# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 16:41:54 2020
#   Inital geometry file: a 120 line input string
#   Ligand name: 3-{[(4-{[(2,6-dioxo-1,2,3,6-tetrahydropyrimidin-4-yl)methyl]amino}butyl)amino]methyl}benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1cccc(CNCCCCNCC2=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
 3FL  3FL  '3-{[(4-{[(2,6-dioxo-1,2,3,6-tetrahydropyrimidin-4-yl)methyl]amino}butyl)amino]methyl}benzoic acid'  ligand  46  25  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_3FL
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
 3FL  C8    C  CH2    0  -0.252   2.0587  -0.0416  -0.8131
 3FL  C5    C  CR6    0  -0.084  -7.0745   0.1156  -0.2106
 3FL  C6    C  CR16   0  -0.306  -7.6350  -1.1578  -0.3017
 3FL  C2    C  CR16   0  -0.318  -5.6970  -2.1131   0.7567
 3FL  C4    C  CR16   0  -0.339  -5.8156   0.2473   0.3659
 3FL  O40   O  OC    -1  -0.596  -8.9397   1.1312  -1.2444
 3FL  C38   C  C      0   0.396  -7.8237   1.3374  -0.7293
 3FL  O39   O  O      0  -0.594  -7.2567   2.4389  -0.5958
 3FL  C1    C  CR16   0  -0.232  -6.9518  -2.2647   0.1782
 3FL  C3    C  CR6    0   0.118  -5.1176  -0.8526   0.8572
 3FL  C17   C  CH2    0  -0.332  -3.7422  -0.6837   1.4421
 3FL  N18   N  NH1    0  -0.589  -2.7542  -0.5186   0.3893
 3FL  C7    C  CH2    0  -0.249  -1.4052  -0.3914   0.9083
 3FL  C22   C  CH2    0  -0.445  -0.3867  -0.2767  -0.2142
 3FL  C23   C  CH2    0  -0.445   1.0373  -0.1365   0.3076
 3FL  N31   N  NH1    0  -0.599   3.4075   0.0722  -0.2819
 3FL  C30   C  CH2    0  -0.348   4.4028   0.1839  -1.3332
 3FL  C16   C  CR6    0   0.442   5.7845   0.0787  -0.7614
 3FL  N11   N  NR16   0  -0.712   6.2172   1.1472  -0.0295
 3FL  C15   C  CR16   0  -0.545   6.5715  -1.0037  -0.9196
 3FL  C14   C  CR6    0   0.580   7.8793  -1.0476  -0.3124
 3FL  O33   O  O      0  -0.468   8.6686  -1.9716  -0.3942
 3FL  N13   N  NR16   0  -0.716   8.2042   0.0871   0.4180
 3FL  C12   C  CR6    0   0.673   7.4368   1.2078   0.5938
 3FL  O34   O  O      0  -0.475   7.8001   2.1682   1.2398
 3FL  H8    H  HCH2   0   0.223   2.0112  -0.9469  -1.4262
 3FL  H8A   H  HCH2   0   0.196   1.7992   0.7957  -1.4797
 3FL  H6    H  HCR6   0   0.241  -8.6123  -1.2793  -0.7499
 3FL  H2    H  HCR6   0   0.244  -5.1675  -2.9809   1.1337
 3FL  H4    H  HCR6   0   0.233  -5.3731   1.2330   0.4454
 3FL  H1    H  HCR6   0   0.246  -7.3951  -3.2499   0.1034
 3FL  H17   H  HCH2   0   0.231  -3.7159   0.2102   2.0725
 3FL  H17A  H  HCH2   0   0.205  -3.5189  -1.5351   2.1039
 3FL  HN18  H  HNH1   0   0.337  -2.7961  -1.3291  -0.2191
 3FL  H7    H  HCH2   0   0.214  -1.3618   0.5084   1.5311
 3FL  H7A   H  HCH2   0   0.185  -1.1289  -1.2310   1.5676
 3FL  H22   H  HCH2   0   0.217  -0.4541  -1.1627  -0.8554
 3FL  H22A  H  HCH2   0   0.220  -0.6391   0.5818  -0.8433
 3FL  H23   H  HCH2   0   0.221   1.2845  -0.9904   0.9452
 3FL  H23A  H  HCH2   0   0.219   1.1077   0.7550   0.9407
 3FL  HN31  H  HNH1   0   0.346   3.4466   0.8917   0.3138
 3FL  H30   H  HCH2   0   0.268   4.2629  -0.6410  -2.0320
 3FL  H30A  H  HCH2   0   0.242   4.3247   1.1120  -1.9198
 3FL  HN13  H  HNR6   0   0.426   9.1107   0.0988   0.8689
 3FL  H21   H  HNR6   0   0.433   5.6390   1.9724   0.0468
 3FL  H15   H  HCR6   0   0.286   6.2335  -1.8514  -1.4963

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
 3FL  C8   C23   single    1.519  0.020  1.519
 3FL  C8   N31   single    1.454  0.020  1.454
 3FL  C8   H8    single    0.970  0.020  1.090
 3FL  C8   H8A   single    0.970  0.020  1.090
 3FL  C5   C4    aromatic  1.391  0.020  1.391
 3FL  C5   C38   single    1.524  0.020  1.524
 3FL  C6   C5    aromatic  1.394  0.020  1.394
 3FL  C6   H6    single    0.930  0.020  1.080
 3FL  C2   C3    aromatic  1.391  0.020  1.391
 3FL  C2   H2    single    0.930  0.020  1.080
 3FL  C4   H4    single    0.930  0.020  1.080
 3FL  C38  O40   deloc     1.246  0.020  1.246
 3FL  O39  C38   deloc     1.246  0.020  1.246
 3FL  C1   C6    aromatic  1.386  0.020  1.386
 3FL  C1   C2    aromatic  1.390  0.020  1.390
 3FL  C1   H1    single    0.930  0.020  1.080
 3FL  C3   C4    aromatic  1.392  0.020  1.392
 3FL  C3   C17   single    1.504  0.020  1.504
 3FL  C17  N18   single    1.453  0.020  1.453
 3FL  C17  H17   single    0.970  0.020  1.090
 3FL  C17  H17A  single    0.970  0.020  1.090
 3FL  N18  C7    single    1.451  0.020  1.451
 3FL  N18  HN18  single    0.890  0.020  1.040
 3FL  C7   C22   single    1.520  0.020  1.520
 3FL  C7   H7    single    0.970  0.020  1.090
 3FL  C7   H7A   single    0.970  0.020  1.090
 3FL  C22  C23   single    1.523  0.020  1.523
 3FL  C22  H22   single    0.970  0.020  1.090
 3FL  C22  H22A  single    0.970  0.020  1.090
 3FL  C23  H23   single    0.970  0.020  1.090
 3FL  C23  H23A  single    0.970  0.020  1.090
 3FL  N31  HN31  single    0.890  0.020  1.040
 3FL  C30  N31   single    1.452  0.020  1.452
 3FL  C30  H30   single    0.970  0.020  1.090
 3FL  C30  H30A  single    0.970  0.020  1.090
 3FL  C16  C30   single    1.499  0.020  1.499
 3FL  C16  C15   double    1.348  0.020  1.348
 3FL  N11  C16   single    1.366  0.020  1.366
 3FL  C14  C15   single    1.443  0.020  1.443
 3FL  C14  O33   double    1.218  0.020  1.218
 3FL  N13  C14   single    1.388  0.020  1.388
 3FL  N13  HN13  single    0.860  0.020  1.020
 3FL  C12  N11   single    1.371  0.020  1.371
 3FL  C12  N13   single    1.370  0.020  1.370
 3FL  O34  C12   double    1.213  0.020  1.213
 3FL  N11  H21   single    0.860  0.020  1.020
 3FL  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
 3FL  H8A   C8   H8   106.24  3.000
 3FL  H8A   C8   N31  112.34  3.000
 3FL  H8    C8   N31  108.04  3.000
 3FL  H8A   C8   C23  109.61  3.000
 3FL  H8    C8   C23  109.41  3.000
 3FL  N31   C8   C23  111.04  3.000
 3FL  C38   C5   C4   120.67  3.000
 3FL  C38   C5   C6   120.81  3.000
 3FL  C4    C5   C6   118.52  3.000
 3FL  H6    C6   C1   119.92  3.000
 3FL  C1    C6   C5   120.56  3.000
 3FL  H6    C6   C5   119.52  3.000
 3FL  H2    C2   C3   119.79  3.000
 3FL  H2    C2   C1   119.88  3.000
 3FL  C3    C2   C1   120.33  3.000
 3FL  H4    C4   C3   119.21  3.000
 3FL  C3    C4   C5   121.69  3.000
 3FL  H4    C4   C5   119.09  3.000
 3FL  O39   C38  O40  126.73  3.000
 3FL  O39   C38  C5   116.64  3.000
 3FL  O40   C38  C5   116.63  3.000
 3FL  H1    C1   C2   119.84  3.000
 3FL  H1    C1   C6   120.04  3.000
 3FL  C2    C1   C6   120.12  3.000
 3FL  C17   C3   C4   120.46  3.000
 3FL  C17   C3   C2   120.72  3.000
 3FL  C4    C3   C2   118.79  3.000
 3FL  H17A  C17  H17  106.29  3.000
 3FL  H17A  C17  N18  112.66  3.000
 3FL  H17   C17  N18  107.95  3.000
 3FL  H17A  C17  C3   109.41  3.000
 3FL  H17   C17  C3   109.75  3.000
 3FL  N18   C17  C3   110.66  3.000
 3FL  HN18  N18  C7   108.85  3.000
 3FL  HN18  N18  C17  108.40  3.000
 3FL  C7    N18  C17  112.52  3.000
 3FL  H7A   C7   H7   105.99  3.000
 3FL  H7A   C7   C22  109.34  3.000
 3FL  H7    C7   C22  109.35  3.000
 3FL  H7A   C7   N18  112.34  3.000
 3FL  H7    C7   N18  108.20  3.000
 3FL  C22   C7   N18  111.44  3.000
 3FL  H22A  C22  H22  106.49  3.000
 3FL  H22A  C22  C23  109.91  3.000
 3FL  H22   C22  C23  109.41  3.000
 3FL  H22A  C22  C7   109.23  3.000
 3FL  H22   C22  C7   109.26  3.000
 3FL  C23   C22  C7   112.36  3.000
 3FL  H23A  C23  H23  106.49  3.000
 3FL  H23A  C23  C22  109.44  3.000
 3FL  H23   C23  C22  109.82  3.000
 3FL  H23A  C23  C8   109.41  3.000
 3FL  H23   C23  C8   109.07  3.000
 3FL  C22   C23  C8   112.43  3.000
 3FL  HN31  N31  C30  109.68  3.000
 3FL  C30   N31  C8   112.17  3.000
 3FL  HN31  N31  C8   108.28  3.000
 3FL  H30A  C30  H30  106.70  3.000
 3FL  H30A  C30  C16  109.14  3.000
 3FL  H30   C30  C16  108.04  3.000
 3FL  C16   C30  N31  110.50  3.000
 3FL  H30A  C30  N31  113.71  3.000
 3FL  H30   C30  N31  108.54  3.000
 3FL  C15   C16  N11  120.42  3.000
 3FL  N11   C16  C30  116.21  3.000
 3FL  C15   C16  C30  123.36  3.000
 3FL  H21   N11  C12  116.01  3.000
 3FL  H21   N11  C16  119.88  3.000
 3FL  C12   N11  C16  124.07  3.000
 3FL  H15   C15  C14  119.00  3.000
 3FL  H15   C15  C16  120.70  3.000
 3FL  C14   C15  C16  120.30  3.000
 3FL  N13   C14  O33  120.25  3.000
 3FL  N13   C14  C15  114.13  3.000
 3FL  O33   C14  C15  125.62  3.000
 3FL  HN13  N13  C12  115.78  3.000
 3FL  C12   N13  C14  127.25  3.000
 3FL  HN13  N13  C14  116.96  3.000
 3FL  O34   C12  N13  123.25  3.000
 3FL  O34   C12  N11  122.92  3.000
 3FL  N13   C12  N11  113.82  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
 3FL  CONST_01  C2    C3   C4   C5      0.00   0.0  0
 3FL  CONST_02  C2    C1   C6   C5      0.00   0.0  0
 3FL  CONST_03  C3    C4   C5   C6      0.00   0.0  0
 3FL  CONST_04  C3    C2   C1   C6      0.00   0.0  0
 3FL  CONST_05  C1    C6   C5   C4      0.00   0.0  0
 3FL  CONST_06  C1    C2   C3   C4      0.00   0.0  0
 3FL  CONST_07  N13   C12  N11  C16     0.00   0.0  0
 3FL  CONST_08  C14   N13  C12  N11     0.00   0.0  0
 3FL  CONST_09  C12   N13  C14  C15     0.00   0.0  0
 3FL  CONST_10  C17   C3   C4   C5    180.00   0.0  0
 3FL  CONST_11  C3    C4   C5   C38   180.00   0.0  0
 3FL  CONST_12  C1    C6   C5   C38   180.00   0.0  0
 3FL  CONST_13  C17   C3   C2   C1    180.00   0.0  0
 3FL  CONST_14  O34   C12  N11  C16   180.00   0.0  0
 3FL  CONST_15  O34   C12  N13  C14   180.00   0.0  0
 3FL  CONST_16  C12   N13  C14  O33   180.00   0.0  0
 3FL  CONST_17  H1    C1   C6   C5    180.00   0.0  0
 3FL  CONST_18  H4    C4   C5   C6    180.00   0.0  0
 3FL  CONST_19  H2    C2   C1   C6    180.00   0.0  0
 3FL  CONST_20  H6    C6   C1   C2    180.00   0.0  0
 3FL  CONST_21  HN13  N13  C12  N11   180.00   0.0  0
 3FL  CONST_22  H21   N11  C12  N13   180.00   0.0  0
 3FL  Var_01    O40   C38  C5   C6     -0.81  30.0  2
 3FL  Var_02    N18   C17  C3   C2    101.01  30.0  2
 3FL  Var_03    C15   C16  C30  N31   107.17  30.0  2
 3FL  Var_04    C16   C30  N31  C8   -170.97  30.0  1
 3FL  Var_05    C7    N18  C17  C3   -178.30  30.0  3
 3FL  Var_06    C7    C22  C23  C8    179.18  30.0  1
 3FL  Var_07    C22   C7   N18  C17   177.70  30.0  3
 3FL  Var_08    C23   C22  C7   N18   179.78  30.0  3
 3FL  Var_09    N31   C8   C23  C22  -179.20  30.0  1
 3FL  Var_10    C30   N31  C8   C23  -179.18  30.0  3

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
 3FL  plan-1  C5    0.020
 3FL  plan-1  C6    0.020
 3FL  plan-1  C2    0.020
 3FL  plan-1  C4    0.020
 3FL  plan-1  C38   0.020
 3FL  plan-1  C1    0.020
 3FL  plan-1  C3    0.020
 3FL  plan-1  C17   0.020
 3FL  plan-1  H6    0.020
 3FL  plan-1  H2    0.020
 3FL  plan-1  H4    0.020
 3FL  plan-1  H1    0.020
 3FL  plan-2  C30   0.020
 3FL  plan-2  C16   0.020
 3FL  plan-2  N11   0.020
 3FL  plan-2  C15   0.020
 3FL  plan-2  C14   0.020
 3FL  plan-2  O33   0.020
 3FL  plan-2  N13   0.020
 3FL  plan-2  C12   0.020
 3FL  plan-2  O34   0.020
 3FL  plan-2  HN13  0.020
 3FL  plan-2  H21   0.020
 3FL  plan-2  H15   0.020
 3FL  plan-3  C5    0.020
 3FL  plan-3  O40   0.020
 3FL  plan-3  C38   0.020
 3FL  plan-3  O39   0.020

