# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 16:02:51 2020
#   Inital geometry file: a 106 line input string
#   Ligand name: 1-{4-[(2-hydroxyethyl)carbamoyl]benzyl}-1-methylpiperidinium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[N+]1(CCCCC1)Cc2ccc(cc2)C(=O)NCCO
#
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
 KHA  KHA  1-{4-[(2-hydroxyethyl)carbamoyl]benzyl}-1-methylpiperidinium  ligand  45  20  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_KHA
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
 KHA  O1    O  O     0  -0.487  -3.8384   2.2348   0.1723
 KHA  C8    C  C     0   0.527  -3.3004   1.1445   0.0352
 KHA  N1    N  NH1   0  -0.642  -3.9563  -0.0218   0.1197
 KHA  C9    C  CH2   0  -0.296  -5.3754  -0.1259   0.3782
 KHA  C10   C  CH2   0  -0.177  -5.9503  -1.3538  -0.2925
 KHA  O2    O  OH1   0  -0.673  -5.2995  -2.4937   0.2268
 KHA  C6    C  CR6   0  -0.037  -1.8325   1.0421  -0.2444
 KHA  C3    C  CR16  0  -0.255  -0.9980   2.0548   0.2184
 KHA  C1    C  CR16  0  -0.275   0.3638   2.0062  -0.0259
 KHA  C2    C  CR16  0  -0.274  -1.2862   0.0014  -0.9908
 KHA  C5    C  CR16  0  -0.273   0.0744  -0.0349  -1.2495
 KHA  C4    C  CR6   0   0.092   0.9178   0.9536  -0.7510
 KHA  C7    C  CH2   0  -0.418   2.3873   0.9237  -1.0455
 KHA  N2    N  NT    1  -0.389   3.2255   0.1638  -0.0393
 KHA  C11   C  CH3   0  -0.565   3.0887   0.7912   1.3017
 KHA  C16   C  CH2   0  -0.324   4.6546   0.2513  -0.5144
 KHA  C15   C  CH2   0  -0.333   2.8005  -1.2786   0.0018
 KHA  C13   C  CH2   0  -0.469   3.7259  -2.1442   0.8345
 KHA  C14   C  CH2   0  -0.442   5.1659  -2.0462   0.3548
 KHA  C12   C  CH2   0  -0.478   5.6122  -0.5919   0.3035
 KHA  H1    H  HNH1  0   0.402  -3.4284  -0.8791   0.1661
 KHA  H9C1  H  HCH2  0   0.244  -5.5702  -0.1590   1.4550
 KHA  H9C2  H  HCH2  0   0.255  -5.8769   0.7575  -0.0138
 KHA  H101  H  HCH2  0   0.213  -7.0299  -1.3771  -0.1011
 KHA  H102  H  HCH2  0   0.212  -5.8129  -1.2700  -1.3765
 KHA  H2    H  HOH1  0   0.461  -5.4852  -3.2395  -0.3502
 KHA  H3    H  HCR6  0   0.268  -1.4117   2.8852   0.7741
 KHA  HB    H  HCR6  0   0.275   0.9965   2.8046   0.3424
 KHA  HA    H  HCR6  0   0.266  -1.9147  -0.7750  -1.4080
 KHA  H5    H  HCR6  0   0.275   0.4761  -0.8378  -1.8551
 KHA  H7C1  H  HCH2  0   0.324   2.7941   1.9341  -1.0735
 KHA  H7C2  H  HCH2  0   0.325   2.5777   0.4597  -2.0128
 KHA  H111  H  HCH3  0   0.296   3.3622   1.8407   1.2295
 KHA  H112  H  HCH3  0   0.299   2.0620   0.6956   1.6427
 KHA  H113  H  HCH3  0   0.306   3.7394   0.3000   2.0161
 KHA  H161  H  HCH2  0   0.295   4.6511  -0.0872  -1.5515
 KHA  H162  H  HCH2  0   0.307   4.9314   1.3053  -0.5017
 KHA  H151  H  HCH2  0   0.309   1.7826  -1.3088   0.3852
 KHA  H152  H  HCH2  0   0.295   2.7894  -1.6226  -1.0336
 KHA  H131  H  HCH2  0   0.279   3.3578  -3.1673   0.7441
 KHA  H132  H  HCH2  0   0.255   3.6484  -1.8885   1.8933
 KHA  H141  H  HCH2  0   0.235   5.2473  -2.4855  -0.6436
 KHA  H142  H  HCH2  0   0.258   5.8228  -2.6200   1.0087
 KHA  H121  H  HCH2  0   0.280   6.5875  -0.5058  -0.1779
 KHA  H122  H  HCH2  0   0.256   5.7367  -0.1839   1.3085

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
 KHA  O1   C8    double    1.224  0.020  1.224
 KHA  C8   N1    single    1.341  0.020  1.341
 KHA  C8   C6    single    1.498  0.020  1.498
 KHA  N1   C9    single    1.446  0.020  1.446
 KHA  N1   H1    single    0.860  0.020  1.020
 KHA  C9   C10   single    1.513  0.020  1.513
 KHA  C9   H9C1  single    0.970  0.020  1.090
 KHA  C9   H9C2  single    0.970  0.020  1.090
 KHA  C10  O2    single    1.412  0.020  1.412
 KHA  C10  H101  single    0.970  0.020  1.090
 KHA  C10  H102  single    0.970  0.020  1.090
 KHA  O2   H2    single    0.850  0.020  0.980
 KHA  C6   C3    aromatic  1.391  0.020  1.391
 KHA  C6   C2    aromatic  1.392  0.020  1.392
 KHA  C3   C1    aromatic  1.384  0.020  1.384
 KHA  C3   H3    single    0.930  0.020  1.080
 KHA  C1   C4    aromatic  1.393  0.020  1.393
 KHA  C1   HB    single    0.930  0.020  1.080
 KHA  C2   C5    aromatic  1.386  0.020  1.386
 KHA  C2   HA    single    0.930  0.020  1.080
 KHA  C5   C4    aromatic  1.392  0.020  1.392
 KHA  C5   H5    single    0.930  0.020  1.080
 KHA  C4   C7    single    1.499  0.020  1.499
 KHA  C7   N2    single    1.514  0.020  1.514
 KHA  C7   H7C1  single    0.970  0.020  1.090
 KHA  C7   H7C2  single    0.970  0.020  1.090
 KHA  N2   C11   single    1.487  0.020  1.487
 KHA  N2   C16   single    1.509  0.020  1.509
 KHA  N2   C15   single    1.504  0.020  1.504
 KHA  C11  H111  single    0.970  0.020  1.090
 KHA  C11  H112  single    0.970  0.020  1.090
 KHA  C11  H113  single    0.970  0.020  1.090
 KHA  C16  C12   single    1.516  0.020  1.516
 KHA  C16  H161  single    0.970  0.020  1.090
 KHA  C16  H162  single    0.970  0.020  1.090
 KHA  C15  C13   single    1.516  0.020  1.516
 KHA  C15  H151  single    0.970  0.020  1.090
 KHA  C15  H152  single    0.970  0.020  1.090
 KHA  C13  C14   single    1.521  0.020  1.521
 KHA  C13  H131  single    0.970  0.020  1.090
 KHA  C13  H132  single    0.970  0.020  1.090
 KHA  C14  C12   single    1.522  0.020  1.522
 KHA  C14  H141  single    0.970  0.020  1.090
 KHA  C14  H142  single    0.970  0.020  1.090
 KHA  C12  H121  single    0.970  0.020  1.090
 KHA  C12  H122  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
 KHA  C6    C8   N1    115.57  3.000
 KHA  C6    C8   O1    120.85  3.000
 KHA  N1    C8   O1    123.58  3.000
 KHA  H1    N1   C9    116.39  3.000
 KHA  H1    N1   C8    119.12  3.000
 KHA  C9    N1   C8    123.63  3.000
 KHA  H9C2  C9   H9C1  107.26  3.000
 KHA  H9C2  C9   C10   108.90  3.000
 KHA  H9C1  C9   C10   110.12  3.000
 KHA  H9C2  C9   N1    109.23  3.000
 KHA  H9C1  C9   N1    110.64  3.000
 KHA  C10   C9   N1    110.62  3.000
 KHA  H102  C10  H101  107.32  3.000
 KHA  H102  C10  O2    111.59  3.000
 KHA  H101  C10  O2    111.87  3.000
 KHA  H102  C10  C9    109.20  3.000
 KHA  H101  C10  C9    108.30  3.000
 KHA  O2    C10  C9    108.49  3.000
 KHA  H2    O2   C10   108.46  3.000
 KHA  C2    C6   C3    119.15  3.000
 KHA  C2    C6   C8    122.39  3.000
 KHA  C3    C6   C8    118.42  3.000
 KHA  H3    C3   C1    119.60  3.000
 KHA  H3    C3   C6    120.02  3.000
 KHA  C1    C3   C6    120.38  3.000
 KHA  HB    C1   C4    120.10  3.000
 KHA  HB    C1   C3    119.26  3.000
 KHA  C4    C1   C3    120.63  3.000
 KHA  HA    C2   C5    118.65  3.000
 KHA  HA    C2   C6    120.99  3.000
 KHA  C5    C2   C6    120.33  3.000
 KHA  H5    C5   C4    120.14  3.000
 KHA  H5    C5   C2    119.21  3.000
 KHA  C4    C5   C2    120.64  3.000
 KHA  C7    C4   C5    120.63  3.000
 KHA  C7    C4   C1    120.48  3.000
 KHA  C5    C4   C1    118.83  3.000
 KHA  H7C2  C7   H7C1  107.87  3.000
 KHA  H7C2  C7   N2    106.24  3.000
 KHA  H7C1  C7   N2    106.01  3.000
 KHA  H7C2  C7   C4    110.74  3.000
 KHA  H7C1  C7   C4    110.64  3.000
 KHA  N2    C7   C4    114.97  3.000
 KHA  C15   N2   C16   109.38  3.000
 KHA  C15   N2   C11   110.73  3.000
 KHA  C16   N2   C11   110.29  3.000
 KHA  C15   N2   C7    110.06  3.000
 KHA  C16   N2   C7    106.62  3.000
 KHA  C11   N2   C7    109.68  3.000
 KHA  H113  C11  H112  108.70  3.000
 KHA  H113  C11  H111  109.28  3.000
 KHA  H112  C11  H111  110.10  3.000
 KHA  H113  C11  N2    110.37  3.000
 KHA  H112  C11  N2    109.45  3.000
 KHA  H111  C11  N2    108.93  3.000
 KHA  H162  C16  H161  108.18  3.000
 KHA  H162  C16  C12   111.79  3.000
 KHA  H161  C16  C12   110.03  3.000
 KHA  H162  C16  N2    107.04  3.000
 KHA  H161  C16  N2    106.16  3.000
 KHA  C12   C16  N2    113.35  3.000
 KHA  H152  C15  H151  108.42  3.000
 KHA  H152  C15  C13   110.33  3.000
 KHA  H151  C15  C13   111.20  3.000
 KHA  H152  C15  N2    106.22  3.000
 KHA  H151  C15  N2    107.49  3.000
 KHA  C13   C15  N2    112.95  3.000
 KHA  H132  C13  H131  106.02  3.000
 KHA  H132  C13  C14   110.98  3.000
 KHA  H131  C13  C14   110.72  3.000
 KHA  H132  C13  C15   110.82  3.000
 KHA  H131  C13  C15   106.49  3.000
 KHA  C14   C13  C15   111.58  3.000
 KHA  H142  C14  H141  106.94  3.000
 KHA  H142  C14  C12   110.27  3.000
 KHA  H141  C14  C12   109.34  3.000
 KHA  H142  C14  C13   110.32  3.000
 KHA  H141  C14  C13   109.42  3.000
 KHA  C12   C14  C13   110.48  3.000
 KHA  H122  C12  H121  105.95  3.000
 KHA  H122  C12  C14   111.06  3.000
 KHA  H121  C12  C14   110.63  3.000
 KHA  H122  C12  C16   111.16  3.000
 KHA  H121  C12  C16   106.43  3.000
 KHA  C14   C12  C16   111.38  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
 KHA  CONST_01  C4   C1   C3   C6     0.00   0.0  0
 KHA  CONST_02  C4   C5   C2   C6     0.00   0.0  0
 KHA  CONST_03  C5   C2   C6   C3     0.00   0.0  0
 KHA  CONST_04  C5   C4   C1   C3     0.00   0.0  0
 KHA  CONST_05  C2   C6   C3   C1     0.00   0.0  0
 KHA  CONST_06  C2   C5   C4   C1     0.00   0.0  0
 KHA  CONST_07  C1   C3   C6   C8   180.00   0.0  0
 KHA  CONST_08  C5   C2   C6   C8   180.00   0.0  0
 KHA  CONST_09  C7   C4   C1   C3   180.00   0.0  0
 KHA  CONST_10  C7   C4   C5   C2   180.00   0.0  0
 KHA  CONST_11  HB   C1   C3   C6   180.00   0.0  0
 KHA  CONST_12  H5   C5   C2   C6   180.00   0.0  0
 KHA  CONST_13  HA   C2   C6   C3   180.00   0.0  0
 KHA  CONST_14  H3   C3   C6   C2   180.00   0.0  0
 KHA  CONST_15  C6   C8   N1   C9   180.00   0.0  0
 KHA  CONST_16  H1   N1   C8   C6     0.00   0.0  0
 KHA  CONST_17  C9   N1   C8   O1     0.00   0.0  0
 KHA  Var_01    C14  C12  C16  N2    55.17  30.0  1
 KHA  Var_02    C14  C13  C15  N2   -55.80  30.0  1
 KHA  Var_03    C13  C14  C12  C16  -53.44  30.0  1
 KHA  Var_04    C12  C14  C13  C15   53.87  30.0  1
 KHA  Var_05    N2   C7   C4   C1    92.89  30.0  2
 KHA  Var_06    C3   C6   C8   O1    28.09  30.0  2
 KHA  Var_07    C10  C9   N1   C8   149.16  30.0  3
 KHA  Var_08    O2   C10  C9   N1    60.27  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
 KHA  chir_01  N2  C11  C16  C15  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
 KHA  plan-1  C8  0.020
 KHA  plan-1  C6  0.020
 KHA  plan-1  C3  0.020
 KHA  plan-1  C1  0.020
 KHA  plan-1  C2  0.020
 KHA  plan-1  C5  0.020
 KHA  plan-1  C4  0.020
 KHA  plan-1  C7  0.020
 KHA  plan-1  H3  0.020
 KHA  plan-1  HB  0.020
 KHA  plan-1  HA  0.020
 KHA  plan-1  H5  0.020
 KHA  plan-2  O1  0.020
 KHA  plan-2  C8  0.020
 KHA  plan-2  N1  0.020
 KHA  plan-2  C9  0.020
 KHA  plan-2  C6  0.020
 KHA  plan-2  H1  0.020

