# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 16:59:12 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: 3-{(E)-[(3-{[(2,6-dioxo-1,2,3,6-tetrahydropyrimidin-4-yl)methyl]amino}propoxy)imino]methyl}benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1cccc(\C=N\OCCCNCC2=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
 3FI  3FI  '3-{(E)-[(3-{[(2,6-dioxo-1,2,3,6-tetrahydropyrimidin-4-yl)methyl]amino}propoxy)imino]methyl}benzoic acid'  ligand  42  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 PERFECT
;

data_comp_3FI
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
 3FI  C1    C  CR16   0  -0.214  -6.5735  -1.7533  -0.9353
 3FI  C2    C  CR16   0  -0.290  -5.2424  -1.3973  -0.8122
 3FI  C3    C  CR6    0   0.076  -4.8974  -0.2301  -0.1253
 3FI  C4    C  CR16   0  -0.366  -5.9062   0.5593   0.4220
 3FI  C5    C  CR6    0  -0.089  -7.2477   0.2070   0.3080
 3FI  C6    C  CR16   0  -0.293  -7.5701  -0.9596  -0.3770
 3FI  O40   O  OC    -1  -0.615  -9.5076   0.6782   0.8002
 3FI  C38   C  C      0   0.392  -8.3357   1.0810   0.9232
 3FI  O39   O  O      0  -0.529  -7.9566   2.1204   1.4951
 3FI  C9    C  C1     0  -0.062  -3.5103   0.1978   0.0465
 3FI  N18   N  N      0  -0.088  -2.5443  -0.5235  -0.3515
 3FI  O1    O  O2     0  -0.390  -1.3324   0.0531  -0.1185
 3FI  C22   C  CH2    0  -0.095  -0.2832  -0.8420  -0.4555
 3FI  C23   C  CH2    0  -0.487   1.0281  -0.1138  -0.2437
 3FI  C8    C  CH2    0  -0.259   2.2114  -1.0307  -0.5109
 3FI  N31   N  NH1    0  -0.551   3.4630  -0.3286  -0.2825
 3FI  C30   C  CH2    0  -0.345   4.6160  -1.1879  -0.4852
 3FI  C16   C  CR6    0   0.440   5.8728  -0.4825  -0.0735
 3FI  N11   N  NR16   0  -0.715   6.3169   0.4976  -0.9138
 3FI  C15   C  CR16   0  -0.508   6.5354  -0.7549   1.0680
 3FI  C14   C  CR6    0   0.582   7.7221  -0.0122   1.4159
 3FI  O33   O  O      0  -0.409   8.3952  -0.1802   2.4171
 3FI  N13   N  NR16   0  -0.717   8.0718   0.9632   0.4924
 3FI  C12   C  CR6    0   0.665   7.4286   1.2647  -0.6787
 3FI  O34   O  O      0  -0.428   7.8069   2.1285  -1.4420
 3FI  H1    H  HCR6   0   0.233  -6.8395  -2.6565  -1.4697
 3FI  H2    H  HCR6   0   0.240  -4.4708  -2.0184  -1.2484
 3FI  H4    H  HCR6   0   0.255  -5.6430   1.4670   0.9519
 3FI  H6    H  HCR6   0   0.239  -8.6076  -1.2491  -0.4757
 3FI  H9    H  H      0   0.225  -3.3413   1.1587   0.5337
 3FI  H22   H  HCH2   0   0.196  -0.3309  -1.7336   0.1796
 3FI  H22A  H  HCH2   0   0.197  -0.3828  -1.1669  -1.4965
 3FI  H23   H  HCH2   0   0.221   1.0751   0.7542  -0.9086
 3FI  H23A  H  HCH2   0   0.248   1.0879   0.2566   0.7829
 3FI  H8    H  HCH2   0   0.219   2.1737  -1.8823   0.1747
 3FI  H8A   H  HCH2   0   0.187   2.1414  -1.4467  -1.5277
 3FI  HN31  H  HNH1   0   0.319   3.5081   0.4602  -0.9181
 3FI  H30   H  HCH2   0   0.254   4.5061  -2.0710   0.1444
 3FI  H30A  H  HCH2   0   0.210   4.7243  -1.5465  -1.5201
 3FI  HN11  H  HNR6   0   0.390   5.8420   0.6629  -1.7903
 3FI  H15   H  HCR6   0   0.260   6.1840  -1.5251   1.7376
 3FI  HN13  H  HNR6   0   0.403   8.9015   1.5072   0.6926

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
 3FI  C1   C6    aromatic  1.391  0.020  1.391
 3FI  C1   C2    aromatic  1.383  0.020  1.383
 3FI  C1   H1    single    0.930  0.020  1.080
 3FI  C2   C3    aromatic  1.398  0.020  1.398
 3FI  C2   H2    single    0.930  0.020  1.080
 3FI  C3   C4    aromatic  1.393  0.020  1.393
 3FI  C3   C9    single    1.462  0.020  1.462
 3FI  C5   C4    aromatic  1.392  0.020  1.392
 3FI  C4   H4    single    0.930  0.020  1.080
 3FI  C6   C5    aromatic  1.391  0.020  1.391
 3FI  C5   C38   single    1.525  0.020  1.525
 3FI  C6   H6    single    0.930  0.020  1.080
 3FI  C38  O40   deloc     1.245  0.020  1.245
 3FI  O39  C38   deloc     1.246  0.020  1.246
 3FI  C9   N18   double    1.270  0.020  1.270
 3FI  C9   H9    single    0.930  0.020  1.080
 3FI  N18  O1    single    1.362  0.020  1.362
 3FI  C22  O1    single    1.420  0.020  1.420
 3FI  C22  C23   single    1.515  0.020  1.515
 3FI  C22  H22   single    0.970  0.020  1.090
 3FI  C22  H22A  single    0.970  0.020  1.090
 3FI  C23  C8    single    1.521  0.020  1.521
 3FI  C23  H23   single    0.970  0.020  1.090
 3FI  C23  H23A  single    0.970  0.020  1.090
 3FI  C8   N31   single    1.453  0.020  1.453
 3FI  C8   H8    single    0.970  0.020  1.090
 3FI  C8   H8A   single    0.970  0.020  1.090
 3FI  N31  C30   single    1.452  0.020  1.452
 3FI  N31  HN31  single    0.890  0.020  1.040
 3FI  C30  C16   single    1.499  0.020  1.499
 3FI  C30  H30   single    0.970  0.020  1.090
 3FI  C30  H30A  single    0.970  0.020  1.090
 3FI  C15  C16   double    1.348  0.020  1.348
 3FI  C16  N11   single    1.365  0.020  1.365
 3FI  N11  C12   single    1.371  0.020  1.371
 3FI  N11  HN11  single    0.860  0.020  1.020
 3FI  C15  C14   single    1.443  0.020  1.443
 3FI  C15  H15   single    0.930  0.020  1.080
 3FI  O33  C14   double    1.218  0.020  1.218
 3FI  C14  N13   single    1.388  0.020  1.388
 3FI  N13  C12   single    1.370  0.020  1.370
 3FI  N13  HN13  single    0.860  0.020  1.020
 3FI  C12  O34   double    1.213  0.020  1.213

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
 3FI  H1    C1   C6   119.88  3.000
 3FI  H1    C1   C2   119.67  3.000
 3FI  C6    C1   C2   120.45  3.000
 3FI  H2    C2   C3   120.09  3.000
 3FI  H2    C2   C1   120.16  3.000
 3FI  C3    C2   C1   119.75  3.000
 3FI  C9    C3   C4   118.37  3.000
 3FI  C9    C3   C2   122.45  3.000
 3FI  C4    C3   C2   119.18  3.000
 3FI  H4    C4   C5   119.10  3.000
 3FI  H4    C4   C3   119.40  3.000
 3FI  C5    C4   C3   121.50  3.000
 3FI  C38   C5   C6   120.93  3.000
 3FI  C38   C5   C4   120.63  3.000
 3FI  C6    C5   C4   118.44  3.000
 3FI  H6    C6   C5   119.46  3.000
 3FI  H6    C6   C1   119.86  3.000
 3FI  C5    C6   C1   120.68  3.000
 3FI  O39   C38  O40  126.99  3.000
 3FI  O39   C38  C5   116.51  3.000
 3FI  O40   C38  C5   116.50  3.000
 3FI  H9    C9   N18  121.52  3.000
 3FI  H9    C9   C3   117.22  3.000
 3FI  N18   C9   C3   121.26  3.000
 3FI  O1    N18  C9   112.51  3.000
 3FI  C22   O1   N18  110.48  3.000
 3FI  H22A  C22  H22  107.80  3.000
 3FI  H22A  C22  C23  110.75  3.000
 3FI  H22   C22  C23  110.35  3.000
 3FI  H22A  C22  O1   110.21  3.000
 3FI  H22   C22  O1   110.08  3.000
 3FI  C23   C22  O1   107.66  3.000
 3FI  H23A  C23  H23  107.43  3.000
 3FI  H23A  C23  C8   109.08  3.000
 3FI  H23   C23  C8   109.75  3.000
 3FI  H23A  C23  C22  109.97  3.000
 3FI  H23   C23  C22  109.48  3.000
 3FI  C8    C23  C22  111.05  3.000
 3FI  H8A   C8   H8   106.41  3.000
 3FI  H8A   C8   N31  112.49  3.000
 3FI  H8    C8   N31  107.90  3.000
 3FI  H8A   C8   C23  109.92  3.000
 3FI  H8    C8   C23  109.42  3.000
 3FI  N31   C8   C23  110.56  3.000
 3FI  HN31  N31  C30  109.72  3.000
 3FI  HN31  N31  C8   108.40  3.000
 3FI  C30   N31  C8   112.09  3.000
 3FI  H30A  C30  H30  106.80  3.000
 3FI  H30A  C30  C16  109.22  3.000
 3FI  H30   C30  C16  107.89  3.000
 3FI  H30A  C30  N31  113.71  3.000
 3FI  H30   C30  N31  108.58  3.000
 3FI  C16   C30  N31  110.42  3.000
 3FI  C15   C16  N11  120.43  3.000
 3FI  N11   C16  C30  116.20  3.000
 3FI  C15   C16  C30  123.35  3.000
 3FI  HN11  N11  C12  116.00  3.000
 3FI  HN11  N11  C16  119.89  3.000
 3FI  C12   N11  C16  124.05  3.000
 3FI  H15   C15  C14  119.05  3.000
 3FI  H15   C15  C16  120.64  3.000
 3FI  C14   C15  C16  120.31  3.000
 3FI  N13   C14  O33  120.30  3.000
 3FI  N13   C14  C15  114.12  3.000
 3FI  O33   C14  C15  125.58  3.000
 3FI  HN13  N13  C12  115.83  3.000
 3FI  HN13  N13  C14  116.92  3.000
 3FI  C12   N13  C14  127.25  3.000
 3FI  O34   C12  N13  123.25  3.000
 3FI  O34   C12  N11  122.91  3.000
 3FI  N13   C12  N11  113.84  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
 3FI  CONST_01  C4    C5   C6   C1      0.00   0.0  0
 3FI  CONST_02  C4    C3   C2   C1      0.00   0.0  0
 3FI  CONST_03  C5    C6   C1   C2      0.00   0.0  0
 3FI  CONST_04  C5    C4   C3   C2      0.00   0.0  0
 3FI  CONST_05  C6    C1   C2   C3      0.00   0.0  0
 3FI  CONST_06  C6    C5   C4   C3      0.00   0.0  0
 3FI  CONST_07  N13   C12  N11  C16     0.00   0.0  0
 3FI  CONST_08  C14   N13  C12  N11     0.00   0.0  0
 3FI  CONST_09  C12   N13  C14  C15     0.00   0.0  0
 3FI  CONST_10  C38   C5   C6   C1    180.00   0.0  0
 3FI  CONST_11  C9    C3   C2   C1    180.00   0.0  0
 3FI  CONST_12  C38   C5   C4   C3    180.00   0.0  0
 3FI  CONST_13  C9    C3   C4   C5    180.00   0.0  0
 3FI  CONST_14  O34   C12  N11  C16   180.00   0.0  0
 3FI  CONST_15  O34   C12  N13  C14   180.00   0.0  0
 3FI  CONST_16  C12   N13  C14  O33   180.00   0.0  0
 3FI  CONST_17  H6    C6   C1   C2    180.00   0.0  0
 3FI  CONST_18  H4    C4   C3   C2    180.00   0.0  0
 3FI  CONST_19  H1    C1   C2   C3    180.00   0.0  0
 3FI  CONST_20  H2    C2   C3   C4    180.00   0.0  0
 3FI  CONST_21  HN13  N13  C12  N11   180.00   0.0  0
 3FI  CONST_22  HN11  N11  C12  N13   180.00   0.0  0
 3FI  CONST_23  O1    N18  C9   C3    180.00   0.0  0
 3FI  CONST_24  H9    C9   N18  O1      0.00   0.0  0
 3FI  Var_01    N18   C9   C3   C2     -4.57  30.0  2
 3FI  Var_02    O40   C38  C5   C4   -178.48  30.0  2
 3FI  Var_03    C15   C16  C30  N31   104.79  30.0  3
 3FI  Var_04    C16   C30  N31  C8   -172.82  30.0  3
 3FI  Var_05    C23   C22  O1   N18   177.02  30.0  1
 3FI  Var_06    C8    C23  C22  O1    176.91  30.0  3
 3FI  Var_07    N31   C8   C23  C22  -179.02  30.0  3
 3FI  Var_08    C30   N31  C8   C23   178.08  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
 3FI  plan-1  C1    0.020
 3FI  plan-1  C2    0.020
 3FI  plan-1  C3    0.020
 3FI  plan-1  C4    0.020
 3FI  plan-1  C5    0.020
 3FI  plan-1  C6    0.020
 3FI  plan-1  C38   0.020
 3FI  plan-1  C9    0.020
 3FI  plan-1  H1    0.020
 3FI  plan-1  H2    0.020
 3FI  plan-1  H4    0.020
 3FI  plan-1  H6    0.020
 3FI  plan-2  C3    0.020
 3FI  plan-2  C9    0.020
 3FI  plan-2  N18   0.020
 3FI  plan-2  O1    0.020
 3FI  plan-2  H9    0.020
 3FI  plan-3  C30   0.020
 3FI  plan-3  C16   0.020
 3FI  plan-3  N11   0.020
 3FI  plan-3  C15   0.020
 3FI  plan-3  C14   0.020
 3FI  plan-3  O33   0.020
 3FI  plan-3  N13   0.020
 3FI  plan-3  C12   0.020
 3FI  plan-3  O34   0.020
 3FI  plan-3  HN11  0.020
 3FI  plan-3  H15   0.020
 3FI  plan-3  HN13  0.020
 3FI  plan-4  C5    0.020
 3FI  plan-4  O40   0.020
 3FI  plan-4  C38   0.020
 3FI  plan-4  O39   0.020

