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: 7658K

Calculation Name: 4EQY-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4EQY

Chain ID: A

ChEMBL ID:

UniProt ID: Q2SWY6

Base Structure: X-ray

Registration Date: 2023-09-23

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 261
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3111177.133941
FMO2-HF: Nuclear repulsion 3014056.158049
FMO2-HF: Total energy -97120.975893
FMO2-MP2: Total energy -97406.372287


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:3:SER)


Summations of interaction energy for fragment #1(A:3:SER)
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.
-15.776-9.5021.401-3.799-3.876-0.025
Interaction energy analysis for fragmet #1(A:3:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.003 / q_NPA : -0.002
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].
3A5ILE00.0570.0373.202-0.4882.1720.001-1.279-1.3830.005
4A6HIS00.0250.0362.258-10.223-7.4681.341-2.249-1.847-0.032
5A7PRO00.024-0.0092.994-0.2560.5580.060-0.270-0.6040.002
6A8THR0-0.038-0.0355.2430.2380.283-0.001-0.001-0.0420.000
7A9ALA0-0.045-0.0026.9880.2500.2500.0000.0000.0000.000
8A10ILE0-0.017-0.0088.6400.0340.0340.0000.0000.0000.000
9A11ILE00.008-0.0038.780-0.013-0.0130.0000.0000.0000.000
10A12GLU-1-0.851-0.91211.616-0.455-0.4550.0000.0000.0000.000
11A13PRO0-0.024-0.03315.228-0.029-0.0290.0000.0000.0000.000
12A14GLY00.0050.00316.5430.0520.0520.0000.0000.0000.000
13A15ALA00.0200.04014.2360.0260.0260.0000.0000.0000.000
14A16GLN0-0.107-0.05615.145-0.020-0.0200.0000.0000.0000.000
15A17LEU00.006-0.00410.266-0.013-0.0130.0000.0000.0000.000
16A18HIS00.0840.07212.392-0.103-0.1030.0000.0000.0000.000
17A19GLU-1-0.871-0.9519.742-0.933-0.9330.0000.0000.0000.000
18A20THR0-0.109-0.0948.324-0.272-0.2720.0000.0000.0000.000
19A21VAL0-0.0300.0089.737-0.084-0.0840.0000.0000.0000.000
20A22GLU-1-0.900-0.9346.304-2.746-2.7460.0000.0000.0000.000
21A23VAL00.0200.0016.7450.7920.7920.0000.0000.0000.000
22A24GLY00.0060.0156.405-0.990-0.9900.0000.0000.0000.000
23A25PRO0-0.018-0.0368.3200.0240.0240.0000.0000.0000.000
24A26TYR0-0.003-0.0169.1930.1570.1570.0000.0000.0000.000
25A27ALA0-0.0090.02410.5400.1470.1470.0000.0000.0000.000
26A28ILE0-0.006-0.00911.416-0.103-0.1030.0000.0000.0000.000
27A29VAL0-0.013-0.00612.0030.0340.0340.0000.0000.0000.000
28A30GLY00.0740.03414.3760.0090.0090.0000.0000.0000.000
29A31SER0-0.026-0.04217.271-0.026-0.0260.0000.0000.0000.000
30A32ASN0-0.103-0.04018.8780.0400.0400.0000.0000.0000.000
31A33VAL0-0.0140.01017.0620.0310.0310.0000.0000.0000.000
32A34THR0-0.019-0.01017.725-0.023-0.0230.0000.0000.0000.000
33A35ILE0-0.035-0.02113.4350.0170.0170.0000.0000.0000.000
34A36GLY00.0610.03215.444-0.049-0.0490.0000.0000.0000.000
35A37ALA0-0.004-0.00914.219-0.120-0.1200.0000.0000.0000.000
36A38ARG10.7390.81212.4130.6120.6120.0000.0000.0000.000
37A39THR0-0.0110.02313.4640.0510.0510.0000.0000.0000.000
38A40THR0-0.047-0.01910.853-0.205-0.2050.0000.0000.0000.000
39A41ILE00.0190.00511.3680.2570.2570.0000.0000.0000.000
40A42GLY00.0000.00011.090-0.298-0.2980.0000.0000.0000.000
41A43SER00.001-0.02311.8550.0210.0210.0000.0000.0000.000
42A44HIS0-0.044-0.04912.7480.1820.1820.0000.0000.0000.000
43A45SER0-0.0280.00714.3840.1310.1310.0000.0000.0000.000
44A46VAL0-0.0070.01114.956-0.092-0.0920.0000.0000.0000.000
45A47ILE0-0.009-0.00315.2850.0620.0620.0000.0000.0000.000
46A48GLU-1-0.888-0.96117.635-0.472-0.4720.0000.0000.0000.000
47A49GLY00.0620.05020.3350.0120.0120.0000.0000.0000.000
48A50HIS0-0.040-0.01622.245-0.040-0.0400.0000.0000.0000.000
49A51THR0-0.009-0.03220.9610.0500.0500.0000.0000.0000.000
50A52THR0-0.053-0.02121.112-0.034-0.0340.0000.0000.0000.000
51A53ILE0-0.013-0.00917.6820.0300.0300.0000.0000.0000.000
52A54GLY00.0690.04119.512-0.036-0.0360.0000.0000.0000.000
53A55GLU-1-0.857-0.93817.815-0.598-0.5980.0000.0000.0000.000
54A56ASP-1-0.815-0.88216.936-0.478-0.4780.0000.0000.0000.000
55A57ASN0-0.039-0.01317.6170.1010.1010.0000.0000.0000.000
56A58ARG10.9400.96515.0290.5100.5100.0000.0000.0000.000
57A59ILE00.0240.00616.1720.1130.1130.0000.0000.0000.000
58A60GLY00.0050.01015.632-0.120-0.1200.0000.0000.0000.000
59A61HIS00.0120.01213.825-0.136-0.1360.0000.0000.0000.000
60A62TYR0-0.036-0.02217.1050.0820.0820.0000.0000.0000.000
61A63ALA00.0180.01218.0880.0660.0660.0000.0000.0000.000
62A64SER0-0.041-0.00718.935-0.040-0.0400.0000.0000.0000.000
63A65VAL00.025-0.00819.6310.0450.0450.0000.0000.0000.000
64A66GLY00.0530.01620.940-0.036-0.0360.0000.0000.0000.000
65A67GLY00.0340.03323.5820.0110.0110.0000.0000.0000.000
66A68ARG10.9440.97325.3050.2780.2780.0000.0000.0000.000
67A69PRO0-0.0050.00228.6960.0050.0050.0000.0000.0000.000
68A70GLN00.0070.00831.7850.0030.0030.0000.0000.0000.000
69A71ASP-1-0.815-0.90734.045-0.163-0.1630.0000.0000.0000.000
70A72MET00.009-0.00236.898-0.002-0.0020.0000.0000.0000.000
71A73LYS10.8400.89739.2450.1680.1680.0000.0000.0000.000
72A74TYR0-0.041-0.01930.4480.0010.0010.0000.0000.0000.000
73A75LYS10.7510.85836.0050.1730.1730.0000.0000.0000.000
74A76ASP-1-0.884-0.94731.266-0.224-0.2240.0000.0000.0000.000
75A77GLU-1-0.815-0.89731.751-0.204-0.2040.0000.0000.0000.000
76A78PRO0-0.0240.01229.177-0.014-0.0140.0000.0000.0000.000
77A79THR0-0.068-0.05129.977-0.005-0.0050.0000.0000.0000.000
78A80ARG10.9680.97027.4250.2580.2580.0000.0000.0000.000
79A81LEU0-0.0010.01023.6330.0220.0220.0000.0000.0000.000
80A82VAL0-0.050-0.02625.043-0.025-0.0250.0000.0000.0000.000
81A83ILE0-0.017-0.01321.9510.0210.0210.0000.0000.0000.000
82A84GLY00.0560.04323.565-0.025-0.0250.0000.0000.0000.000
83A85ASP-1-0.816-0.90721.942-0.488-0.4880.0000.0000.0000.000
84A86ARG10.7350.83021.2240.3730.3730.0000.0000.0000.000
85A87ASN0-0.037-0.00622.0290.0720.0720.0000.0000.0000.000
86A88THR0-0.037-0.01120.787-0.068-0.0680.0000.0000.0000.000
87A89ILE0-0.010-0.00520.6650.0520.0520.0000.0000.0000.000
88A90ARG10.8460.90720.4140.3650.3650.0000.0000.0000.000
89A91GLU-1-0.762-0.86119.490-0.513-0.5130.0000.0000.0000.000
90A92PHE0-0.020-0.02222.0470.0430.0430.0000.0000.0000.000
91A93THR0-0.042-0.00422.5560.0240.0240.0000.0000.0000.000
92A94THR0-0.002-0.01523.794-0.024-0.0240.0000.0000.0000.000
93A95ILE00.0130.01423.6030.0240.0240.0000.0000.0000.000
94A96HIS00.0160.01225.449-0.007-0.0070.0000.0000.0000.000
95A97THR00.0440.03726.2940.0040.0040.0000.0000.0000.000
96A98GLY00.0210.01428.6720.0160.0160.0000.0000.0000.000
97A99THR0-0.078-0.07632.2430.0020.0020.0000.0000.0000.000
98A100VAL00.017-0.00635.3180.0020.0020.0000.0000.0000.000
99A101GLN0-0.045-0.02137.4820.0040.0040.0000.0000.0000.000
100A102ASP-1-0.854-0.89037.742-0.173-0.1730.0000.0000.0000.000
101A103ALA00.0440.02036.8340.0050.0050.0000.0000.0000.000
102A104GLY0-0.040-0.01634.460-0.007-0.0070.0000.0000.0000.000
103A105VAL0-0.078-0.05129.791-0.017-0.0170.0000.0000.0000.000
104A106THR0-0.003-0.00229.0150.0230.0230.0000.0000.0000.000
105A107THR0-0.007-0.00829.028-0.016-0.0160.0000.0000.0000.000
106A108LEU0-0.019-0.00825.5650.0140.0140.0000.0000.0000.000
107A109GLY00.0380.02927.686-0.015-0.0150.0000.0000.0000.000
108A110ASP-1-0.759-0.86626.246-0.363-0.3630.0000.0000.0000.000
109A111ASP-1-0.809-0.89525.657-0.271-0.2710.0000.0000.0000.000
110A112ASN0-0.055-0.02126.4590.0460.0460.0000.0000.0000.000
111A113TRP0-0.015-0.01223.542-0.036-0.0360.0000.0000.0000.000
112A114ILE00.019-0.00225.2320.0290.0290.0000.0000.0000.000
113A115MET0-0.040-0.01025.099-0.024-0.0240.0000.0000.0000.000
114A116ALA00.0540.02425.421-0.008-0.0080.0000.0000.0000.000
115A117TYR0-0.025-0.03226.3270.0310.0310.0000.0000.0000.000
116A118VAL0-0.0530.00527.7120.0170.0170.0000.0000.0000.000
117A119HIS00.0070.02427.805-0.036-0.0360.0000.0000.0000.000
118A120ILE00.012-0.00127.8260.0200.0200.0000.0000.0000.000
119A121GLY00.0730.02829.867-0.014-0.0140.0000.0000.0000.000
120A122HIS10.8590.92431.9660.2040.2040.0000.0000.0000.000
121A123ASP-1-0.710-0.81932.587-0.203-0.2030.0000.0000.0000.000
122A124CYS0-0.084-0.01132.3420.0150.0150.0000.0000.0000.000
123A125ARG10.8470.92232.9030.1740.1740.0000.0000.0000.000
124A126VAL0-0.027-0.02930.8100.0150.0150.0000.0000.0000.000
125A127GLY00.0420.03431.816-0.011-0.0110.0000.0000.0000.000
126A128SER00.0400.00130.613-0.027-0.0270.0000.0000.0000.000
127A129HIS0-0.020-0.00529.9190.0260.0260.0000.0000.0000.000
128A130VAL0-0.041-0.00231.0730.0160.0160.0000.0000.0000.000
129A131VAL0-0.034-0.01830.306-0.018-0.0180.0000.0000.0000.000
130A132LEU00.0100.00529.8290.0180.0180.0000.0000.0000.000
131A133SER00.013-0.03230.077-0.016-0.0160.0000.0000.0000.000
132A134SER00.017-0.01529.998-0.007-0.0070.0000.0000.0000.000
133A135ASN0-0.024-0.02730.5210.0130.0130.0000.0000.0000.000
134A136ALA0-0.0330.01332.3200.0130.0130.0000.0000.0000.000
135A137GLN0-0.033-0.02232.336-0.013-0.0130.0000.0000.0000.000
136A138MET0-0.020-0.01032.7980.0220.0220.0000.0000.0000.000
137A139ALA00.0220.01334.371-0.010-0.0100.0000.0000.0000.000
138A140GLY00.0340.01335.740-0.006-0.0060.0000.0000.0000.000
139A141HIS0-0.071-0.06336.3560.0130.0130.0000.0000.0000.000
140A142VAL0-0.021-0.01036.4460.0110.0110.0000.0000.0000.000
141A143GLU-1-0.873-0.91336.369-0.175-0.1750.0000.0000.0000.000
142A144ILE0-0.011-0.01934.1960.0100.0100.0000.0000.0000.000
143A145GLY00.0380.02035.941-0.009-0.0090.0000.0000.0000.000
144A146ASP-1-0.802-0.91335.034-0.203-0.2030.0000.0000.0000.000
145A147TRP0-0.006-0.02133.6210.0160.0160.0000.0000.0000.000
146A148ALA0-0.0430.00535.8100.0080.0080.0000.0000.0000.000
147A149ILE0-0.026-0.01234.950-0.011-0.0110.0000.0000.0000.000
148A150VAL00.0260.01035.1450.0130.0130.0000.0000.0000.000
149A151GLY00.0050.01135.099-0.011-0.0110.0000.0000.0000.000
150A152GLY00.0250.00134.795-0.006-0.0060.0000.0000.0000.000
151A153MET0-0.026-0.00935.1340.0080.0080.0000.0000.0000.000
152A154SER00.0160.02736.7980.0120.0120.0000.0000.0000.000
153A155GLY00.0150.02637.033-0.012-0.0120.0000.0000.0000.000
154A156VAL0-0.022-0.02038.0760.0110.0110.0000.0000.0000.000
155A157HIS0-0.054-0.04739.220-0.002-0.0020.0000.0000.0000.000
156A158GLN00.0310.01640.060-0.007-0.0070.0000.0000.0000.000
157A159TYR00.010-0.01240.6120.0130.0130.0000.0000.0000.000
158A160VAL0-0.069-0.00741.6670.0060.0060.0000.0000.0000.000
159A161ARG10.8180.90840.8890.1200.1200.0000.0000.0000.000
160A162ILE0-0.008-0.01538.2290.0090.0090.0000.0000.0000.000
161A163GLY00.0560.03040.390-0.007-0.0070.0000.0000.0000.000
162A164ALA00.0510.02839.572-0.003-0.0030.0000.0000.0000.000
163A165HIS00.0170.00038.7370.0110.0110.0000.0000.0000.000
164A166SER0-0.050-0.00740.5500.0060.0060.0000.0000.0000.000
165A167MET0-0.046-0.03439.346-0.006-0.0060.0000.0000.0000.000
166A168LEU0-0.0010.01239.8760.0090.0090.0000.0000.0000.000
167A169GLY00.019-0.00139.883-0.006-0.0060.0000.0000.0000.000
168A170GLY00.001-0.01439.265-0.005-0.0050.0000.0000.0000.000
169A171ALA0-0.029-0.00539.6970.0090.0090.0000.0000.0000.000
170A172SER0-0.028-0.00841.2270.0110.0110.0000.0000.0000.000
171A173ALA0-0.033-0.01241.660-0.008-0.0080.0000.0000.0000.000
172A174LEU00.0250.02041.6020.0080.0080.0000.0000.0000.000
173A175VAL00.023-0.00943.478-0.006-0.0060.0000.0000.0000.000
174A176GLN0-0.036-0.01346.1460.0030.0030.0000.0000.0000.000
175A177ASP-1-0.702-0.82645.169-0.133-0.1330.0000.0000.0000.000
176A178ILE0-0.023-0.01542.2970.0070.0070.0000.0000.0000.000
177A179PRO00.0140.00744.870-0.005-0.0050.0000.0000.0000.000
178A180PRO00.0420.02344.018-0.002-0.0020.0000.0000.0000.000
179A181PHE0-0.015-0.01743.8000.0060.0060.0000.0000.0000.000
180A182VAL0-0.062-0.00645.2530.0060.0060.0000.0000.0000.000
181A183ILE00.0140.01344.113-0.008-0.0080.0000.0000.0000.000
182A184ALA0-0.003-0.00344.6250.0060.0060.0000.0000.0000.000
183A185ALA00.0190.00844.542-0.006-0.0060.0000.0000.0000.000
184A186GLY00.0490.03745.6660.0060.0060.0000.0000.0000.000
185A187ASN00.0410.03245.768-0.005-0.0050.0000.0000.0000.000
186A188LYS10.8880.91947.5300.1110.1110.0000.0000.0000.000
187A189ALA0-0.009-0.00445.4430.0030.0030.0000.0000.0000.000
188A190GLU-1-0.851-0.88647.596-0.085-0.0850.0000.0000.0000.000
189A191PRO0-0.009-0.00949.153-0.003-0.0030.0000.0000.0000.000
190A192HIS0-0.037-0.02348.3000.0070.0070.0000.0000.0000.000
191A193GLY0-0.007-0.00149.7290.0000.0000.0000.0000.0000.000
192A194ILE00.0220.00747.786-0.004-0.0040.0000.0000.0000.000
193A195ASN0-0.021-0.01740.6650.0060.0060.0000.0000.0000.000
194A196VAL00.007-0.01344.480-0.002-0.0020.0000.0000.0000.000
195A197GLU-1-0.760-0.86243.075-0.091-0.0910.0000.0000.0000.000
196A198GLY0-0.0330.00740.234-0.003-0.0030.0000.0000.0000.000
197A199LEU00.0270.01240.538-0.004-0.0040.0000.0000.0000.000
198A200ARG10.8530.90142.7590.0860.0860.0000.0000.0000.000
199A201ARG10.8560.89738.5550.1200.1200.0000.0000.0000.000
200A202ARG10.8430.94136.2850.1530.1530.0000.0000.0000.000
201A203GLY00.0210.02939.364-0.002-0.0020.0000.0000.0000.000
202A204PHE0-0.037-0.01141.2810.0040.0040.0000.0000.0000.000
203A205SER0-0.017-0.04844.9800.0020.0020.0000.0000.0000.000
204A206PRO00.015-0.01948.264-0.002-0.0020.0000.0000.0000.000
205A207ASP-1-0.864-0.93250.933-0.066-0.0660.0000.0000.0000.000
206A208ALA00.0310.02348.7560.0000.0000.0000.0000.0000.000
207A209ILE00.001-0.00746.332-0.001-0.0010.0000.0000.0000.000
208A210SER0-0.091-0.03850.2070.0000.0000.0000.0000.0000.000
209A211ALA00.0570.04053.0930.0010.0010.0000.0000.0000.000
210A212LEU00.0550.02447.7020.0000.0000.0000.0000.0000.000
211A213ARG10.9140.94051.9150.0760.0760.0000.0000.0000.000
212A214SER0-0.036-0.01453.8320.0020.0020.0000.0000.0000.000
213A215ALA00.0670.04653.3740.0010.0010.0000.0000.0000.000
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