# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 14:24:36 2021
#   Inital geometry file: a 122 line input string
#   Ligand name: [(3~{S})-1-(2,3-dihydro-1~{H}-inden-2-yl)piperidin-1-ium-3-yl] ~{N}-phenylcarbamate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(Nc1ccccc1)O[C@H]2CCC[NH+](C2)C3Cc4ccccc4C3
#
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
 L3H  L3H  '[(3~{S})-1-(2,3-dihydro-1~{H}-inden-2-yl)piperidin-1-ium-3-yl] ~{N}-phenylcarbamate'  ligand  50  25  .  2022-03-22  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_L3H
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
 L3H  C02  C  C     0   0.755  137.1911  112.8866  40.1759
 L3H  C04  C  CR6   0   0.365  139.3526  113.6425  41.1023
 L3H  C05  C  CR16  0  -0.310  138.9670  114.8788  41.6195
 L3H  C06  C  CR16  0  -0.247  139.9351  115.7536  42.0958
 L3H  C07  C  CR16  0  -0.270  141.2811  115.4197  42.0760
 L3H  C08  C  CR16  0  -0.246  141.6597  114.1830  41.5698
 L3H  C09  C  CR16  0  -0.338  140.7069  113.3032  41.0849
 L3H  C11  C  CH1   0  -0.011  135.4083  111.7423  39.0809
 L3H  C12  C  CH2   0  -0.466  135.3417  110.5190  38.1849
 L3H  C13  C  CH2   0  -0.478  135.3454  109.2346  39.0030
 L3H  C14  C  CH2   0  -0.321  134.2543  109.2486  40.0537
 L3H  C16  C  CH2   0  -0.350  134.3193  111.7124  40.1409
 L3H  C17  C  CR15  0  -0.132  133.4445  110.4015  42.1162
 L3H  C18  C  CH2   0  -0.516  133.7801  111.5047  43.1312
 L3H  C19  C  CR56  0   0.077  132.7615  112.5753  42.8587
 L3H  C20  C  CR56  0   0.099  131.7392  112.0812  42.0563
 L3H  C21  C  CH2   0  -0.514  131.9799  110.6367  41.7184
 L3H  C22  C  CR16  0  -0.319  130.6875  112.8969  41.6713
 L3H  C23  C  CR16  0  -0.256  130.6727  114.2199  42.1007
 L3H  C24  C  CR16  0  -0.258  131.6951  114.7134  42.9047
 L3H  C25  C  CR16  0  -0.314  132.7495  113.8921  43.2898
 L3H  N03  N  NH1   0  -0.765  138.4576  112.6866  40.6062
 L3H  N15  N  NT1   1  -0.545  134.3882  110.4517  40.9394
 L3H  O01  O  O     0  -0.481  136.5687  113.9220  40.2089
 L3H  O10  O  O2    0  -0.497  136.6996  111.7312  39.6982
 L3H  H1   H  HCR6  0   0.276  137.9294  115.1680  41.6631
 L3H  H2   H  HCR6  0   0.260  139.6212  116.7104  42.4926
 L3H  H3   H  HCR6  0   0.256  142.0245  116.1114  42.4495
 L3H  H4   H  HCR6  0   0.261  142.7036  113.8989  41.5442
 L3H  H5   H  HCR6  0   0.272  141.0160  112.3445  40.6855
 L3H  H6   H  HCH1  0   0.303  135.2756  112.6522  38.4925
 L3H  H7   H  HCH2  0   0.261  134.4231  110.5832  37.5968
 L3H  H8   H  HCH2  0   0.278  136.1720  110.5340  37.4785
 L3H  H9   H  HCH2  0   0.285  135.1682  108.3751  38.3564
 L3H  H10  H  HCH2  0   0.261  136.3170  109.0719  39.4749
 L3H  H11  H  HCH2  0   0.296  133.2666  109.2929  39.5960
 L3H  H12  H  HCH2  0   0.312  134.3017  108.3727  40.6976
 L3H  H13  H  HCH2  0   0.318  134.4009  112.5614  40.8151
 L3H  H14  H  HCH2  0   0.318  133.3445  111.7479  39.6567
 L3H  H15  H  HCR5  0   0.325  133.6022  109.4096  42.5340
 L3H  H16  H  HCH2  0   0.303  133.6598  111.1003  44.1393
 L3H  H17  H  HCH2  0   0.271  134.8150  111.8518  43.0699
 L3H  H18  H  HCH2  0   0.279  131.7509  110.3868  40.6817
 L3H  H19  H  HCH2  0   0.302  131.3519  109.9840  42.3300
 L3H  H20  H  HCR6  0   0.254  129.8930  112.5187  41.0394
 L3H  H21  H  HCR6  0   0.257  129.8635  114.8734  41.8011
 L3H  H22  H  HCR6  0   0.258  131.6737  115.7466  43.2263
 L3H  H23  H  HCR6  0   0.255  133.5499  114.2825  43.9062
 L3H  H24  H  HNH1  0   0.419  138.8516  111.7760  40.4189
 L3H  H25  H  HNT1  0   0.458  135.3249  110.4003  41.3497

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
 L3H  C12  C11  single    1.518  0.020  1.518
 L3H  C12  C13  single    1.523  0.020  1.523
 L3H  C11  O10  single    1.431  0.020  1.431
 L3H  C11  C16  single    1.520  0.020  1.520
 L3H  C13  C14  single    1.515  0.020  1.515
 L3H  O10  C02  single    1.343  0.020  1.343
 L3H  O01  C02  double    1.209  0.020  1.209
 L3H  C02  N03  single    1.352  0.020  1.352
 L3H  C16  N15  single    1.494  0.020  1.494
 L3H  C14  N15  single    1.500  0.020  1.500
 L3H  N03  C04  single    1.400  0.020  1.400
 L3H  N15  C17  single    1.509  0.020  1.509
 L3H  C04  C09  aromatic  1.396  0.020  1.396
 L3H  C04  C05  aromatic  1.394  0.020  1.394
 L3H  C09  C08  aromatic  1.385  0.020  1.385
 L3H  C21  C17  single    1.536  0.020  1.536
 L3H  C21  C20  single    1.503  0.020  1.503
 L3H  C05  C06  aromatic  1.389  0.020  1.389
 L3H  C17  C18  single    1.536  0.020  1.536
 L3H  C22  C20  aromatic  1.386  0.020  1.386
 L3H  C22  C23  aromatic  1.391  0.020  1.391
 L3H  C20  C19  aromatic  1.390  0.020  1.390
 L3H  C08  C07  aromatic  1.389  0.020  1.389
 L3H  C06  C07  aromatic  1.387  0.020  1.387
 L3H  C23  C24  aromatic  1.391  0.020  1.391
 L3H  C18  C19  single    1.503  0.020  1.503
 L3H  C19  C25  aromatic  1.386  0.020  1.386
 L3H  C24  C25  aromatic  1.391  0.020  1.391
 L3H  C05  H1   single    0.930  0.020  1.080
 L3H  C06  H2   single    0.930  0.020  1.080
 L3H  C07  H3   single    0.930  0.020  1.080
 L3H  C08  H4   single    0.930  0.020  1.080
 L3H  C09  H5   single    0.930  0.020  1.080
 L3H  C11  H6   single    0.970  0.020  1.090
 L3H  C12  H7   single    0.970  0.020  1.090
 L3H  C12  H8   single    0.970  0.020  1.090
 L3H  C13  H9   single    0.970  0.020  1.090
 L3H  C13  H10  single    0.970  0.020  1.090
 L3H  C14  H11  single    0.970  0.020  1.090
 L3H  C14  H12  single    0.970  0.020  1.090
 L3H  C16  H13  single    0.970  0.020  1.090
 L3H  C16  H14  single    0.970  0.020  1.090
 L3H  C17  H15  single    0.970  0.020  1.090
 L3H  C18  H16  single    0.970  0.020  1.090
 L3H  C18  H17  single    0.970  0.020  1.090
 L3H  C21  H18  single    0.970  0.020  1.090
 L3H  C21  H19  single    0.970  0.020  1.090
 L3H  C22  H20  single    0.930  0.020  1.080
 L3H  C23  H21  single    0.930  0.020  1.080
 L3H  C24  H22  single    0.930  0.020  1.080
 L3H  C25  H23  single    0.930  0.020  1.080
 L3H  N03  H24  single    0.860  0.020  1.020
 L3H  N15  H25  single    0.890  0.020  1.040

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
 L3H  O10  C02  O01  123.93  3.000
 L3H  O01  C02  N03  126.89  3.000
 L3H  O10  C02  N03  109.18  3.000
 L3H  N03  C04  C09  116.72  3.000
 L3H  C09  C04  C05  119.22  3.000
 L3H  N03  C04  C05  124.05  3.000
 L3H  H1   C05  C06  119.21  3.000
 L3H  H1   C05  C04  121.26  3.000
 L3H  C06  C05  C04  119.53  3.000
 L3H  H2   C06  C07  119.96  3.000
 L3H  H2   C06  C05  118.71  3.000
 L3H  C07  C06  C05  121.32  3.000
 L3H  H3   C07  C08  120.52  3.000
 L3H  H3   C07  C06  120.53  3.000
 L3H  C08  C07  C06  118.95  3.000
 L3H  H4   C08  C09  119.25  3.000
 L3H  H4   C08  C07  120.36  3.000
 L3H  C09  C08  C07  120.39  3.000
 L3H  H5   C09  C08  119.67  3.000
 L3H  H5   C09  C04  119.76  3.000
 L3H  C08  C09  C04  120.58  3.000
 L3H  H6   C11  O10  110.41  3.000
 L3H  H6   C11  C16  107.77  3.000
 L3H  O10  C11  C16  110.21  3.000
 L3H  H6   C11  C12  110.38  3.000
 L3H  C16  C11  C12  111.37  3.000
 L3H  O10  C11  C12  106.73  3.000
 L3H  H8   C12  H7   106.91  3.000
 L3H  H8   C12  C13  110.97  3.000
 L3H  H7   C12  C13  109.92  3.000
 L3H  H8   C12  C11  109.75  3.000
 L3H  H7   C12  C11  107.90  3.000
 L3H  C13  C12  C11  111.26  3.000
 L3H  H10  C13  H9   106.46  3.000
 L3H  H10  C13  C14  110.02  3.000
 L3H  H9   C13  C14  107.56  3.000
 L3H  H10  C13  C12  111.09  3.000
 L3H  H9   C13  C12  110.24  3.000
 L3H  C14  C13  C12  111.29  3.000
 L3H  H12  C14  H11  108.71  3.000
 L3H  H12  C14  N15  107.00  3.000
 L3H  H11  C14  N15  107.24  3.000
 L3H  H12  C14  C13  111.82  3.000
 L3H  H11  C14  C13  111.22  3.000
 L3H  N15  C14  C13  110.65  3.000
 L3H  H14  C16  H13  108.51  3.000
 L3H  H14  C16  N15  107.84  3.000
 L3H  H13  C16  N15  108.91  3.000
 L3H  H14  C16  C11  109.31  3.000
 L3H  H13  C16  C11  111.30  3.000
 L3H  N15  C16  C11  110.87  3.000
 L3H  H15  C17  N15  103.83  3.000
 L3H  H15  C17  C21  112.17  3.000
 L3H  N15  C17  C21  112.91  3.000
 L3H  H15  C17  C18  111.68  3.000
 L3H  C21  C17  C18  105.63  3.000
 L3H  N15  C17  C18  110.78  3.000
 L3H  H17  C18  H16  105.87  3.000
 L3H  H17  C18  C19  113.91  3.000
 L3H  H16  C18  C19  110.87  3.000
 L3H  H17  C18  C17  113.44  3.000
 L3H  H16  C18  C17  108.65  3.000
 L3H  C19  C18  C17  104.11  3.000
 L3H  C25  C19  C20  120.72  3.000
 L3H  C25  C19  C18  128.80  3.000
 L3H  C20  C19  C18  110.48  3.000
 L3H  C22  C20  C21  128.68  3.000
 L3H  C22  C20  C19  120.62  3.000
 L3H  C21  C20  C19  110.70  3.000
 L3H  H19  C21  H18  105.92  3.000
 L3H  H19  C21  C20  110.87  3.000
 L3H  H18  C21  C20  113.59  3.000
 L3H  H19  C21  C17  108.16  3.000
 L3H  H18  C21  C17  114.29  3.000
 L3H  C20  C21  C17  103.99  3.000
 L3H  H20  C22  C23  120.29  3.000
 L3H  H20  C22  C20  120.88  3.000
 L3H  C23  C22  C20  118.83  3.000
 L3H  H21  C23  C24  119.69  3.000
 L3H  H21  C23  C22  119.78  3.000
 L3H  C24  C23  C22  120.53  3.000
 L3H  H22  C24  C25  119.76  3.000
 L3H  H22  C24  C23  119.73  3.000
 L3H  C25  C24  C23  120.51  3.000
 L3H  H23  C25  C24  120.32  3.000
 L3H  H23  C25  C19  120.88  3.000
 L3H  C24  C25  C19  118.79  3.000
 L3H  H24  N03  C04  115.59  3.000
 L3H  H24  N03  C02  116.09  3.000
 L3H  C04  N03  C02  127.61  3.000
 L3H  H25  N15  C17  104.94  3.000
 L3H  H25  N15  C16  107.38  3.000
 L3H  C17  N15  C16  114.58  3.000
 L3H  H25  N15  C14  106.14  3.000
 L3H  C17  N15  C14  112.21  3.000
 L3H  C16  N15  C14  110.92  3.000
 L3H  C11  O10  C02  118.47  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
 L3H  CONST_01  C07  C08  C09  C04    0.00   0.0  0
 L3H  CONST_02  C07  C06  C05  C04    0.00   0.0  0
 L3H  CONST_03  C08  C09  C04  C05    0.00   0.0  0
 L3H  CONST_04  C08  C07  C06  C05    0.00   0.0  0
 L3H  CONST_05  C09  C04  C05  C06    0.00   0.0  0
 L3H  CONST_06  C09  C08  C07  C06    0.00   0.0  0
 L3H  CONST_07  C23  C22  C20  C19    0.00   0.0  0
 L3H  CONST_08  C23  C24  C25  C19    0.00   0.0  0
 L3H  CONST_09  C24  C23  C22  C20    0.00   0.0  0
 L3H  CONST_10  C24  C25  C19  C20    0.00   0.0  0
 L3H  CONST_11  C25  C19  C20  C22    0.00   0.0  0
 L3H  CONST_12  C25  C24  C23  C22    0.00   0.0  0
 L3H  CONST_13  N03  C04  C05  C06  180.00   0.0  0
 L3H  CONST_14  N03  C04  C09  C08  180.00   0.0  0
 L3H  CONST_15  H4   C08  C09  C04  180.00   0.0  0
 L3H  CONST_16  H2   C06  C05  C04  180.00   0.0  0
 L3H  CONST_17  H5   C09  C04  C05  180.00   0.0  0
 L3H  CONST_18  H3   C07  C06  C05  180.00   0.0  0
 L3H  CONST_19  H1   C05  C06  C07  180.00   0.0  0
 L3H  CONST_20  H23  C25  C19  C18    0.00   0.0  0
 L3H  CONST_21  H20  C22  C20  C19  180.00   0.0  0
 L3H  CONST_22  H22  C24  C25  C19  180.00   0.0  0
 L3H  CONST_23  H21  C23  C22  C20  180.00   0.0  0
 L3H  CONST_26  H24  N03  C04  C05  180.00   0.0  0
 L3H  CONST_27  O10  C02  N03  C04  180.00   0.0  0
 L3H  CONST_28  O01  C02  N03  C04    0.00   0.0  0
 L3H  Var_01    C14  C13  C12  C11   53.47  30.0  1
 L3H  Var_02    N15  C14  C13  C12  -56.03  30.0  1
 L3H  Var_03    C22  C20  C21  C17  165.99  30.0  1
 L3H  Var_04    C20  C19  C18  C17   13.77  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
 L3H  chir_01  C11  C12  O10  C16  positiv
 L3H  chir_02  C17  N15  C21  C18  positiv
 L3H  chir_03  N15  C17  C14  C16  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
 L3H  plan-1  C04  0.020
 L3H  plan-1  C05  0.020
 L3H  plan-1  C06  0.020
 L3H  plan-1  C07  0.020
 L3H  plan-1  C08  0.020
 L3H  plan-1  C09  0.020
 L3H  plan-1  N03  0.020
 L3H  plan-1  H1   0.020
 L3H  plan-1  H2   0.020
 L3H  plan-1  H3   0.020
 L3H  plan-1  H4   0.020
 L3H  plan-1  H5   0.020
 L3H  plan-2  C18  0.020
 L3H  plan-2  C19  0.020
 L3H  plan-2  C20  0.020
 L3H  plan-2  C21  0.020
 L3H  plan-2  C22  0.020
 L3H  plan-2  C23  0.020
 L3H  plan-2  C24  0.020
 L3H  plan-2  C25  0.020
 L3H  plan-2  H20  0.020
 L3H  plan-2  H21  0.020
 L3H  plan-2  H22  0.020
 L3H  plan-2  H23  0.020
 L3H  plan-3  C02  0.020
 L3H  plan-3  C04  0.020
 L3H  plan-3  N03  0.020
 L3H  plan-3  H24  0.020
 L3H  plan-4  C02  0.020
 L3H  plan-4  N03  0.020
 L3H  plan-4  O01  0.020
 L3H  plan-4  O10  0.020

