Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: K91V3

Calculation Name: 4XH3-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4XH3

Chain ID: A

ChEMBL ID:

UniProt ID: Q9NQW6

Base Structure: X-ray

Registration Date: 2023-09-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptHSide
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 214
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2320940.176831
FMO2-HF: Nuclear repulsion 2237275.103687
FMO2-HF: Total energy -83665.073143
FMO2-MP2: Total energy -83906.251781


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:-2:GLY)


Summations of interaction energy for fragment #1(A:-2:GLY)
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.
0.1211.629-0.023-0.76-0.725-0.001
Interaction energy analysis for fragmet #1(A:-2:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.010 / 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].
3A0MET0-0.0070.0043.812-0.1291.379-0.023-0.760-0.725-0.001
4A1CYS00.0200.0156.9940.2550.2550.0000.0000.0000.000
5A2GLN00.0310.0159.501-0.074-0.0740.0000.0000.0000.000
6A3VAL00.0130.00312.9880.0330.0330.0000.0000.0000.000
7A4ASN0-0.009-0.01915.3260.0410.0410.0000.0000.0000.000
8A5ILE00.1130.04518.093-0.011-0.0110.0000.0000.0000.000
9A6LYS10.9640.99220.1570.0760.0760.0000.0000.0000.000
10A7GLN0-0.009-0.01216.222-0.005-0.0050.0000.0000.0000.000
11A8LYS10.9040.94715.771-0.060-0.0600.0000.0000.0000.000
12A9MET0-0.010-0.00318.5170.0040.0040.0000.0000.0000.000
13A10GLN0-0.025-0.02321.4220.0070.0070.0000.0000.0000.000
14A11GLU-1-0.920-0.94815.563-0.185-0.1850.0000.0000.0000.000
15A12LEU00.0060.00119.8760.0020.0020.0000.0000.0000.000
16A13ASN0-0.026-0.01421.8260.0110.0110.0000.0000.0000.000
17A14ASN0-0.015-0.01822.1130.0140.0140.0000.0000.0000.000
18A15GLU-1-0.771-0.86820.722-0.043-0.0430.0000.0000.0000.000
19A16ILE0-0.008-0.00122.8790.0070.0070.0000.0000.0000.000
20A17ASN0-0.069-0.04726.1970.0070.0070.0000.0000.0000.000
21A18MET00.0030.01223.406-0.001-0.0010.0000.0000.0000.000
22A19GLN00.004-0.01823.4210.0100.0100.0000.0000.0000.000
23A20GLN00.0330.02427.2370.0090.0090.0000.0000.0000.000
24A21THR0-0.0240.00129.2670.0010.0010.0000.0000.0000.000
25A22VAL00.0140.01227.1160.0010.0010.0000.0000.0000.000
26A23ILE0-0.0040.00930.4240.0020.0020.0000.0000.0000.000
27A24TYR0-0.009-0.00232.8870.0010.0010.0000.0000.0000.000
28A25GLN00.010-0.01031.6670.0010.0010.0000.0000.0000.000
29A26ALA00.0140.01233.3580.0010.0010.0000.0000.0000.000
30A27SER00.001-0.01535.3190.0030.0030.0000.0000.0000.000
31A28GLN0-0.019-0.00838.1600.0030.0030.0000.0000.0000.000
32A29ALA00.0170.01637.6870.0000.0000.0000.0000.0000.000
33A30LEU0-0.006-0.01337.4880.0010.0010.0000.0000.0000.000
34A31ASN0-0.057-0.03440.9920.0030.0030.0000.0000.0000.000
35A32CYS0-0.052-0.01742.8550.0000.0000.0000.0000.0000.000
36A33CYS0-0.0400.01342.5660.0000.0000.0000.0000.0000.000
37A34VAL0-0.029-0.02545.4470.0020.0020.0000.0000.0000.000
38A35ASP-1-0.832-0.93948.992-0.008-0.0080.0000.0000.0000.000
39A36GLU-1-0.856-0.92848.439-0.003-0.0030.0000.0000.0000.000
40A37GLU-1-0.918-0.94148.407-0.014-0.0140.0000.0000.0000.000
41A38HIS10.7680.88647.1410.0120.0120.0000.0000.0000.000
42A39GLY00.0860.05544.028-0.001-0.0010.0000.0000.0000.000
43A40LYS10.9120.97343.9490.0020.0020.0000.0000.0000.000
44A41GLY0-0.033-0.01544.8040.0000.0000.0000.0000.0000.000
45A42SER0-0.012-0.01142.0680.0010.0010.0000.0000.0000.000
46A43LEU00.0380.00736.7150.0010.0010.0000.0000.0000.000
47A44GLU-1-0.933-0.96537.287-0.018-0.0180.0000.0000.0000.000
48A45GLU-1-0.795-0.90237.399-0.002-0.0020.0000.0000.0000.000
49A46ALA00.0240.00538.0470.0010.0010.0000.0000.0000.000
50A47GLU-1-0.807-0.92532.0300.0050.0050.0000.0000.0000.000
51A48ALA0-0.0160.00933.2810.0000.0000.0000.0000.0000.000
52A49GLU-1-0.711-0.85534.7360.0040.0040.0000.0000.0000.000
53A50ARG10.8140.92127.074-0.009-0.0090.0000.0000.0000.000
54A51LEU0-0.028-0.01928.5260.0030.0030.0000.0000.0000.000
55A52LEU0-0.0040.01430.4080.0000.0000.0000.0000.0000.000
56A53LEU0-0.0100.01031.8440.0010.0010.0000.0000.0000.000
57A54ILE0-0.008-0.00725.9600.0050.0050.0000.0000.0000.000
58A55ALA00.0050.01027.3320.0050.0050.0000.0000.0000.000
59A56THR0-0.022-0.03428.402-0.001-0.0010.0000.0000.0000.000
60A57GLY00.0030.00928.9010.0020.0020.0000.0000.0000.000
61A58LYS10.9080.93620.8500.0120.0120.0000.0000.0000.000
62A59ARG10.8940.93425.3040.0030.0030.0000.0000.0000.000
63A60THR0-0.049-0.03127.422-0.002-0.0020.0000.0000.0000.000
64A61LEU00.0080.01723.4120.0030.0030.0000.0000.0000.000
65A62LEU00.0070.00621.0230.0040.0040.0000.0000.0000.000
66A63ILE0-0.014-0.01224.405-0.002-0.0020.0000.0000.0000.000
67A64ASP-1-0.896-0.94627.1690.0460.0460.0000.0000.0000.000
68A65GLU-1-0.831-0.92019.3870.0830.0830.0000.0000.0000.000
69A66LEU0-0.0050.00323.9540.0000.0000.0000.0000.0000.000
70A67ASN0-0.016-0.02325.137-0.008-0.0080.0000.0000.0000.000
71A68LYS10.9811.00123.397-0.102-0.1020.0000.0000.0000.000
72A69LEU00.0470.01619.959-0.002-0.0020.0000.0000.0000.000
73A70LYS10.8080.91823.977-0.017-0.0170.0000.0000.0000.000
74A71ASN0-0.094-0.06327.084-0.006-0.0060.0000.0000.0000.000
75A72GLU-1-0.950-0.95021.6490.0890.0890.0000.0000.0000.000
76A73GLY0-0.012-0.00525.913-0.009-0.0090.0000.0000.0000.000
77A74PRO0-0.040-0.03625.443-0.001-0.0010.0000.0000.0000.000
78A75GLN00.0100.01918.2460.0040.0040.0000.0000.0000.000
79A90LYS10.8760.9139.182-1.294-1.2940.0000.0000.0000.000
80A91GLY00.016-0.00415.448-0.050-0.0500.0000.0000.0000.000
81A92SER0-0.054-0.02314.9440.0720.0720.0000.0000.0000.000
82A93VAL00.0110.00616.830-0.043-0.0430.0000.0000.0000.000
83A94THR00.0060.00018.7560.0220.0220.0000.0000.0000.000
84A95LEU00.0050.01620.777-0.017-0.0170.0000.0000.0000.000
85A96SER00.0190.00223.264-0.002-0.0020.0000.0000.0000.000
86A97GLU-1-0.797-0.88625.6900.0850.0850.0000.0000.0000.000
87A98ILE00.0360.02426.445-0.002-0.0020.0000.0000.0000.000
88A99ARG10.9290.95430.384-0.062-0.0620.0000.0000.0000.000
89A100LEU00.0220.01434.1390.0030.0030.0000.0000.0000.000
90A101PRO00.0000.01736.592-0.004-0.0040.0000.0000.0000.000
91A102LEU0-0.008-0.00740.2300.0000.0000.0000.0000.0000.000
92A103LYS10.8790.92542.982-0.030-0.0300.0000.0000.0000.000
93A104ALA00.0440.00946.682-0.001-0.0010.0000.0000.0000.000
94A105ASP-1-0.863-0.93748.9000.0220.0220.0000.0000.0000.000
95A106PHE00.002-0.00344.192-0.001-0.0010.0000.0000.0000.000
96A107VAL00.0450.01545.145-0.002-0.0020.0000.0000.0000.000
97A108CYS0-0.0130.00747.865-0.002-0.0020.0000.0000.0000.000
98A109SER0-0.026-0.01450.958-0.002-0.0020.0000.0000.0000.000
99A110THR0-0.090-0.05346.393-0.001-0.0010.0000.0000.0000.000
100A111VAL00.0140.01549.661-0.001-0.0010.0000.0000.0000.000
101A112GLN0-0.022-0.02151.646-0.001-0.0010.0000.0000.0000.000
102A113LYS10.8900.94053.430-0.012-0.0120.0000.0000.0000.000
103A114PRO00.0230.02550.6580.0000.0000.0000.0000.0000.000
104A115ASP-1-0.876-0.92950.1570.0040.0040.0000.0000.0000.000
105A116ALA0-0.098-0.03852.124-0.001-0.0010.0000.0000.0000.000
106A117ALA0-0.068-0.06147.5300.0000.0000.0000.0000.0000.000
107A118ASN00.0190.04543.4250.0010.0010.0000.0000.0000.000
108A119TYR0-0.012-0.03242.6310.0010.0010.0000.0000.0000.000
109A120TYR00.0140.01237.2090.0000.0000.0000.0000.0000.000
110A121TYR0-0.010-0.01836.3310.0010.0010.0000.0000.0000.000
111A122LEU0-0.0110.00630.587-0.002-0.0020.0000.0000.0000.000
112A123ILE00.0060.00029.0860.0020.0020.0000.0000.0000.000
113A124ILE0-0.017-0.01526.729-0.001-0.0010.0000.0000.0000.000
114A125LEU0-0.024-0.01523.8080.0050.0050.0000.0000.0000.000
115A126LYS10.8740.91623.259-0.067-0.0670.0000.0000.0000.000
116A127ALA0-0.0030.01020.1210.0030.0030.0000.0000.0000.000
117A128GLY00.0630.03519.292-0.004-0.0040.0000.0000.0000.000
118A129ALA0-0.009-0.00820.344-0.015-0.0150.0000.0000.0000.000
119A130GLU-1-0.862-0.91116.3180.0500.0500.0000.0000.0000.000
120A131ASN0-0.110-0.05615.4860.0270.0270.0000.0000.0000.000
121A132MET00.0320.02818.9690.0010.0010.0000.0000.0000.000
122A133VAL0-0.024-0.00520.828-0.010-0.0100.0000.0000.0000.000
123A134ALA00.0180.01722.7430.0030.0030.0000.0000.0000.000
124A135THR0-0.024-0.00725.847-0.003-0.0030.0000.0000.0000.000
125A136PRO00.011-0.00326.918-0.004-0.0040.0000.0000.0000.000
126A137LEU00.0030.01929.6770.0060.0060.0000.0000.0000.000
127A138ALA0-0.0030.01533.413-0.001-0.0010.0000.0000.0000.000
128A139SER00.014-0.00635.290-0.001-0.0010.0000.0000.0000.000
129A140THR00.035-0.01439.0520.0010.0010.0000.0000.0000.000
130A141SER00.0020.01341.5190.0000.0000.0000.0000.0000.000
131A142ASN00.0100.00735.9690.0010.0010.0000.0000.0000.000
132A143SER00.0080.00535.5230.0010.0010.0000.0000.0000.000
133A144LEU0-0.029-0.00237.0270.0040.0040.0000.0000.0000.000
134A145ASN0-0.025-0.00836.392-0.003-0.0030.0000.0000.0000.000
135A146GLY0-0.024-0.00939.9050.0030.0030.0000.0000.0000.000
136A147ASP-1-0.896-0.94642.1940.0360.0360.0000.0000.0000.000
137A148ALA00.000-0.00437.9310.0010.0010.0000.0000.0000.000
138A149LEU0-0.048-0.00936.183-0.002-0.0020.0000.0000.0000.000
139A150THR00.0060.00532.1880.0060.0060.0000.0000.0000.000
140A151PHE00.0230.00229.236-0.004-0.0040.0000.0000.0000.000
141A152THR0-0.002-0.01026.3150.0020.0020.0000.0000.0000.000
142A153THR0-0.025-0.01323.5040.0010.0010.0000.0000.0000.000
143A154THR0-0.017-0.00420.1700.0040.0040.0000.0000.0000.000
144A155PHE0-0.005-0.00719.653-0.001-0.0010.0000.0000.0000.000
145A156THR0-0.019-0.01815.045-0.009-0.0090.0000.0000.0000.000
146A157LEU00.0030.01115.9300.0200.0200.0000.0000.0000.000
147A158GLN00.019-0.0149.789-0.007-0.0070.0000.0000.0000.000
148A159ASP-1-0.857-0.90210.4731.2681.2680.0000.0000.0000.000
149A160VAL0-0.0180.00413.011-0.049-0.0490.0000.0000.0000.000
150A161SER00.0350.02316.7290.0220.0220.0000.0000.0000.000
151A162ASN0-0.032-0.03319.563-0.001-0.0010.0000.0000.0000.000
152A163ASP-1-0.898-0.95622.7590.2000.2000.0000.0000.0000.000
153A164PHE0-0.064-0.02121.235-0.012-0.0120.0000.0000.0000.000
154A165GLU-1-0.877-0.94923.0010.1060.1060.0000.0000.0000.000
155A166ILE0-0.094-0.05421.8690.0090.0090.0000.0000.0000.000
156A167ASN0-0.0060.01225.090-0.018-0.0180.0000.0000.0000.000
157A168ILE0-0.0010.00027.1690.0000.0000.0000.0000.0000.000
158A169GLU-1-0.822-0.88829.4470.0540.0540.0000.0000.0000.000
159A170VAL00.0070.00331.547-0.001-0.0010.0000.0000.0000.000
160A171TYR0-0.006-0.02831.617-0.005-0.0050.0000.0000.0000.000
161A172SER0-0.036-0.01735.718-0.001-0.0010.0000.0000.0000.000
162A173LEU00.0230.02138.362-0.001-0.0010.0000.0000.0000.000
163A174VAL0-0.021-0.02140.2520.0000.0000.0000.0000.0000.000
164A175GLN0-0.033-0.02042.0460.0000.0000.0000.0000.0000.000
165A176LYS10.9470.96845.392-0.011-0.0110.0000.0000.0000.000
166A177LYS10.8820.94649.177-0.001-0.0010.0000.0000.0000.000
167A222ALA0-0.021-0.02342.614-0.001-0.0010.0000.0000.0000.000
168A223VAL00.0050.00136.707-0.001-0.0010.0000.0000.0000.000
169A224ARG10.8820.95439.1050.0050.0050.0000.0000.0000.000
170A225THR0-0.007-0.01337.740-0.001-0.0010.0000.0000.0000.000
171A226SER0-0.024-0.02735.4940.0000.0000.0000.0000.0000.000
172A227ASN0-0.058-0.05137.6270.0030.0030.0000.0000.0000.000
173A228PHE0-0.056-0.01935.7260.0020.0020.0000.0000.0000.000
174A229ALA00.0270.01837.7380.0010.0010.0000.0000.0000.000
175A230LEU0-0.028-0.01934.4460.0020.0020.0000.0000.0000.000
176A231VAL0-0.039-0.04737.500-0.001-0.0010.0000.0000.0000.000
177A232GLY00.0710.02037.1910.0000.0000.0000.0000.0000.000
178A233SER0-0.060-0.01133.8260.0000.0000.0000.0000.0000.000
179A234TYR00.0420.02531.7320.0010.0010.0000.0000.0000.000
180A235THR00.0330.02228.7190.0000.0000.0000.0000.0000.000
181A236LEU0-0.036-0.00726.7800.0000.0000.0000.0000.0000.000
182A237SER00.0950.03926.6190.0080.0080.0000.0000.0000.000
183A238LEU00.0460.01324.8810.0000.0000.0000.0000.0000.000
184A239SER0-0.041-0.02027.166-0.005-0.0050.0000.0000.0000.000
185A240SER00.0310.01928.872-0.007-0.0070.0000.0000.0000.000
186A241VAL00.000-0.01325.604-0.004-0.0040.0000.0000.0000.000
187A242GLY0-0.025-0.00128.564-0.005-0.0050.0000.0000.0000.000
188A243ASN0-0.061-0.01130.683-0.014-0.0140.0000.0000.0000.000
189A244THR0-0.005-0.02231.3810.0040.0040.0000.0000.0000.000
190A245LYS10.8490.93933.379-0.056-0.0560.0000.0000.0000.000
191A246PHE00.0060.00731.2290.0020.0020.0000.0000.0000.000
192A247VAL00.022-0.00136.053-0.004-0.0040.0000.0000.0000.000
193A248LEU0-0.047-0.00434.8790.0030.0030.0000.0000.0000.000
194A249ASP-1-0.849-0.92536.5920.0610.0610.0000.0000.0000.000
195A250LYS10.8580.89636.255-0.053-0.0530.0000.0000.0000.000
196A251VAL00.0270.03240.188-0.002-0.0020.0000.0000.0000.000
197A252PRO0-0.031-0.00241.454-0.001-0.0010.0000.0000.0000.000
198A253PHE00.0280.00344.6310.0000.0000.0000.0000.0000.000
199A254LEU0-0.035-0.01148.254-0.001-0.0010.0000.0000.0000.000
200A255SER00.0210.02243.876-0.001-0.0010.0000.0000.0000.000
201A256SER00.0470.01742.6040.0000.0000.0000.0000.0000.000
202A257LEU00.0030.01038.8250.0000.0000.0000.0000.0000.000
203A258GLU-1-0.840-0.90741.9890.0440.0440.0000.0000.0000.000
204A259GLY00.0020.00441.480-0.001-0.0010.0000.0000.0000.000
205A260HIS0-0.032-0.02738.7090.0050.0050.0000.0000.0000.000
206A261ILE0-0.001-0.00232.001-0.002-0.0020.0000.0000.0000.000
207A262TYR0-0.014-0.01634.2280.0030.0030.0000.0000.0000.000
208A263LEU0-0.0020.00528.1280.0000.0000.0000.0000.0000.000
209A264LYS10.8280.89826.609-0.094-0.0940.0000.0000.0000.000
210A265ILE00.014-0.00124.8620.0080.0080.0000.0000.0000.000
211A266LYS10.9310.97322.216-0.152-0.1520.0000.0000.0000.000
212A267CYS0-0.012-0.00321.1370.0120.0120.0000.0000.0000.000
213A268GLN0-0.0260.00116.223-0.033-0.0330.0000.0000.0000.000
214A269VAL00.0600.03518.5940.0430.0430.0000.0000.0000.000