# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 02:37:35 2020
#   Inital geometry file: a 99 line input string
#   Ligand name: (3~{S},4~{S})-4-(3,4-dimethylphenoxy)-1-prop-2-ynyl-piperidin-3-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(O[C@H]2CCN(CC#C)C[C@@H]2O)cc1C
#
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
 JMN  JMN  (3~{S},4~{S})-4-(3,4-dimethylphenoxy)-1-prop-2-ynyl-piperidin-3-ol  ligand  40  19  .  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_JMN
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
 JMN  C1   C  CH1   0   0.006  -0.5796  -0.5114   0.2244
 JMN  C3   C  CH1   0   0.052  -1.5465  -1.6709   0.0716
 JMN  O2   O  O2    0  -0.495   0.6459  -0.8916  -0.3776
 JMN  C12  C  CR6   0   0.089   4.1659  -0.0640  -0.5291
 JMN  C13  C  CR16  0  -0.289   3.1501   1.3336   1.1270
 JMN  C15  C  CR6   0   0.047   4.2906   0.9444   0.4407
 JMN  C16  C  CH3   0  -0.737   5.3664  -0.5260  -1.3017
 JMN  C17  C  CSP   0   0.279  -5.4337   1.1851  -0.4745
 JMN  C18  C  CH3   0  -0.735   5.6200   1.5774   0.7310
 JMN  C19  C  CSP1  0  -0.551  -5.9752   2.0038  -1.1679
 JMN  C4   C  CH2   0  -0.482  -1.1656   0.7323  -0.4300
 JMN  C5   C  CR6   0   0.393   1.7876  -0.2400  -0.0641
 JMN  C6   C  CH2   0  -0.329  -2.9079  -1.2637   0.6351
 JMN  O7   O  OH1   0  -0.667  -1.0239  -2.7789   0.7617
 JMN  C8   C  CH2   0  -0.292  -2.5434   1.0428   0.1295
 JMN  C9   C  CR16  0  -0.408   2.9260  -0.6367  -0.7685
 JMN  C10  C  CR16  0  -0.381   1.9037   0.7611   0.8923
 JMN  N11  N  NT    0  -0.426  -3.4286  -0.0951  -0.0465
 JMN  H1   H  HCH1  0   0.227  -0.4374  -0.3367   1.3000
 JMN  H2   H  HCH1  0   0.213  -1.6688  -1.8867  -0.9995
 JMN  H3   H  HCR6  0   0.247   3.2230   2.1139   1.8754
 JMN  H4   H  HCH2  0   0.243  -4.8367   0.5361   1.4247
 JMN  H5   H  HCH2  0   0.280  -5.3693  -0.7318   0.3340
 JMN  H6   H  HCH3  0   0.245   6.1047  -0.9938  -0.6469
 JMN  H7   H  HCH3  0   0.250   5.0958  -1.2536  -2.0653
 JMN  H8   H  HCH3  0   0.242   5.8691   0.3060  -1.7978
 JMN  H9   H  HCH3  0   0.238   6.0725   2.0090  -0.1644
 JMN  H10  H  HCH3  0   0.247   5.5243   2.3732   1.4685
 JMN  H11  H  HCH3  0   0.240   6.3357   0.8512   1.1238
 JMN  H12  H  H     0   0.280  -6.4549   2.7321  -1.7808
 JMN  H13  H  HCH2  0   0.257  -0.5137   1.5943  -0.2782
 JMN  H14  H  HCH2  0   0.240  -1.2398   0.5688  -1.5085
 JMN  H15  H  HCH2  0   0.251  -3.6068  -2.0938   0.4978
 JMN  H16  H  HCH2  0   0.204  -2.8103  -1.1023   1.7232
 JMN  H17  H  HOH1  0   0.455  -1.5844  -3.5399   0.5805
 JMN  H18  H  HCH2  0   0.203  -2.4617   1.3288   1.1927
 JMN  H19  H  HCH2  0   0.255  -2.9560   1.9046  -0.3980
 JMN  H20  H  HCR6  0   0.249   2.8306  -1.4165  -1.5157
 JMN  H21  H  HCR6  0   0.268   1.0568   1.1130   1.4652
 JMN  C14  C  CH2   0  -0.407  -4.7857   0.1915   0.3787

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
 JMN  C16  C12  single    1.500  0.020  1.500
 JMN  C18  C15  single    1.501  0.020  1.501
 JMN  C12  C15  aromatic  1.405  0.020  1.405
 JMN  C12  C9   aromatic  1.387  0.020  1.387
 JMN  C15  C13  aromatic  1.387  0.020  1.387
 JMN  C9   C5   aromatic  1.396  0.020  1.396
 JMN  C13  C10  aromatic  1.391  0.020  1.391
 JMN  C5   C10  aromatic  1.389  0.020  1.389
 JMN  C5   O2   single    1.351  0.020  1.351
 JMN  O2   C1   single    1.417  0.020  1.417
 JMN  C1   C3   single    1.517  0.020  1.517
 JMN  C1   C4   single    1.523  0.020  1.523
 JMN  C3   O7   single    1.406  0.020  1.406
 JMN  C3   C6   single    1.529  0.020  1.529
 JMN  C4   C8   single    1.519  0.020  1.519
 JMN  C6   N11  single    1.450  0.020  1.450
 JMN  C8   N11  single    1.452  0.020  1.452
 JMN  N11  C14  single    1.451  0.020  1.451
 JMN  C17  C14  single    1.461  0.020  1.461
 JMN  C17  C19  triple    1.202  0.020  1.202
 JMN  C1   H1   single    0.939  0.020  1.096
 JMN  C3   H2   single    0.939  0.020  1.096
 JMN  C13  H3   single    0.929  0.020  1.085
 JMN  C14  H4   single    0.939  0.020  1.096
 JMN  C14  H5   single    0.939  0.020  1.096
 JMN  C16  H6   single    0.939  0.020  1.096
 JMN  C16  H7   single    0.939  0.020  1.096
 JMN  C16  H8   single    0.939  0.020  1.096
 JMN  C18  H9   single    0.939  0.020  1.096
 JMN  C18  H10  single    0.939  0.020  1.096
 JMN  C18  H11  single    0.939  0.020  1.096
 JMN  C19  H12  single    0.913  0.020  1.066
 JMN  C4   H13  single    0.939  0.020  1.096
 JMN  C4   H14  single    0.939  0.020  1.096
 JMN  C6   H15  single    0.939  0.020  1.096
 JMN  C6   H16  single    0.939  0.020  1.096
 JMN  O7   H17  single    0.832  0.020  0.971
 JMN  C8   H18  single    0.939  0.020  1.096
 JMN  C8   H19  single    0.939  0.020  1.096
 JMN  C9   H20  single    0.929  0.020  1.085
 JMN  C10  H21  single    0.929  0.020  1.085

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
 JMN  H1   C1   C4   109.91  3.000
 JMN  H1   C1   O2   110.28  3.000
 JMN  C4   C1   O2   111.68  3.000
 JMN  H1   C1   C3   107.60  3.000
 JMN  C4   C1   C3   109.61  3.000
 JMN  O2   C1   C3   107.65  3.000
 JMN  H2   C3   O7   111.40  3.000
 JMN  H2   C3   C6   108.20  3.000
 JMN  O7   C3   C6   111.10  3.000
 JMN  H2   C3   C1   108.60  3.000
 JMN  C6   C3   C1   109.08  3.000
 JMN  O7   C3   C1   108.42  3.000
 JMN  C5   O2   C1   120.17  3.000
 JMN  C9   C12  C16  119.96  3.000
 JMN  C9   C12  C15  119.67  3.000
 JMN  C16  C12  C15  120.37  3.000
 JMN  H3   C13  C10  118.23  3.000
 JMN  H3   C13  C15  119.24  3.000
 JMN  C10  C13  C15  122.53  3.000
 JMN  C18  C15  C13  120.96  3.000
 JMN  C13  C15  C12  118.04  3.000
 JMN  C18  C15  C12  121.00  3.000
 JMN  H8   C16  H7   107.76  3.000
 JMN  H8   C16  H6   106.72  3.000
 JMN  H7   C16  H6   107.59  3.000
 JMN  H8   C16  C12  111.58  3.000
 JMN  H7   C16  C12  111.60  3.000
 JMN  H6   C16  C12  111.35  3.000
 JMN  C19  C17  C14  180.00  3.000
 JMN  H11  C18  H10  107.45  3.000
 JMN  H11  C18  H9   106.61  3.000
 JMN  H10  C18  H9   107.63  3.000
 JMN  H11  C18  C15  111.68  3.000
 JMN  H10  C18  C15  111.18  3.000
 JMN  H9   C18  C15  112.03  3.000
 JMN  H12  C19  C17  180.00  3.000
 JMN  H14  C4   H13  107.21  3.000
 JMN  H14  C4   C8   109.40  3.000
 JMN  H13  C4   C8   109.21  3.000
 JMN  H14  C4   C1   109.14  3.000
 JMN  H13  C4   C1   110.82  3.000
 JMN  C8   C4   C1   110.96  3.000
 JMN  C10  C5   C9   118.93  3.000
 JMN  C10  C5   O2   125.29  3.000
 JMN  C9   C5   O2   115.77  3.000
 JMN  H16  C6   H15  106.92  3.000
 JMN  H16  C6   N11  112.16  3.000
 JMN  H15  C6   N11  108.86  3.000
 JMN  H16  C6   C3   108.87  3.000
 JMN  H15  C6   C3   108.70  3.000
 JMN  N11  C6   C3   111.18  3.000
 JMN  H17  O7   C3   108.32  3.000
 JMN  H19  C8   H18  106.79  3.000
 JMN  H19  C8   N11  109.25  3.000
 JMN  H18  C8   N11  111.39  3.000
 JMN  H19  C8   C4   109.04  3.000
 JMN  H18  C8   C4   109.91  3.000
 JMN  N11  C8   C4   110.36  3.000
 JMN  H20  C9   C5   118.70  3.000
 JMN  H20  C9   C12  119.65  3.000
 JMN  C5   C9   C12  121.65  3.000
 JMN  H21  C10  C5   122.25  3.000
 JMN  H21  C10  C13  118.58  3.000
 JMN  C5   C10  C13  119.17  3.000
 JMN  C8   N11  C6   110.84  3.000
 JMN  C8   N11  C14  112.32  3.000
 JMN  C6   N11  C14  110.95  3.000
 JMN  H5   C14  H4   106.15  3.000
 JMN  H5   C14  N11  108.70  3.000
 JMN  H4   C14  N11  112.53  3.000
 JMN  H5   C14  C17  108.28  3.000
 JMN  H4   C14  C17  108.72  3.000
 JMN  N11  C14  C17  112.21  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
 JMN  CONST_01  C10  C13  C15  C12     0.00   0.0  0
 JMN  CONST_02  C10  C5   C9   C12     0.00   0.0  0
 JMN  CONST_03  C9   C12  C15  C13     0.00   0.0  0
 JMN  CONST_04  C9   C5   C10  C13     0.00   0.0  0
 JMN  CONST_05  C5   C9   C12  C15     0.00   0.0  0
 JMN  CONST_06  C5   C10  C13  C15     0.00   0.0  0
 JMN  CONST_07  C12  C9   C5   O2    180.00   0.0  0
 JMN  CONST_08  C13  C10  C5   O2    180.00   0.0  0
 JMN  CONST_09  C16  C12  C15  C13   180.00   0.0  0
 JMN  CONST_10  C5   C9   C12  C16   180.00   0.0  0
 JMN  CONST_11  C9   C12  C15  C18   180.00   0.0  0
 JMN  CONST_12  C10  C13  C15  C18   180.00   0.0  0
 JMN  CONST_13  H3   C13  C15  C12   180.00   0.0  0
 JMN  CONST_14  H20  C9   C12  C15   180.00   0.0  0
 JMN  CONST_15  H21  C10  C13  C15   180.00   0.0  0
 JMN  Var_01    N11  C8   C4   C1    -56.92  30.0  1
 JMN  Var_02    C8   N11  C6   C3    -61.34  30.0  1
 JMN  Var_03    C6   N11  C8   C4     59.77  30.0  1
 JMN  Var_04    C9   C5   O2   C1   -176.35  30.0  2
 JMN  Var_05    H9   C18  C15  C12    56.48  30.0  2
 JMN  Var_06    H6   C16  C12  C15    64.14  30.0  2
 JMN  Var_07    N11  C14  C17  C19  -165.00  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
 JMN  chir_01  C1  O2  C3  C4  positiv
 JMN  chir_02  C3  O7  C1  C6  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
 JMN  plan-1  O2   0.020
 JMN  plan-1  C12  0.020
 JMN  plan-1  C13  0.020
 JMN  plan-1  C15  0.020
 JMN  plan-1  C16  0.020
 JMN  plan-1  C18  0.020
 JMN  plan-1  C5   0.020
 JMN  plan-1  C9   0.020
 JMN  plan-1  C10  0.020
 JMN  plan-1  H3   0.020
 JMN  plan-1  H20  0.020
 JMN  plan-1  H21  0.020

