31  H31   single    0.930  0.020  1.080
 DFM  C6   C33   aromatic  1.388  0.020  1.388
 DFM  C6   H6    single    0.930  0.020  1.080
 DFM  C33  C34   aromatic  1.389  0.020  1.389
 DFM  C33  H33   single    0.930  0.020  1.080
 DFM  C34  H34   single    0.930  0.020  1.080
 DFM  C67  O70   double    1.223  0.020  1.223
 DFM  C67  C71   single    1.506  0.020  1.506
 DFM  C71  H711  single    0.970  0.020  1.090
 DFM  C71  H712  single    0.970  0.020  1.090
 DFM  C71  H713  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
 DFM  P68   C1   F67   108.57  3.000
 DFM  P68   C1   F66   106.20  3.000
 DFM  F67   C1   F66   106.60  3.000
 DFM  P68   C1   C11   113.50  3.000
 DFM  F67   C1   C11   110.71  3.000
 DFM  F66   C1   C11   110.93  3.000
 DFM  HO6   O6   P68   114.68  3.000
 DFM  HO7   O7   P68   114.57  3.000
 DFM  C16   C11  C12   119.44  3.000
 DFM  C16   C11  C1    120.74  3.000
 DFM  C12   C11  C1    119.81  3.000
 DFM  H12   C12  C13   119.07  3.000
 DFM  H12   C12  C11   120.94  3.000
 DFM  C13   C12  C11   119.98  3.000
 DFM  H13   C13  C14   119.72  3.000
 DFM  H13   C13  C12   119.16  3.000
 DFM  C14   C13  C12   121.11  3.000
 DFM  C21   C14  C15   121.27  3.000
 DFM  C21   C14  C13   120.37  3.000
 DFM  C15   C14  C13   118.35  3.000
 DFM  H15   C15  C16   118.69  3.000
 DFM  H15   C15  C14   120.29  3.000
 DFM  C16   C15  C14   121.02  3.000
 DFM  H16   C16  C15   118.75  3.000
 DFM  H16   C16  C11   121.16  3.000
 DFM  C15   C16  C11   120.09  3.000
 DFM  H212  C21  H211  106.96  3.000
 DFM  H212  C21  C22   108.70  3.000
 DFM  H211  C21  C22   108.68  3.000
 DFM  H212  C21  C14   110.50  3.000
 DFM  H211  C21  C14   109.77  3.000
 DFM  C22   C21  C14   112.08  3.000
 DFM  H22   C22  N45   107.88  3.000
 DFM  H22   C22  C25   110.32  3.000
 DFM  N45   C22  C25   109.62  3.000
 DFM  H22   C22  C21   109.16  3.000
 DFM  N45   C22  C21   111.19  3.000
 DFM  C25   C22  C21   108.67  3.000
 DFM  N27   C25  O26   124.14  3.000
 DFM  N27   C25  C22   114.72  3.000
 DFM  O26   C25  C22   121.09  3.000
 DFM  H272  N27  H271  117.30  3.000
 DFM  H272  N27  C25   122.08  3.000
 DFM  H271  N27  C25   120.61  3.000
 DFM  H45   N45  C47   118.86  3.000
 DFM  H45   N45  C22   116.64  3.000
 DFM  C47   N45  C22   124.46  3.000
 DFM  O49   C47  C48   121.16  3.000
 DFM  O49   C47  N45   124.42  3.000
 DFM  C48   C47  N45   114.40  3.000
 DFM  H48   C48  C4    108.84  3.000
 DFM  H48   C48  N51   107.51  3.000
 DFM  C4    C48  N51   110.70  3.000
 DFM  H48   C48  C47   110.18  3.000
 DFM  C4    C48  C47   109.34  3.000
 DFM  N51   C48  C47   110.23  3.000
 DFM  H51   N51  C67   118.31  3.000
 DFM  H51   N51  C48   117.45  3.000
 DFM  C67   N51  C48   123.77  3.000
 DFM  H4C2  C4   H4C1  106.67  3.000
 DFM  H4C2  C4   C5    110.29  3.000
 DFM  H4C1  C4   C5    110.19  3.000
 DFM  H4C2  C4   C48   109.35  3.000
 DFM  H4C1  C4   C48   108.45  3.000
 DFM  C5    C4   C48   111.74  3.000
 DFM  C34   C5   C30   118.63  3.000
 DFM  C34   C5   C4    120.93  3.000
 DFM  C30   C5   C4    120.42  3.000
 DFM  H30   C30  C31   119.65  3.000
 DFM  H30   C30  C5    119.53  3.000
 DFM  C31   C30  C5    120.82  3.000
 DFM  H31   C31  C6    120.09  3.000
 DFM  H31   C31  C30   119.84  3.000
 DFM  C6    C31  C30   120.07  3.000
 DFM  H6    C6   C33   120.19  3.000
 DFM  H6    C6   C31   120.22  3.000
 DFM  C33   C6   C31   119.59  3.000
 DFM  H33   C33  C34   119.83  3.000
 DFM  H33   C33  C6    120.05  3.000
 DFM  C34   C33  C6    120.11  3.000
 DFM  H34   C34  C33   119.55  3.000
 DFM  H34   C34  C5    119.67  3.000
 DFM  C33   C34  C5    120.78  3.000
 DFM  C71   C67  O70   122.42  3.000
 DFM  C71   C67  N51   114.65  3.000
 DFM  O70   C67  N51   122.93  3.000
 DFM  H713  C71  H712  107.65  3.000
 DFM  H713  C71  H711  109.04  3.000
 DFM  H712  C71  H711  108.07  3.000
 DFM  H713  C71  C67   112.73  3.000
 DFM  H712  C71  C67   109.12  3.000
 DFM  H711  C71  C67   110.10  3.000
 DFM  O9    P68  O7    118.29  3.000
 DFM  O9    P68  O6    117.15  3.000
 DFM  O7    P68  O6    101.40  3.000
 DFM  O9    P68  C1    112.64  3.000
 DFM  O7    P68  C1    100.83  3.000
 DFM  O6    P68  C1    104.33  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
 DFM  CONST_01  C14   C13  C12  C11     0.00   0.0  0
 DFM  CONST_02  C14   C15  C16  C11     0.00   0.0  0
 DFM  CONST_03  C15   C16  C11  C12     0.00   0.0  0
 DFM  CONST_04  C15   C14  C13  C12     0.00   0.0  0
 DFM  CONST_05  C16   C11  C12  C13     0.00   0.0  0
 DFM  CONST_06  C16   C15  C14  C13     0.00   0.0  0
 DFM  CONST_07  C6    C31  C30  C5      0.00   0.0  0
 DFM  CONST_08  C6    C33  C34  C5      0.00   0.0  0
 DFM  CONST_09  C33   C34  C5   C30     0.00   0.0  0
 DFM  CONST_10  C33   C6   C31  C30     0.00   0.0  0
 DFM  CONST_11  C34   C5   C30  C31     0.00   0.0  0
 DFM  CONST_12  C34   C33  C6   C31     0.00   0.0  0
 DFM  CONST_13  C13   C12  C11  C1    180.00   0.0  0
 DFM  CONST_14  C15   C16  C11  C1    180.00   0.0  0
 DFM  CONST_15  C21   C14  C13  C12   180.00   0.0  0
 DFM  CONST_16  C21   C14  C15  C16   180.00   0.0  0
 DFM  CONST_17  C31   C30  C5   C4    180.00   0.0  0
 DFM  CONST_18  C33   C34  C5   C4    180.00   0.0  0
 DFM  CONST_19  H13   C13  C12  C11   180.00   0.0  0
 DFM  CONST_20  H15   C15  C16  C11   180.00   0.0  0
 DFM  CONST_21  H16   C16  C11  C12   180.00   0.0  0
 DFM  CONST_22  H12   C12  C13  C14   180.00   0.0  0
 DFM  CONST_23  H31   C31  C30  C5    180.00   0.0  0
 DFM  CONST_24  H33   C33  C34  C5    180.00   0.0  0
 DFM  CONST_25  H34   C34  C5   C30   180.00   0.0  0
 DFM  CONST_26  H6    C6   C31  C30   180.00   0.0  0
 DFM  CONST_27  H30   C30  C31  C6    180.00   0.0  0
 DFM  CONST_28  C48   C47  N45  C22   180.00   0.0  0
 DFM  CONST_29  O49   C47  N45  C22     0.00   0.0  0
 DFM  CONST_30  O70   C67  N51  C48     0.00   0.0  0
 DFM  CONST_31  C71   C67  N51  C48   180.00   0.0  0
 DFM  CONST_32  H271  N27  C25  C22   180.00   0.0  0
 DFM  CONST_33  H272  N27  C25  C22     0.00   0.0  0
 DFM  CONST_34  H45   N45  C47  C48     0.00   0.0  0
 DFM  CONST_35  H51   N51  C67  O70   180.00   0.0  0
 DFM  Var_01    F66   C1   C11  C12  -157.67  30.0  2
 DFM  Var_02    C22   C21  C14  C13   -96.75  30.0  2
 DFM  Var_03    C30   C5   C4   C48   -82.67  30.0  2
 DFM  Var_04    C11   C1   P68  O6   -176.76  30.0  1
 DFM  Var_05    H711  C71  C67  N51   150.38  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
 DFM  chir_01  C22  C21  C25  N45  negativ
 DFM  chir_02  C48  N51  C47  C4   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
 DFM  plan-1  C1    0.020
 DFM  plan-1  C11   0.020
 DFM  plan-1  C12   0.020
 DFM  plan-1  C13   0.020
 DFM  plan-1  C14   0.020
 DFM  plan-1  C15   0.020
 DFM  plan-1  C16   0.020
 DFM  plan-1  C21   0.020
 DFM  plan-1  H12   0.020
 DFM  plan-1  H16   0.020
 DFM  plan-1  H13   0.020
 DFM  plan-1  H15   0.020
 DFM  plan-2  C4    0.020
 DFM  plan-2  C5    0.020
 DFM  plan-2  C30   0.020
 DFM  plan-2  C31   0.020
 DFM  plan-2  C6    0.020
 DFM  plan-2  C33   0.020
 DFM  plan-2  C34   0.020
 DFM  plan-2  H30   0.020
 DFM  plan-2  H34   0.020
 DFM  plan-2  H31   0.020
 DFM  plan-2  H6    0.020
 DFM  plan-2  H33   0.020
 DFM  plan-3  C22   0.020
 DFM  plan-3  C25   0.020
 DFM  plan-3  O26   0.020
 DFM  plan-3  N27   0.020
 DFM  plan-3  H271  0.020
 DFM  plan-3  H272  0.020
 DFM  plan-4  C22   0.020
 DFM  plan-4  N45   0.020
 DFM  plan-4  C47   0.020
 DFM  plan-4  C48   0.020
 DFM  plan-4  O49   0.020
 DFM  plan-4  H45   0.020
 DFM  plan-5  C48   0.020
 DFM  plan-5  N51   0.020
 DFM  plan-5  C67   0.020
 DFM  plan-5  O70   0.020
 DFM  plan-5  C71   0.020
 DFM  plan-5  H51   0.020

