# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 16:18:06 2020
#   Inital geometry file: a 127 line input string
#   Ligand name: (3R)-4-[(3R)-3-amino-4-(2,4,5-trifluorophenyl)butanoyl]-3-(tert-butoxymethyl)piperazin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(C)OC[C@H]1N(CCNC1=O)C(=O)C[C@H](N)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
 8VU  8VU  (3R)-4-[(3R)-3-amino-4-(2,4,5-trifluorophenyl)butanoyl]-3-(tert-butoxymethyl)piperazin-2-one  ligand  54  28  .  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_8VU
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
 8VU  C10   C  C     0   0.605   0.8610   0.4573  -0.6250
 8VU  C13   C  CH1   0  -0.235   3.1909   0.4558  -1.2110
 8VU  C17   C  CH2   0  -0.302   2.4209   1.5107   0.9567
 8VU  C26   C  CH3   0  -0.677   4.5094  -3.7187  -0.7308
 8VU  C28   C  CH3   0  -0.660   5.1761  -2.7945   1.4915
 8VU  C01   C  CR6   0   0.399  -6.6611   1.0628  -0.8769
 8VU  C02   C  CR16  0  -0.552  -6.0259  -0.1581  -0.7899
 8VU  C03   C  CR6   0   0.531  -4.7564  -0.1942  -0.2447
 8VU  C04   C  CR6   0  -0.063  -4.0953   0.9310   0.2251
 8VU  C05   C  CR16  0  -0.457  -4.7688   2.1458   0.1155
 8VU  C06   C  CR6   0   0.405  -6.0349   2.2107  -0.4265
 8VU  C07   C  CH2   0  -0.518  -2.7054   0.8605   0.7823
 8VU  C08   C  CH1   0  -0.081  -1.6252   0.8531  -0.3185
 8VU  C09   C  CH2   0  -0.609  -0.2506   0.8312   0.3363
 8VU  N11   N  NT    0  -0.485   2.1336   0.7387  -0.2438
 8VU  O12   O  O     0  -0.496   0.6265  -0.1099  -1.6826
 8VU  C14   C  C     0   0.527   4.4810   1.2380  -0.9922
 8VU  N15   N  NH1   0  -0.612   4.7164   1.6934   0.2405
 8VU  C16   C  CH2   0  -0.301   3.8675   1.3721   1.3630
 8VU  O18   O  O     0  -0.496   5.2510   1.3933  -1.9298
 8VU  N19   N  NH2   0  -0.785  -1.6908   1.9794  -1.2316
 8VU  F20   F  F     0  -0.306  -6.6717   3.3830  -0.5221
 8VU  F22   F  F     0  -0.305  -4.1427  -1.3845  -0.1661
 8VU  C23   C  CH2   0  -0.142   3.5487  -1.0311  -1.2763
 8VU  O24   O  O2    0  -0.497   4.2650  -1.3696  -0.1198
 8VU  C25   C  CT    0   0.205   4.1580  -2.7094   0.3616
 8VU  C27   C  CH3   0  -0.665   2.7554  -2.9726   0.9084
 8VU  H131  H  HCH1  0   0.289   2.8369   0.7402  -2.2049
 8VU  H172  H  HCH2  0   0.250   2.1978   2.5703   0.7954
 8VU  H171  H  HCH2  0   0.271   1.8010   1.1636   1.7834
 8VU  H3    H  HCH3  0   0.234   5.4895  -3.5040  -1.1608
 8VU  H1    H  HCH3  0   0.236   4.5404  -4.7266  -0.3145
 8VU  H2    H  HCH3  0   0.232   3.7773  -3.7269  -1.5408
 8VU  H5    H  HCH3  0   0.230   6.1884  -2.6186   1.1236
 8VU  H6    H  HCH3  0   0.232   4.9616  -2.0577   2.2678
 8VU  H4    H  HCH3  0   0.224   5.1532  -3.7822   1.9523
 8VU  H021  H  HCR6  0   0.313  -6.5117  -1.0605  -1.1376
 8VU  H051  H  HCR6  0   0.296  -4.3006   3.0556   0.4697
 8VU  H072  H  HCH2  0   0.254  -2.5445   1.7222   1.4364
 8VU  H071  H  HCH2  0   0.256  -2.5915  -0.0272   1.4086
 8VU  H7    H  HCH1  0   0.245  -1.7496  -0.0551  -0.9120
 8VU  H092  H  HCH2  0   0.283  -0.2315   0.1130   1.1641
 8VU  H091  H  HCH2  0   0.267  -0.0695   1.8087   0.7909
 8VU  H8    H  HNH1  0   0.403   5.6011   2.1488   0.4107
 8VU  H161  H  HCH2  0   0.274   4.0703   2.0785   2.1651
 8VU  H162  H  HCH2  0   0.257   4.0700   0.3685   1.7398
 8VU  H10   H  HNH2  0   0.351  -2.5575   1.9597  -1.7546
 8VU  H9    H  HNH2  0   0.337  -1.6996   2.8484  -0.7083
 8VU  H231  H  HCH2  0   0.234   2.6267  -1.6058  -1.3852
 8VU  H232  H  HCH2  0   0.221   4.1450  -1.2026  -2.1811
 8VU  H14   H  HCH3  0   0.230   2.6993  -3.9776   1.3288
 8VU  H12   H  HCH3  0   0.230   2.5073  -2.2625   1.6992
 8VU  H13   H  HCH3  0   0.229   1.9867  -2.9027   0.1371
 8VU  F21   F  F     0  -0.302  -7.8893   1.1418  -1.3937

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
 8VU  F20  C06   single    1.337  0.020  1.337
 8VU  C06  C05   aromatic  1.379  0.020  1.379
 8VU  C06  C01   aromatic  1.383  0.020  1.383
 8VU  F21  C01   single    1.335  0.020  1.335
 8VU  C05  C04   aromatic  1.393  0.020  1.393
 8VU  C01  C02   aromatic  1.379  0.020  1.379
 8VU  C04  C07   single    1.499  0.020  1.499
 8VU  C04  C03   aromatic  1.387  0.020  1.387
 8VU  O12  C10   double    1.223  0.020  1.223
 8VU  C02  C03   aromatic  1.382  0.020  1.382
 8VU  O18  C14   double    1.223  0.020  1.223
 8VU  C08  C07   single    1.542  0.020  1.542
 8VU  C08  C09   single    1.523  0.020  1.523
 8VU  C08  N19   single    1.451  0.020  1.451
 8VU  C03  F22   single    1.341  0.020  1.341
 8VU  C10  C09   single    1.516  0.020  1.516
 8VU  C10  N11   single    1.358  0.020  1.358
 8VU  C14  C13   single    1.524  0.020  1.524
 8VU  C14  N15   single    1.335  0.020  1.335
 8VU  C13  N11   single    1.461  0.020  1.461
 8VU  C13  C23   single    1.531  0.020  1.531
 8VU  N11  C17   single    1.456  0.020  1.456
 8VU  N15  C16   single    1.444  0.020  1.444
 8VU  C26  C25   single    1.528  0.020  1.528
 8VU  C17  C16   single    1.509  0.020  1.509
 8VU  O24  C23   single    1.402  0.020  1.402
 8VU  O24  C25   single    1.428  0.020  1.428
 8VU  C25  C28   single    1.523  0.020  1.523
 8VU  C25  C27   single    1.528  0.020  1.528
 8VU  C13  H131  single    0.970  0.020  1.090
 8VU  C17  H172  single    0.970  0.020  1.090
 8VU  C17  H171  single    0.970  0.020  1.090
 8VU  C26  H3    single    0.970  0.020  1.090
 8VU  C26  H1    single    0.970  0.020  1.090
 8VU  C26  H2    single    0.970  0.020  1.090
 8VU  C28  H5    single    0.970  0.020  1.090
 8VU  C28  H6    single    0.970  0.020  1.090
 8VU  C28  H4    single    0.970  0.020  1.090
 8VU  C02  H021  single    0.930  0.020  1.080
 8VU  C05  H051  single    0.930  0.020  1.080
 8VU  C07  H072  single    0.970  0.020  1.090
 8VU  C07  H071  single    0.970  0.020  1.090
 8VU  C08  H7    single    0.970  0.020  1.090
 8VU  C09  H092  single    0.970  0.020  1.090
 8VU  C09  H091  single    0.970  0.020  1.090
 8VU  N15  H8    single    0.860  0.020  1.020
 8VU  C16  H161  single    0.970  0.020  1.090
 8VU  C16  H162  single    0.970  0.020  1.090
 8VU  N19  H10   single    0.890  0.020  1.040
 8VU  N19  H9    single    0.890  0.020  1.040
 8VU  C23  H231  single    0.970  0.020  1.090
 8VU  C23  H232  single    0.970  0.020  1.090
 8VU  C27  H14   single    0.970  0.020  1.090
 8VU  C27  H12   single    0.970  0.020  1.090
 8VU  C27  H13   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
 8VU  O12   C10  N11   121.24  3.000
 8VU  N11   C10  C09   117.25  3.000
 8VU  O12   C10  C09   121.48  3.000
 8VU  H131  C13  C23   106.84  3.000
 8VU  H131  C13  C14   105.73  3.000
 8VU  C23   C13  C14   107.86  3.000
 8VU  H131  C13  N11   108.50  3.000
 8VU  C23   C13  N11   112.68  3.000
 8VU  C14   C13  N11   114.72  3.000
 8VU  H171  C17  H172  107.71  3.000
 8VU  H171  C17  C16   108.17  3.000
 8VU  H172  C17  C16   108.90  3.000
 8VU  H171  C17  N11   110.14  3.000
 8VU  H172  C17  N11   110.57  3.000
 8VU  C16   C17  N11   111.25  3.000
 8VU  H2    C26  H1    107.17  3.000
 8VU  H2    C26  H3    108.13  3.000
 8VU  H1    C26  H3    107.85  3.000
 8VU  H2    C26  C25   112.40  3.000
 8VU  H1    C26  C25   110.12  3.000
 8VU  H3    C26  C25   110.99  3.000
 8VU  H4    C28  H6    107.86  3.000
 8VU  H4    C28  H5    107.94  3.000
 8VU  H6    C28  H5    108.25  3.000
 8VU  H4    C28  C25   110.49  3.000
 8VU  H6    C28  C25   111.01  3.000
 8VU  H5    C28  C25   111.16  3.000
 8VU  F21   C01  C06   119.58  3.000
 8VU  F21   C01  C02   120.04  3.000
 8VU  C06   C01  C02   120.38  3.000
 8VU  H021  C02  C03   121.15  3.000
 8VU  H021  C02  C01   120.75  3.000
 8VU  C03   C02  C01   118.11  3.000
 8VU  F22   C03  C04   118.81  3.000
 8VU  F22   C03  C02   117.81  3.000
 8VU  C04   C03  C02   123.38  3.000
 8VU  C07   C04  C05   121.23  3.000
 8VU  C07   C04  C03   121.99  3.000
 8VU  C05   C04  C03   116.76  3.000
 8VU  H051  C05  C06   119.08  3.000
 8VU  H051  C05  C04   119.86  3.000
 8VU  C06   C05  C04   121.06  3.000
 8VU  F20   C06  C05   120.44  3.000
 8VU  C05   C06  C01   120.31  3.000
 8VU  F20   C06  C01   119.25  3.000
 8VU  H071  C07  H072  106.38  3.000
 8VU  H071  C07  C08   109.41  3.000
 8VU  H072  C07  C08   109.12  3.000
 8VU  H071  C07  C04   110.37  3.000
 8VU  H072  C07  C04   108.76  3.000
 8VU  C08   C07  C04   112.60  3.000
 8VU  H7    C08  N19   107.36  3.000
 8VU  H7    C08  C09   108.94  3.000
 8VU  N19   C08  C09   108.81  3.000
 8VU  H7    C08  C07   108.18  3.000
 8VU  N19   C08  C07   114.43  3.000
 8VU  C09   C08  C07   108.98  3.000
 8VU  H091  C09  H092  105.61  3.000
 8VU  H091  C09  C08   108.39  3.000
 8VU  H092  C09  C08   110.48  3.000
 8VU  H091  C09  C10   111.27  3.000
 8VU  H092  C09  C10   107.72  3.000
 8VU  C08   C09  C10   113.12  3.000
 8VU  C17   N11  C13   120.39  3.000
 8VU  C17   N11  C10   121.75  3.000
 8VU  C13   N11  C10   116.90  3.000
 8VU  O18   C14  N15   123.60  3.000
 8VU  N15   C14  C13   117.18  3.000
 8VU  O18   C14  C13   119.20  3.000
 8VU  H8    N15  C16   118.99  3.000
 8VU  H8    N15  C14   117.65  3.000
 8VU  C16   N15  C14   122.57  3.000
 8VU  H162  C16  H161  107.95  3.000
 8VU  H162  C16  N15   111.36  3.000
 8VU  H161  C16  N15   108.61  3.000
 8VU  H162  C16  C17   110.82  3.000
 8VU  H161  C16  C17   108.51  3.000
 8VU  N15   C16  C17   109.51  3.000
 8VU  H9    N19  H10   106.01  3.000
 8VU  H9    N19  C08   109.92  3.000
 8VU  H10   N19  C08   110.40  3.000
 8VU  H232  C23  H231  107.13  3.000
 8VU  H232  C23  O24   111.40  3.000
 8VU  H231  C23  O24   112.74  3.000
 8VU  H232  C23  C13   108.30  3.000
 8VU  H231  C23  C13   108.55  3.000
 8VU  O24   C23  C13   108.59  3.000
 8VU  C25   O24  C23   117.81  3.000
 8VU  C27   C25  O24   110.55  3.000
 8VU  C27   C25  C28   109.78  3.000
 8VU  O24   C25  C28   104.62  3.000
 8VU  C27   C25  C26   110.67  3.000
 8VU  C28   C25  C26   109.85  3.000
 8VU  O24   C25  C26   111.20  3.000
 8VU  H13   C27  H12   108.08  3.000
 8VU  H13   C27  H14   107.17  3.000
 8VU  H12   C27  H14   107.97  3.000
 8VU  H13   C27  C25   112.49  3.000
 8VU  H12   C27  C25   110.85  3.000
 8VU  H14   C27  C25   110.11  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
 8VU  CONST_01  C04   C05  C06  C01    0.00   0.0  0
 8VU  CONST_02  C04   C03  C02  C01    0.00   0.0  0
 8VU  CONST_03  C05   C06  C01  C02    0.00   0.0  0
 8VU  CONST_04  C05   C04  C03  C02    0.00   0.0  0
 8VU  CONST_05  C06   C05  C04  C03    0.00   0.0  0
 8VU  CONST_06  C06   C01  C02  C03    0.00   0.0  0
 8VU  CONST_07  C16   N15  C14  C13    0.00   0.0  0
 8VU  CONST_08  F22   C03  C02  C01  180.00   0.0  0
 8VU  CONST_09  F20   C06  C01  C02  180.00   0.0  0
 8VU  CONST_10  C07   C04  C03  C02  180.00   0.0  0
 8VU  CONST_11  F21   C01  C02  C03  180.00   0.0  0
 8VU  CONST_12  F20   C06  C05  C04  180.00   0.0  0
 8VU  CONST_13  F21   C01  C06  C05  180.00   0.0  0
 8VU  CONST_14  F22   C03  C04  C05  180.00   0.0  0
 8VU  CONST_15  C07   C04  C05  C06  180.00   0.0  0
 8VU  CONST_16  O18   C14  N15  C16  180.00   0.0  0
 8VU  CONST_17  H051  C05  C06  C01  180.00   0.0  0
 8VU  CONST_18  H021  C02  C03  C04  180.00   0.0  0
 8VU  CONST_19  H8    N15  C14  C13  180.00   0.0  0
 8VU  CONST_20  O12   C10  N11  C13    0.00   0.0  0
 8VU  CONST_21  C09   C10  N11  C13  180.00   0.0  0
 8VU  CONST_22  O12   C10  N11  C17  180.00   0.0  0
 8VU  CONST_23  C09   C10  N11  C17    0.00   0.0  0
 8VU  Var_01    C16   C17  N11  C13  -26.91  30.0  1
 8VU  Var_02    C14   N15  C16  C17  -44.54  30.0  1
 8VU  Var_03    N15   C16  C17  N11   53.04  30.0  1
 8VU  Var_04    C08   C07  C04  C03   81.53  30.0  2
 8VU  Var_05    N11   C10  C09  C08  163.49  30.0  1
 8VU  Var_06    C27   C25  O24  C23  -69.07  30.0  3
 8VU  Var_07    H5    C28  C25  C26   57.57  30.0  3
 8VU  Var_08    H14   C27  C25  C26   59.75  30.0  3
 8VU  Var_09    H3    C26  C25  C28  -61.53  30.0  3
 8VU  Var_10    H231  C23  O24  C25   30.35  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
 8VU  chir_01  C13  C14  N11  C23  positiv
 8VU  chir_02  C08  N19  C09  C07  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
 8VU  plan-1  C01   0.020
 8VU  plan-1  C02   0.020
 8VU  plan-1  C03   0.020
 8VU  plan-1  C04   0.020
 8VU  plan-1  C05   0.020
 8VU  plan-1  C06   0.020
 8VU  plan-1  C07   0.020
 8VU  plan-1  F20   0.020
 8VU  plan-1  F22   0.020
 8VU  plan-1  H021  0.020
 8VU  plan-1  H051  0.020
 8VU  plan-1  F21   0.020
 8VU  plan-2  C10   0.020
 8VU  plan-2  C13   0.020
 8VU  plan-2  C17   0.020
 8VU  plan-2  C09   0.020
 8VU  plan-2  N11   0.020
 8VU  plan-2  O12   0.020
 8VU  plan-3  C13   0.020
 8VU  plan-3  C14   0.020
 8VU  plan-3  N15   0.020
 8VU  plan-3  C16   0.020
 8VU  plan-3  O18   0.020
 8VU  plan-3  H8    0.020

