# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 10:42:44 2021
#   Inital geometry file: a 109 line input string
#   Ligand name: (3R)-3-(2,4-dichlorophenyl)-N~1~-hydroxy-N~5~-pentylpentanediamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCNC(=O)C[C@H](CC(=O)NO)c1ccc(Cl)cc1Cl
#
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
 UZP  UZP  (3R)-3-(2,4-dichlorophenyl)-N~1~-hydroxy-N~5~-pentylpentanediamide  ligand  45  23  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_UZP
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
 UZP  C11   C   CR16  0  -0.180   5.5431  -13.2643  20.8332
 UZP  O16   O   OH1   0  -0.543   7.1574   -5.6335  20.1252
 UZP  O17   O   O     0  -0.474   5.6379   -6.7990  22.0465
 UZP  C03   C   CH2   0  -0.557   4.1979   -9.2313  19.9309
 UZP  C04   C   CH1   0  -0.333   4.8702   -9.5451  21.2759
 UZP  C05   C   CR6   0   0.257   4.8496  -11.0338  21.5300
 UZP  C06   C   CR6   0  -0.145   4.1245  -11.6313  22.5581
 UZP  C08   C   CR16  0  -0.144   4.0929  -13.0082  22.7393
 UZP  C09   C   CR6   0  -0.069   4.8036  -13.8127  21.8686
 UZP  C12   C   CR16  0  -0.335   5.5528  -11.8896  20.6822
 UZP  C13   C   CH2   0  -0.563   6.2991   -8.9952  21.3322
 UZP  C14   C   C     0   0.520   6.3047   -7.4825  21.2892
 UZP  C19   C   CH2   0  -0.229   1.1908  -11.3691  19.0512
 UZP  C20   C   CH2   0  -0.479   1.1688  -12.4589  17.9924
 UZP  C21   C   CH2   0  -0.420  -0.2168  -13.0803  17.8606
 UZP  C22   C   CH2   0  -0.427  -0.2866  -14.2339  16.8644
 UZP  C23   C   CH3   0  -0.669   0.0370  -13.8351  15.4304
 UZP  N15   N   NH1   0  -0.371   7.1325   -6.9731  20.3613
 UZP  N18   N   NH1   0  -0.632   2.4943  -10.7422  19.1210
 UZP  O01   O   O     0  -0.498   1.9185   -9.2009  20.6574
 UZP  CL07  CL  CL    0  -0.118   3.2139  -10.6774  23.6841
 UZP  CL10  CL  CL    0  -0.117   4.7654  -15.5289  22.0829
 UZP  H1    H   HCR6  0   0.285   6.0983  -13.8945  20.1526
 UZP  H2    H   HOH1  0   0.479   7.8978   -5.2807  20.6360
 UZP  H3    H   HCH2  0   0.255   4.7686   -9.6734  19.1113
 UZP  H4    H   HCH2  0   0.281   4.1864   -8.1513  19.7660
 UZP  H5    H   HCH1  0   0.273   4.2990   -9.0442  22.0566
 UZP  H6    H   HCR6  0   0.300   3.5195  -13.4410  23.5470
 UZP  H7    H   HCR6  0   0.275   6.1337  -11.4714  19.8690
 UZP  H8    H   HCH2  0   0.294   6.7606   -9.2945  22.2766
 UZP  H9    H   HCH2  0   0.261   6.9135   -9.4203  20.5354
 UZP  H10   H   HCH2  0   0.229   0.4349  -10.6138  18.8197
 UZP  H11   H   HCH2  0   0.229   0.9270  -11.7911  20.0258
 UZP  H12   H   HCH2  0   0.226   1.8975  -13.2367  18.2465
 UZP  H13   H   HCH2  0   0.234   1.4850  -12.0346  17.0351
 UZP  H14   H   HCH2  0   0.214  -0.9322  -12.3035  17.5694
 UZP  H15   H   HCH2  0   0.223  -0.5406  -13.4393  18.8423
 UZP  H16   H   HCH2  0   0.223  -1.2910  -14.6638  16.8977
 UZP  H17   H   HCH2  0   0.213   0.3927  -15.0296  17.1860
 UZP  H18   H   HCH3  0   0.229  -0.1059  -14.6737  14.7481
 UZP  H19   H   HCH3  0   0.216  -0.6099  -13.0226  15.0930
 UZP  H20   H   HCH3  0   0.221   1.0692  -13.5001  15.3213
 UZP  H21   H   HNH1  0   0.418   7.5697   -7.5398  19.6491
 UZP  H22   H   HNH1  0   0.399   3.2412  -11.1364  18.5730
 UZP  C02   C   C     0   0.548   2.7632   -9.7138  19.9348

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
 UZP  C23  C22   single    1.523  0.020  1.523
 UZP  C22  C21   single    1.526  0.020  1.526
 UZP  C21  C20   single    1.524  0.020  1.524
 UZP  C20  C19   single    1.520  0.020  1.520
 UZP  C19  N18   single    1.448  0.020  1.448
 UZP  N18  C02   single    1.339  0.020  1.339
 UZP  C02  C03   single    1.514  0.020  1.514
 UZP  C02  O01   double    1.224  0.020  1.224
 UZP  C03  C04   single    1.536  0.020  1.536
 UZP  N15  O16   single    1.360  0.020  1.360
 UZP  N15  C14   single    1.344  0.020  1.344
 UZP  C12  C11   aromatic  1.383  0.020  1.383
 UZP  C12  C05   aromatic  1.395  0.020  1.395
 UZP  C11  C09   aromatic  1.386  0.020  1.386
 UZP  C04  C13   single    1.532  0.020  1.532
 UZP  C04  C05   single    1.510  0.020  1.510
 UZP  C13  C14   single    1.513  0.020  1.513
 UZP  C14  O17   double    1.219  0.020  1.219
 UZP  C05  C06   aromatic  1.393  0.020  1.393
 UZP  C09  CL10  single    1.730  0.020  1.730
 UZP  C09  C08   aromatic  1.382  0.020  1.382
 UZP  C06  C08   aromatic  1.389  0.020  1.389
 UZP  C06  CL07  single    1.734  0.020  1.734
 UZP  C11  H1    single    0.930  0.020  1.080
 UZP  O16  H2    single    0.850  0.020  0.980
 UZP  C03  H3    single    0.970  0.020  1.090
 UZP  C03  H4    single    0.970  0.020  1.090
 UZP  C04  H5    single    0.970  0.020  1.090
 UZP  C08  H6    single    0.930  0.020  1.080
 UZP  C12  H7    single    0.930  0.020  1.080
 UZP  C13  H8    single    0.970  0.020  1.090
 UZP  C13  H9    single    0.970  0.020  1.090
 UZP  C19  H10   single    0.970  0.020  1.090
 UZP  C19  H11   single    0.970  0.020  1.090
 UZP  C20  H12   single    0.970  0.020  1.090
 UZP  C20  H13   single    0.970  0.020  1.090
 UZP  C21  H14   single    0.970  0.020  1.090
 UZP  C21  H15   single    0.970  0.020  1.090
 UZP  C22  H16   single    0.970  0.020  1.090
 UZP  C22  H17   single    0.970  0.020  1.090
 UZP  C23  H18   single    0.970  0.020  1.090
 UZP  C23  H19   single    0.970  0.020  1.090
 UZP  C23  H20   single    0.970  0.020  1.090
 UZP  N15  H21   single    0.860  0.020  1.020
 UZP  N18  H22   single    0.860  0.020  1.020

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
 UZP  H1    C11  C12  120.47  3.000
 UZP  H1    C11  C09  120.92  3.000
 UZP  C12   C11  C09  118.60  3.000
 UZP  H2    O16  N15  106.37  3.000
 UZP  H4    C03  H3   107.00  3.000
 UZP  H4    C03  C04  109.79  3.000
 UZP  H3    C03  C04  110.23  3.000
 UZP  H4    C03  C02  107.79  3.000
 UZP  H3    C03  C02  111.60  3.000
 UZP  C04   C03  C02  110.33  3.000
 UZP  H5    C04  C13  107.32  3.000
 UZP  H5    C04  C05  108.99  3.000
 UZP  C13   C04  C05  111.12  3.000
 UZP  H5    C04  C03  107.71  3.000
 UZP  C05   C04  C03  110.04  3.000
 UZP  C13   C04  C03  111.53  3.000
 UZP  C12   C05  C06  116.61  3.000
 UZP  C06   C05  C04  123.65  3.000
 UZP  C12   C05  C04  119.71  3.000
 UZP  CL07  C06  C08  116.65  3.000
 UZP  CL07  C06  C05  121.11  3.000
 UZP  C08   C06  C05  122.23  3.000
 UZP  H6    C08  C09  120.69  3.000
 UZP  H6    C08  C06  120.42  3.000
 UZP  C09   C08  C06  118.89  3.000
 UZP  CL10  C09  C08  119.22  3.000
 UZP  C08   C09  C11  120.99  3.000
 UZP  CL10  C09  C11  119.80  3.000
 UZP  H7    C12  C05  119.32  3.000
 UZP  H7    C12  C11  118.00  3.000
 UZP  C05   C12  C11  122.68  3.000
 UZP  H9    C13  H8   106.63  3.000
 UZP  H9    C13  C14  111.48  3.000
 UZP  H8    C13  C14  107.27  3.000
 UZP  H9    C13  C04  110.98  3.000
 UZP  H8    C13  C04  109.10  3.000
 UZP  C14   C13  C04  111.17  3.000
 UZP  N15   C14  C13  113.63  3.000
 UZP  C13   C14  O17  122.74  3.000
 UZP  N15   C14  O17  123.61  3.000
 UZP  H11   C19  H10  106.76  3.000
 UZP  H11   C19  N18  109.95  3.000
 UZP  H10   C19  N18  109.48  3.000
 UZP  H11   C19  C20  109.90  3.000
 UZP  H10   C19  C20  109.75  3.000
 UZP  N18   C19  C20  110.92  3.000
 UZP  H13   C20  H12  106.62  3.000
 UZP  H13   C20  C21  110.19  3.000
 UZP  H12   C20  C21  109.58  3.000
 UZP  H13   C20  C19  109.11  3.000
 UZP  H12   C20  C19  109.75  3.000
 UZP  C21   C20  C19  111.46  3.000
 UZP  H15   C21  H14  106.13  3.000
 UZP  H15   C21  C22  108.92  3.000
 UZP  H14   C21  C22  109.43  3.000
 UZP  H15   C21  C20  108.98  3.000
 UZP  H14   C21  C20  109.12  3.000
 UZP  C22   C21  C20  113.97  3.000
 UZP  H17   C22  H16  105.99  3.000
 UZP  H17   C22  C23  109.58  3.000
 UZP  H16   C22  C23  109.07  3.000
 UZP  H17   C22  C21  109.24  3.000
 UZP  H16   C22  C21  108.64  3.000
 UZP  C23   C22  C21  114.02  3.000
 UZP  H20   C23  H19  107.53  3.000
 UZP  H20   C23  H18  107.32  3.000
 UZP  H19   C23  H18  107.53  3.000
 UZP  H20   C23  C22  112.06  3.000
 UZP  H19   C23  C22  111.09  3.000
 UZP  H18   C23  C22  111.09  3.000
 UZP  H21   N15  C14  122.76  3.000
 UZP  H21   N15  O16  114.98  3.000
 UZP  C14   N15  O16  120.29  3.000
 UZP  H22   N18  C19  118.17  3.000
 UZP  H22   N18  C02  118.86  3.000
 UZP  C19   N18  C02  122.87  3.000
 UZP  O01   C02  N18  122.82  3.000
 UZP  O01   C02  C03  121.47  3.000
 UZP  N18   C02  C03  115.70  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
 UZP  CONST_01  C06   C05  C12  C11     0.00   0.0  0
 UZP  CONST_02  C06   C08  C09  C11     0.00   0.0  0
 UZP  CONST_03  C09   C11  C12  C05     0.00   0.0  0
 UZP  CONST_04  C09   C08  C06  C05     0.00   0.0  0
 UZP  CONST_05  C12   C11  C09  C08     0.00   0.0  0
 UZP  CONST_06  C12   C05  C06  C08     0.00   0.0  0
 UZP  CONST_07  C04   C05  C12  C11   180.00   0.0  0
 UZP  CONST_08  C08   C06  C05  C04   180.00   0.0  0
 UZP  CONST_09  CL10  C09  C08  C06   180.00   0.0  0
 UZP  CONST_10  CL07  C06  C08  C09   180.00   0.0  0
 UZP  CONST_11  CL10  C09  C11  C12   180.00   0.0  0
 UZP  CONST_12  CL07  C06  C05  C12   180.00   0.0  0
 UZP  CONST_13  H6    C08  C09  C11   180.00   0.0  0
 UZP  CONST_14  H1    C11  C12  C05   180.00   0.0  0
 UZP  CONST_15  H7    C12  C05  C06   180.00   0.0  0
 UZP  CONST_16  C13   C14  N15  O16   180.00   0.0  0
 UZP  CONST_17  O17   C14  N15  O16     0.00   0.0  0
 UZP  CONST_18  C19   N18  C02  C03   180.00   0.0  0
 UZP  CONST_19  O01   C02  N18  C19     0.00   0.0  0
 UZP  CONST_20  H21   N15  C14  O17   180.00   0.0  0
 UZP  CONST_21  H22   N18  C02  C03     0.00   0.0  0
 UZP  Var_01    C04   C13  C14  O17    52.13  30.0  2
 UZP  Var_02    C20   C19  N18  C02   177.15  30.0  1
 UZP  Var_03    N18   C02  C03  C04  -111.72  30.0  1
 UZP  Var_04    C22   C21  C20  C19  -176.90  30.0  1
 UZP  Var_05    C23   C22  C21  C20   -62.63  30.0  1
 UZP  Var_06    N18   C19  C20  C21  -177.19  30.0  3
 UZP  Var_07    H18   C23  C22  C21  -175.36  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
 UZP  chir_01  C04  C03  C13  C05  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
 UZP  plan-1  C11   0.020
 UZP  plan-1  C04   0.020
 UZP  plan-1  C05   0.020
 UZP  plan-1  C06   0.020
 UZP  plan-1  C08   0.020
 UZP  plan-1  C09   0.020
 UZP  plan-1  C12   0.020
 UZP  plan-1  CL07  0.020
 UZP  plan-1  CL10  0.020
 UZP  plan-1  H1    0.020
 UZP  plan-1  H6    0.020
 UZP  plan-1  H7    0.020
 UZP  plan-2  O16   0.020
 UZP  plan-2  O17   0.020
 UZP  plan-2  C13   0.020
 UZP  plan-2  C14   0.020
 UZP  plan-2  N15   0.020
 UZP  plan-2  H21   0.020
 UZP  plan-3  C03   0.020
 UZP  plan-3  C19   0.020
 UZP  plan-3  N18   0.020
 UZP  plan-3  O01   0.020
 UZP  plan-3  H22   0.020
 UZP  plan-3  C02   0.020

