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: QY9LY

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 OptH
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 -2318735.0156
FMO2-HF: Nuclear repulsion 2235070.987254
FMO2-HF: Total energy -83664.028346
FMO2-MP2: Total energy -83905.186146


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.
0.3981.84-0.023-0.724-0.695-0.001
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 : -0.019
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].
3A0MET00.0090.0113.8120.0121.454-0.023-0.724-0.695-0.001
4A1CYS0-0.0020.0056.9930.2570.2570.0000.0000.0000.000
5A2GLN00.0560.0229.500-0.077-0.0770.0000.0000.0000.000
6A3VAL00.0130.00812.9870.0390.0390.0000.0000.0000.000
7A4ASN0-0.011-0.01915.3260.0420.0420.0000.0000.0000.000
8A5ILE00.1180.04418.092-0.013-0.0130.0000.0000.0000.000
9A6LYS10.9640.99020.1560.0820.0820.0000.0000.0000.000
10A7GLN0-0.012-0.01716.348-0.018-0.0180.0000.0000.0000.000
11A8LYS11.0191.03615.635-0.032-0.0320.0000.0000.0000.000
12A9MET0-0.002-0.00318.5170.0040.0040.0000.0000.0000.000
13A10GLN0-0.024-0.02121.3890.0030.0030.0000.0000.0000.000
14A11GLU-1-0.955-0.96315.586-0.222-0.2220.0000.0000.0000.000
15A12LEU00.0330.01419.9610.0030.0030.0000.0000.0000.000
16A13ASN0-0.039-0.01921.7680.0120.0120.0000.0000.0000.000
17A14ASN0-0.026-0.02521.7100.0150.0150.0000.0000.0000.000
18A15GLU-1-0.834-0.90620.438-0.077-0.0770.0000.0000.0000.000
19A16ILE00.000-0.00222.8240.0090.0090.0000.0000.0000.000
20A17ASN0-0.033-0.02526.1400.0110.0110.0000.0000.0000.000
21A18MET0-0.008-0.00123.3120.0000.0000.0000.0000.0000.000
22A19GLN00.001-0.00923.1750.0110.0110.0000.0000.0000.000
23A20GLN00.0180.01527.1830.0090.0090.0000.0000.0000.000
24A21THR0-0.0150.01129.1770.0020.0020.0000.0000.0000.000
25A22VAL00.0090.01127.0620.0020.0020.0000.0000.0000.000
26A23ILE0-0.0120.00330.3750.0030.0030.0000.0000.0000.000
27A24TYR0-0.019-0.01332.8350.0020.0020.0000.0000.0000.000
28A25GLN00.011-0.01031.9500.0020.0020.0000.0000.0000.000
29A26ALA00.0200.01633.3640.0010.0010.0000.0000.0000.000
30A27SER00.0120.00035.2720.0040.0040.0000.0000.0000.000
31A28GLN0-0.041-0.02138.1180.0040.0040.0000.0000.0000.000
32A29ALA00.0320.01837.6770.0010.0010.0000.0000.0000.000
33A30LEU00.004-0.00537.5630.0010.0010.0000.0000.0000.000
34A31ASN0-0.060-0.03240.9460.0040.0040.0000.0000.0000.000
35A32CYS0-0.050-0.01442.7720.0000.0000.0000.0000.0000.000
36A33CYS0-0.0260.02142.4850.0000.0000.0000.0000.0000.000
37A34VAL0-0.029-0.02645.4030.0020.0020.0000.0000.0000.000
38A35ASP-1-0.856-0.95248.947-0.011-0.0110.0000.0000.0000.000
39A36GLU-1-0.943-0.97648.399-0.006-0.0060.0000.0000.0000.000
40A37GLU-1-0.977-0.96748.370-0.016-0.0160.0000.0000.0000.000
41A38HIS10.8270.91246.9780.0150.0150.0000.0000.0000.000
42A39GLY00.0890.05443.989-0.001-0.0010.0000.0000.0000.000
43A40LYS10.9030.96943.9090.0050.0050.0000.0000.0000.000
44A41GLY0-0.038-0.02744.7190.0000.0000.0000.0000.0000.000
45A42SER0-0.018-0.02142.1020.0010.0010.0000.0000.0000.000
46A43LEU00.030-0.00236.6910.0010.0010.0000.0000.0000.000
47A44GLU-1-0.928-0.96437.223-0.024-0.0240.0000.0000.0000.000
48A45GLU-1-0.842-0.92237.359-0.007-0.0070.0000.0000.0000.000
49A46ALA00.0180.00237.9460.0010.0010.0000.0000.0000.000
50A47GLU-1-0.887-0.96732.611-0.004-0.0040.0000.0000.0000.000
51A48ALA0-0.0170.00333.237-0.001-0.0010.0000.0000.0000.000
52A49GLU-1-0.760-0.88034.689-0.002-0.0020.0000.0000.0000.000
53A50ARG10.8870.96426.553-0.002-0.0020.0000.0000.0000.000
54A51LEU0-0.047-0.02928.4600.0030.0030.0000.0000.0000.000
55A52LEU00.0040.01730.358-0.001-0.0010.0000.0000.0000.000
56A53LEU0-0.0020.00931.5620.0010.0010.0000.0000.0000.000
57A54ILE0-0.018-0.01325.9020.0040.0040.0000.0000.0000.000
58A55ALA0-0.0020.00627.2810.0040.0040.0000.0000.0000.000
59A56THR0-0.021-0.02928.349-0.001-0.0010.0000.0000.0000.000
60A57GLY0-0.009-0.00628.8520.0020.0020.0000.0000.0000.000
61A58LYS10.9870.97621.7280.0070.0070.0000.0000.0000.000
62A59ARG10.9070.94125.2440.0110.0110.0000.0000.0000.000
63A60THR0-0.035-0.01427.363-0.002-0.0020.0000.0000.0000.000
64A61LEU00.0060.01023.7140.0030.0030.0000.0000.0000.000
65A62LEU00.0150.01521.1850.0050.0050.0000.0000.0000.000
66A63ILE0-0.014-0.01124.344-0.001-0.0010.0000.0000.0000.000
67A64ASP-1-0.903-0.95027.0590.0390.0390.0000.0000.0000.000
68A65GLU-1-0.911-0.96419.2230.0720.0720.0000.0000.0000.000
69A66LEU0-0.0130.00023.9520.0000.0000.0000.0000.0000.000
70A67ASN0-0.040-0.04325.135-0.007-0.0070.0000.0000.0000.000
71A68LYS10.9580.98023.375-0.090-0.0900.0000.0000.0000.000
72A69LEU00.0530.01819.977-0.001-0.0010.0000.0000.0000.000
73A70LYS10.8430.94123.975-0.008-0.0080.0000.0000.0000.000
74A71ASN0-0.085-0.04927.075-0.006-0.0060.0000.0000.0000.000
75A72GLU-1-0.943-0.94921.3520.0770.0770.0000.0000.0000.000
76A73GLY0-0.020-0.00725.912-0.008-0.0080.0000.0000.0000.000
77A74PRO0-0.036-0.03325.442-0.001-0.0010.0000.0000.0000.000
78A75GLN00.0080.01718.4460.0100.0100.0000.0000.0000.000
79A90LYS10.9150.9509.710-1.183-1.1830.0000.0000.0000.000
80A91GLY00.0440.02615.504-0.047-0.0470.0000.0000.0000.000
81A92SER0-0.081-0.03115.0740.0540.0540.0000.0000.0000.000
82A93VAL00.0640.02516.871-0.041-0.0410.0000.0000.0000.000
83A94THR0-0.040-0.02118.8760.0130.0130.0000.0000.0000.000
84A95LEU0-0.0040.00420.746-0.016-0.0160.0000.0000.0000.000
85A96SER00.0130.00023.231-0.003-0.0030.0000.0000.0000.000
86A97GLU-1-0.904-0.96525.6610.0790.0790.0000.0000.0000.000
87A98ILE00.0270.01926.441-0.001-0.0010.0000.0000.0000.000
88A99ARG10.9330.95530.351-0.060-0.0600.0000.0000.0000.000
89A100LEU00.0200.01034.1050.0030.0030.0000.0000.0000.000
90A101PRO00.0090.01636.554-0.004-0.0040.0000.0000.0000.000
91A102LEU0-0.009-0.00740.194-0.001-0.0010.0000.0000.0000.000
92A103LYS10.9300.97542.944-0.027-0.0270.0000.0000.0000.000
93A104ALA00.0530.01046.643-0.001-0.0010.0000.0000.0000.000
94A105ASP-1-0.872-0.93748.8640.0200.0200.0000.0000.0000.000
95A106PHE00.004-0.00144.082-0.001-0.0010.0000.0000.0000.000
96A107VAL00.0440.01645.139-0.002-0.0020.0000.0000.0000.000
97A108CYS0-0.0160.01847.828-0.002-0.0020.0000.0000.0000.000
98A109SER0-0.001-0.00550.867-0.002-0.0020.0000.0000.0000.000
99A110THR0-0.104-0.06846.380-0.001-0.0010.0000.0000.0000.000
100A111VAL00.0200.01949.624-0.001-0.0010.0000.0000.0000.000
101A112GLN0-0.039-0.03551.612-0.001-0.0010.0000.0000.0000.000
102A113LYS10.8790.93653.395-0.010-0.0100.0000.0000.0000.000
103A114PRO00.0290.02650.6150.0000.0000.0000.0000.0000.000
104A115ASP-1-0.866-0.92050.1210.0010.0010.0000.0000.0000.000
105A116ALA0-0.120-0.05152.131-0.001-0.0010.0000.0000.0000.000
106A117ALA0-0.067-0.05847.4370.0000.0000.0000.0000.0000.000
107A118ASN00.0210.04443.5190.0010.0010.0000.0000.0000.000
108A119TYR0-0.013-0.03442.5580.0010.0010.0000.0000.0000.000
109A120TYR0-0.0020.00837.1630.0000.0000.0000.0000.0000.000
110A121TYR00.0140.01436.2130.0010.0010.0000.0000.0000.000
111A122LEU0-0.025-0.00130.518-0.002-0.0020.0000.0000.0000.000
112A123ILE00.0170.00828.7070.0020.0020.0000.0000.0000.000
113A124ILE0-0.009-0.01626.666-0.002-0.0020.0000.0000.0000.000
114A125LEU0-0.031-0.01623.8080.0050.0050.0000.0000.0000.000
115A126LYS10.9300.95823.193-0.063-0.0630.0000.0000.0000.000
116A127ALA0-0.0020.01720.0490.0030.0030.0000.0000.0000.000
117A128GLY00.0580.02719.277-0.003-0.0030.0000.0000.0000.000
118A129ALA0-0.010-0.00920.316-0.014-0.0140.0000.0000.0000.000
119A130GLU-1-0.901-0.95116.1880.0080.0080.0000.0000.0000.000
120A131ASN0-0.118-0.04815.3780.0300.0300.0000.0000.0000.000
121A132MET00.0320.02218.9130.0020.0020.0000.0000.0000.000
122A133VAL0-0.038-0.01320.812-0.012-0.0120.0000.0000.0000.000
123A134ALA00.0190.01522.6940.0030.0030.0000.0000.0000.000
124A135THR0-0.0070.00925.805-0.004-0.0040.0000.0000.0000.000
125A136PRO00.000-0.00326.764-0.004-0.0040.0000.0000.0000.000
126A137LEU00.0080.01929.6400.0060.0060.0000.0000.0000.000
127A138ALA00.0240.02933.3740.0000.0000.0000.0000.0000.000
128A139SER00.0230.00035.254-0.001-0.0010.0000.0000.0000.000
129A140THR00.020-0.01839.0160.0010.0010.0000.0000.0000.000
130A141SER0-0.0090.00541.5410.0010.0010.0000.0000.0000.000
131A142ASN00.0110.01036.6980.0020.0020.0000.0000.0000.000
132A143SER00.0180.00435.5220.0010.0010.0000.0000.0000.000
133A144LEU0-0.035-0.01036.9980.0040.0040.0000.0000.0000.000
134A145ASN0-0.0190.00436.783-0.002-0.0020.0000.0000.0000.000
135A146GLY0-0.025-0.00839.8790.0030.0030.0000.0000.0000.000
136A147ASP-1-0.898-0.94942.4270.0330.0330.0000.0000.0000.000
137A148ALA00.0040.00337.8570.0010.0010.0000.0000.0000.000
138A149LEU0-0.052-0.01136.074-0.002-0.0020.0000.0000.0000.000
139A150THR0-0.001-0.00632.1110.0060.0060.0000.0000.0000.000
140A151PHE00.0130.00129.199-0.004-0.0040.0000.0000.0000.000
141A152THR0-0.013-0.01526.1880.0020.0020.0000.0000.0000.000
142A153THR0-0.020-0.01123.3340.0010.0010.0000.0000.0000.000
143A154THR0-0.0070.00420.0140.0050.0050.0000.0000.0000.000
144A155PHE0-0.012-0.01019.972-0.004-0.0040.0000.0000.0000.000
145A156THR00.003-0.00315.158-0.009-0.0090.0000.0000.0000.000
146A157LEU00.0140.01315.8890.0160.0160.0000.0000.0000.000
147A158GLN00.007-0.01810.076-0.005-0.0050.0000.0000.0000.000
148A159ASP-1-0.908-0.9599.6801.3841.3840.0000.0000.0000.000
149A160VAL0-0.0300.00213.011-0.054-0.0540.0000.0000.0000.000
150A161SER00.0300.01216.7290.0240.0240.0000.0000.0000.000
151A162ASN0-0.018-0.02819.563-0.006-0.0060.0000.0000.0000.000
152A163ASP-1-0.891-0.94822.8340.1970.1970.0000.0000.0000.000
153A164PHE0-0.075-0.02721.279-0.013-0.0130.0000.0000.0000.000
154A165GLU-1-0.889-0.95623.0010.1030.1030.0000.0000.0000.000
155A166ILE0-0.085-0.04721.6750.0080.0080.0000.0000.0000.000
156A167ASN0-0.0140.00125.090-0.015-0.0150.0000.0000.0000.000
157A168ILE00.003-0.00427.117-0.001-0.0010.0000.0000.0000.000
158A169GLU-1-0.878-0.93829.3980.0480.0480.0000.0000.0000.000
159A170VAL00.0050.00031.497-0.001-0.0010.0000.0000.0000.000
160A171TYR0-0.007-0.01731.629-0.004-0.0040.0000.0000.0000.000
161A172SER0-0.027-0.01535.669-0.001-0.0010.0000.0000.0000.000
162A173LEU00.0340.02838.553-0.001-0.0010.0000.0000.0000.000
163A174VAL0-0.024-0.01940.2050.0000.0000.0000.0000.0000.000
164A175GLN00.0460.03642.170-0.001-0.0010.0000.0000.0000.000
165A176LYS10.9470.96445.347-0.008-0.0080.0000.0000.0000.000
166A177LYS10.9921.00949.1320.0000.0000.0000.0000.0000.000
167A222ALA0-0.001-0.01842.536-0.001-0.0010.0000.0000.0000.000
168A223VAL0-0.0080.00236.680-0.001-0.0010.0000.0000.0000.000
169A224ARG10.9250.97439.0650.0100.0100.0000.0000.0000.000
170A225THR0-0.025-0.01937.6050.0000.0000.0000.0000.0000.000
171A226SER0-0.039-0.04235.4300.0000.0000.0000.0000.0000.000
172A227ASN0-0.048-0.04837.5750.0040.0040.0000.0000.0000.000
173A228PHE0-0.066-0.02235.7100.0020.0020.0000.0000.0000.000
174A229ALA00.0260.01937.6850.0010.0010.0000.0000.0000.000
175A230LEU0-0.031-0.02134.4310.0010.0010.0000.0000.0000.000
176A231VAL0-0.040-0.04937.454-0.001-0.0010.0000.0000.0000.000
177A232GLY00.0660.01737.1430.0000.0000.0000.0000.0000.000
178A233SER0-0.041-0.00833.762-0.001-0.0010.0000.0000.0000.000
179A234TYR00.0330.01431.5250.0010.0010.0000.0000.0000.000
180A235THR00.0420.03628.604-0.001-0.0010.0000.0000.0000.000
181A236LEU0-0.047-0.01726.9660.0000.0000.0000.0000.0000.000
182A237SER00.1050.04926.6260.0090.0090.0000.0000.0000.000
183A238LEU00.0450.01324.8380.0000.0000.0000.0000.0000.000
184A239SER0-0.037-0.02227.166-0.005-0.0050.0000.0000.0000.000
185A240SER00.0070.00828.847-0.007-0.0070.0000.0000.0000.000
186A241VAL00.013-0.00825.742-0.003-0.0030.0000.0000.0000.000
187A242GLY0-0.032-0.00628.596-0.005-0.0050.0000.0000.0000.000
188A243ASN0-0.0290.00630.720-0.011-0.0110.0000.0000.0000.000
189A244THR0-0.009-0.02431.3920.0030.0030.0000.0000.0000.000
190A245LYS10.9280.97333.359-0.057-0.0570.0000.0000.0000.000
191A246PHE0-0.021-0.00431.1760.0020.0020.0000.0000.0000.000
192A247VAL00.0250.00636.028-0.004-0.0040.0000.0000.0000.000
193A248LEU0-0.045-0.00634.7100.0030.0030.0000.0000.0000.000
194A249ASP-1-0.861-0.92936.7770.0580.0580.0000.0000.0000.000
195A250LYS10.8870.91837.453-0.043-0.0430.0000.0000.0000.000
196A251VAL00.0240.03140.175-0.002-0.0020.0000.0000.0000.000
197A252PRO0-0.042-0.00341.399-0.001-0.0010.0000.0000.0000.000
198A253PHE00.0260.00144.5800.0000.0000.0000.0000.0000.000
199A254LEU0-0.044-0.02248.204-0.001-0.0010.0000.0000.0000.000
200A255SER00.0130.02143.900-0.001-0.0010.0000.0000.0000.000
201A256SER00.025-0.01842.8290.0010.0010.0000.0000.0000.000
202A257LEU00.0010.00438.5310.0000.0000.0000.0000.0000.000
203A258GLU-1-0.864-0.93742.0670.0420.0420.0000.0000.0000.000
204A259GLY0-0.010-0.00341.4420.0000.0000.0000.0000.0000.000
205A260HIS0-0.045-0.02338.6500.0050.0050.0000.0000.0000.000
206A261ILE00.0000.00031.898-0.002-0.0020.0000.0000.0000.000
207A262TYR0-0.044-0.02934.1930.0030.0030.0000.0000.0000.000
208A263LEU00.0000.00128.047-0.001-0.0010.0000.0000.0000.000
209A264LYS10.9460.98626.852-0.103-0.1030.0000.0000.0000.000
210A265ILE00.0290.00624.8710.0070.0070.0000.0000.0000.000
211A266LYS10.9090.96022.318-0.152-0.1520.0000.0000.0000.000
212A267CYS00.0250.00821.1690.0170.0170.0000.0000.0000.000
213A268GLN0-0.059-0.00716.854-0.001-0.0010.0000.0000.0000.000
214A269VAL00.0610.03618.6450.0430.0430.0000.0000.0000.000