# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 10:12:46 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  55  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   0.458  -2.7287   2.3521  -3.9837
 DFM  O6    O  OP    -1  -0.870  -5.0120   1.0186  -4.5529
 DFM  O7    O  OP    -1  -0.843  -2.8684  -0.3317  -4.0734
 DFM  O9    O  O      0  -0.813  -4.0830   0.9308  -2.1689
 DFM  C11   C  CR6    0  -0.057  -1.5267   2.4274  -3.1026
 DFM  C12   C  CR16   0  -0.267  -0.3425   1.7951  -3.4684
 DFM  C13   C  CR16   0  -0.270   0.7245   1.7346  -2.5884
 DFM  C14   C  CR6    0   0.125   0.6283   2.2762  -1.3104
 DFM  C15   C  CR16   0  -0.299  -0.5427   2.9393  -0.9651
 DFM  C16   C  CR16   0  -0.271  -1.6068   3.0203  -1.8486
 DFM  C21   C  CH2    0  -0.524   1.6986   2.0398  -0.2865
 DFM  C22   C  CH1    0  -0.197   1.6844   0.5593   0.1712
 DFM  C25   C  C      0   0.516   2.5394   0.4172   1.4258
 DFM  O26   O  O      0  -0.480   2.0454   0.4254   2.5427
 DFM  N27   N  NH2    0  -0.798   3.8556   0.3417   1.1947
 DFM  N45   N  NH1    0  -0.650   0.3549   0.0810   0.4261
 DFM  C47   C  C      0   0.606  -0.3064  -0.7371  -0.4158
 DFM  C48   C  CH1    0  -0.210  -1.7677  -0.9943  -0.0163
 DFM  O49   O  O      0  -0.489   0.2090  -1.2640  -1.3877
 DFM  N51   N  NH1    0  -0.640  -2.5570   0.2176  -0.0459
 DFM  C4    C  CH2    0  -0.568  -2.4096  -2.0586  -0.9082
 DFM  C5    C  CR6    0   0.131  -3.7089  -2.5521  -0.3333
 DFM  C30   C  CR16   0  -0.314  -3.7223  -3.6459   0.5312
 DFM  C31   C  CR16   0  -0.244  -4.9078  -4.1017   1.0932
 DFM  C6    C  CR16   0  -0.274  -6.1065  -3.4659   0.7966
 DFM  C33   C  CR16   0  -0.248  -6.1057  -2.3756  -0.0641
 DFM  C34   C  CR16   0  -0.332  -4.9180  -1.9219  -0.6242
 DFM  C67   C  C      0   0.517  -2.6516   1.0335   1.0027
 DFM  O70   O  O      0  -0.550  -2.0054   0.8833   2.0475
 DFM  C71   C  CH3    0  -0.789  -3.6304   2.1707   0.8598
 DFM  F66   F  F      0  -0.377  -3.4894   3.4925  -3.8140
 DFM  F67   F  F      0  -0.378  -2.3314   2.3948  -5.3070
 DFM  P68   P  P      0   1.173  -3.7823   0.8157  -3.6771
 DFM  H12   H  HCR6   0   0.235  -0.2517   1.3263  -4.4385
 DFM  H16   H  HCR6   0   0.238  -2.5142   3.5173  -1.5336
 DFM  H13   H  HCR6   0   0.234   1.6308   1.2229  -2.8910
 DFM  H15   H  HCR6   0   0.237  -0.6382   3.3731   0.0241
 DFM  H211  H  HCH2   0   0.261   2.6910   2.2730  -0.6797
 DFM  H212  H  HCH2   0   0.255   1.5366   2.6929   0.5749
 DFM  H22   H  HCH1   0   0.280   2.1059  -0.0504  -0.6288
 DFM  H45   H  HNH1   0   0.397  -0.1527   0.4577   1.2186
 DFM  H271  H  HNH2   0   0.404   4.5098   0.2944   1.9589
 DFM  H272  H  HNH2   0   0.411   4.2285   0.2910   0.2623
 DFM  H48   H  HCH1   0   0.265  -1.7504  -1.3651   1.0150
 DFM  H51   H  HNH1   0   0.464  -3.0771   0.4607  -0.9248
 DFM  H4C1  H  HCH2   0   0.247  -1.7164  -2.8958  -0.9998
 DFM  H4C2  H  HCH2   0   0.283  -2.5530  -1.6471  -1.9107
 DFM  H30   H  HCR6   0   0.239  -2.7919  -4.1525   0.7641
 DFM  H34   H  HCR6   0   0.275  -4.9197  -1.0642  -1.2871
 DFM  H31   H  HCR6   0   0.248  -4.8953  -4.9548   1.7597
 DFM  H6    H  HCR6   0   0.248  -7.0335  -3.8184   1.2310
 DFM  H33   H  HCR6   0   0.245  -7.0363  -1.8744  -0.3004
 DFM  H711  H  HCH3   0   0.245  -3.1319   3.1171   1.0715
 DFM  H712  H  HCH3   0   0.259  -4.0783   2.2147  -0.1295
 DFM  H713  H  HCH3   0   0.256  -4.4217   2.0527   1.6021

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    1.492  0.020  1.492
 DFM  C1   F66   single    1.381  0.020  1.381
 DFM  C1   F67   single    1.382  0.020  1.382
 DFM  C1   P68   single    1.888  0.020  1.888
 DFM  O6   P68   deloc     1.523  0.020  1.523
 DFM  O7   P68   deloc     1.520  0.020  1.520
 DFM  O9   P68   deloc     1.542  0.020  1.542
 DFM  C11  C12   aromatic  1.391  0.020  1.391
 DFM  C11  C16   aromatic  1.389  0.020  1.389
 DFM  C12  C13   aromatic  1.384  0.020  1.384
 DFM  C12  H12   single    0.930  0.020  1.080
 DFM  C13  C14   aromatic  1.391  0.020  1.391
 DFM  C13  H13   single    0.930  0.020  1.080
 DFM  C14  C15   aromatic  1.389  0.020  1.389
 DFM  C14  C21   single    1.500  0.020  1.500
 DFM  C15  C16   aromatic  1.385  0.020  1.385
 DFM  C15  H15   single    0.930  0.020  1.080
 DFM  C16  H16   single    0.930  0.020  1.080
 DFM  C21  C22   single    1.550  0.020  1.550
 DFM  C21  H211  single    0.970  0.020  1.090
 DFM  C21  H212  single    0.970  0.020  1.090
 DFM  C22  C25   single    1.525  0.020  1.525
 DFM  C22  N45   single    1.436  0.020  1.436
 DFM  C22  H22   single    0.970  0.020  1.090
 DFM  C25  O26   double    1.221  0.020  1.221
 DFM  C25  N27   single    1.338  0.020  1.338
 DFM  N27  H271  single    0.860  0.020  1.020
 DFM  N27  H272  single    0.860  0.020  1.020
 DFM  N45  C47   single    1.347  0.020  1.347
 DFM  N45  H45   single    0.860  0.020  1.020
 DFM  C47  C48   single    1.537  0.020  1.537
 DFM  C47  O49   double    1.220  0.020  1.220
 DFM  C48  N51   single    1.447  0.020  1.447
 DFM  C48  C4    single    1.530  0.020  1.530
 DFM  C48  H48   single    0.970  0.020  1.090
 DFM  N51  C67   single    1.332  0.020  1.332
 DFM  N51  H51   single    0.860  0.020  1.020
 DFM  C4   C5    single    1.504  0.020  1.504
 DFM  C4   H4C1  single    0.970  0.020  1.090
 DFM  C4   H4C2  single    0.970  0.020  1.090
 DFM  C5   C30   aromatic  1.394  0.020  1.394
 DFM  C5   C34   aromatic  1.394  0.020  1.394
 DFM  C30  C31   aromatic  1.389  0.020  1.389
 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  1.389  0.020  1.389
 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    1.238  0.020  1.238
 DFM  C67  C71   single    1.507  0.020  1.507
 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   109.93  3.000
 DFM  P68   C1   F66   110.16  3.000
 DFM  F67   C1   F66   104.49  3.000
 DFM  P68   C1   C11   113.25  3.000
 DFM  F67   C1   C11   109.40  3.000
 DFM  F66   C1   C11   109.23  3.000
 DFM  C16   C11  C12   118.70  3.000
 DFM  C16   C11  C1    120.53  3.000
 DFM  C12   C11  C1    120.49  3.000
 DFM  H12   C12  C13   119.12  3.000
 DFM  H12   C12  C11   120.29  3.000
 DFM  C13   C12  C11   120.58  3.000
 DFM  H13   C13  C14   119.87  3.000
 DFM  H13   C13  C12   119.18  3.000
 DFM  C14   C13  C12   120.90  3.000
 DFM  C21   C14  C15   120.46  3.000
 DFM  C21   C14  C13   121.09  3.000
 DFM  C15   C14  C13   118.19  3.000
 DFM  H15   C15  C16   119.38  3.000
 DFM  H15   C15  C14   119.47  3.000
 DFM  C16   C15  C14   121.12  3.000
 DFM  H16   C16  C15   119.05  3.000
 DFM  H16   C16  C11   120.48  3.000
 DFM  C15   C16  C11   120.42  3.000
 DFM  H212  C21  H211  106.90  3.000
 DFM  H212  C21  C22   109.67  3.000
 DFM  H211  C21  C22   108.57  3.000
 DFM  H212  C21  C14   109.76  3.000
 DFM  H211  C21  C14   111.64  3.000
 DFM  C22   C21  C14   110.22  3.000
 DFM  H22   C22  N45   107.57  3.000
 DFM  H22   C22  C25   109.56  3.000
 DFM  N45   C22  C25   110.01  3.000
 DFM  H22   C22  C21   108.29  3.000
 DFM  N45   C22  C21   112.28  3.000
 DFM  C25   C22  C21   109.08  3.000
 DFM  N27   C25  O26   123.78  3.000
 DFM  N27   C25  C22   114.49  3.000
 DFM  O26   C25  C22   121.67  3.000
 DFM  H272  N27  H271  117.41  3.000
 DFM  H272  N27  C25   121.85  3.000
 DFM  H271  N27  C25   120.69  3.000
 DFM  H45   N45  C47   117.93  3.000
 DFM  H45   N45  C22   118.60  3.000
 DFM  C47   N45  C22   123.08  3.000
 DFM  O49   C47  C48   122.46  3.000
 DFM  O49   C47  N45   123.56  3.000
 DFM  C48   C47  N45   113.95  3.000
 DFM  H48   C48  C4    108.66  3.000
 DFM  H48   C48  N51   108.13  3.000
 DFM  C4    C48  N51   110.00  3.000
 DFM  H48   C48  C47   106.63  3.000
 DFM  C4    C48  C47   111.34  3.000
 DFM  N51   C48  C47   111.92  3.000
 DFM  H51   N51  C67   118.82  3.000
 DFM  H51   N51  C48   118.78  3.000
 DFM  C67   N51  C48   122.40  3.000
 DFM  H4C2  C4   H4C1  107.17  3.000
 DFM  H4C2  C4   C5    111.15  3.000
 DFM  H4C1  C4   C5    109.22  3.000
 DFM  H4C2  C4   C48   109.14  3.000
 DFM  H4C1  C4   C48   108.44  3.000
 DFM  C5    C4   C48   111.59  3.000
 DFM  C34   C5   C30   118.40  3.000
 DFM  C34   C5   C4    121.40  3.000
 DFM  C30   C5   C4    120.18  3.000
 DFM  H30   C30  C31   119.48  3.000
 DFM  H30   C30  C5    119.42  3.000
 DFM  C31   C30  C5    121.10  3.000
 DFM  H31   C31  C6    120.14  3.000
 DFM  H31   C31  C30   119.86  3.000
 DFM  C6    C31  C30   120.01  3.000
 DFM  H6    C6   C33   120.31  3.000
 DFM  H6    C6   C31   120.28  3.000
 DFM  C33   C6   C31   119.41  3.000
 DFM  H33   C33  C34   119.70  3.000
 DFM  H33   C33  C6    119.86  3.000
 DFM  C34   C33  C6    120.44  3.000
 DFM  H34   C34  C33   120.24  3.000
 DFM  H34   C34  C5    119.12  3.000
 DFM  C33   C34  C5    120.64  3.000
 DFM  C71   C67  O70   120.70  3.000
 DFM  C71   C67  N51   115.70  3.000
 DFM  O70   C67  N51   123.58  3.000
 DFM  H713  C71  H712  108.94  3.000
 DFM  H713  C71  H711  107.06  3.000
 DFM  H712  C71  H711  109.27  3.000
 DFM  H713  C71  C67   108.95  3.000
 DFM  H712  C71  C67   112.61  3.000
 DFM  H711  C71  C67   109.85  3.000
 DFM  O9    P68  O7    115.38  3.000
 DFM  O9    P68  O6    113.26  3.000
 DFM  O7    P68  O6    115.86  3.000
 DFM  O9    P68  C1    101.94  3.000
 DFM  O7    P68  C1    103.68  3.000
 DFM  O6    P68  C1    104.41  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  -150.63  30.0  1
 DFM  Var_02    C22   C21  C14  C13   -69.73  30.0  2
 DFM  Var_03    C30   C5   C4   C48   -90.24  30.0  2
 DFM  Var_04    C11   C1   P68  O6    173.86  30.0  3
 DFM  Var_05    H711  C71  C67  N51  -126.55  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

