# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 04:24:37 2020
#   Inital geometry file: a 91 line input string
#   Ligand name: 4-[(E)-{[(2S)-tetrahydro-2H-pyran-2-yloxy]imino}methyl]benzenecarboximidamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=N)c1ccc(cc1)/C=N/O[C@H]2CCCCO2
#
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
 O04  O04  4-[(E)-{[(2S)-tetrahydro-2H-pyran-2-yloxy]imino}methyl]benzenecarboximidamide  ligand  35  18  .  2021-08-17  2021-08-17  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_O04
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
 O04  C1    C  C     0   0.337  -5.3249   0.6804  -0.1417
 O04  N1    N  NH2   0  -0.822  -6.2813  -0.2731   0.0586
 O04  O1    O  O2    0  -0.406   2.2942  -1.0404   0.2347
 O04  C2    C  CR6   0   0.042  -3.9191   0.1910  -0.1023
 O04  N2    N  N     0  -0.099   1.0905  -0.3942   0.2714
 O04  O2    O  O2    0  -0.489   3.4746   0.6277  -0.7127
 O04  C3    C  CR16  0  -0.255  -2.8871   1.0889   0.1792
 O04  N3    N  N     0  -0.649  -5.5309   1.9134  -0.4051
 O04  C4    C  CR16  0  -0.271  -1.5727   0.6699   0.2147
 O04  C5    C  CR6   0   0.045  -1.2485  -0.6652  -0.0453
 O04  C6    C  C1    0  -0.070   0.1262  -1.1603  -0.0325
 O04  C7    C  CH1   0   0.332   3.3457  -0.1464   0.4465
 O04  C8    C  CH2   0  -0.194   4.5171   1.5828  -0.6135
 O04  C9    C  CH2   0  -0.454   5.8608   0.9111  -0.3927
 O04  C10   C  CH2   0  -0.462   5.7944   0.0003   0.8284
 O04  C11   C  CH2   0  -0.499   4.6021  -0.9493   0.7253
 O04  C12   C  CR16  0  -0.286  -2.2751  -1.5584  -0.3379
 O04  C13   C  CR16  0  -0.278  -3.5962  -1.1375  -0.3630
 O04  HN1   H  HNH2  0   0.392  -7.2308   0.0446   0.1732
 O04  HN1A  H  HNH2  0   0.396  -6.0532  -1.0676   0.6333
 O04  H3    H  HCR6  0   0.260  -3.1270   2.1245   0.3774
 O04  HN3   H  H     0   0.326  -6.5230   2.1345  -0.3829
 O04  H4    H  HCR6  0   0.259  -0.7901   1.3819   0.4419
 O04  H6    H  H     0   0.257   0.2846  -2.2062  -0.2949
 O04  H7    H  HCH1  0   0.189   3.1167   0.5051   1.3067
 O04  H8    H  HCH2  0   0.243   4.5041   2.1564  -1.5408
 O04  H8A   H  HCH2  0   0.204   4.3137   2.2831   0.2098
 O04  H9    H  HCH2  0   0.227   6.1319   0.3325  -1.2802
 O04  H9A   H  HCH2  0   0.240   6.6286   1.6767  -0.2633
 O04  H10   H  HCH2  0   0.247   6.7178  -0.5703   0.9369
 O04  H10A  H  HCH2  0   0.226   5.6954   0.6107   1.7317
 O04  H11   H  HCH2  0   0.250   4.4806  -1.5164   1.6507
 O04  H11A  H  HCH2  0   0.236   4.7627  -1.6667  -0.0853
 O04  H12   H  HCR6  0   0.263  -2.0439  -2.5944  -0.5532
 O04  H13   H  HCR6  0   0.263  -4.3664  -1.8560  -0.6108

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
 O04  C9   C10   single    1.525  0.020  1.525
 O04  C9   C8    single    1.518  0.020  1.518
 O04  C10  C11   single    1.528  0.020  1.528
 O04  C8   O2    single    1.417  0.020  1.417
 O04  C11  C7    single    1.517  0.020  1.517
 O04  O2   C7    single    1.400  0.020  1.400
 O04  C7   O1    single    1.396  0.020  1.396
 O04  O1   N2    single    1.367  0.020  1.367
 O04  N2   C6    double    1.269  0.020  1.269
 O04  C6   C5    single    1.461  0.020  1.461
 O04  C5   C12   aromatic  1.392  0.020  1.392
 O04  C5   C4    aromatic  1.398  0.020  1.398
 O04  C12  C13   aromatic  1.387  0.020  1.387
 O04  C4   C3    aromatic  1.380  0.020  1.380
 O04  C13  C2    aromatic  1.392  0.020  1.392
 O04  C3   C2    aromatic  1.397  0.020  1.397
 O04  C2   C1    single    1.489  0.020  1.489
 O04  C1   N1    single    1.365  0.020  1.365
 O04  C1   N3    double    1.277  0.020  1.277
 O04  N1   HN1   single    0.890  0.020  1.040
 O04  N1   HN1A  single    0.890  0.020  1.040
 O04  C3   H3    single    0.930  0.020  1.080
 O04  N3   HN3   single    0.890  0.020  1.040
 O04  C4   H4    single    0.930  0.020  1.080
 O04  C6   H6    single    0.930  0.020  1.080
 O04  C7   H7    single    0.970  0.020  1.090
 O04  C8   H8    single    0.970  0.020  1.090
 O04  C8   H8A   single    0.970  0.020  1.090
 O04  C9   H9    single    0.970  0.020  1.090
 O04  C9   H9A   single    0.970  0.020  1.090
 O04  C10  H10   single    0.970  0.020  1.090
 O04  C10  H10A  single    0.970  0.020  1.090
 O04  C11  H11   single    0.970  0.020  1.090
 O04  C11  H11A  single    0.970  0.020  1.090
 O04  C12  H12   single    0.930  0.020  1.080
 O04  C13  H13   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
 O04  N3    C1   C2   118.35  3.000
 O04  N3    C1   N1   126.25  3.000
 O04  C2    C1   N1   115.34  3.000
 O04  HN1A  N1   HN1  113.41  3.000
 O04  HN1A  N1   C1   118.44  3.000
 O04  HN1   N1   C1   117.16  3.000
 O04  C7    O1   N2   110.88  3.000
 O04  C13   C2   C3   118.69  3.000
 O04  C3    C2   C1   119.45  3.000
 O04  C13   C2   C1   121.85  3.000
 O04  C6    N2   O1   112.18  3.000
 O04  C8    O2   C7   112.48  3.000
 O04  H3    C3   C4   119.82  3.000
 O04  H3    C3   C2   119.26  3.000
 O04  C4    C3   C2   120.92  3.000
 O04  HN3   N3   C1   111.27  3.000
 O04  H4    C4   C5   119.97  3.000
 O04  H4    C4   C3   119.64  3.000
 O04  C5    C4   C3   120.39  3.000
 O04  C12   C5   C6   118.58  3.000
 O04  C12   C5   C4   118.74  3.000
 O04  C6    C5   C4   122.68  3.000
 O04  H6    C6   C5   117.37  3.000
 O04  H6    C6   N2   121.79  3.000
 O04  C5    C6   N2   120.84  3.000
 O04  H7    C7   C11  109.95  3.000
 O04  H7    C7   O2   109.77  3.000
 O04  C11   C7   O2   111.64  3.000
 O04  H7    C7   O1   109.88  3.000
 O04  O2    C7   O1   107.32  3.000
 O04  C11   C7   O1   108.22  3.000
 O04  H8A   C8   H8   107.42  3.000
 O04  H8A   C8   C9   109.66  3.000
 O04  H8    C8   C9   111.53  3.000
 O04  H8A   C8   O2   110.21  3.000
 O04  H8    C8   O2   106.63  3.000
 O04  C9    C8   O2   111.28  3.000
 O04  H9A   C9   H9   107.03  3.000
 O04  H9A   C9   C10  110.77  3.000
 O04  H9    C9   C10  110.16  3.000
 O04  H9A   C9   C8   109.23  3.000
 O04  H9    C9   C8   109.59  3.000
 O04  C10   C9   C8   110.01  3.000
 O04  H10A  C10  H10  106.62  3.000
 O04  H10A  C10  C11  109.38  3.000
 O04  H10   C10  C11  110.01  3.000
 O04  H10A  C10  C9   109.37  3.000
 O04  H10   C10  C9   110.81  3.000
 O04  C11   C10  C9   110.57  3.000
 O04  H11A  C11  H11  107.68  3.000
 O04  H11A  C11  C10  110.05  3.000
 O04  H11   C11  C10  110.64  3.000
 O04  H11A  C11  C7   109.41  3.000
 O04  H11   C11  C7   109.78  3.000
 O04  C10   C11  C7   109.26  3.000
 O04  H12   C12  C13  119.35  3.000
 O04  H12   C12  C5   119.88  3.000
 O04  C13   C12  C5   120.77  3.000
 O04  H13   C13  C12  118.73  3.000
 O04  H13   C13  C2   120.77  3.000
 O04  C12   C13  C2   120.49  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
 O04  CONST_01  C5   C12  C13  C2     0.00   0.0  0
 O04  CONST_02  C5   C4   C3   C2     0.00   0.0  0
 O04  CONST_03  C12  C5   C4   C3     0.00   0.0  0
 O04  CONST_04  C12  C13  C2   C3     0.00   0.0  0
 O04  CONST_05  C13  C12  C5   C4     0.00   0.0  0
 O04  CONST_06  C13  C2   C3   C4     0.00   0.0  0
 O04  CONST_07  C12  C13  C2   C1   180.00   0.0  0
 O04  CONST_08  C4   C3   C2   C1   180.00   0.0  0
 O04  CONST_09  C6   C5   C4   C3   180.00   0.0  0
 O04  CONST_10  C13  C12  C5   C6   180.00   0.0  0
 O04  CONST_11  H12  C12  C13  C2   180.00   0.0  0
 O04  CONST_12  H4   C4   C3   C2   180.00   0.0  0
 O04  CONST_13  H13  C13  C2   C3   180.00   0.0  0
 O04  CONST_14  H3   C3   C4   C5   180.00   0.0  0
 O04  CONST_15  HN1  N1   C1   C2   180.00   0.0  0
 O04  CONST_17  HN3  N3   C1   C2   180.00   0.0  0
 O04  Var_01    C10  C9   C8   O2   -54.96  30.0  1
 O04  Var_02    C9   C10  C11  C7   -52.08  30.0  1
 O04  Var_03    C9   C8   O2   C7    60.62  30.0  1
 O04  Var_04    C11  C10  C9   C8    51.66  30.0  1
 O04  Var_05    C13  C2   C1   N1    23.79  30.0  2
 O04  Var_06    C12  C5   C6   N2  -177.68  30.0  2
 O04  Var_07    C5   C6   N2   O1   179.63   0.0  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
 O04  chir_01  C7  C11  O2  O1  negativ

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
 O04  plan-1  C1    0.020
 O04  plan-1  C2    0.020
 O04  plan-1  C3    0.020
 O04  plan-1  C4    0.020
 O04  plan-1  C5    0.020
 O04  plan-1  C6    0.020
 O04  plan-1  C12   0.020
 O04  plan-1  C13   0.020
 O04  plan-1  H3    0.020
 O04  plan-1  H4    0.020
 O04  plan-1  H12   0.020
 O04  plan-1  H13   0.020
 O04  plan-2  C1    0.020
 O04  plan-2  N1    0.020
 O04  plan-2  C2    0.020
 O04  plan-2  N3    0.020
 O04  plan-2  HN1   0.020
 O04  plan-2  HN1A  0.020
 O04  plan-2  HN3   0.020
 O04  plan-3  O1    0.020
 O04  plan-3  N2    0.020
 O04  plan-3  C5    0.020
 O04  plan-3  C6    0.020
 O04  plan-3  H6    0.020

