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: Q178Y

Calculation Name: 3KG4-A-Xray317

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3KG4

Chain ID: A

ChEMBL ID:

UniProt ID: Q65TW5

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 192
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2153683.84941
FMO2-HF: Nuclear repulsion 2077294.909887
FMO2-HF: Total energy -76388.939522
FMO2-MP2: Total energy -76611.129034


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:ACE )


Summations of interaction energy for fragment #1(A:-1: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.
1.5812.495-0.005-0.346-0.5610
Interaction energy analysis for fragmet #1(A:-1:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.032 / q_NPA : 0.006
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].
3A1LEU 00.0470.0133.8490.8931.612-0.005-0.320-0.3940.000
4A2ALA 00.0260.0257.1700.2920.2920.0000.0000.0000.000
5A3ASN 0-0.059-0.0334.5490.2960.4150.000-0.009-0.1100.000
6A4ARG 11.0171.0004.9820.4380.4880.000-0.005-0.0440.000
7A5ILE 0-0.087-0.0257.374-0.109-0.1090.0000.0000.0000.000
8A6ARG 10.9250.94910.8430.0910.0910.0000.0000.0000.000
9A7LEU 0-0.0270.00313.392-0.031-0.0310.0000.0000.0000.000
10A8HIS 00.0620.03616.8060.0270.0270.0000.0000.0000.000
11A9ILE 00.003-0.01319.731-0.003-0.0030.0000.0000.0000.000
12A10TRP 00.000-0.01422.1410.0020.0020.0000.0000.0000.000
13A11GLY 00.0230.00725.551-0.001-0.0010.0000.0000.0000.000
14A12ASP -1-0.871-0.92028.8690.0350.0350.0000.0000.0000.000
15A13TYR 0-0.050-0.01431.487-0.001-0.0010.0000.0000.0000.000
16A14ALA 0-0.0090.00027.2610.0030.0030.0000.0000.0000.000
17A15CYS 0-0.015-0.01528.991-0.003-0.0030.0000.0000.0000.000
18A16PHE 00.0320.02924.1140.0040.0040.0000.0000.0000.000
19A17THR 0-0.026-0.01827.278-0.002-0.0020.0000.0000.0000.000
20A18ARG 10.9040.94428.703-0.089-0.0890.0000.0000.0000.000
21A19PRO 0-0.0060.00728.128-0.007-0.0070.0000.0000.0000.000
22A20GLU -1-0.795-0.90630.8900.0900.0900.0000.0000.0000.000
23A21MET 0-0.0240.00033.527-0.005-0.0050.0000.0000.0000.000
24A22LYS 10.9060.95334.103-0.079-0.0790.0000.0000.0000.000
25A23VAL 0-0.0090.01237.931-0.002-0.0020.0000.0000.0000.000
26A24GLU -1-0.978-0.99238.7440.0480.0480.0000.0000.0000.000
27A25ARG 10.9140.96033.544-0.064-0.0640.0000.0000.0000.000
28A26VAL 00.0850.02832.956-0.004-0.0040.0000.0000.0000.000
29A27SER 0-0.016-0.01828.5910.0060.0060.0000.0000.0000.000
30A28TYR 00.005-0.01125.7430.0010.0010.0000.0000.0000.000
31A29ASP -1-0.816-0.90326.2110.0840.0840.0000.0000.0000.000
32A30VAL 00.0060.00521.516-0.005-0.0050.0000.0000.0000.000
33A31ILE 0-0.045-0.01219.3760.0010.0010.0000.0000.0000.000
34A32THR 00.0280.01920.3730.0130.0130.0000.0000.0000.000
35A33PRO 00.0330.00715.608-0.006-0.0060.0000.0000.0000.000
36A34SER 0-0.0160.00917.239-0.008-0.0080.0000.0000.0000.000
37A35ALA 0-0.008-0.01219.555-0.009-0.0090.0000.0000.0000.000
38A36ALA 00.0120.00716.482-0.014-0.0140.0000.0000.0000.000
39A37ARG 10.9050.94414.957-0.260-0.2600.0000.0000.0000.000
40A38GLY 00.0140.01716.735-0.015-0.0150.0000.0000.0000.000
41A39ILE 0-0.022-0.01319.355-0.018-0.0180.0000.0000.0000.000
42A40LEU 0-0.033-0.02013.105-0.015-0.0150.0000.0000.0000.000
43A41SER 0-0.022-0.03217.219-0.015-0.0150.0000.0000.0000.000
44A42ALA 0-0.0080.01418.720-0.015-0.0150.0000.0000.0000.000
45A43ILE 0-0.0090.00918.969-0.016-0.0160.0000.0000.0000.000
46A44HIS 0-0.055-0.05615.885-0.020-0.0200.0000.0000.0000.000
47A45TRP 00.0690.04916.6800.0050.0050.0000.0000.0000.000
48A46LYS 10.9310.95217.834-0.064-0.0640.0000.0000.0000.000
49A47PRO 00.0500.03717.7770.0170.0170.0000.0000.0000.000
50A48ALA 00.0580.03316.7200.0150.0150.0000.0000.0000.000
51A49ILE 0-0.043-0.01112.7830.0150.0150.0000.0000.0000.000
52A50ASN 00.0250.00812.563-0.043-0.0430.0000.0000.0000.000
53A51TRP 0-0.035-0.02610.4250.0580.0580.0000.0000.0000.000
54A52VAL 0-0.010-0.0198.220-0.028-0.0280.0000.0000.0000.000
55A53ILE 0-0.017-0.0149.2710.0620.0620.0000.0000.0000.000
56A54ASP -1-0.793-0.8726.7561.6131.6130.0000.0000.0000.000
57A55LYS 10.9220.9648.818-0.305-0.3050.0000.0000.0000.000
58A56ILE 0-0.020-0.00611.873-0.026-0.0260.0000.0000.0000.000
59A57TYR 0-0.050-0.03311.748-0.021-0.0210.0000.0000.0000.000
60A58VAL 00.019-0.00717.391-0.007-0.0070.0000.0000.0000.000
61A59LEU 00.0110.01120.139-0.008-0.0080.0000.0000.0000.000
62A60LYS 10.9320.97723.307-0.047-0.0470.0000.0000.0000.000
63A61PRO 00.0050.00626.6940.0060.0060.0000.0000.0000.000
64A62ILE 0-0.037-0.00825.5170.0010.0010.0000.0000.0000.000
65A63ARG 10.8840.94329.317-0.046-0.0460.0000.0000.0000.000
66A64PHE 00.007-0.00230.3560.0010.0010.0000.0000.0000.000
67A65GLU -1-0.834-0.92134.5630.0330.0330.0000.0000.0000.000
68A66SER 0-0.0150.00237.0820.0020.0020.0000.0000.0000.000
69A67VAL 00.0420.02437.248-0.003-0.0030.0000.0000.0000.000
70A68ARG 10.9060.93140.251-0.029-0.0290.0000.0000.0000.000
71A69ARG 10.9460.96537.803-0.052-0.0520.0000.0000.0000.000
72A70ASN 0-0.003-0.00140.783-0.003-0.0030.0000.0000.0000.000
73A71NME 00.0420.03241.1230.0020.0020.0000.0000.0000.000
74A103ACE 00.0580.02547.5360.0000.0000.0000.0000.0000.000
75A104ARG 10.8760.92141.799-0.039-0.0390.0000.0000.0000.000
76A105ALA 00.0510.04341.538-0.001-0.0010.0000.0000.0000.000
77A106ALA 0-0.016-0.00236.0350.0020.0020.0000.0000.0000.000
78A107THR 00.0130.02035.120-0.004-0.0040.0000.0000.0000.000
79A108VAL 0-0.047-0.02532.7410.0060.0060.0000.0000.0000.000
80A109LEU 00.0160.01027.042-0.003-0.0030.0000.0000.0000.000
81A110LYS 10.8440.91431.220-0.039-0.0390.0000.0000.0000.000
82A111ASP -1-0.912-0.97630.9780.0380.0380.0000.0000.0000.000
83A112VAL 0-0.0180.00725.7270.0020.0020.0000.0000.0000.000
84A113ALA 0-0.006-0.04024.047-0.006-0.0060.0000.0000.0000.000
85A114TYR 00.008-0.00619.2730.0060.0060.0000.0000.0000.000
86A115VAL 00.0200.02614.699-0.013-0.0130.0000.0000.0000.000
87A116ILE 0-0.0170.00313.6150.0280.0280.0000.0000.0000.000
88A117GLU -1-0.790-0.8928.4990.1530.1530.0000.0000.0000.000
89A118ALA 00.0340.0309.0900.0880.0880.0000.0000.0000.000
90A119HIS 10.8230.8985.204-1.807-1.7810.000-0.012-0.0130.000
91A120ALA 00.0020.0057.056-0.010-0.0100.0000.0000.0000.000
92A121VAL 0-0.0090.0027.2200.1020.1020.0000.0000.0000.000
93A122MET 00.0120.0099.253-0.080-0.0800.0000.0000.0000.000
94A123THR 0-0.029-0.02212.3050.0290.0290.0000.0000.0000.000
95A124SER 00.035-0.00215.387-0.019-0.0190.0000.0000.0000.000
96A125LYS 10.8690.94418.235-0.152-0.1520.0000.0000.0000.000
97A126ALA 0-0.037-0.00316.189-0.009-0.0090.0000.0000.0000.000
98A127GLY 00.0200.00318.189-0.005-0.0050.0000.0000.0000.000
99A128VAL 00.0050.00217.9500.0000.0000.0000.0000.0000.000
100A129ASP -1-0.864-0.92417.516-0.034-0.0340.0000.0000.0000.000
101A130GLU -1-0.916-0.92915.653-0.001-0.0010.0000.0000.0000.000
102A131ASN 00.039-0.00411.4940.0430.0430.0000.0000.0000.000
103A132THR 00.045-0.0047.888-0.007-0.0070.0000.0000.0000.000
104A133THR 00.0100.02510.8560.0160.0160.0000.0000.0000.000
105A134LYS 10.9220.94512.4700.0290.0290.0000.0000.0000.000
106A135HIS 0-0.034-0.01713.0690.0140.0140.0000.0000.0000.000
107A136ILE 00.0130.0179.0370.0280.0280.0000.0000.0000.000
108A137GLU -1-0.848-0.92412.608-0.096-0.0960.0000.0000.0000.000
109A138MET 0-0.068-0.03015.7200.0160.0160.0000.0000.0000.000
110A139PHE 0-0.003-0.00614.6250.0090.0090.0000.0000.0000.000
111A140LYS 11.0061.00112.3870.1650.1650.0000.0000.0000.000
112A141ARG 10.9130.96417.0980.0630.0630.0000.0000.0000.000
113A142ARG 10.8750.93320.359-0.023-0.0230.0000.0000.0000.000
114A143ALA 00.0600.02918.7960.0030.0030.0000.0000.0000.000
115A144LEU 00.0260.00920.0840.0040.0040.0000.0000.0000.000
116A145LYS 10.8360.93322.3450.0170.0170.0000.0000.0000.000
117A146GLY 00.0380.02724.3660.0020.0020.0000.0000.0000.000
118A147GLN 0-0.056-0.01224.6150.0070.0070.0000.0000.0000.000
119A148CYS 0-0.029-0.02823.6760.0050.0050.0000.0000.0000.000
120A149PHE 0-0.064-0.02623.973-0.006-0.0060.0000.0000.0000.000
121A150GLN 00.0100.00524.8290.0040.0040.0000.0000.0000.000
122A151GLN 0-0.010-0.00425.603-0.001-0.0010.0000.0000.0000.000
123A152PRO 00.0110.02322.9320.0060.0060.0000.0000.0000.000
124A153CYS 0-0.050-0.02325.006-0.007-0.0070.0000.0000.0000.000
125A154MET 00.0400.02224.2000.0150.0150.0000.0000.0000.000
126A155GLY 00.0070.00125.705-0.002-0.0020.0000.0000.0000.000
127A156VAL 0-0.052-0.01926.8170.0000.0000.0000.0000.0000.000
128A157ARG 10.9380.96528.514-0.060-0.0600.0000.0000.0000.000
129A158GLU -1-0.918-0.96631.4200.0540.0540.0000.0000.0000.000
130A159PHE 0-0.0110.00330.349-0.004-0.0040.0000.0000.0000.000
131A160PRO 0-0.0080.00229.0540.0070.0070.0000.0000.0000.000
132A161ALA 0-0.007-0.00924.1770.0000.0000.0000.0000.0000.000
133A162HIS 00.0250.01525.982-0.003-0.0030.0000.0000.0000.000
134A163PHE 0-0.005-0.02621.3210.0100.0100.0000.0000.0000.000
135A164ALA 00.0080.01221.562-0.008-0.0080.0000.0000.0000.000
136A165LEU 0-0.044-0.02315.2950.0130.0130.0000.0000.0000.000
137A166ILE 0-0.023-0.00115.9720.0010.0010.0000.0000.0000.000
138A167ASP -1-0.896-0.97015.349-0.141-0.1410.0000.0000.0000.000
139A168ASP -1-1.024-1.02112.651-0.347-0.3470.0000.0000.0000.000
140A169ASN 0-0.028-0.01115.035-0.016-0.0160.0000.0000.0000.000
141A170ASP -1-0.871-0.91117.854-0.053-0.0530.0000.0000.0000.000
142A171PRO 0-0.048-0.02817.657-0.008-0.0080.0000.0000.0000.000
143A172LEU 0-0.029-0.02114.5040.0090.0090.0000.0000.0000.000
144A173PRO 0-0.008-0.00518.531-0.004-0.0040.0000.0000.0000.000
145A174LEU 00.0120.01620.9940.0050.0050.0000.0000.0000.000
146A175SER 00.025-0.00422.4610.0070.0070.0000.0000.0000.000
147A176GLN 0-0.090-0.05423.881-0.005-0.0050.0000.0000.0000.000
148A177LEU 0-0.0260.00123.2810.0000.0000.0000.0000.0000.000
149A178SER 00.0480.01627.155-0.005-0.0050.0000.0000.0000.000
150A179GLU -1-0.844-0.92228.2050.0370.0370.0000.0000.0000.000
151A180SER 0-0.038-0.03328.1100.0040.0040.0000.0000.0000.000
152A181GLU -1-0.944-0.96127.0700.0620.0620.0000.0000.0000.000
153A182PHE 00.0030.01321.8980.0100.0100.0000.0000.0000.000
154A183ASN 00.0020.00422.6980.0180.0180.0000.0000.0000.000
155A184ARG 10.9320.96723.627-0.087-0.0870.0000.0000.0000.000
156A185ASP -1-0.741-0.82523.6280.1330.1330.0000.0000.0000.000
157A186LEU 0-0.019-0.02621.744-0.009-0.0090.0000.0000.0000.000
158A187GLY 00.0040.01424.898-0.004-0.0040.0000.0000.0000.000
159A188TRP 0-0.037-0.03122.2470.0160.0160.0000.0000.0000.000
160A189MET 0-0.030-0.01321.906-0.013-0.0130.0000.0000.0000.000
161A190LEU 0-0.007-0.00122.2280.0130.0130.0000.0000.0000.000
162A191HIS 0-0.024-0.02514.264-0.039-0.0390.0000.0000.0000.000
163A192ASP -1-0.751-0.90517.7290.2440.2440.0000.0000.0000.000
164A193ILE 0-0.048-0.01620.124-0.010-0.0100.0000.0000.0000.000
165A194ASP -1-0.899-0.93320.5920.2190.2190.0000.0000.0000.000
166A195PHE 0-0.020-0.03823.015-0.014-0.0140.0000.0000.0000.000
167A196GLU -1-0.928-0.95823.0990.1330.1330.0000.0000.0000.000
168A197HIS 0-0.020-0.00423.578-0.012-0.0120.0000.0000.0000.000
169A198GLY 0-0.012-0.00728.297-0.004-0.0040.0000.0000.0000.000
170A199ASN 0-0.044-0.04027.9940.0080.0080.0000.0000.0000.000
171A200THR 00.0110.01325.339-0.009-0.0090.0000.0000.0000.000
172A201PRO 0-0.020-0.00824.3300.0140.0140.0000.0000.0000.000
173A202HIS 00.0620.05818.323-0.025-0.0250.0000.0000.0000.000
174A203PHE 0-0.017-0.01221.6720.0040.0040.0000.0000.0000.000
175A204PHE 00.008-0.01217.0890.0200.0200.0000.0000.0000.000
176A205ARG 10.7860.87019.960-0.152-0.1520.0000.0000.0000.000
177A206ALA 0-0.0150.00819.2780.0210.0210.0000.0000.0000.000
178A207GLU -1-0.900-0.96518.9560.1200.1200.0000.0000.0000.000
179A208LEU 0-0.058-0.01218.6420.0190.0190.0000.0000.0000.000
180A209LYS 10.9970.97717.308-0.163-0.1630.0000.0000.0000.000
181A210ASN 0-0.024-0.03018.365-0.001-0.0010.0000.0000.0000.000
182A211GLY 00.0430.02119.347-0.004-0.0040.0000.0000.0000.000
183A212VAL 0-0.046-0.02513.6640.0030.0030.0000.0000.0000.000
184A213ILE 0-0.0080.01616.201-0.001-0.0010.0000.0000.0000.000
185A214ASP -1-0.886-0.95110.8480.4000.4000.0000.0000.0000.000
186A215VAL 0-0.046-0.02311.856-0.051-0.0510.0000.0000.0000.000
187A216PRO 0-0.0150.00911.1420.1200.1200.0000.0000.0000.000
188A217PRO 00.018-0.0209.715-0.005-0.0050.0000.0000.0000.000
189A218PHE 0-0.035-0.00311.927-0.065-0.0650.0000.0000.0000.000
190A219TYR 0-0.008-0.00113.905-0.042-0.0420.0000.0000.0000.000
191A220ALA 00.0010.00515.3230.0270.0270.0000.0000.0000.000
192A221NME 00.0030.00916.0640.0020.0020.0000.0000.0000.000