# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 10 11:17:50 2022
#   Inital geometry file: a 120 line input string
#   Ligand name: N-[1-(2,6-dimethoxybenzyl)piperidin-4-yl]-4-sulfanylbutanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cccc(OC)c1CN2CCC(CC2)NC(=O)CCCS
#
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
 F1I  F1I  N-[1-(2,6-dimethoxybenzyl)piperidin-4-yl]-4-sulfanylbutanamide  ligand  52  24  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_F1I
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
 F1I  C28   C  CH3   0  -0.435  -4.1133   3.7241   1.3704
 F1I  C27   C  CH3   0  -0.435  -4.4538  -2.7049  -1.7578
 F1I  O25   O  O2    0  -0.469  -3.7868   2.3523   1.2980
 F1I  C16   C  CR6   0   0.379  -4.3613  -0.5335  -0.7969
 F1I  C17   C  CR16  0  -0.413  -5.1587  -0.0024  -1.8106
 F1I  C20   C  CR6   0   0.375  -4.2569   1.6210   0.2679
 F1I  C15   C  CR6   0  -0.123  -3.8984   0.2681   0.2553
 F1I  C12   C  CH2   0  -0.282  -0.9656  -1.4798   1.7592
 F1I  C13   C  CH2   0  -0.444   0.3827  -1.8909   1.1891
 F1I  C14   C  CH2   0  -0.315  -3.0278  -0.3405   1.3233
 F1I  C10   C  CH2   0  -0.277  -0.9286   0.6017   0.5870
 F1I  C9    C  CH2   0  -0.427   0.4247   0.2815  -0.0293
 F1I  C7    C  CH2   0  -0.552   7.1357  -0.8528  -1.2013
 F1I  C5    C  CH2   0  -0.581   4.8199  -1.0974  -0.2865
 F1I  C6    C  CH2   0  -0.415   6.0044  -0.1581  -0.4592
 F1I  C1    C  CH1   0  -0.069   1.2243  -0.6647   0.8611
 F1I  O4    O  O     0  -0.504   3.7995   0.4968   1.1978
 F1I  S8    S  S2    0  -0.257   8.5464   0.2950  -1.3464
 F1I  N2    N  NH1   0  -0.643   2.4735  -1.0642   0.2451
 F1I  N11   N  NT    0  -0.404  -1.6804  -0.6105   0.8469
 F1I  C18   C  CR16  0  -0.236  -5.4896   1.3422  -1.7680
 F1I  C19   C  CR16  0  -0.411  -5.0524   2.1637  -0.7435
 F1I  H28   H  HCH3  0   0.226  -3.7395   4.2828   0.5085
 F1I  H28A  H  HCH3  0   0.227  -5.1913   3.8858   1.4532
 F1I  H28B  H  HCH3  0   0.258  -3.6325   4.1065   2.2675
 F1I  H27   H  HCH3  0   0.226  -4.0972  -2.4123  -2.7486
 F1I  H27A  H  HCH3  0   0.257  -4.0498  -3.6855  -1.5180
 F1I  H27B  H  HCH3  0   0.226  -5.5446  -2.7727  -1.7834
 F1I  H17   H  HCR6  0   0.272  -5.5243  -0.6119  -2.6247
 F1I  H12   H  HCH2  0   0.237  -1.5689  -2.3730   1.9384
 F1I  H12A  H  HCH2  0   0.185  -0.8110  -1.0020   2.7443
 F1I  H13   H  HCH2  0   0.242   0.9050  -2.5281   1.9064
 F1I  H13A  H  HCH2  0   0.222   0.2239  -2.4820   0.2808
 F1I  H14   H  HCH2  0   0.217  -3.0203   0.2952   2.2199
 F1I  H14A  H  HCH2  0   0.239  -3.4628  -1.2930   1.6347
 F1I  H10   H  HCH2  0   0.182  -0.7852   1.1941   1.5094
 F1I  H10A  H  HCH2  0   0.242  -1.4927   1.2330  -0.1024
 F1I  H9    H  HCH2  0   0.217   0.2740  -0.1858  -1.0074
 F1I  H9A   H  HCH2  0   0.237   0.9817   1.2066  -0.1925
 F1I  H7    H  HCH2  0   0.264   7.4515  -1.7477  -0.6643
 F1I  H7A   H  HCH2  0   0.265   6.8126  -1.1515  -2.1988
 F1I  H5    H  HCH2  0   0.257   4.4835  -1.4641  -1.2601
 F1I  H5A   H  HCH2  0   0.274   5.1283  -1.9848   0.2775
 F1I  H6    H  HCH2  0   0.241   6.3560   0.1791   0.5174
 F1I  H6A   H  HCH2  0   0.241   5.6970   0.7324  -1.0128
 F1I  H1    H  HCH1  0   0.238   1.4689  -0.1492   1.7935
 F1I  HS8   H  HSH1  0   0.222   9.3518  -0.4957  -2.0635
 F1I  HN2   H  HNH1  0   0.393   2.4328  -1.8160  -0.4253
 F1I  H18   H  HCR6  0   0.258  -6.1040   1.7606  -2.5548
 F1I  H19   H  HCR6  0   0.273  -5.3322   3.2075  -0.7448
 F1I  O26   O  O2    0  -0.460  -3.9973  -1.8280  -0.7494
 F1I  C3    C  C     0   0.561   3.6567  -0.4631   0.4525

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
 F1I  C28  O25   single    1.412  0.020  1.412
 F1I  C27  O26   single    1.412  0.020  1.412
 F1I  O25  C20   single    1.348  0.020  1.348
 F1I  C16  C17   aromatic  1.395  0.020  1.395
 F1I  C16  C15   aromatic  1.401  0.020  1.401
 F1I  C16  O26   single    1.346  0.020  1.346
 F1I  C17  C18   aromatic  1.385  0.020  1.385
 F1I  C20  C15   aromatic  1.400  0.020  1.400
 F1I  C20  C19   aromatic  1.397  0.020  1.397
 F1I  C15  C14   single    1.506  0.020  1.506
 F1I  C12  C13   single    1.521  0.020  1.521
 F1I  C12  N11   single    1.449  0.020  1.449
 F1I  C13  C1    single    1.523  0.020  1.523
 F1I  C14  N11   single    1.454  0.020  1.454
 F1I  C10  C9    single    1.521  0.020  1.521
 F1I  C10  N11   single    1.450  0.020  1.450
 F1I  C9   C1    single    1.526  0.020  1.526
 F1I  C7   C6    single    1.521  0.020  1.521
 F1I  C7   S8    single    1.824  0.020  1.824
 F1I  C5   C6    single    1.522  0.020  1.522
 F1I  C5   C3    single    1.517  0.020  1.517
 F1I  C3   O4    double    1.224  0.020  1.224
 F1I  C3   N2    single    1.343  0.020  1.343
 F1I  C1   N2    single    1.449  0.020  1.449
 F1I  C18  C19   aromatic  1.384  0.020  1.384
 F1I  C28  H28   single    0.970  0.020  1.090
 F1I  C28  H28A  single    0.970  0.020  1.090
 F1I  C28  H28B  single    0.970  0.020  1.090
 F1I  C27  H27   single    0.970  0.020  1.090
 F1I  C27  H27A  single    0.970  0.020  1.090
 F1I  C27  H27B  single    0.970  0.020  1.090
 F1I  C17  H17   single    0.930  0.020  1.080
 F1I  C12  H12   single    0.970  0.020  1.090
 F1I  C12  H12A  single    0.970  0.020  1.090
 F1I  C13  H13   single    0.970  0.020  1.090
 F1I  C13  H13A  single    0.970  0.020  1.090
 F1I  C14  H14   single    0.970  0.020  1.090
 F1I  C14  H14A  single    0.970  0.020  1.090
 F1I  C10  H10   single    0.970  0.020  1.090
 F1I  C10  H10A  single    0.970  0.020  1.090
 F1I  C9   H9    single    0.970  0.020  1.090
 F1I  C9   H9A   single    0.970  0.020  1.090
 F1I  C7   H7    single    0.970  0.020  1.090
 F1I  C7   H7A   single    0.970  0.020  1.090
 F1I  C5   H5    single    0.970  0.020  1.090
 F1I  C5   H5A   single    0.970  0.020  1.090
 F1I  C6   H6    single    0.970  0.020  1.090
 F1I  C6   H6A   single    0.970  0.020  1.090
 F1I  C1   H1    single    0.970  0.020  1.090
 F1I  S8   HS8   single    1.200  0.020  1.300
 F1I  N2   HN2   single    0.860  0.020  1.020
 F1I  C18  H18   single    0.930  0.020  1.080
 F1I  C19  H19   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
 F1I  H28B  C28  H28A  108.76  3.000
 F1I  H28B  C28  H28   108.64  3.000
 F1I  H28A  C28  H28   108.74  3.000
 F1I  H28B  C28  O25   106.37  3.000
 F1I  H28A  C28  O25   112.06  3.000
 F1I  H28   C28  O25   112.15  3.000
 F1I  H27B  C27  H27A  108.66  3.000
 F1I  H27B  C27  H27   108.71  3.000
 F1I  H27A  C27  H27   108.67  3.000
 F1I  H27B  C27  O26   112.20  3.000
 F1I  H27A  C27  O26   106.41  3.000
 F1I  H27   C27  O26   112.06  3.000
 F1I  C20   O25  C28   119.05  3.000
 F1I  O26   C16  C15   115.75  3.000
 F1I  O26   C16  C17   123.14  3.000
 F1I  C15   C16  C17   121.11  3.000
 F1I  H17   C17  C18   119.32  3.000
 F1I  H17   C17  C16   121.75  3.000
 F1I  C18   C17  C16   118.93  3.000
 F1I  C19   C20  C15   121.00  3.000
 F1I  C19   C20  O25   122.77  3.000
 F1I  C15   C20  O25   116.23  3.000
 F1I  C14   C15  C20   122.16  3.000
 F1I  C14   C15  C16   119.48  3.000
 F1I  C20   C15  C16   118.36  3.000
 F1I  H12A  C12  H12   106.52  3.000
 F1I  H12A  C12  N11   111.76  3.000
 F1I  H12   C12  N11   108.74  3.000
 F1I  H12A  C12  C13   109.08  3.000
 F1I  H12   C12  C13   109.28  3.000
 F1I  N11   C12  C13   111.33  3.000
 F1I  H13A  C13  H13   107.40  3.000
 F1I  H13A  C13  C1    109.63  3.000
 F1I  H13   C13  C1    110.30  3.000
 F1I  H13A  C13  C12   109.16  3.000
 F1I  H13   C13  C12   109.60  3.000
 F1I  C1    C13  C12   110.68  3.000
 F1I  H14A  C14  H14   105.93  3.000
 F1I  H14A  C14  N11   107.48  3.000
 F1I  H14   C14  N11   111.61  3.000
 F1I  H14A  C14  C15   108.92  3.000
 F1I  H14   C14  C15   110.40  3.000
 F1I  N11   C14  C15   112.23  3.000
 F1I  H10A  C10  H10   106.51  3.000
 F1I  H10A  C10  N11   109.19  3.000
 F1I  H10   C10  N11   111.45  3.000
 F1I  H10A  C10  C9    109.00  3.000
 F1I  H10   C10  C9    109.60  3.000
 F1I  N11   C10  C9    110.97  3.000
 F1I  H9A   C9   H9    107.36  3.000
 F1I  H9A   C9   C1    110.20  3.000
 F1I  H9    C9   C1    109.20  3.000
 F1I  H9A   C9   C10   109.63  3.000
 F1I  H9    C9   C10   109.24  3.000
 F1I  C1    C9   C10   111.12  3.000
 F1I  H7A   C7   H7    108.16  3.000
 F1I  H7A   C7   S8    109.19  3.000
 F1I  H7    C7   S8    109.36  3.000
 F1I  H7A   C7   C6    110.56  3.000
 F1I  H7    C7   C6    110.48  3.000
 F1I  S8    C7   C6    109.06  3.000
 F1I  H5A   C5   H5    105.86  3.000
 F1I  H5A   C5   C3    107.68  3.000
 F1I  H5    C5   C3    109.76  3.000
 F1I  H5A   C5   C6    109.84  3.000
 F1I  H5    C5   C6    110.21  3.000
 F1I  C3    C5   C6    113.21  3.000
 F1I  H6A   C6   H6    106.98  3.000
 F1I  H6A   C6   C5    109.98  3.000
 F1I  H6    C6   C5    109.88  3.000
 F1I  H6A   C6   C7    109.53  3.000
 F1I  H6    C6   C7    109.76  3.000
 F1I  C5    C6   C7    110.64  3.000
 F1I  H1    C1   N2    107.44  3.000
 F1I  H1    C1   C9    108.82  3.000
 F1I  N2    C1   C9    112.01  3.000
 F1I  H1    C1   C13   108.64  3.000
 F1I  N2    C1   C13   110.24  3.000
 F1I  C9    C1   C13   109.60  3.000
 F1I  HS8   S8   C7     97.84  3.000
 F1I  HN2   N2   C1    116.97  3.000
 F1I  HN2   N2   C3    118.16  3.000
 F1I  C1    N2   C3    124.78  3.000
 F1I  C10   N11  C14   112.57  3.000
 F1I  C10   N11  C12   111.02  3.000
 F1I  C14   N11  C12   111.24  3.000
 F1I  H18   C18  C19   119.21  3.000
 F1I  H18   C18  C17   119.24  3.000
 F1I  C19   C18  C17   121.56  3.000
 F1I  H19   C19  C18   119.38  3.000
 F1I  H19   C19  C20   121.58  3.000
 F1I  C18   C19  C20   119.04  3.000
 F1I  C16   O26  C27   119.00  3.000
 F1I  N2    C3   O4    123.22  3.000
 F1I  N2    C3   C5    114.40  3.000
 F1I  O4    C3   C5    122.36  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
 F1I  CONST_01  C19  C18  C17  C16     0.00   0.0  0
 F1I  CONST_02  C19  C20  C15  C16     0.00   0.0  0
 F1I  CONST_03  C20  C15  C16  C17     0.00   0.0  0
 F1I  CONST_04  C20  C19  C18  C17     0.00   0.0  0
 F1I  CONST_05  C18  C17  C16  C15     0.00   0.0  0
 F1I  CONST_06  C18  C19  C20  C15     0.00   0.0  0
 F1I  CONST_07  C16  C15  C20  O25   180.00   0.0  0
 F1I  CONST_08  C18  C19  C20  O25   180.00   0.0  0
 F1I  CONST_09  C14  C15  C16  C17   180.00   0.0  0
 F1I  CONST_10  O26  C16  C15  C20   180.00   0.0  0
 F1I  CONST_11  C19  C20  C15  C14   180.00   0.0  0
 F1I  CONST_12  C18  C17  C16  O26   180.00   0.0  0
 F1I  CONST_13  H18  C18  C17  C16   180.00   0.0  0
 F1I  CONST_14  H19  C19  C18  C17   180.00   0.0  0
 F1I  CONST_15  H17  C17  C16  C15   180.00   0.0  0
 F1I  CONST_16  C1   N2   C3   C5    180.00   0.0  0
 F1I  CONST_17  O4   C3   N2   C1      0.00   0.0  0
 F1I  CONST_18  HN2  N2   C3   C5      0.00   0.0  0
 F1I  Var_01    C9   C10  N11  C12    59.79  30.0  1
 F1I  Var_02    C10  N11  C12  C13   -60.25  30.0  1
 F1I  Var_03    N11  C12  C13  C1     57.01  30.0  1
 F1I  Var_04    N11  C10  C9   C1    -56.52  30.0  1
 F1I  Var_05    N11  C14  C15  C16    73.24  30.0  2
 F1I  Var_06    C12  N11  C14  C15  -165.96  30.0  3
 F1I  Var_07    C15  C20  O25  C28  -179.93  30.0  2
 F1I  Var_08    C17  C16  O26  C27    -0.95  30.0  2
 F1I  Var_09    H27  C27  O26  C16    61.77  30.0  3
 F1I  Var_10    H28  C28  O25  C20   -61.27  30.0  3
 F1I  Var_11    C3   C5   C6   C7    179.83  30.0  1
 F1I  Var_12    S8   C7   C6   C5   -178.55  30.0  2
 F1I  Var_13    O4   C3   C5   C6    -22.57  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
 F1I  chir_01  C1  C13  C9  N2  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
 F1I  plan-1  O25  0.020
 F1I  plan-1  C16  0.020
 F1I  plan-1  C17  0.020
 F1I  plan-1  C20  0.020
 F1I  plan-1  C15  0.020
 F1I  plan-1  C14  0.020
 F1I  plan-1  C18  0.020
 F1I  plan-1  C19  0.020
 F1I  plan-1  H17  0.020
 F1I  plan-1  H18  0.020
 F1I  plan-1  H19  0.020
 F1I  plan-1  O26  0.020
 F1I  plan-2  C5   0.020
 F1I  plan-2  C1   0.020
 F1I  plan-2  O4   0.020
 F1I  plan-2  N2   0.020
 F1I  plan-2  HN2  0.020
 F1I  plan-2  C3   0.020

