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

tag_button

FMODB ID: Q1R8Y

Calculation Name: 4EQ6-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4EQ6

Chain ID: A

ChEMBL ID:

UniProt ID: P40465

Base Structure: X-ray

Registration Date: 2023-06-20

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 OptAll
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 192
LigandCharge DGL=-1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2309132.305881
FMO2-HF: Nuclear repulsion 2230271.737622
FMO2-HF: Total energy -78860.568259
FMO2-MP2: Total energy -79091.937521


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:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-16.528-4.9456.932-5.732-12.78-0.037
Interaction energy analysis for fragmet #1(A:1:MET)
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 : -0.003
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].
3A3TYR00.023-0.0113.8840.1432.9630.209-1.421-1.608-0.003
4A4GLU-1-0.795-0.8936.039-0.338-0.3380.0000.0000.0000.000
5A5ASP-1-0.927-0.9482.626-1.477-0.4551.046-0.601-1.467-0.007
6A6LEU0-0.104-0.0492.549-7.866-5.1583.562-1.980-4.290-0.020
7A7GLU-1-0.879-0.9334.093-1.892-1.7430.0080.027-0.1850.000
8A8LEU0-0.042-0.0186.2540.3310.3310.0000.0000.0000.000
9A9ILE0-0.046-0.0299.2190.1510.1510.0000.0000.0000.000
10A10THR00.0020.0084.151-0.296-0.151-0.001-0.013-0.1310.000
11A11ILE0-0.006-0.0087.1330.2160.2160.0000.0000.0000.000
12A12TRP0-0.003-0.0144.8480.1930.1930.0000.0000.0000.000
13A13PRO0-0.008-0.0068.528-0.031-0.0310.0000.0000.0000.000
14A14SER0-0.038-0.02311.4460.1120.1120.0000.0000.0000.000
15A15PRO00.0360.0558.5200.1090.1090.0000.0000.0000.000
16A16THR00.012-0.01010.375-0.127-0.1270.0000.0000.0000.000
17A17LYS10.9880.98010.507-0.144-0.1440.0000.0000.0000.000
18A18ASN0-0.003-0.00311.425-0.078-0.0780.0000.0000.0000.000
19A19LYS10.9540.9705.508-3.184-3.1840.0000.0000.0000.000
20A20LEU00.0420.0476.296-0.019-0.0190.0000.0000.0000.000
21A21CYS0-0.040-0.0217.976-0.220-0.2200.0000.0000.0000.000
22A22GLN00.0050.0105.6740.4380.4380.0000.0000.0000.000
23A23PHE00.0340.0222.522-1.2210.2860.653-0.542-1.617-0.001
24A24ILE00.0400.0194.787-0.356-0.351-0.001-0.0030.0000.000
25A25LYS10.8210.9078.2500.0480.0480.0000.0000.0000.000
26A26GLN0-0.0090.0083.0560.1830.7770.039-0.210-0.423-0.001
27A27ASN0-0.002-0.0163.9950.4360.790-0.001-0.167-0.1860.000
28A28LEU0-0.041-0.0197.8620.1710.1710.0000.0000.0000.000
29A29SER0-0.077-0.04910.7760.0770.0770.0000.0000.0000.000
30A30LYS10.7910.8979.3400.4980.4980.0000.0000.0000.000
31A31DGL-1-0.862-0.92912.023-0.120-0.1200.0000.0000.0000.000
32A32HIS0-0.058-0.04415.027-0.020-0.0200.0000.0000.0000.000
33A33VAL00.0300.04112.4610.0000.0000.0000.0000.0000.000
34A34VAL0-0.033-0.01615.9520.0090.0090.0000.0000.0000.000
35A35THR00.003-0.0039.3530.0210.0210.0000.0000.0000.000
36A36GLN0-0.053-0.03912.3820.0370.0370.0000.0000.0000.000
37A37LEU0-0.032-0.0029.646-0.026-0.0260.0000.0000.0000.000
38A38PHE0-0.002-0.01412.4580.0350.0350.0000.0000.0000.000
39A39PHE00.0210.00912.686-0.003-0.0030.0000.0000.0000.000
40A40ILE0-0.020-0.01214.8080.0090.0090.0000.0000.0000.000
41A41ASP-1-0.730-0.84816.7670.0630.0630.0000.0000.0000.000
42A42ALA00.0070.02118.826-0.006-0.0060.0000.0000.0000.000
43A43THR0-0.038-0.03520.715-0.003-0.0030.0000.0000.0000.000
44A44SER0-0.031-0.00221.0460.0040.0040.0000.0000.0000.000
45A45SER0-0.011-0.03517.8340.0040.0040.0000.0000.0000.000
46A46PHE0-0.0070.01413.6110.0320.0320.0000.0000.0000.000
47A47PRO00.0010.00313.3880.0020.0020.0000.0000.0000.000
48A48LEU00.0300.01316.6770.0080.0080.0000.0000.0000.000
49A49SER00.0580.02618.5440.0020.0020.0000.0000.0000.000
50A50GLN0-0.036-0.02715.6390.0100.0100.0000.0000.0000.000
51A51PHE00.0590.01011.6610.0190.0190.0000.0000.0000.000
52A52GLN00.0550.01915.387-0.003-0.0030.0000.0000.0000.000
53A53LYS10.8660.94016.672-0.201-0.2010.0000.0000.0000.000
54A54LEU0-0.078-0.04812.3500.0310.0310.0000.0000.0000.000
55A55VAL00.0160.02812.532-0.017-0.0170.0000.0000.0000.000
56A56PRO00.0450.03415.568-0.008-0.0080.0000.0000.0000.000
57A57PRO00.003-0.00419.440-0.012-0.0120.0000.0000.0000.000
58A58THR0-0.030-0.01321.165-0.006-0.0060.0000.0000.0000.000
59A59LEU0-0.0270.00419.5910.0040.0040.0000.0000.0000.000
60A60PRO00.0480.00520.791-0.010-0.0100.0000.0000.0000.000
61A61GLU-1-0.805-0.89516.429-0.045-0.0450.0000.0000.0000.000
62A62ASN00.007-0.00415.852-0.047-0.0470.0000.0000.0000.000
63A63VAL0-0.0290.00517.713-0.006-0.0060.0000.0000.0000.000
64A64ARG10.9380.95915.1220.2330.2330.0000.0000.0000.000
65A65ILE00.0010.01112.578-0.013-0.0130.0000.0000.0000.000
66A66TYR0-0.043-0.05015.7220.0040.0040.0000.0000.0000.000
67A67GLU-1-0.887-0.94418.340-0.091-0.0910.0000.0000.0000.000
68A68ASN0-0.048-0.01315.559-0.001-0.0010.0000.0000.0000.000
69A69ILE00.0150.02313.768-0.018-0.0180.0000.0000.0000.000
70A70ARG10.8020.89315.9730.1290.1290.0000.0000.0000.000
71A71ILE00.0070.00316.634-0.001-0.0010.0000.0000.0000.000
72A72ASN0-0.035-0.03318.961-0.005-0.0050.0000.0000.0000.000
73A73THR00.0100.01620.2000.0020.0020.0000.0000.0000.000
74A74CYS0-0.035-0.00821.074-0.011-0.0110.0000.0000.0000.000
75A75LEU00.0230.00522.9760.0070.0070.0000.0000.0000.000
76A76ASP-1-0.838-0.89725.365-0.036-0.0360.0000.0000.0000.000
77A77LEU00.0280.01022.397-0.006-0.0060.0000.0000.0000.000
78A78GLU-1-0.770-0.87424.582-0.068-0.0680.0000.0000.0000.000
79A79GLU-1-0.870-0.92925.258-0.039-0.0390.0000.0000.0000.000
80A80LEU00.0540.01418.296-0.006-0.0060.0000.0000.0000.000
81A81SER0-0.013-0.00421.709-0.015-0.0150.0000.0000.0000.000
82A82ALA00.0020.00023.905-0.008-0.0080.0000.0000.0000.000
83A83ILE0-0.041-0.02519.506-0.005-0.0050.0000.0000.0000.000
84A84THR00.009-0.01219.324-0.013-0.0130.0000.0000.0000.000
85A85VAL0-0.053-0.02421.011-0.011-0.0110.0000.0000.0000.000
86A86LYS10.9700.99722.3190.0800.0800.0000.0000.0000.000
87A87LEU00.0090.00316.598-0.001-0.0010.0000.0000.0000.000
88A88LEU00.0440.02620.051-0.008-0.0080.0000.0000.0000.000
89A89GLN0-0.019-0.01021.9010.0010.0010.0000.0000.0000.000
90A90ILE0-0.011-0.00419.6240.0020.0020.0000.0000.0000.000
91A91LEU00.0160.01216.5210.0020.0020.0000.0000.0000.000
92A92SER00.000-0.01220.7010.0000.0000.0000.0000.0000.000
93A93MET0-0.042-0.02124.2970.0080.0080.0000.0000.0000.000
94A94ASN00.0000.01120.6720.0040.0040.0000.0000.0000.000
95A95LYS10.8490.92118.3670.2460.2460.0000.0000.0000.000
96A96ILE0-0.030-0.00924.2440.0050.0050.0000.0000.0000.000
97A97ASN0-0.095-0.06627.0450.0110.0110.0000.0000.0000.000
98A98ALA0-0.0180.01124.4230.0050.0050.0000.0000.0000.000
99A99GLN0-0.109-0.04425.1550.0030.0030.0000.0000.0000.000
100A108GLU-1-0.861-0.92219.689-0.168-0.1680.0000.0000.0000.000
101A109PRO0-0.0160.00516.619-0.001-0.0010.0000.0000.0000.000
102A110LEU0-0.028-0.02115.829-0.012-0.0120.0000.0000.0000.000
103A111LYS10.7650.85710.8540.3270.3270.0000.0000.0000.000
104A112ILE00.004-0.00211.717-0.008-0.0080.0000.0000.0000.000
105A113ILE00.0330.0096.553-0.018-0.0180.0000.0000.0000.000
106A114LEU0-0.018-0.0019.7190.0420.0420.0000.0000.0000.000
107A115TYR0-0.068-0.0727.7940.0020.0020.0000.0000.0000.000
108A116ILE0-0.004-0.00311.3530.0130.0130.0000.0000.0000.000
109A117ASN00.001-0.01013.3830.0370.0370.0000.0000.0000.000
110A118GLY00.0580.02915.680-0.016-0.0160.0000.0000.0000.000
111A119LEU00.0540.02016.506-0.010-0.0100.0000.0000.0000.000
112A120GLU-1-0.810-0.91119.0500.0340.0340.0000.0000.0000.000
113A121VAL0-0.069-0.03821.3200.0000.0000.0000.0000.0000.000
114A122MET0-0.0230.00818.927-0.011-0.0110.0000.0000.0000.000
115A123PHE00.0340.00122.632-0.002-0.0020.0000.0000.0000.000
116A124ARG10.9110.95924.187-0.014-0.0140.0000.0000.0000.000
117A125ASN0-0.003-0.01026.8920.0030.0030.0000.0000.0000.000
118A126SER00.0630.00927.1970.0000.0000.0000.0000.0000.000
119A127GLN0-0.064-0.00328.650-0.007-0.0070.0000.0000.0000.000
120A128PHE0-0.046-0.02030.8250.0050.0050.0000.0000.0000.000
121A129LYS10.8430.90630.3830.0280.0280.0000.0000.0000.000
122A130SER0-0.034-0.02331.748-0.003-0.0030.0000.0000.0000.000
123A131SER00.0280.01233.8440.0020.0020.0000.0000.0000.000
124A132PRO00.0640.01030.670-0.003-0.0030.0000.0000.0000.000
125A133GLN00.0090.01829.744-0.004-0.0040.0000.0000.0000.000
126A134ARG10.8520.92129.8180.0600.0600.0000.0000.0000.000
127A135SER00.0280.01026.777-0.007-0.0070.0000.0000.0000.000
128A136HIS0-0.042-0.04125.091-0.009-0.0090.0000.0000.0000.000
129A137GLU-1-0.881-0.92324.969-0.086-0.0860.0000.0000.0000.000
130A138LEU00.0000.01725.063-0.010-0.0100.0000.0000.0000.000
131A139LEU0-0.0140.00019.313-0.009-0.0090.0000.0000.0000.000
132A140ARG10.8280.88620.7950.0890.0890.0000.0000.0000.000
133A141ASP-1-0.789-0.86321.226-0.137-0.1370.0000.0000.0000.000
134A142THR0-0.044-0.03319.784-0.011-0.0110.0000.0000.0000.000
135A143LEU00.0070.00315.597-0.016-0.0160.0000.0000.0000.000
136A144LEU00.0080.00116.842-0.035-0.0350.0000.0000.0000.000
137A145LYS10.9000.96418.5660.1200.1200.0000.0000.0000.000
138A146LEU00.029-0.00114.866-0.005-0.0050.0000.0000.0000.000
139A147ARG10.8040.88211.8700.4650.4650.0000.0000.0000.000
140A148VAL00.002-0.00215.086-0.026-0.0260.0000.0000.0000.000
141A149MET0-0.058-0.02216.8750.0010.0010.0000.0000.0000.000
142A150GLY00.0150.01612.8870.0040.0040.0000.0000.0000.000
143A151ASN0-0.050-0.03513.129-0.088-0.0880.0000.0000.0000.000
144A152ASP-1-0.854-0.90115.124-0.219-0.2190.0000.0000.0000.000
145A153GLU-1-0.916-0.95716.614-0.282-0.2820.0000.0000.0000.000
146A154ASN0-0.097-0.05618.0450.0010.0010.0000.0000.0000.000
147A155GLU-1-0.758-0.88415.161-0.321-0.3210.0000.0000.0000.000
148A156ASN0-0.042-0.01517.577-0.002-0.0020.0000.0000.0000.000
149A157ALA00.0100.00217.2330.0080.0080.0000.0000.0000.000
150A158SER00.0360.03813.304-0.019-0.0190.0000.0000.0000.000
151A159ILE0-0.014-0.00912.5900.0250.0250.0000.0000.0000.000
152A160ARG10.8730.9437.3030.6350.6350.0000.0000.0000.000
153A161THR00.0080.0029.3210.0960.0960.0000.0000.0000.000
154A162LEU0-0.036-0.0074.396-0.225-0.079-0.001-0.008-0.1360.000
155A163LEU0-0.012-0.0108.5280.0550.0550.0000.0000.0000.000
156A164GLU-1-0.837-0.89410.7540.2920.2920.0000.0000.0000.000
157A165PHE00.033-0.00611.980-0.056-0.0560.0000.0000.0000.000
158A166PRO00.0150.01514.2520.0610.0610.0000.0000.0000.000
159A167LYS10.9370.96313.610-0.528-0.5280.0000.0000.0000.000
160A168GLU-1-0.876-0.94316.2740.1730.1730.0000.0000.0000.000
161A169GLN0-0.095-0.06318.145-0.042-0.0420.0000.0000.0000.000
162A170LEU00.0200.02213.192-0.029-0.0290.0000.0000.0000.000
163A171LEU00.0180.01217.3590.0030.0030.0000.0000.0000.000
164A172ASP-1-0.784-0.86420.0040.0080.0080.0000.0000.0000.000
165A173TYR0-0.054-0.05312.294-0.044-0.0440.0000.0000.0000.000
166A174TYR0-0.070-0.07613.1700.0040.0040.0000.0000.0000.000
167A175LEU00.0090.00918.4040.0050.0050.0000.0000.0000.000
168A176LYS10.8380.94015.255-0.007-0.0070.0000.0000.0000.000
169A177LYS10.8490.92914.176-0.315-0.3150.0000.0000.0000.000
170A178ASN0-0.0080.01219.4180.0160.0160.0000.0000.0000.000
171A192ARG10.8520.89522.396-0.037-0.0370.0000.0000.0000.000
172A193ILE0-0.0020.00229.526-0.006-0.0060.0000.0000.0000.000
173A194LYS10.7490.83723.1390.0180.0180.0000.0000.0000.000
174A195ASN0-0.020-0.01229.214-0.003-0.0030.0000.0000.0000.000
175A196GLY00.0430.02927.779-0.004-0.0040.0000.0000.0000.000
176A197ASP-1-0.811-0.89422.005-0.047-0.0470.0000.0000.0000.000
177A198SER0-0.023-0.02219.773-0.005-0.0050.0000.0000.0000.000
178A199LEU00.0470.01518.215-0.011-0.0110.0000.0000.0000.000
179A200ALA00.0350.02315.856-0.022-0.0220.0000.0000.0000.000
180A201GLU-1-0.774-0.87616.202-0.007-0.0070.0000.0000.0000.000
181A202TYR00.0070.00218.045-0.029-0.0290.0000.0000.0000.000
182A203ILE00.0360.00814.037-0.021-0.0210.0000.0000.0000.000
183A204TRP00.007-0.01512.1350.0010.0010.0000.0000.0000.000
184A205LYS10.7910.88714.4110.0380.0380.0000.0000.0000.000
185A206TYR0-0.052-0.02317.2250.0030.0030.0000.0000.0000.000
186A207TYR0-0.017-0.00215.7550.0070.0070.0000.0000.0000.000
187A208ALA0-0.012-0.00510.488-0.022-0.0220.0000.0000.0000.000
188A209ASP-1-0.750-0.8448.159-0.656-0.6560.0000.0000.0000.000
189A210SER00.0010.0085.534-0.119-0.1190.0000.0000.0000.000
190A211LEU0-0.042-0.0197.6100.1360.1360.0000.0000.0000.000
191A212PHE00.0290.0262.927-2.640-0.5071.419-0.814-2.737-0.005
192A213GLU-1-0.786-0.8476.2411.0891.0890.0000.0000.0000.000