# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 18:29:14 2020
#   Inital geometry file: a 133 line input string
#   Ligand name: 6-[1-(3,5,5,8,8-pentamethyl-5,6,7,8-tetrahydronaphthalen-2-yl)cyclopropyl]pyridine-3-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc2c(cc1C3(CC3)c4ccc(cn4)C(O)=O)C(C)(C)CCC2(C)C
#
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
 LG2  LG2  '6-[1-(3,5,5,8,8-pentamethyl-5,6,7,8-tetrahydronaphthalen-2-yl)cyclopropyl]pyridine-3-carboxylic acid'  ligand  55  27  .  2022-09-22  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_LG2
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
 LG2  C1    C  CR6    0   0.136  -0.1612  -0.6039   2.4442
 LG2  C2    C  CR16   0  -0.367   0.3325  -1.0774   1.2255
 LG2  C3    C  CR6    0   0.053   1.0750  -0.3028   0.3518
 LG2  C4    C  CR6    0   0.077   1.3479   1.0285   0.6971
 LG2  C5    C  CR16   0  -0.361   0.8378   1.5067   1.8932
 LG2  C6    C  CR6    0   0.137   0.0708   0.7348   2.7712
 LG2  C7    C  CT     0  -0.169  -0.4540   1.3860   4.0457
 LG2  C8    C  CH2    0  -0.424  -1.5158   0.4952   4.6979
 LG2  C9    C  CH2    0  -0.425  -1.1005  -0.9610   4.7411
 LG2  C10   C  CT     0  -0.168  -0.9351  -1.5612   3.3418
 LG2  C11   C  CT     0  -0.138   1.5513  -0.8670  -0.9481
 LG2  C12   C  C      0   0.301   0.7848  -0.4585  -2.1641
 LG2  N13   N  N      0  -0.441   1.3087  -0.7697  -3.3479
 LG2  C14   C  C1     0  -0.103   0.6456  -0.4506  -4.4511
 LG2  C15   C  C      0  -0.193  -0.5835   0.1994  -4.4661
 LG2  C16   C  C1     0  -0.177  -1.1256   0.5194  -3.2274
 LG2  C17   C  C1     0  -0.326  -0.4449   0.1914  -2.0676
 LG2  C18   C  C      0   0.396  -1.2932   0.5366  -5.7661
 LG2  O19   O  O      0  -0.592  -2.3996   1.0992  -5.6622
 LG2  O20   O  OC    -1  -0.594  -0.7068   0.2199  -6.8186
 LG2  C21   C  CH2    0  -0.455   3.0320  -1.1108  -1.1023
 LG2  C22   C  CH2    0  -0.473   2.1123  -2.2708  -0.9649
 LG2  C23   C  CH3    0  -0.637   0.7170   1.6110   5.0128
 LG2  C24   C  CH3    0  -0.645  -1.1079   2.7389   3.7388
 LG2  C25   C  CH3    0  -0.636  -2.3140  -1.8367   2.7250
 LG2  C26   C  CH3    0  -0.647  -0.1908  -2.8935   3.4927
 LG2  C27   C  CH3    0  -0.746   2.1485   1.9302  -0.1963
 LG2  HC2   H  HCR6   0   0.233   0.1271  -2.1015   0.9355
 LG2  HC5   H  HCR6   0   0.231   1.0474   2.5386   2.1518
 LG2  HC81  H  HCH2   0   0.226  -2.4563   0.5917   4.1458
 LG2  HC82  H  HCH2   0   0.230  -1.7192   0.8655   5.7068
 LG2  HC91  H  HCH2   0   0.230  -1.8360  -1.5531   5.2938
 LG2  HC92  H  HCH2   0   0.226  -0.1607  -1.0598   5.2938
 LG2  HC41  H  H      0   0.248   1.1175  -0.7263  -5.3877
 LG2  HC61  H  H      0   0.254  -2.0810   1.0247  -3.1712
 LG2  HC71  H  H      0   0.261  -0.8651   0.4331  -1.1010
 LG2  H211  H  HCH2   0   0.254   3.4735  -0.9150  -2.0705
 LG2  H212  H  HCH2   0   0.254   3.6541  -0.8535  -0.2537
 LG2  H221  H  HCH2   0   0.253   2.1126  -2.8253  -0.0348
 LG2  H222  H  HCH2   0   0.255   1.9120  -2.8677  -1.8454
 LG2  H231  H  HCH3   0   0.224   0.3743   2.1100   5.9223
 LG2  H232  H  HCH3   0   0.229   1.1918   0.6733   5.3059
 LG2  H233  H  HCH3   0   0.229   1.4852   2.2405   4.5605
 LG2  H241  H  HCH3   0   0.228  -1.5434   3.1552   4.6498
 LG2  H242  H  HCH3   0   0.228  -0.3989   3.4729   3.3547
 LG2  H243  H  HCH3   0   0.227  -1.9094   2.6286   3.0062
 LG2  H251  H  HCH3   0   0.223  -2.8617  -2.5619   3.3319
 LG2  H252  H  HCH3   0   0.229  -2.9187  -0.9316   2.6598
 LG2  H253  H  HCH3   0   0.229  -2.2228  -2.2455   1.7173
 LG2  H261  H  HCH3   0   0.228  -0.6983  -3.5173   4.2324
 LG2  H262  H  HCH3   0   0.227  -0.1545  -3.4646   2.5643
 LG2  H263  H  HCH3   0   0.227   0.8345  -2.7394   3.8339
 LG2  H271  H  HCH3   0   0.249   3.1152   1.4953  -0.4534
 LG2  H272  H  HCH3   0   0.242   1.6341   2.1286  -1.1389
 LG2  H273  H  HCH3   0   0.246   2.3314   2.8910   0.2834

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
 LG2  C1   C2    aromatic  1.398  0.020  1.398
 LG2  C1   C6    aromatic  1.397  0.020  1.397
 LG2  C1   C10   single    1.523  0.020  1.523
 LG2  C2   C3    aromatic  1.384  0.020  1.384
 LG2  C2   HC2   single    0.930  0.020  1.080
 LG2  C3   C4    aromatic  1.402  0.020  1.402
 LG2  C3   C11   single    1.495  0.020  1.495
 LG2  C4   C5    aromatic  1.385  0.020  1.385
 LG2  C4   C27   single    1.501  0.020  1.501
 LG2  C5   C6    aromatic  1.398  0.020  1.398
 LG2  C5   HC5   single    0.930  0.020  1.080
 LG2  C6   C7    single    1.524  0.020  1.524
 LG2  C7   C8    single    1.532  0.020  1.532
 LG2  C7   C23   single    1.535  0.020  1.535
 LG2  C7   C24   single    1.534  0.020  1.534
 LG2  C8   C9    single    1.515  0.020  1.515
 LG2  C8   HC81  single    0.970  0.020  1.090
 LG2  C8   HC82  single    0.970  0.020  1.090
 LG2  C9   C10   single    1.532  0.020  1.532
 LG2  C9   HC91  single    0.970  0.020  1.090
 LG2  C9   HC92  single    0.970  0.020  1.090
 LG2  C10  C25   single    1.535  0.020  1.535
 LG2  C10  C26   single    1.534  0.020  1.534
 LG2  C11  C12   single    1.494  0.020  1.494
 LG2  C11  C21   single    1.509  0.020  1.509
 LG2  C11  C22   single    1.512  0.020  1.512
 LG2  C12  N13   aromatic  1.331  0.020  1.331
 LG2  C12  C17   aromatic  1.394  0.020  1.394
 LG2  N13  C14   aromatic  1.326  0.020  1.326
 LG2  C14  C15   aromatic  1.390  0.020  1.390
 LG2  C14  HC41  single    0.930  0.020  1.080
 LG2  C15  C16   aromatic  1.389  0.020  1.389
 LG2  C15  C18   single    1.519  0.020  1.519
 LG2  C16  C17   aromatic  1.384  0.020  1.384
 LG2  C16  HC61  single    0.930  0.020  1.080
 LG2  C17  HC71  single    0.930  0.020  1.080
 LG2  C18  O19   deloc     1.246  0.020  1.246
 LG2  C18  O20   deloc     1.246  0.020  1.246
 LG2  C21  C22   single    1.487  0.020  1.487
 LG2  C21  H211  single    0.970  0.020  1.090
 LG2  C21  H212  single    0.970  0.020  1.090
 LG2  C22  H221  single    0.970  0.020  1.090
 LG2  C22  H222  single    0.970  0.020  1.090
 LG2  C23  H231  single    0.970  0.020  1.090
 LG2  C23  H232  single    0.970  0.020  1.090
 LG2  C23  H233  single    0.970  0.020  1.090
 LG2  C24  H241  single    0.970  0.020  1.090
 LG2  C24  H242  single    0.970  0.020  1.090
 LG2  C24  H243  single    0.970  0.020  1.090
 LG2  C25  H251  single    0.970  0.020  1.090
 LG2  C25  H252  single    0.970  0.020  1.090
 LG2  C25  H253  single    0.970  0.020  1.090
 LG2  C26  H261  single    0.970  0.020  1.090
 LG2  C26  H262  single    0.970  0.020  1.090
 LG2  C26  H263  single    0.970  0.020  1.090
 LG2  C27  H271  single    0.970  0.020  1.090
 LG2  C27  H272  single    0.970  0.020  1.090
 LG2  C27  H273  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
 LG2  C10   C1   C6    123.26  3.000
 LG2  C10   C1   C2    118.70  3.000
 LG2  C6    C1   C2    118.03  3.000
 LG2  HC2   C2   C3    117.49  3.000
 LG2  HC2   C2   C1    119.10  3.000
 LG2  C3    C2   C1    123.40  3.000
 LG2  C11   C3   C4    120.70  3.000
 LG2  C11   C3   C2    120.58  3.000
 LG2  C4    C3   C2    118.71  3.000
 LG2  C27   C4   C5    120.19  3.000
 LG2  C27   C4   C3    121.85  3.000
 LG2  C5    C4   C3    117.95  3.000
 LG2  HC5   C5   C6    118.79  3.000
 LG2  HC5   C5   C4    117.60  3.000
 LG2  C6    C5   C4    123.61  3.000
 LG2  C7    C6   C5    118.56  3.000
 LG2  C7    C6   C1    123.21  3.000
 LG2  C5    C6   C1    118.23  3.000
 LG2  C24   C7   C23   108.78  3.000
 LG2  C24   C7   C8    107.62  3.000
 LG2  C23   C7   C8    110.22  3.000
 LG2  C24   C7   C6    110.88  3.000
 LG2  C23   C7   C6    109.07  3.000
 LG2  C8    C7   C6    110.26  3.000
 LG2  HC82  C8   HC81  106.00  3.000
 LG2  HC82  C8   C9    110.50  3.000
 LG2  HC81  C8   C9    109.55  3.000
 LG2  HC82  C8   C7    108.95  3.000
 LG2  HC81  C8   C7    109.24  3.000
 LG2  C9    C8   C7    112.40  3.000
 LG2  HC92  C9   HC91  105.85  3.000
 LG2  HC92  C9   C10   109.46  3.000
 LG2  HC91  C9   C10   108.79  3.000
 LG2  HC92  C9   C8    109.66  3.000
 LG2  HC91  C9   C8    110.50  3.000
 LG2  C10   C9   C8    112.35  3.000
 LG2  C26   C10  C25   108.64  3.000
 LG2  C26   C10  C9    107.64  3.000
 LG2  C25   C10  C9    109.90  3.000
 LG2  C26   C10  C1    110.94  3.000
 LG2  C25   C10  C1    109.41  3.000
 LG2  C9    C10  C1    110.30  3.000
 LG2  C22   C11  C21    58.98  3.000
 LG2  C22   C11  C12   115.79  3.000
 LG2  C21   C11  C12   117.68  3.000
 LG2  C22   C11  C3    118.58  3.000
 LG2  C21   C11  C3    117.55  3.000
 LG2  C12   C11  C3    116.16  3.000
 LG2  C17   C12  N13   121.17  3.000
 LG2  C17   C12  C11   121.57  3.000
 LG2  N13   C12  C11   117.24  3.000
 LG2  C14   N13  C12   119.12  3.000
 LG2  HC41  C14  C15   119.62  3.000
 LG2  HC41  C14  N13   116.09  3.000
 LG2  C15   C14  N13   124.29  3.000
 LG2  C18   C15  C16   121.97  3.000
 LG2  C18   C15  C14   121.73  3.000
 LG2  C16   C15  C14   116.29  3.000
 LG2  HC61  C16  C17   120.08  3.000
 LG2  HC61  C16  C15   119.88  3.000
 LG2  C17   C16  C15   120.03  3.000
 LG2  HC71  C17  C16   120.32  3.000
 LG2  HC71  C17  C12   120.59  3.000
 LG2  C16   C17  C12   119.09  3.000
 LG2  O20   C18  O19   127.11  3.000
 LG2  O20   C18  C15   116.53  3.000
 LG2  O19   C18  C15   116.35  3.000
 LG2  H212  C21  H211  115.07  3.000
 LG2  H212  C21  C22   117.92  3.000
 LG2  H211  C21  C22   118.44  3.000
 LG2  H212  C21  C11   116.44  3.000
 LG2  H211  C21  C11   117.56  3.000
 LG2  C22   C21  C11    60.62  3.000
 LG2  H222  C22  H221  114.60  3.000
 LG2  H222  C22  C21   118.01  3.000
 LG2  H221  C22  C21   118.60  3.000
 LG2  H222  C22  C11   116.90  3.000
 LG2  H221  C22  C11   117.78  3.000
 LG2  C21   C22  C11    60.40  3.000
 LG2  H233  C23  H232  107.50  3.000
 LG2  H233  C23  H231  107.60  3.000
 LG2  H232  C23  H231  107.78  3.000
 LG2  H233  C23  C7    111.12  3.000
 LG2  H232  C23  C7    112.04  3.000
 LG2  H231  C23  C7    110.61  3.000
 LG2  H243  C24  H242  108.01  3.000
 LG2  H243  C24  H241  107.79  3.000
 LG2  H242  C24  H241  107.25  3.000
 LG2  H243  C24  C7    110.99  3.000
 LG2  H242  C24  C7    112.77  3.000
 LG2  H241  C24  C7    109.84  3.000
 LG2  H253  C25  H252  107.58  3.000
 LG2  H253  C25  H251  107.82  3.000
 LG2  H252  C25  H251  107.83  3.000
 LG2  H253  C25  C10   111.29  3.000
 LG2  H252  C25  C10   111.91  3.000
 LG2  H251  C25  C10   110.25  3.000
 LG2  H263  C26  H262  107.99  3.000
 LG2  H263  C26  H261  107.78  3.000
 LG2  H262  C26  H261  107.03  3.000
 LG2  H263  C26  C10   111.34  3.000
 LG2  H262  C26  C10   112.79  3.000
 LG2  H261  C26  C10   109.70  3.000
 LG2  H273  C27  H272  107.39  3.000
 LG2  H273  C27  H271  107.86  3.000
 LG2  H272  C27  H271  106.64  3.000
 LG2  H273  C27  C4    110.94  3.000
 LG2  H272  C27  C4    111.82  3.000
 LG2  H271  C27  C4    111.94  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
 LG2  CONST_01  C4    C3   C2   C1     0.00   0.0  0
 LG2  CONST_02  C4    C5   C6   C1     0.00   0.0  0
 LG2  CONST_03  C5    C6   C1   C2     0.00   0.0  0
 LG2  CONST_04  C5    C4   C3   C2     0.00   0.0  0
 LG2  CONST_05  C6    C1   C2   C3     0.00   0.0  0
 LG2  CONST_06  C6    C5   C4   C3     0.00   0.0  0
 LG2  CONST_07  C15   C14  N13  C12    0.00   0.0  0
 LG2  CONST_08  C15   C16  C17  C12    0.00   0.0  0
 LG2  CONST_09  C16   C17  C12  N13    0.00   0.0  0
 LG2  CONST_10  C16   C15  C14  N13    0.00   0.0  0
 LG2  CONST_11  C17   C12  N13  C14    0.00   0.0  0
 LG2  CONST_12  C17   C16  C15  C14    0.00   0.0  0
 LG2  CONST_13  C11   C3   C2   C1   180.00   0.0  0
 LG2  CONST_14  C11   C3   C4   C5   180.00   0.0  0
 LG2  CONST_15  C14   N13  C12  C11  180.00   0.0  0
 LG2  CONST_16  C16   C17  C12  C11  180.00   0.0  0
 LG2  CONST_17  C27   C4   C3   C2   180.00   0.0  0
 LG2  CONST_18  C27   C4   C5   C6   180.00   0.0  0
 LG2  CONST_19  C27   C4   C3   C11    0.00   0.0  0
 LG2  CONST_20  C18   C15  C14  N13  180.00   0.0  0
 LG2  CONST_21  C18   C15  C16  C17  180.00   0.0  0
 LG2  CONST_22  HC5   C5   C6   C1   180.00   0.0  0
 LG2  CONST_23  HC2   C2   C3   C4   180.00   0.0  0
 LG2  CONST_24  HC71  C17  C12  C11    0.00   0.0  0
 LG2  CONST_25  HC41  C14  N13  C12  180.00   0.0  0
 LG2  CONST_26  HC61  C16  C17  C12  180.00   0.0  0
 LG2  Var_01    C8    C7   C6   C1   -13.83  30.0  1
 LG2  Var_02    C8    C9   C10  C1    44.99  30.0  1
 LG2  Var_03    C9    C10  C1   C2   166.84  30.0  1
 LG2  Var_04    C12   C11  C3   C2   102.50  30.0  2
 LG2  Var_05    N13   C12  C11  C3   169.59  30.0  2
 LG2  Var_06    C22   C21  C11  C3   108.41  30.0  1
 LG2  Var_07    C9    C8   C7   C6    45.01  30.0  1
 LG2  Var_08    C10   C9   C8   C7   -63.54  30.0  1
 LG2  Var_09    O19   C18  C15  C14  178.82  30.0  2
 LG2  Var_10    H251  C25  C10  C1   177.13  30.0  3
 LG2  Var_11    H261  C26  C10  C1   173.18  30.0  3
 LG2  Var_12    H271  C27  C4   C3   -54.17  30.0  2
 LG2  Var_13    H231  C23  C7   C6   177.98  30.0  3
 LG2  Var_14    H241  C24  C7   C6   175.78  30.0  3

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
 LG2  plan-1  C11   0.020
 LG2  plan-1  C12   0.020
 LG2  plan-1  N13   0.020
 LG2  plan-1  C14   0.020
 LG2  plan-1  C15   0.020
 LG2  plan-1  C16   0.020
 LG2  plan-1  C17   0.020
 LG2  plan-1  C18   0.020
 LG2  plan-1  HC41  0.020
 LG2  plan-1  HC61  0.020
 LG2  plan-1  HC71  0.020
 LG2  plan-2  C1    0.020
 LG2  plan-2  C2    0.020
 LG2  plan-2  C3    0.020
 LG2  plan-2  C4    0.020
 LG2  plan-2  C5    0.020
 LG2  plan-2  C6    0.020
 LG2  plan-2  C7    0.020
 LG2  plan-2  C10   0.020
 LG2  plan-2  C11   0.020
 LG2  plan-2  C27   0.020
 LG2  plan-2  HC2   0.020
 LG2  plan-2  HC5   0.020
 LG2  plan-3  C15   0.020
 LG2  plan-3  C18   0.020
 LG2  plan-3  O19   0.020
 LG2  plan-3  O20   0.020

