# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 13:41:10 2022
#   Inital geometry file: a 101 line input string
#   Ligand name: ~{N}-cyclopropyl-3-oxidanylidene-~{N}-(thiophen-2-ylmethyl)-4~{H}-1,4-benzoxazine-7-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1COc2cc(ccc2N1)C(=O)N(Cc3sccc3)C4CC4
#
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
 Y6V  Y6V  ~{N}-cyclopropyl-3-oxidanylidene-~{N}-(thiophen-2-ylmethyl)-4~{H}-1,4-benzoxazine-7-carboxamide  ligand  39  23  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_Y6V
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
 Y6V  O1   O  O     0  -0.469   0.0190  -3.6430  18.3513
 Y6V  C1   C  C     0   0.522  -0.8739  -3.2664  19.0959
 Y6V  N1   N  NT    0  -0.471  -1.1836  -1.9541  19.2621
 Y6V  C2   C  CH2   0  -0.361  -0.2730  -0.9305  18.7751
 Y6V  C3   C  CR5   0  -0.152   0.1122   0.0182  19.8639
 Y6V  C4   C  CR15  0  -0.234  -0.0047   1.3745  19.8805
 Y6V  C5   C  CR15  0  -0.178   0.4715   1.9608  21.0868
 Y6V  C6   C  CR15  0  -0.467   0.9322   1.0342  21.9692
 Y6V  S1   S  S2    0   0.207   0.8013  -0.5558  21.3370
 Y6V  C7   C  CH1   0  -0.102  -2.4034  -1.4804  19.8484
 Y6V  C8   C  CH2   0  -0.475  -3.7175  -2.0414  19.4165
 Y6V  C9   C  CH2   0  -0.490  -3.3267  -0.6624  18.9944
 Y6V  C10  C  CR6   0  -0.053  -1.6419  -4.2733  19.8860
 Y6V  C11  C  CR16  0  -0.282  -2.0315  -5.4536  19.2620
 Y6V  C12  C  CR16  0  -0.317  -2.6686  -6.4512  19.9807
 Y6V  C13  C  CR6   0   0.317  -2.8882  -6.2920  21.3414
 Y6V  N2   N  NH1   0  -0.717  -3.4641  -7.2884  22.1224
 Y6V  C14  C  C     0   0.482  -3.9477  -7.0580  23.3667
 Y6V  O2   O  O     0  -0.441  -4.4917  -7.9059  24.0423
 Y6V  C15  C  CH2   0  -0.311  -3.8066  -5.6186  23.8216
 Y6V  O3   O  O2    0  -0.472  -2.6491  -4.9876  23.3091
 Y6V  C16  C  CR6   0   0.349  -2.4810  -5.1159  21.9712
 Y6V  C17  C  CR16  0  -0.357  -1.8725  -4.1075  21.2493
 Y6V  H1   H  HCH2  0   0.286   0.6052  -1.4211  18.3588
 Y6V  H2   H  HCH2  0   0.268  -0.7347  -0.3576  17.9675
 Y6V  H3   H  HCR5  0   0.263  -0.4220   1.9370  19.0563
 Y6V  H4   H  HCR5  0   0.265   0.4616   3.0225  21.2881
 Y6V  H5   H  HCR5  0   0.292   1.3381   1.1972  22.9557
 Y6V  H6   H  HCH1  0   0.272  -2.3243  -1.1688  20.8853
 Y6V  H7   H  HCH2  0   0.261  -4.4761  -2.1646  20.1782
 Y6V  H8   H  HCH2  0   0.262  -3.7193  -2.8147  18.6597
 Y6V  H9   H  HCH2  0   0.260  -3.0598  -0.5177  17.9551
 Y6V  H10  H  HCH2  0   0.260  -3.8087   0.1886  19.4568
 Y6V  H11  H  HCR6  0   0.263  -1.8484  -5.5962  18.2057
 Y6V  H12  H  HCR6  0   0.278  -2.9824  -7.3643  19.4903
 Y6V  H13  H  HNH1  0   0.417  -3.5972  -8.2079  21.7217
 Y6V  H14  H  HCH2  0   0.284  -3.7362  -5.5891  24.9068
 Y6V  H15  H  HCH2  0   0.269  -4.7131  -5.0756  23.5217
 Y6V  H16  H  HCR6  0   0.274  -1.5512  -3.2137  21.7698

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
 Y6V  C9   C8   single    1.494  0.020  1.494
 Y6V  C9   C7   single    1.500  0.020  1.500
 Y6V  O1   C1   double    1.222  0.020  1.222
 Y6V  C2   N1   single    1.454  0.020  1.454
 Y6V  C2   C3   single    1.495  0.020  1.495
 Y6V  C8   C7   single    1.493  0.020  1.493
 Y6V  N1   C1   single    1.359  0.020  1.359
 Y6V  N1   C7   single    1.434  0.020  1.434
 Y6V  C1   C10  single    1.493  0.020  1.493
 Y6V  C11  C10  aromatic  1.391  0.020  1.391
 Y6V  C11  C12  aromatic  1.385  0.020  1.385
 Y6V  C3   C4   aromatic  1.361  0.020  1.361
 Y6V  C3   S1   aromatic  1.725  0.020  1.725
 Y6V  C4   C5   aromatic  1.423  0.020  1.423
 Y6V  C10  C17  aromatic  1.393  0.020  1.393
 Y6V  C12  C13  aromatic  1.387  0.020  1.387
 Y6V  S1   C6   aromatic  1.716  0.020  1.716
 Y6V  C5   C6   aromatic  1.360  0.020  1.360
 Y6V  C17  C16  aromatic  1.381  0.020  1.381
 Y6V  C13  C16  aromatic  1.395  0.020  1.395
 Y6V  C13  N2   single    1.391  0.020  1.391
 Y6V  C16  O3   single    1.354  0.020  1.354
 Y6V  N2   C14  single    1.355  0.020  1.355
 Y6V  O3   C15  single    1.414  0.020  1.414
 Y6V  C14  C15  single    1.516  0.020  1.516
 Y6V  C14  O2   double    1.213  0.020  1.213
 Y6V  C2   H1   single    0.970  0.020  1.090
 Y6V  C2   H2   single    0.970  0.020  1.090
 Y6V  C4   H3   single    0.930  0.020  1.080
 Y6V  C5   H4   single    0.930  0.020  1.080
 Y6V  C6   H5   single    0.930  0.020  1.080
 Y6V  C7   H6   single    0.970  0.020  1.090
 Y6V  C8   H7   single    0.970  0.020  1.090
 Y6V  C8   H8   single    0.970  0.020  1.090
 Y6V  C9   H9   single    0.970  0.020  1.090
 Y6V  C9   H10  single    0.970  0.020  1.090
 Y6V  C11  H11  single    0.930  0.020  1.080
 Y6V  C12  H12  single    0.930  0.020  1.080
 Y6V  N2   H13  single    0.860  0.020  1.020
 Y6V  C15  H14  single    0.970  0.020  1.090
 Y6V  C15  H15  single    0.970  0.020  1.090
 Y6V  C17  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
 Y6V  C10  C1   N1   118.00  3.000
 Y6V  C10  C1   O1   119.38  3.000
 Y6V  N1   C1   O1   122.60  3.000
 Y6V  C7   N1   C2   115.92  3.000
 Y6V  C7   N1   C1   124.27  3.000
 Y6V  C2   N1   C1   119.75  3.000
 Y6V  H2   C2   H1   107.12  3.000
 Y6V  H2   C2   C3   108.33  3.000
 Y6V  H1   C2   C3   110.90  3.000
 Y6V  H2   C2   N1   110.62  3.000
 Y6V  H1   C2   N1   108.42  3.000
 Y6V  C3   C2   N1   111.36  3.000
 Y6V  S1   C3   C4   110.82  3.000
 Y6V  S1   C3   C2   120.93  3.000
 Y6V  C4   C3   C2   128.25  3.000
 Y6V  H3   C4   C5   124.11  3.000
 Y6V  H3   C4   C3   122.81  3.000
 Y6V  C5   C4   C3   113.08  3.000
 Y6V  H4   C5   C6   123.48  3.000
 Y6V  H4   C5   C4   124.02  3.000
 Y6V  C6   C5   C4   112.49  3.000
 Y6V  H5   C6   S1   120.35  3.000
 Y6V  H5   C6   C5   128.15  3.000
 Y6V  S1   C6   C5   111.50  3.000
 Y6V  C6   S1   C3    92.10  3.000
 Y6V  H6   C7   C9   115.60  3.000
 Y6V  H6   C7   C8   116.64  3.000
 Y6V  C9   C7   C8    59.90  3.000
 Y6V  H6   C7   N1   115.05  3.000
 Y6V  C8   C7   N1   120.43  3.000
 Y6V  C9   C7   N1   118.09  3.000
 Y6V  H8   C8   H7   114.19  3.000
 Y6V  H8   C8   C9   117.54  3.000
 Y6V  H7   C8   C9   119.16  3.000
 Y6V  H8   C8   C7   118.19  3.000
 Y6V  H7   C8   C7   117.15  3.000
 Y6V  C9   C8   C7    60.31  3.000
 Y6V  H10  C9   H9   114.52  3.000
 Y6V  H10  C9   C8   119.25  3.000
 Y6V  H9   C9   C8   117.32  3.000
 Y6V  H10  C9   C7   117.37  3.000
 Y6V  H9   C9   C7   117.88  3.000
 Y6V  C8   C9   C7    59.80  3.000
 Y6V  C17  C10  C11  119.59  3.000
 Y6V  C17  C10  C1   121.54  3.000
 Y6V  C11  C10  C1   118.63  3.000
 Y6V  H11  C11  C12  119.33  3.000
 Y6V  H11  C11  C10  120.17  3.000
 Y6V  C12  C11  C10  120.49  3.000
 Y6V  H12  C12  C13  119.67  3.000
 Y6V  H12  C12  C11  120.38  3.000
 Y6V  C13  C12  C11  119.94  3.000
 Y6V  C16  C13  N2   118.12  3.000
 Y6V  N2   C13  C12  122.28  3.000
 Y6V  C16  C13  C12  119.56  3.000
 Y6V  H13  N2   C14  118.12  3.000
 Y6V  H13  N2   C13  118.89  3.000
 Y6V  C14  N2   C13  122.81  3.000
 Y6V  C15  C14  O2   122.56  3.000
 Y6V  O2   C14  N2   123.56  3.000
 Y6V  C15  C14  N2   113.82  3.000
 Y6V  H15  C15  H14  108.20  3.000
 Y6V  H15  C15  O3   110.85  3.000
 Y6V  H14  C15  O3   107.24  3.000
 Y6V  H15  C15  C14  108.10  3.000
 Y6V  H14  C15  C14  109.33  3.000
 Y6V  O3   C15  C14  113.01  3.000
 Y6V  C16  O3   C15  114.66  3.000
 Y6V  C17  C16  O3   120.11  3.000
 Y6V  O3   C16  C13  119.31  3.000
 Y6V  C17  C16  C13  120.54  3.000
 Y6V  H16  C17  C16  118.81  3.000
 Y6V  H16  C17  C10  121.31  3.000
 Y6V  C16  C17  C10  119.84  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
 Y6V  CONST_01  C6   C5   C4   C3      0.00   0.0  0
 Y6V  CONST_02  C5   C6   S1   C3      0.00   0.0  0
 Y6V  CONST_03  C6   S1   C3   C4      0.00   0.0  0
 Y6V  CONST_04  S1   C6   C5   C4      0.00   0.0  0
 Y6V  CONST_05  S1   C3   C4   C5      0.00   0.0  0
 Y6V  CONST_06  C13  C12  C11  C10     0.00   0.0  0
 Y6V  CONST_07  C13  C16  C17  C10     0.00   0.0  0
 Y6V  CONST_08  C16  C17  C10  C11     0.00   0.0  0
 Y6V  CONST_09  C16  C13  C12  C11     0.00   0.0  0
 Y6V  CONST_10  C17  C10  C11  C12     0.00   0.0  0
 Y6V  CONST_11  C17  C16  C13  C12     0.00   0.0  0
 Y6V  CONST_12  C15  C14  N2   C13     0.00   0.0  0
 Y6V  CONST_13  C12  C11  C10  C1    180.00   0.0  0
 Y6V  CONST_14  C16  C17  C10  C1    180.00   0.0  0
 Y6V  CONST_15  C5   C4   C3   C2    180.00   0.0  0
 Y6V  CONST_16  C6   S1   C3   C2    180.00   0.0  0
 Y6V  CONST_17  O2   C14  N2   C13   180.00   0.0  0
 Y6V  CONST_18  H4   C5   C4   C3    180.00   0.0  0
 Y6V  CONST_19  H5   C6   S1   C3    180.00   0.0  0
 Y6V  CONST_20  H3   C4   C5   C6    180.00   0.0  0
 Y6V  CONST_21  H12  C12  C11  C10   180.00   0.0  0
 Y6V  CONST_22  H16  C17  C10  C11   180.00   0.0  0
 Y6V  CONST_23  H11  C11  C12  C13   180.00   0.0  0
 Y6V  CONST_24  H13  N2   C14  C15   180.00   0.0  0
 Y6V  CONST_27  C10  C1   N1   C2    180.00   0.0  0
 Y6V  CONST_28  C2   N1   C1   O1      0.00   0.0  0
 Y6V  Var_01    C14  N2   C13  C12  -165.33  30.0  1
 Y6V  Var_02    O3   C15  C14  N2    -32.90  30.0  1
 Y6V  Var_03    C17  C16  O3   C15   147.93  30.0  1
 Y6V  Var_04    C8   C9   C7   N1    110.74  30.0  1
 Y6V  Var_05    H7   C8   C9   C7    106.46  30.0  1
 Y6V  Var_06    C11  C10  C1   O1    -42.35  30.0  2
 Y6V  Var_07    C9   C7   N1   C1   -117.10  30.0  3
 Y6V  Var_08    C4   C3   C2   N1   -124.85  30.0  2
 Y6V  Var_09    C7   N1   C2   C3     57.70  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
 Y6V  chir_01  C7  C9  C8  N1  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
 Y6V  plan-1  C2   0.020
 Y6V  plan-1  C3   0.020
 Y6V  plan-1  C4   0.020
 Y6V  plan-1  C5   0.020
 Y6V  plan-1  C6   0.020
 Y6V  plan-1  S1   0.020
 Y6V  plan-1  H3   0.020
 Y6V  plan-1  H4   0.020
 Y6V  plan-1  H5   0.020
 Y6V  plan-2  C1   0.020
 Y6V  plan-2  C10  0.020
 Y6V  plan-2  C11  0.020
 Y6V  plan-2  C12  0.020
 Y6V  plan-2  C13  0.020
 Y6V  plan-2  N2   0.020
 Y6V  plan-2  O3   0.020
 Y6V  plan-2  C16  0.020
 Y6V  plan-2  C17  0.020
 Y6V  plan-2  H11  0.020
 Y6V  plan-2  H12  0.020
 Y6V  plan-2  H16  0.020
 Y6V  plan-3  O1   0.020
 Y6V  plan-3  C1   0.020
 Y6V  plan-3  N1   0.020
 Y6V  plan-3  C2   0.020
 Y6V  plan-3  C7   0.020
 Y6V  plan-3  C10  0.020
 Y6V  plan-4  C13  0.020
 Y6V  plan-4  N2   0.020
 Y6V  plan-4  C14  0.020
 Y6V  plan-4  O2   0.020
 Y6V  plan-4  C15  0.020
 Y6V  plan-4  H13  0.020

