# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 10:42:46 2020
#   Inital geometry file: a 89 line input string
#   Ligand name: ethyl 4-[(4-chloropyridin-2-yl)amino]piperidine-1-carboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCOC(=O)N1CCC(CC1)Nc2cc(Cl)ccn2
#
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
 A11  A11  'ethyl 4-[(4-chloropyridin-2-yl)amino]piperidine-1-carboxylate'  ligand  37  19  .  2021-08-06  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_A11
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
 A11  CL    CL  CL    0  -0.111   4.7062   2.0671  -0.6909
 A11  C2    C   CR6   0   0.070   4.1069   0.6548   0.1057
 A11  C3    C   CR16  0  -0.346   4.9082   0.0018   1.0333
 A11  C4    C   CR16  0  -0.060   4.3546  -1.1175   1.6304
 A11  N5    N   N     0  -0.467   3.1438  -1.5875   1.3737
 A11  C6    C   CR6   0   0.510   2.3865  -0.9500   0.4747
 A11  C7    C   CR16  0  -0.374   2.8411   0.2047  -0.1927
 A11  N8    N   NH1   0  -0.666   1.1721  -1.4952   0.2282
 A11  C9    C   CH1   0  -0.080   0.1147  -0.8727  -0.5344
 A11  C10   C   CH2   0  -0.436  -0.5604   0.2812   0.2115
 A11  C11   C   CH2   0  -0.324  -1.7234   0.8453  -0.5967
 A11  N12   N   NT    0  -0.482  -2.6636  -0.2083  -0.9420
 A11  C13   C   CH2   0  -0.321  -2.0647  -1.2915  -1.6995
 A11  C14   C   CH2   0  -0.443  -0.9164  -1.9266  -0.9259
 A11  C15   C   C     0   0.763  -3.8830  -0.3680  -0.3826
 A11  O16   O   O     0  -0.532  -4.6036  -1.3324  -0.5631
 A11  O17   O   O2    0  -0.481  -4.2323   0.6679   0.3815
 A11  C18   C   CH2   0  -0.166  -5.5254   0.6281   0.9943
 A11  C19   C   CH3   0  -0.689  -5.7023   1.9099   1.7722
 A11  H3    H   HCR6  0   0.281   5.9020   0.3422   1.2827
 A11  H4    H   HCR6  0   0.267   4.9322  -1.6661   2.3665
 A11  H7    H   HCR6  0   0.291   2.2276   0.7261  -0.9126
 A11  HN8   H   HNH1  0   0.381   0.9095  -2.2446   0.8502
 A11  H9    H   HCH1  0   0.242   0.5444  -0.4831  -1.4651
 A11  H101  H   HCH2  0   0.234  -0.9243  -0.0779   1.1789
 A11  H102  H   HCH2  0   0.249   0.1567   1.0816   0.4092
 A11  H111  H   HCH2  0   0.243  -1.3478   1.2829  -1.5279
 A11  H112  H   HCH2  0   0.276  -2.2196   1.6413  -0.0510
 A11  H131  H   HCH2  0   0.271  -2.8198  -2.0326  -1.9449
 A11  H132  H   HCH2  0   0.246  -1.6889  -0.8827  -2.6431
 A11  H141  H   HCH2  0   0.236  -1.3077  -2.4162  -0.0275
 A11  H142  H   HCH2  0   0.255  -0.4466  -2.6976  -1.5402
 A11  H181  H   HCH2  0   0.229  -5.5973  -0.2375   1.6562
 A11  H182  H   HCH2  0   0.229  -6.2990   0.5317   0.2297
 A11  H191  H   HCH3  0   0.234  -5.6601   2.7839   1.1221
 A11  H192  H   HCH3  0   0.238  -6.6783   1.9017   2.2570
 A11  H193  H   HCH3  0   0.234  -4.9447   2.0170   2.5486

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
 A11  CL   C2    single    1.729  0.020  1.729
 A11  C2   C3    aromatic  1.389  0.020  1.389
 A11  C2   C7    aromatic  1.376  0.020  1.376
 A11  C3   C4    aromatic  1.384  0.020  1.384
 A11  C3   H3    single    0.930  0.020  1.080
 A11  C4   N5    aromatic  1.324  0.020  1.324
 A11  C4   H4    single    0.930  0.020  1.080
 A11  N5   C6    aromatic  1.337  0.020  1.337
 A11  C6   C7    aromatic  1.409  0.020  1.409
 A11  C6   N8    single    1.354  0.020  1.354
 A11  C7   H7    single    0.930  0.020  1.080
 A11  N8   C9    single    1.445  0.020  1.445
 A11  N8   HN8   single    0.890  0.020  1.040
 A11  C9   C10   single    1.531  0.020  1.531
 A11  C9   C14   single    1.526  0.020  1.526
 A11  C9   H9    single    0.970  0.020  1.090
 A11  C10  C11   single    1.525  0.020  1.525
 A11  C10  H101  single    0.970  0.020  1.090
 A11  C10  H102  single    0.970  0.020  1.090
 A11  C11  N12   single    1.454  0.020  1.454
 A11  C11  H111  single    0.970  0.020  1.090
 A11  C11  H112  single    0.970  0.020  1.090
 A11  N12  C13   single    1.451  0.020  1.451
 A11  N12  C15   single    1.351  0.020  1.351
 A11  C13  C14   single    1.523  0.020  1.523
 A11  C13  H131  single    0.970  0.020  1.090
 A11  C13  H132  single    0.970  0.020  1.090
 A11  C14  H141  single    0.970  0.020  1.090
 A11  C14  H142  single    0.970  0.020  1.090
 A11  C15  O16   double    1.217  0.020  1.217
 A11  C15  O17   single    1.334  0.020  1.334
 A11  O17  C18   single    1.432  0.020  1.432
 A11  C18  C19   single    1.510  0.020  1.510
 A11  C18  H181  single    0.970  0.020  1.090
 A11  C18  H182  single    0.970  0.020  1.090
 A11  C19  H191  single    0.970  0.020  1.090
 A11  C19  H192  single    0.970  0.020  1.090
 A11  C19  H193  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
 A11  C7    C2   C3    121.45  3.000
 A11  C7    C2   CL    119.09  3.000
 A11  C3    C2   CL    119.46  3.000
 A11  H3    C3   C4    121.56  3.000
 A11  H3    C3   C2    122.49  3.000
 A11  C4    C3   C2    115.95  3.000
 A11  H4    C4   N5    116.04  3.000
 A11  H4    C4   C3    119.26  3.000
 A11  N5    C4   C3    124.70  3.000
 A11  C6    N5   C4    118.62  3.000
 A11  N8    C6   C7    122.22  3.000
 A11  N8    C6   N5    116.00  3.000
 A11  C7    C6   N5    121.77  3.000
 A11  H7    C7   C6    121.88  3.000
 A11  H7    C7   C2    120.60  3.000
 A11  C6    C7   C2    117.52  3.000
 A11  HN8   N8   C9    117.07  3.000
 A11  HN8   N8   C6    114.86  3.000
 A11  C9    N8   C6    125.39  3.000
 A11  H9    C9   C14   107.01  3.000
 A11  H9    C9   C10   108.57  3.000
 A11  C14   C9   C10   110.35  3.000
 A11  H9    C9   N8    108.32  3.000
 A11  C14   C9   N8    109.42  3.000
 A11  C10   C9   N8    112.98  3.000
 A11  H102  C10  H101  107.38  3.000
 A11  H102  C10  C11   109.00  3.000
 A11  H101  C10  C11   109.66  3.000
 A11  H102  C10  C9    110.54  3.000
 A11  H101  C10  C9    109.27  3.000
 A11  C11   C10  C9    110.92  3.000
 A11  H112  C11  H111  106.94  3.000
 A11  H112  C11  N12   110.82  3.000
 A11  H111  C11  N12   108.03  3.000
 A11  H112  C11  C10   110.71  3.000
 A11  H111  C11  C10   109.69  3.000
 A11  N12   C11  C10   110.56  3.000
 A11  C15   N12  C13   120.03  3.000
 A11  C15   N12  C11   124.82  3.000
 A11  C13   N12  C11   113.46  3.000
 A11  H132  C13  H131  107.38  3.000
 A11  H132  C13  C14   109.55  3.000
 A11  H131  C13  C14   110.76  3.000
 A11  H132  C13  N12   108.23  3.000
 A11  H131  C13  N12   109.90  3.000
 A11  C14   C13  N12   110.93  3.000
 A11  H142  C14  H141  107.43  3.000
 A11  H142  C14  C13   109.45  3.000
 A11  H141  C14  C13   109.48  3.000
 A11  H142  C14  C9    109.96  3.000
 A11  H141  C14  C9    109.86  3.000
 A11  C13   C14  C9    110.60  3.000
 A11  O17   C15  O16   123.04  3.000
 A11  O17   C15  N12   112.44  3.000
 A11  O16   C15  N12   124.50  3.000
 A11  C18   O17  C15   117.40  3.000
 A11  H182  C18  H181  107.93  3.000
 A11  H182  C18  C19   110.66  3.000
 A11  H181  C18  C19   110.67  3.000
 A11  H182  C18  O17   110.04  3.000
 A11  H181  C18  O17   109.93  3.000
 A11  C19   C18  O17   107.62  3.000
 A11  H193  C19  H192  107.84  3.000
 A11  H193  C19  H191  108.61  3.000
 A11  H192  C19  H191  107.82  3.000
 A11  H193  C19  C18   111.65  3.000
 A11  H192  C19  C18   109.13  3.000
 A11  H191  C19  C18   111.64  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
 A11  CONST_01  N5    C4   C3   C2      0.00   0.0  0
 A11  CONST_02  N5    C6   C7   C2      0.00   0.0  0
 A11  CONST_03  C6    C7   C2   C3      0.00   0.0  0
 A11  CONST_04  C6    N5   C4   C3      0.00   0.0  0
 A11  CONST_05  C7    C2   C3   C4      0.00   0.0  0
 A11  CONST_06  C7    C6   N5   C4      0.00   0.0  0
 A11  CONST_07  C4    C3   C2   CL    180.00   0.0  0
 A11  CONST_08  C6    C7   C2   CL    180.00   0.0  0
 A11  CONST_09  N8    C6   C7   C2    180.00   0.0  0
 A11  CONST_10  N8    C6   N5   C4    180.00   0.0  0
 A11  CONST_11  C9    N8   C6   N5    180.00   0.0  0
 A11  CONST_12  C9    N8   C6   C7      0.00   0.0  0
 A11  CONST_13  H4    C4   C3   C2    180.00   0.0  0
 A11  CONST_14  H7    C7   C2   C3    180.00   0.0  0
 A11  CONST_15  H3    C3   C4   N5    180.00   0.0  0
 A11  CONST_16  HN8   N8   C6   N5      0.00   0.0  0
 A11  Var_01    N12   C11  C10  C9     54.96  30.0  1
 A11  Var_02    N12   C13  C14  C9    -55.40  30.0  1
 A11  Var_03    C13   N12  C11  C10   -58.08  30.0  1
 A11  Var_04    C14   C13  N12  C11    58.46  30.0  1
 A11  Var_05    O16   C15  N12  C11  -171.32  30.0  2
 A11  Var_06    C19   C18  O17  C15  -178.66  30.0  3
 A11  Var_07    H191  C19  C18  O17    61.39  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
 A11  chir_01  C9  N8  C10  C14  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
 A11  plan-1  CL   0.020
 A11  plan-1  C2   0.020
 A11  plan-1  C3   0.020
 A11  plan-1  C4   0.020
 A11  plan-1  N5   0.020
 A11  plan-1  C6   0.020
 A11  plan-1  C7   0.020
 A11  plan-1  N8   0.020
 A11  plan-1  H3   0.020
 A11  plan-1  H4   0.020
 A11  plan-1  H7   0.020
 A11  plan-2  C6   0.020
 A11  plan-2  N8   0.020
 A11  plan-2  C9   0.020
 A11  plan-2  HN8  0.020
 A11  plan-3  N12  0.020
 A11  plan-3  C15  0.020
 A11  plan-3  O16  0.020
 A11  plan-3  O17  0.020

