# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Jun  2 07:54:02 2020
#   Inital geometry file: a 112 line input string
#   Ligand name: (3R)-9-fluoro-3-methyl-10-(4-methylpiperazin-1-yl)-7-oxo-2,3-dihydro-7H-[1,4]oxazino[2,3,4-ij]quinoline-6-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1COc2c(N3CCN(C)CC3)c(F)cc4C(=O)C(=CN1c24)C(O)=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
 XED  XED  '(3R)-9-fluoro-3-methyl-10-(4-methylpiperazin-1-yl)-7-oxo-2,3-dihydro-7H-[1,4]oxazino[2,3,4-ij]quinoline-6-carboxylic acid'  ligand  46  26  .  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_XED
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
 XED  C1    C  CH2   0  -0.288  -0.4472   1.2308  -3.4708
 XED  C2    C  CH2   0  -0.283   0.2893   1.1837  -4.7965
 XED  N3    N  NT    0  -0.483  -0.1800   0.0121  -2.7271
 XED  N4    N  NT    0  -0.416  -0.0845   0.0019  -5.5474
 XED  C5    C  CH2   0  -0.287  -0.5178  -1.1933  -3.4638
 XED  C6    C  CH2   0  -0.283   0.2180  -1.1965  -4.7908
 XED  C7    C  CH3   0  -0.516   0.5366  -0.0211  -6.8512
 XED  C8    C  CR6   0  -0.026  -0.5351   0.0263  -1.3685
 XED  C9    C  CR66  0   0.331   0.4750   0.0044  -0.4107
 XED  C10   C  CR6   0   0.588  -1.8546   0.0715  -0.9068
 XED  F11   F  F     0  -0.305  -2.8353   0.0946  -1.8190
 XED  C12   C  C     0   0.330   0.1609   0.0046   0.9616
 XED  C13   C  CR16  0  -0.521  -2.1885   0.1093   0.4201
 XED  C14   C  CR66  0  -0.112  -1.1712   0.0735   1.3733
 XED  O15   O  O     0  -0.442   1.7436  -0.0218  -0.8376
 XED  N16   N  N     0  -0.562   1.1744  -0.0776   1.9068
 XED  C17   C  CR16  0   0.066   0.8713  -0.0538   3.1984
 XED  C18   C  CR16  0  -0.120   2.5507  -0.3166   1.4295
 XED  C19   C  C     0  -0.195   2.7026   0.4106   0.1100
 XED  C20   C  CH3   0  -0.729   3.6146   0.1462   2.4063
 XED  C21   C  CR6   0  -0.361  -0.4036   0.0499   3.7042
 XED  C22   C  CR6   0   0.443  -1.5348   0.1068   2.8057
 XED  O23   O  O     0  -0.462   0.4773   0.0474   5.9019
 XED  C24   C  C     0   0.534  -0.4930   0.0788   5.1737
 XED  O25   O  OH1   0  -0.584  -1.7277   0.1397   5.6482
 XED  O26   O  OC    0  -0.437  -2.7104   0.1774   3.1401
 XED  H1C1  H  HCH2  0   0.206  -1.5183   1.3852  -3.6634
 XED  H1C2  H  HCH2  0   0.244  -0.0886   2.0854  -2.8947
 XED  H2C1  H  HCH2  0   0.236   0.0290   2.0726  -5.3763
 XED  H2C2  H  HCH2  0   0.190   1.3764   1.2221  -4.6089
 XED  H5C1  H  HCH2  0   0.244  -0.2082  -2.0638  -2.8832
 XED  H5C2  H  HCH2  0   0.205  -1.5962  -1.2881  -3.6543
 XED  H6C1  H  HCH2  0   0.236  -0.0977  -2.0709  -5.3651
 XED  H6C2  H  HCH2  0   0.190   1.3011  -1.3001  -4.6049
 XED  H7C1  H  HCH3  0   0.232   0.1969  -0.8937  -7.4115
 XED  H7C2  H  HCH3  0   0.232   0.2547   0.8691  -7.4158
 XED  H7C3  H  HCH3  0   0.191   1.6364  -0.0577  -6.8079
 XED  H13   H  HCR6  0   0.283  -3.2236   0.1603   0.7287
 XED  H17   H  HCR6  0   0.325   1.7033  -0.1250   3.8819
 XED  H18   H  HCR6  0   0.300   2.6577  -1.3915   1.2572
 XED  H191  H  H     0   0.251   2.6217   1.4926   0.2631
 XED  H192  H  H     0   0.275   3.6788   0.1915  -0.3172
 XED  H201  H  HCH3  0   0.277   4.5892   0.0436   1.9305
 XED  H202  H  HCH3  0   0.256   3.4818   1.1923   2.6837
 XED  H203  H  HCH3  0   0.268   3.6441  -0.4588   3.3105
 XED  H25   H  HOH1  0   0.480  -1.6864   0.1517   6.6163

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
 XED  C1   C2    single    1.517  0.020  1.517
 XED  C1   N3    single    1.452  0.020  1.452
 XED  C1   H1C1  single    0.970  0.020  1.090
 XED  C1   H1C2  single    0.970  0.020  1.090
 XED  C2   N4    single    1.449  0.020  1.449
 XED  C2   H2C1  single    0.970  0.020  1.090
 XED  C2   H2C2  single    0.970  0.020  1.090
 XED  N3   C5    single    1.453  0.020  1.453
 XED  N3   C8    single    1.404  0.020  1.404
 XED  N4   C6    single    1.449  0.020  1.449
 XED  N4   C7    single    1.444  0.020  1.444
 XED  C5   C6    single    1.517  0.020  1.517
 XED  C5   H5C1  single    0.970  0.020  1.090
 XED  C5   H5C2  single    0.970  0.020  1.090
 XED  C6   H6C1  single    0.970  0.020  1.090
 XED  C6   H6C2  single    0.970  0.020  1.090
 XED  C7   H7C1  single    0.970  0.020  1.090
 XED  C7   H7C2  single    0.970  0.020  1.090
 XED  C7   H7C3  single    0.970  0.020  1.090
 XED  C8   C9    aromatic  1.392  0.020  1.392
 XED  C8   C10   aromatic  1.399  0.020  1.399
 XED  C9   C12   aromatic  1.408  0.020  1.408
 XED  C9   O15   single    1.339  0.020  1.339
 XED  C10  F11   single    1.340  0.020  1.340
 XED  C10  C13   aromatic  1.369  0.020  1.369
 XED  C12  C14   aromatic  1.396  0.020  1.396
 XED  C12  N16   aromatic  1.388  0.020  1.388
 XED  C13  C14   aromatic  1.395  0.020  1.395
 XED  C13  H13   single    0.930  0.020  1.080
 XED  C14  C22   aromatic  1.478  0.020  1.478
 XED  O15  C19   single    1.416  0.020  1.416
 XED  N16  C17   aromatic  1.327  0.020  1.327
 XED  N16  C18   single    1.476  0.020  1.476
 XED  C17  C21   aromatic  1.375  0.020  1.375
 XED  C17  H17   single    0.930  0.020  1.080
 XED  C18  C19   single    1.514  0.020  1.514
 XED  C18  C20   single    1.517  0.020  1.517
 XED  C18  H18   single    0.970  0.020  1.090
 XED  C19  H191  single    0.970  0.020  1.090
 XED  C19  H192  single    0.970  0.020  1.090
 XED  C20  H201  single    0.970  0.020  1.090
 XED  C20  H202  single    0.970  0.020  1.090
 XED  C20  H203  single    0.970  0.020  1.090
 XED  C21  C22   aromatic  1.446  0.020  1.446
 XED  C21  C24   single    1.473  0.020  1.473
 XED  C22  O26   double    1.224  0.020  1.224
 XED  O23  C24   double    1.214  0.020  1.214
 XED  C24  O25   single    1.324  0.020  1.324
 XED  O25  H25   single    0.850  0.020  0.980

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
 XED  H1C2  C1   H1C1  107.62  3.000
 XED  H1C2  C1   N3    109.05  3.000
 XED  H1C1  C1   N3    112.76  3.000
 XED  H1C2  C1   C2    109.03  3.000
 XED  H1C1  C1   C2    108.92  3.000
 XED  N3    C1   C2    109.39  3.000
 XED  H2C2  C2   H2C1  107.24  3.000
 XED  H2C2  C2   N4    111.74  3.000
 XED  H2C1  C2   N4    109.09  3.000
 XED  H2C2  C2   C1    109.17  3.000
 XED  H2C1  C2   C1    108.83  3.000
 XED  N4    C2   C1    110.66  3.000
 XED  C8    N3   C5    116.12  3.000
 XED  C8    N3   C1    116.13  3.000
 XED  C5    N3   C1    113.19  3.000
 XED  C7    N4   C6    111.62  3.000
 XED  C7    N4   C2    111.70  3.000
 XED  C6    N4   C2    110.49  3.000
 XED  H5C2  C5   H5C1  107.56  3.000
 XED  H5C2  C5   C6    108.90  3.000
 XED  H5C1  C5   C6    109.03  3.000
 XED  H5C2  C5   N3    112.81  3.000
 XED  H5C1  C5   N3    109.04  3.000
 XED  C6    C5   N3    109.43  3.000
 XED  H6C2  C6   H6C1  107.27  3.000
 XED  H6C2  C6   C5    109.19  3.000
 XED  H6C1  C6   C5    108.74  3.000
 XED  H6C2  C6   N4    111.74  3.000
 XED  H6C1  C6   N4    109.09  3.000
 XED  C5    C6   N4    110.71  3.000
 XED  H7C3  C7   H7C2  107.79  3.000
 XED  H7C3  C7   H7C1  107.73  3.000
 XED  H7C2  C7   H7C1  107.84  3.000
 XED  H7C3  C7   N4    113.23  3.000
 XED  H7C2  C7   N4    110.06  3.000
 XED  H7C1  C7   N4    110.02  3.000
 XED  C10   C8   C9    117.25  3.000
 XED  C10   C8   N3    123.93  3.000
 XED  C9    C8   N3    118.81  3.000
 XED  O15   C9   C12   121.48  3.000
 XED  O15   C9   C8    117.94  3.000
 XED  C12   C9   C8    120.58  3.000
 XED  C13   C10  F11   118.76  3.000
 XED  C13   C10  C8    123.44  3.000
 XED  F11   C10  C8    117.80  3.000
 XED  N16   C12  C14   119.92  3.000
 XED  N16   C12  C9    120.05  3.000
 XED  C14   C12  C9    120.03  3.000
 XED  H13   C13  C14   120.30  3.000
 XED  H13   C13  C10   120.76  3.000
 XED  C14   C13  C10   118.94  3.000
 XED  C22   C14  C13   118.84  3.000
 XED  C22   C14  C12   121.44  3.000
 XED  C13   C14  C12   119.72  3.000
 XED  C19   O15  C9    114.99  3.000
 XED  C18   N16  C17   122.04  3.000
 XED  C18   N16  C12   118.04  3.000
 XED  C17   N16  C12   119.67  3.000
 XED  H17   C17  C21   119.12  3.000
 XED  H17   C17  N16   116.06  3.000
 XED  C21   C17  N16   124.82  3.000
 XED  H18   C18  C20   109.43  3.000
 XED  H18   C18  C19   108.96  3.000
 XED  C20   C18  C19   110.14  3.000
 XED  H18   C18  N16   107.53  3.000
 XED  C20   C18  N16   113.35  3.000
 XED  C19   C18  N16   107.31  3.000
 XED  H192  C19  H191  108.66  3.000
 XED  H192  C19  C18   109.60  3.000
 XED  H191  C19  C18   110.19  3.000
 XED  H192  C19  O15   106.47  3.000
 XED  H191  C19  O15   110.19  3.000
 XED  C18   C19  O15   111.63  3.000
 XED  H203  C20  H202  108.98  3.000
 XED  H203  C20  H201  106.63  3.000
 XED  H202  C20  H201  108.09  3.000
 XED  H203  C20  C18   112.61  3.000
 XED  H202  C20  C18   111.79  3.000
 XED  H201  C20  C18   108.51  3.000
 XED  C24   C21  C22   124.88  3.000
 XED  C24   C21  C17   115.14  3.000
 XED  C22   C21  C17   119.98  3.000
 XED  O26   C22  C21   125.73  3.000
 XED  O26   C22  C14   120.14  3.000
 XED  C21   C22  C14   114.13  3.000
 XED  O25   C24  O23   122.12  3.000
 XED  O25   C24  C21   114.53  3.000
 XED  O23   C24  C21   123.35  3.000
 XED  H25   O25  C24   108.59  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
 XED  CONST_01  C14   C12  C9   C8      0.00   0.0  0
 XED  CONST_02  N16   C12  C9   C8    180.00   0.0  0
 XED  CONST_03  C14   C13  C10  C8      0.00   0.0  0
 XED  CONST_04  C13   C10  C8   C9      0.00   0.0  0
 XED  CONST_05  C13   C14  C12  C9      0.00   0.0  0
 XED  CONST_06  C22   C14  C12  C9    180.00   0.0  0
 XED  CONST_07  C17   N16  C12  C9    180.00   0.0  0
 XED  CONST_08  C12   C9   C8   C10     0.00   0.0  0
 XED  CONST_09  C12   C14  C13  C10     0.00   0.0  0
 XED  CONST_10  C22   C14  C13  C10   180.00   0.0  0
 XED  CONST_11  C21   C22  C14  C12     0.00   0.0  0
 XED  CONST_12  C21   C17  N16  C12     0.00   0.0  0
 XED  CONST_13  N16   C12  C14  C13   180.00   0.0  0
 XED  CONST_14  C21   C22  C14  C13   180.00   0.0  0
 XED  CONST_15  C17   N16  C12  C14     0.00   0.0  0
 XED  CONST_16  C17   C21  C22  C14     0.00   0.0  0
 XED  CONST_17  C22   C14  C12  N16     0.00   0.0  0
 XED  CONST_18  C22   C21  C17  N16     0.00   0.0  0
 XED  CONST_19  C12   C9   C8   N3    180.00   0.0  0
 XED  CONST_20  O15   C9   C8   N3      0.00   0.0  0
 XED  CONST_21  C13   C10  C8   N3    180.00   0.0  0
 XED  CONST_22  F11   C10  C8   N3      0.00   0.0  0
 XED  CONST_23  F11   C10  C8   C9    180.00   0.0  0
 XED  CONST_24  C14   C13  C10  F11   180.00   0.0  0
 XED  CONST_25  O26   C22  C14  C12   180.00   0.0  0
 XED  CONST_26  O26   C22  C14  C13     0.00   0.0  0
 XED  CONST_27  C24   C21  C22  C14   180.00   0.0  0
 XED  CONST_28  C24   C21  C17  N16   180.00   0.0  0
 XED  CONST_29  O26   C22  C21  C17   180.00   0.0  0
 XED  CONST_30  H13   C13  C10  C8    180.00   0.0  0
 XED  CONST_31  H17   C17  N16  C12   180.00   0.0  0
 XED  CONST_32  H25   O25  C24  C21   180.00   0.0  0
 XED  Var_01    C6    N4   C2   C1    -58.90  30.0  1
 XED  Var_02    C6    C5   N3   C1     55.76  30.0  1
 XED  Var_03    C9    C8   N3   C1   -111.37  30.0  2
 XED  Var_04    C5    N3   C1   C2    -55.84  30.0  1
 XED  Var_05    C5    C6   N4   C2     58.82  30.0  1
 XED  Var_06    N4    C2   C1   N3     56.38  30.0  1
 XED  Var_07    N4    C6   C5   N3    -56.22  30.0  1
 XED  Var_08    C18   C19  O15  C9     51.96  30.0  1
 XED  Var_09    O23   C24  C21  C17     1.73  30.0  2
 XED  Var_10    H7C1  C7   N4   C2   -177.08  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
 XED  chir_01  C18  N16  C19  C20  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
 XED  plan-1  N3   0.020
 XED  plan-1  C8   0.020
 XED  plan-1  C9   0.020
 XED  plan-1  C10  0.020
 XED  plan-1  F11  0.020
 XED  plan-1  C12  0.020
 XED  plan-1  C13  0.020
 XED  plan-1  C14  0.020
 XED  plan-1  O15  0.020
 XED  plan-1  N16  0.020
 XED  plan-1  C17  0.020
 XED  plan-1  C18  0.020
 XED  plan-1  C21  0.020
 XED  plan-1  C22  0.020
 XED  plan-1  C24  0.020
 XED  plan-1  O26  0.020
 XED  plan-1  H13  0.020
 XED  plan-1  H17  0.020
 XED  plan-2  C21  0.020
 XED  plan-2  O23  0.020
 XED  plan-2  C24  0.020
 XED  plan-2  O25  0.020
 XED  plan-2  H25  0.020

