# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 20 00:18:09 2022
#   Inital geometry file: a 107 line input string
#   Ligand name: 3-(cyclopentyloxy)-N-(3,5-dichloropyridin-4-yl)-4-methoxybenzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(cc1OC2CCCC2)C(=O)Nc3c(Cl)cncc3Cl
#
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
 PIL  PIL  3-(cyclopentyloxy)-N-(3,5-dichloropyridin-4-yl)-4-methoxybenzamide  ligand  43  25  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PIL
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
 PIL  CL25  CL  CL    0  -0.079   0.6394   2.6004  -3.5249
 PIL  C24   C   CR6   0  -0.194   0.1495   1.1099  -4.2297
 PIL  C23   C   CR16  0  -0.031  -0.2959   1.0830  -5.5415
 PIL  N22   N   N     0  -0.397  -0.7053  -0.0305  -6.1264
 PIL  C21   C   CR16  0  -0.035  -0.6686  -1.1601  -5.4388
 PIL  C19   C   CR6   0  -0.167  -0.2197  -1.2251  -4.1282
 PIL  CL20  CL  CL    0  -0.079  -0.1189  -2.7512  -3.3501
 PIL  C18   C   CR6   0   0.604   0.1932  -0.0631  -3.4784
 PIL  N16   N   NH1   0  -0.761   0.6559  -0.0667  -2.1687
 PIL  C15   C   C     0   0.536  -0.1412  -0.4389  -1.1148
 PIL  O17   O   O     0  -0.438  -1.3012  -0.7588  -1.2799
 PIL  C14   C   CR6   0  -0.055   0.5070  -0.4139   0.2169
 PIL  C13   C   CR16  0  -0.307   1.8812  -0.4540   0.3869
 PIL  C12   C   CR16  0  -0.374   2.4291  -0.4554   1.6648
 PIL  C9    C   CR6   0   0.307   1.6101  -0.4112   2.7822
 PIL  O10   O   O2    0  -0.448   2.0403  -0.4076   4.0481
 PIL  C11   C   CH3   0  -0.441   3.4343  -0.4444   4.2886
 PIL  C2    C   CR6   0   0.351   0.2048  -0.3738   2.6173
 PIL  C1    C   CR16  0  -0.402  -0.3257  -0.3840   1.3430
 PIL  O3    O   O2    0  -0.469  -0.5012  -0.3533   3.7568
 PIL  C4    C   CH1   0  -0.033  -1.9157  -0.1602   3.7177
 PIL  C5    C   CH2   0  -0.478  -2.2676   1.2938   3.4203
 PIL  C6    C   CH2   0  -0.440  -1.9781   2.0388   4.7337
 PIL  C7    C   CH2   0  -0.449  -2.0331   0.9693   5.8497
 PIL  C8    C   CH2   0  -0.453  -2.4098  -0.3401   5.1435
 PIL  H23   H   HCR6  0   0.298  -0.3302   1.9971  -6.1221
 PIL  H21   H   HCR6  0   0.296  -0.9931  -2.0630  -5.9423
 PIL  H16   H   HNH1  0   0.417   1.4841   0.4775  -1.9780
 PIL  H13   H   HCR6  0   0.262   2.5572  -0.5141  -0.4556
 PIL  H12   H   HCR6  0   0.291   3.5044  -0.4972   1.7676
 PIL  H111  H   HCH3  0   0.263   3.5589  -0.4325   5.3682
 PIL  H112  H   HCH3  0   0.232   3.8930  -1.3531   3.8905
 PIL  H113  H   HCH3  0   0.233   3.9439   0.4250   3.8654
 PIL  H1    H   HCR6  0   0.285  -1.3964  -0.3633   1.1961
 PIL  H4    H   HCH1  0   0.251  -2.3748  -0.8724   3.0244
 PIL  H51   H   HCH2  0   0.251  -1.7312   1.7076   2.5651
 PIL  H52   H   HCH2  0   0.242  -3.3315   1.3381   3.1757
 PIL  H61   H   HCH2  0   0.232  -2.7002   2.8387   4.8969
 PIL  H62   H   HCH2  0   0.233  -0.9938   2.5067   4.6999
 PIL  H71   H   HCH2  0   0.231  -2.7515   1.2219   6.6297
 PIL  H72   H   HCH2  0   0.233  -1.0617   0.8750   6.3359
 PIL  H81   H   HCH2  0   0.238  -3.4947  -0.4611   5.1100
 PIL  H82   H   HCH2  0   0.245  -2.0022  -1.2321   5.6220

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
 PIL  CL25  C24   single    1.720  0.020  1.720
 PIL  C24   C23   aromatic  1.386  0.020  1.386
 PIL  C24   C18   aromatic  1.394  0.020  1.394
 PIL  C23   N22   aromatic  1.323  0.020  1.323
 PIL  C23   H23   single    0.930  0.020  1.080
 PIL  N22   C21   aromatic  1.323  0.020  1.323
 PIL  C21   C19   aromatic  1.387  0.020  1.387
 PIL  C21   H21   single    0.930  0.020  1.080
 PIL  C19   CL20  single    1.716  0.020  1.716
 PIL  C19   C18   aromatic  1.394  0.020  1.394
 PIL  C18   N16   single    1.389  0.020  1.389
 PIL  N16   C15   single    1.373  0.020  1.373
 PIL  N16   H16   single    0.860  0.020  1.020
 PIL  C15   O17   double    1.215  0.020  1.215
 PIL  C15   C14   single    1.481  0.020  1.481
 PIL  C14   C13   aromatic  1.385  0.020  1.385
 PIL  C14   C1    aromatic  1.401  0.020  1.401
 PIL  C13   C12   aromatic  1.390  0.020  1.390
 PIL  C13   H13   single    0.930  0.020  1.080
 PIL  C12   C9    aromatic  1.386  0.020  1.386
 PIL  C12   H12   single    0.930  0.020  1.080
 PIL  C9    O10   single    1.337  0.020  1.337
 PIL  C9    C2    aromatic  1.415  0.020  1.415
 PIL  O10   C11   single    1.415  0.020  1.415
 PIL  C11   H111  single    0.970  0.020  1.090
 PIL  C11   H112  single    0.970  0.020  1.090
 PIL  C11   H113  single    0.970  0.020  1.090
 PIL  C2    C1    aromatic  1.380  0.020  1.380
 PIL  C2    O3    single    1.341  0.020  1.341
 PIL  C1    H1    single    0.930  0.020  1.080
 PIL  O3    C4    single    1.428  0.020  1.428
 PIL  C4    C5    single    1.525  0.020  1.525
 PIL  C4    C8    single    1.520  0.020  1.520
 PIL  C4    H4    single    0.970  0.020  1.090
 PIL  C5    C6    single    1.537  0.020  1.537
 PIL  C5    H51   single    0.970  0.020  1.090
 PIL  C5    H52   single    0.970  0.020  1.090
 PIL  C6    C7    single    1.547  0.020  1.547
 PIL  C6    H61   single    0.970  0.020  1.090
 PIL  C6    H62   single    0.970  0.020  1.090
 PIL  C7    C8    single    1.535  0.020  1.535
 PIL  C7    H71   single    0.970  0.020  1.090
 PIL  C7    H72   single    0.970  0.020  1.090
 PIL  C8    H81   single    0.970  0.020  1.090
 PIL  C8    H82   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
 PIL  C18   C24  C23   120.27  3.000
 PIL  C18   C24  CL25  119.97  3.000
 PIL  C23   C24  CL25  119.76  3.000
 PIL  H23   C23  N22   117.61  3.000
 PIL  H23   C23  C24   120.08  3.000
 PIL  N22   C23  C24   122.31  3.000
 PIL  C21   N22  C23   118.71  3.000
 PIL  H21   C21  C19   119.80  3.000
 PIL  H21   C21  N22   117.49  3.000
 PIL  C19   C21  N22   122.70  3.000
 PIL  C18   C19  CL20  120.84  3.000
 PIL  C18   C19  C21   119.82  3.000
 PIL  CL20  C19  C21   119.29  3.000
 PIL  N16   C18  C19   122.42  3.000
 PIL  N16   C18  C24   121.39  3.000
 PIL  C19   C18  C24   116.17  3.000
 PIL  H16   N16  C15   118.53  3.000
 PIL  H16   N16  C18   116.76  3.000
 PIL  C15   N16  C18   122.08  3.000
 PIL  C14   C15  O17   122.99  3.000
 PIL  C14   C15  N16   115.56  3.000
 PIL  O17   C15  N16   121.44  3.000
 PIL  C1    C14  C13   119.44  3.000
 PIL  C1    C14  C15   117.58  3.000
 PIL  C13   C14  C15   122.95  3.000
 PIL  H13   C13  C12   117.99  3.000
 PIL  H13   C13  C14   121.73  3.000
 PIL  C12   C13  C14   120.25  3.000
 PIL  H12   C12  C9    120.82  3.000
 PIL  H12   C12  C13   118.65  3.000
 PIL  C9    C12  C13   120.53  3.000
 PIL  C2    C9   O10   115.45  3.000
 PIL  C2    C9   C12   119.57  3.000
 PIL  O10   C9   C12   124.98  3.000
 PIL  C11   O10  C9    118.54  3.000
 PIL  H113  C11  H112  108.94  3.000
 PIL  H113  C11  H111  108.81  3.000
 PIL  H112  C11  H111  108.83  3.000
 PIL  H113  C11  O10   111.89  3.000
 PIL  H112  C11  O10   111.91  3.000
 PIL  H111  C11  O10   106.35  3.000
 PIL  O3    C2   C1    125.61  3.000
 PIL  O3    C2   C9    115.10  3.000
 PIL  C1    C2   C9    119.27  3.000
 PIL  H1    C1   C2    120.40  3.000
 PIL  H1    C1   C14   118.68  3.000
 PIL  C2    C1   C14   120.92  3.000
 PIL  C4    O3   C2    120.03  3.000
 PIL  H4    C4   C8    112.39  3.000
 PIL  H4    C4   C5    113.57  3.000
 PIL  C8    C4   C5    102.75  3.000
 PIL  H4    C4   O3    110.16  3.000
 PIL  C8    C4   O3    106.28  3.000
 PIL  C5    C4   O3    111.27  3.000
 PIL  H52   C5   H51   106.73  3.000
 PIL  H52   C5   C6    110.80  3.000
 PIL  H51   C5   C6    113.16  3.000
 PIL  H52   C5   C4    107.88  3.000
 PIL  H51   C5   C4    113.63  3.000
 PIL  C6    C5   C4    104.59  3.000
 PIL  H62   C6   H61   106.72  3.000
 PIL  H62   C6   C7    110.56  3.000
 PIL  H61   C6   C7    112.07  3.000
 PIL  H62   C6   C5    110.58  3.000
 PIL  H61   C6   C5    111.03  3.000
 PIL  C7    C6   C5    105.94  3.000
 PIL  H72   C7   H71   106.74  3.000
 PIL  H72   C7   C8    110.49  3.000
 PIL  H71   C7   C8    111.42  3.000
 PIL  H72   C7   C6    110.48  3.000
 PIL  H71   C7   C6    112.31  3.000
 PIL  C8    C7   C6    105.47  3.000
 PIL  H82   C8   H81   107.10  3.000
 PIL  H82   C8   C7    113.83  3.000
 PIL  H81   C8   C7    110.64  3.000
 PIL  H82   C8   C4    112.75  3.000
 PIL  H81   C8   C4    107.89  3.000
 PIL  C7    C8   C4    104.53  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
 PIL  CONST_01  C21   N22  C23  C24     0.00   0.0  0
 PIL  CONST_02  C21   C19  C18  C24     0.00   0.0  0
 PIL  CONST_03  C19   C18  C24  C23     0.00   0.0  0
 PIL  CONST_04  C19   C21  N22  C23     0.00   0.0  0
 PIL  CONST_05  C18   C24  C23  N22     0.00   0.0  0
 PIL  CONST_06  C18   C19  C21  N22     0.00   0.0  0
 PIL  CONST_07  C9    C12  C13  C14     0.00   0.0  0
 PIL  CONST_08  C9    C2   C1   C14     0.00   0.0  0
 PIL  CONST_09  C2    C1   C14  C13     0.00   0.0  0
 PIL  CONST_10  C2    C9   C12  C13     0.00   0.0  0
 PIL  CONST_11  C1    C14  C13  C12     0.00   0.0  0
 PIL  CONST_12  C1    C2   C9   C12     0.00   0.0  0
 PIL  CONST_13  N22   C23  C24  CL25  180.00   0.0  0
 PIL  CONST_14  C19   C18  C24  CL25  180.00   0.0  0
 PIL  CONST_15  CL20  C19  C18  C24   180.00   0.0  0
 PIL  CONST_16  N16   C18  C24  C23   180.00   0.0  0
 PIL  CONST_17  CL20  C19  C21  N22   180.00   0.0  0
 PIL  CONST_18  N16   C18  C19  C21   180.00   0.0  0
 PIL  CONST_19  C12   C13  C14  C15   180.00   0.0  0
 PIL  CONST_20  C2    C1   C14  C15   180.00   0.0  0
 PIL  CONST_21  O3    C2   C1   C14   180.00   0.0  0
 PIL  CONST_22  O10   C9   C12  C13   180.00   0.0  0
 PIL  CONST_23  O3    C2   C9   C12   180.00   0.0  0
 PIL  CONST_24  C1    C2   C9   O10   180.00   0.0  0
 PIL  CONST_25  H21   C21  N22  C23   180.00   0.0  0
 PIL  CONST_26  H23   C23  N22  C21   180.00   0.0  0
 PIL  CONST_27  H12   C12  C13  C14   180.00   0.0  0
 PIL  CONST_28  H1    C1   C14  C13   180.00   0.0  0
 PIL  CONST_29  H13   C13  C12  C9    180.00   0.0  0
 PIL  CONST_30  C14   C15  N16  C18   180.00   0.0  0
 PIL  CONST_34  O17   C15  N16  C18     0.00   0.0  0
 PIL  Var_01    C7    C6   C5   C4    -22.32  30.0  1
 PIL  Var_02    C6    C7   C8   C4     26.17  30.0  1
 PIL  Var_03    C8    C7   C6   C5     -2.28  30.0  1
 PIL  Var_04    C13   C14  C15  N16   -20.58  30.0  2
 PIL  Var_05    C2    C9   O10  C11   179.97  30.0  2
 PIL  Var_06    H111  C11  O10  C9    179.90  30.0  3

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
 PIL  chir_01  C4  O3  C5  C8  positiv

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
 PIL  plan-1  CL25  0.020
 PIL  plan-1  C24   0.020
 PIL  plan-1  C23   0.020
 PIL  plan-1  N22   0.020
 PIL  plan-1  C21   0.020
 PIL  plan-1  C19   0.020
 PIL  plan-1  CL20  0.020
 PIL  plan-1  C18   0.020
 PIL  plan-1  N16   0.020
 PIL  plan-1  H23   0.020
 PIL  plan-1  H21   0.020
 PIL  plan-2  C15   0.020
 PIL  plan-2  C14   0.020
 PIL  plan-2  C13   0.020
 PIL  plan-2  C12   0.020
 PIL  plan-2  C9    0.020
 PIL  plan-2  O10   0.020
 PIL  plan-2  C2    0.020
 PIL  plan-2  C1    0.020
 PIL  plan-2  O3    0.020
 PIL  plan-2  H13   0.020
 PIL  plan-2  H12   0.020
 PIL  plan-2  H1    0.020
 PIL  plan-3  C18   0.020
 PIL  plan-3  N16   0.020
 PIL  plan-3  C15   0.020
 PIL  plan-3  O17   0.020
 PIL  plan-3  C14   0.020
 PIL  plan-3  H16   0.020

