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: QVK1Y

Calculation Name: 4J80-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4J80

Chain ID: A

ChEMBL ID:

UniProt ID: Q56237

Base Structure: X-ray

Registration Date: 2023-09-22

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 271
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2774457.812597
FMO2-HF: Nuclear repulsion 2670381.071524
FMO2-HF: Total energy -104076.741073
FMO2-MP2: Total energy -104383.359381


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:ALA)


Summations of interaction energy for fragment #1(A:2:ALA)
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.
-6.356-2.3740.464-1.871-2.575-0.004
Interaction energy analysis for fragmet #1(A:2:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.020 / q_NPA : 0.004
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].
3A4LYS10.8160.8933.8220.2221.455-0.010-0.671-0.5510.003
4A5LYS10.8010.9015.273-0.231-0.2310.0000.0000.0000.000
5A6ASP-1-0.826-0.8937.398-0.141-0.1410.0000.0000.0000.000
6A7TYR00.008-0.0498.2890.0010.0010.0000.0000.0000.000
7A8TYR0-0.064-0.05412.7830.0110.0110.0000.0000.0000.000
8A9ALA0-0.018-0.01014.0900.0040.0040.0000.0000.0000.000
9A10ILE0-0.057-0.01210.515-0.003-0.0030.0000.0000.0000.000
10A11LEU0-0.038-0.02915.083-0.013-0.0130.0000.0000.0000.000
11A12GLY0-0.0070.01218.038-0.014-0.0140.0000.0000.0000.000
12A13VAL0-0.087-0.04019.126-0.019-0.0190.0000.0000.0000.000
13A14PRO00.0340.01119.7030.0060.0060.0000.0000.0000.000
14A15ARG10.9060.94316.1190.1250.1250.0000.0000.0000.000
15A16ASN0-0.018-0.01719.919-0.016-0.0160.0000.0000.0000.000
16A17ALA00.0180.03421.6780.0000.0000.0000.0000.0000.000
17A18THR00.020-0.01923.312-0.017-0.0170.0000.0000.0000.000
18A19GLN00.0460.00921.2560.0040.0040.0000.0000.0000.000
19A20GLU-1-0.778-0.86324.563-0.003-0.0030.0000.0000.0000.000
20A21GLU-1-0.851-0.90124.7880.0050.0050.0000.0000.0000.000
21A22ILE00.0500.02919.8430.0150.0150.0000.0000.0000.000
22A23LYS10.8480.92022.4490.0210.0210.0000.0000.0000.000
23A24ARG10.8100.87924.4680.0000.0000.0000.0000.0000.000
24A25ALA00.0090.01422.2040.0070.0070.0000.0000.0000.000
25A26TYR00.0430.01519.4450.0090.0090.0000.0000.0000.000
26A27LYS10.9180.95922.063-0.002-0.0020.0000.0000.0000.000
27A28ARG10.9120.95625.242-0.064-0.0640.0000.0000.0000.000
28A29LEU00.0190.01519.5800.0040.0040.0000.0000.0000.000
29A30ALA00.0220.01122.1250.0130.0130.0000.0000.0000.000
30A31ARG10.9230.94923.019-0.053-0.0530.0000.0000.0000.000
31A32GLN0-0.0310.00323.980-0.008-0.0080.0000.0000.0000.000
32A33TYR0-0.013-0.02120.8730.0130.0130.0000.0000.0000.000
33A34HIS0-0.018-0.00222.2270.0030.0030.0000.0000.0000.000
34A35PRO00.1210.05522.3430.0010.0010.0000.0000.0000.000
35A36ASP-1-0.874-0.92924.8180.0650.0650.0000.0000.0000.000
36A37VAL0-0.078-0.02827.082-0.006-0.0060.0000.0000.0000.000
37A38ASN0-0.069-0.02724.8700.0050.0050.0000.0000.0000.000
38A39LYS10.8540.93525.605-0.080-0.0800.0000.0000.0000.000
39A40SER00.004-0.01223.776-0.004-0.0040.0000.0000.0000.000
40A41PRO00.002-0.00622.061-0.002-0.0020.0000.0000.0000.000
41A42GLU-1-0.837-0.92019.0980.2610.2610.0000.0000.0000.000
42A43ALA0-0.075-0.04818.5480.0250.0250.0000.0000.0000.000
43A44GLU-1-0.884-0.92818.0460.1470.1470.0000.0000.0000.000
44A45GLU-1-0.878-0.94614.0510.3820.3820.0000.0000.0000.000
45A46LYS10.8990.94314.289-0.427-0.4270.0000.0000.0000.000
46A47PHE00.0420.02416.243-0.025-0.0250.0000.0000.0000.000
47A48LYS10.8410.93811.483-0.268-0.2680.0000.0000.0000.000
48A49GLU-1-0.829-0.9019.7510.7320.7320.0000.0000.0000.000
49A50ILE0-0.040-0.01912.871-0.065-0.0650.0000.0000.0000.000
50A51ASN0-0.021-0.02315.978-0.063-0.0630.0000.0000.0000.000
51A52GLU-1-0.674-0.7728.0450.0800.0800.0000.0000.0000.000
52A53ALA00.012-0.00512.928-0.062-0.0620.0000.0000.0000.000
53A54TYR0-0.028-0.03013.720-0.044-0.0440.0000.0000.0000.000
54A55ALA00.0150.03114.515-0.020-0.0200.0000.0000.0000.000
55A56VAL0-0.0260.00011.368-0.030-0.0300.0000.0000.0000.000
56A57MET0-0.039-0.02014.831-0.016-0.0160.0000.0000.0000.000
57A58SER0-0.056-0.03617.1790.0050.0050.0000.0000.0000.000
58A59ASP-1-0.800-0.89519.017-0.155-0.1550.0000.0000.0000.000
59A60PRO0-0.001-0.01219.255-0.016-0.0160.0000.0000.0000.000
60A61GLU-1-0.814-0.87920.281-0.223-0.2230.0000.0000.0000.000
61A62LYS10.8110.90515.6450.1590.1590.0000.0000.0000.000
62A63ARG10.8270.89515.4000.0450.0450.0000.0000.0000.000
63A64ARG10.8390.89916.3730.2300.2300.0000.0000.0000.000
64A65ILE0-0.0040.01213.168-0.014-0.0140.0000.0000.0000.000
65A66TYR0-0.003-0.0209.367-0.042-0.0420.0000.0000.0000.000
66A67ASP-1-0.807-0.88312.640-0.202-0.2020.0000.0000.0000.000
67A68THR0-0.152-0.08715.3800.0110.0110.0000.0000.0000.000
68A69TYR00.0150.0185.8170.2980.2980.0000.0000.0000.000
69A70GLY00.0220.01310.2050.0070.0070.0000.0000.0000.000
70A71THR0-0.042-0.02911.0940.0360.0360.0000.0000.0000.000
71A72THR0-0.024-0.00814.1540.0620.0620.0000.0000.0000.000
72A73GLU-1-0.957-0.9809.850-0.663-0.6630.0000.0000.0000.000
73A74ALA00.0260.0219.380-0.185-0.1850.0000.0000.0000.000
74A75PRO00.0190.0138.6390.0880.0880.0000.0000.0000.000
75A76PRO0-0.034-0.00711.0460.0900.0900.0000.0000.0000.000
76A77PRO0-0.015-0.02514.759-0.013-0.0130.0000.0000.0000.000
77A78PRO0-0.0070.02016.8870.0060.0060.0000.0000.0000.000
78A79PRO0-0.0020.00918.3410.0250.0250.0000.0000.0000.000
79A80PRO0-0.001-0.02721.688-0.001-0.0010.0000.0000.0000.000
80A81GLY0-0.043-0.01124.3970.0080.0080.0000.0000.0000.000
81A82GLY0-0.0010.00220.046-0.002-0.0020.0000.0000.0000.000
82A83TYR0-0.024-0.01614.8240.0340.0340.0000.0000.0000.000
83A84ASP-1-0.848-0.89218.713-0.122-0.1220.0000.0000.0000.000
84A85PHE0-0.005-0.01813.8970.0050.0050.0000.0000.0000.000
85A86SER0-0.015-0.04018.9200.0170.0170.0000.0000.0000.000
86A87GLY0-0.068-0.02921.9560.0060.0060.0000.0000.0000.000
87A88PHE0-0.007-0.01216.8330.0160.0160.0000.0000.0000.000
88A89ASP-1-0.877-0.92217.284-0.034-0.0340.0000.0000.0000.000
89A90VAL0-0.028-0.03113.5890.0100.0100.0000.0000.0000.000
90A91GLU-1-0.959-0.98012.733-0.179-0.1790.0000.0000.0000.000
91A92ASP-1-0.846-0.91513.0280.1290.1290.0000.0000.0000.000
92A93PHE0-0.040-0.0139.8680.1010.1010.0000.0000.0000.000
93A94SER0-0.036-0.0545.430-0.089-0.0890.0000.0000.0000.000
94A95GLU-1-0.874-0.9513.066-1.337-0.8930.049-0.121-0.3720.000
95A96PHE00.0010.0032.412-1.966-0.4270.380-0.782-1.137-0.004
96A97PHE00.0270.0183.3580.1710.3450.039-0.014-0.199-0.001
97A98GLN0-0.009-0.0096.7670.0300.0300.0000.0000.0000.000
98A99GLU-1-0.945-0.9563.733-4.241-3.6490.006-0.283-0.316-0.002
99A100LEU0-0.048-0.0146.7280.2940.2940.0000.0000.0000.000
100A101PHE00.002-0.0328.7260.2010.2010.0000.0000.0000.000
101A102GLY00.0670.03910.4540.1170.1170.0000.0000.0000.000
102A103PRO0-0.041-0.03411.2130.1070.1070.0000.0000.0000.000
103A104GLY0-0.033-0.01214.4270.0640.0640.0000.0000.0000.000
104A105LEU0-0.0150.00812.3430.0450.0450.0000.0000.0000.000
105A106PHE0-0.0080.00116.315-0.003-0.0030.0000.0000.0000.000
106A107GLY00.0670.03119.4150.0090.0090.0000.0000.0000.000
107A108LYS10.9210.96721.1260.0900.0900.0000.0000.0000.000
108A109GLY00.0390.03824.524-0.002-0.0020.0000.0000.0000.000
109A110ARG10.9170.95426.9030.1140.1140.0000.0000.0000.000
110A111ASP-1-0.805-0.91230.020-0.074-0.0740.0000.0000.0000.000
111A112LEU0-0.063-0.02432.870-0.003-0.0030.0000.0000.0000.000
112A113ARG10.9600.98135.9480.0540.0540.0000.0000.0000.000
113A114ALA0-0.005-0.00139.518-0.002-0.0020.0000.0000.0000.000
114A115GLU-1-0.841-0.90842.300-0.042-0.0420.0000.0000.0000.000
115A116LEU0-0.017-0.01646.111-0.002-0.0020.0000.0000.0000.000
116A117PRO00.003-0.01048.0700.0020.0020.0000.0000.0000.000
117A118LEU0-0.0180.00451.3330.0000.0000.0000.0000.0000.000
118A119THR0-0.012-0.03354.0560.0010.0010.0000.0000.0000.000
119A120LEU00.025-0.00157.7150.0000.0000.0000.0000.0000.000
120A121GLU-1-0.748-0.85159.861-0.026-0.0260.0000.0000.0000.000
121A122GLU-1-0.813-0.88454.940-0.035-0.0350.0000.0000.0000.000
122A123ALA0-0.019-0.01255.0440.0000.0000.0000.0000.0000.000
123A124PHE0-0.078-0.02556.0660.0010.0010.0000.0000.0000.000
124A125HIS00.0230.00158.2490.0010.0010.0000.0000.0000.000
125A126GLY0-0.0380.00154.0570.0000.0000.0000.0000.0000.000
126A127GLY0-0.007-0.01253.0450.0000.0000.0000.0000.0000.000
127A128GLU-1-0.906-0.97247.787-0.037-0.0370.0000.0000.0000.000
128A129ARG10.8530.91348.5420.0370.0370.0000.0000.0000.000
129A130VAL0-0.016-0.01844.888-0.001-0.0010.0000.0000.0000.000
130A131VAL0-0.023-0.02543.6460.0010.0010.0000.0000.0000.000
131A132GLU-1-0.894-0.95342.432-0.062-0.0620.0000.0000.0000.000
132A133VAL00.0010.00540.0580.0010.0010.0000.0000.0000.000
133A134ALA00.000-0.01539.014-0.003-0.0030.0000.0000.0000.000
134A135GLY00.007-0.00136.162-0.003-0.0030.0000.0000.0000.000
135A136ARG10.8580.95133.3040.0830.0830.0000.0000.0000.000
136A137ARG11.0001.00837.5630.0570.0570.0000.0000.0000.000
137A138VAL0-0.013-0.01238.562-0.002-0.0020.0000.0000.0000.000
138A139SER0-0.0140.01141.0950.0020.0020.0000.0000.0000.000
139A140VAL0-0.033-0.01342.889-0.001-0.0010.0000.0000.0000.000
140A141ARG10.9740.99644.9780.0330.0330.0000.0000.0000.000
141A142MET0-0.0390.00447.525-0.001-0.0010.0000.0000.0000.000
142A143PRO0-0.009-0.00249.6610.0010.0010.0000.0000.0000.000
143A144PRO00.0280.01352.649-0.001-0.0010.0000.0000.0000.000
144A145GLY0-0.0060.00156.2610.0010.0010.0000.0000.0000.000
145A146VAL0-0.047-0.00750.7190.0000.0000.0000.0000.0000.000
146A147ARG10.9660.96253.3840.0240.0240.0000.0000.0000.000
147A148GLU-1-0.771-0.87152.451-0.035-0.0350.0000.0000.0000.000
148A149GLY0-0.017-0.00449.3820.0010.0010.0000.0000.0000.000
149A150SER0-0.066-0.04248.8050.0010.0010.0000.0000.0000.000
150A151VAL0-0.024-0.01742.603-0.002-0.0020.0000.0000.0000.000
151A152ILE0-0.004-0.00643.8770.0020.0020.0000.0000.0000.000
152A153ARG10.8650.91335.3200.0440.0440.0000.0000.0000.000
153A154VAL00.0110.00137.9810.0020.0020.0000.0000.0000.000
154A155PRO0-0.033-0.02034.983-0.004-0.0040.0000.0000.0000.000
155A156GLY00.0510.02331.5760.0010.0010.0000.0000.0000.000
156A157MET0-0.030-0.00831.841-0.007-0.0070.0000.0000.0000.000
157A158GLY0-0.041-0.01632.8930.0010.0010.0000.0000.0000.000
158A159GLY0-0.022-0.02529.901-0.004-0.0040.0000.0000.0000.000
159A160GLN00.021-0.00225.684-0.001-0.0010.0000.0000.0000.000
160A161GLY00.0230.00523.194-0.004-0.0040.0000.0000.0000.000
161A162ASN0-0.0290.02518.6590.0230.0230.0000.0000.0000.000
162A163PRO00.0490.01322.4620.0030.0030.0000.0000.0000.000
163A164PRO00.025-0.00325.182-0.004-0.0040.0000.0000.0000.000
164A165GLY0-0.032-0.01227.7090.0080.0080.0000.0000.0000.000
165A166ASP-1-0.821-0.88530.538-0.059-0.0590.0000.0000.0000.000
166A167LEU0-0.021-0.02234.206-0.002-0.0020.0000.0000.0000.000
167A168LEU0-0.043-0.02237.1180.0050.0050.0000.0000.0000.000
168A169LEU00.0280.01239.934-0.001-0.0010.0000.0000.0000.000
169A170VAL0-0.010-0.00743.2850.0030.0030.0000.0000.0000.000
170A171VAL00.0250.01446.152-0.001-0.0010.0000.0000.0000.000
171A172ARG10.7980.88948.0480.0400.0400.0000.0000.0000.000
172A173MET0-0.049-0.01651.9760.0000.0000.0000.0000.0000.000
173A174LEU0-0.006-0.01254.4350.0000.0000.0000.0000.0000.000
174A175PRO0-0.032-0.01057.4930.0010.0010.0000.0000.0000.000
175A176HIS0-0.013-0.03461.0430.0000.0000.0000.0000.0000.000
176A177PRO0-0.018-0.00363.7280.0010.0010.0000.0000.0000.000
177A178VAL0-0.028-0.00967.0700.0010.0010.0000.0000.0000.000
178A179PHE0-0.030-0.01165.6770.0010.0010.0000.0000.0000.000
179A180ARG10.8430.89964.9890.0190.0190.0000.0000.0000.000
180A181LEU0-0.020-0.01759.3660.0010.0010.0000.0000.0000.000
181A182GLU-1-0.843-0.89562.709-0.020-0.0200.0000.0000.0000.000
182A183GLY00.0000.00360.5900.0010.0010.0000.0000.0000.000
183A184GLN0-0.039-0.05160.287-0.001-0.0010.0000.0000.0000.000
184A185ASP-1-0.831-0.89662.535-0.017-0.0170.0000.0000.0000.000
185A186LEU0-0.018-0.00763.659-0.001-0.0010.0000.0000.0000.000
186A187TYR00.001-0.00167.0120.0010.0010.0000.0000.0000.000
187A188ALA00.0650.02769.301-0.001-0.0010.0000.0000.0000.000
188A189THR00.0060.01271.8720.0010.0010.0000.0000.0000.000
189A190LEU0-0.012-0.00875.1890.0000.0000.0000.0000.0000.000
190A191ASP-1-0.786-0.86577.892-0.016-0.0160.0000.0000.0000.000
191A192VAL0-0.018-0.01280.5840.0000.0000.0000.0000.0000.000
192A193PRO00.0200.01483.9090.0000.0000.0000.0000.0000.000
193A194ALA00.0520.02087.1050.0000.0000.0000.0000.0000.000
194A195PRO00.0200.00789.8060.0000.0000.0000.0000.0000.000
195A196ILE00.003-0.00787.1980.0000.0000.0000.0000.0000.000
196A197ALA00.0160.02487.6600.0000.0000.0000.0000.0000.000
197A198VAL0-0.024-0.00789.0340.0000.0000.0000.0000.0000.000
198A199VAL0-0.006-0.01192.6890.0000.0000.0000.0000.0000.000
199A200GLY00.0080.01389.6110.0000.0000.0000.0000.0000.000
200A201GLY00.0130.00888.5930.0000.0000.0000.0000.0000.000
201A202LYS10.8130.89783.8330.0120.0120.0000.0000.0000.000
202A203VAL00.0140.01781.1500.0000.0000.0000.0000.0000.000
203A204ARG10.9110.96277.2430.0160.0160.0000.0000.0000.000
204A205ALA00.0350.03176.2190.0000.0000.0000.0000.0000.000
205A206MET0-0.005-0.01670.5380.0000.0000.0000.0000.0000.000
206A207THR0-0.037-0.03269.5420.0000.0000.0000.0000.0000.000
207A208LEU00.0340.00562.8740.0000.0000.0000.0000.0000.000
208A209GLU-1-0.813-0.90265.525-0.020-0.0200.0000.0000.0000.000
209A210GLY00.0320.02067.3010.0000.0000.0000.0000.0000.000
210A211PRO0-0.039-0.00270.3260.0000.0000.0000.0000.0000.000
211A212VAL00.0260.00673.4740.0000.0000.0000.0000.0000.000
212A213GLU-1-0.872-0.94076.207-0.013-0.0130.0000.0000.0000.000
213A214VAL00.0080.00277.7880.0000.0000.0000.0000.0000.000
214A215ALA00.001-0.00180.6690.0000.0000.0000.0000.0000.000
215A216VAL0-0.019-0.01483.2200.0000.0000.0000.0000.0000.000
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