# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 20:25:47 2020
#   Inital geometry file: a 83 line input string
#   Ligand name: 2-(2-fluorophenyl)-N-[(5-methylthiophen-2-yl)methyl]ethanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1sc(CNCCc2ccccc2F)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
 49Z  49Z  2-(2-fluorophenyl)-N-[(5-methylthiophen-2-yl)methyl]ethanamine  ligand  33  17  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_49Z
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
 49Z  C16  C  CR16  0  -0.255   5.3980   1.1722   0.4381
 49Z  C17  C  CR16  0  -0.256   5.9226   0.0614  -0.2079
 49Z  C14  C  CR16  0  -0.291   4.0549   1.1973   0.7888
 49Z  C13  C  CR16  0  -0.399   5.1031  -1.0204  -0.5004
 49Z  C4   C  CR15  0  -0.220  -5.1296   1.0815  -0.4015
 49Z  C5   C  CR15  0  -0.229  -3.9089   1.5049  -1.0031
 49Z  C7   C  CR6   0  -0.070   3.2061   0.1282   0.5112
 49Z  C6   C  CR6   0   0.506   3.7722  -0.9611  -0.1364
 49Z  C3   C  CR5   0  -0.169  -4.9771   0.0226   0.4409
 49Z  C2   C  CR5   0  -0.176  -2.8387   0.7599  -0.6176
 49Z  C12  C  CH2   0  -0.522   1.7475   0.1677   0.8663
 49Z  C10  C  CH2   0  -0.308  -1.4144   0.8442  -1.0548
 49Z  C15  C  CH2   0  -0.247   0.8726   0.5232  -0.3341
 49Z  N9   N  NH1   0  -0.601  -0.5229   0.5696   0.0539
 49Z  F8   F  F     0  -0.315   2.9864  -2.0167  -0.4228
 49Z  S1   S  S2    0   0.191  -3.3193  -0.4629   0.5037
 49Z  H1   H  HCR6  0   0.259   6.0332   2.0160   0.6723
 49Z  H2   H  HCR6  0   0.266   6.9679   0.0305  -0.4849
 49Z  H3   H  HCR6  0   0.259   3.6481   2.0656   1.2934
 49Z  H4   H  HCR6  0   0.276   5.4908  -1.8985  -1.0005
 49Z  H5   H  HCR5  0   0.255  -6.0857   1.5550  -0.5813
 49Z  H6   H  HCR5  0   0.255  -3.8336   2.3305  -1.6978
 49Z  H7   H  HCH3  0   0.250  -6.0344  -1.7422   1.0706
 49Z  H8   H  HCH3  0   0.251  -5.8514  -0.5270   2.3281
 49Z  H9   H  HCH3  0   0.253  -7.0010  -0.2708   1.0187
 49Z  H10  H  HCH2  0   0.250   1.4183  -0.7887   1.2776
 49Z  H11  H  HCH2  0   0.250   1.5984   0.9145   1.6503
 49Z  H12  H  HCH2  0   0.247  -1.2224   0.0938  -1.8289
 49Z  H13  H  HCH2  0   0.222  -1.2498   1.8228  -1.5294
 49Z  H14  H  HCH2  0   0.204   1.2269   1.4684  -0.7729
 49Z  H15  H  HCH2  0   0.229   0.9847  -0.2399  -1.1089
 49Z  H16  H  HNH1  0   0.347  -0.6495   1.2837   0.7624
 49Z  C11  C  CH3   0  -0.714  -6.0157  -0.6680   1.2586

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
 49Z  C11  C3   single    1.491  0.020  1.491
 49Z  C3   C4   aromatic  1.362  0.020  1.362
 49Z  C3   S1   aromatic  1.729  0.020  1.729
 49Z  C4   C5   aromatic  1.425  0.020  1.425
 49Z  C5   C2   aromatic  1.360  0.020  1.360
 49Z  S1   C2   aromatic  1.727  0.020  1.727
 49Z  C2   C10  single    1.492  0.020  1.492
 49Z  C10  N9   single    1.449  0.020  1.449
 49Z  N9   C15  single    1.449  0.020  1.449
 49Z  C15  C12  single    1.527  0.020  1.527
 49Z  C12  C7   single    1.502  0.020  1.502
 49Z  C14  C7   aromatic  1.393  0.020  1.393
 49Z  C14  C16  aromatic  1.388  0.020  1.388
 49Z  C7   C6   aromatic  1.388  0.020  1.388
 49Z  C16  C17  aromatic  1.388  0.020  1.388
 49Z  C6   F8   single    1.347  0.020  1.347
 49Z  C6   C13  aromatic  1.381  0.020  1.381
 49Z  C17  C13  aromatic  1.388  0.020  1.388
 49Z  C16  H1   single    0.930  0.020  1.080
 49Z  C17  H2   single    0.930  0.020  1.080
 49Z  C14  H3   single    0.930  0.020  1.080
 49Z  C13  H4   single    0.930  0.020  1.080
 49Z  C4   H5   single    0.930  0.020  1.080
 49Z  C5   H6   single    0.930  0.020  1.080
 49Z  C11  H7   single    0.970  0.020  1.090
 49Z  C11  H8   single    0.970  0.020  1.090
 49Z  C11  H9   single    0.970  0.020  1.090
 49Z  C12  H10  single    0.970  0.020  1.090
 49Z  C12  H11  single    0.970  0.020  1.090
 49Z  C10  H12  single    0.970  0.020  1.090
 49Z  C10  H13  single    0.970  0.020  1.090
 49Z  C15  H14  single    0.970  0.020  1.090
 49Z  C15  H15  single    0.970  0.020  1.090
 49Z  N9   H16  single    0.890  0.020  1.040

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
 49Z  H1   C16  C14  119.95  3.000
 49Z  H1   C16  C17  120.21  3.000
 49Z  C14  C16  C17  119.85  3.000
 49Z  H2   C17  C13  119.62  3.000
 49Z  H2   C17  C16  120.48  3.000
 49Z  C13  C17  C16  119.91  3.000
 49Z  H3   C14  C7   118.62  3.000
 49Z  H3   C14  C16  119.69  3.000
 49Z  C7   C14  C16  121.68  3.000
 49Z  H4   C13  C6   120.12  3.000
 49Z  H4   C13  C17  121.21  3.000
 49Z  C6   C13  C17  118.68  3.000
 49Z  H5   C4   C3   122.83  3.000
 49Z  H5   C4   C5   123.82  3.000
 49Z  C3   C4   C5   113.34  3.000
 49Z  H6   C5   C2   123.06  3.000
 49Z  H6   C5   C4   123.88  3.000
 49Z  C2   C5   C4   113.06  3.000
 49Z  C12  C7   C6   121.81  3.000
 49Z  C6   C7   C14  116.54  3.000
 49Z  C12  C7   C14  121.64  3.000
 49Z  F8   C6   C7   118.45  3.000
 49Z  F8   C6   C13  118.20  3.000
 49Z  C7   C6   C13  123.35  3.000
 49Z  S1   C3   C11  121.19  3.000
 49Z  S1   C3   C4   110.39  3.000
 49Z  C11  C3   C4   128.41  3.000
 49Z  S1   C2   C10  119.72  3.000
 49Z  C10  C2   C5   129.58  3.000
 49Z  S1   C2   C5   110.67  3.000
 49Z  H11  C12  H10  106.68  3.000
 49Z  H11  C12  C15  109.06  3.000
 49Z  H10  C12  C15  109.10  3.000
 49Z  H11  C12  C7   108.67  3.000
 49Z  H10  C12  C7   111.03  3.000
 49Z  C15  C12  C7   112.13  3.000
 49Z  H13  C10  H12  106.16  3.000
 49Z  H13  C10  N9   113.99  3.000
 49Z  H12  C10  N9   107.65  3.000
 49Z  H13  C10  C2   108.63  3.000
 49Z  H12  C10  C2   109.62  3.000
 49Z  N9   C10  C2   110.63  3.000
 49Z  H15  C15  H14  106.49  3.000
 49Z  H15  C15  N9   108.11  3.000
 49Z  H14  C15  N9   112.90  3.000
 49Z  H15  C15  C12  109.62  3.000
 49Z  H14  C15  C12  109.20  3.000
 49Z  N9   C15  C12  110.41  3.000
 49Z  H16  N9   C15  109.26  3.000
 49Z  H16  N9   C10  108.93  3.000
 49Z  C15  N9   C10  113.19  3.000
 49Z  C2   S1   C3    92.54  3.000
 49Z  H9   C11  H8   107.75  3.000
 49Z  H9   C11  H7   107.80  3.000
 49Z  H8   C11  H7   107.39  3.000
 49Z  H9   C11  C3   109.90  3.000
 49Z  H8   C11  C3   111.88  3.000
 49Z  H7   C11  C3   111.93  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
 49Z  CONST_01  C6   C7   C14  C16     0.00   0.0  0
 49Z  CONST_02  C6   C13  C17  C16     0.00   0.0  0
 49Z  CONST_03  C7   C14  C16  C17     0.00   0.0  0
 49Z  CONST_04  C7   C6   C13  C17     0.00   0.0  0
 49Z  CONST_05  C13  C6   C7   C14     0.00   0.0  0
 49Z  CONST_06  C13  C17  C16  C14     0.00   0.0  0
 49Z  CONST_07  C2   S1   C3   C4      0.00   0.0  0
 49Z  CONST_08  S1   C2   C5   C4      0.00   0.0  0
 49Z  CONST_09  S1   C3   C4   C5      0.00   0.0  0
 49Z  CONST_10  C3   S1   C2   C5      0.00   0.0  0
 49Z  CONST_11  C2   C5   C4   C3      0.00   0.0  0
 49Z  CONST_12  C12  C7   C14  C16   180.00   0.0  0
 49Z  CONST_13  F8   C6   C13  C17   180.00   0.0  0
 49Z  CONST_14  F8   C6   C7   C14   180.00   0.0  0
 49Z  CONST_15  C12  C7   C6   C13   180.00   0.0  0
 49Z  CONST_16  C10  C2   C5   C4    180.00   0.0  0
 49Z  CONST_17  C11  C3   C4   C5    180.00   0.0  0
 49Z  CONST_18  C10  C2   S1   C3    180.00   0.0  0
 49Z  CONST_19  C11  C3   S1   C2    180.00   0.0  0
 49Z  CONST_20  H4   C13  C17  C16   180.00   0.0  0
 49Z  CONST_21  H3   C14  C16  C17   180.00   0.0  0
 49Z  CONST_22  H2   C17  C16  C14   180.00   0.0  0
 49Z  CONST_23  H1   C16  C17  C13   180.00   0.0  0
 49Z  CONST_24  H6   C5   C4   C3    180.00   0.0  0
 49Z  CONST_25  H5   C4   C5   C2    180.00   0.0  0
 49Z  Var_01    C15  C12  C7   C14    99.45  30.0  2
 49Z  Var_02    N9   C10  C2   C5    143.59  30.0  2
 49Z  Var_03    H7   C11  C3   C4    125.81  30.0  2
 49Z  Var_04    N9   C15  C12  C7   -179.18  30.0  1
 49Z  Var_05    C15  N9   C10  C2    175.00  30.0  3
 49Z  Var_06    C10  N9   C15  C12  -177.42  30.0  1

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
 49Z  plan-1  C4   0.020
 49Z  plan-1  C5   0.020
 49Z  plan-1  C3   0.020
 49Z  plan-1  C2   0.020
 49Z  plan-1  C10  0.020
 49Z  plan-1  S1   0.020
 49Z  plan-1  H5   0.020
 49Z  plan-1  H6   0.020
 49Z  plan-1  C11  0.020
 49Z  plan-2  C16  0.020
 49Z  plan-2  C17  0.020
 49Z  plan-2  C14  0.020
 49Z  plan-2  C13  0.020
 49Z  plan-2  C7   0.020
 49Z  plan-2  C6   0.020
 49Z  plan-2  C12  0.020
 49Z  plan-2  F8   0.020
 49Z  plan-2  H1   0.020
 49Z  plan-2  H2   0.020
 49Z  plan-2  H3   0.020
 49Z  plan-2  H4   0.020

