# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 08:26:12 2021
#   Inital geometry file: a 116 line input string
#   Ligand name: N~2~-{(2R)-2-hydroxy-2-[4-(trifluoromethyl)phenyl]acetyl}-N-[(pyridin-2-yl)methyl]-L-cysteinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H](C(=O)N[C@@H](CS)C(=O)NCc1ccccn1)c2ccc(cc2)C(F)(F)F
#
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
 R7D  R7D  N~2~-{(2R)-2-hydroxy-2-[4-(trifluoromethyl)phenyl]acetyl}-N-[(pyridin-2-yl)methyl]-L-cysteinamide  ligand  46  28  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_R7D
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
 R7D  SD   S  S2    0  -0.232  -4.1896   -9.2944  -26.9484
 R7D  CE   C  CH2   0  -0.589  -4.2197   -9.7929  -28.7036
 R7D  CAA  C  CH1   0  -0.132  -5.6830   -5.2257  -29.3007
 R7D  CAB  C  C     0   0.513  -4.7195   -6.2976  -29.8169
 R7D  CAM  C  CH2   0  -0.346  -5.2975   -9.6065  -32.9513
 R7D  CAN  C  CR6   0   0.238  -5.3447  -11.1134  -32.8243
 R7D  CAP  C  CR16  0  -0.080  -5.8079  -12.9380  -31.5370
 R7D  CAQ  C  CR16  0  -0.330  -5.5056  -13.8205  -32.5617
 R7D  CAR  C  CR16  0  -0.150  -5.1007  -13.2914  -33.7789
 R7D  CAS  C  CR16  0  -0.335  -5.0149  -11.9158  -33.9120
 R7D  CAY  C  CR6   0   0.109  -5.2289   -4.8379  -27.9072
 R7D  CBA  C  CR16  0  -0.283  -4.2156   -3.8995  -27.7318
 R7D  CBB  C  CR16  0  -0.252  -3.7779   -3.5729  -26.4614
 R7D  CBC  C  CR6   0  -0.204  -4.3497   -4.1821  -25.3472
 R7D  CBD  C  CR16  0  -0.264  -5.3604   -5.1169  -25.5133
 R7D  CBE  C  CR16  0  -0.291  -5.7955   -5.4372  -26.7912
 R7D  CBF  C  CT    0   1.051  -3.8592   -3.7927  -23.9894
 R7D  CX   C  C     0   0.553  -3.9292   -9.0663  -31.0345
 R7D  CXA  C  CH1   0  -0.172  -3.9271   -8.5808  -29.5838
 R7D  FBG  F  F     0  -0.314  -2.5425   -4.0118  -23.8557
 R7D  FBH  F  F     0  -0.301  -4.4679   -4.4598  -23.0057
 R7D  FBI  F  F     0  -0.315  -4.0496   -2.4856  -23.7527
 R7D  NAO  N  N     0  -0.412  -5.7345  -11.6177  -31.6609
 R7D  NX   N  NH1   0  -0.649  -4.8881   -7.5336  -29.3280
 R7D  OAD  O  O     0  -0.467  -3.8401   -6.0014  -30.6087
 R7D  OAZ  O  OH1   0  -0.654  -5.7011   -4.1464  -30.1788
 R7D  OX   O  O     0  -0.481  -2.9333   -9.5885  -31.5076
 R7D  H1   H  HSH1  0   0.237  -4.6376  -10.4522  -26.4528
 R7D  H2   H  HCH2  0   0.291  -5.1939  -10.2153  -28.9529
 R7D  H3   H  HCH2  0   0.303  -3.4598  -10.5499  -28.8858
 R7D  H4   H  HCH1  0   0.291  -6.6904   -5.6523  -29.2347
 R7D  H5   H  HCH2  0   0.265  -4.5250   -9.3210  -33.6669
 R7D  H6   H  HCH2  0   0.286  -6.2446   -9.2483  -33.3577
 R7D  H7   H  HCR6  0   0.261  -6.1255  -13.3130  -30.5702
 R7D  H8   H  HCR6  0   0.269  -5.5822  -14.8877  -32.4059
 R7D  H9   H  HCR6  0   0.273  -4.8478  -13.9399  -34.6075
 R7D  H10  H  HCR6  0   0.266  -4.6905  -11.4669  -34.8421
 R7D  H11  H  HCR6  0   0.266  -3.7619   -3.4112  -28.5841
 R7D  H12  H  HCR6  0   0.277  -2.9890   -2.8400  -26.3504
 R7D  H13  H  HCR6  0   0.274  -5.8251   -5.5984  -24.6643
 R7D  H14  H  HCR6  0   0.267  -6.5978   -6.1560  -26.9075
 R7D  H15  H  HCH1  0   0.298  -2.9183   -8.2172  -29.3700
 R7D  H16  H  HNH1  0   0.404  -5.8913   -8.5879  -31.2054
 R7D  H17  H  HNH1  0   0.414  -5.6159   -7.7033  -28.6484
 R7D  H18  H  HOH1  0   0.453  -4.9047   -4.1978  -30.7264
 R7D  NAL  N  NH1   0  -0.610  -5.0858   -8.9420  -31.6945

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
 R7D  CAR  CAS  aromatic  1.385  0.020  1.385
 R7D  CAR  CAQ  aromatic  1.388  0.020  1.388
 R7D  CAS  CAN  aromatic  1.391  0.020  1.391
 R7D  CAQ  CAP  aromatic  1.386  0.020  1.386
 R7D  CAN  CAM  single    1.513  0.020  1.513
 R7D  CAN  NAO  aromatic  1.327  0.020  1.327
 R7D  CAM  NAL  single    1.437  0.020  1.437
 R7D  CAP  NAO  aromatic  1.328  0.020  1.328
 R7D  NAL  CX   single    1.337  0.020  1.337
 R7D  OX   CX   double    1.220  0.020  1.220
 R7D  CX   CXA  single    1.530  0.020  1.530
 R7D  OAZ  CAA  single    1.391  0.020  1.391
 R7D  CXA  NX   single    1.444  0.020  1.444
 R7D  CXA  CE   single    1.526  0.020  1.526
 R7D  OAD  CAB  double    1.220  0.020  1.220
 R7D  NX   CAB  single    1.340  0.020  1.340
 R7D  CAB  CAA  single    1.531  0.020  1.531
 R7D  CAA  CAY  single    1.516  0.020  1.516
 R7D  CE   SD   single    1.825  0.020  1.825
 R7D  CBA  CAY  aromatic  1.392  0.020  1.392
 R7D  CBA  CBB  aromatic  1.383  0.020  1.383
 R7D  CAY  CBE  aromatic  1.388  0.020  1.388
 R7D  CBB  CBC  aromatic  1.393  0.020  1.393
 R7D  CBE  CBD  aromatic  1.387  0.020  1.387
 R7D  CBC  CBD  aromatic  1.387  0.020  1.387
 R7D  CBC  CBF  single    1.495  0.020  1.495
 R7D  FBI  CBF  single    1.342  0.020  1.342
 R7D  CBF  FBG  single    1.341  0.020  1.341
 R7D  CBF  FBH  single    1.335  0.020  1.335
 R7D  SD   H1   single    1.200  0.020  1.300
 R7D  CE   H2   single    0.970  0.020  1.090
 R7D  CE   H3   single    0.970  0.020  1.090
 R7D  CAA  H4   single    0.970  0.020  1.090
 R7D  CAM  H5   single    0.970  0.020  1.090
 R7D  CAM  H6   single    0.970  0.020  1.090
 R7D  CAP  H7   single    0.930  0.020  1.080
 R7D  CAQ  H8   single    0.930  0.020  1.080
 R7D  CAR  H9   single    0.930  0.020  1.080
 R7D  CAS  H10  single    0.930  0.020  1.080
 R7D  CBA  H11  single    0.930  0.020  1.080
 R7D  CBB  H12  single    0.930  0.020  1.080
 R7D  CBD  H13  single    0.930  0.020  1.080
 R7D  CBE  H14  single    0.930  0.020  1.080
 R7D  CXA  H15  single    0.970  0.020  1.090
 R7D  NAL  H16  single    0.860  0.020  1.020
 R7D  NX   H17  single    0.860  0.020  1.020
 R7D  OAZ  H18  single    0.850  0.020  0.980

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
 R7D  H1   SD   CE    96.57  3.000
 R7D  H3   CE   H2   108.43  3.000
 R7D  H3   CE   CXA  108.79  3.000
 R7D  H2   CE   CXA  110.31  3.000
 R7D  H3   CE   SD   109.85  3.000
 R7D  H2   CE   SD   109.90  3.000
 R7D  CXA  CE   SD   109.54  3.000
 R7D  H4   CAA  OAZ  109.14  3.000
 R7D  H4   CAA  CAY  108.63  3.000
 R7D  OAZ  CAA  CAY  112.68  3.000
 R7D  H4   CAA  CAB  109.04  3.000
 R7D  CAY  CAA  CAB  107.49  3.000
 R7D  OAZ  CAA  CAB  109.79  3.000
 R7D  OAD  CAB  NX   123.47  3.000
 R7D  NX   CAB  CAA  116.34  3.000
 R7D  OAD  CAB  CAA  120.17  3.000
 R7D  H6   CAM  H5   106.52  3.000
 R7D  H6   CAM  NAL  107.56  3.000
 R7D  H5   CAM  NAL  110.38  3.000
 R7D  H6   CAM  CAN  109.33  3.000
 R7D  H5   CAM  CAN  109.74  3.000
 R7D  NAL  CAM  CAN  113.06  3.000
 R7D  NAO  CAN  CAS  122.41  3.000
 R7D  NAO  CAN  CAM  117.48  3.000
 R7D  CAS  CAN  CAM  120.09  3.000
 R7D  H7   CAP  NAO  116.30  3.000
 R7D  H7   CAP  CAQ  120.19  3.000
 R7D  NAO  CAP  CAQ  123.51  3.000
 R7D  H8   CAQ  CAR  121.56  3.000
 R7D  H8   CAQ  CAP  120.44  3.000
 R7D  CAR  CAQ  CAP  118.00  3.000
 R7D  H9   CAR  CAS  120.48  3.000
 R7D  H9   CAR  CAQ  120.76  3.000
 R7D  CAS  CAR  CAQ  118.76  3.000
 R7D  H10  CAS  CAR  120.87  3.000
 R7D  H10  CAS  CAN  120.24  3.000
 R7D  CAR  CAS  CAN  118.89  3.000
 R7D  CBE  CAY  CBA  119.14  3.000
 R7D  CBE  CAY  CAA  120.43  3.000
 R7D  CBA  CAY  CAA  120.41  3.000
 R7D  H11  CBA  CBB  118.98  3.000
 R7D  H11  CBA  CAY  120.67  3.000
 R7D  CBB  CBA  CAY  120.35  3.000
 R7D  H12  CBB  CBC  120.89  3.000
 R7D  H12  CBB  CBA  118.99  3.000
 R7D  CBC  CBB  CBA  120.12  3.000
 R7D  CBF  CBC  CBD  121.56  3.000
 R7D  CBF  CBC  CBB  118.55  3.000
 R7D  CBD  CBC  CBB  119.89  3.000
 R7D  H13  CBD  CBE  119.06  3.000
 R7D  H13  CBD  CBC  121.30  3.000
 R7D  CBE  CBD  CBC  119.63  3.000
 R7D  H14  CBE  CBD  118.96  3.000
 R7D  H14  CBE  CAY  120.17  3.000
 R7D  CBD  CBE  CAY  120.87  3.000
 R7D  FBI  CBF  FBH  106.98  3.000
 R7D  FBH  CBF  FBG  107.00  3.000
 R7D  FBI  CBF  FBG  106.31  3.000
 R7D  FBH  CBF  CBC  112.91  3.000
 R7D  FBG  CBF  CBC  111.71  3.000
 R7D  FBI  CBF  CBC  111.55  3.000
 R7D  OX   CX   NAL  123.67  3.000
 R7D  OX   CX   CXA  120.16  3.000
 R7D  NAL  CX   CXA  116.08  3.000
 R7D  H15  CXA  NX   109.76  3.000
 R7D  H15  CXA  CX   106.99  3.000
 R7D  NX   CXA  CX   113.40  3.000
 R7D  H15  CXA  CE   109.16  3.000
 R7D  NX   CXA  CE   110.25  3.000
 R7D  CX   CXA  CE   107.13  3.000
 R7D  CAP  NAO  CAN  118.42  3.000
 R7D  H17  NX   CXA  118.47  3.000
 R7D  H17  NX   CAB  119.42  3.000
 R7D  CXA  NX   CAB  121.37  3.000
 R7D  H18  OAZ  CAA  107.76  3.000
 R7D  H16  NAL  CX   119.01  3.000
 R7D  H16  NAL  CAM  118.01  3.000
 R7D  CX   NAL  CAM  121.05  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
 R7D  CONST_01  CAQ  CAR  CAS  CAN     0.00   0.0  0
 R7D  CONST_02  CAQ  CAP  NAO  CAN     0.00   0.0  0
 R7D  CONST_03  CAS  CAR  CAQ  CAP     0.00   0.0  0
 R7D  CONST_04  CAS  CAN  NAO  CAP     0.00   0.0  0
 R7D  CONST_05  NAO  CAN  CAS  CAR     0.00   0.0  0
 R7D  CONST_06  NAO  CAP  CAQ  CAR     0.00   0.0  0
 R7D  CONST_07  CBC  CBB  CBA  CAY     0.00   0.0  0
 R7D  CONST_08  CBC  CBD  CBE  CAY     0.00   0.0  0
 R7D  CONST_09  CBD  CBE  CAY  CBA     0.00   0.0  0
 R7D  CONST_10  CBD  CBC  CBB  CBA     0.00   0.0  0
 R7D  CONST_11  CBE  CAY  CBA  CBB     0.00   0.0  0
 R7D  CONST_12  CBE  CBD  CBC  CBB     0.00   0.0  0
 R7D  CONST_13  CBB  CBA  CAY  CAA   180.00   0.0  0
 R7D  CONST_14  CBD  CBE  CAY  CAA   180.00   0.0  0
 R7D  CONST_15  CAR  CAS  CAN  CAM   180.00   0.0  0
 R7D  CONST_16  CAP  NAO  CAN  CAM   180.00   0.0  0
 R7D  CONST_17  CBF  CBC  CBB  CBA   180.00   0.0  0
 R7D  CONST_18  CBF  CBC  CBD  CBE   180.00   0.0  0
 R7D  CONST_19  H9   CAR  CAS  CAN   180.00   0.0  0
 R7D  CONST_20  H7   CAP  NAO  CAN   180.00   0.0  0
 R7D  CONST_21  H10  CAS  CAR  CAQ   180.00   0.0  0
 R7D  CONST_22  H8   CAQ  CAR  CAS   180.00   0.0  0
 R7D  CONST_23  H12  CBB  CBA  CAY   180.00   0.0  0
 R7D  CONST_24  H13  CBD  CBE  CAY   180.00   0.0  0
 R7D  CONST_25  H14  CBE  CAY  CBA   180.00   0.0  0
 R7D  CONST_26  H11  CBA  CBB  CBC   180.00   0.0  0
 R7D  CONST_27  CXA  NX   CAB  CAA   180.00   0.0  0
 R7D  CONST_28  OX   CX   NAL  CAM     0.00   0.0  0
 R7D  CONST_29  CXA  CX   NAL  CAM   180.00   0.0  0
 R7D  CONST_30  OAD  CAB  NX   CXA     0.00   0.0  0
 R7D  CONST_31  H17  NX   CAB  CAA     0.00   0.0  0
 R7D  CONST_32  H16  NAL  CX   CXA     0.00   0.0  0
 R7D  Var_01    NAL  CAM  CAN  CAS  -154.57  30.0  2
 R7D  Var_02    FBI  CBF  CBC  CBB    60.51  30.0  2
 R7D  Var_03    CX   NAL  CAM  CAN    66.92  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
 R7D  chir_01  CAA  OAZ  CAB  CAY  negativ
 R7D  chir_02  CXA  NX   CX   CE   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
 R7D  plan-1  CAM  0.020
 R7D  plan-1  CAN  0.020
 R7D  plan-1  CAP  0.020
 R7D  plan-1  CAQ  0.020
 R7D  plan-1  CAR  0.020
 R7D  plan-1  CAS  0.020
 R7D  plan-1  NAO  0.020
 R7D  plan-1  H7   0.020
 R7D  plan-1  H8   0.020
 R7D  plan-1  H9   0.020
 R7D  plan-1  H10  0.020
 R7D  plan-2  CAA  0.020
 R7D  plan-2  CAY  0.020
 R7D  plan-2  CBA  0.020
 R7D  plan-2  CBB  0.020
 R7D  plan-2  CBC  0.020
 R7D  plan-2  CBD  0.020
 R7D  plan-2  CBE  0.020
 R7D  plan-2  CBF  0.020
 R7D  plan-2  H11  0.020
 R7D  plan-2  H12  0.020
 R7D  plan-2  H13  0.020
 R7D  plan-2  H14  0.020
 R7D  plan-3  CAA  0.020
 R7D  plan-3  CAB  0.020
 R7D  plan-3  CXA  0.020
 R7D  plan-3  NX   0.020
 R7D  plan-3  OAD  0.020
 R7D  plan-3  H17  0.020
 R7D  plan-4  CAM  0.020
 R7D  plan-4  CX   0.020
 R7D  plan-4  CXA  0.020
 R7D  plan-4  OX   0.020
 R7D  plan-4  H16  0.020
 R7D  plan-4  NAL  0.020

