# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 15:52:02 2020
#   Inital geometry file: a 129 line input string
#   Ligand name: 2-{(R)-(3-aminophenyl)[2-(piperidin-1-yl)ethoxy]methyl}thieno[3,2-b]pyridine-7-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1cccc(c1)[C@@H](OCCN2CCCCC2)c3sc4c(c3)nccc4C(O)=O
#
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
 H6V  H6V  '2-{(R)-(3-aminophenyl)[2-(piperidin-1-yl)ethoxy]methyl}thieno[3,2-b]pyridine-7-carboxylic acid'  ligand  53  29  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_H6V
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
 H6V  C02  C  C      0   0.417   1.7980   3.9270  -0.7809
 H6V  C04  C  C      0  -0.001   2.5766   2.6221  -0.8058
 H6V  C05  C  CR5    0  -0.239   1.9232   1.3961  -0.7395
 H6V  C06  C  CR5    0   0.270   2.6632   0.1974  -0.7716
 H6V  C07  C  CR15   0  -0.234   1.8191  -0.9593  -0.6931
 H6V  C08  C  CR5    0  -0.197   0.5131  -0.6239  -0.6051
 H6V  C09  C  CH1    0  -0.007  -0.6927  -1.5168  -0.6008
 H6V  C10  C  CR6    0   0.086  -0.3831  -2.8907  -0.0527
 H6V  C11  C  CR16   0  -0.327  -0.3898  -3.1216   1.3195
 H6V  C12  C  CR16   0  -0.237  -0.0639  -4.3865   1.7882
 H6V  C13  C  CR16   0  -0.335   0.2710  -5.4113   0.9167
 H6V  C14  C  CR6    0   0.318   0.2796  -5.1892  -0.4646
 H6V  C20  C  CR16   0  -0.376  -0.0580  -3.9124  -0.9311
 H6V  C23  C  CH2    0  -0.295  -3.9557  -0.2981   0.5615
 H6V  C25  C  CH2    0  -0.272  -4.5557   1.8861   1.2963
 H6V  C26  C  CH2    0  -0.435  -4.1831   3.3602   1.3051
 H6V  C27  C  CH2    0  -0.439  -4.1851   3.9239  -0.1095
 H6V  C28  C  CH2    0  -0.449  -3.2971   3.0666  -1.0012
 H6V  C29  C  CH2    0  -0.273  -3.6948   1.6001  -0.9237
 H6V  C32  C  C1     0  -0.095   4.6119   1.3392  -0.9262
 H6V  C33  C  C1     0  -0.391   3.9571   2.5720  -0.9043
 H6V  N15  N  NH2    0  -0.861   0.5528  -6.2122  -1.3479
 H6V  N24  N  NT     0  -0.401  -3.6694   1.1156   0.4438
 H6V  N31  N  N      0  -0.439   3.9950   0.1715  -0.8627
 H6V  O01  O  OC    -1  -0.578   2.4512   4.9786  -0.8701
 H6V  O03  O  O      0  -0.566   0.5630   3.7960  -0.6745
 H6V  O21  O  O2     0  -0.482  -1.6778  -0.8404   0.1299
 H6V  S30  S  S2     0   0.241   0.2259   1.0980  -0.5959
 H6V  H1   H  HCR5   0   0.259   2.1923  -1.9739  -0.7101
 H6V  H2   H  HCH1   0   0.251  -1.0170  -1.6297  -1.6489
 H6V  H3   H  HCR6   0   0.242  -0.6459  -2.3300   2.0113
 H6V  H4   H  HCR6   0   0.250  -0.0653  -4.5811   2.8536
 H6V  H5   H  HCR6   0   0.254   0.5257  -6.3910   1.3042
 H6V  H6   H  HCR6   0   0.252  -0.0679  -3.7227  -1.9999
 H6V  H7   H  HCH2   0   0.226  -3.2165  -2.2369   0.0734
 H6V  H8   H  HCH2   0   0.213  -3.1546  -1.1142  -1.2827
 H6V  H9   H  HCH2   0   0.193  -4.9744  -0.5547   0.2192
 H6V  H10  H  HCH2   0   0.232  -3.9149  -0.5612   1.6231
 H6V  H13  H  HCH2   0   0.226  -4.8808   3.9048   1.9455
 H6V  H14  H  HCH2   0   0.212  -3.1872   3.4759   1.7432
 H6V  H15  H  HCH2   0   0.206  -5.2087   3.9242  -0.5001
 H6V  H16  H  HCH2   0   0.227  -3.8492   4.9634  -0.1114
 H6V  H17  H  HCH2   0   0.221  -3.3563   3.3966  -2.0412
 H6V  H18  H  HCH2   0   0.235  -2.2528   3.1679  -0.6917
 H6V  H19  H  HCH2   0   0.175  -4.6957   1.4667  -1.3762
 H6V  H20  H  HCH2   0   0.234  -2.9982   1.0178  -1.5285
 H6V  H21  H  H      0   0.255   5.6936   1.3093  -1.0006
 H6V  H22  H  H      0   0.258   4.5318   3.4858  -0.9663
 H6V  H23  H  HNH2   0   0.378   1.0918  -6.9768  -0.9739
 H6V  H24  H  HNH2   0   0.378   0.8925  -5.9281  -2.2528
 H6V  C22  C  CH2    0  -0.186  -3.0008  -1.1960  -0.1988
 H6V  H11  H  HCH2   0   0.228  -4.4973   1.4846   2.3117
 H6V  H12  H  HCH2   0   0.175  -5.6109   1.7834   0.9791

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
 H6V  C27  C26  single    1.523  0.020  1.523
 H6V  C27  C28  single    1.523  0.020  1.523
 H6V  C26  C25  single    1.521  0.020  1.521
 H6V  C28  C29  single    1.521  0.020  1.521
 H6V  C25  N24  single    1.451  0.020  1.451
 H6V  C29  N24  single    1.451  0.020  1.451
 H6V  N24  C23  single    1.447  0.020  1.447
 H6V  C22  C23  single    1.515  0.020  1.515
 H6V  C22  O21  single    1.409  0.020  1.409
 H6V  C07  C06  aromatic  1.434  0.020  1.434
 H6V  C07  C08  aromatic  1.351  0.020  1.351
 H6V  N31  C06  aromatic  1.335  0.020  1.335
 H6V  N31  C32  aromatic  1.322  0.020  1.322
 H6V  C09  O21  single    1.401  0.020  1.401
 H6V  C09  C08  single    1.500  0.020  1.500
 H6V  C09  C10  single    1.511  0.020  1.511
 H6V  C06  C05  aromatic  1.409  0.020  1.409
 H6V  C08  S30  aromatic  1.746  0.020  1.746
 H6V  C20  C10  aromatic  1.386  0.020  1.386
 H6V  C20  C14  aromatic  1.401  0.020  1.401
 H6V  C32  C33  aromatic  1.396  0.020  1.396
 H6V  N15  C14  single    1.379  0.020  1.379
 H6V  C10  C11  aromatic  1.391  0.020  1.391
 H6V  C14  C13  aromatic  1.399  0.020  1.399
 H6V  C05  S30  aromatic  1.729  0.020  1.729
 H6V  C05  C04  aromatic  1.391  0.020  1.391
 H6V  C11  C12  aromatic  1.388  0.020  1.388
 H6V  C33  C04  aromatic  1.385  0.020  1.385
 H6V  C13  C12  aromatic  1.386  0.020  1.386
 H6V  C04  C02  single    1.520  0.020  1.520
 H6V  C02  O03  deloc     1.247  0.020  1.247
 H6V  C02  O01  deloc     1.241  0.020  1.241
 H6V  C07  H1   single    0.930  0.020  1.080
 H6V  C09  H2   single    0.970  0.020  1.090
 H6V  C11  H3   single    0.930  0.020  1.080
 H6V  C12  H4   single    0.930  0.020  1.080
 H6V  C13  H5   single    0.930  0.020  1.080
 H6V  C20  H6   single    0.930  0.020  1.080
 H6V  C22  H7   single    0.970  0.020  1.090
 H6V  C22  H8   single    0.970  0.020  1.090
 H6V  C23  H9   single    0.970  0.020  1.090
 H6V  C23  H10  single    0.970  0.020  1.090
 H6V  C25  H11  single    0.970  0.020  1.090
 H6V  C25  H12  single    0.970  0.020  1.090
 H6V  C26  H13  single    0.970  0.020  1.090
 H6V  C26  H14  single    0.970  0.020  1.090
 H6V  C27  H15  single    0.970  0.020  1.090
 H6V  C27  H16  single    0.970  0.020  1.090
 H6V  C28  H17  single    0.970  0.020  1.090
 H6V  C28  H18  single    0.970  0.020  1.090
 H6V  C29  H19  single    0.970  0.020  1.090
 H6V  C29  H20  single    0.970  0.020  1.090
 H6V  C32  H21  single    0.930  0.020  1.080
 H6V  C33  H22  single    0.930  0.020  1.080
 H6V  N15  H23  single    0.890  0.020  1.040
 H6V  N15  H24  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
 H6V  O03  C02  O01  128.06  3.000
 H6V  O01  C02  C04  117.18  3.000
 H6V  O03  C02  C04  114.76  3.000
 H6V  C33  C04  C05  116.09  3.000
 H6V  C33  C04  C02  122.88  3.000
 H6V  C05  C04  C02  121.02  3.000
 H6V  S30  C05  C06  111.76  3.000
 H6V  S30  C05  C04  128.10  3.000
 H6V  C06  C05  C04  120.13  3.000
 H6V  N31  C06  C07  125.11  3.000
 H6V  N31  C06  C05  122.81  3.000
 H6V  C07  C06  C05  112.07  3.000
 H6V  H1   C07  C08  124.58  3.000
 H6V  H1   C07  C06  123.56  3.000
 H6V  C08  C07  C06  111.85  3.000
 H6V  S30  C08  C09  117.05  3.000
 H6V  S30  C08  C07  113.84  3.000
 H6V  C09  C08  C07  128.99  3.000
 H6V  H2   C09  O21  109.78  3.000
 H6V  H2   C09  C10  108.17  3.000
 H6V  O21  C09  C10  113.20  3.000
 H6V  H2   C09  C08  107.13  3.000
 H6V  C10  C09  C08  112.17  3.000
 H6V  O21  C09  C08  106.22  3.000
 H6V  C20  C10  C11  120.25  3.000
 H6V  C11  C10  C09  120.50  3.000
 H6V  C20  C10  C09  119.23  3.000
 H6V  H3   C11  C12  120.43  3.000
 H6V  H3   C11  C10  120.68  3.000
 H6V  C12  C11  C10  118.89  3.000
 H6V  H4   C12  C13  119.07  3.000
 H6V  H4   C12  C11  119.72  3.000
 H6V  C13  C12  C11  121.21  3.000
 H6V  H5   C13  C14  119.67  3.000
 H6V  H5   C13  C12  120.01  3.000
 H6V  C14  C13  C12  120.31  3.000
 H6V  N15  C14  C20  120.71  3.000
 H6V  N15  C14  C13  121.06  3.000
 H6V  C20  C14  C13  118.17  3.000
 H6V  H6   C20  C14  119.31  3.000
 H6V  H6   C20  C10  119.54  3.000
 H6V  C14  C20  C10  121.16  3.000
 H6V  H10  C23  H9   106.21  3.000
 H6V  H10  C23  N24  107.84  3.000
 H6V  H9   C23  N24  112.59  3.000
 H6V  H10  C23  C22  108.71  3.000
 H6V  H9   C23  C22  106.73  3.000
 H6V  N24  C23  C22  114.41  3.000
 H6V  H12  C25  H11  106.45  3.000
 H6V  H12  C25  N24  111.39  3.000
 H6V  H11  C25  N24  108.54  3.000
 H6V  H12  C25  C26  108.98  3.000
 H6V  H11  C25  C26  109.72  3.000
 H6V  N24  C25  C26  111.62  3.000
 H6V  H14  C26  H13  107.09  3.000
 H6V  H14  C26  C27  109.51  3.000
 H6V  H13  C26  C27  111.05  3.000
 H6V  H14  C26  C25  109.15  3.000
 H6V  H13  C26  C25  109.28  3.000
 H6V  C27  C26  C25  110.68  3.000
 H6V  H16  C27  H15  106.64  3.000
 H6V  H16  C27  C28  110.81  3.000
 H6V  H15  C27  C28  109.64  3.000
 H6V  H16  C27  C26  110.70  3.000
 H6V  H15  C27  C26  109.43  3.000
 H6V  C28  C27  C26  109.56  3.000
 H6V  H18  C28  H17  107.04  3.000
 H6V  H18  C28  C29  108.93  3.000
 H6V  H17  C28  C29  108.99  3.000
 H6V  H18  C28  C27  109.81  3.000
 H6V  H17  C28  C27  110.84  3.000
 H6V  C29  C28  C27  111.12  3.000
 H6V  H20  C29  H19  106.65  3.000
 H6V  H20  C29  N24  109.46  3.000
 H6V  H19  C29  N24  111.16  3.000
 H6V  H20  C29  C28  108.63  3.000
 H6V  H19  C29  C28  109.38  3.000
 H6V  N24  C29  C28  111.43  3.000
 H6V  H21  C32  N31  116.38  3.000
 H6V  H21  C32  C33  119.54  3.000
 H6V  N31  C32  C33  124.08  3.000
 H6V  H22  C33  C32  119.74  3.000
 H6V  H22  C33  C04  120.22  3.000
 H6V  C32  C33  C04  120.04  3.000
 H6V  H24  N15  H23  111.54  3.000
 H6V  H24  N15  C14  115.65  3.000
 H6V  H23  N15  C14  115.54  3.000
 H6V  C29  N24  C25  111.45  3.000
 H6V  C29  N24  C23  113.54  3.000
 H6V  C25  N24  C23  110.49  3.000
 H6V  C32  N31  C06  116.84  3.000
 H6V  C22  O21  C09  114.63  3.000
 H6V  C08  S30  C05   90.47  3.000
 H6V  H8   C22  H7   106.74  3.000
 H6V  H8   C22  O21  110.07  3.000
 H6V  H7   C22  O21  111.48  3.000
 H6V  H8   C22  C23  111.28  3.000
 H6V  H7   C22  C23  108.28  3.000
 H6V  O21  C22  C23  108.97  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
 H6V  CONST_01  C07  C06  C05  C04   180.00   0.0  0
 H6V  CONST_02  N31  C06  C05  C04     0.00   0.0  0
 H6V  CONST_03  C08  S30  C05  C04   180.00   0.0  0
 H6V  CONST_04  N31  C32  C33  C04     0.00   0.0  0
 H6V  CONST_05  C08  C07  C06  C05     0.00   0.0  0
 H6V  CONST_06  C32  N31  C06  C05     0.00   0.0  0
 H6V  CONST_07  C07  C08  S30  C05     0.00   0.0  0
 H6V  CONST_08  C32  C33  C04  C05     0.00   0.0  0
 H6V  CONST_09  S30  C08  C07  C06     0.00   0.0  0
 H6V  CONST_10  C33  C32  N31  C06     0.00   0.0  0
 H6V  CONST_11  C08  S30  C05  C06     0.00   0.0  0
 H6V  CONST_12  C33  C04  C05  C06     0.00   0.0  0
 H6V  CONST_13  C32  N31  C06  C07   180.00   0.0  0
 H6V  CONST_14  S30  C05  C06  C07     0.00   0.0  0
 H6V  CONST_15  N31  C06  C07  C08   180.00   0.0  0
 H6V  CONST_16  C13  C14  C20  C10     0.00   0.0  0
 H6V  CONST_17  C13  C12  C11  C10     0.00   0.0  0
 H6V  CONST_18  C14  C20  C10  C11     0.00   0.0  0
 H6V  CONST_19  C14  C13  C12  C11     0.00   0.0  0
 H6V  CONST_20  C20  C10  C11  C12     0.00   0.0  0
 H6V  CONST_21  C20  C14  C13  C12     0.00   0.0  0
 H6V  CONST_22  S30  C05  C04  C33   180.00   0.0  0
 H6V  CONST_23  S30  C05  C06  N31   180.00   0.0  0
 H6V  CONST_24  C06  C05  C04  C02   180.00   0.0  0
 H6V  CONST_25  S30  C05  C04  C02     0.00   0.0  0
 H6V  CONST_26  C32  C33  C04  C02   180.00   0.0  0
 H6V  CONST_27  C09  C08  S30  C05   180.00   0.0  0
 H6V  CONST_28  C09  C08  C07  C06   180.00   0.0  0
 H6V  CONST_29  C14  C20  C10  C09   180.00   0.0  0
 H6V  CONST_30  C12  C11  C10  C09   180.00   0.0  0
 H6V  CONST_31  N15  C14  C20  C10   180.00   0.0  0
 H6V  CONST_32  N15  C14  C13  C12   180.00   0.0  0
 H6V  CONST_33  H21  C32  C33  C04   180.00   0.0  0
 H6V  CONST_34  H1   C07  C06  C05   180.00   0.0  0
 H6V  CONST_35  H22  C33  C04  C05   180.00   0.0  0
 H6V  CONST_36  H4   C12  C11  C10   180.00   0.0  0
 H6V  CONST_37  H6   C20  C10  C11   180.00   0.0  0
 H6V  CONST_38  H5   C13  C12  C11   180.00   0.0  0
 H6V  CONST_39  H3   C11  C12  C13   180.00   0.0  0
 H6V  Var_01    C28  C27  C26  C25   -53.49  30.0  1
 H6V  Var_02    C28  C29  N24  C25    58.26  30.0  1
 H6V  Var_03    C29  C28  C27  C26    53.37  30.0  1
 H6V  Var_04    C29  N24  C25  C26   -58.76  30.0  1
 H6V  Var_05    N24  C25  C26  C27    56.62  30.0  1
 H6V  Var_06    N24  C29  C28  C27   -56.02  30.0  1
 H6V  Var_07    O03  C02  C04  C05     1.20  30.0  2
 H6V  Var_08    C25  N24  C23  C22  -174.87  30.0  1
 H6V  Var_09    O21  C22  C23  N24    50.50  30.0  1
 H6V  Var_10    C23  C22  O21  C09  -174.47  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
 H6V  chir_01  C09  O21  C08  C10  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
 H6V  plan-1  C09  0.020
 H6V  plan-1  C10  0.020
 H6V  plan-1  C11  0.020
 H6V  plan-1  C12  0.020
 H6V  plan-1  C13  0.020
 H6V  plan-1  C14  0.020
 H6V  plan-1  C20  0.020
 H6V  plan-1  N15  0.020
 H6V  plan-1  H3   0.020
 H6V  plan-1  H4   0.020
 H6V  plan-1  H5   0.020
 H6V  plan-1  H6   0.020
 H6V  plan-2  C02  0.020
 H6V  plan-2  C04  0.020
 H6V  plan-2  C05  0.020
 H6V  plan-2  C06  0.020
 H6V  plan-2  C07  0.020
 H6V  plan-2  C08  0.020
 H6V  plan-2  C09  0.020
 H6V  plan-2  C32  0.020
 H6V  plan-2  C33  0.020
 H6V  plan-2  N31  0.020
 H6V  plan-2  S30  0.020
 H6V  plan-2  H1   0.020
 H6V  plan-2  H21  0.020
 H6V  plan-2  H22  0.020
 H6V  plan-3  C14  0.020
 H6V  plan-3  N15  0.020
 H6V  plan-3  H23  0.020
 H6V  plan-3  H24  0.020
 H6V  plan-4  C02  0.020
 H6V  plan-4  C04  0.020
 H6V  plan-4  O01  0.020
 H6V  plan-4  O03  0.020

