# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 12:44:28 2021
#   Inital geometry file: a 73 line input string
#   Ligand name: 4-cyclopentylcarbonylpiperazin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1CN(CCN1)C(=O)C2CCCC2
#
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
 LX4  LX4  4-cyclopentylcarbonylpiperazin-2-one  ligand  30  14  .  2022-03-22  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_LX4
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
 LX4  N1   N  NH1   0  -0.620   -9.1694  -32.0427  -14.9294
 LX4  C4   C  CH2   0  -0.443   -6.5426  -30.8929  -18.9812
 LX4  C5   C  C     0   0.597   -5.6214  -31.7739  -16.8102
 LX4  C6   C  CH2   0  -0.351   -7.7944  -33.0132  -16.6758
 LX4  C7   C  CH2   0  -0.252   -9.1033  -32.3301  -16.3463
 LX4  C8   C  C     0   0.506   -8.1224  -31.9335  -14.1042
 LX4  N    N  NT    0  -0.482   -6.6981  -32.2429  -16.1291
 LX4  C    C  CH2   0  -0.454   -5.7231  -29.6015  -18.9568
 LX4  O    O  O     0  -0.489   -4.7025  -31.2199  -16.2218
 LX4  C1   C  CH2   0  -0.433   -4.2565  -30.0484  -19.1221
 LX4  C2   C  CH2   0  -0.425   -4.2540  -31.5764  -18.9259
 LX4  C3   C  CH1   0  -0.443   -5.6149  -31.9297  -18.3214
 LX4  C9   C  CH2   0  -0.397   -6.7354  -32.1175  -14.6885
 LX4  O1   O  O     0  -0.506   -8.2373  -31.7085  -12.9063
 LX4  H1   H  HNH1  0   0.403  -10.0806  -31.8811  -14.5258
 LX4  H3   H  HCH2  0   0.243   -6.7334  -31.2075  -20.0099
 LX4  H4   H  HCH2  0   0.269   -7.7805  -34.0217  -16.2490
 LX4  H5   H  HCH2  0   0.288   -7.7064  -33.1199  -17.7517
 LX4  H6   H  HCH2  0   0.245   -9.2094  -31.4121  -16.9311
 LX4  H7   H  HCH2  0   0.263   -9.9325  -32.9859  -16.6113
 LX4  H8   H  HCH2  0   0.228   -5.8621  -29.0903  -18.0022
 LX4  H9   H  HCH2  0   0.236   -6.0401  -28.9034  -19.7323
 LX4  H10  H  HCH2  0   0.228   -3.6139  -29.5539  -18.3945
 LX4  H11  H  HCH2  0   0.224   -3.8728  -29.7870  -20.1090
 LX4  H12  H  HCH2  0   0.235   -4.1776  -32.0780  -19.8929
 LX4  H13  H  HCH2  0   0.237   -3.4164  -31.9267  -18.3239
 LX4  H14  H  HCH1  0   0.278   -5.8996  -32.9492  -18.5898
 LX4  H15  H  HCH2  0   0.279   -6.2970  -32.9990  -14.2054
 LX4  H16  H  HCH2  0   0.293   -6.1404  -31.2607  -14.3776
 LX4  H2   H  HCH2  0   0.243   -7.5128  -30.7853  -18.4939

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
 LX4  C1  C2   single  1.541  0.020  1.541
 LX4  C1  C    single  1.542  0.020  1.542
 LX4  C2  C3   single  1.530  0.020  1.530
 LX4  C   C4   single  1.530  0.020  1.530
 LX4  C4  C3   single  1.540  0.020  1.540
 LX4  C3  C5   single  1.519  0.020  1.519
 LX4  C5  O    double  1.224  0.020  1.224
 LX4  C5  N    single  1.358  0.020  1.358
 LX4  C6  C7   single  1.513  0.020  1.513
 LX4  C6  N    single  1.447  0.020  1.447
 LX4  C7  N1   single  1.447  0.020  1.447
 LX4  N   C9   single  1.446  0.020  1.446
 LX4  N1  C8   single  1.338  0.020  1.338
 LX4  C9  C8   single  1.516  0.020  1.516
 LX4  C8  O1   double  1.224  0.020  1.224
 LX4  N1  H1   single  0.860  0.020  1.020
 LX4  C4  H2   single  0.970  0.020  1.090
 LX4  C4  H3   single  0.970  0.020  1.090
 LX4  C6  H4   single  0.970  0.020  1.090
 LX4  C6  H5   single  0.970  0.020  1.090
 LX4  C7  H6   single  0.970  0.020  1.090
 LX4  C7  H7   single  0.970  0.020  1.090
 LX4  C   H8   single  0.970  0.020  1.090
 LX4  C   H9   single  0.970  0.020  1.090
 LX4  C1  H10  single  0.970  0.020  1.090
 LX4  C1  H11  single  0.970  0.020  1.090
 LX4  C2  H12  single  0.970  0.020  1.090
 LX4  C2  H13  single  0.970  0.020  1.090
 LX4  C3  H14  single  0.970  0.020  1.090
 LX4  C9  H15  single  0.970  0.020  1.090
 LX4  C9  H16  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
 LX4  H1   N1  C8   116.54  3.000
 LX4  H1   N1  C7   117.67  3.000
 LX4  C8   N1  C7   125.77  3.000
 LX4  H3   C4  H2   107.07  3.000
 LX4  H3   C4  C3   108.35  3.000
 LX4  H2   C4  C3   114.25  3.000
 LX4  H3   C4  C    110.59  3.000
 LX4  H2   C4  C    112.70  3.000
 LX4  C3   C4  C    103.82  3.000
 LX4  C3   C5  O    121.44  3.000
 LX4  O    C5  N    120.71  3.000
 LX4  C3   C5  N    117.84  3.000
 LX4  H5   C6  H4   107.15  3.000
 LX4  H5   C6  N    111.44  3.000
 LX4  H4   C6  N    109.47  3.000
 LX4  H5   C6  C7   109.31  3.000
 LX4  H4   C6  C7   110.00  3.000
 LX4  N    C6  C7   109.44  3.000
 LX4  H7   C7  H6   107.54  3.000
 LX4  H7   C7  C6   109.48  3.000
 LX4  H6   C7  C6   110.28  3.000
 LX4  H7   C7  N1   108.84  3.000
 LX4  H6   C7  N1   110.63  3.000
 LX4  C6   C7  N1   110.02  3.000
 LX4  O1   C8  C9   119.03  3.000
 LX4  O1   C8  N1   123.04  3.000
 LX4  C9   C8  N1   117.93  3.000
 LX4  C9   N   C6   113.76  3.000
 LX4  C9   N   C5   119.35  3.000
 LX4  C6   N   C5   126.53  3.000
 LX4  H9   C   H8   106.57  3.000
 LX4  H9   C   C1   112.69  3.000
 LX4  H8   C   C1   110.51  3.000
 LX4  H9   C   C4   111.93  3.000
 LX4  H8   C   C4   109.94  3.000
 LX4  C1   C   C4   105.26  3.000
 LX4  H11  C1  H10  106.74  3.000
 LX4  H11  C1  C2   110.63  3.000
 LX4  H10  C1  C2   111.36  3.000
 LX4  H11  C1  C    111.23  3.000
 LX4  H10  C1  C    110.97  3.000
 LX4  C2   C1  C    105.98  3.000
 LX4  H13  C2  H12  106.73  3.000
 LX4  H13  C2  C3   113.03  3.000
 LX4  H12  C2  C3   107.81  3.000
 LX4  H13  C2  C1   112.99  3.000
 LX4  H12  C2  C1   110.05  3.000
 LX4  C3   C2  C1   106.13  3.000
 LX4  H14  C3  C2   110.50  3.000
 LX4  H14  C3  C5   109.82  3.000
 LX4  C2   C3  C5   111.90  3.000
 LX4  H14  C3  C4   111.49  3.000
 LX4  C5   C3  C4   110.77  3.000
 LX4  C2   C3  C4   102.18  3.000
 LX4  H16  C9  H15  106.76  3.000
 LX4  H16  C9  N    109.79  3.000
 LX4  H15  C9  N    111.02  3.000
 LX4  H16  C9  C8   107.13  3.000
 LX4  H15  C9  C8   107.06  3.000
 LX4  N    C9  C8   114.70  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
 LX4  CONST_01  C9  C8  N1  C7    0.00   0.0  0
 LX4  CONST_02  C3  C5  N   C6    0.00   0.0  0
 LX4  CONST_03  C9  N   C5  C3  180.00   0.0  0
 LX4  CONST_04  O1  C8  N1  C7  180.00   0.0  0
 LX4  CONST_05  H1  N1  C8  C9  180.00   0.0  0
 LX4  CONST_06  O   C5  N   C6  180.00   0.0  0
 LX4  CONST_07  C9  N   C5  O     0.00   0.0  0
 LX4  Var_01    N   C6  C7  N1  -51.22  30.0  1
 LX4  Var_02    N   C9  C8  N1    6.79  30.0  1
 LX4  Var_03    C2  C1  C   C4  -12.08  30.0  1
 LX4  Var_04    C8  N1  C7  C6   22.14  30.0  1
 LX4  Var_05    C8  C9  N   C6  -38.45  30.0  1
 LX4  Var_06    C9  N   C6  C7   61.45  30.0  1
 LX4  Var_07    C3  C2  C1  C   -13.59  30.0  1
 LX4  Var_08    C3  C4  C   C1   33.07  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
 LX4  chir_01  C3  C2  C4  C5  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
 LX4  plan-1  C5  0.020
 LX4  plan-1  C6  0.020
 LX4  plan-1  N   0.020
 LX4  plan-1  O   0.020
 LX4  plan-1  C3  0.020
 LX4  plan-1  C9  0.020
 LX4  plan-2  N1  0.020
 LX4  plan-2  C7  0.020
 LX4  plan-2  C8  0.020
 LX4  plan-2  C9  0.020
 LX4  plan-2  O1  0.020
 LX4  plan-2  H1  0.020

