# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 13:57:59 2022
#   Inital geometry file: a 123 line input string
#   Ligand name: (3S)-10-[(3R)-3-(1-aminocyclopropyl)pyrrolidin-1-yl]-9-fluoro-3-methyl-5-oxo-2,3-dihydro-5H-[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(N3CC[C@H](C3)C4(N)CC4)c(F)cc5C=C(C(O)=O)C(=O)N1c25
#
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
 Y21  Y21  '(3S)-10-[(3R)-3-(1-aminocyclopropyl)pyrrolidin-1-yl]-9-fluoro-3-methyl-5-oxo-2,3-dihydro-5H-[1,4]oxazino[2,3,4-ij]quinoline-6-carboxylic acid'  ligand  49  28  .  2022-08-11  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_Y21
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
 Y21  C1   C  CR6    0   0.500  87.0181  -56.2128  59.9553
 Y21  C2   C  CR6    0   0.071  86.3381  -55.0118  59.6847
 Y21  C3   C  CR6    0   0.297  86.0422  -54.2060  60.7933
 Y21  C12  C  CH1    0  -0.161  85.6873  -52.3933  62.8605
 Y21  C13  C  CR6    0   0.533  86.5424  -54.0267  64.4687
 Y21  C14  C  CR6    0  -0.276  87.0931  -55.3609  64.7003
 Y21  C16  C  CH2    0  -0.203  84.7061  -52.5421  61.7161
 Y21  C17  C  CH3    0  -0.649  86.8064  -51.4035  62.5649
 Y21  C18  C  CH2    0  -0.260  85.4403  -55.5455  57.4100
 Y21  C19  C  CH2    0  -0.475  84.9425  -54.5945  56.3333
 Y21  C20  C  CH1    0  -0.290  86.0138  -53.5055  56.3487
 Y21  C21  C  CH2    0  -0.221  86.2814  -53.3279  57.8477
 Y21  C22  C  CT     0   0.149  85.7174  -52.1931  55.6486
 Y21  C24  C  CH2    0  -0.490  84.8183  -52.1776  54.4509
 Y21  C25  C  CH2    0  -0.494  84.3548  -51.5820  55.7514
 Y21  C26  C  C      0   0.380  87.2988  -55.8769  66.1206
 Y21  C4   C  CR66   0   0.333  86.4504  -54.5622  62.0873
 Y21  C5   C  CR66   0   0.029  87.0815  -55.7915  62.3038
 Y21  C6   C  CR16   0  -0.534  87.3568  -56.6230  61.2147
 Y21  C7   C  CR16   0  -0.193  87.3995  -56.1487  63.6472
 Y21  F8   F  F      0  -0.316  87.3510  -57.0047  58.9207
 Y21  N11  N  NR6    0  -0.605  86.2163  -53.7224  63.1595
 Y21  N23  N  NH2    0  -0.805  86.7984  -51.2420  55.6127
 Y21  N9   N  NT     0  -0.526  85.9602  -54.6312  58.4155
 Y21  O10  O  O2     0  -0.465  85.3401  -53.0760  60.5678
 Y21  O15  O  O      0  -0.482  86.4027  -53.1793  65.3412
 Y21  O27  O  O      0  -0.592  88.3519  -56.5057  66.3299
 Y21  O28  O  OC    -1  -0.582  86.3640  -55.6670  66.9113
 Y21  H1   H  HCH1   0   0.282  85.1263  -52.0562  63.7312
 Y21  H2   H  HCH2   0   0.261  84.3064  -51.5707  61.4300
 Y21  H3   H  HCH2   0   0.251  83.8713  -53.1850  62.0170
 Y21  H4   H  HCH3   0   0.248  87.4700  -51.3065  63.4228
 Y21  H5   H  HCH3   0   0.234  87.4052  -51.7086  61.7065
 Y21  H6   H  HCH3   0   0.240  86.3883  -50.4191  62.3526
 Y21  H7   H  HCH2   0   0.235  84.6465  -56.1712  57.8241
 Y21  H8   H  HCH2   0   0.215  86.2002  -56.2075  56.9842
 Y21  H9   H  HCH2   0   0.235  83.9647  -54.1925  56.6103
 Y21  H10  H  HCH2   0   0.246  84.8464  -55.0882  55.3665
 Y21  H11  H  HCH1   0   0.238  86.9144  -53.9258  55.8817
 Y21  H12  H  HCH2   0   0.223  87.3194  -53.0478  58.0506
 Y21  H13  H  HCH2   0   0.220  85.6434  -52.5325  58.2442
 Y21  H14  H  HCH2   0   0.246  85.0734  -51.5004  53.6458
 Y21  H15  H  HCH2   0   0.244  84.3632  -53.1052  54.1268
 Y21  H16  H  HCH2   0   0.247  84.3015  -50.5032  55.8238
 Y21  H17  H  HCH2   0   0.243  83.5838  -52.1018  56.3061
 Y21  H18  H  HCR6   0   0.274  87.8638  -57.5681  61.3635
 Y21  H19  H  HCR6   0   0.260  87.8726  -57.1095  63.8159
 Y21  H20  H  HNH2   0   0.346  87.0535  -50.9675  56.5545
 Y21  H21  H  HNH2   0   0.341  87.6227  -51.6755  55.2120

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
 Y21  C24  C22  single    1.498  0.020  1.498
 Y21  C24  C25  single    1.504  0.020  1.504
 Y21  C22  C25  single    1.497  0.020  1.497
 Y21  C22  N23  single    1.440  0.020  1.440
 Y21  C22  C20  single    1.517  0.020  1.517
 Y21  C20  C19  single    1.528  0.020  1.528
 Y21  C20  C21  single    1.533  0.020  1.533
 Y21  C19  C18  single    1.520  0.020  1.520
 Y21  C18  N9   single    1.455  0.020  1.455
 Y21  C21  N9   single    1.458  0.020  1.458
 Y21  N9   C2   single    1.378  0.020  1.378
 Y21  F8   C1   single    1.345  0.020  1.345
 Y21  C2   C1   aromatic  1.406  0.020  1.406
 Y21  C2   C3   aromatic  1.402  0.020  1.402
 Y21  C1   C6   aromatic  1.367  0.020  1.367
 Y21  O10  C3   single    1.349  0.020  1.349
 Y21  O10  C16  single    1.416  0.020  1.416
 Y21  C3   C4   aromatic  1.403  0.020  1.403
 Y21  C6   C5   aromatic  1.398  0.020  1.398
 Y21  C16  C12  single    1.515  0.020  1.515
 Y21  C4   C5   aromatic  1.399  0.020  1.399
 Y21  C4   N11  single    1.382  0.020  1.382
 Y21  C5   C7   single    1.426  0.020  1.426
 Y21  C17  C12  single    1.523  0.020  1.523
 Y21  C12  N11  single    1.461  0.020  1.461
 Y21  N11  C13  single    1.383  0.020  1.383
 Y21  C7   C14  double    1.350  0.020  1.350
 Y21  C13  C14  single    1.462  0.020  1.462
 Y21  C13  O15  double    1.224  0.020  1.224
 Y21  C14  C26  single    1.525  0.020  1.525
 Y21  C26  O27  deloc     1.244  0.020  1.244
 Y21  C26  O28  deloc     1.242  0.020  1.242
 Y21  C12  H1   single    0.970  0.020  1.090
 Y21  C16  H2   single    0.970  0.020  1.090
 Y21  C16  H3   single    0.970  0.020  1.090
 Y21  C17  H4   single    0.970  0.020  1.090
 Y21  C17  H5   single    0.970  0.020  1.090
 Y21  C17  H6   single    0.970  0.020  1.090
 Y21  C18  H7   single    0.970  0.020  1.090
 Y21  C18  H8   single    0.970  0.020  1.090
 Y21  C19  H9   single    0.970  0.020  1.090
 Y21  C19  H10  single    0.970  0.020  1.090
 Y21  C20  H11  single    0.970  0.020  1.090
 Y21  C21  H12  single    0.970  0.020  1.090
 Y21  C21  H13  single    0.970  0.020  1.090
 Y21  C24  H14  single    0.970  0.020  1.090
 Y21  C24  H15  single    0.970  0.020  1.090
 Y21  C25  H16  single    0.970  0.020  1.090
 Y21  C25  H17  single    0.970  0.020  1.090
 Y21  C6   H18  single    0.930  0.020  1.080
 Y21  C7   H19  single    0.930  0.020  1.080
 Y21  N23  H20  single    0.890  0.020  1.040
 Y21  N23  H21  single    0.890  0.020  1.040

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
 Y21  F8   C1   C6   118.08  3.000
 Y21  C6   C1   C2   123.59  3.000
 Y21  F8   C1   C2   118.33  3.000
 Y21  N9   C2   C3   120.78  3.000
 Y21  C3   C2   C1   116.14  3.000
 Y21  N9   C2   C1   123.07  3.000
 Y21  O10  C3   C4   121.21  3.000
 Y21  C4   C3   C2   121.47  3.000
 Y21  O10  C3   C2   117.32  3.000
 Y21  H1   C12  N11  107.72  3.000
 Y21  H1   C12  C17  109.42  3.000
 Y21  N11  C12  C17  111.40  3.000
 Y21  H1   C12  C16  107.50  3.000
 Y21  N11  C12  C16  107.44  3.000
 Y21  C17  C12  C16  113.15  3.000
 Y21  O15  C13  N11  119.69  3.000
 Y21  O15  C13  C14  124.18  3.000
 Y21  N11  C13  C14  116.08  3.000
 Y21  C7   C14  C26  119.89  3.000
 Y21  C26  C14  C13  120.47  3.000
 Y21  C7   C14  C13  119.63  3.000
 Y21  H3   C16  H2   108.42  3.000
 Y21  H3   C16  O10  110.03  3.000
 Y21  H2   C16  O10  106.72  3.000
 Y21  H3   C16  C12  110.11  3.000
 Y21  H2   C16  C12  110.41  3.000
 Y21  O10  C16  C12  111.08  3.000
 Y21  H6   C17  H5   108.06  3.000
 Y21  H6   C17  H4   107.86  3.000
 Y21  H5   C17  H4   108.09  3.000
 Y21  H6   C17  C12  110.05  3.000
 Y21  H5   C17  C12  111.99  3.000
 Y21  H4   C17  C12  110.65  3.000
 Y21  H8   C18  H7   107.80  3.000
 Y21  H8   C18  N9   113.64  3.000
 Y21  H7   C18  N9   110.96  3.000
 Y21  H8   C18  C19  109.28  3.000
 Y21  H7   C18  C19  112.89  3.000
 Y21  N9   C18  C19  102.32  3.000
 Y21  H10  C19  H9   108.21  3.000
 Y21  H10  C19  C20  113.18  3.000
 Y21  H9   C19  C20  111.26  3.000
 Y21  H10  C19  C18  111.95  3.000
 Y21  H9   C19  C18  110.09  3.000
 Y21  C20  C19  C18  102.07  3.000
 Y21  H11  C20  C22  107.17  3.000
 Y21  H11  C20  C21  108.49  3.000
 Y21  C22  C20  C21  112.65  3.000
 Y21  H11  C20  C19  107.34  3.000
 Y21  C21  C20  C19  102.41  3.000
 Y21  C22  C20  C19  118.37  3.000
 Y21  H13  C21  H12  107.46  3.000
 Y21  H13  C21  N9   112.36  3.000
 Y21  H12  C21  N9   111.45  3.000
 Y21  H13  C21  C20  109.68  3.000
 Y21  H12  C21  C20  112.12  3.000
 Y21  N9   C21  C20  103.81  3.000
 Y21  N23  C22  C25  114.54  3.000
 Y21  N23  C22  C24  115.07  3.000
 Y21  C25  C22  C24   60.28  3.000
 Y21  N23  C22  C20  115.86  3.000
 Y21  C25  C22  C20  119.97  3.000
 Y21  C24  C22  C20  119.70  3.000
 Y21  H15  C24  H14  114.35  3.000
 Y21  H15  C24  C25  117.95  3.000
 Y21  H14  C24  C25  117.91  3.000
 Y21  H15  C24  C22  118.87  3.000
 Y21  H14  C24  C22  117.37  3.000
 Y21  C25  C24  C22   59.83  3.000
 Y21  H17  C25  H16  114.15  3.000
 Y21  H17  C25  C24  118.19  3.000
 Y21  H16  C25  C24  117.89  3.000
 Y21  H17  C25  C22  119.17  3.000
 Y21  H16  C25  C22  117.14  3.000
 Y21  C24  C25  C22   59.89  3.000
 Y21  O28  C26  O27  127.97  3.000
 Y21  O28  C26  C14  115.73  3.000
 Y21  O27  C26  C14  116.22  3.000
 Y21  N11  C4   C5   119.37  3.000
 Y21  N11  C4   C3   120.81  3.000
 Y21  C5   C4   C3   119.82  3.000
 Y21  C7   C5   C6   122.77  3.000
 Y21  C7   C5   C4   117.81  3.000
 Y21  C6   C5   C4   119.41  3.000
 Y21  H18  C6   C5   120.29  3.000
 Y21  H18  C6   C1   120.29  3.000
 Y21  C5   C6   C1   119.38  3.000
 Y21  H19  C7   C5   117.77  3.000
 Y21  H19  C7   C14  119.65  3.000
 Y21  C5   C7   C14  122.55  3.000
 Y21  C4   N11  C13  124.11  3.000
 Y21  C13  N11  C12  118.63  3.000
 Y21  C4   N11  C12  117.08  3.000
 Y21  H21  N23  H20  106.17  3.000
 Y21  H21  N23  C22  109.74  3.000
 Y21  H20  N23  C22  110.16  3.000
 Y21  C21  N9   C18  111.81  3.000
 Y21  C21  N9   C2   123.05  3.000
 Y21  C18  N9   C2   124.13  3.000
 Y21  C16  O10  C3   114.40  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
 Y21  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 Y21  CONST_02  C4   C5   C6   C1      0.00   0.0  0
 Y21  CONST_03  C5   C6   C1   C2      0.00   0.0  0
 Y21  CONST_04  C5   C4   C3   C2      0.00   0.0  0
 Y21  CONST_05  C6   C1   C2   C3      0.00   0.0  0
 Y21  CONST_06  C6   C5   C4   C3      0.00   0.0  0
 Y21  CONST_07  N9   C2   C3   C4    180.00   0.0  0
 Y21  CONST_08  N9   C2   C1   C6    180.00   0.0  0
 Y21  CONST_09  O10  C3   C2   N9      0.00   0.0  0
 Y21  CONST_10  C14  C13  N11  C12   180.00   0.0  0
 Y21  CONST_11  C4   N11  C13  C14     0.00   0.0  0
 Y21  CONST_12  F8   C1   C2   C3    180.00   0.0  0
 Y21  CONST_13  F8   C1   C6   C5    180.00   0.0  0
 Y21  CONST_14  N9   C2   C1   F8      0.00   0.0  0
 Y21  CONST_15  O15  C13  N11  C12     0.00   0.0  0
 Y21  CONST_16  O15  C13  N11  C4    180.00   0.0  0
 Y21  CONST_17  H18  C6   C1   C2    180.00   0.0  0
 Y21  Var_01    C18  N9   C2   C1     39.28  30.0  2
 Y21  Var_02    C19  C18  N9   C2    169.50  30.0  1
 Y21  Var_03    C20  C21  N9   C2    165.03  30.0  1
 Y21  Var_04    C12  C16  O10  C3     51.45  30.0  1
 Y21  Var_05    C4   C3   O10  C16   -19.09  30.0  1
 Y21  Var_06    C25  C24  C22  C20   109.66  30.0  1
 Y21  Var_07    N9   C18  C19  C20    38.27  30.0  1
 Y21  Var_08    O27  C26  C14  C13  -138.90  30.0  2
 Y21  Var_09    H20  N23  C22  C20   -62.20  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
 Y21  chir_01  C12  C16  C17  N11  positiv
 Y21  chir_02  C20  C22  C19  C21  positiv
 Y21  chir_03  C22  C25  N23  C20  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
 Y21  plan-1  C1   0.020
 Y21  plan-1  C2   0.020
 Y21  plan-1  C3   0.020
 Y21  plan-1  C12  0.020
 Y21  plan-1  C13  0.020
 Y21  plan-1  C14  0.020
 Y21  plan-1  C26  0.020
 Y21  plan-1  C4   0.020
 Y21  plan-1  C5   0.020
 Y21  plan-1  C6   0.020
 Y21  plan-1  C7   0.020
 Y21  plan-1  F8   0.020
 Y21  plan-1  N11  0.020
 Y21  plan-1  N9   0.020
 Y21  plan-1  O10  0.020
 Y21  plan-1  O15  0.020
 Y21  plan-1  H18  0.020
 Y21  plan-1  H19  0.020
 Y21  plan-2  C14  0.020
 Y21  plan-2  C26  0.020
 Y21  plan-2  O27  0.020
 Y21  plan-2  O28  0.020

