FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: ZY21N

Calculation Name: 5B26-A-Xray323

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5B26

Chain ID: A

ChEMBL ID:

UniProt ID: Q9Z2G6

Base Structure: X-ray

Registration Date: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 175
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -1671594.421419
FMO2-HF: Nuclear repulsion 1603882.027655
FMO2-HF: Total energy -67712.393765
FMO2-MP2: Total energy -67909.817771


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
ligand interaction
Ligand binding energy
"
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
N/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(A:351:ACE )


Summations of interaction energy for fragment #1(A:351:ACE )
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
1.2344.0912.694-2.922-2.628-0.019
Interaction energy analysis for fragmet #1(A:351:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.043 / q_NPA : 0.018
Distance from base fragment(s) [Å]
Dist
Interaction energy by IFIE and PIEDA
[kcal/mol]
| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >
Fragment charge [e]
FCHARGE q_Mulliken
q_NPA q(I=>J)
Residue
Res #    RES   
Sort
Graph Options
X Axis Label
Y Axis Max Y Axis Min
Display   
frag_NumFragment number. ChainChain species. Res #Residue number. RES3-letter code of amino acid residue, ligand and solvent molecule. FCHARGEFormal charge [e]. q_MullikenFragment charge evaluated by Mulliken charge [e]. q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. DISTDistance from Ligand [Å]. TotalIFIE at MP2 level [kcal/mol]. ESElectro static interaction energy by PIEDA [kcal/mol]. EXExchange-repulsion energy by PIEDA [kcal/mol]. CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. DI(MP2)Dispersion energy by PIEDA [kcal/mol]. q(I=>J)Charge transfer value from I to J fragmens [e].
3A353GLU -1-0.915-0.9573.4540.4621.6330.002-0.594-0.5790.000
4A354GLU -1-0.912-0.9802.4862.4674.1202.692-2.297-2.047-0.019
5A355ASP -1-0.812-0.9054.476-2.778-2.7450.000-0.031-0.0020.000
6A356LEU 0-0.043-0.0206.2790.3720.3720.0000.0000.0000.000
7A357ILE 0-0.037-0.0107.3150.1540.1540.0000.0000.0000.000
8A358GLN 00.0270.0198.441-0.017-0.0170.0000.0000.0000.000
9A359TYR 0-0.015-0.00710.2000.0710.0710.0000.0000.0000.000
10A360TYR 00.009-0.00812.2090.0660.0660.0000.0000.0000.000
11A361GLN 0-0.009-0.01211.8850.0160.0160.0000.0000.0000.000
12A362PHE 00.0080.01114.2220.0290.0290.0000.0000.0000.000
13A363LEU 0-0.011-0.01816.0410.0250.0250.0000.0000.0000.000
14A364ALA 0-0.033-0.01217.8280.0210.0210.0000.0000.0000.000
15A365GLU -1-0.974-0.98218.047-0.082-0.0820.0000.0000.0000.000
16A366LYS 10.8590.93520.2870.1230.1230.0000.0000.0000.000
17A367GLY 0-0.013-0.00122.4600.0030.0030.0000.0000.0000.000
18A368ASP -1-0.884-0.93420.905-0.111-0.1110.0000.0000.0000.000
19A369VAL 00.0530.01022.4410.0040.0040.0000.0000.0000.000
20A370GLN 00.007-0.01021.7070.0060.0060.0000.0000.0000.000
21A371ALA 0-0.0010.01617.9870.0050.0050.0000.0000.0000.000
22A372GLN 0-0.007-0.00119.1390.0130.0130.0000.0000.0000.000
23A373VAL 0-0.013-0.00821.2820.0120.0120.0000.0000.0000.000
24A374GLY 0-0.005-0.00219.0030.0110.0110.0000.0000.0000.000
25A375LEU 0-0.011-0.01213.8840.0160.0160.0000.0000.0000.000
26A376GLY 00.0430.02517.6100.0200.0200.0000.0000.0000.000
27A377GLN 0-0.024-0.01520.0680.0160.0160.0000.0000.0000.000
28A378LEU 0-0.035-0.02713.4670.0110.0110.0000.0000.0000.000
29A379HIS 0-0.070-0.02015.3480.0020.0020.0000.0000.0000.000
30A380LEU 0-0.009-0.00218.6590.0090.0090.0000.0000.0000.000
31A381HIS 0-0.004-0.00720.0560.0070.0070.0000.0000.0000.000
32A382GLY 0-0.0150.01916.8470.0120.0120.0000.0000.0000.000
33A383GLY 0-0.035-0.03315.046-0.013-0.0130.0000.0000.0000.000
34A384ARG 10.9130.94611.3540.0840.0840.0000.0000.0000.000
35A385GLY 00.1070.0628.5740.0540.0540.0000.0000.0000.000
36A386VAL 0-0.100-0.0399.4550.0320.0320.0000.0000.0000.000
37A387GLU -1-0.886-0.94112.4790.1630.1630.0000.0000.0000.000
38A388GLN 0-0.006-0.01715.108-0.038-0.0380.0000.0000.0000.000
39A389ASN 0-0.002-0.01118.745-0.007-0.0070.0000.0000.0000.000
40A390HIS 00.1280.03120.669-0.014-0.0140.0000.0000.0000.000
41A391GLN 0-0.0010.02423.369-0.004-0.0040.0000.0000.0000.000
42A392ARG 10.9590.97414.928-0.023-0.0230.0000.0000.0000.000
43A393ALA 0-0.0150.01021.661-0.011-0.0110.0000.0000.0000.000
44A394PHE 00.0610.03122.823-0.009-0.0090.0000.0000.0000.000
45A395ASP -1-0.871-0.92423.578-0.001-0.0010.0000.0000.0000.000
46A396TYR 0-0.018-0.01616.938-0.015-0.0150.0000.0000.0000.000
47A397PHE 0-0.009-0.01023.550-0.007-0.0070.0000.0000.0000.000
48A398ASN 0-0.037-0.04426.480-0.004-0.0040.0000.0000.0000.000
49A399LEU 0-0.044-0.01023.621-0.003-0.0030.0000.0000.0000.000
50A400ALA 00.0480.02125.517-0.003-0.0030.0000.0000.0000.000
51A401ALA 0-0.061-0.03827.444-0.001-0.0010.0000.0000.0000.000
52A402ASN 0-0.045-0.02930.8300.0020.0020.0000.0000.0000.000
53A403ALA 0-0.0150.01029.2400.0000.0000.0000.0000.0000.000
54A404GLY 0-0.0050.00431.234-0.002-0.0020.0000.0000.0000.000
55A405ASN 00.0160.00627.5400.0040.0040.0000.0000.0000.000
56A406SER 00.0640.01230.6310.0030.0030.0000.0000.0000.000
57A407HIS 00.0430.01827.2250.0070.0070.0000.0000.0000.000
58A408ALA 00.0000.02027.6270.0050.0050.0000.0000.0000.000
59A409MET 0-0.0190.00428.5090.0050.0050.0000.0000.0000.000
60A410ALA 00.0220.01030.8290.0040.0040.0000.0000.0000.000
61A411PHE 0-0.007-0.00324.9120.0040.0040.0000.0000.0000.000
62A412LEU 00.0070.01629.1350.0050.0050.0000.0000.0000.000
63A413GLY 00.0280.00531.0990.0030.0030.0000.0000.0000.000
64A414LYS 10.8650.93729.990-0.015-0.0150.0000.0000.0000.000
65A415MET 00.0210.00926.5110.0000.0000.0000.0000.0000.000
66A416TYR 00.0450.03031.2090.0010.0010.0000.0000.0000.000
67A417SER 0-0.092-0.06134.7460.0010.0010.0000.0000.0000.000
68A418GLU -1-0.960-0.98631.4340.0280.0280.0000.0000.0000.000
69A419GLY 00.0020.00032.9100.0010.0010.0000.0000.0000.000
70A420SER 0-0.043-0.02229.1960.0020.0020.0000.0000.0000.000
71A421ASP -1-0.875-0.93929.4690.0430.0430.0000.0000.0000.000
72A422ILE 0-0.054-0.02426.828-0.003-0.0030.0000.0000.0000.000
73A423VAL 0-0.013-0.00429.735-0.005-0.0050.0000.0000.0000.000
74A424PRO 00.0120.01832.3760.0010.0010.0000.0000.0000.000
75A425GLN 0-0.052-0.03335.956-0.003-0.0030.0000.0000.0000.000
76A426SER 00.0540.02637.573-0.001-0.0010.0000.0000.0000.000
77A427ASN 0-0.033-0.02539.097-0.002-0.0020.0000.0000.0000.000
78A428GLU -1-0.795-0.90140.7010.0010.0010.0000.0000.0000.000
79A429THR 0-0.055-0.02637.358-0.001-0.0010.0000.0000.0000.000
80A430ALA 0-0.0010.00636.723-0.002-0.0020.0000.0000.0000.000
81A431LEU 0-0.023-0.00637.755-0.002-0.0020.0000.0000.0000.000
82A432HIS 0-0.0010.01137.880-0.001-0.0010.0000.0000.0000.000
83A433TYR 00.003-0.00834.262-0.003-0.0030.0000.0000.0000.000
84A434PHE 0-0.0040.00033.862-0.002-0.0020.0000.0000.0000.000
85A435LYS 10.8720.95137.5170.0070.0070.0000.0000.0000.000
86A436LYS 10.9400.98036.3910.0150.0150.0000.0000.0000.000
87A437ALA 00.013-0.00234.448-0.002-0.0020.0000.0000.0000.000
88A438ALA 0-0.043-0.02436.032-0.002-0.0020.0000.0000.0000.000
89A439ASP -1-0.892-0.94838.880-0.013-0.0130.0000.0000.0000.000
90A440MET 0-0.066-0.03734.395-0.002-0.0020.0000.0000.0000.000
91A441GLY 0-0.0170.00336.932-0.002-0.0020.0000.0000.0000.000
92A442ASN 0-0.010-0.01630.6620.0030.0030.0000.0000.0000.000
93A443PRO 00.0410.01932.5840.0030.0030.0000.0000.0000.000
94A444VAL 00.0290.01730.2180.0030.0030.0000.0000.0000.000
95A445GLY 00.0320.01533.6510.0030.0030.0000.0000.0000.000
96A446GLN 0-0.011-0.01236.1700.0020.0020.0000.0000.0000.000
97A447SER 00.0390.01336.1640.0010.0010.0000.0000.0000.000
98A448GLY 0-0.0090.00537.1610.0020.0020.0000.0000.0000.000
99A449LEU 0-0.003-0.01138.1550.0010.0010.0000.0000.0000.000
100A450GLY 00.0040.00341.1240.0010.0010.0000.0000.0000.000
101A451MET 0-0.007-0.01638.5760.0010.0010.0000.0000.0000.000
102A452ALA 0-0.0250.00441.8220.0010.0010.0000.0000.0000.000
103A453TYR 00.0230.00343.5280.0000.0000.0000.0000.0000.000
104A454LEU 0-0.044-0.01844.0180.0000.0000.0000.0000.0000.000
105A455TYR 0-0.037-0.04342.6240.0010.0010.0000.0000.0000.000
106A456GLY 00.0090.01546.7110.0010.0010.0000.0000.0000.000
107A457ARG 10.8900.94639.324-0.011-0.0110.0000.0000.0000.000
108A458GLY 00.0510.03444.526-0.001-0.0010.0000.0000.0000.000
109A459VAL 0-0.005-0.00346.202-0.001-0.0010.0000.0000.0000.000
110A460GLN 0-0.0040.00148.3900.0010.0010.0000.0000.0000.000
111A461VAL 00.0150.00349.962-0.001-0.0010.0000.0000.0000.000
112A462ASN 00.0170.00950.125-0.001-0.0010.0000.0000.0000.000
113A463TYR 00.0750.03449.7560.0000.0000.0000.0000.0000.000
114A464ASP -1-0.881-0.93250.031-0.001-0.0010.0000.0000.0000.000
115A465LEU 0-0.065-0.04147.761-0.001-0.0010.0000.0000.0000.000
116A466ALA 00.0040.01345.511-0.001-0.0010.0000.0000.0000.000
117A467LEU 00.0200.01445.1080.0000.0000.0000.0000.0000.000
118A468LYS 10.9510.96846.1210.0030.0030.0000.0000.0000.000
119A469TYR 0-0.043-0.01742.153-0.002-0.0020.0000.0000.0000.000
120A470PHE 00.0330.00640.365-0.001-0.0010.0000.0000.0000.000
121A471GLN 0-0.025-0.01641.452-0.001-0.0010.0000.0000.0000.000
122A472LYS 10.9380.97341.2020.0090.0090.0000.0000.0000.000
123A473ALA 00.0350.02136.986-0.001-0.0010.0000.0000.0000.000
124A474ALA 0-0.041-0.02337.309-0.001-0.0010.0000.0000.0000.000
125A475GLU -1-0.961-0.98638.665-0.011-0.0110.0000.0000.0000.000
126A476GLN 0-0.101-0.04134.972-0.004-0.0040.0000.0000.0000.000
127A477GLY 0-0.0080.00534.283-0.001-0.0010.0000.0000.0000.000
128A478TRP 0-0.002-0.00329.3520.0010.0010.0000.0000.0000.000
129A479VAL 00.0730.02732.3180.0010.0010.0000.0000.0000.000
130A480ASP -1-0.875-0.94733.9820.0100.0100.0000.0000.0000.000
131A481GLY 00.0370.02635.7020.0000.0000.0000.0000.0000.000
132A482GLN 0-0.038-0.02436.9700.0020.0020.0000.0000.0000.000
133A483LEU 00.0070.01136.2570.0000.0000.0000.0000.0000.000
134A484GLN 0-0.025-0.00838.8110.0000.0000.0000.0000.0000.000
135A485LEU 0-0.0180.00241.8570.0000.0000.0000.0000.0000.000
136A486GLY 00.0100.00543.1010.0000.0000.0000.0000.0000.000
137A487SER 0-0.0050.00043.8800.0000.0000.0000.0000.0000.000
138A488MET 0-0.024-0.00845.6210.0000.0000.0000.0000.0000.000
139A489TYR 00.0300.01347.2560.0000.0000.0000.0000.0000.000
140A490TYR 00.012-0.01247.8420.0000.0000.0000.0000.0000.000
141A491ASN 0-0.052-0.04547.7490.0010.0010.0000.0000.0000.000
142A492GLY 0-0.0210.00351.3080.0000.0000.0000.0000.0000.000
143A493ILE 0-0.0150.01148.3310.0000.0000.0000.0000.0000.000
144A494GLY 0-0.005-0.02351.0730.0000.0000.0000.0000.0000.000
145A495VAL 0-0.0180.00652.055-0.001-0.0010.0000.0000.0000.000
146A496LYN 00.0240.02254.7310.0010.0010.0000.0000.0000.000
147A497ARG 10.9040.95052.002-0.006-0.0060.0000.0000.0000.000
148A498ASP -1-0.870-0.93252.0320.0000.0000.0000.0000.0000.000
149A499TYR 0-0.005-0.02250.9660.0000.0000.0000.0000.0000.000
150A500LYS 10.9880.99250.1280.0010.0010.0000.0000.0000.000
151A501GLN 00.0100.02148.6410.0000.0000.0000.0000.0000.000
152A502ALA 0-0.029-0.00846.6890.0000.0000.0000.0000.0000.000
153A503LEU 00.011-0.00445.3540.0000.0000.0000.0000.0000.000
154A504LYS 10.9340.98544.2180.0050.0050.0000.0000.0000.000
155A505TYR 00.011-0.00541.700-0.001-0.0010.0000.0000.0000.000
156A506PHE 00.0380.00840.5980.0000.0000.0000.0000.0000.000
157A507ASN 0-0.0250.00340.0980.0020.0020.0000.0000.0000.000
158A508LEU 0-0.0050.02238.3610.0000.0000.0000.0000.0000.000
159A509ALA 00.0250.01436.2280.0000.0000.0000.0000.0000.000
160A510SER 0-0.104-0.06435.1240.0010.0010.0000.0000.0000.000
161A511GLN 0-0.012-0.01435.1810.0010.0010.0000.0000.0000.000
162A512GLY 00.0130.01331.667-0.001-0.0010.0000.0000.0000.000
163A513GLY 0-0.002-0.00831.887-0.002-0.0020.0000.0000.0000.000
164A514HIS 00.037-0.00733.630-0.002-0.0020.0000.0000.0000.000
165A515ILE 00.0150.02134.4180.0010.0010.0000.0000.0000.000
166A516LEU 0-0.023-0.02932.4110.0010.0010.0000.0000.0000.000
167A517ALA 0-0.0040.00730.174-0.002-0.0020.0000.0000.0000.000
168A518PHE 00.0430.02028.7160.0000.0000.0000.0000.0000.000
169A519TYR 0-0.007-0.00928.0080.0020.0020.0000.0000.0000.000
170A520ASN 0-0.0030.00425.720-0.005-0.0050.0000.0000.0000.000
171A521LEU 0-0.034-0.02324.053-0.002-0.0020.0000.0000.0000.000
172A522ALA 0-0.0180.00523.8810.0060.0060.0000.0000.0000.000
173A523GLN 0-0.047-0.02821.118-0.002-0.0020.0000.0000.0000.000
174A524MET 0-0.045-0.00519.475-0.010-0.0100.0000.0000.0000.000
175A525NME 00.0030.00915.8420.0120.0120.0000.0000.0000.000