# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May 14 11:03:45 2020
#   Inital geometry file: a 121 line input string
#   Ligand name: [6-(4-chlorophenyl)-2,2-dimethyl-7-phenyl-2,3-dihydro-1H-pyrrolizin-5-yl]acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1(C)Cn2c(CC(O)=O)c(c3ccc(Cl)cc3)c(c4ccccc4)c2C1
#
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
 LCF  LCF  '[6-(4-chlorophenyl)-2,2-dimethyl-7-phenyl-2,3-dihydro-1H-pyrrolizin-5-yl]acetic acid'  ligand  49  27  .  2021-08-13  2021-08-13  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_LCF
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
 LCF  C1    C   CR5   0   0.366   0.5772  -3.2636   0.4501
 LCF  C2    C   CH2   0  -0.247   3.0035  -3.3630  -0.4731
 LCF  C3    C   CR5   0  -0.124   3.8842  -2.0982  -0.6086
 LCF  C4    C   CH2   0  -0.507   2.8722  -1.0065  -1.0467
 LCF  C5    C   CR55  0   0.349   1.6049  -1.4877  -0.4303
 LCF  C6    C   CR5   0  -0.051   0.3459  -1.0629  -0.0859
 LCF  C7    C   CR5   0  -0.063  -0.3117  -2.2035   0.4863
 LCF  N     N   N     0  -0.501   1.7199  -2.7992  -0.1146
 LCF  C8    C   CH2   0  -0.727   0.4160  -4.6723   0.8874
 LCF  C9    C   C     0   0.564   1.1308  -4.9906   2.1804
 LCF  O1    O   OH1   0  -0.591   0.9663  -6.2624   2.5224
 LCF  O2    O   O     0  -0.432   1.7704  -4.2028   2.8288
 LCF  C10   C   CH3   0  -0.654   5.0059  -2.2899  -1.6177
 LCF  C11   C   CH3   0  -0.639   4.4583  -1.7397   0.7625
 LCF  C12   C   CR6   0   0.020  -0.1490   0.3183  -0.2107
 LCF  C13   C   CR16  0  -0.318   0.3989   1.3301   0.5794
 LCF  C14   C   CR16  0  -0.241  -0.0354   2.6437   0.4619
 LCF  C15   C   CR16  0  -0.270  -1.0319   2.9702  -0.4487
 LCF  C16   C   CR16  0  -0.243  -1.5828   1.9748  -1.2449
 LCF  C17   C   CR16  0  -0.318  -1.1411   0.6637  -1.1287
 LCF  C18   C   CR6   0   0.033  -1.6377  -2.2406   1.1173
 LCF  C19   C   CR16  0  -0.316  -2.8000  -1.9109   0.4189
 LCF  C20   C   CR16  0  -0.194  -4.0440  -1.9426   1.0303
 LCF  C21   C   CR6   0  -0.060  -4.1337  -2.3198   2.3609
 LCF  C22   C   CR16  0  -0.191  -3.0014  -2.6634   3.0821
 LCF  C23   C   CR16  0  -0.336  -1.7648  -2.6152   2.4564
 LCF  CL1   CL  CL    0  -0.134  -5.6863  -2.3634   3.1336
 LCF  H21   H   HCH2  0   0.257   2.9316  -3.9140  -1.4155
 LCF  H22A  H   HCH2  0   0.255   3.3757  -4.0448   0.2919
 LCF  H41   H   HCH2  0   0.254   2.7876  -0.9692  -2.1382
 LCF  H42   H   HCH2  0   0.255   3.1698  -0.0109  -0.7128
 LCF  H81   H   HCH2  0   0.309   0.7737  -5.3689   0.1209
 LCF  H82   H   HCH2  0   0.311  -0.6442  -4.9048   1.0166
 LCF  HO1   H   HOH1  0   0.482   1.4271  -6.4467   3.3547
 LCF  H101  H   HCH3  0   0.230   4.6141  -2.5205  -2.6099
 LCF  H102  H   HCH3  0   0.233   5.6093  -1.3841  -1.6978
 LCF  H103  H   HCH3  0   0.232   5.6715  -3.1032  -1.3223
 LCF  H111  H   HCH3  0   0.231   5.1390  -2.5166   1.1151
 LCF  H112  H   HCH3  0   0.232   5.0168  -0.8031   0.7151
 LCF  H113  H   HCH3  0   0.235   3.6737  -1.6212   1.5130
 LCF  H13   H   HCR6  0   0.241   1.1703   1.0834   1.2989
 LCF  H14   H   HCR6  0   0.254   0.4020   3.4114   1.0873
 LCF  H15   H   HCR6  0   0.254  -1.3746   3.9929  -0.5391
 LCF  H16   H   HCR6  0   0.253  -2.3535   2.2184  -1.9652
 LCF  H17   H   HCR6  0   0.250  -1.5602  -0.0969  -1.7753
 LCF  H19   H   HCR6  0   0.252  -2.7423  -1.6466  -0.6275
 LCF  H20   H   HCR6  0   0.277  -4.9329  -1.6869   0.4696
 LCF  H22   H   HCR6  0   0.278  -3.0758  -2.9530   4.1216
 LCF  H23   H   HCR6  0   0.253  -0.8769  -2.8549   3.0281

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
 LCF  C1   C7    aromatic  1.384  0.020  1.384
 LCF  C1   N     aromatic  1.357  0.020  1.357
 LCF  C1   C8    single    1.484  0.020  1.484
 LCF  C2   C3    single    1.547  0.020  1.547
 LCF  C2   N     single    1.447  0.020  1.447
 LCF  C2   H21   single    0.970  0.020  1.090
 LCF  C2   H22A  single    0.970  0.020  1.090
 LCF  C3   C4    single    1.552  0.020  1.552
 LCF  C3   C10   single    1.521  0.020  1.521
 LCF  C3   C11   single    1.529  0.020  1.529
 LCF  C4   C5    single    1.489  0.020  1.489
 LCF  C4   H41   single    0.970  0.020  1.090
 LCF  C4   H42   single    0.970  0.020  1.090
 LCF  C5   C6    aromatic  1.373  0.020  1.373
 LCF  C5   N     aromatic  1.354  0.020  1.354
 LCF  C6   C7    aromatic  1.436  0.020  1.436
 LCF  C6   C12   single    1.473  0.020  1.473
 LCF  C7   C18   single    1.469  0.020  1.469
 LCF  C8   C9    single    1.511  0.020  1.511
 LCF  C8   H81   single    0.970  0.020  1.090
 LCF  C8   H82   single    0.970  0.020  1.090
 LCF  C9   O1    single    1.327  0.020  1.327
 LCF  C9   O2    double    1.204  0.020  1.204
 LCF  O1   HO1   single    0.850  0.020  0.980
 LCF  C10  H101  single    0.970  0.020  1.090
 LCF  C10  H102  single    0.970  0.020  1.090
 LCF  C10  H103  single    0.970  0.020  1.090
 LCF  C11  H111  single    0.970  0.020  1.090
 LCF  C11  H112  single    0.970  0.020  1.090
 LCF  C11  H113  single    0.970  0.020  1.090
 LCF  C12  C13   aromatic  1.396  0.020  1.396
 LCF  C12  C17   aromatic  1.395  0.020  1.395
 LCF  C13  C14   aromatic  1.388  0.020  1.388
 LCF  C13  H13   single    0.930  0.020  1.080
 LCF  C14  C15   aromatic  1.389  0.020  1.389
 LCF  C14  H14   single    0.930  0.020  1.080
 LCF  C15  C16   aromatic  1.389  0.020  1.389
 LCF  C15  H15   single    0.930  0.020  1.080
 LCF  C16  C17   aromatic  1.388  0.020  1.388
 LCF  C16  H16   single    0.930  0.020  1.080
 LCF  C17  H17   single    0.930  0.020  1.080
 LCF  C18  C19   aromatic  1.395  0.020  1.395
 LCF  C18  C23   aromatic  1.396  0.020  1.396
 LCF  C19  C20   aromatic  1.386  0.020  1.386
 LCF  C19  H19   single    0.930  0.020  1.080
 LCF  C20  C21   aromatic  1.386  0.020  1.386
 LCF  C20  H20   single    0.930  0.020  1.080
 LCF  C21  C22   aromatic  1.386  0.020  1.386
 LCF  C21  CL1   single    1.735  0.020  1.735
 LCF  C22  C23   aromatic  1.387  0.020  1.387
 LCF  C22  H22   single    0.930  0.020  1.080
 LCF  C23  H23   single    0.930  0.020  1.080

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
 LCF  C8    C1   N     122.63  3.000
 LCF  C8    C1   C7    130.53  3.000
 LCF  N     C1   C7    106.84  3.000
 LCF  H22A  C2   H21   108.17  3.000
 LCF  H22A  C2   N     111.88  3.000
 LCF  H21   C2   N     110.57  3.000
 LCF  H22A  C2   C3    112.23  3.000
 LCF  H21   C2   C3    111.95  3.000
 LCF  N     C2   C3    102.01  3.000
 LCF  C11   C3   C10   110.34  3.000
 LCF  C11   C3   C4    109.46  3.000
 LCF  C10   C3   C4    112.48  3.000
 LCF  C11   C3   C2    109.08  3.000
 LCF  C10   C3   C2    112.02  3.000
 LCF  C4    C3   C2    103.22  3.000
 LCF  H42   C4   H41   107.15  3.000
 LCF  H42   C4   C5    113.59  3.000
 LCF  H41   C4   C5    110.96  3.000
 LCF  H42   C4   C3    112.18  3.000
 LCF  H41   C4   C3    110.84  3.000
 LCF  C5    C4   C3    102.17  3.000
 LCF  N     C5   C6    108.61  3.000
 LCF  N     C5   C4    109.71  3.000
 LCF  C6    C5   C4    141.67  3.000
 LCF  C12   C6   C7    128.69  3.000
 LCF  C12   C6   C5    125.26  3.000
 LCF  C7    C6   C5    105.92  3.000
 LCF  C18   C7   C6    127.22  3.000
 LCF  C18   C7   C1    124.87  3.000
 LCF  C6    C7   C1    107.70  3.000
 LCF  C5    N    C2    113.26  3.000
 LCF  C5    N    C1    110.92  3.000
 LCF  C2    N    C1    135.80  3.000
 LCF  H82   C8   H81   105.31  3.000
 LCF  H82   C8   C9    108.23  3.000
 LCF  H81   C8   C9    108.07  3.000
 LCF  H82   C8   C1    110.01  3.000
 LCF  H81   C8   C1    111.22  3.000
 LCF  C9    C8   C1    113.63  3.000
 LCF  O2    C9   O1    123.64  3.000
 LCF  O2    C9   C8    125.03  3.000
 LCF  O1    C9   C8    111.32  3.000
 LCF  HO1   O1   C9    110.16  3.000
 LCF  H103  C10  H102  107.52  3.000
 LCF  H103  C10  H101  107.91  3.000
 LCF  H102  C10  H101  107.88  3.000
 LCF  H103  C10  C3    111.35  3.000
 LCF  H102  C10  C3    110.60  3.000
 LCF  H101  C10  C3    111.41  3.000
 LCF  H113  C11  H112  107.72  3.000
 LCF  H113  C11  H111  107.66  3.000
 LCF  H112  C11  H111  107.80  3.000
 LCF  H113  C11  C3    111.83  3.000
 LCF  H112  C11  C3    110.75  3.000
 LCF  H111  C11  C3    110.91  3.000
 LCF  C17   C12  C13   118.17  3.000
 LCF  C17   C12  C6    121.81  3.000
 LCF  C13   C12  C6    120.00  3.000
 LCF  H13   C13  C14   119.63  3.000
 LCF  H13   C13  C12   119.36  3.000
 LCF  C14   C13  C12   121.00  3.000
 LCF  H14   C14  C15   120.13  3.000
 LCF  H14   C14  C13   119.71  3.000
 LCF  C15   C14  C13   120.16  3.000
 LCF  H15   C15  C16   120.25  3.000
 LCF  H15   C15  C14   120.27  3.000
 LCF  C16   C15  C14   119.48  3.000
 LCF  H16   C16  C17   119.65  3.000
 LCF  H16   C16  C15   120.17  3.000
 LCF  C17   C16  C15   120.18  3.000
 LCF  H17   C17  C16   119.36  3.000
 LCF  H17   C17  C12   119.62  3.000
 LCF  C16   C17  C12   121.01  3.000
 LCF  C23   C18  C19   117.87  3.000
 LCF  C23   C18  C7    120.06  3.000
 LCF  C19   C18  C7    122.07  3.000
 LCF  H19   C19  C20   118.71  3.000
 LCF  H19   C19  C18   119.85  3.000
 LCF  C20   C19  C18   121.42  3.000
 LCF  H20   C20  C21   120.58  3.000
 LCF  H20   C20  C19   120.23  3.000
 LCF  C21   C20  C19   119.18  3.000
 LCF  CL1   C21  C22   119.55  3.000
 LCF  CL1   C21  C20   119.50  3.000
 LCF  C22   C21  C20   120.95  3.000
 LCF  H22   C22  C23   120.28  3.000
 LCF  H22   C22  C21   120.69  3.000
 LCF  C23   C22  C21   119.02  3.000
 LCF  H23   C23  C22   119.03  3.000
 LCF  H23   C23  C18   119.41  3.000
 LCF  C22   C23  C18   121.55  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
 LCF  CONST_01  C5    C6   C7   C1      0.00   0.0  0
 LCF  CONST_02  C12   C6   C7   C1    180.00   0.0  0
 LCF  CONST_05  C6    C5   N    C1      0.00   0.0  0
 LCF  CONST_06  C18   C7   C6   C5    180.00   0.0  0
 LCF  CONST_09  C7    C1   N    C5      0.00   0.0  0
 LCF  CONST_10  N     C1   C7   C6      0.00   0.0  0
 LCF  CONST_13  C14   C13  C12  C6    180.00   0.0  0
 LCF  CONST_14  C16   C17  C12  C6    180.00   0.0  0
 LCF  CONST_15  N     C5   C6   C7      0.00   0.0  0
 LCF  CONST_18  C20   C19  C18  C7    180.00   0.0  0
 LCF  CONST_19  C22   C23  C18  C7    180.00   0.0  0
 LCF  CONST_20  C18   C7   C1   N     180.00   0.0  0
 LCF  CONST_21  C12   C6   C5   N     180.00   0.0  0
 LCF  CONST_22  C18   C7   C6   C12     0.00   0.0  0
 LCF  CONST_23  C15   C14  C13  C12     0.00   0.0  0
 LCF  CONST_24  C15   C16  C17  C12     0.00   0.0  0
 LCF  CONST_25  C16   C17  C12  C13     0.00   0.0  0
 LCF  CONST_26  C16   C15  C14  C13     0.00   0.0  0
 LCF  CONST_27  C17   C12  C13  C14     0.00   0.0  0
 LCF  CONST_28  C17   C16  C15  C14     0.00   0.0  0
 LCF  CONST_29  C21   C20  C19  C18     0.00   0.0  0
 LCF  CONST_30  C21   C22  C23  C18     0.00   0.0  0
 LCF  CONST_31  C22   C23  C18  C19     0.00   0.0  0
 LCF  CONST_32  C22   C21  C20  C19     0.00   0.0  0
 LCF  CONST_33  C23   C18  C19  C20     0.00   0.0  0
 LCF  CONST_34  C23   C22  C21  C20     0.00   0.0  0
 LCF  CONST_35  C12   C6   C5   C4      0.00   0.0  0
 LCF  CONST_36  C8    C1   N    C2      0.00   0.0  0
 LCF  CONST_37  C8    C1   N    C5    180.00   0.0  0
 LCF  CONST_38  C8    C1   C7   C6    180.00   0.0  0
 LCF  CONST_39  C18   C7   C1   C8      0.00   0.0  0
 LCF  CONST_40  CL1   C21  C20  C19   180.00   0.0  0
 LCF  CONST_41  CL1   C21  C22  C23   180.00   0.0  0
 LCF  CONST_42  H13   C13  C12  C6      0.00   0.0  0
 LCF  CONST_43  H17   C17  C12  C6      0.00   0.0  0
 LCF  CONST_44  H19   C19  C18  C7      0.00   0.0  0
 LCF  CONST_45  H23   C23  C18  C7      0.00   0.0  0
 LCF  CONST_46  H14   C14  C13  C12   180.00   0.0  0
 LCF  CONST_47  H16   C16  C17  C12   180.00   0.0  0
 LCF  CONST_48  H15   C15  C14  C13   180.00   0.0  0
 LCF  CONST_49  H20   C20  C19  C18   180.00   0.0  0
 LCF  CONST_50  H22   C22  C23  C18   180.00   0.0  0
 LCF  CONST_51  HO1   O1   C9   C8    180.00   0.0  0
 LCF  Var_01    C3    C2   N    C1   -161.49  30.0  1
 LCF  Var_02    C5    C4   C3   C2     28.91  30.0  1
 LCF  Var_03    C6    C5   C4   C3    162.97  30.0  1
 LCF  Var_04    N     C2   C3   C4    -29.32  30.0  1
 LCF  Var_05    C9    C8   C1   C7   -105.18  30.0  2
 LCF  Var_06    H101  C10  C3   C2     59.79  30.0  3
 LCF  Var_07    H111  C11  C3   C2     65.09  30.0  3
 LCF  Var_08    O1    C9   C8   C1   -179.46  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
 LCF  plan-1  C6   0.020
 LCF  plan-1  C12  0.020
 LCF  plan-1  C13  0.020
 LCF  plan-1  C14  0.020
 LCF  plan-1  C15  0.020
 LCF  plan-1  C16  0.020
 LCF  plan-1  C17  0.020
 LCF  plan-1  H13  0.020
 LCF  plan-1  H14  0.020
 LCF  plan-1  H15  0.020
 LCF  plan-1  H16  0.020
 LCF  plan-1  H17  0.020
 LCF  plan-2  C7   0.020
 LCF  plan-2  C18  0.020
 LCF  plan-2  C19  0.020
 LCF  plan-2  C20  0.020
 LCF  plan-2  C21  0.020
 LCF  plan-2  C22  0.020
 LCF  plan-2  C23  0.020
 LCF  plan-2  CL1  0.020
 LCF  plan-2  H19  0.020
 LCF  plan-2  H20  0.020
 LCF  plan-2  H22  0.020
 LCF  plan-2  H23  0.020
 LCF  plan-3  C1   0.020
 LCF  plan-3  C2   0.020
 LCF  plan-3  C4   0.020
 LCF  plan-3  C5   0.020
 LCF  plan-3  C6   0.020
 LCF  plan-3  C7   0.020
 LCF  plan-3  N    0.020
 LCF  plan-3  C8   0.020
 LCF  plan-3  C12  0.020
 LCF  plan-3  C18  0.020
 LCF  plan-4  C8   0.020
 LCF  plan-4  C9   0.020
 LCF  plan-4  O1   0.020
 LCF  plan-4  O2   0.020
 LCF  plan-4  HO1  0.020

