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: M365Z

Calculation Name: 3KBG-A-Xray320

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3KBG

Chain ID: A

ChEMBL ID:

UniProt ID: Q56230

Base Structure: X-ray

Registration Date: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 196
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2072553.260749
FMO2-HF: Nuclear repulsion 1997452.291543
FMO2-HF: Total energy -75100.969206
FMO2-MP2: Total energy -75320.636891


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:33:ACE )


Summations of interaction energy for fragment #1(A:33:ACE )
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.
-1.024-0.222-0.005-0.337-0.460
Interaction energy analysis for fragmet #1(A:33:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.011 / 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].
3A35ASP -1-0.864-0.9143.840-0.0040.773-0.005-0.324-0.4480.000
4A36GLN 0-0.0310.0045.1550.3300.3300.0000.0000.0000.000
5A37SER 0-0.037-0.0108.6940.1380.1380.0000.0000.0000.000
6A38VAL 00.0460.03111.260-0.078-0.0780.0000.0000.0000.000
7A39THR 0-0.019-0.00713.6560.0740.0740.0000.0000.0000.000
8A40LEU 00.0840.04317.289-0.018-0.0180.0000.0000.0000.000
9A41LEU 0-0.009-0.01219.7740.0010.0010.0000.0000.0000.000
10A42SER 0-0.081-0.04715.820-0.014-0.0140.0000.0000.0000.000
11A43ILE 00.1110.06614.535-0.003-0.0030.0000.0000.0000.000
12A44ILE 00.0090.00317.3690.0170.0170.0000.0000.0000.000
13A45ARG 10.9350.96820.1830.2210.2210.0000.0000.0000.000
14A46ASP -1-0.914-0.95515.100-0.398-0.3980.0000.0000.0000.000
15A47TYR 00.004-0.00118.5790.0180.0180.0000.0000.0000.000
16A48LEU 00.0170.00020.5310.0150.0150.0000.0000.0000.000
17A49LYS 10.9120.94619.5240.2530.2530.0000.0000.0000.000
18A50LEU 0-0.0380.00519.5060.0100.0100.0000.0000.0000.000
19A51SER 0-0.058-0.01923.3830.0160.0160.0000.0000.0000.000
20A52ASP -1-0.801-0.89226.007-0.112-0.1120.0000.0000.0000.000
21A53LYS 10.9470.97326.8070.1020.1020.0000.0000.0000.000
22A54GLU -1-0.833-0.91723.653-0.160-0.1600.0000.0000.0000.000
23A55ARG 10.7160.83625.4690.1280.1280.0000.0000.0000.000
24A56GLU -1-0.846-0.90828.426-0.089-0.0890.0000.0000.0000.000
25A57ALA 00.0140.01624.2080.0040.0040.0000.0000.0000.000
26A58ALA 0-0.007-0.01226.3310.0030.0030.0000.0000.0000.000
27A59ARG 10.9180.94127.6860.0920.0920.0000.0000.0000.000
28A60ILE 00.0240.00228.2310.0070.0070.0000.0000.0000.000
29A61LEU 00.0110.00424.6360.0050.0050.0000.0000.0000.000
30A62ALA 0-0.023-0.01028.2300.0080.0080.0000.0000.0000.000
31A63ASN 0-0.0020.01131.2950.0090.0090.0000.0000.0000.000
32A64GLY 0-0.0050.00631.6940.0040.0040.0000.0000.0000.000
33A65LEU 0-0.050-0.01630.9730.0040.0040.0000.0000.0000.000
34A66VAL 00.0100.01224.611-0.003-0.0030.0000.0000.0000.000
35A67LYS 10.8800.95526.8810.0670.0670.0000.0000.0000.000
36A68VAL 00.0400.01621.513-0.010-0.0100.0000.0000.0000.000
37A69ASP -1-0.779-0.86922.606-0.059-0.0590.0000.0000.0000.000
38A70GLY 00.0290.01625.1700.0070.0070.0000.0000.0000.000
39A71LYS 10.9500.98627.6230.0670.0670.0000.0000.0000.000
40A72THR 00.007-0.00427.841-0.007-0.0070.0000.0000.0000.000
41A73VAL 0-0.040-0.02124.4290.0040.0040.0000.0000.0000.000
42A74ARG 10.9080.93127.4390.0720.0720.0000.0000.0000.000
43A75GLU -1-0.877-0.92424.105-0.117-0.1170.0000.0000.0000.000
44A76LYS 10.9910.98022.6610.1520.1520.0000.0000.0000.000
45A77LYS 10.8920.92120.5360.1120.1120.0000.0000.0000.000
46A78PHE 00.0120.02319.894-0.005-0.0050.0000.0000.0000.000
47A79ALA 00.0140.01315.785-0.018-0.0180.0000.0000.0000.000
48A80VAL 0-0.013-0.00315.9510.0290.0290.0000.0000.0000.000
49A81GLY 00.0640.00513.404-0.057-0.0570.0000.0000.0000.000
50A82PHE 00.0300.01811.9760.0190.0190.0000.0000.0000.000
51A83MET 0-0.039-0.00513.9560.0300.0300.0000.0000.0000.000
52A84ASP -1-0.808-0.88417.271-0.101-0.1010.0000.0000.0000.000
53A85VAL 0-0.004-0.00719.325-0.011-0.0110.0000.0000.0000.000
54A86ILE 00.0060.00119.116-0.001-0.0010.0000.0000.0000.000
55A87GLU -1-0.921-0.97522.950-0.061-0.0610.0000.0000.0000.000
56A88ILE 00.0220.00323.160-0.005-0.0050.0000.0000.0000.000
57A89ASN 0-0.026-0.02727.501-0.001-0.0010.0000.0000.0000.000
58A90GLY 00.0340.03031.0040.0040.0040.0000.0000.0000.000
59A91GLU -1-0.854-0.92328.379-0.061-0.0610.0000.0000.0000.000
60A92SER 0-0.007-0.00726.163-0.003-0.0030.0000.0000.0000.000
61A93TYR 00.0080.00821.2630.0020.0020.0000.0000.0000.000
62A94ARG 10.7770.88618.2020.0670.0670.0000.0000.0000.000
63A95VAL 0-0.0160.00513.934-0.020-0.0200.0000.0000.0000.000
64A96VAL 00.006-0.01814.1010.0380.0380.0000.0000.0000.000
65A97TYR 0-0.034-0.0537.370-0.006-0.0060.0000.0000.0000.000
66A98ASN 00.0520.0319.890-0.006-0.0060.0000.0000.0000.000
67A99ASP -1-0.782-0.9049.768-0.126-0.1260.0000.0000.0000.000
68A100GLN 0-0.083-0.0378.2810.0170.0170.0000.0000.0000.000
69A101GLY 00.0310.0125.273-0.471-0.4710.0000.0000.0000.000
70A102ALA 0-0.065-0.0376.073-0.358-0.3580.0000.0000.0000.000
71A103LEU 0-0.0050.0078.2340.2350.2350.0000.0000.0000.000
72A104VAL 00.0110.00411.019-0.014-0.0140.0000.0000.0000.000
73A105LEU 0-0.020-0.00514.3470.0390.0390.0000.0000.0000.000
74A106MET 0-0.0030.01117.8760.0000.0000.0000.0000.0000.000
75A107LYS 10.8470.92519.7710.0830.0830.0000.0000.0000.000
76A108GLU -1-0.795-0.90023.066-0.050-0.0500.0000.0000.0000.000
77A109THR 0-0.024-0.01824.7940.0030.0030.0000.0000.0000.000
78A110LYS 10.9180.93727.9670.0570.0570.0000.0000.0000.000
79A111GLU -1-0.911-0.94030.421-0.019-0.0190.0000.0000.0000.000
80A112ARG 10.9940.98625.3710.0290.0290.0000.0000.0000.000
81A113ALA 0-0.039-0.01625.7270.0000.0000.0000.0000.0000.000
82A114SER 0-0.0320.00226.814-0.001-0.0010.0000.0000.0000.000
83A115MET 00.0160.02424.2300.0060.0060.0000.0000.0000.000
84A116LYS 10.7740.86619.5080.0520.0520.0000.0000.0000.000
85A117LEU 0-0.0380.01019.8010.0090.0090.0000.0000.0000.000
86A118LEU 00.000-0.00519.517-0.007-0.0070.0000.0000.0000.000
87A119LYS 10.8920.96413.341-0.209-0.2090.0000.0000.0000.000
88A120VAL 00.0040.00218.587-0.006-0.0060.0000.0000.0000.000
89A121ARG 10.9700.98014.372-0.020-0.0200.0000.0000.0000.000
90A122SER 0-0.038-0.01417.7970.0130.0130.0000.0000.0000.000
91A123LYS 10.9000.92420.594-0.087-0.0870.0000.0000.0000.000
92A124VAL 00.0290.03324.2880.0060.0060.0000.0000.0000.000
93A125ILE 0-0.035-0.02227.088-0.004-0.0040.0000.0000.0000.000
94A126ALA 00.0280.02430.1470.0010.0010.0000.0000.0000.000
95A127PRO 00.025-0.00833.4490.0010.0010.0000.0000.0000.000
96A128GLY 00.0310.01436.965-0.002-0.0020.0000.0000.0000.000
97A129ASN 0-0.038-0.01434.5040.0020.0020.0000.0000.0000.000
98A130ARG 11.0421.03933.399-0.022-0.0220.0000.0000.0000.000
99A131ILE 0-0.023-0.01628.2400.0040.0040.0000.0000.0000.000
100A132GLN 0-0.0140.00227.358-0.004-0.0040.0000.0000.0000.000
101A133LEU 0-0.001-0.01024.5570.0090.0090.0000.0000.0000.000
102A134GLY 00.0510.02621.840-0.009-0.0090.0000.0000.0000.000
103A135THR 00.018-0.02319.9410.0160.0160.0000.0000.0000.000
104A136HIS 0-0.071-0.04814.4660.0190.0190.0000.0000.0000.000
105A137ASP -1-0.744-0.86815.806-0.037-0.0370.0000.0000.0000.000
106A138GLY 0-0.053-0.02318.119-0.012-0.0120.0000.0000.0000.000
107A139ARG 10.8520.92820.1230.0380.0380.0000.0000.0000.000
108A140THR 0-0.023-0.01722.9140.0120.0120.0000.0000.0000.000
109A141PHE 00.0050.00924.610-0.004-0.0040.0000.0000.0000.000
110A142ILE 0-0.024-0.01528.1910.0050.0050.0000.0000.0000.000
111A143THR 0-0.0040.00729.413-0.003-0.0030.0000.0000.0000.000
112A144ASP -1-0.840-0.92532.0410.0280.0280.0000.0000.0000.000
113A145ASP -1-0.807-0.88031.5140.0460.0460.0000.0000.0000.000
114A146LYS 10.9340.95730.839-0.039-0.0390.0000.0000.0000.000
115A147SER 0-0.121-0.09330.2890.0080.0080.0000.0000.0000.000
116A148ILE 00.0300.02225.3980.0080.0080.0000.0000.0000.000
117A149LYS 10.8710.94423.793-0.076-0.0760.0000.0000.0000.000
118A150VAL 00.0220.01018.294-0.005-0.0050.0000.0000.0000.000
119A151GLY 0-0.030-0.02217.9840.0150.0150.0000.0000.0000.000
120A152ASP -1-0.752-0.84519.0050.0810.0810.0000.0000.0000.000
121A153VAL 0-0.025-0.01719.1080.0020.0020.0000.0000.0000.000
122A154LEU 0-0.0110.01021.825-0.002-0.0020.0000.0000.0000.000
123A155ALA 00.0270.02023.494-0.005-0.0050.0000.0000.0000.000
124A156VAL 0-0.001-0.01224.5450.0010.0010.0000.0000.0000.000
125A157SER 00.0190.01926.901-0.006-0.0060.0000.0000.0000.000
126A158VAL 0-0.020-0.02725.561-0.001-0.0010.0000.0000.0000.000
127A159PRO 0-0.039-0.02828.311-0.002-0.0020.0000.0000.0000.000
128A160ASP -1-0.845-0.92331.622-0.013-0.0130.0000.0000.0000.000
129A161MET 0-0.063-0.02526.6550.0030.0030.0000.0000.0000.000
130A162LYS 10.9410.99029.7680.0050.0050.0000.0000.0000.000
131A163ILE 0-0.008-0.01627.888-0.001-0.0010.0000.0000.0000.000
132A164SER 0-0.061-0.02529.3930.0000.0000.0000.0000.0000.000
133A165GLU -1-0.844-0.92828.1620.0240.0240.0000.0000.0000.000
134A166ILE 00.0160.00525.8960.0010.0010.0000.0000.0000.000
135A167ILE 0-0.057-0.03422.7160.0010.0010.0000.0000.0000.000
136A168LYS 10.8500.91723.404-0.065-0.0650.0000.0000.0000.000
137A169MET 00.014-0.00916.6600.0050.0050.0000.0000.0000.000
138A170GLN 0-0.038-0.01622.1690.0070.0070.0000.0000.0000.000
139A171PRO 00.016-0.01824.1460.0000.0000.0000.0000.0000.000
140A172GLY 00.0020.01025.333-0.007-0.0070.0000.0000.0000.000
141A173ASN 0-0.052-0.02223.854-0.013-0.0130.0000.0000.0000.000
142A174LYS 10.9700.99120.776-0.030-0.0300.0000.0000.0000.000
143A175ALA 0-0.022-0.02016.734-0.003-0.0030.0000.0000.0000.000
144A176TYR 00.009-0.01611.996-0.005-0.0050.0000.0000.0000.000
145A177ILE 0-0.0140.0069.4540.0260.0260.0000.0000.0000.000
146A178THR 00.017-0.0019.038-0.039-0.0390.0000.0000.0000.000
147A179ALA 0-0.011-0.0074.561-0.057-0.0630.000-0.0060.0120.000
148A180GLY 00.0090.0044.151-0.071-0.0400.000-0.007-0.0240.000
149A181SER 00.012-0.0115.732-0.290-0.2900.0000.0000.0000.000
150A182HIS 10.8750.9288.374-0.426-0.4260.0000.0000.0000.000
151A183VAL 0-0.0050.0126.608-0.052-0.0520.0000.0000.0000.000
152A184ASN 0-0.0070.0019.001-0.054-0.0540.0000.0000.0000.000
153A185GLN 00.0690.07812.1190.0040.0040.0000.0000.0000.000
154A186THR 0-0.039-0.04314.5320.0070.0070.0000.0000.0000.000
155A187GLY 00.0260.02117.2420.0040.0040.0000.0000.0000.000
156A188THR 0-0.033-0.01819.520-0.004-0.0040.0000.0000.0000.000
157A189ILE 0-0.042-0.00219.6070.0090.0090.0000.0000.0000.000
158A190SER 0-0.001-0.01522.027-0.010-0.0100.0000.0000.0000.000
159A191LYS 10.9390.97222.771-0.145-0.1450.0000.0000.0000.000
160A192ILE 00.0030.00420.6180.0160.0160.0000.0000.0000.000
161A193GLU -1-0.883-0.93521.1750.1650.1650.0000.0000.0000.000
162A194ALA 0-0.027-0.02420.9450.0200.0200.0000.0000.0000.000
163A195LYS 10.9240.96922.168-0.151-0.1510.0000.0000.0000.000
164A196GLU -1-0.916-0.95422.8380.1240.1240.0000.0000.0000.000
165A197GLY 00.0190.00422.510-0.002-0.0020.0000.0000.0000.000
166A198SER 00.0110.00318.4770.0100.0100.0000.0000.0000.000
167A199SER 0-0.023-0.03618.6450.0240.0240.0000.0000.0000.000
168A200ALA 00.0910.06916.920-0.023-0.0230.0000.0000.0000.000
169A201ASN 0-0.086-0.05316.4230.0080.0080.0000.0000.0000.000
170A202LEU 00.0060.00715.4010.0350.0350.0000.0000.0000.000
171A203VAL 0-0.018-0.00516.391-0.038-0.0380.0000.0000.0000.000
172A204HIS 0-0.026-0.02517.1600.0210.0210.0000.0000.0000.000
173A205PHE 00.012-0.00215.590-0.016-0.0160.0000.0000.0000.000
174A206GLN 00.015-0.00920.470-0.003-0.0030.0000.0000.0000.000
175A207GLU -1-0.838-0.91719.9680.0880.0880.0000.0000.0000.000
176A208GLY 0-0.0090.01321.2190.0000.0000.0000.0000.0000.000
177A209PHE 0-0.034-0.02014.1340.0200.0200.0000.0000.0000.000
178A210SER 00.0120.00116.187-0.006-0.0060.0000.0000.0000.000
179A211THR 0-0.001-0.00211.2950.0350.0350.0000.0000.0000.000
180A212ILE 00.0310.0249.488-0.054-0.0540.0000.0000.0000.000
181A213LYS 11.0210.99712.639-0.186-0.1860.0000.0000.0000.000
182A214ASP -1-0.917-0.95110.3500.4210.4210.0000.0000.0000.000
183A215HIS 0-0.024-0.0156.917-0.130-0.1300.0000.0000.0000.000
184A216VAL 0-0.0040.01910.271-0.068-0.0680.0000.0000.0000.000
185A217PHE 0-0.020-0.01313.640-0.016-0.0160.0000.0000.0000.000
186A218MET 0-0.0050.00515.383-0.006-0.0060.0000.0000.0000.000
187A219ILE 00.009-0.01218.041-0.015-0.0150.0000.0000.0000.000
188A220GLY 0-0.0080.00120.841-0.012-0.0120.0000.0000.0000.000
189A221SER 0-0.034-0.01724.2440.0100.0100.0000.0000.0000.000
190A222SER 00.0390.00127.205-0.003-0.0030.0000.0000.0000.000
191A223LYS 10.8740.95929.028-0.040-0.0400.0000.0000.0000.000
192A224PHE 00.0510.02425.287-0.003-0.0030.0000.0000.0000.000
193A225SER 0-0.027-0.02025.6780.0090.0090.0000.0000.0000.000
194A226PHE 00.0080.00420.581-0.004-0.0040.0000.0000.0000.000
195A227VAL 0-0.046-0.01622.245-0.007-0.0070.0000.0000.0000.000
196A228NME 00.0350.01925.063-0.003-0.0030.0000.0000.0000.000