Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: R8198

Calculation Name: 3ENP-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3ENP

Chain ID: A

ChEMBL ID:

UniProt ID: Q9Y3C4

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 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 175
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1867731.707421
FMO2-HF: Nuclear repulsion 1798606.63814
FMO2-HF: Total energy -69125.069281
FMO2-MP2: Total energy -69325.628618


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.
-12.347-11.51417.889-7.686-11.035-0.063
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 : -0.047 / q_NPA : -0.027
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].
3A3LEU0-0.029-0.0103.8480.2253.2510.086-1.457-1.6560.001
4A4THR0-0.011-0.0256.841-0.283-0.2830.0000.0000.0000.000
5A5HIS0-0.027-0.0169.8270.1100.1100.0000.0000.0000.000
6A6GLN00.0150.01013.251-0.033-0.0330.0000.0000.0000.000
7A7LEU0-0.0080.00216.769-0.005-0.0050.0000.0000.0000.000
8A8ASP-1-0.874-0.91819.938-0.055-0.0550.0000.0000.0000.000
9A9LEU0-0.036-0.02022.5770.0070.0070.0000.0000.0000.000
10A10PHE0-0.058-0.03122.9510.0010.0010.0000.0000.0000.000
11A11PRO00.0640.02820.302-0.008-0.0080.0000.0000.0000.000
12A12GLU-1-0.765-0.88319.367-0.080-0.0800.0000.0000.0000.000
13A13CYS0-0.114-0.05819.665-0.009-0.0090.0000.0000.0000.000
14A14ARG10.7860.88513.9280.1380.1380.0000.0000.0000.000
15A15VAL00.001-0.00213.450-0.020-0.0200.0000.0000.0000.000
16A16THR00.0160.0158.5290.0680.0680.0000.0000.0000.000
17A17LEU0-0.027-0.0088.406-0.004-0.0040.0000.0000.0000.000
18A18LEU00.0430.0164.324-0.636-0.543-0.001-0.015-0.0770.000
19A19LEU0-0.024-0.0054.0390.9381.078-0.001-0.020-0.1190.000
20A20PHE00.0310.0124.470-0.609-0.491-0.001-0.011-0.1060.000
21A21LYS10.8340.9157.2240.0060.0060.0000.0000.0000.000
22A22ASP-1-0.819-0.9049.6810.2000.2000.0000.0000.0000.000
23A23VAL0-0.043-0.00611.1890.0200.0200.0000.0000.0000.000
24A24LYS10.8160.88613.570-0.067-0.0670.0000.0000.0000.000
25A25ASN00.0480.02215.224-0.013-0.0130.0000.0000.0000.000
26A26ALA00.0430.03016.681-0.017-0.0170.0000.0000.0000.000
27A27GLY00.0110.00417.548-0.011-0.0110.0000.0000.0000.000
28A28ASP-1-0.816-0.90019.815-0.064-0.0640.0000.0000.0000.000
29A29LEU0-0.039-0.01213.628-0.009-0.0090.0000.0000.0000.000
30A30ARG10.8780.92817.5200.1050.1050.0000.0000.0000.000
31A31ARG10.7590.85120.0050.0740.0740.0000.0000.0000.000
32A32LYS10.8850.93416.3490.1320.1320.0000.0000.0000.000
33A33ALA00.0100.00718.304-0.002-0.0020.0000.0000.0000.000
34A34MET0-0.113-0.05719.9850.0060.0060.0000.0000.0000.000
35A35GLU-1-0.866-0.91323.358-0.074-0.0740.0000.0000.0000.000
36A36GLY0-0.0140.01021.6310.0070.0070.0000.0000.0000.000
37A37THR0-0.040-0.02720.967-0.005-0.0050.0000.0000.0000.000
38A38ILE0-0.034-0.01613.3620.0000.0000.0000.0000.0000.000
39A39ASP-1-0.879-0.92614.477-0.205-0.2050.0000.0000.0000.000
40A40GLY00.000-0.00814.376-0.043-0.0430.0000.0000.0000.000
41A41SER0-0.076-0.05515.0910.0470.0470.0000.0000.0000.000
42A42LEU00.0130.00913.291-0.074-0.0740.0000.0000.0000.000
43A43ILE0-0.002-0.01713.5980.0640.0640.0000.0000.0000.000
44A44ASN00.0510.04113.496-0.059-0.0590.0000.0000.0000.000
45A45PRO00.018-0.00311.1770.0110.0110.0000.0000.0000.000
46A46THR0-0.041-0.03213.2540.0350.0350.0000.0000.0000.000
47A47VAL0-0.013-0.00516.3420.0300.0300.0000.0000.0000.000
48A48ILE0-0.038-0.01813.5920.0070.0070.0000.0000.0000.000
49A49VAL00.020-0.00414.942-0.002-0.0020.0000.0000.0000.000
50A50ASP-1-0.845-0.91713.819-0.022-0.0220.0000.0000.0000.000
51A51PRO00.005-0.00810.332-0.039-0.0390.0000.0000.0000.000
52A52PHE00.0390.01712.974-0.020-0.0200.0000.0000.0000.000
53A53GLN00.0220.00616.3830.0000.0000.0000.0000.0000.000
54A54ILE0-0.004-0.01112.7700.0020.0020.0000.0000.0000.000
55A55LEU00.0180.01414.1370.0060.0060.0000.0000.0000.000
56A56VAL00.0360.03117.4110.0120.0120.0000.0000.0000.000
57A57ALA0-0.014-0.00219.0640.0080.0080.0000.0000.0000.000
58A58ALA0-0.007-0.01117.5440.0060.0060.0000.0000.0000.000
59A59ASN00.008-0.01619.6910.0110.0110.0000.0000.0000.000
60A60LYS10.8610.95122.3750.0800.0800.0000.0000.0000.000
61A61ALA0-0.011-0.00921.9940.0070.0070.0000.0000.0000.000
62A62VAL00.0290.00021.0270.0060.0060.0000.0000.0000.000
63A63HIS0-0.020-0.02224.0660.0130.0130.0000.0000.0000.000
64A64LEU0-0.0240.00027.2490.0070.0070.0000.0000.0000.000
65A65TYR0-0.015-0.02624.9800.0040.0040.0000.0000.0000.000
66A66LYS10.8320.92624.7200.0900.0900.0000.0000.0000.000
67A67LEU00.0220.02928.9280.0060.0060.0000.0000.0000.000
68A68GLY0-0.0140.00730.9400.0050.0050.0000.0000.0000.000
69A69LYS10.7910.87131.1730.0590.0590.0000.0000.0000.000
70A70MET0-0.0200.02626.332-0.004-0.0040.0000.0000.0000.000
71A71LYS10.8540.91229.0360.0680.0680.0000.0000.0000.000
72A72THR0-0.076-0.06326.2780.0000.0000.0000.0000.0000.000
73A73ARG10.9660.97327.4710.0770.0770.0000.0000.0000.000
74A74THR00.0380.01323.1720.0010.0010.0000.0000.0000.000
75A75LEU00.1020.05720.469-0.002-0.0020.0000.0000.0000.000
76A76SER00.0250.01618.588-0.004-0.0040.0000.0000.0000.000
77A77THR0-0.037-0.00619.839-0.011-0.0110.0000.0000.0000.000
78A78GLU-1-0.747-0.85222.644-0.096-0.0960.0000.0000.0000.000
79A79ILE00.0420.02417.1180.0100.0100.0000.0000.0000.000
80A80ILE00.0090.00118.3130.0030.0030.0000.0000.0000.000
81A81PHE0-0.038-0.03220.5850.0140.0140.0000.0000.0000.000
82A82ASN0-0.037-0.03922.8730.0190.0190.0000.0000.0000.000
83A83LEU00.0380.04117.0130.0050.0050.0000.0000.0000.000
84A84SER0-0.0390.00821.5140.0120.0120.0000.0000.0000.000
85A85PRO00.0180.01224.5200.0030.0030.0000.0000.0000.000
86A86ASN0-0.020-0.02127.4400.0080.0080.0000.0000.0000.000
87A87ASN00.039-0.00928.847-0.009-0.0090.0000.0000.0000.000
88A88ASN00.0140.03131.250-0.004-0.0040.0000.0000.0000.000
89A89ILE00.0950.04127.745-0.005-0.0050.0000.0000.0000.000
90A90SER0-0.031-0.02727.412-0.006-0.0060.0000.0000.0000.000
91A91GLU-1-0.853-0.89128.083-0.062-0.0620.0000.0000.0000.000
92A92ALA00.0700.03724.586-0.004-0.0040.0000.0000.0000.000
93A93LEU00.015-0.00222.814-0.011-0.0110.0000.0000.0000.000
94A94LYS10.8340.90923.3440.0660.0660.0000.0000.0000.000
95A95LYS10.8380.90922.8640.0780.0780.0000.0000.0000.000
96A96PHE00.0570.02419.049-0.001-0.0010.0000.0000.0000.000
97A97GLY00.0140.02017.873-0.033-0.0330.0000.0000.0000.000
98A98ILE0-0.0250.00915.0110.0170.0170.0000.0000.0000.000
99A99SER0-0.057-0.06418.1750.0260.0260.0000.0000.0000.000
100A100ALA00.012-0.01719.622-0.009-0.0090.0000.0000.0000.000
101A101ASN0-0.024-0.01620.9930.0030.0030.0000.0000.0000.000
102A102ASP-1-0.798-0.84815.966-0.134-0.1340.0000.0000.0000.000
103A103THR00.0530.02315.320-0.013-0.0130.0000.0000.0000.000
104A104SER0-0.056-0.03911.1270.0390.0390.0000.0000.0000.000
105A105ILE0-0.013-0.00110.2950.0330.0330.0000.0000.0000.000
106A106LEU00.0090.0118.043-0.191-0.1910.0000.0000.0000.000
107A107ILE00.0080.0098.8860.1880.1880.0000.0000.0000.000
108A108VAL00.001-0.0039.389-0.190-0.1900.0000.0000.0000.000
109A109TYR00.004-0.0029.3220.0540.0540.0000.0000.0000.000
110A110ILE0-0.023-0.01913.801-0.003-0.0030.0000.0000.0000.000
111A111GLU-1-0.838-0.89714.254-0.190-0.1900.0000.0000.0000.000
112A112GLU-1-0.779-0.89317.622-0.086-0.0860.0000.0000.0000.000
113A113GLY00.005-0.00320.6860.0000.0000.0000.0000.0000.000
114A114GLU-1-0.894-0.92522.243-0.078-0.0780.0000.0000.0000.000
115A115LYS10.7770.86321.0110.1030.1030.0000.0000.0000.000
116A116GLN00.0560.03716.363-0.010-0.0100.0000.0000.0000.000
117A117ILE0-0.016-0.00913.4860.0100.0100.0000.0000.0000.000
118A118ASN0-0.020-0.01912.232-0.041-0.0410.0000.0000.0000.000
119A119GLN0-0.029-0.0225.9960.1050.1050.0000.0000.0000.000
120A120GLU-1-0.785-0.8839.165-0.190-0.1900.0000.0000.0000.000
121A121TYR00.0270.01110.1880.0200.0200.0000.0000.0000.000
122A122LEU0-0.0020.00710.2400.0070.0070.0000.0000.0000.000
123A123ILE0-0.022-0.0215.309-0.046-0.0460.0000.0000.0000.000
124A124SER0-0.069-0.0468.8080.0590.0590.0000.0000.0000.000
125A125GLN00.0250.03212.2120.0370.0370.0000.0000.0000.000
126A126VAL0-0.054-0.0279.9510.0090.0090.0000.0000.0000.000
127A127GLU-1-0.893-0.93711.7350.0780.0780.0000.0000.0000.000
128A128GLY0-0.006-0.02411.326-0.019-0.0190.0000.0000.0000.000
129A129HIS00.0200.0337.131-0.090-0.0900.0000.0000.0000.000
130A130GLN00.0280.0152.042-6.947-7.6566.967-3.237-3.020-0.035
131A131VAL0-0.012-0.0123.3741.4672.5700.042-0.337-0.8080.000
132A132SER00.0260.0092.018-8.464-9.47310.639-4.888-4.742-0.029
133A133LEU00.0570.0192.9762.2650.3360.1582.279-0.5070.000
134A134LYS10.9220.9615.267-0.613-0.6130.0000.0000.0000.000
135A135ASN0-0.017-0.0146.775-0.035-0.0350.0000.0000.0000.000
136A136LEU00.0360.0228.539-0.002-0.0020.0000.0000.0000.000
137A137PRO00.010-0.01410.3090.0220.0220.0000.0000.0000.000
138A138GLU-1-0.883-0.92011.4560.2060.2060.0000.0000.0000.000
139A139ILE0-0.039-0.02710.1360.0030.0030.0000.0000.0000.000
140A140MET0-0.0390.01614.180-0.014-0.0140.0000.0000.0000.000
141A141ASN00.0640.03016.1020.0330.0330.0000.0000.0000.000
142A142ILE00.0770.02319.666-0.006-0.0060.0000.0000.0000.000
143A143THR0-0.001-0.00521.8710.0020.0020.0000.0000.0000.000
144A144GLU-1-0.815-0.89921.903-0.053-0.0530.0000.0000.0000.000
145A145VAL00.0220.01319.650-0.003-0.0030.0000.0000.0000.000
146A146LYS10.8270.90722.7380.0140.0140.0000.0000.0000.000
147A147LYS10.7960.89126.2920.0490.0490.0000.0000.0000.000
148A148ILE0-0.064-0.03523.0720.0020.0020.0000.0000.0000.000
149A149TYR00.010-0.01721.059-0.001-0.0010.0000.0000.0000.000
150A150LYS10.8380.93026.5940.0490.0490.0000.0000.0000.000
151A151LEU00.0410.04124.7800.0020.0020.0000.0000.0000.000
152A152SER00.0270.01629.3530.0010.0010.0000.0000.0000.000
153A153SER00.004-0.00729.779-0.001-0.0010.0000.0000.0000.000
154A154GLN0-0.032-0.02130.4460.0000.0000.0000.0000.0000.000
155A155GLU-1-0.834-0.91426.016-0.010-0.0100.0000.0000.0000.000
156A156GLU-1-0.798-0.86926.6850.0040.0040.0000.0000.0000.000
157A157SER0-0.026-0.01823.7450.0030.0030.0000.0000.0000.000
158A158ILE00.008-0.00917.538-0.005-0.0050.0000.0000.0000.000
159A159GLY00.0120.01920.955-0.009-0.0090.0000.0000.0000.000
160A160THR00.0590.00721.871-0.007-0.0070.0000.0000.0000.000
161A161LEU0-0.030-0.01322.794-0.006-0.0060.0000.0000.0000.000
162A162LEU0-0.0070.00218.153-0.011-0.0110.0000.0000.0000.000
163A163ASP-1-0.852-0.92321.741-0.027-0.0270.0000.0000.0000.000
164A164ALA0-0.012-0.00424.758-0.004-0.0040.0000.0000.0000.000
165A165ILE0-0.039-0.02520.966-0.003-0.0030.0000.0000.0000.000
166A166ILE00.0450.01520.610-0.007-0.0070.0000.0000.0000.000
167A167CYS0-0.0150.00224.4640.0000.0000.0000.0000.0000.000
168A168ARG10.8100.90626.6480.0410.0410.0000.0000.0000.000
169A169MET0-0.055-0.01820.5770.0000.0000.0000.0000.0000.000
170A170SER0-0.050-0.03626.189-0.002-0.0020.0000.0000.0000.000
171A171THR0-0.054-0.04728.5260.0020.0020.0000.0000.0000.000
172A172LYS10.8130.92926.7900.0860.0860.0000.0000.0000.000
173A173ASP-1-0.874-0.92630.820-0.062-0.0620.0000.0000.0000.000
174A174VAL00.0180.02332.650-0.002-0.0020.0000.0000.0000.000
175A175LEU00.0020.01034.4340.0010.0010.0000.0000.0000.000