# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 07:47:03 2020
#   Inital geometry file: a 134 line input string
#   Ligand name: N-[(3R)-3-amino-4-(2,4,5-trifluorophenyl)butyl]-3'-(trifluoromethyl)biphenyl-4-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCNC(=O)c1ccc(cc1)c2cccc(c2)C(F)(F)F)Cc3cc(F)c(F)cc3F
#
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
 D5C  D5C  N-[(3R)-3-amino-4-(2,4,5-trifluorophenyl)butyl]-3'-(trifluoromethyl)biphenyl-4-carboxamide  ligand  53  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_D5C
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
 D5C  FBE  F  F     0  -0.302  -10.3527   0.2461  -0.3665
 D5C  CBD  C  CT    0   1.054   -9.1621  -0.3534  -0.4463
 D5C  FBF  F  F     0  -0.314   -9.2035  -1.4171   0.3697
 D5C  FBG  F  F     0  -0.314   -9.0500  -0.8365  -1.6924
 D5C  CBB  C  CR6   0  -0.171   -8.0283   0.5614  -0.1024
 D5C  CBC  C  CR16  0  -0.338   -6.7352   0.0535  -0.1530
 D5C  CBA  C  CR16  0  -0.297   -8.2509   1.8835   0.2546
 D5C  CAZ  C  CR16  0  -0.224   -7.1662   2.6939   0.5602
 D5C  CAY  C  CR16  0  -0.299   -5.8778   2.1906   0.5117
 D5C  CAX  C  CR6   0   0.110   -5.6443   0.8609   0.1549
 D5C  CAU  C  CR6   0   0.087   -4.2721   0.3193   0.1099
 D5C  CAV  C  CR16  0  -0.293   -3.2114   1.0978  -0.3522
 D5C  CAW  C  CR16  0  -0.276   -1.9222   0.5923  -0.3865
 D5C  CAT  C  CR16  0  -0.296   -4.0042  -0.9862   0.5250
 D5C  CAS  C  CR16  0  -0.254   -2.7191  -1.4963   0.4781
 D5C  CAR  C  CR6   0  -0.042   -1.6596  -0.7086   0.0355
 D5C  CAP  C  C     0   0.533   -0.2928  -1.3137  -0.0061
 D5C  OAQ  O  O     0  -0.492   -0.1404  -2.5222  -0.1340
 D5C  NAO  N  NH1   0  -0.660    0.7376  -0.4645   0.1068
 D5C  CAN  C  CH2   0  -0.222    2.1178  -0.9089   0.0719
 D5C  CAL  C  CH2   0  -0.484    3.0532   0.2742   0.2612
 D5C  CAK  C  CH1   0  -0.093    4.5210  -0.1129   0.1091
 D5C  NAM  N  NH2   0  -0.783    4.8562  -1.1627   1.0533
 D5C  CAJ  C  CH2   0  -0.510    5.4025   1.1481   0.2249
 D5C  CAD  C  CR6   0  -0.063    6.8568   0.8541   0.0105
 D5C  CAE  C  CR6   0   0.532    7.3893   0.6935  -1.2606
 D5C  FAG  F  F     0  -0.306    6.5841   0.8470  -2.3227
 D5C  CAF  C  CR16  0  -0.552    8.7145   0.3824  -1.4970
 D5C  CAA  C  CR6   0   0.399    9.5477   0.2200  -0.4100
 D5C  FAH  F  F     0  -0.301   10.8356  -0.0780  -0.5933
 D5C  CAB  C  CR6   0   0.405    9.0572   0.3688   0.8743
 D5C  FAI  F  F     0  -0.307    9.8848   0.2099   1.9130
 D5C  CAC  C  CR16  0  -0.462    7.7294   0.6783   1.0824
 D5C  H1   H  HCR6  0   0.277   -6.5659  -0.9741  -0.4514
 D5C  H2   H  HCR6  0   0.274   -9.2502   2.2928   0.3018
 D5C  H3   H  HCR6  0   0.272   -7.3322   3.7240   0.8451
 D5C  H4   H  HCR6  0   0.268   -5.0473   2.8335   0.7745
 D5C  H5   H  HCR6  0   0.265   -3.3920   2.1011  -0.7163
 D5C  H6   H  HCR6  0   0.259   -1.1331   1.2201  -0.7810
 D5C  H7   H  HCR6  0   0.263   -4.8039  -1.6085   0.9068
 D5C  H8   H  HCR6  0   0.263   -2.5358  -2.5114   0.8039
 D5C  H9   H  HNH1  0   0.405    0.5597   0.5002   0.3330
 D5C  H10  H  HCH2  0   0.240    2.2945  -1.6546   0.8481
 D5C  H11  H  HCH2  0   0.230    2.3232  -1.3911  -0.8879
 D5C  H12  H  HCH2  0   0.241    2.8185   1.0496  -0.4740
 D5C  H13  H  HCH2  0   0.234    2.8925   0.7175   1.2508
 D5C  H14  H  HCH1  0   0.238    4.6539  -0.5275  -0.8956
 D5C  H15  H  HNH2  0   0.352    5.7991  -1.4975   0.9004
 D5C  H16  H  HNH2  0   0.337    4.8313  -0.7995   1.9999
 D5C  H18  H  HCH2  0   0.254    5.0570   1.9028  -0.4856
 D5C  H19  H  HCH2  0   0.252    5.2675   1.5758   1.2219
 D5C  H20  H  HCR6  0   0.313    9.0912   0.2678  -2.5051
 D5C  H21  H  HCR6  0   0.300    7.3705   0.7978   2.0972

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
 D5C  FBG  CBD  single    1.341  0.020  1.341
 D5C  FBE  CBD  single    1.335  0.020  1.335
 D5C  FBF  CBD  single    1.341  0.020  1.341
 D5C  CBD  CBB  single    1.497  0.020  1.497
 D5C  CBB  CBA  aromatic  1.387  0.020  1.387
 D5C  CBB  CBC  aromatic  1.390  0.020  1.390
 D5C  CBA  CAZ  aromatic  1.388  0.020  1.388
 D5C  CBC  CAX  aromatic  1.392  0.020  1.392
 D5C  CAZ  CAY  aromatic  1.384  0.020  1.384
 D5C  CAX  CAY  aromatic  1.396  0.020  1.396
 D5C  CAX  CAU  single    1.476  0.020  1.476
 D5C  CAT  CAU  aromatic  1.396  0.020  1.396
 D5C  CAT  CAS  aromatic  1.383  0.020  1.383
 D5C  CAU  CAV  aromatic  1.395  0.020  1.395
 D5C  CAS  CAR  aromatic  1.392  0.020  1.392
 D5C  CAV  CAW  aromatic  1.385  0.020  1.385
 D5C  CAR  CAW  aromatic  1.393  0.020  1.393
 D5C  CAR  CAP  single    1.495  0.020  1.495
 D5C  OAQ  CAP  double    1.225  0.020  1.225
 D5C  CAP  NAO  single    1.340  0.020  1.340
 D5C  NAO  CAN  single    1.450  0.020  1.450
 D5C  CAN  CAL  single    1.520  0.020  1.520
 D5C  CAL  CAK  single    1.526  0.020  1.526
 D5C  CAK  CAJ  single    1.543  0.020  1.543
 D5C  CAK  NAM  single    1.451  0.020  1.451
 D5C  CAJ  CAD  single    1.499  0.020  1.499
 D5C  CAC  CAD  aromatic  1.393  0.020  1.393
 D5C  CAC  CAB  aromatic  1.379  0.020  1.379
 D5C  FAI  CAB  single    1.338  0.020  1.338
 D5C  CAD  CAE  aromatic  1.387  0.020  1.387
 D5C  CAB  CAA  aromatic  1.383  0.020  1.383
 D5C  CAE  FAG  single    1.342  0.020  1.342
 D5C  CAE  CAF  aromatic  1.382  0.020  1.382
 D5C  CAA  CAF  aromatic  1.379  0.020  1.379
 D5C  CAA  FAH  single    1.335  0.020  1.335
 D5C  CBC  H1   single    0.930  0.020  1.080
 D5C  CBA  H2   single    0.930  0.020  1.080
 D5C  CAZ  H3   single    0.930  0.020  1.080
 D5C  CAY  H4   single    0.930  0.020  1.080
 D5C  CAV  H5   single    0.930  0.020  1.080
 D5C  CAW  H6   single    0.930  0.020  1.080
 D5C  CAT  H7   single    0.930  0.020  1.080
 D5C  CAS  H8   single    0.930  0.020  1.080
 D5C  NAO  H9   single    0.860  0.020  1.020
 D5C  CAN  H10  single    0.970  0.020  1.090
 D5C  CAN  H11  single    0.970  0.020  1.090
 D5C  CAL  H12  single    0.970  0.020  1.090
 D5C  CAL  H13  single    0.970  0.020  1.090
 D5C  CAK  H14  single    0.970  0.020  1.090
 D5C  NAM  H15  single    0.890  0.020  1.040
 D5C  NAM  H16  single    0.890  0.020  1.040
 D5C  CAJ  H18  single    0.970  0.020  1.090
 D5C  CAJ  H19  single    0.970  0.020  1.090
 D5C  CAF  H20  single    0.930  0.020  1.080
 D5C  CAC  H21  single    0.930  0.020  1.080

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
 D5C  CBB  CBD  FBG  111.73  3.000
 D5C  CBB  CBD  FBF  111.61  3.000
 D5C  FBG  CBD  FBF  106.39  3.000
 D5C  CBB  CBD  FBE  112.78  3.000
 D5C  FBF  CBD  FBE  106.99  3.000
 D5C  FBG  CBD  FBE  106.96  3.000
 D5C  CBA  CBB  CBC  120.45  3.000
 D5C  CBC  CBB  CBD  118.22  3.000
 D5C  CBA  CBB  CBD  121.33  3.000
 D5C  H1   CBC  CAX  119.26  3.000
 D5C  H1   CBC  CBB  120.13  3.000
 D5C  CAX  CBC  CBB  120.60  3.000
 D5C  H2   CBA  CAZ  119.46  3.000
 D5C  H2   CBA  CBB  121.36  3.000
 D5C  CAZ  CBA  CBB  119.18  3.000
 D5C  H3   CAZ  CAY  119.90  3.000
 D5C  H3   CAZ  CBA  119.61  3.000
 D5C  CAY  CAZ  CBA  120.49  3.000
 D5C  H4   CAY  CAX  119.95  3.000
 D5C  H4   CAY  CAZ  119.32  3.000
 D5C  CAX  CAY  CAZ  120.72  3.000
 D5C  CAU  CAX  CAY  120.84  3.000
 D5C  CAU  CAX  CBC  120.61  3.000
 D5C  CAY  CAX  CBC  118.55  3.000
 D5C  CAT  CAU  CAV  118.34  3.000
 D5C  CAV  CAU  CAX  120.83  3.000
 D5C  CAT  CAU  CAX  120.84  3.000
 D5C  H5   CAV  CAW  119.03  3.000
 D5C  H5   CAV  CAU  120.13  3.000
 D5C  CAW  CAV  CAU  120.82  3.000
 D5C  H6   CAW  CAR  120.97  3.000
 D5C  H6   CAW  CAV  118.41  3.000
 D5C  CAR  CAW  CAV  120.59  3.000
 D5C  H7   CAT  CAS  119.08  3.000
 D5C  H7   CAT  CAU  120.04  3.000
 D5C  CAS  CAT  CAU  120.87  3.000
 D5C  H8   CAS  CAR  119.84  3.000
 D5C  H8   CAS  CAT  119.55  3.000
 D5C  CAR  CAS  CAT  120.60  3.000
 D5C  CAP  CAR  CAS  118.39  3.000
 D5C  CAP  CAR  CAW  122.82  3.000
 D5C  CAS  CAR  CAW  118.77  3.000
 D5C  NAO  CAP  OAQ  122.58  3.000
 D5C  NAO  CAP  CAR  116.36  3.000
 D5C  OAQ  CAP  CAR  121.06  3.000
 D5C  H9   NAO  CAN  117.85  3.000
 D5C  H9   NAO  CAP  119.36  3.000
 D5C  CAN  NAO  CAP  122.38  3.000
 D5C  H11  CAN  H10  107.02  3.000
 D5C  H11  CAN  CAL  109.69  3.000
 D5C  H10  CAN  CAL  110.11  3.000
 D5C  H11  CAN  NAO  109.57  3.000
 D5C  H10  CAN  NAO  110.27  3.000
 D5C  CAL  CAN  NAO  110.13  3.000
 D5C  H13  CAL  H12  106.77  3.000
 D5C  H13  CAL  CAK  109.49  3.000
 D5C  H12  CAL  CAK  108.62  3.000
 D5C  H13  CAL  CAN  109.69  3.000
 D5C  H12  CAL  CAN  109.63  3.000
 D5C  CAK  CAL  CAN  112.47  3.000
 D5C  H14  CAK  CAJ  108.00  3.000
 D5C  H14  CAK  NAM  107.16  3.000
 D5C  CAJ  CAK  NAM  114.23  3.000
 D5C  H14  CAK  CAL  107.72  3.000
 D5C  NAM  CAK  CAL  109.93  3.000
 D5C  CAJ  CAK  CAL  109.56  3.000
 D5C  H16  NAM  H15  106.40  3.000
 D5C  H16  NAM  CAK  110.03  3.000
 D5C  H15  NAM  CAK  110.86  3.000
 D5C  H19  CAJ  H18  106.49  3.000
 D5C  H19  CAJ  CAD  109.08  3.000
 D5C  H18  CAJ  CAD  110.44  3.000
 D5C  H19  CAJ  CAK  108.53  3.000
 D5C  H18  CAJ  CAK  109.58  3.000
 D5C  CAD  CAJ  CAK  112.53  3.000
 D5C  CAC  CAD  CAE  116.73  3.000
 D5C  CAE  CAD  CAJ  121.74  3.000
 D5C  CAC  CAD  CAJ  121.49  3.000
 D5C  CAF  CAE  FAG  117.77  3.000
 D5C  CAF  CAE  CAD  123.43  3.000
 D5C  FAG  CAE  CAD  118.80  3.000
 D5C  H20  CAF  CAA  120.76  3.000
 D5C  H20  CAF  CAE  121.14  3.000
 D5C  CAA  CAF  CAE  118.10  3.000
 D5C  CAB  CAA  FAH  119.60  3.000
 D5C  FAH  CAA  CAF  120.07  3.000
 D5C  CAB  CAA  CAF  120.34  3.000
 D5C  CAC  CAB  FAI  120.34  3.000
 D5C  FAI  CAB  CAA  119.27  3.000
 D5C  CAC  CAB  CAA  120.38  3.000
 D5C  H21  CAC  CAB  119.03  3.000
 D5C  H21  CAC  CAD  119.96  3.000
 D5C  CAB  CAC  CAD  121.01  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
 D5C  CONST_01  CAY  CAZ  CBA  CBB     0.00   0.0  0
 D5C  CONST_02  CAY  CAX  CBC  CBB     0.00   0.0  0
 D5C  CONST_03  CAU  CAX  CBC  CBB   180.00   0.0  0
 D5C  CONST_04  CAZ  CBA  CBB  CBC     0.00   0.0  0
 D5C  CONST_05  CAZ  CAY  CAX  CBC     0.00   0.0  0
 D5C  CONST_08  CAX  CBC  CBB  CBA     0.00   0.0  0
 D5C  CONST_09  CAX  CAY  CAZ  CBA     0.00   0.0  0
 D5C  CONST_10  CAU  CAX  CAY  CAZ   180.00   0.0  0
 D5C  CONST_13  CAS  CAT  CAU  CAX   180.00   0.0  0
 D5C  CONST_14  CAW  CAV  CAU  CAX   180.00   0.0  0
 D5C  CONST_15  CAR  CAS  CAT  CAU     0.00   0.0  0
 D5C  CONST_16  CAR  CAW  CAV  CAU     0.00   0.0  0
 D5C  CONST_17  CAS  CAT  CAU  CAV     0.00   0.0  0
 D5C  CONST_18  CAS  CAR  CAW  CAV     0.00   0.0  0
 D5C  CONST_19  CAT  CAU  CAV  CAW     0.00   0.0  0
 D5C  CONST_20  CAT  CAS  CAR  CAW     0.00   0.0  0
 D5C  CONST_21  CAA  CAB  CAC  CAD     0.00   0.0  0
 D5C  CONST_22  CAA  CAF  CAE  CAD     0.00   0.0  0
 D5C  CONST_23  CAB  CAC  CAD  CAE     0.00   0.0  0
 D5C  CONST_24  CAB  CAA  CAF  CAE     0.00   0.0  0
 D5C  CONST_25  CAC  CAD  CAE  CAF     0.00   0.0  0
 D5C  CONST_26  CAC  CAB  CAA  CAF     0.00   0.0  0
 D5C  CONST_27  CAZ  CBA  CBB  CBD   180.00   0.0  0
 D5C  CONST_28  CAX  CBC  CBB  CBD   180.00   0.0  0
 D5C  CONST_29  CAP  CAR  CAW  CAV   180.00   0.0  0
 D5C  CONST_30  CAP  CAR  CAS  CAT   180.00   0.0  0
 D5C  CONST_31  CAB  CAC  CAD  CAJ   180.00   0.0  0
 D5C  CONST_32  CAF  CAE  CAD  CAJ   180.00   0.0  0
 D5C  CONST_33  FAI  CAB  CAC  CAD   180.00   0.0  0
 D5C  CONST_34  FAH  CAA  CAF  CAE   180.00   0.0  0
 D5C  CONST_35  CAC  CAD  CAE  FAG   180.00   0.0  0
 D5C  CONST_36  CAA  CAF  CAE  FAG   180.00   0.0  0
 D5C  CONST_37  FAI  CAB  CAA  CAF   180.00   0.0  0
 D5C  CONST_38  CAC  CAB  CAA  FAH   180.00   0.0  0
 D5C  CONST_39  H3   CAZ  CBA  CBB   180.00   0.0  0
 D5C  CONST_40  H2   CBA  CBB  CBC   180.00   0.0  0
 D5C  CONST_41  H4   CAY  CAX  CBC   180.00   0.0  0
 D5C  CONST_42  H1   CBC  CBB  CBA   180.00   0.0  0
 D5C  CONST_43  H7   CAT  CAU  CAX     0.00   0.0  0
 D5C  CONST_44  H5   CAV  CAU  CAX     0.00   0.0  0
 D5C  CONST_45  H8   CAS  CAT  CAU   180.00   0.0  0
 D5C  CONST_46  H6   CAW  CAV  CAU   180.00   0.0  0
 D5C  CONST_47  H20  CAF  CAE  CAD   180.00   0.0  0
 D5C  CONST_48  H21  CAC  CAD  CAE   180.00   0.0  0
 D5C  CONST_49  CAN  NAO  CAP  CAR   180.00   0.0  0
 D5C  CONST_50  H9   NAO  CAP  CAR     0.00   0.0  0
 D5C  CONST_51  CAN  NAO  CAP  OAQ     0.00   0.0  0
 D5C  Var_01    CBA  CBB  CBD  FBE     0.01  30.0  2
 D5C  Var_02    OAQ  CAP  CAR  CAW  -151.71  30.0  2
 D5C  Var_03    CAC  CAD  CAJ  CAK   -98.20  30.0  2
 D5C  Var_04    CAL  CAN  NAO  CAP  -178.47  30.0  3
 D5C  Var_05    CAK  CAL  CAN  NAO  -174.87  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
 D5C  chir_01  CAK  CAL  CAJ  NAM  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
 D5C  plan-1  CBD  0.020
 D5C  plan-1  CBB  0.020
 D5C  plan-1  CBC  0.020
 D5C  plan-1  CBA  0.020
 D5C  plan-1  CAZ  0.020
 D5C  plan-1  CAY  0.020
 D5C  plan-1  CAX  0.020
 D5C  plan-1  CAU  0.020
 D5C  plan-1  H1   0.020
 D5C  plan-1  H2   0.020
 D5C  plan-1  H3   0.020
 D5C  plan-1  H4   0.020
 D5C  plan-2  CAX  0.020
 D5C  plan-2  CAU  0.020
 D5C  plan-2  CAV  0.020
 D5C  plan-2  CAW  0.020
 D5C  plan-2  CAT  0.020
 D5C  plan-2  CAS  0.020
 D5C  plan-2  CAR  0.020
 D5C  plan-2  CAP  0.020
 D5C  plan-2  H5   0.020
 D5C  plan-2  H6   0.020
 D5C  plan-2  H7   0.020
 D5C  plan-2  H8   0.020
 D5C  plan-3  CAJ  0.020
 D5C  plan-3  CAD  0.020
 D5C  plan-3  CAE  0.020
 D5C  plan-3  FAG  0.020
 D5C  plan-3  CAF  0.020
 D5C  plan-3  CAA  0.020
 D5C  plan-3  FAH  0.020
 D5C  plan-3  CAB  0.020
 D5C  plan-3  FAI  0.020
 D5C  plan-3  CAC  0.020
 D5C  plan-3  H20  0.020
 D5C  plan-3  H21  0.020
 D5C  plan-4  CAR  0.020
 D5C  plan-4  CAP  0.020
 D5C  plan-4  OAQ  0.020
 D5C  plan-4  NAO  0.020
 D5C  plan-4  CAN  0.020
 D5C  plan-4  H9   0.020

