# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 23:13:57 2020
#   Inital geometry file: a 81 line input string
#   Ligand name: [(3S,4R)-4-(4-fluorophenyl)-1-methylpiperidin-3-yl]methanol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CC[C@H]([C@H](CO)C1)c2ccc(F)cc2
#
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
 JLD  JLD  '[(3S,4R)-4-(4-fluorophenyl)-1-methylpiperidin-3-yl]methanol'  ligand  34  16  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_JLD
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
 JLD  C10   C  CR6   0   0.167   0.9431  -0.3329   0.3018
 JLD  C13   C  CR6   0   0.505   3.6879  -0.2761  -0.1106
 JLD  C15   C  CR16  0  -0.396   2.8451  -0.3054  -1.2054
 JLD  N02   N  NT    0  -0.412  -3.2881  -0.6835  -0.3869
 JLD  C03   C  CH2   0  -0.280  -2.6318  -1.7740   0.3052
 JLD  C04   C  CH2   0  -0.411  -1.1302  -1.7258   0.0863
 JLD  C05   C  CH1   0  -0.331  -0.5473  -0.3821   0.5316
 JLD  C06   C  CH1   0  -0.274  -1.3063   0.7664  -0.1494
 JLD  C07   C  CH2   0  -0.127  -0.8154   2.1107   0.3621
 JLD  O08   O  OH1   0  -0.673  -1.5018   3.1472  -0.3055
 JLD  C09   C  CH2   0  -0.248  -2.8064   0.6011   0.0782
 JLD  C11   C  CR16  0  -0.315   1.8290  -0.3043   1.3747
 JLD  C12   C  CR16  0  -0.395   3.2048  -0.2760   1.1814
 JLD  F14   F  F     0  -0.319   5.0175  -0.2449  -0.3116
 JLD  C16   C  CR16  0  -0.298   1.4758  -0.3352  -0.9872
 JLD  H151  H  HCR6  0   0.276   3.2480  -0.3045  -2.2100
 JLD  H013  H  HCH3  0   0.189  -5.0913  -0.6817   0.7567
 JLD  H011  H  HCH3  0   0.231  -5.1980   0.0144  -0.8676
 JLD  H012  H  HCH3  0   0.231  -5.0717  -1.7331  -0.6670
 JLD  H032  H  HCH2  0   0.235  -3.0287  -2.7201  -0.0719
 JLD  H042  H  HCH2  0   0.239  -0.6527  -2.5387   0.6378
 JLD  H041  H  HCH2  0   0.222  -0.9144  -1.8897  -0.9736
 JLD  H051  H  HCH1  0   0.234  -0.7172  -0.2901   1.6127
 JLD  H061  H  HCH1  0   0.226  -1.1200   0.7156  -1.2293
 JLD  H072  H  HCH2  0   0.186  -0.9738   2.1588   1.4496
 JLD  H071  H  HCH2  0   0.209   0.2669   2.1851   0.1980
 JLD  H081  H  HOH1  0   0.454  -1.1863   3.9864   0.0410
 JLD  H092  H  HCH2  0   0.238  -3.3449   1.3853  -0.4572
 JLD  H091  H  HCH2  0   0.177  -3.0224   0.7471   1.1548
 JLD  H111  H  HCR6  0   0.257   1.4436  -0.3013   2.3874
 JLD  H121  H  HCR6  0   0.277   3.8847  -0.2516   2.0230
 JLD  H161  H  HCR6  0   0.259   0.8171  -0.3549  -1.8469
 JLD  H031  H  HCH2  0   0.185  -2.8445  -1.7524   1.3901
 JLD  C01   C  CH3   0  -0.517  -4.7261  -0.7738  -0.2786

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
 JLD  F14  C13   single    1.345  0.020  1.345
 JLD  C13  C15   aromatic  1.382  0.020  1.382
 JLD  C13  C12   aromatic  1.379  0.020  1.379
 JLD  C15  C16   aromatic  1.387  0.020  1.387
 JLD  C07  O08   single    1.411  0.020  1.411
 JLD  C07  C06   single    1.520  0.020  1.520
 JLD  C12  C11   aromatic  1.390  0.020  1.390
 JLD  C16  C10   aromatic  1.395  0.020  1.395
 JLD  C11  C10   aromatic  1.392  0.020  1.392
 JLD  C10  C05   single    1.509  0.020  1.509
 JLD  C06  C05   single    1.536  0.020  1.536
 JLD  C06  C09   single    1.526  0.020  1.526
 JLD  C05  C04   single    1.531  0.020  1.531
 JLD  C09  N02   single    1.449  0.020  1.449
 JLD  C04  C03   single    1.518  0.020  1.518
 JLD  N02  C03   single    1.449  0.020  1.449
 JLD  N02  C01   single    1.445  0.020  1.445
 JLD  C15  H151  single    0.930  0.020  1.080
 JLD  C01  H013  single    0.970  0.020  1.090
 JLD  C01  H011  single    0.970  0.020  1.090
 JLD  C01  H012  single    0.970  0.020  1.090
 JLD  C03  H031  single    0.970  0.020  1.090
 JLD  C03  H032  single    0.970  0.020  1.090
 JLD  C04  H042  single    0.970  0.020  1.090
 JLD  C04  H041  single    0.970  0.020  1.090
 JLD  C05  H051  single    0.970  0.020  1.090
 JLD  C06  H061  single    0.970  0.020  1.090
 JLD  C07  H072  single    0.970  0.020  1.090
 JLD  C07  H071  single    0.970  0.020  1.090
 JLD  O08  H081  single    0.850  0.020  0.980
 JLD  C09  H092  single    0.970  0.020  1.090
 JLD  C09  H091  single    0.970  0.020  1.090
 JLD  C11  H111  single    0.930  0.020  1.080
 JLD  C12  H121  single    0.930  0.020  1.080
 JLD  C16  H161  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
 JLD  C16   C10  C11   118.00  3.000
 JLD  C11   C10  C05   120.80  3.000
 JLD  C16   C10  C05   121.20  3.000
 JLD  F14   C13  C12   119.09  3.000
 JLD  C12   C13  C15   121.90  3.000
 JLD  F14   C13  C15   119.01  3.000
 JLD  H151  C15  C16   120.90  3.000
 JLD  H151  C15  C13   120.55  3.000
 JLD  C16   C15  C13   118.55  3.000
 JLD  C09   N02  C03   111.31  3.000
 JLD  C03   N02  C01   111.59  3.000
 JLD  C09   N02  C01   111.24  3.000
 JLD  H032  C03  H031  106.59  3.000
 JLD  H032  C03  C04   109.68  3.000
 JLD  H031  C03  C04   109.33  3.000
 JLD  H032  C03  N02   108.79  3.000
 JLD  H031  C03  N02   111.52  3.000
 JLD  C04   C03  N02   110.82  3.000
 JLD  H041  C04  H042  106.94  3.000
 JLD  H041  C04  C05   109.77  3.000
 JLD  H042  C04  C05   109.87  3.000
 JLD  H041  C04  C03   109.27  3.000
 JLD  H042  C04  C03   109.63  3.000
 JLD  C05   C04  C03   111.25  3.000
 JLD  H051  C05  C06   107.30  3.000
 JLD  H051  C05  C04   107.51  3.000
 JLD  C06   C05  C04   109.83  3.000
 JLD  H051  C05  C10   107.46  3.000
 JLD  C04   C05  C10   111.13  3.000
 JLD  C06   C05  C10   113.34  3.000
 JLD  H061  C06  C09   107.98  3.000
 JLD  H061  C06  C07   108.51  3.000
 JLD  C09   C06  C07   111.29  3.000
 JLD  H061  C06  C05   108.54  3.000
 JLD  C09   C06  C05   109.79  3.000
 JLD  C07   C06  C05   110.64  3.000
 JLD  H071  C07  H072  106.68  3.000
 JLD  H071  C07  O08   111.05  3.000
 JLD  H072  C07  O08   111.44  3.000
 JLD  H071  C07  C06   109.17  3.000
 JLD  H072  C07  C06   108.96  3.000
 JLD  O08   C07  C06   109.47  3.000
 JLD  H081  O08  C07   108.13  3.000
 JLD  H091  C09  H092  106.61  3.000
 JLD  H091  C09  C06   108.80  3.000
 JLD  H092  C09  C06   109.51  3.000
 JLD  H091  C09  N02   111.35  3.000
 JLD  H092  C09  N02   108.39  3.000
 JLD  C06   C09  N02   112.02  3.000
 JLD  H111  C11  C12   118.82  3.000
 JLD  H111  C11  C10   119.62  3.000
 JLD  C12   C11  C10   121.56  3.000
 JLD  H121  C12  C11   120.95  3.000
 JLD  H121  C12  C13   120.55  3.000
 JLD  C11   C12  C13   118.49  3.000
 JLD  H161  C16  C15   118.42  3.000
 JLD  H161  C16  C10   120.08  3.000
 JLD  C15   C16  C10   121.50  3.000
 JLD  H012  C01  H011  107.82  3.000
 JLD  H012  C01  H013  107.64  3.000
 JLD  H011  C01  H013  107.66  3.000
 JLD  H012  C01  N02   110.09  3.000
 JLD  H011  C01  N02   110.17  3.000
 JLD  H013  C01  N02   113.28  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
 JLD  CONST_01  C13   C15  C16  C10    0.00   0.0  0
 JLD  CONST_02  C13   C12  C11  C10    0.00   0.0  0
 JLD  CONST_03  C11   C12  C13  C15    0.00   0.0  0
 JLD  CONST_04  C11   C10  C16  C15    0.00   0.0  0
 JLD  CONST_05  C16   C15  C13  C12    0.00   0.0  0
 JLD  CONST_06  C16   C10  C11  C12    0.00   0.0  0
 JLD  CONST_07  C05   C10  C16  C15  180.00   0.0  0
 JLD  CONST_08  C12   C11  C10  C05  180.00   0.0  0
 JLD  CONST_09  F14   C13  C12  C11  180.00   0.0  0
 JLD  CONST_10  C16   C15  C13  F14  180.00   0.0  0
 JLD  CONST_11  H151  C15  C16  C10  180.00   0.0  0
 JLD  CONST_12  H121  C12  C11  C10  180.00   0.0  0
 JLD  CONST_13  H161  C16  C15  C13  180.00   0.0  0
 JLD  CONST_14  H111  C11  C12  C13  180.00   0.0  0
 JLD  Var_01    C05   C04  C03  N02   56.72  30.0  1
 JLD  Var_02    C06   C09  N02  C03   60.23  30.0  1
 JLD  Var_03    C09   N02  C03  C04  -59.66  30.0  1
 JLD  Var_04    H013  C01  N02  C03   63.49  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
 JLD  chir_01  C05  C10  C06  C04  negativ
 JLD  chir_02  C06  C07  C05  C09  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
 JLD  plan-1  C10   0.020
 JLD  plan-1  C13   0.020
 JLD  plan-1  C15   0.020
 JLD  plan-1  C05   0.020
 JLD  plan-1  C11   0.020
 JLD  plan-1  C12   0.020
 JLD  plan-1  F14   0.020
 JLD  plan-1  C16   0.020
 JLD  plan-1  H151  0.020
 JLD  plan-1  H111  0.020
 JLD  plan-1  H121  0.020
 JLD  plan-1  H161  0.020

