# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 19:17:56 2020
#   Inital geometry file: a 94 line input string
#   Ligand name: [(~{Z})-[(3~{S},4~{R},5~{S},6~{S})-6-methyl-3,4,5-tris(oxidanyl)oxan-2-ylidene]amino] ~{N}-phenylcarbamate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1OC(=N\OC(=O)Nc2ccccc2)/[C@@H](O)[C@H](O)[C@@H]1O
#
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
 GYZ  GYZ  '[(~{Z})-[(3~{S},4~{R},5~{S},6~{S})-6-methyl-3,4,5-tris(oxidanyl)oxan-2-ylidene]amino] ~{N}-phenylcarbamate'  ligand  37  21  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GYZ
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
 GYZ  C2   C  CH1   0  -0.066  -2.9815  -1.2919  -0.2551
 GYZ  C1   C  C     0   0.471  -1.7700  -0.3921  -0.1115
 GYZ  C10  C  CH3   0  -0.700  -3.1334   2.9383   0.2483
 GYZ  C5   C  CH1   0   0.015  -3.0795   1.4746   0.6180
 GYZ  C4   C  CH1   0  -0.035  -4.3529   0.7090   0.2756
 GYZ  C3   C  CH1   0   0.032  -4.1353  -0.7616   0.5903
 GYZ  O6   O  OH1   0  -0.658  -2.7206  -2.6066   0.1367
 GYZ  O8   O  OH1   0  -0.664  -5.3209  -1.4645   0.3475
 GYZ  O9   O  OH1   0  -0.666  -4.7132   0.8316  -1.0758
 GYZ  O11  O  O2    0  -0.457  -1.9245   0.9219  -0.0511
 GYZ  N12  N  N     0  -0.203  -0.6334  -0.9567  -0.1641
 GYZ  O14  O  O2    0  -0.407   0.3924  -0.0370  -0.0646
 GYZ  C15  C  C     0   0.750   1.6159  -0.6015  -0.1770
 GYZ  O16  O  O     0  -0.467   1.8187  -1.7627  -0.4165
 GYZ  N17  N  NH1   0  -0.775   2.5382   0.3706   0.0206
 GYZ  C18  C  CR6   0   0.371   3.9310   0.2522  -0.0013
 GYZ  C19  C  CR16  0  -0.316   4.6193  -0.8880  -0.4165
 GYZ  C20  C  CR16  0  -0.244   6.0084  -0.8912  -0.4065
 GYZ  C21  C  CR16  0  -0.273   6.7311   0.2185   0.0047
 GYZ  C22  C  CR16  0  -0.245   6.0423   1.3537   0.4123
 GYZ  C23  C  CR16  0  -0.341   4.6582   1.3717   0.4106
 GYZ  H1   H  HCH1  0   0.262  -3.2793  -1.2408  -1.3128
 GYZ  H2   H  HCH3  0   0.238  -3.2606   3.0817  -0.8247
 GYZ  H3   H  HCH3  0   0.247  -3.9696   3.4126   0.7620
 GYZ  H4   H  HCH3  0   0.258  -2.2229   3.4517   0.5548
 GYZ  H5   H  HCH1  0   0.254  -2.9130   1.3800   1.6967
 GYZ  H6   H  HCH1  0   0.261  -5.1380   1.0947   0.9397
 GYZ  H7   H  HCH1  0   0.237  -3.8433  -0.8301   1.6497
 GYZ  H8   H  HOH1  0   0.462  -2.0334  -2.9724  -0.4303
 GYZ  H9   H  HOH1  0   0.456  -5.1942  -2.3787   0.6209
 GYZ  H10  H  HOH1  0   0.463  -5.1561   1.6751  -1.2060
 GYZ  H11  H  HNH1  0   0.419   2.1835   1.2842   0.2642
 GYZ  H12  H  HCR6  0   0.279   4.0940  -1.7679  -0.7497
 GYZ  H13  H  HCR6  0   0.259   6.5268  -1.7839  -0.7320
 GYZ  H14  H  HCR6  0   0.255   7.8127   0.2012   0.0064
 GYZ  H15  H  HCR6  0   0.260   6.5813   2.2337   0.7380
 GYZ  H16  H  HCR6  0   0.271   4.1340   2.2630   0.7350

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
 GYZ  O8   C3   single    1.400  0.020  1.400
 GYZ  O9   C4   single    1.404  0.020  1.404
 GYZ  O6   C2   single    1.396  0.020  1.396
 GYZ  C2   C3   single    1.526  0.020  1.526
 GYZ  C2   C1   single    1.516  0.020  1.516
 GYZ  C3   C4   single    1.520  0.020  1.520
 GYZ  C4   C5   single    1.525  0.020  1.525
 GYZ  C1   N12  double    1.270  0.020  1.270
 GYZ  C1   O11  single    1.324  0.020  1.324
 GYZ  C10  C5   single    1.511  0.020  1.511
 GYZ  C5   O11  single    1.445  0.020  1.445
 GYZ  N12  O14  single    1.381  0.020  1.381
 GYZ  O14  C15  single    1.352  0.020  1.352
 GYZ  O16  C15  double    1.203  0.020  1.203
 GYZ  C15  N17  single    1.354  0.020  1.354
 GYZ  N17  C18  single    1.398  0.020  1.398
 GYZ  C18  C19  aromatic  1.395  0.020  1.395
 GYZ  C18  C23  aromatic  1.397  0.020  1.397
 GYZ  C19  C20  aromatic  1.389  0.020  1.389
 GYZ  C23  C22  aromatic  1.384  0.020  1.384
 GYZ  C20  C21  aromatic  1.387  0.020  1.387
 GYZ  C22  C21  aromatic  1.389  0.020  1.389
 GYZ  C2   H1   single    0.970  0.020  1.090
 GYZ  C10  H2   single    0.970  0.020  1.090
 GYZ  C10  H3   single    0.970  0.020  1.090
 GYZ  C10  H4   single    0.970  0.020  1.090
 GYZ  C5   H5   single    0.970  0.020  1.090
 GYZ  C4   H6   single    0.970  0.020  1.090
 GYZ  C3   H7   single    0.970  0.020  1.090
 GYZ  O6   H8   single    0.850  0.020  0.980
 GYZ  O8   H9   single    0.850  0.020  0.980
 GYZ  O9   H10  single    0.850  0.020  0.980
 GYZ  N17  H11  single    0.860  0.020  1.020
 GYZ  C19  H12  single    0.930  0.020  1.080
 GYZ  C20  H13  single    0.930  0.020  1.080
 GYZ  C21  H14  single    0.930  0.020  1.080
 GYZ  C22  H15  single    0.930  0.020  1.080
 GYZ  C23  H16  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
 GYZ  H1   C2   O6   111.35  3.000
 GYZ  H1   C2   C3   108.18  3.000
 GYZ  O6   C2   C3   108.25  3.000
 GYZ  H1   C2   C1   106.25  3.000
 GYZ  C3   C2   C1   110.22  3.000
 GYZ  O6   C2   C1   112.51  3.000
 GYZ  N12  C1   O11  123.17  3.000
 GYZ  O11  C1   C2   120.00  3.000
 GYZ  N12  C1   C2   116.58  3.000
 GYZ  H4   C10  H3   107.67  3.000
 GYZ  H4   C10  H2   108.21  3.000
 GYZ  H3   C10  H2   108.49  3.000
 GYZ  H4   C10  C5   110.98  3.000
 GYZ  H3   C10  C5   109.49  3.000
 GYZ  H2   C10  C5   111.87  3.000
 GYZ  H5   C5   O11  107.55  3.000
 GYZ  H5   C5   C4   107.74  3.000
 GYZ  O11  C5   C4   111.81  3.000
 GYZ  H5   C5   C10  109.27  3.000
 GYZ  O11  C5   C10  106.61  3.000
 GYZ  C4   C5   C10  113.69  3.000
 GYZ  H6   C4   O9   111.59  3.000
 GYZ  H6   C4   C3   108.48  3.000
 GYZ  O9   C4   C3   108.70  3.000
 GYZ  H6   C4   C5   106.55  3.000
 GYZ  C3   C4   C5   108.65  3.000
 GYZ  O9   C4   C5   112.75  3.000
 GYZ  H7   C3   O8   111.12  3.000
 GYZ  H7   C3   C4   107.30  3.000
 GYZ  O8   C3   C4   109.20  3.000
 GYZ  H7   C3   C2   108.12  3.000
 GYZ  C4   C3   C2   109.27  3.000
 GYZ  O8   C3   C2   111.71  3.000
 GYZ  H8   O6   C2   109.01  3.000
 GYZ  H9   O8   C3   108.43  3.000
 GYZ  H10  O9   C4   108.97  3.000
 GYZ  C5   O11  C1   119.60  3.000
 GYZ  O14  N12  C1   111.45  3.000
 GYZ  C15  O14  N12  112.83  3.000
 GYZ  N17  C15  O16  127.38  3.000
 GYZ  N17  C15  O14  107.72  3.000
 GYZ  O16  C15  O14  124.90  3.000
 GYZ  H11  N17  C18  115.49  3.000
 GYZ  H11  N17  C15  116.44  3.000
 GYZ  C18  N17  C15  127.97  3.000
 GYZ  C23  C18  C19  119.07  3.000
 GYZ  C23  C18  N17  116.50  3.000
 GYZ  C19  C18  N17  124.43  3.000
 GYZ  H12  C19  C20  119.19  3.000
 GYZ  H12  C19  C18  121.26  3.000
 GYZ  C20  C19  C18  119.55  3.000
 GYZ  H13  C20  C21  119.97  3.000
 GYZ  H13  C20  C19  118.60  3.000
 GYZ  C21  C20  C19  121.43  3.000
 GYZ  H14  C21  C22  120.56  3.000
 GYZ  H14  C21  C20  120.58  3.000
 GYZ  C22  C21  C20  118.86  3.000
 GYZ  H15  C22  C23  119.20  3.000
 GYZ  H15  C22  C21  120.39  3.000
 GYZ  C23  C22  C21  120.41  3.000
 GYZ  H16  C23  C22  119.61  3.000
 GYZ  H16  C23  C18  119.70  3.000
 GYZ  C22  C23  C18  120.69  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
 GYZ  CONST_01  C21  C20  C19  C18     0.00   0.0  0
 GYZ  CONST_02  C21  C22  C23  C18     0.00   0.0  0
 GYZ  CONST_03  C22  C23  C18  C19     0.00   0.0  0
 GYZ  CONST_04  C22  C21  C20  C19     0.00   0.0  0
 GYZ  CONST_05  C23  C18  C19  C20     0.00   0.0  0
 GYZ  CONST_06  C23  C22  C21  C20     0.00   0.0  0
 GYZ  CONST_07  C20  C19  C18  N17   180.00   0.0  0
 GYZ  CONST_08  C22  C23  C18  N17   180.00   0.0  0
 GYZ  CONST_09  H13  C20  C19  C18   180.00   0.0  0
 GYZ  CONST_10  H15  C22  C23  C18   180.00   0.0  0
 GYZ  CONST_11  H16  C23  C18  C19   180.00   0.0  0
 GYZ  CONST_12  H14  C21  C20  C19   180.00   0.0  0
 GYZ  CONST_13  H12  C19  C20  C21   180.00   0.0  0
 GYZ  CONST_14  C19  C18  N17  C15     0.00   0.0  0
 GYZ  CONST_15  C23  C18  N17  C15   180.00   0.0  0
 GYZ  CONST_16  H11  N17  C18  C19   180.00   0.0  0
 GYZ  CONST_17  C18  N17  C15  O14   180.00   0.0  0
 GYZ  CONST_18  C18  N17  C15  O16     0.00   0.0  0
 GYZ  Var_01    N12  C1   O11  C5   -150.65  30.0  1
 GYZ  Var_02    O16  C15  O14  N12     4.16  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
 GYZ  chir_01  C2  O6   C3  C1   negativ
 GYZ  chir_02  C5  O11  C4  C10  positiv
 GYZ  chir_03  C4  O9   C5  C3   positiv
 GYZ  chir_04  C3  O8   C2  C4   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
 GYZ  plan-1  N17  0.020
 GYZ  plan-1  C18  0.020
 GYZ  plan-1  C19  0.020
 GYZ  plan-1  C20  0.020
 GYZ  plan-1  C21  0.020
 GYZ  plan-1  C22  0.020
 GYZ  plan-1  C23  0.020
 GYZ  plan-1  H12  0.020
 GYZ  plan-1  H13  0.020
 GYZ  plan-1  H14  0.020
 GYZ  plan-1  H15  0.020
 GYZ  plan-1  H16  0.020
 GYZ  plan-2  C15  0.020
 GYZ  plan-2  N17  0.020
 GYZ  plan-2  C18  0.020
 GYZ  plan-2  H11  0.020
 GYZ  plan-3  O14  0.020
 GYZ  plan-3  C15  0.020
 GYZ  plan-3  O16  0.020
 GYZ  plan-3  N17  0.020

