# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 09:25:23 2020
#   Inital geometry file: a 125 line input string
#   Ligand name: (4S,4a'R,10a'S)-2-amino-8'-(2-fluoropyridin-3-yl)-1,4a'-dimethyl-3',4',4a',10a'-tetrahydro-2'H-spiro[imidazole-4,10'-pyrano[3,2-b]chromen]-5(1H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=N[C@@]2([C@@H]3OCCC[C@@]3(C)Oc4ccc(cc24)c5cccnc5F)C1=O)N
#
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
 3UX  3UX  (4S,4a'R,10a'S)-2-amino-8'-(2-fluoropyridin-3-yl)-1,4a'-dimethyl-3',4',4a',10a'-tetrahydro-2'H-spiro[imidazole-4,10'-pyrano[3,2-b]chromen]-5(1H)-one  ligand  50  29  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_3UX
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
 3UX  C1   C  CR6   0   0.115  -2.2276   1.1182   0.0639
 3UX  C2   C  CR16  0  -0.286  -1.9002   2.4704  -0.0591
 3UX  C3   C  CR16  0  -0.349  -0.5845   2.8813  -0.1283
 3UX  C4   C  CR6   0   0.334   0.4491   1.9459  -0.0963
 3UX  C5   C  CR6   0   0.154   0.1472   0.5875   0.0129
 3UX  C6   C  CR16  0  -0.353  -1.1843   0.2006   0.1013
 3UX  C7   C  CR6   0  -0.217  -3.6387   0.7095   0.1805
 3UX  O8   O  O2    0  -0.495   1.7035   2.4270  -0.1936
 3UX  C9   C  CT    0   0.183   2.7737   1.5744   0.2389
 3UX  C10  C  CH1   0   0.112   2.5449   0.1962  -0.3891
 3UX  C11  C  CR5   0  -0.266   1.2413  -0.4534   0.0732
 3UX  C12  C  CH2   0  -0.464   4.0514   2.1377  -0.3794
 3UX  C13  C  CH2   0  -0.469   5.2044   1.1497  -0.2138
 3UX  C14  C  CH2   0  -0.166   4.8081  -0.2272  -0.7232
 3UX  O15  O  O2    0  -0.465   3.6035  -0.6731  -0.1365
 3UX  N16  N  N     0  -0.406   1.3301  -1.0435   1.3898
 3UX  C17  C  CR5   0   0.677   1.2028  -2.3033   1.2346
 3UX  N18  N  NR5   0  -0.533   0.9648  -2.7335  -0.0666
 3UX  C19  C  CR5   0   0.559   0.9622  -1.6292  -0.8784
 3UX  O20  O  O     0  -0.371   0.8021  -1.6090  -2.0688
 3UX  N21  N  NH2   0  -0.833   1.3199  -3.2271   2.2171
 3UX  C22  C  CH3   0  -0.645   2.8402   1.5774   1.7595
 3UX  C23  C  CH3   0  -0.537   0.8618  -4.0948  -0.5216
 3UX  C24  C  CR16  0  -0.157  -4.5331   1.3942   0.9967
 3UX  C25  C  CR16  0  -0.309  -5.8613   1.0009   1.0704
 3UX  C26  C  CR16  0  -0.039  -6.2616  -0.0864   0.3161
 3UX  N27  N  N     0  -0.381  -5.4275  -0.7559  -0.4717
 3UX  C28  C  CR6   0   0.575  -4.1906  -0.3636  -0.5232
 3UX  F29  F  F     0  -0.280  -3.4003  -1.0608  -1.3377
 3UX  H1   H  HCR6  0   0.242  -2.6829   3.2164  -0.1091
 3UX  H2   H  HCR6  0   0.247  -0.3469   3.9340  -0.2164
 3UX  H3   H  HCR6  0   0.232  -1.4028  -0.8536   0.2198
 3UX  H4   H  HCH1  0   0.232   2.4393   0.3675  -1.4762
 3UX  H5   H  HCH2  0   0.233   3.8767   2.3131  -1.4458
 3UX  H6   H  HCH2  0   0.238   4.3005   3.1030   0.0676
 3UX  H7   H  HCH2  0   0.239   6.0771   1.5007  -0.7688
 3UX  H8   H  HCH2  0   0.232   5.5080   1.0858   0.8337
 3UX  H9   H  HCH2  0   0.195   4.7082  -0.2042  -1.8182
 3UX  H10  H  HCH2  0   0.233   5.5672  -0.9709  -0.4799
 3UX  H11  H  HNH2  0   0.380   1.3770  -2.8463   3.1464
 3UX  H12  H  HNH2  0   0.374   0.8039  -4.0872   2.1478
 3UX  H13  H  HCH3  0   0.255   1.9000   1.2808   2.2192
 3UX  H14  H  HCH3  0   0.241   3.5942   0.8813   2.1207
 3UX  H15  H  HCH3  0   0.222   3.0991   2.5752   2.1182
 3UX  H16  H  HCH3  0   0.248   1.7188  -4.6810  -0.1905
 3UX  H17  H  HCH3  0   0.232  -0.0567  -4.5710  -0.1740
 3UX  H18  H  HCH3  0   0.284   0.8447  -4.0915  -1.6086
 3UX  H19  H  HCR6  0   0.251  -4.1793   2.2291   1.5880
 3UX  H20  H  HCR6  0   0.248  -6.5635   1.5194   1.7068
 3UX  H21  H  HCR6  0   0.254  -7.2860  -0.4370   0.3392

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
 3UX  O20  C19  double    1.201  0.020  1.201
 3UX  C14  C13  single    1.521  0.020  1.521
 3UX  C14  O15  single    1.412  0.020  1.412
 3UX  C13  C12  single    1.527  0.020  1.527
 3UX  C12  C9   single    1.527  0.020  1.527
 3UX  O15  C10  single    1.393  0.020  1.393
 3UX  C19  N18  single    1.371  0.020  1.371
 3UX  C19  C11  single    1.538  0.020  1.538
 3UX  C10  C9   single    1.532  0.020  1.532
 3UX  C10  C11  single    1.528  0.020  1.528
 3UX  C23  N18  single    1.439  0.020  1.439
 3UX  O8   C9   single    1.435  0.020  1.435
 3UX  O8   C4   single    1.347  0.020  1.347
 3UX  N18  C17  single    1.391  0.020  1.391
 3UX  C9   C22  single    1.522  0.020  1.522
 3UX  C11  C5   single    1.511  0.020  1.511
 3UX  C11  N16  single    1.445  0.020  1.445
 3UX  C4   C5   aromatic  1.396  0.020  1.396
 3UX  C4   C3   aromatic  1.394  0.020  1.394
 3UX  C5   C6   aromatic  1.389  0.020  1.389
 3UX  C3   C2   aromatic  1.380  0.020  1.380
 3UX  C24  C25  aromatic  1.387  0.020  1.387
 3UX  C24  C7   aromatic  1.391  0.020  1.391
 3UX  C6   C1   aromatic  1.390  0.020  1.390
 3UX  C2   C1   aromatic  1.397  0.020  1.397
 3UX  C17  N16  double    1.276  0.020  1.276
 3UX  C17  N21  single    1.354  0.020  1.354
 3UX  C1   C7   single    1.474  0.020  1.474
 3UX  C25  C26  aromatic  1.382  0.020  1.382
 3UX  C7   C28  aromatic  1.397  0.020  1.397
 3UX  C26  N27  aromatic  1.328  0.020  1.328
 3UX  C28  N27  aromatic  1.299  0.020  1.299
 3UX  C28  F29  single    1.332  0.020  1.332
 3UX  C2   H1   single    0.930  0.020  1.080
 3UX  C3   H2   single    0.930  0.020  1.080
 3UX  C6   H3   single    0.930  0.020  1.080
 3UX  C10  H4   single    0.970  0.020  1.090
 3UX  C12  H5   single    0.970  0.020  1.090
 3UX  C12  H6   single    0.970  0.020  1.090
 3UX  C13  H7   single    0.970  0.020  1.090
 3UX  C13  H8   single    0.970  0.020  1.090
 3UX  C14  H9   single    0.970  0.020  1.090
 3UX  C14  H10  single    0.970  0.020  1.090
 3UX  N21  H11  single    0.890  0.020  1.040
 3UX  N21  H12  single    0.890  0.020  1.040
 3UX  C22  H13  single    0.970  0.020  1.090
 3UX  C22  H14  single    0.970  0.020  1.090
 3UX  C22  H15  single    0.970  0.020  1.090
 3UX  C23  H16  single    0.970  0.020  1.090
 3UX  C23  H17  single    0.970  0.020  1.090
 3UX  C23  H18  single    0.970  0.020  1.090
 3UX  C24  H19  single    0.930  0.020  1.080
 3UX  C25  H20  single    0.930  0.020  1.080
 3UX  C26  H21  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
 3UX  C7   C1   C6   122.24  3.000
 3UX  C7   C1   C2   119.99  3.000
 3UX  C6   C1   C2   117.75  3.000
 3UX  H1   C2   C3   118.80  3.000
 3UX  H1   C2   C1   120.12  3.000
 3UX  C3   C2   C1   121.08  3.000
 3UX  H2   C3   C4   119.43  3.000
 3UX  H2   C3   C2   120.18  3.000
 3UX  C4   C3   C2   120.38  3.000
 3UX  O8   C4   C5   123.69  3.000
 3UX  C5   C4   C3   119.63  3.000
 3UX  O8   C4   C3   116.68  3.000
 3UX  C11  C5   C6   119.96  3.000
 3UX  C6   C5   C4   118.90  3.000
 3UX  C11  C5   C4   121.12  3.000
 3UX  H3   C6   C5   118.13  3.000
 3UX  H3   C6   C1   119.61  3.000
 3UX  C5   C6   C1   122.26  3.000
 3UX  C28  C7   C24  114.82  3.000
 3UX  C28  C7   C1   123.46  3.000
 3UX  C24  C7   C1   121.71  3.000
 3UX  C9   O8   C4   117.42  3.000
 3UX  C22  C9   C12  111.54  3.000
 3UX  C22  C9   C10  114.70  3.000
 3UX  C12  C9   C10  106.91  3.000
 3UX  C22  C9   O8   109.42  3.000
 3UX  C10  C9   O8   107.44  3.000
 3UX  C12  C9   O8   106.43  3.000
 3UX  H4   C10  O15  110.34  3.000
 3UX  H4   C10  C11  106.37  3.000
 3UX  O15  C10  C11  109.16  3.000
 3UX  H4   C10  C9   106.14  3.000
 3UX  C11  C10  C9   112.70  3.000
 3UX  O15  C10  C9   111.94  3.000
 3UX  C19  C11  N16  105.22  3.000
 3UX  N16  C11  C10  113.37  3.000
 3UX  C19  C11  C10  107.01  3.000
 3UX  N16  C11  C5   111.22  3.000
 3UX  C10  C11  C5   108.22  3.000
 3UX  C19  C11  C5   111.74  3.000
 3UX  H6   C12  H5   107.06  3.000
 3UX  H6   C12  C13  110.79  3.000
 3UX  H5   C12  C13  109.25  3.000
 3UX  H6   C12  C9   110.55  3.000
 3UX  H5   C12  C9   108.66  3.000
 3UX  C13  C12  C9   110.43  3.000
 3UX  H8   C13  H7   106.50  3.000
 3UX  H8   C13  C14  109.92  3.000
 3UX  H7   C13  C14  109.21  3.000
 3UX  H8   C13  C12  110.58  3.000
 3UX  H7   C13  C12  109.89  3.000
 3UX  C14  C13  C12  110.64  3.000
 3UX  H10  C14  H9   107.44  3.000
 3UX  H10  C14  O15  106.61  3.000
 3UX  H9   C14  O15  110.05  3.000
 3UX  H10  C14  C13  111.19  3.000
 3UX  H9   C14  C13  109.77  3.000
 3UX  O15  C14  C13  111.66  3.000
 3UX  C14  O15  C10  112.08  3.000
 3UX  C17  N16  C11  106.63  3.000
 3UX  N21  C17  N18  118.86  3.000
 3UX  N21  C17  N16  125.24  3.000
 3UX  N18  C17  N16  115.87  3.000
 3UX  C23  N18  C19  125.08  3.000
 3UX  C23  N18  C17  126.91  3.000
 3UX  C19  N18  C17  107.77  3.000
 3UX  O20  C19  N18  126.93  3.000
 3UX  N18  C19  C11  104.42  3.000
 3UX  O20  C19  C11  128.63  3.000
 3UX  H12  N21  H11  114.63  3.000
 3UX  H12  N21  C17  119.30  3.000
 3UX  H11  N21  C17  114.65  3.000
 3UX  H15  C22  H14  108.14  3.000
 3UX  H15  C22  H13  108.39  3.000
 3UX  H14  C22  H13  106.51  3.000
 3UX  H15  C22  C9   109.91  3.000
 3UX  H14  C22  C9   111.14  3.000
 3UX  H13  C22  C9   112.58  3.000
 3UX  H18  C23  H17  107.85  3.000
 3UX  H18  C23  H16  108.54  3.000
 3UX  H17  C23  H16  109.29  3.000
 3UX  H18  C23  N18  108.33  3.000
 3UX  H17  C23  N18  111.85  3.000
 3UX  H16  C23  N18  110.88  3.000
 3UX  H19  C24  C25  120.17  3.000
 3UX  H19  C24  C7   119.34  3.000
 3UX  C25  C24  C7   120.48  3.000
 3UX  H20  C25  C26  120.71  3.000
 3UX  H20  C25  C24  121.17  3.000
 3UX  C26  C25  C24  118.12  3.000
 3UX  H21  C26  N27  116.32  3.000
 3UX  H21  C26  C25  121.12  3.000
 3UX  N27  C26  C25  122.56  3.000
 3UX  C28  N27  C26  117.99  3.000
 3UX  F29  C28  N27  115.55  3.000
 3UX  F29  C28  C7   118.41  3.000
 3UX  N27  C28  C7   126.04  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
 3UX  CONST_01  C4   C5   C6   C1     0.00   0.0  0
 3UX  CONST_02  C4   C3   C2   C1     0.00   0.0  0
 3UX  CONST_03  C25  C24  C7   C1   180.00   0.0  0
 3UX  CONST_04  N27  C28  C7   C1   180.00   0.0  0
 3UX  CONST_05  C5   C4   C3   C2     0.00   0.0  0
 3UX  CONST_06  C5   C6   C1   C2     0.00   0.0  0
 3UX  CONST_09  C6   C5   C4   C3     0.00   0.0  0
 3UX  CONST_10  C6   C1   C2   C3     0.00   0.0  0
 3UX  CONST_11  C7   C1   C2   C3   180.00   0.0  0
 3UX  CONST_12  C7   C1   C6   C5   180.00   0.0  0
 3UX  CONST_15  C26  C25  C24  C7     0.00   0.0  0
 3UX  CONST_16  C26  N27  C28  C7     0.00   0.0  0
 3UX  CONST_17  N27  C26  C25  C24    0.00   0.0  0
 3UX  CONST_18  N27  C28  C7   C24    0.00   0.0  0
 3UX  CONST_19  C28  C7   C24  C25    0.00   0.0  0
 3UX  CONST_20  C28  N27  C26  C25    0.00   0.0  0
 3UX  CONST_21  C17  N18  C19  C11    0.00   0.0  0
 3UX  CONST_22  N18  C17  N16  C11    0.00   0.0  0
 3UX  CONST_23  C19  N18  C17  N16    0.00   0.0  0
 3UX  CONST_24  F29  C28  C7   C1     0.00   0.0  0
 3UX  CONST_25  F29  C28  C7   C24  180.00   0.0  0
 3UX  CONST_26  F29  C28  N27  C26  180.00   0.0  0
 3UX  CONST_27  C23  N18  C19  C11  180.00   0.0  0
 3UX  CONST_28  N21  C17  N16  C11  180.00   0.0  0
 3UX  CONST_29  C23  N18  C17  N16  180.00   0.0  0
 3UX  CONST_30  O20  C19  N18  C17  180.00   0.0  0
 3UX  CONST_31  N21  C17  N18  C19  180.00   0.0  0
 3UX  CONST_32  H2   C3   C2   C1   180.00   0.0  0
 3UX  CONST_33  H19  C24  C7   C1     0.00   0.0  0
 3UX  CONST_34  H3   C6   C1   C2   180.00   0.0  0
 3UX  CONST_35  H1   C2   C3   C4   180.00   0.0  0
 3UX  CONST_36  H20  C25  C24  C7   180.00   0.0  0
 3UX  CONST_37  H21  C26  C25  C24  180.00   0.0  0
 3UX  CONST_38  C23  N18  C19  O20    0.00   0.0  0
 3UX  CONST_39  C23  N18  C17  N21    0.00   0.0  0
 3UX  CONST_40  H11  N21  C17  N16    0.00   0.0  0
 3UX  Var_01    C14  C13  C12  C9    52.03  30.0  1
 3UX  Var_02    C13  C14  O15  C10   58.89  30.0  1
 3UX  Var_03    O15  C14  C13  C12  -52.89  30.0  1
 3UX  Var_04    H16  C23  N18  C17  -51.35  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
 3UX  chir_01  C9   C10  O8   C12  positiv
 3UX  chir_02  C10  O15  C11  C9   negativ
 3UX  chir_03  C11  C5   C10  C19  positiv

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
 3UX  plan-1  C1   0.020
 3UX  plan-1  C7   0.020
 3UX  plan-1  C24  0.020
 3UX  plan-1  C25  0.020
 3UX  plan-1  C26  0.020
 3UX  plan-1  N27  0.020
 3UX  plan-1  C28  0.020
 3UX  plan-1  F29  0.020
 3UX  plan-1  H19  0.020
 3UX  plan-1  H20  0.020
 3UX  plan-1  H21  0.020
 3UX  plan-2  C1   0.020
 3UX  plan-2  C2   0.020
 3UX  plan-2  C3   0.020
 3UX  plan-2  C4   0.020
 3UX  plan-2  C5   0.020
 3UX  plan-2  C6   0.020
 3UX  plan-2  C7   0.020
 3UX  plan-2  O8   0.020
 3UX  plan-2  C11  0.020
 3UX  plan-2  H1   0.020
 3UX  plan-2  H2   0.020
 3UX  plan-2  H3   0.020
 3UX  plan-3  C11  0.020
 3UX  plan-3  N16  0.020
 3UX  plan-3  C17  0.020
 3UX  plan-3  N18  0.020
 3UX  plan-3  C19  0.020
 3UX  plan-3  O20  0.020
 3UX  plan-3  N21  0.020
 3UX  plan-3  C23  0.020
 3UX  plan-3  H11  0.020
 3UX  plan-3  H12  0.020

