# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 13:55:01 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: 3-({[3-({[(1E)-(2,6-dioxo-1,2,3,6-tetrahydropyrimidin-4-yl)methylidene]amino}oxy)propyl]amino}methyl)benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1cccc(CNCCCO/N=C/C2=CC(=O)NC(=O)N2)c1
#
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
 FCK  FCK  '3-({[3-({[(1E)-(2,6-dioxo-1,2,3,6-tetrahydropyrimidin-4-yl)methylidene]amino}oxy)propyl]amino}methyl)benzoic acid'  ligand  43  25  .  2021-08-09  2021-08-09  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_FCK
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
 FCK  C1    C  CR16  0  -0.228   -6.3790   0.9062   1.9078
 FCK  C2    C  CR16  0  -0.275   -5.1755   1.1220   1.2562
 FCK  C3    C  CR6   0   0.120   -5.0053   0.7333  -0.0723
 FCK  C4    C  CR16  0  -0.330   -6.0593   0.1127  -0.7241
 FCK  C5    C  CR6   0  -0.065   -7.2738  -0.1141  -0.0749
 FCK  C6    C  CR16  0  -0.277   -7.4323   0.2878   1.2485
 FCK  C7    C  CH2   0  -0.260   -1.2973   0.6933  -0.5729
 FCK  O39   O  O     0  -0.440   -8.2531  -1.1466  -1.9811
 FCK  C38   C  C     0   0.534   -8.3554  -0.7918  -0.8305
 FCK  O40   O  OH1   0  -0.595   -9.4549  -0.9745  -0.1124
 FCK  C17   C  CH2   0  -0.328   -3.6938   0.9810  -0.7676
 FCK  N18   N  NH1   0  -0.592   -2.6038   0.3637  -0.0377
 FCK  C22   C  CH2   0  -0.503   -0.2043   0.0210   0.2450
 FCK  C23   C  CH2   0  -0.133    1.1692   0.4083  -0.2567
 FCK  O27   O  O2    0  -0.383    2.1298  -0.2274   0.5883
 FCK  N31   N  N     0  -0.080    3.3780   0.0148   0.1662
 FCK  C30   C  C1    0  -0.055    4.2768  -0.4731   0.9183
 FCK  C16   C  CR6   0   0.419    5.6693  -0.2715   0.5437
 FCK  N11   N  NR16  0  -0.736    5.9217   0.4044  -0.6141
 FCK  C15   C  CR16  0  -0.542    6.6766  -0.7340   1.3146
 FCK  C14   C  CR6   0   0.595    8.0464  -0.5152   0.9143
 FCK  O33   O  O     0  -0.460    9.0278  -0.8879   1.5299
 FCK  N13   N  NR16  0  -0.720    8.1841   0.1812  -0.2770
 FCK  C12   C  CR6   0   0.670    7.1816   0.6614  -1.0817
 FCK  O34   O  O     0  -0.472    7.3931   1.2604  -2.1146
 FCK  H1    H  HCR6  0   0.264   -6.5025   1.2201   2.9358
 FCK  H2    H  HCR6  0   0.258   -4.3570   1.5993   1.7804
 FCK  H4    H  HCR6  0   0.259   -5.9344  -0.2031  -1.7527
 FCK  H6    H  HCR6  0   0.267   -8.3640   0.1252   1.7724
 FCK  H7    H  HCH2  0   0.198   -1.1876   0.4208  -1.6343
 FCK  H7A   H  HCH2  0   0.224   -1.1764   1.7801  -0.5220
 FCK  HO40  H  HOH1  0   0.487  -10.1238  -1.4332  -0.6420
 FCK  H17   H  HCH2  0   0.219   -3.7632   0.6504  -1.8141
 FCK  H17A  H  HCH2  0   0.242   -3.5059   2.0589  -0.8005
 FCK  HN18  H  HNH1  0   0.344   -2.7264  -0.6426  -0.0524
 FCK  H22   H  HCH2  0   0.240   -0.3157   0.3119   1.2924
 FCK  H22A  H  HCH2  0   0.239   -0.3228  -1.0656   0.1927
 FCK  H23   H  HCH2  0   0.228    1.3172   0.0864  -1.2913
 FCK  H23A  H  HCH2  0   0.226    1.3037   1.4934  -0.2148
 FCK  HN13  H  HNR6  0   0.428    9.1279   0.3554  -0.5992
 FCK  H30   H  H     0   0.284    4.0699  -1.0318   1.8273
 FCK  H171  H  HNR6  0   0.432    5.1419   0.7289  -1.1712
 FCK  H15   H  HCR6  0   0.294    6.4733  -1.2690   2.2300

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
 FCK  C1   H1    single    0.930  0.020  1.080
 FCK  C2   C1    aromatic  1.386  0.020  1.386
 FCK  C2   H2    single    0.930  0.020  1.080
 FCK  C3   C2    aromatic  1.395  0.020  1.395
 FCK  C4   C3    aromatic  1.386  0.020  1.386
 FCK  C4   C5    aromatic  1.396  0.020  1.396
 FCK  C4   H4    single    0.930  0.020  1.080
 FCK  C5   C6    aromatic  1.392  0.020  1.392
 FCK  C6   C1    aromatic  1.388  0.020  1.388
 FCK  C6   H6    single    0.930  0.020  1.080
 FCK  C7   N18   single    1.450  0.020  1.450
 FCK  C7   H7    single    0.970  0.020  1.090
 FCK  C7   H7A   single    0.970  0.020  1.090
 FCK  O39  C38   double    1.208  0.020  1.208
 FCK  C38  C5    single    1.483  0.020  1.483
 FCK  C38  O40   single    1.326  0.020  1.326
 FCK  O40  HO40  single    0.850  0.020  0.980
 FCK  C17  C3    single    1.505  0.020  1.505
 FCK  C17  H17   single    0.970  0.020  1.090
 FCK  C17  H17A  single    0.970  0.020  1.090
 FCK  N18  C17   single    1.450  0.020  1.450
 FCK  N18  HN18  single    0.890  0.020  1.040
 FCK  C22  C7    single    1.522  0.020  1.522
 FCK  C22  H22   single    0.970  0.020  1.090
 FCK  C22  H22A  single    0.970  0.020  1.090
 FCK  C23  C22   single    1.513  0.020  1.513
 FCK  C23  H23   single    0.970  0.020  1.090
 FCK  C23  H23A  single    0.970  0.020  1.090
 FCK  O27  C23   single    1.429  0.020  1.429
 FCK  N31  O27   single    1.340  0.020  1.340
 FCK  C30  N31   double    1.269  0.020  1.269
 FCK  C16  C30   single    1.456  0.020  1.456
 FCK  N11  C16   single    1.364  0.020  1.364
 FCK  C15  C16   double    1.350  0.020  1.350
 FCK  C14  C15   single    1.444  0.020  1.444
 FCK  C14  N13   single    1.387  0.020  1.387
 FCK  O33  C14   double    1.217  0.020  1.217
 FCK  N13  C12   single    1.372  0.020  1.372
 FCK  N13  HN13  single    0.860  0.020  1.020
 FCK  C12  N11   single    1.368  0.020  1.368
 FCK  O34  C12   double    1.213  0.020  1.213
 FCK  C30  H30   single    0.930  0.020  1.080
 FCK  N11  H171  single    0.860  0.020  1.020
 FCK  C15  H15   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
 FCK  H1    C1   C6   119.61  3.000
 FCK  C6    C1   C2   120.34  3.000
 FCK  H1    C1   C2   120.06  3.000
 FCK  H2    C2   C3   119.46  3.000
 FCK  C3    C2   C1   120.71  3.000
 FCK  H2    C2   C1   119.84  3.000
 FCK  C17   C3   C4   121.28  3.000
 FCK  C17   C3   C2   120.03  3.000
 FCK  C4    C3   C2   118.69  3.000
 FCK  H4    C4   C5   119.65  3.000
 FCK  H4    C4   C3   119.30  3.000
 FCK  C5    C4   C3   121.05  3.000
 FCK  C38   C5   C6   122.22  3.000
 FCK  C38   C5   C4   118.15  3.000
 FCK  C6    C5   C4   119.63  3.000
 FCK  H6    C6   C5   121.02  3.000
 FCK  H6    C6   C1   119.39  3.000
 FCK  C5    C6   C1   119.59  3.000
 FCK  H7A   C7   H7   106.23  3.000
 FCK  H7A   C7   C22  109.53  3.000
 FCK  H7    C7   C22  109.70  3.000
 FCK  C22   C7   N18  110.38  3.000
 FCK  H7A   C7   N18  107.95  3.000
 FCK  H7    C7   N18  112.91  3.000
 FCK  O40   C38  O39  123.05  3.000
 FCK  O40   C38  C5   113.06  3.000
 FCK  O39   C38  C5   123.88  3.000
 FCK  HO40  O40  C38  109.98  3.000
 FCK  H17A  C17  H17  106.16  3.000
 FCK  H17A  C17  N18  107.78  3.000
 FCK  H17   C17  N18  113.48  3.000
 FCK  N18   C17  C3   110.64  3.000
 FCK  H17A  C17  C3   109.00  3.000
 FCK  H17   C17  C3   109.58  3.000
 FCK  HN18  N18  C17  108.93  3.000
 FCK  HN18  N18  C7   109.23  3.000
 FCK  C17   N18  C7   113.25  3.000
 FCK  H22A  C22  H22  107.41  3.000
 FCK  H22A  C22  C23  109.67  3.000
 FCK  H22   C22  C23  110.01  3.000
 FCK  C23   C22  C7   111.15  3.000
 FCK  H22A  C22  C7   109.59  3.000
 FCK  H22   C22  C7   108.93  3.000
 FCK  H23A  C23  H23  108.14  3.000
 FCK  H23A  C23  O27  109.63  3.000
 FCK  H23   C23  O27  109.73  3.000
 FCK  O27   C23  C22  107.49  3.000
 FCK  H23A  C23  C22  110.66  3.000
 FCK  H23   C23  C22  111.18  3.000
 FCK  N31   O27  C23  111.09  3.000
 FCK  C30   N31  O27  113.80  3.000
 FCK  H30   C30  C16  117.93  3.000
 FCK  H30   C30  N31  123.94  3.000
 FCK  C16   C30  N31  118.13  3.000
 FCK  C15   C16  N11  121.09  3.000
 FCK  C15   C16  C30  121.27  3.000
 FCK  N11   C16  C30  117.64  3.000
 FCK  H171  N11  C12  117.47  3.000
 FCK  H171  N11  C16  118.92  3.000
 FCK  C12   N11  C16  123.60  3.000
 FCK  H15   C15  C14  119.27  3.000
 FCK  H15   C15  C16  120.89  3.000
 FCK  C14   C15  C16  119.84  3.000
 FCK  N13   C14  O33  120.55  3.000
 FCK  O33   C14  C15  125.34  3.000
 FCK  N13   C14  C15  114.11  3.000
 FCK  HN13  N13  C12  115.73  3.000
 FCK  HN13  N13  C14  116.90  3.000
 FCK  C12   N13  C14  127.37  3.000
 FCK  O34   C12  N13  123.02  3.000
 FCK  O34   C12  N11  122.99  3.000
 FCK  N13   C12  N11  113.99  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
 FCK  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 FCK  CONST_02  C4    C5   C6   C1      0.00   0.0  0
 FCK  CONST_03  C5    C6   C1   C2      0.00   0.0  0
 FCK  CONST_04  C5    C4   C3   C2      0.00   0.0  0
 FCK  CONST_05  C6    C1   C2   C3      0.00   0.0  0
 FCK  CONST_06  C6    C5   C4   C3      0.00   0.0  0
 FCK  CONST_07  N13   C12  N11  C16     0.00   0.0  0
 FCK  CONST_08  C14   N13  C12  N11     0.00   0.0  0
 FCK  CONST_09  C12   N13  C14  C15     0.00   0.0  0
 FCK  CONST_10  C17   C3   C2   C1    180.00   0.0  0
 FCK  CONST_11  C38   C5   C6   C1    180.00   0.0  0
 FCK  CONST_12  C38   C5   C4   C3    180.00   0.0  0
 FCK  CONST_13  C17   C3   C4   C5    180.00   0.0  0
 FCK  CONST_14  O34   C12  N11  C16   180.00   0.0  0
 FCK  CONST_15  O34   C12  N13  C14   180.00   0.0  0
 FCK  CONST_16  C12   N13  C14  O33   180.00   0.0  0
 FCK  CONST_17  H6    C6   C1   C2    180.00   0.0  0
 FCK  CONST_18  H4    C4   C3   C2    180.00   0.0  0
 FCK  CONST_19  H1    C1   C2   C3    180.00   0.0  0
 FCK  CONST_20  H2    C2   C3   C4    180.00   0.0  0
 FCK  CONST_21  HN13  N13  C12  N11   180.00   0.0  0
 FCK  CONST_22  H171  N11  C12  N13   180.00   0.0  0
 FCK  CONST_23  C16   C30  N31  O27   180.00   0.0  0
 FCK  CONST_24  HO40  O40  C38  C5    180.00   0.0  0
 FCK  CONST_25  H30   C30  N31  O27     0.00   0.0  0
 FCK  Var_01    N18   C17  C3   C2     56.63  30.0  2
 FCK  Var_02    O39   C38  C5   C4     -0.86  30.0  3
 FCK  Var_03    N11   C16  C30  N31    -1.55  30.0  2
 FCK  Var_04    C7    N18  C17  C3   -173.41  30.0  1
 FCK  Var_05    O27   C23  C22  C7    178.14  30.0  2
 FCK  Var_06    C22   C7   N18  C17   179.62  30.0  1
 FCK  Var_07    C23   C22  C7   N18  -177.19  30.0  1

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
 FCK  plan-1  C1    0.020
 FCK  plan-1  C2    0.020
 FCK  plan-1  C3    0.020
 FCK  plan-1  C4    0.020
 FCK  plan-1  C5    0.020
 FCK  plan-1  C6    0.020
 FCK  plan-1  C38   0.020
 FCK  plan-1  C17   0.020
 FCK  plan-1  H1    0.020
 FCK  plan-1  H2    0.020
 FCK  plan-1  H4    0.020
 FCK  plan-1  H6    0.020
 FCK  plan-2  O27   0.020
 FCK  plan-2  N31   0.020
 FCK  plan-2  C30   0.020
 FCK  plan-2  C16   0.020
 FCK  plan-2  H30   0.020
 FCK  plan-3  C30   0.020
 FCK  plan-3  C16   0.020
 FCK  plan-3  N11   0.020
 FCK  plan-3  C15   0.020
 FCK  plan-3  C14   0.020
 FCK  plan-3  O33   0.020
 FCK  plan-3  N13   0.020
 FCK  plan-3  C12   0.020
 FCK  plan-3  O34   0.020
 FCK  plan-3  HN13  0.020
 FCK  plan-3  H171  0.020
 FCK  plan-3  H15   0.020
 FCK  plan-4  C5    0.020
 FCK  plan-4  O39   0.020
 FCK  plan-4  C38   0.020
 FCK  plan-4  O40   0.020
 FCK  plan-4  HO40  0.020

