# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Jun  9 19:55:08 2020
#   Inital geometry file: a 83 line input string
#   Ligand name: N-(5-chloro-1,3-benzoxazol-2-yl)-2-cyclopentylacetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1ccc2oc(NC(=O)CC3CCCC3)nc2c1
#
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
 ZYI  ZYI  N-(5-chloro-1,3-benzoxazol-2-yl)-2-cyclopentylacetamide  ligand  34  19  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_ZYI
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
 ZYI  N1    N   N     0  -0.490   1.2742  -1.4384  -0.3741
 ZYI  C2    C   CR5   0   0.722   0.3360  -0.6495   0.0284
 ZYI  O3    O   O     0  -0.432   0.7201   0.5659   0.4432
 ZYI  C4    C   CR56  0   0.355   2.0748   0.5594   0.2879
 ZYI  C5    C   CR16  0  -0.337   2.9779   1.5597   0.5609
 ZYI  C6    C   CR16  0  -0.234   4.3103   1.2638   0.2972
 ZYI  C7    C   CR6   0  -0.046   4.6707   0.0161  -0.2133
 ZYI  CL8   CL  CL    0  -0.126   6.3505  -0.2944  -0.5206
 ZYI  C9    C   CR16  0  -0.286   3.7509  -0.9855  -0.4849
 ZYI  C10   C   CR56  0   0.170   2.4217  -0.6868  -0.2211
 ZYI  N11   N   NH1   0  -0.752  -0.9844  -0.9704   0.0408
 ZYI  C12   C   C     0   0.571  -2.0486  -0.2137   0.4957
 ZYI  C13   C   CH2   0  -0.615  -3.3697  -0.9308   0.3718
 ZYI  C14   C   CR15  0  -0.232  -4.5789  -0.0115   0.3835
 ZYI  C15   C   CH2   0  -0.434  -5.9020  -0.7930   0.3701
 ZYI  C16   C   CH2   0  -0.445  -6.9401   0.1404  -0.2909
 ZYI  C17   C   CH2   0  -0.449  -6.1546   1.3829  -0.7485
 ZYI  C18   C   CH2   0  -0.425  -4.7058   0.9101  -0.8285
 ZYI  O19   O   O     0  -0.423  -1.9109   0.8913   0.9632
 ZYI  H5    H   HCR6  0   0.290   2.6831   2.5219   0.9557
 ZYI  H6    H   HCR6  0   0.286   5.0707   2.0075   0.4899
 ZYI  H9    H   HCR6  0   0.289   4.0516  -1.9459  -0.8796
 ZYI  HN11  H   HNH1  0   0.438  -1.1837  -1.8922  -0.3217
 ZYI  H13   H   HCH2  0   0.267  -3.3769  -1.5450  -0.5340
 ZYI  H13A  H   HCH2  0   0.298  -3.4255  -1.6358   1.2101
 ZYI  H14   H   HCR5  0   0.234  -4.5474   0.6089   1.2850
 ZYI  H15   H   HCH2  0   0.222  -5.7852  -1.7063  -0.2201
 ZYI  H15A  H   HCH2  0   0.234  -6.1947  -1.1053   1.3735
 ZYI  H16   H   HCH2  0   0.226  -7.4053  -0.3550  -1.1443
 ZYI  H16A  H   HCH2  0   0.228  -7.7479   0.4050   0.3926
 ZYI  H17   H   HCH2  0   0.229  -6.5233   1.7903  -1.6908
 ZYI  H17A  H   HCH2  0   0.220  -6.2362   2.1772  -0.0021
 ZYI  H18   H   HCH2  0   0.235  -3.9864   1.7304  -0.8268
 ZYI  H18A  H   HCH2  0   0.212  -4.5462   0.3340  -1.7467

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
 ZYI  N1   C2    aromatic  1.290  0.020  1.290
 ZYI  N1   C10   aromatic  1.380  0.020  1.380
 ZYI  N11  C2    single    1.359  0.020  1.359
 ZYI  C2   O3    aromatic  1.340  0.020  1.340
 ZYI  O3   C4    aromatic  1.364  0.020  1.364
 ZYI  C10  C4    aromatic  1.390  0.020  1.390
 ZYI  C4   C5    aromatic  1.375  0.020  1.375
 ZYI  C6   C5    aromatic  1.390  0.020  1.390
 ZYI  C5   H5    single    0.930  0.020  1.080
 ZYI  C7   C6    aromatic  1.395  0.020  1.395
 ZYI  C6   H6    single    0.930  0.020  1.080
 ZYI  C9   C7    aromatic  1.387  0.020  1.387
 ZYI  CL8  C7    single    1.736  0.020  1.736
 ZYI  C9   C10   aromatic  1.388  0.020  1.388
 ZYI  C9   H9    single    0.930  0.020  1.080
 ZYI  C12  N11   single    1.383  0.020  1.383
 ZYI  N11  HN11  single    0.860  0.020  1.020
 ZYI  O19  C12   double    1.208  0.020  1.208
 ZYI  C13  C12   single    1.508  0.020  1.508
 ZYI  C14  C13   single    1.519  0.020  1.519
 ZYI  C13  H13   single    0.970  0.020  1.090
 ZYI  C13  H13A  single    0.970  0.020  1.090
 ZYI  C15  C14   single    1.537  0.020  1.537
 ZYI  C18  C14   single    1.528  0.020  1.528
 ZYI  C14  H14   single    0.970  0.020  1.090
 ZYI  C16  C15   single    1.545  0.020  1.545
 ZYI  C15  H15   single    0.970  0.020  1.090
 ZYI  C15  H15A  single    0.970  0.020  1.090
 ZYI  C16  C17   single    1.540  0.020  1.540
 ZYI  C16  H16   single    0.970  0.020  1.090
 ZYI  C16  H16A  single    0.970  0.020  1.090
 ZYI  C17  C18   single    1.526  0.020  1.526
 ZYI  C17  H17   single    0.970  0.020  1.090
 ZYI  C17  H17A  single    0.970  0.020  1.090
 ZYI  C18  H18   single    0.970  0.020  1.090
 ZYI  C18  H18A  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
 ZYI  C10   N1   C2   103.71  3.000
 ZYI  N11   C2   O3   119.32  3.000
 ZYI  O3    C2   N1   116.27  3.000
 ZYI  N11   C2   N1   124.40  3.000
 ZYI  C4    O3   C2   104.19  3.000
 ZYI  C10   C4   C5   124.12  3.000
 ZYI  C5    C4   O3   128.79  3.000
 ZYI  C10   C4   O3   107.09  3.000
 ZYI  H5    C5   C6   121.34  3.000
 ZYI  H5    C5   C4   122.75  3.000
 ZYI  C6    C5   C4   115.91  3.000
 ZYI  H6    C6   C7   119.91  3.000
 ZYI  H6    C6   C5   119.60  3.000
 ZYI  C7    C6   C5   120.48  3.000
 ZYI  C9    C7   CL8  118.56  3.000
 ZYI  CL8   C7   C6   118.34  3.000
 ZYI  C9    C7   C6   123.10  3.000
 ZYI  H9    C9   C10  121.80  3.000
 ZYI  H9    C9   C7   121.92  3.000
 ZYI  C10   C9   C7   116.27  3.000
 ZYI  C9    C10  C4   120.11  3.000
 ZYI  C9    C10  N1   131.15  3.000
 ZYI  C4    C10  N1   108.74  3.000
 ZYI  HN11  N11  C12  117.74  3.000
 ZYI  HN11  N11  C2   113.81  3.000
 ZYI  C12   N11  C2   128.43  3.000
 ZYI  O19   C12  C13  124.52  3.000
 ZYI  C13   C12  N11  112.76  3.000
 ZYI  O19   C12  N11  122.70  3.000
 ZYI  H13A  C13  H13  105.75  3.000
 ZYI  H13A  C13  C14  110.04  3.000
 ZYI  H13   C13  C14  109.92  3.000
 ZYI  H13A  C13  C12  106.71  3.000
 ZYI  H13   C13  C12  109.91  3.000
 ZYI  C14   C13  C12  114.14  3.000
 ZYI  H14   C14  C18  108.28  3.000
 ZYI  H14   C14  C15  108.67  3.000
 ZYI  C18   C14  C15  103.20  3.000
 ZYI  H14   C14  C13  109.05  3.000
 ZYI  C18   C14  C13  115.16  3.000
 ZYI  C15   C14  C13  112.19  3.000
 ZYI  H15A  C15  H15  106.62  3.000
 ZYI  H15A  C15  C16  112.73  3.000
 ZYI  H15   C15  C16  110.21  3.000
 ZYI  H15A  C15  C14  111.63  3.000
 ZYI  H15   C15  C14  109.71  3.000
 ZYI  C16   C15  C14  105.97  3.000
 ZYI  H16A  C16  H16  106.53  3.000
 ZYI  H16A  C16  C17  111.62  3.000
 ZYI  H16   C16  C17  110.58  3.000
 ZYI  H16A  C16  C15  112.10  3.000
 ZYI  H16   C16  C15  110.30  3.000
 ZYI  C17   C16  C15  105.78  3.000
 ZYI  H17A  C17  H17  107.05  3.000
 ZYI  H17A  C17  C18  109.38  3.000
 ZYI  H17   C17  C18  113.04  3.000
 ZYI  H17A  C17  C16  110.20  3.000
 ZYI  H17   C17  C16  112.69  3.000
 ZYI  C18   C17  C16  104.47  3.000
 ZYI  H18A  C18  H18  107.49  3.000
 ZYI  H18A  C18  C17  110.19  3.000
 ZYI  H18   C18  C17  113.14  3.000
 ZYI  H18A  C18  C14  109.60  3.000
 ZYI  H18   C18  C14  113.42  3.000
 ZYI  C17   C18  C14  102.95  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
 ZYI  CONST_01  C4    O3   C2   N1      0.00   0.0  0
 ZYI  CONST_02  O3    C4   C10  N1      0.00   0.0  0
 ZYI  CONST_03  C5    C4   C10  N1    180.00   0.0  0
 ZYI  CONST_04  C7    C9   C10  N1    180.00   0.0  0
 ZYI  CONST_05  C4    C10  N1   C2      0.00   0.0  0
 ZYI  CONST_06  C9    C10  N1   C2    180.00   0.0  0
 ZYI  CONST_07  C10   C4   O3   C2      0.00   0.0  0
 ZYI  CONST_08  C5    C4   O3   C2    180.00   0.0  0
 ZYI  CONST_09  C10   N1   C2   O3      0.00   0.0  0
 ZYI  CONST_10  C9    C10  C4   O3    180.00   0.0  0
 ZYI  CONST_11  C6    C5   C4   O3    180.00   0.0  0
 ZYI  CONST_12  C7    C9   C10  C4      0.00   0.0  0
 ZYI  CONST_13  C7    C6   C5   C4      0.00   0.0  0
 ZYI  CONST_14  C9    C10  C4   C5      0.00   0.0  0
 ZYI  CONST_15  C9    C7   C6   C5      0.00   0.0  0
 ZYI  CONST_16  C10   C4   C5   C6      0.00   0.0  0
 ZYI  CONST_17  C10   C9   C7   C6      0.00   0.0  0
 ZYI  CONST_18  N11   C2   O3   C4    180.00   0.0  0
 ZYI  CONST_19  CL8   C7   C6   C5    180.00   0.0  0
 ZYI  CONST_20  C10   C9   C7   CL8   180.00   0.0  0
 ZYI  CONST_21  N11   C2   N1   C10   180.00   0.0  0
 ZYI  CONST_22  H9    C9   C10  N1      0.00   0.0  0
 ZYI  CONST_23  H5    C5   C4   O3      0.00   0.0  0
 ZYI  CONST_24  H6    C6   C5   C4    180.00   0.0  0
 ZYI  CONST_25  C12   N11  C2   N1    180.00   0.0  0
 ZYI  CONST_26  C12   N11  C2   O3      0.00   0.0  0
 ZYI  CONST_27  HN11  N11  C2   N1      0.00   0.0  0
 ZYI  CONST_28  O19   C12  N11  C2      0.00   0.0  0
 ZYI  CONST_29  C13   C12  N11  C2    180.00   0.0  0
 ZYI  Var_01    C17   C16  C15  C14     4.79  30.0  1
 ZYI  Var_02    C16   C17  C18  C14   -38.72  30.0  1
 ZYI  Var_03    C18   C17  C16  C15    20.84  30.0  1
 ZYI  Var_04    C14   C13  C12  N11  -159.48  30.0  2

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
 ZYI  chir_01  C14  C13  C15  C18  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
 ZYI  plan-1  N1    0.020
 ZYI  plan-1  C2    0.020
 ZYI  plan-1  O3    0.020
 ZYI  plan-1  C4    0.020
 ZYI  plan-1  C5    0.020
 ZYI  plan-1  C6    0.020
 ZYI  plan-1  C7    0.020
 ZYI  plan-1  CL8   0.020
 ZYI  plan-1  C9    0.020
 ZYI  plan-1  C10   0.020
 ZYI  plan-1  N11   0.020
 ZYI  plan-1  H5    0.020
 ZYI  plan-1  H6    0.020
 ZYI  plan-1  H9    0.020
 ZYI  plan-2  C2    0.020
 ZYI  plan-2  N11   0.020
 ZYI  plan-2  C12   0.020
 ZYI  plan-2  C13   0.020
 ZYI  plan-2  O19   0.020
 ZYI  plan-2  HN11  0.020

