# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 14:37:10 2020
#   Inital geometry file: a 95 line input string
#   Ligand name: 4-[(3R)-3-amino-4-(2,4,5-trifluorophenyl)butanoyl]piperazin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CC(=O)N1CCNC(=O)C1)Cc2cc(F)c(F)cc2F
#
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
 8O3  8O3  4-[(3R)-3-amino-4-(2,4,5-trifluorophenyl)butanoyl]piperazin-2-one  ligand  38  22  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_8O3
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
 8O3  C10   C  C     0   0.595  -2.2592  -0.8114   0.5493
 8O3  C13   C  CH2   0  -0.399  -4.1339  -0.2581  -0.9935
 8O3  C17   C  CH2   0  -0.343  -4.5898  -1.1841   1.1866
 8O3  C01   C  CR6   0   0.400   5.1619   0.3567   0.1950
 8O3  C02   C  CR16  0  -0.552   4.4573   1.4832  -0.1690
 8O3  C03   C  CR6   0   0.507   3.1587   1.3245  -0.6188
 8O3  C04   C  CR6   0  -0.061   2.5346   0.0909  -0.7261
 8O3  C05   C  CR16  0  -0.436   3.2818  -1.0243  -0.3490
 8O3  C06   C  CR6   0   0.406   4.5759  -0.8940   0.1040
 8O3  C07   C  CH2   0  -0.520   1.1098  -0.0637  -1.1696
 8O3  C08   C  CH1   0  -0.077   0.1399  -0.1745   0.0252
 8O3  C09   C  CH2   0  -0.614  -1.2830  -0.3157  -0.4996
 8O3  N11   N  NT    0  -0.485  -3.5822  -0.6964   0.2676
 8O3  O12   O  O     0  -0.489  -1.8738  -1.3177   1.5917
 8O3  C14   C  C     0   0.515  -5.4115   0.5539  -0.8629
 8O3  N15   N  NH1   0  -0.620  -5.9938   0.6054   0.3395
 8O3  C16   C  CH2   0  -0.252  -5.5156  -0.0434   1.5449
 8O3  O18   O  O     0  -0.504  -5.8708   1.1039  -1.8552
 8O3  N19   N  NH2   0  -0.786   0.1952   0.9362   0.9574
 8O3  F20   F  F     0  -0.306   5.2831  -1.9734   0.4562
 8O3  F22   F  F     0  -0.306   2.4863   2.4319  -0.9698
 8O3  H132  H  HCH2  0   0.295  -3.4305   0.3621  -1.5431
 8O3  H131  H  HCH2  0   0.284  -4.3671  -1.1157  -1.6367
 8O3  H171  H  HCH2  0   0.259  -5.1524  -1.9965   0.7149
 8O3  H172  H  HCH2  0   0.282  -4.1207  -1.5772   2.0828
 8O3  H021  H  HCR6  0   0.313   4.9092   2.4643  -0.1009
 8O3  H051  H  HCR6  0   0.295   2.8454  -2.0134  -0.4181
 8O3  H071  H  HCH2  0   0.254   0.8134   0.7698  -1.8104
 8O3  H072  H  HCH2  0   0.258   1.0257  -0.9665  -1.7796
 8O3  H1    H  HCH1  0   0.244   0.4032  -1.0783   0.5793
 8O3  H092  H  HCH2  0   0.284  -1.3087  -1.0134  -1.3441
 8O3  H091  H  HCH2  0   0.267  -1.5990   0.6499  -0.9025
 8O3  H2    H  HNH1  0   0.403  -6.8309   1.1656   0.4099
 8O3  H161  H  HCH2  0   0.260  -6.3729  -0.4237   2.1002
 8O3  H162  H  HCH2  0   0.246  -4.9961   0.6737   2.1861
 8O3  H3    H  HNH2  0   0.350   1.0901   0.9570   1.4299
 8O3  H4    H  HNH2  0   0.337   0.1176   1.8142   0.4570
 8O3  F21   F  F     0  -0.301   6.4175   0.4624   0.6348

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
 8O3  O18  C14   double    1.224  0.020  1.224
 8O3  N15  C14   single    1.337  0.020  1.337
 8O3  N15  C16   single    1.450  0.020  1.450
 8O3  C14  C13   single    1.519  0.020  1.519
 8O3  C16  C17   single    1.512  0.020  1.512
 8O3  C17  N11   single    1.448  0.020  1.448
 8O3  C13  N11   single    1.445  0.020  1.445
 8O3  N11  C10   single    1.358  0.020  1.358
 8O3  C10  O12   double    1.221  0.020  1.221
 8O3  C10  C09   single    1.516  0.020  1.516
 8O3  C09  C08   single    1.523  0.020  1.523
 8O3  C08  C07   single    1.543  0.020  1.543
 8O3  C08  N19   single    1.451  0.020  1.451
 8O3  C07  C04   single    1.500  0.020  1.500
 8O3  C04  C05   aromatic  1.394  0.020  1.394
 8O3  C04  C03   aromatic  1.387  0.020  1.387
 8O3  F22  C03   single    1.342  0.020  1.342
 8O3  C05  C06   aromatic  1.377  0.020  1.377
 8O3  C03  C02   aromatic  1.383  0.020  1.383
 8O3  C06  F20   single    1.338  0.020  1.338
 8O3  C06  C01   aromatic  1.384  0.020  1.384
 8O3  C02  C01   aromatic  1.378  0.020  1.378
 8O3  C01  F21   single    1.335  0.020  1.335
 8O3  C13  H132  single    0.970  0.020  1.090
 8O3  C13  H131  single    0.970  0.020  1.090
 8O3  C17  H171  single    0.970  0.020  1.090
 8O3  C17  H172  single    0.970  0.020  1.090
 8O3  C02  H021  single    0.930  0.020  1.080
 8O3  C05  H051  single    0.930  0.020  1.080
 8O3  C07  H071  single    0.970  0.020  1.090
 8O3  C07  H072  single    0.970  0.020  1.090
 8O3  C08  H1    single    0.970  0.020  1.090
 8O3  C09  H092  single    0.970  0.020  1.090
 8O3  C09  H091  single    0.970  0.020  1.090
 8O3  N15  H2    single    0.860  0.020  1.020
 8O3  C16  H161  single    0.970  0.020  1.090
 8O3  C16  H162  single    0.970  0.020  1.090
 8O3  N19  H3    single    0.890  0.020  1.040
 8O3  N19  H4    single    0.890  0.020  1.040

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
 8O3  O12   C10  N11   121.32  3.000
 8O3  O12   C10  C09   121.52  3.000
 8O3  N11   C10  C09   117.14  3.000
 8O3  H131  C13  H132  106.69  3.000
 8O3  H131  C13  C14   106.82  3.000
 8O3  H132  C13  C14   106.42  3.000
 8O3  H131  C13  N11   110.85  3.000
 8O3  H132  C13  N11   111.55  3.000
 8O3  C14   C13  N11   114.09  3.000
 8O3  H172  C17  H171  108.00  3.000
 8O3  H172  C17  C16   110.01  3.000
 8O3  H171  C17  C16   110.31  3.000
 8O3  H172  C17  N11   110.20  3.000
 8O3  H171  C17  N11   109.50  3.000
 8O3  C16   C17  N11   108.80  3.000
 8O3  F21   C01  C06   119.44  3.000
 8O3  F21   C01  C02   120.23  3.000
 8O3  C06   C01  C02   120.33  3.000
 8O3  H021  C02  C03   121.08  3.000
 8O3  H021  C02  C01   120.74  3.000
 8O3  C03   C02  C01   118.18  3.000
 8O3  F22   C03  C04   119.23  3.000
 8O3  F22   C03  C02   117.43  3.000
 8O3  C04   C03  C02   123.34  3.000
 8O3  C07   C04  C05   120.43  3.000
 8O3  C05   C04  C03   116.71  3.000
 8O3  C07   C04  C03   122.82  3.000
 8O3  H051  C05  C06   119.07  3.000
 8O3  H051  C05  C04   119.81  3.000
 8O3  C06   C05  C04   121.12  3.000
 8O3  F20   C06  C05   120.47  3.000
 8O3  F20   C06  C01   119.21  3.000
 8O3  C05   C06  C01   120.32  3.000
 8O3  H072  C07  H071  106.38  3.000
 8O3  H072  C07  C08   108.94  3.000
 8O3  H071  C07  C08   109.78  3.000
 8O3  H072  C07  C04   108.86  3.000
 8O3  H071  C07  C04   110.64  3.000
 8O3  C08   C07  C04   112.05  3.000
 8O3  H1    C08  N19   107.35  3.000
 8O3  H1    C08  C09   108.85  3.000
 8O3  N19   C08  C09   109.14  3.000
 8O3  H1    C08  C07   107.50  3.000
 8O3  N19   C08  C07   114.75  3.000
 8O3  C09   C08  C07   109.09  3.000
 8O3  H091  C09  H092  105.76  3.000
 8O3  H091  C09  C08   108.37  3.000
 8O3  H092  C09  C08   110.28  3.000
 8O3  H091  C09  C10   110.96  3.000
 8O3  H092  C09  C10   108.06  3.000
 8O3  C08   C09  C10   113.17  3.000
 8O3  C17   N11  C13   112.98  3.000
 8O3  C13   N11  C10   125.39  3.000
 8O3  C17   N11  C10   121.18  3.000
 8O3  O18   C14  N15   123.25  3.000
 8O3  N15   C14  C13   117.65  3.000
 8O3  O18   C14  C13   119.08  3.000
 8O3  H2    N15  C16   117.62  3.000
 8O3  H2    N15  C14   116.44  3.000
 8O3  C16   N15  C14   125.93  3.000
 8O3  H162  C16  H161  107.69  3.000
 8O3  H162  C16  N15   110.53  3.000
 8O3  H161  C16  N15   108.68  3.000
 8O3  H162  C16  C17   110.05  3.000
 8O3  H161  C16  C17   109.83  3.000
 8O3  N15   C16  C17   110.02  3.000
 8O3  H4    N19  H3    106.28  3.000
 8O3  H4    N19  C08   110.05  3.000
 8O3  H3    N19  C08   110.44  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
 8O3  CONST_01  C04   C05  C06  C01    0.00   0.0  0
 8O3  CONST_02  C04   C03  C02  C01    0.00   0.0  0
 8O3  CONST_03  C05   C04  C03  C02    0.00   0.0  0
 8O3  CONST_04  C05   C06  C01  C02    0.00   0.0  0
 8O3  CONST_05  C06   C05  C04  C03    0.00   0.0  0
 8O3  CONST_06  C06   C01  C02  C03    0.00   0.0  0
 8O3  CONST_07  C16   N15  C14  C13    0.00   0.0  0
 8O3  CONST_08  F22   C03  C02  C01  180.00   0.0  0
 8O3  CONST_09  C07   C04  C03  C02  180.00   0.0  0
 8O3  CONST_10  F20   C06  C01  C02  180.00   0.0  0
 8O3  CONST_11  F21   C01  C02  C03  180.00   0.0  0
 8O3  CONST_12  F20   C06  C05  C04  180.00   0.0  0
 8O3  CONST_13  F22   C03  C04  C05  180.00   0.0  0
 8O3  CONST_14  F21   C01  C06  C05  180.00   0.0  0
 8O3  CONST_15  C07   C04  C05  C06  180.00   0.0  0
 8O3  CONST_16  O18   C14  N15  C16  180.00   0.0  0
 8O3  CONST_17  H051  C05  C06  C01  180.00   0.0  0
 8O3  CONST_18  H021  C02  C03  C04  180.00   0.0  0
 8O3  CONST_19  H2    N15  C14  C13  180.00   0.0  0
 8O3  CONST_20  O12   C10  N11  C13  180.00   0.0  0
 8O3  CONST_21  C09   C10  N11  C13    0.00   0.0  0
 8O3  CONST_22  O12   C10  N11  C17    0.00   0.0  0
 8O3  CONST_23  C09   C10  N11  C17  180.00   0.0  0
 8O3  Var_01    C16   C17  N11  C13  -64.03  30.0  1
 8O3  Var_02    C14   N15  C16  C17  -21.11  30.0  1
 8O3  Var_03    C14   C13  N11  C17   42.57  30.0  1
 8O3  Var_04    N15   C16  C17  N11   51.05  30.0  1
 8O3  Var_05    N15   C14  C13  N11   -9.91  30.0  1
 8O3  Var_06    C08   C07  C04  C03  -96.15  30.0  2
 8O3  Var_07    N11   C10  C09  C08  166.22  30.0  1

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
 8O3  chir_01  C08  C09  C07  N19  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
 8O3  plan-1  C01   0.020
 8O3  plan-1  C02   0.020
 8O3  plan-1  C03   0.020
 8O3  plan-1  C04   0.020
 8O3  plan-1  C05   0.020
 8O3  plan-1  C06   0.020
 8O3  plan-1  C07   0.020
 8O3  plan-1  F20   0.020
 8O3  plan-1  F22   0.020
 8O3  plan-1  H021  0.020
 8O3  plan-1  H051  0.020
 8O3  plan-1  F21   0.020
 8O3  plan-2  C10   0.020
 8O3  plan-2  C13   0.020
 8O3  plan-2  C17   0.020
 8O3  plan-2  C09   0.020
 8O3  plan-2  N11   0.020
 8O3  plan-2  O12   0.020
 8O3  plan-3  C13   0.020
 8O3  plan-3  C14   0.020
 8O3  plan-3  N15   0.020
 8O3  plan-3  C16   0.020
 8O3  plan-3  O18   0.020
 8O3  plan-3  H2    0.020

