# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 20:51:42 2020
#   Inital geometry file: a 75 line input string
#   Ligand name: 1-(4-fluorophenyl)-~{N}-[[(2~{R})-oxolan-2-yl]methyl]methanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1ccc(CNC[C@H]2CCCO2)cc1
#
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
 AXS  AXS  1-(4-fluorophenyl)-~{N}-[[(2~{R})-oxolan-2-yl]methyl]methanamine  ligand  31  15  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_AXS
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
 AXS  N1   N  NH1   0  -0.594   0.7173  -0.4990   0.1444
 AXS  C4   C  CR16  0  -0.397  -4.0748  -1.0236  -0.0048
 AXS  C5   C  CR16  0  -0.292  -2.7938  -1.5360  -0.1615
 AXS  C6   C  CR6   0   0.065  -1.6878  -0.6999  -0.2831
 AXS  C7   C  CH2   0  -0.300  -0.3144  -1.2787  -0.5032
 AXS  C8   C  CH2   0  -0.268   2.0507  -0.9937  -0.1258
 AXS  C10  C  CH2   0  -0.503   4.5252  -0.7106   0.3552
 AXS  C1   C  CR16  0  -0.279  -1.8905   0.6776  -0.2316
 AXS  C2   C  CR16  0  -0.396  -3.1617   1.2111  -0.0716
 AXS  C3   C  CR6   0   0.507  -4.2344   0.3470   0.0361
 AXS  C9   C  CH1   0   0.047   3.1158  -0.1365   0.5306
 AXS  C11  C  CH2   0  -0.488   5.3804   0.5380   0.1808
 AXS  C12  C  CH2   0  -0.162   4.4217   1.4420  -0.5750
 AXS  O1   O  O2    0  -0.502   3.1417   1.1741  -0.0282
 AXS  F1   F  F     0  -0.319  -5.4698   0.8561   0.1897
 AXS  H1   H  HNH1  0   0.341   0.5581  -0.5034   1.1458
 AXS  H4   H  HCR6  0   0.259  -2.6588  -2.6108  -0.1856
 AXS  H5   H  HCH2  0   0.241  -0.1023  -1.2845  -1.5783
 AXS  H6   H  HCH2  0   0.212  -0.3179  -2.3372  -0.1988
 AXS  H7   H  HCH2  0   0.197   2.1975  -2.0346   0.2073
 AXS  H8   H  HCH2  0   0.222   2.2106  -0.9949  -1.2096
 AXS  H9   H  HCH2  0   0.252   4.8242  -1.3298   1.2002
 AXS  H10  H  HCH2  0   0.234   4.5762  -1.3333  -0.5427
 AXS  H11  H  HCR6  0   0.259  -1.0417   1.3441  -0.3097
 AXS  H12  H  HCR6  0   0.276  -3.3135   2.2821  -0.0324
 AXS  H13  H  HCH1  0   0.212   2.8829  -0.0416   1.6005
 AXS  H14  H  HCH2  0   0.235   5.6369   0.9727   1.1495
 AXS  H15  H  HCH2  0   0.245   6.3070   0.3551  -0.3629
 AXS  H16  H  HCH2  0   0.225   4.6412   2.5052  -0.4570
 AXS  H17  H  HCH2  0   0.197   4.4457   1.2124  -1.6486
 AXS  H3   H  HCR6  0   0.277  -4.9285  -1.6817   0.0903

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
 AXS  C11  C12  single    1.519  0.020  1.519
 AXS  C11  C10  single    1.523  0.020  1.523
 AXS  C12  O1   single    1.417  0.020  1.417
 AXS  C10  C9   single    1.532  0.020  1.532
 AXS  O1   C9   single    1.425  0.020  1.425
 AXS  C9   C8   single    1.517  0.020  1.517
 AXS  C8   N1   single    1.448  0.020  1.448
 AXS  N1   C7   single    1.446  0.020  1.446
 AXS  C7   C6   single    1.507  0.020  1.507
 AXS  C6   C1   aromatic  1.393  0.020  1.393
 AXS  C6   C5   aromatic  1.392  0.020  1.392
 AXS  C1   C2   aromatic  1.388  0.020  1.388
 AXS  C5   C4   aromatic  1.389  0.020  1.389
 AXS  C2   C3   aromatic  1.382  0.020  1.382
 AXS  C4   C3   aromatic  1.380  0.020  1.380
 AXS  C3   F1   single    1.345  0.020  1.345
 AXS  N1   H1   single    0.890  0.020  1.040
 AXS  C4   H3   single    0.930  0.020  1.080
 AXS  C5   H4   single    0.930  0.020  1.080
 AXS  C7   H5   single    0.970  0.020  1.090
 AXS  C7   H6   single    0.970  0.020  1.090
 AXS  C8   H7   single    0.970  0.020  1.090
 AXS  C8   H8   single    0.970  0.020  1.090
 AXS  C10  H9   single    0.970  0.020  1.090
 AXS  C10  H10  single    0.970  0.020  1.090
 AXS  C1   H11  single    0.930  0.020  1.080
 AXS  C2   H12  single    0.930  0.020  1.080
 AXS  C9   H13  single    0.970  0.020  1.090
 AXS  C11  H14  single    0.970  0.020  1.090
 AXS  C11  H15  single    0.970  0.020  1.090
 AXS  C12  H16  single    0.970  0.020  1.090
 AXS  C12  H17  single    0.970  0.020  1.090

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
 AXS  H1   N1   C8   109.12  3.000
 AXS  H1   N1   C7   109.14  3.000
 AXS  C8   N1   C7   112.91  3.000
 AXS  H3   C4   C3   120.67  3.000
 AXS  H3   C4   C5   120.88  3.000
 AXS  C3   C4   C5   118.45  3.000
 AXS  H4   C5   C6   119.67  3.000
 AXS  H4   C5   C4   118.91  3.000
 AXS  C6   C5   C4   121.42  3.000
 AXS  C1   C6   C7   121.19  3.000
 AXS  C1   C6   C5   118.37  3.000
 AXS  C7   C6   C5   120.42  3.000
 AXS  H6   C7   H5   105.47  3.000
 AXS  H6   C7   C6   109.03  3.000
 AXS  H5   C7   C6   108.77  3.000
 AXS  H6   C7   N1   113.36  3.000
 AXS  H5   C7   N1   107.70  3.000
 AXS  C6   C7   N1   112.19  3.000
 AXS  H8   C8   H7   106.16  3.000
 AXS  H8   C8   C9   109.05  3.000
 AXS  H7   C8   C9   108.02  3.000
 AXS  H8   C8   N1   108.63  3.000
 AXS  H7   C8   N1   112.88  3.000
 AXS  C9   C8   N1   111.90  3.000
 AXS  H10  C10  H9   107.48  3.000
 AXS  H10  C10  C11  110.27  3.000
 AXS  H9   C10  C11  113.61  3.000
 AXS  H10  C10  C9   110.50  3.000
 AXS  H9   C10  C9   112.13  3.000
 AXS  C11  C10  C9   102.85  3.000
 AXS  H11  C1   C2   119.34  3.000
 AXS  H11  C1   C6   119.49  3.000
 AXS  C2   C1   C6   121.17  3.000
 AXS  H12  C2   C3   120.47  3.000
 AXS  H12  C2   C1   120.86  3.000
 AXS  C3   C2   C1   118.67  3.000
 AXS  F1   C3   C2   119.03  3.000
 AXS  F1   C3   C4   119.04  3.000
 AXS  C2   C3   C4   121.93  3.000
 AXS  H13  C9   O1   107.83  3.000
 AXS  H13  C9   C10  109.81  3.000
 AXS  O1   C9   C10  106.44  3.000
 AXS  H13  C9   C8   108.75  3.000
 AXS  O1   C9   C8   111.28  3.000
 AXS  C10  C9   C8   112.63  3.000
 AXS  H15  C11  H14  108.03  3.000
 AXS  H15  C11  C12  112.85  3.000
 AXS  H14  C11  C12  110.65  3.000
 AXS  H15  C11  C10  113.38  3.000
 AXS  H14  C11  C10  110.88  3.000
 AXS  C12  C11  C10  100.97  3.000
 AXS  H17  C12  H16  107.75  3.000
 AXS  H17  C12  O1   110.94  3.000
 AXS  H16  C12  O1   108.90  3.000
 AXS  H17  C12  C11  110.38  3.000
 AXS  H16  C12  C11  113.50  3.000
 AXS  O1   C12  C11  105.40  3.000
 AXS  C12  O1   C9   109.97  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
 AXS  CONST_01  C1   C6   C5   C4      0.00   0.0  0
 AXS  CONST_02  C1   C2   C3   C4      0.00   0.0  0
 AXS  CONST_03  C2   C1   C6   C5      0.00   0.0  0
 AXS  CONST_04  C2   C3   C4   C5      0.00   0.0  0
 AXS  CONST_05  C3   C2   C1   C6      0.00   0.0  0
 AXS  CONST_06  C3   C4   C5   C6      0.00   0.0  0
 AXS  CONST_07  C7   C6   C5   C4    180.00   0.0  0
 AXS  CONST_08  F1   C3   C4   C5    180.00   0.0  0
 AXS  CONST_09  C2   C1   C6   C7    180.00   0.0  0
 AXS  CONST_10  F1   C3   C2   C1    180.00   0.0  0
 AXS  CONST_11  H12  C2   C3   C4    180.00   0.0  0
 AXS  CONST_12  H11  C1   C6   C5    180.00   0.0  0
 AXS  CONST_13  H3   C4   C5   C6    180.00   0.0  0
 AXS  CONST_14  H4   C5   C6   C1    180.00   0.0  0
 AXS  Var_01    O1   C12  C11  C10    36.93  30.0  1
 AXS  Var_02    C12  C11  C10  C9    -34.48  30.0  1
 AXS  Var_03    C11  C12  O1   C9    -24.94  30.0  1
 AXS  Var_04    C1   C6   C7   N1     35.93  30.0  2
 AXS  Var_05    C8   N1   C7   C6   -176.39  30.0  1
 AXS  Var_06    C9   C8   N1   C7    178.34  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
 AXS  chir_01  C9  C10  O1  C8  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
 AXS  plan-1  C4   0.020
 AXS  plan-1  C5   0.020
 AXS  plan-1  C6   0.020
 AXS  plan-1  C7   0.020
 AXS  plan-1  C1   0.020
 AXS  plan-1  C2   0.020
 AXS  plan-1  C3   0.020
 AXS  plan-1  F1   0.020
 AXS  plan-1  H4   0.020
 AXS  plan-1  H11  0.020
 AXS  plan-1  H12  0.020
 AXS  plan-1  H3   0.020

