# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 13:43:32 2022
#   Inital geometry file: a 92 line input string
#   Ligand name: 1-[(3-methoxyphenyl)methyl]piperidine-4-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cccc(CN2CCC(CC2)C(N)=O)c1
#
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
 I81  I81  "1-[(3-methoxyphenyl)methyl]piperidine-4-carboxamide"
  ligand  38  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 OK (reasonable std)
;

data_comp_I81
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
 I81  N1   N  NR6   0  -0.413  -4.0542  34.9289  18.6118
 I81  C4   C  CR16  0  -0.225   0.0117  33.1305  16.9716
 I81  C5   C  CR16  0  -0.334  -0.7531  34.1987  17.4139
 I81  C6   C  CR6   0   0.107  -2.1379  34.1658  17.2701
 I81  C7   C  CH2   0  -0.332  -2.9894  35.3275  17.7130
 I81  C8   C  C     0  -0.276  -3.5265  34.4909  19.8923
 I81  C10  C  CR16  0  -0.386  -5.6717  35.1025  21.0191
 I81  C13  C  C     0   0.513  -6.7905  34.7084  21.9654
 I81  C1   C  CH3   0  -0.434  -1.9172  29.8500  15.1993
 I81  C2   C  CR6   0   0.397  -1.9666  31.9832  16.2407
 I81  C3   C  CR16  0  -0.394  -0.5797  32.0196  16.3840
 I81  C9   C  C     0  -0.427  -4.6305  33.9996  20.8142
 I81  C11  C  C     0  -0.429  -6.1872  35.5570  19.6514
 I81  C12  C  C     0  -0.278  -5.0255  35.9958  18.7751
 I81  O2   O  O     0  -0.481  -7.0103  35.3260  22.9982
 I81  N2   N  NH2   0  -0.800  -7.5238  33.6445  21.5946
 I81  C14  C  CR16  0  -0.381  -2.7357  33.0559  16.6897
 I81  H2   H  HCR6  0   0.254   1.0880  33.1536  17.0861
 I81  H3   H  HCR6  0   0.244  -0.2782  35.0560  17.8748
 I81  H4   H  HCH2  0   0.214  -2.3454  36.1026  18.1611
 I81  H5   H  HCH2  0   0.250  -3.4479  35.7827  16.8299
 I81  H6   H  H     0   0.245  -2.8098  33.6850  19.7214
 I81  H7   H  H     0   0.191  -2.9702  35.3057  20.3907
 I81  H8   H  HCR6  0   0.247  -5.1695  35.9541  21.4889
 I81  H9   H  HCH3  0   0.256  -2.6480  29.1551  14.7924
 I81  H10  H  HCH3  0   0.226  -1.2190  30.1286  14.4050
 I81  H11  H  HCH3  0   0.226  -1.3606  29.3459  15.9940
 I81  H12  H  HCR6  0   0.274   0.0461  31.2030  16.0505
 I81  H13  H  H     0   0.225  -5.0930  33.1110  20.3756
 I81  H14  H  H     0   0.244  -4.1940  33.6987  21.7691
 I81  H15  H  H     0   0.244  -6.8904  36.3855  19.7609
 I81  H16  H  H     0   0.225  -6.7221  34.7421  19.1550
 I81  H17  H  H     0   0.191  -4.5650  36.9000  19.2117
 I81  H18  H  H     0   0.240  -5.3995  36.2792  17.7883
 I81  H19  H  HNH2  0   0.398  -8.2938  33.3327  22.1638
 I81  H20  H  HNH2  0   0.405  -7.3573  33.1472  20.7371
 I81  H21  H  HCR6  0   0.247  -3.8139  33.0168  16.5837
 I81  O1   O  O2    0  -0.470  -2.6435  30.9606  15.6813

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
 I81  O1   C1   single    1.412  0.020  1.412
 I81  O1   C2   single    1.348  0.020  1.348
 I81  C2   C14  aromatic  1.394  0.020  1.394
 I81  C2   C3   aromatic  1.395  0.020  1.395
 I81  C14  C6   aromatic  1.388  0.020  1.388
 I81  C3   C4   aromatic  1.389  0.020  1.389
 I81  C6   C7   single    1.507  0.020  1.507
 I81  C6   C5   aromatic  1.393  0.020  1.393
 I81  C4   C5   aromatic  1.386  0.020  1.386
 I81  C7   N1   single    1.449  0.020  1.449
 I81  N1   C12  single    1.452  0.020  1.452
 I81  N1   C8   single    1.453  0.020  1.453
 I81  C12  C11  single    1.520  0.020  1.520
 I81  C8   C9   single    1.520  0.020  1.520
 I81  C11  C10  single    1.531  0.020  1.531
 I81  C9   C10  single    1.530  0.020  1.530
 I81  C10  C13  single    1.517  0.020  1.517
 I81  N2   C13  single    1.344  0.020  1.344
 I81  C13  O2   double    1.223  0.020  1.223
 I81  C4   H2   single    0.930  0.020  1.080
 I81  C5   H3   single    0.930  0.020  1.080
 I81  C7   H4   single    0.970  0.020  1.090
 I81  C7   H5   single    0.970  0.020  1.090
 I81  C8   H6   single    0.970  0.020  1.090
 I81  C8   H7   single    0.970  0.020  1.090
 I81  C10  H8   single    0.970  0.020  1.090
 I81  C1   H9   single    0.970  0.020  1.090
 I81  C1   H10  single    0.970  0.020  1.090
 I81  C1   H11  single    0.970  0.020  1.090
 I81  C3   H12  single    0.930  0.020  1.080
 I81  C9   H13  single    0.970  0.020  1.090
 I81  C9   H14  single    0.970  0.020  1.090
 I81  C11  H15  single    0.970  0.020  1.090
 I81  C11  H16  single    0.970  0.020  1.090
 I81  C12  H17  single    0.970  0.020  1.090
 I81  C12  H18  single    0.970  0.020  1.090
 I81  N2   H19  single    0.860  0.020  1.020
 I81  N2   H20  single    0.860  0.020  1.020
 I81  C14  H21  single    0.930  0.020  1.080

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
 I81  C12  N1   C8   111.43  3.000
 I81  C8   N1   C7   111.27  3.000
 I81  C12  N1   C7   111.05  3.000
 I81  H2   C4   C3   119.02  3.000
 I81  H2   C4   C5   119.89  3.000
 I81  C3   C4   C5   121.09  3.000
 I81  H3   C5   C6   119.91  3.000
 I81  H3   C5   C4   120.25  3.000
 I81  C6   C5   C4   119.83  3.000
 I81  C14  C6   C7   119.73  3.000
 I81  C7   C6   C5   120.89  3.000
 I81  C14  C6   C5   119.37  3.000
 I81  H5   C7   H4   106.27  3.000
 I81  H5   C7   C6   108.68  3.000
 I81  H4   C7   C6   109.35  3.000
 I81  H5   C7   N1   107.88  3.000
 I81  H4   C7   N1   111.73  3.000
 I81  C6   C7   N1   112.67  3.000
 I81  H7   C8   H6   106.51  3.000
 I81  H7   C8   C9   109.29  3.000
 I81  H6   C8   C9   109.46  3.000
 I81  H7   C8   N1   110.98  3.000
 I81  H6   C8   N1   108.85  3.000
 I81  C9   C8   N1   111.61  3.000
 I81  H8   C10  C11  107.88  3.000
 I81  H8   C10  C9   107.81  3.000
 I81  C11  C10  C9   108.88  3.000
 I81  H8   C10  C13  105.82  3.000
 I81  C9   C10  C13  113.45  3.000
 I81  C11  C10  C13  112.71  3.000
 I81  N2   C13  O2   122.31  3.000
 I81  O2   C13  C10  121.86  3.000
 I81  N2   C13  C10  115.83  3.000
 I81  H11  C1   H10  108.69  3.000
 I81  H11  C1   H9   108.63  3.000
 I81  H10  C1   H9   108.67  3.000
 I81  H11  C1   O1   112.11  3.000
 I81  H10  C1   O1   112.08  3.000
 I81  H9   C1   O1   106.54  3.000
 I81  C14  C2   C3   119.69  3.000
 I81  C3   C2   O1   124.18  3.000
 I81  C14  C2   O1   116.12  3.000
 I81  H12  C3   C2   121.60  3.000
 I81  H12  C3   C4   119.21  3.000
 I81  C2   C3   C4   119.19  3.000
 I81  H14  C9   H13  107.20  3.000
 I81  H14  C9   C10  110.70  3.000
 I81  H13  C9   C10  110.58  3.000
 I81  H14  C9   C8   109.21  3.000
 I81  H13  C9   C8   109.06  3.000
 I81  C10  C9   C8   110.03  3.000
 I81  H16  C11  H15  107.20  3.000
 I81  H16  C11  C12  109.10  3.000
 I81  H15  C11  C12  109.32  3.000
 I81  H16  C11  C10  110.42  3.000
 I81  H15  C11  C10  110.64  3.000
 I81  C12  C11  C10  110.09  3.000
 I81  H18  C12  H17  106.70  3.000
 I81  H18  C12  C11  109.51  3.000
 I81  H17  C12  C11  109.09  3.000
 I81  H18  C12  N1   108.54  3.000
 I81  H17  C12  N1   111.53  3.000
 I81  C11  C12  N1   111.35  3.000
 I81  H20  N2   H19  117.11  3.000
 I81  H20  N2   C13  122.45  3.000
 I81  H19  N2   C13  120.41  3.000
 I81  H21  C14  C2   119.30  3.000
 I81  H21  C14  C6   119.88  3.000
 I81  C2   C14  C6   120.82  3.000
 I81  C2   O1   C1   118.69  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
 I81  CONST_01  C14  C2   C3   C4      0.00   0.0  0
 I81  CONST_02  C14  C6   C5   C4      0.00   0.0  0
 I81  CONST_03  C2   C14  C6   C5      0.00   0.0  0
 I81  CONST_04  C2   C3   C4   C5      0.00   0.0  0
 I81  CONST_05  C3   C2   C14  C6      0.00   0.0  0
 I81  CONST_06  C3   C4   C5   C6      0.00   0.0  0
 I81  CONST_07  O1   C2   C3   C4    180.00   0.0  0
 I81  CONST_08  C7   C6   C5   C4    180.00   0.0  0
 I81  CONST_09  O1   C2   C14  C6    180.00   0.0  0
 I81  CONST_10  C2   C14  C6   C7    180.00   0.0  0
 I81  CONST_11  H21  C14  C6   C5    180.00   0.0  0
 I81  CONST_12  H12  C3   C4   C5    180.00   0.0  0
 I81  CONST_13  H2   C4   C5   C6    180.00   0.0  0
 I81  CONST_14  H2   C4   C3   C2    180.00   0.0  0
 I81  CONST_15  H21  C14  C2   C3    180.00   0.0  0
 I81  CONST_16  H3   C5   C4   C3    180.00   0.0  0
 I81  CONST_17  H12  C3   C2   C14   180.00   0.0  0
 I81  CONST_18  H3   C5   C6   C14   180.00   0.0  0
 I81  CONST_19  H19  N2   C13  C10   180.00   0.0  0
 I81  CONST_20  H20  N2   C13  C10     0.00   0.0  0
 I81  CONST_21  H19  N2   C13  O2      0.00   0.0  0
 I81  CONST_22  H20  N2   C13  O2    180.00   0.0  0
 I81  Var_01    C10  C11  C12  N1     57.65  30.0  1
 I81  Var_02    C10  C9   C8   N1    -57.24  30.0  1
 I81  Var_03    C11  C12  N1   C8    -58.67  30.0  1
 I81  Var_04    C12  N1   C8   C9     58.57  30.0  1
 I81  Var_05    C14  C6   C7   N1     54.24  30.0  3
 I81  Var_06    C5   C6   C7   N1   -126.88  30.0  3
 I81  Var_07    C12  N1   C7   C6   -166.99  30.0  3
 I81  Var_08    C8   N1   C7   C6     68.26  30.0  3
 I81  Var_09    C11  C12  N1   C7    176.67  30.0  1
 I81  Var_10    C9   C8   N1   C7   -176.90  30.0  1
 I81  Var_11    H15  C11  C12  N1    179.39  30.0  1
 I81  Var_12    H16  C11  C12  N1    -63.67  30.0  1
 I81  Var_13    H13  C9   C8   N1     64.21  30.0  1
 I81  Var_14    H14  C9   C8   N1   -178.94  30.0  1
 I81  Var_15    H17  C12  N1   C8     63.45  30.0  1
 I81  Var_16    H18  C12  N1   C8   -179.29  30.0  1
 I81  Var_17    H17  C12  C11  C10   -65.87  30.0  1
 I81  Var_18    H18  C12  C11  C10   177.70  30.0  1
 I81  Var_19    H6   C8   C9   C10  -177.81  30.0  1
 I81  Var_20    H7   C8   C9   C10    65.89  30.0  1
 I81  Var_21    H6   C8   N1   C12   179.49  30.0  1
 I81  Var_22    H7   C8   N1   C12   -63.60  30.0  1
 I81  Var_23    C14  C2   O1   C1    179.56  30.0  2
 I81  Var_24    C3   C2   O1   C1     -0.28  30.0  2
 I81  Var_25    H4   C7   C6   C5     -1.99  30.0  2
 I81  Var_26    H5   C7   C6   C5    113.62  30.0  2
 I81  Var_27    H17  C12  N1   C7    -61.21  30.0  1
 I81  Var_28    H18  C12  N1   C7     56.05  30.0  1
 I81  Var_29    H6   C8   N1   C7    -55.97  30.0  1
 I81  Var_30    H7   C8   N1   C7     60.94  30.0  1
 I81  Var_31    H4   C7   N1   C8    -55.31  30.0  2
 I81  Var_32    H5   C7   N1   C8   -171.77  30.0  2
 I81  Var_33    H4   C7   N1   C12    69.44  30.0  2
 I81  Var_34    H5   C7   N1   C12   -47.02  30.0  2
 I81  Var_35    H4   C7   C6   C14   179.13  30.0  2
 I81  Var_36    H5   C7   C6   C14   -65.26  30.0  2
 I81  Var_37    H9   C1   O1   C2   -179.83  30.0  3
 I81  Var_38    H10  C1   O1   C2    -61.09  30.0  3
 I81  Var_39    H11  C1   O1   C2     61.46  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
 I81  chir_01  C10  C11  C9  C13  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
 I81  plan-1  C4   0.020
 I81  plan-1  C5   0.020
 I81  plan-1  C6   0.020
 I81  plan-1  C7   0.020
 I81  plan-1  C2   0.020
 I81  plan-1  C3   0.020
 I81  plan-1  C14  0.020
 I81  plan-1  H2   0.020
 I81  plan-1  H3   0.020
 I81  plan-1  H12  0.020
 I81  plan-1  H21  0.020
 I81  plan-1  O1   0.020
 I81  plan-2  C10  0.020
 I81  plan-2  C13  0.020
 I81  plan-2  O2   0.020
 I81  plan-2  N2   0.020
 I81  plan-2  H19  0.020
 I81  plan-2  H20  0.020

