# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 23:01:38 2021
#   Inital geometry file: a 85 line input string
#   Ligand name: 4-chloranyl-~{N}-[[cyclopropylmethyl(methanoyl)amino]methyl]benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1ccc(cc1)C(=O)NCN(CC2CC2)C=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
 OAX  OAX  4-chloranyl-~{N}-[[cyclopropylmethyl(methanoyl)amino]methyl]benzamide  ligand  33  18  .  2022-07-22  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_OAX
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
 OAX  C4   C   C1    0   0.265   9.1534  10.5904   1.4781
 OAX  O3   O   O     0  -0.482   8.5289  10.0674   0.5751
 OAX  N2   N   NT    0  -0.417  10.3555  11.1876   1.3582
 OAX  C5   C   CH2   0  -0.321  11.0093  11.3221   0.0680
 OAX  C7   C   CH1   0  -0.239  12.0227  10.2426  -0.2435
 OAX  C8   C   CH2   0  -0.491  12.7615   9.4782   0.8116
 OAX  C6   C   CH2   0  -0.488  11.7478   8.7853  -0.0504
 OAX  C9   C   CH2   0  -0.182  10.9293  11.8630   2.4997
 OAX  N3   N   NH1   0  -0.651  10.6739  13.2805   2.5099
 OAX  C10  C   C     0   0.548  11.6064  14.2158   2.2331
 OAX  O4   O   O     0  -0.478  12.7427  13.9411   1.8785
 OAX  C11  C   CR6   0  -0.022  11.1732  15.6391   2.3792
 OAX  C15  C   CR16  0  -0.272  11.8836  16.6119   1.6801
 OAX  C16  C   CR16  0  -0.198  11.5415  17.9495   1.7780
 OAX  C12  C   CR6   0  -0.040  10.4873  18.3177   2.6008
 OAX  CL1  CL  CL    0  -0.114  10.0566  19.9867   2.7347
 OAX  C13  C   CR16  0  -0.194   9.7766  17.3713   3.3215
 OAX  C14  C   CR16  0  -0.296  10.1232  16.0345   3.2046
 OAX  H1   H   H     0   0.205   8.7760  10.6142   2.5128
 OAX  H2   H   HCH2  0   0.261  11.5090  12.2913   0.0464
 OAX  H3   H   HCH2  0   0.257  10.2470  11.3494  -0.7111
 OAX  H4   H   HCH1  0   0.258  12.6045  10.4885  -1.1260
 OAX  H5   H   HCH2  0   0.252  13.8108   9.2713   0.6450
 OAX  H6   H   HCH2  0   0.245  12.5052   9.6318   1.8525
 OAX  H7   H   HCH2  0   0.247  10.8151   8.4881   0.4108
 OAX  H8   H   HCH2  0   0.250  12.1010   8.1000  -0.8105
 OAX  H9   H   HCH2  0   0.287  10.5150  11.4229   3.4063
 OAX  H10  H   HCH2  0   0.275  12.0049  11.7096   2.5191
 OAX  H11  H   HNH1  0   0.413   9.7315  13.5702   2.7165
 OAX  H12  H   HCR6  0   0.273  12.7115  16.3265   1.0456
 OAX  H13  H   HCR6  0   0.287  12.0918  18.6946   1.2203
 OAX  H14  H   HCR6  0   0.289   8.9643  17.6663   3.9713
 OAX  H15  H   HCR6  0   0.272   9.5682  15.3162   3.7941

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
 OAX  C7   C5   single    1.513  0.020  1.513
 OAX  C7   C6   single    1.495  0.020  1.495
 OAX  C7   C8   single    1.498  0.020  1.498
 OAX  O3   C4   double    1.216  0.020  1.216
 OAX  C5   N2   single    1.453  0.020  1.453
 OAX  C6   C8   single    1.500  0.020  1.500
 OAX  C4   N2   single    1.348  0.020  1.348
 OAX  N2   C9   single    1.445  0.020  1.445
 OAX  O4   C10  double    1.222  0.020  1.222
 OAX  C15  C16  aromatic  1.384  0.020  1.384
 OAX  C15  C11  aromatic  1.393  0.020  1.393
 OAX  C16  C12  aromatic  1.387  0.020  1.387
 OAX  C10  C11  single    1.495  0.020  1.495
 OAX  C10  N3   single    1.349  0.020  1.349
 OAX  C11  C14  aromatic  1.393  0.020  1.393
 OAX  C9   N3   single    1.440  0.020  1.440
 OAX  C12  CL1  single    1.729  0.020  1.729
 OAX  C12  C13  aromatic  1.386  0.020  1.386
 OAX  C14  C13  aromatic  1.386  0.020  1.386
 OAX  C4   H1   single    0.930  0.020  1.080
 OAX  C5   H2   single    0.970  0.020  1.090
 OAX  C5   H3   single    0.970  0.020  1.090
 OAX  C7   H4   single    0.970  0.020  1.090
 OAX  C8   H5   single    0.970  0.020  1.090
 OAX  C8   H6   single    0.970  0.020  1.090
 OAX  C6   H7   single    0.970  0.020  1.090
 OAX  C6   H8   single    0.970  0.020  1.090
 OAX  C9   H9   single    0.970  0.020  1.090
 OAX  C9   H10  single    0.970  0.020  1.090
 OAX  N3   H11  single    0.860  0.020  1.020
 OAX  C15  H12  single    0.930  0.020  1.080
 OAX  C16  H13  single    0.930  0.020  1.080
 OAX  C13  H14  single    0.930  0.020  1.080
 OAX  C14  H15  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
 OAX  H1   C4   N2   112.31  3.000
 OAX  H1   C4   O3   122.06  3.000
 OAX  N2   C4   O3   125.63  3.000
 OAX  C9   N2   C5   118.66  3.000
 OAX  C9   N2   C4   119.41  3.000
 OAX  C5   N2   C4   121.43  3.000
 OAX  H3   C5   H2   106.50  3.000
 OAX  H3   C5   C7   109.82  3.000
 OAX  H2   C5   C7   108.85  3.000
 OAX  H3   C5   N2   108.80  3.000
 OAX  H2   C5   N2   107.82  3.000
 OAX  C7   C5   N2   114.72  3.000
 OAX  H4   C7   C6   115.11  3.000
 OAX  H4   C7   C8   115.09  3.000
 OAX  C6   C7   C8    60.16  3.000
 OAX  H4   C7   C5   111.40  3.000
 OAX  C8   C7   C5   123.33  3.000
 OAX  C6   C7   C5   123.06  3.000
 OAX  H6   C8   H5   113.86  3.000
 OAX  H6   C8   C6   117.25  3.000
 OAX  H5   C8   C6   118.57  3.000
 OAX  H6   C8   C7   119.21  3.000
 OAX  H5   C8   C7   117.86  3.000
 OAX  C6   C8   C7    59.84  3.000
 OAX  H8   C6   H7   113.98  3.000
 OAX  H8   C6   C8   118.38  3.000
 OAX  H7   C6   C8   117.67  3.000
 OAX  H8   C6   C7   117.79  3.000
 OAX  H7   C6   C7   118.76  3.000
 OAX  C8   C6   C7    60.00  3.000
 OAX  H10  C9   H9   107.73  3.000
 OAX  H10  C9   N3   108.32  3.000
 OAX  H9   C9   N3   108.92  3.000
 OAX  H10  C9   N2   109.95  3.000
 OAX  H9   C9   N2   108.51  3.000
 OAX  N3   C9   N2   113.27  3.000
 OAX  H11  N3   C10  119.29  3.000
 OAX  H11  N3   C9   116.77  3.000
 OAX  C10  N3   C9   123.92  3.000
 OAX  C11  C10  O4   120.80  3.000
 OAX  C11  C10  N3   116.08  3.000
 OAX  O4   C10  N3   123.13  3.000
 OAX  C14  C11  C15  118.93  3.000
 OAX  C14  C11  C10  123.14  3.000
 OAX  C15  C11  C10  117.91  3.000
 OAX  H12  C15  C16  119.07  3.000
 OAX  H12  C15  C11  120.04  3.000
 OAX  C16  C15  C11  120.89  3.000
 OAX  H13  C16  C12  120.66  3.000
 OAX  H13  C16  C15  120.24  3.000
 OAX  C12  C16  C15  119.10  3.000
 OAX  C13  C12  CL1  119.42  3.000
 OAX  C13  C12  C16  121.13  3.000
 OAX  CL1  C12  C16  119.44  3.000
 OAX  H14  C13  C14  120.11  3.000
 OAX  H14  C13  C12  120.77  3.000
 OAX  C14  C13  C12  119.12  3.000
 OAX  H15  C14  C13  117.77  3.000
 OAX  H15  C14  C11  121.40  3.000
 OAX  C13  C14  C11  120.82  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
 OAX  CONST_01  C12  C16  C15  C11     0.00   0.0  0
 OAX  CONST_02  C12  C13  C14  C11     0.00   0.0  0
 OAX  CONST_03  C13  C12  C16  C15     0.00   0.0  0
 OAX  CONST_04  C13  C14  C11  C15     0.00   0.0  0
 OAX  CONST_05  C14  C11  C15  C16     0.00   0.0  0
 OAX  CONST_06  C14  C13  C12  C16     0.00   0.0  0
 OAX  CONST_07  C16  C15  C11  C10   180.00   0.0  0
 OAX  CONST_08  C13  C14  C11  C10   180.00   0.0  0
 OAX  CONST_09  CL1  C12  C16  C15   180.00   0.0  0
 OAX  CONST_10  C14  C13  C12  CL1   180.00   0.0  0
 OAX  CONST_11  H13  C16  C15  C11   180.00   0.0  0
 OAX  CONST_12  H14  C13  C14  C11   180.00   0.0  0
 OAX  CONST_13  H15  C14  C11  C15   180.00   0.0  0
 OAX  CONST_14  H12  C15  C16  C12   180.00   0.0  0
 OAX  CONST_15  C11  C10  N3   C9    180.00   0.0  0
 OAX  CONST_16  H11  N3   C10  C11     0.00   0.0  0
 OAX  CONST_17  C5   N2   C4   O3      0.00   0.0  0
 OAX  CONST_18  C9   N2   C4   O3    180.00   0.0  0
 OAX  CONST_19  O4   C10  N3   C9      0.00   0.0  0
 OAX  Var_01    C8   C6   C7   C5   -112.48  30.0  1
 OAX  Var_02    H5   C8   C6   C7   -107.39  30.0  1
 OAX  Var_03    C6   C7   C5   N2     47.35  30.0  1
 OAX  Var_04    C15  C11  C10  N3   -157.59  30.0  2
 OAX  Var_05    C7   C5   N2   C4    -96.03  30.0  2
 OAX  Var_06    N3   C9   N2   C4    -95.97  30.0  3
 OAX  Var_07    C10  N3   C9   N2   -106.44  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
 OAX  chir_01  C7  C5  C6  C8  both

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
 OAX  plan-1  C10  0.020
 OAX  plan-1  C11  0.020
 OAX  plan-1  C15  0.020
 OAX  plan-1  C16  0.020
 OAX  plan-1  C12  0.020
 OAX  plan-1  CL1  0.020
 OAX  plan-1  C13  0.020
 OAX  plan-1  C14  0.020
 OAX  plan-1  H12  0.020
 OAX  plan-1  H13  0.020
 OAX  plan-1  H14  0.020
 OAX  plan-1  H15  0.020
 OAX  plan-2  C9   0.020
 OAX  plan-2  N3   0.020
 OAX  plan-2  C10  0.020
 OAX  plan-2  O4   0.020
 OAX  plan-2  C11  0.020
 OAX  plan-2  H11  0.020
 OAX  plan-3  C4   0.020
 OAX  plan-3  O3   0.020
 OAX  plan-3  N2   0.020
 OAX  plan-3  C5   0.020
 OAX  plan-3  C9   0.020
 OAX  plan-3  H1   0.020

