# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 04:27:29 2022
#   Inital geometry file: a 90 line input string
#   Ligand name: N-hydroxy-4-[(4-methylpiperazin-1-yl)methyl]benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CCN(CC1)Cc2ccc(cc2)C(=O)NO
#
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
 L8C  L8C  "N-hydroxy-4-[(4-methylpiperazin-1-yl)methyl]benzamide"
  ligand  37  18  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_L8C
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
 L8C  C10  C  CR6   0  -0.065  -22.8487  -41.4532  35.1536
 L8C  C13  C  C     0   0.483  -21.3698  -41.5430  34.9709
 L8C  C17  C  CH2   0  -0.285  -29.2506  -40.7990  34.9187
 L8C  C03  C  CH2   0  -0.281  -28.2364  -38.7172  33.3150
 L8C  C04  C  CH2   0  -0.283  -27.4924  -39.2473  34.5252
 L8C  C06  C  CH2   0  -0.323  -27.0909  -41.1989  35.8730
 L8C  C07  C  CR6   0   0.090  -25.6093  -41.2777  35.6181
 L8C  C08  C  CR16  0  -0.268  -25.1217  -41.8233  34.4332
 L8C  C09  C  CR16  0  -0.267  -23.7591  -41.9094  34.2003
 L8C  C11  C  CR16  0  -0.251  -23.3322  -40.9287  36.3479
 L8C  C12  C  CR16  0  -0.299  -24.6970  -40.8312  36.5682
 L8C  C18  C  CH2   0  -0.283  -29.9912  -40.2667  33.7069
 L8C  N02  N  NT    0  -0.409  -29.6667  -38.8727  33.4833
 L8C  N05  N  NT    0  -0.418  -27.8175  -40.6441  34.7506
 L8C  N15  N  NH1   0  -0.377  -20.9571  -41.3557  33.7034
 L8C  O14  O  O     0  -0.462  -20.6087  -41.7354  35.9037
 L8C  O16  O  OH1   0  -0.536  -19.6562  -41.5618  33.3655
 L8C  H1   H  HCH2  0   0.192  -29.6111  -40.2750  35.8201
 L8C  H2   H  HCH2  0   0.237  -29.4830  -41.8591  35.0455
 L8C  H3   H  HCH3  0   0.231  -31.4740  -38.4144  32.5439
 L8C  H4   H  HCH3  0   0.231  -30.1707  -37.2620  32.2551
 L8C  H5   H  HCH3  0   0.189  -30.1744  -38.8186  31.4112
 L8C  H6   H  HCH2  0   0.187  -27.8745  -39.2404  32.4122
 L8C  H7   H  HCH2  0   0.234  -28.0028  -37.6573  33.1878
 L8C  H8   H  HCH2  0   0.241  -26.4193  -39.1444  34.3520
 L8C  H9   H  HCH2  0   0.193  -27.7402  -38.6305  35.4064
 L8C  H10  H  HCH2  0   0.216  -27.2708  -40.6344  36.8032
 L8C  H11  H  HCH2  0   0.256  -27.4701  -42.2104  36.0517
 L8C  H12  H  HCR6  0   0.251  -25.8159  -42.1823  33.6839
 L8C  H13  H  HCR6  0   0.261  -23.4176  -42.3606  33.2766
 L8C  H14  H  HCR6  0   0.259  -22.6416  -40.5788  37.1039
 L8C  H15  H  HCR6  0   0.255  -25.0571  -40.3984  37.4941
 L8C  H16  H  HCH2  0   0.234  -31.0666  -40.3633  33.8749
 L8C  H17  H  HCH2  0   0.188  -29.7434  -40.8889  32.8288
 L8C  H20  H  HNH1  0   0.420  -21.5777  -41.1655  32.9303
 L8C  H21  H  HOH1  0   0.476  -19.2085  -40.7105  33.4659
 L8C  C01  C  CH3   0  -0.515  -30.4010  -38.3226  32.3682

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
 L8C  C01  N02  single    1.444  0.020  1.444
 L8C  O16  N15  single    1.360  0.020  1.360
 L8C  N15  C13  single    1.346  0.020  1.346
 L8C  N02  C03  single    1.449  0.020  1.449
 L8C  N02  C18  single    1.449  0.020  1.449
 L8C  C03  C04  single    1.516  0.020  1.516
 L8C  C18  C17  single    1.517  0.020  1.517
 L8C  C09  C08  aromatic  1.385  0.020  1.385
 L8C  C09  C10  aromatic  1.395  0.020  1.395
 L8C  C08  C07  aromatic  1.393  0.020  1.393
 L8C  C13  C10  single    1.493  0.020  1.493
 L8C  C13  O14  double    1.219  0.020  1.219
 L8C  C04  N05  single    1.452  0.020  1.452
 L8C  N05  C17  single    1.451  0.020  1.451
 L8C  N05  C06  single    1.448  0.020  1.448
 L8C  C10  C11  aromatic  1.391  0.020  1.391
 L8C  C07  C06  single    1.505  0.020  1.505
 L8C  C07  C12  aromatic  1.391  0.020  1.391
 L8C  C11  C12  aromatic  1.386  0.020  1.386
 L8C  C17  H1   single    0.970  0.020  1.090
 L8C  C17  H2   single    0.970  0.020  1.090
 L8C  C01  H3   single    0.970  0.020  1.090
 L8C  C01  H4   single    0.970  0.020  1.090
 L8C  C01  H5   single    0.970  0.020  1.090
 L8C  C03  H6   single    0.970  0.020  1.090
 L8C  C03  H7   single    0.970  0.020  1.090
 L8C  C04  H8   single    0.970  0.020  1.090
 L8C  C04  H9   single    0.970  0.020  1.090
 L8C  C06  H10  single    0.970  0.020  1.090
 L8C  C06  H11  single    0.970  0.020  1.090
 L8C  C08  H12  single    0.930  0.020  1.080
 L8C  C09  H13  single    0.930  0.020  1.080
 L8C  C11  H14  single    0.930  0.020  1.080
 L8C  C12  H15  single    0.930  0.020  1.080
 L8C  C18  H16  single    0.970  0.020  1.090
 L8C  C18  H17  single    0.970  0.020  1.090
 L8C  N15  H20  single    0.860  0.020  1.020
 L8C  O16  H21  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
 L8C  C11  C10  C09  118.89  3.000
 L8C  C11  C10  C13  118.16  3.000
 L8C  C09  C10  C13  122.91  3.000
 L8C  O14  C13  N15  123.43  3.000
 L8C  O14  C13  C10  122.30  3.000
 L8C  N15  C13  C10  114.24  3.000
 L8C  H2   C17  H1   107.25  3.000
 L8C  H2   C17  N05  109.09  3.000
 L8C  H1   C17  N05  111.51  3.000
 L8C  H2   C17  C18  109.23  3.000
 L8C  H1   C17  C18  109.06  3.000
 L8C  N05  C17  C18  110.62  3.000
 L8C  H7   C03  H6   107.12  3.000
 L8C  H7   C03  N02  109.19  3.000
 L8C  H6   C03  N02  111.57  3.000
 L8C  H7   C03  C04  109.09  3.000
 L8C  H6   C03  C04  109.02  3.000
 L8C  N02  C03  C04  110.74  3.000
 L8C  H9   C04  H8   107.14  3.000
 L8C  H9   C04  N05  111.31  3.000
 L8C  H8   C04  N05  109.60  3.000
 L8C  H9   C04  C03  109.37  3.000
 L8C  H8   C04  C03  108.83  3.000
 L8C  N05  C04  C03  110.51  3.000
 L8C  H11  C06  H10  106.18  3.000
 L8C  H11  C06  N05  107.86  3.000
 L8C  H10  C06  N05  112.08  3.000
 L8C  H11  C06  C07  108.67  3.000
 L8C  H10  C06  C07  109.28  3.000
 L8C  N05  C06  C07  112.51  3.000
 L8C  C12  C07  C08  118.51  3.000
 L8C  C12  C07  C06  120.87  3.000
 L8C  C08  C07  C06  120.61  3.000
 L8C  H12  C08  C09  119.59  3.000
 L8C  H12  C08  C07  119.62  3.000
 L8C  C09  C08  C07  120.79  3.000
 L8C  H13  C09  C08  118.65  3.000
 L8C  H13  C09  C10  120.87  3.000
 L8C  C08  C09  C10  120.45  3.000
 L8C  H14  C11  C12  119.65  3.000
 L8C  H14  C11  C10  119.99  3.000
 L8C  C12  C11  C10  120.35  3.000
 L8C  H15  C12  C11  119.42  3.000
 L8C  H15  C12  C07  119.60  3.000
 L8C  C11  C12  C07  120.98  3.000
 L8C  H17  C18  H16  107.05  3.000
 L8C  H17  C18  N02  111.67  3.000
 L8C  H16  C18  N02  109.22  3.000
 L8C  H17  C18  C17  109.15  3.000
 L8C  H16  C18  C17  109.07  3.000
 L8C  N02  C18  C17  110.59  3.000
 L8C  C18  N02  C03  110.02  3.000
 L8C  C18  N02  C01  111.83  3.000
 L8C  C03  N02  C01  111.80  3.000
 L8C  C06  N05  C04  112.13  3.000
 L8C  C06  N05  C17  111.41  3.000
 L8C  C04  N05  C17  109.99  3.000
 L8C  H20  N15  O16  115.24  3.000
 L8C  H20  N15  C13  123.97  3.000
 L8C  O16  N15  C13  120.41  3.000
 L8C  H21  O16  N15  106.48  3.000
 L8C  H5   C01  H4   107.71  3.000
 L8C  H5   C01  H3   107.72  3.000
 L8C  H4   C01  H3   107.82  3.000
 L8C  H5   C01  N02  113.25  3.000
 L8C  H4   C01  N02  110.06  3.000
 L8C  H3   C01  N02  110.09  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
 L8C  CONST_01  C07  C08  C09  C10     0.00   0.0  0
 L8C  CONST_02  C07  C12  C11  C10     0.00   0.0  0
 L8C  CONST_03  C11  C10  C09  C08     0.00   0.0  0
 L8C  CONST_04  C11  C12  C07  C08     0.00   0.0  0
 L8C  CONST_05  C12  C07  C08  C09     0.00   0.0  0
 L8C  CONST_06  C12  C11  C10  C09     0.00   0.0  0
 L8C  CONST_07  C08  C09  C10  C13   180.00   0.0  0
 L8C  CONST_08  C12  C11  C10  C13   180.00   0.0  0
 L8C  CONST_09  C09  C08  C07  C06   180.00   0.0  0
 L8C  CONST_10  C11  C12  C07  C06   180.00   0.0  0
 L8C  CONST_11  H12  C08  C09  C10   180.00   0.0  0
 L8C  CONST_12  H15  C12  C11  C10   180.00   0.0  0
 L8C  CONST_13  H13  C09  C08  C07   180.00   0.0  0
 L8C  CONST_14  H14  C11  C12  C07   180.00   0.0  0
 L8C  CONST_15  H15  C12  C07  C08   180.00   0.0  0
 L8C  CONST_16  H14  C11  C10  C09   180.00   0.0  0
 L8C  CONST_17  H13  C09  C10  C11   180.00   0.0  0
 L8C  CONST_18  H12  C08  C07  C12   180.00   0.0  0
 L8C  CONST_19  O16  N15  C13  C10   180.00   0.0  0
 L8C  CONST_20  H20  N15  C13  C10     0.00   0.0  0
 L8C  CONST_21  O16  N15  C13  O14     0.00   0.0  0
 L8C  CONST_22  H20  N15  C13  O14   180.00   0.0  0
 L8C  Var_01    C03  N02  C18  C17    57.54  30.0  1
 L8C  Var_02    C03  C04  N05  C17   -57.37  30.0  1
 L8C  Var_03    C18  N02  C03  C04   -57.59  30.0  1
 L8C  Var_04    C18  C17  N05  C04    57.48  30.0  1
 L8C  Var_05    N05  C04  C03  N02    57.81  30.0  1
 L8C  Var_06    N05  C17  C18  N02   -57.89  30.0  1
 L8C  Var_07    C01  N02  C18  C17  -177.58  30.0  1
 L8C  Var_08    C07  C06  N05  C17   169.68  30.0  3
 L8C  Var_09    C04  C03  N02  C01   177.52  30.0  1
 L8C  Var_10    C06  N05  C04  C03   178.07  30.0  1
 L8C  Var_11    C07  C06  N05  C04   -66.55  30.0  3
 L8C  Var_12    C18  C17  N05  C06  -177.54  30.0  1
 L8C  Var_13    N05  C06  C07  C08   -48.32  30.0  2
 L8C  Var_14    N05  C06  C07  C12   132.87  30.0  2
 L8C  Var_15    H8   C04  N05  C17  -177.30  30.0  1
 L8C  Var_16    H9   C04  N05  C17    64.37  30.0  1
 L8C  Var_17    H16  C18  N02  C03   177.58  30.0  1
 L8C  Var_18    H17  C18  N02  C03   -64.21  30.0  1
 L8C  Var_19    H1   C17  N05  C04   -64.07  30.0  1
 L8C  Var_20    H2   C17  N05  C04   177.66  30.0  1
 L8C  Var_21    H6   C03  N02  C18    64.05  30.0  1
 L8C  Var_22    H7   C03  N02  C18  -177.73  30.0  1
 L8C  Var_23    H8   C04  C03  N02   178.20  30.0  1
 L8C  Var_24    H9   C04  C03  N02   -65.06  30.0  1
 L8C  Var_25    H1   C17  C18  N02    65.09  30.0  1
 L8C  Var_26    H2   C17  C18  N02  -177.99  30.0  1
 L8C  Var_27    H6   C03  C04  N05   -65.32  30.0  1
 L8C  Var_28    H7   C03  C04  N05   178.01  30.0  1
 L8C  Var_29    H16  C18  C17  N05  -178.02  30.0  1
 L8C  Var_30    H17  C18  C17  N05    65.33  30.0  1
 L8C  Var_31    N15  C13  C10  C09    35.78  30.0  2
 L8C  Var_32    O14  C13  C10  C09  -146.01  30.0  2
 L8C  Var_33    N15  C13  C10  C11  -146.29  30.0  2
 L8C  Var_34    O14  C13  C10  C11    31.91  30.0  2
 L8C  Var_35    H10  C06  N05  C17   -66.70  30.0  3
 L8C  Var_36    H11  C06  N05  C17    49.83  30.0  3
 L8C  Var_37    H6   C03  N02  C01   -60.84  30.0  1
 L8C  Var_38    H7   C03  N02  C01    57.37  30.0  1
 L8C  Var_39    H16  C18  N02  C01   -57.54  30.0  1
 L8C  Var_40    H17  C18  N02  C01    60.67  30.0  1
 L8C  Var_41    H3   C01  N02  C03  -177.49  30.0  3
 L8C  Var_42    H4   C01  N02  C03   -58.77  30.0  3
 L8C  Var_43    H5   C01  N02  C03    61.86  30.0  3
 L8C  Var_44    H10  C06  N05  C04    57.08  30.0  3
 L8C  Var_45    H11  C06  N05  C04   173.61  30.0  3
 L8C  Var_46    H8   C04  N05  C06    58.14  30.0  1
 L8C  Var_47    H9   C04  N05  C06   -60.19  30.0  1
 L8C  Var_48    H1   C17  N05  C06    60.90  30.0  1
 L8C  Var_49    H2   C17  N05  C06   -57.37  30.0  1
 L8C  Var_50    H10  C06  C07  C08  -173.49  30.0  2
 L8C  Var_51    H11  C06  C07  C08    71.06  30.0  2
 L8C  Var_52    H10  C06  C07  C12     7.70  30.0  2
 L8C  Var_53    H11  C06  C07  C12  -107.76  30.0  2
 L8C  Var_54    H3   C01  N02  C18    58.62  30.0  3
 L8C  Var_55    H4   C01  N02  C18   177.34  30.0  3
 L8C  Var_56    H5   C01  N02  C18   -62.03  30.0  3

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
 L8C  plan-1  C10  0.020
 L8C  plan-1  C13  0.020
 L8C  plan-1  C06  0.020
 L8C  plan-1  C07  0.020
 L8C  plan-1  C08  0.020
 L8C  plan-1  C09  0.020
 L8C  plan-1  C11  0.020
 L8C  plan-1  C12  0.020
 L8C  plan-1  H12  0.020
 L8C  plan-1  H13  0.020
 L8C  plan-1  H14  0.020
 L8C  plan-1  H15  0.020
 L8C  plan-2  C10  0.020
 L8C  plan-2  C13  0.020
 L8C  plan-2  N15  0.020
 L8C  plan-2  O14  0.020
 L8C  plan-2  O16  0.020
 L8C  plan-2  H20  0.020

