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: J3N59

Calculation Name: 3KG4-A-Xray372

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: 2023-06-19

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 188
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2140446.661772
FMO2-HF: Nuclear repulsion 2064398.413037
FMO2-HF: Total energy -76048.248735
FMO2-MP2: Total energy -76269.425697


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:0:SER)


Summations of interaction energy for fragment #1(A:0: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.
-6.022-0.4550.491-2.588-3.470.013
Interaction energy analysis for fragmet #1(A:0:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.041 / q_NPA : 0.017
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].
3A2ALA00.0190.0153.020-2.3770.5960.183-1.545-1.6110.007
4A3ASN0-0.074-0.0432.822-2.1600.0960.308-0.967-1.5970.006
5A4ARG10.8570.9144.282-0.2620.0760.000-0.076-0.2620.000
6A5ILE0-0.037-0.0115.8870.6910.6910.0000.0000.0000.000
7A6ARG10.8830.9079.6700.8020.8020.0000.0000.0000.000
8A7LEU0-0.022-0.00412.3880.1020.1020.0000.0000.0000.000
9A8HIS00.0690.04616.006-0.033-0.0330.0000.0000.0000.000
10A9ILE0-0.007-0.01418.8590.0290.0290.0000.0000.0000.000
11A10TRP0-0.004-0.01521.625-0.004-0.0040.0000.0000.0000.000
12A11GLY00.0450.01225.2250.0050.0050.0000.0000.0000.000
13A12ASP-1-0.894-0.94828.562-0.125-0.1250.0000.0000.0000.000
14A13TYR0-0.056-0.04931.3530.0060.0060.0000.0000.0000.000
15A14ALA0-0.006-0.00427.634-0.009-0.0090.0000.0000.0000.000
16A15CYS0-0.021-0.02129.1690.0110.0110.0000.0000.0000.000
17A16PHE00.0580.04324.4250.0000.0000.0000.0000.0000.000
18A17THR0-0.026-0.02127.5820.0050.0050.0000.0000.0000.000
19A18ARG10.9050.94829.5370.1250.1250.0000.0000.0000.000
20A19PRO00.0030.01729.1790.0090.0090.0000.0000.0000.000
21A20GLU-1-0.783-0.89331.630-0.112-0.1120.0000.0000.0000.000
22A21MET0-0.042-0.00934.5450.0050.0050.0000.0000.0000.000
23A22LYS10.8870.92735.6610.0840.0840.0000.0000.0000.000
24A23VAL0-0.0030.00739.5200.0020.0020.0000.0000.0000.000
25A24GLU-1-0.863-0.91638.958-0.079-0.0790.0000.0000.0000.000
26A25ARG10.8140.90733.8920.1020.1020.0000.0000.0000.000
27A26VAL00.0670.02033.8840.0010.0010.0000.0000.0000.000
28A27SER0-0.016-0.01529.088-0.005-0.0050.0000.0000.0000.000
29A28TYR0-0.014-0.01326.6300.0030.0030.0000.0000.0000.000
30A29ASP-1-0.816-0.90426.710-0.155-0.1550.0000.0000.0000.000
31A30VAL0-0.015-0.01222.314-0.004-0.0040.0000.0000.0000.000
32A31ILE0-0.036-0.00519.6330.0110.0110.0000.0000.0000.000
33A32THR00.0340.02020.815-0.020-0.0200.0000.0000.0000.000
34A33PRO00.0230.00616.451-0.014-0.0140.0000.0000.0000.000
35A34SER0-0.012-0.00817.935-0.014-0.0140.0000.0000.0000.000
36A35ALA0-0.019-0.00820.4560.0030.0030.0000.0000.0000.000
37A36ALA00.0120.00716.6550.0060.0060.0000.0000.0000.000
38A37ARG10.8760.91216.0450.2480.2480.0000.0000.0000.000
39A38GLY00.0250.02717.2300.0170.0170.0000.0000.0000.000
40A39ILE0-0.030-0.02619.1540.0200.0200.0000.0000.0000.000
41A40LEU0-0.007-0.00512.9300.0160.0160.0000.0000.0000.000
42A41SER0-0.019-0.03816.9270.0240.0240.0000.0000.0000.000
43A42ALA0-0.029-0.00218.6100.0290.0290.0000.0000.0000.000
44A43ILE00.0180.02018.3880.0270.0270.0000.0000.0000.000
45A44HIS0-0.017-0.02615.1630.0400.0400.0000.0000.0000.000
46A45TRP00.0600.04016.606-0.023-0.0230.0000.0000.0000.000
47A46LYS10.9220.95117.5160.0760.0760.0000.0000.0000.000
48A47PRO00.0620.03517.864-0.017-0.0170.0000.0000.0000.000
49A48ALA00.0330.02516.082-0.006-0.0060.0000.0000.0000.000
50A49ILE0-0.027-0.01312.5340.0000.0000.0000.0000.0000.000
51A50ASN00.0070.00413.3460.0300.0300.0000.0000.0000.000
52A51TRP0-0.023-0.0179.832-0.086-0.0860.0000.0000.0000.000
53A52VAL0-0.018-0.0209.6640.1050.1050.0000.0000.0000.000
54A53ILE0-0.006-0.0089.874-0.210-0.2100.0000.0000.0000.000
55A54ASP-1-0.807-0.8737.291-1.714-1.7140.0000.0000.0000.000
56A55LYS10.8030.8779.6890.8750.8750.0000.0000.0000.000
57A56ILE0-0.007-0.00312.447-0.023-0.0230.0000.0000.0000.000
58A57TYR0-0.017-0.02311.2760.0810.0810.0000.0000.0000.000
59A58VAL00.006-0.01117.3540.0200.0200.0000.0000.0000.000
60A59LEU00.0100.00819.8270.0090.0090.0000.0000.0000.000
61A60LYS10.8620.93923.1210.1850.1850.0000.0000.0000.000
62A61PRO00.0180.01426.827-0.006-0.0060.0000.0000.0000.000
63A62ILE0-0.079-0.01425.6570.0040.0040.0000.0000.0000.000
64A63ARG10.8060.88029.5340.1410.1410.0000.0000.0000.000
65A64PHE00.004-0.01230.920-0.005-0.0050.0000.0000.0000.000
66A65GLU-1-0.785-0.84934.856-0.086-0.0860.0000.0000.0000.000
67A66SER0-0.0090.00137.412-0.002-0.0020.0000.0000.0000.000
68A67VAL00.0240.01737.5720.0040.0040.0000.0000.0000.000
69A68ARG10.9300.94940.6850.0570.0570.0000.0000.0000.000
70A69ARG10.9390.97637.7000.0820.0820.0000.0000.0000.000
71A70ASN00.0820.04941.4850.0050.0050.0000.0000.0000.000
72A104ARG10.9460.97342.5990.0640.0640.0000.0000.0000.000
73A105ALA0-0.026-0.02542.2370.0000.0000.0000.0000.0000.000
74A106ALA0-0.023-0.01636.8620.0000.0000.0000.0000.0000.000
75A107THR00.0080.01036.0800.0010.0010.0000.0000.0000.000
76A108VAL0-0.054-0.03333.467-0.006-0.0060.0000.0000.0000.000
77A109LEU00.0120.00827.6240.0030.0030.0000.0000.0000.000
78A110LYS10.8180.89531.6930.1020.1020.0000.0000.0000.000
79A111ASP-1-0.827-0.90331.099-0.125-0.1250.0000.0000.0000.000
80A112VAL00.0180.03125.994-0.007-0.0070.0000.0000.0000.000
81A113ALA0-0.007-0.03123.8270.0070.0070.0000.0000.0000.000
82A114TYR00.0320.01219.5410.0080.0080.0000.0000.0000.000
83A115VAL00.0090.01014.6670.0110.0110.0000.0000.0000.000
84A116ILE0-0.0150.00913.475-0.021-0.0210.0000.0000.0000.000
85A117GLU-1-0.724-0.8278.459-1.491-1.4910.0000.0000.0000.000
86A118ALA00.0040.0169.1900.0910.0910.0000.0000.0000.000
87A119HIS10.8590.9195.1261.3091.3090.0000.0000.0000.000
88A120ALA00.0230.0186.9680.3870.3870.0000.0000.0000.000
89A121VAL0-0.020-0.0127.591-0.260-0.2600.0000.0000.0000.000
90A122MET00.0220.02510.0840.0550.0550.0000.0000.0000.000
91A123THR0-0.014-0.00912.480-0.019-0.0190.0000.0000.0000.000
92A124SER00.0290.00216.0830.0210.0210.0000.0000.0000.000
93A125LYS10.8810.94118.5580.0910.0910.0000.0000.0000.000
94A126ALA0-0.042-0.00215.545-0.004-0.0040.0000.0000.0000.000
95A127GLY00.000-0.00517.3990.0030.0030.0000.0000.0000.000
96A128VAL00.007-0.00616.6220.0050.0050.0000.0000.0000.000
97A129ASP-1-0.879-0.93215.6670.2000.2000.0000.0000.0000.000
98A130GLU-1-0.877-0.90813.6680.1240.1240.0000.0000.0000.000
99A131ASN00.026-0.0138.161-0.147-0.1470.0000.0000.0000.000
100A132THR00.023-0.0156.1220.1470.1470.0000.0000.0000.000
101A133THR00.0250.0297.251-0.119-0.1190.0000.0000.0000.000
102A134LYS10.8960.9339.243-0.244-0.2440.0000.0000.0000.000
103A135HIS0-0.038-0.02911.988-0.066-0.0660.0000.0000.0000.000
104A136ILE00.0240.0207.349-0.089-0.0890.0000.0000.0000.000
105A137GLU-1-0.795-0.89410.722-0.004-0.0040.0000.0000.0000.000
106A138MET0-0.093-0.03812.916-0.045-0.0450.0000.0000.0000.000
107A139PHE00.0060.00213.451-0.019-0.0190.0000.0000.0000.000
108A140LYS10.8610.93310.6920.0940.0940.0000.0000.0000.000
109A141ARG10.9000.93615.026-0.062-0.0620.0000.0000.0000.000
110A142ARG10.8290.92417.9760.1020.1020.0000.0000.0000.000
111A143ALA00.0710.03017.2960.0040.0040.0000.0000.0000.000
112A144LEU0-0.005-0.00316.8060.0040.0040.0000.0000.0000.000
113A145LYS10.8360.92020.4020.0780.0780.0000.0000.0000.000
114A146GLY00.0320.03022.8340.0090.0090.0000.0000.0000.000
115A147GLN0-0.0280.00223.144-0.001-0.0010.0000.0000.0000.000
116A148CYS0-0.035-0.02922.167-0.015-0.0150.0000.0000.0000.000
117A149PHE0-0.071-0.03323.2410.0210.0210.0000.0000.0000.000
118A150GLN00.000-0.00324.6640.0110.0110.0000.0000.0000.000
119A151GLN00.005-0.00425.119-0.005-0.0050.0000.0000.0000.000
120A152PRO00.0450.03922.6440.0030.0030.0000.0000.0000.000
121A153CYS0-0.029-0.01724.7820.0150.0150.0000.0000.0000.000
122A154MET00.0300.04123.630-0.020-0.0200.0000.0000.0000.000
123A155GLY00.003-0.00125.9590.0070.0070.0000.0000.0000.000
124A156VAL0-0.067-0.02627.1310.0100.0100.0000.0000.0000.000
125A157ARG10.9440.96428.5420.1130.1130.0000.0000.0000.000
126A158GLU-1-0.854-0.93731.411-0.098-0.0980.0000.0000.0000.000
127A159PHE0-0.0150.00630.5860.0040.0040.0000.0000.0000.000
128A160PRO0-0.007-0.00128.970-0.010-0.0100.0000.0000.0000.000
129A161ALA0-0.012-0.00924.037-0.002-0.0020.0000.0000.0000.000
130A162HIS00.0200.01825.5890.0030.0030.0000.0000.0000.000
131A163PHE0-0.032-0.03320.692-0.023-0.0230.0000.0000.0000.000
132A164ALA00.0170.01120.6440.0260.0260.0000.0000.0000.000
133A165LEU0-0.045-0.01713.698-0.037-0.0370.0000.0000.0000.000
134A166ILE0-0.032-0.00714.5800.0310.0310.0000.0000.0000.000
135A167ASP-1-0.786-0.90312.983-0.306-0.3060.0000.0000.0000.000
136A168ASP-1-0.874-0.9388.721-0.952-0.9520.0000.0000.0000.000
137A169ASN0-0.073-0.04011.6340.0200.0200.0000.0000.0000.000
138A170ASP-1-0.868-0.90314.920-0.205-0.2050.0000.0000.0000.000
139A171PRO0-0.042-0.02015.663-0.061-0.0610.0000.0000.0000.000
140A172LEU0-0.005-0.01613.721-0.011-0.0110.0000.0000.0000.000
141A173PRO0-0.020-0.01517.4540.0340.0340.0000.0000.0000.000
142A174LEU00.0060.01220.272-0.022-0.0220.0000.0000.0000.000
143A175SER0-0.019-0.02721.773-0.001-0.0010.0000.0000.0000.000
144A176GLN0-0.058-0.03623.5660.0110.0110.0000.0000.0000.000
145A177LEU0-0.0260.00023.4790.0110.0110.0000.0000.0000.000
146A178SER00.0080.00527.5740.0010.0010.0000.0000.0000.000
147A179GLU-1-0.829-0.92928.452-0.153-0.1530.0000.0000.0000.000
148A180SER0-0.063-0.03228.853-0.004-0.0040.0000.0000.0000.000
149A181GLU-1-0.870-0.93727.392-0.152-0.1520.0000.0000.0000.000
150A182PHE0-0.003-0.00221.812-0.015-0.0150.0000.0000.0000.000
151A183ASN0-0.009-0.00523.347-0.032-0.0320.0000.0000.0000.000
152A184ARG10.9070.94824.5820.1710.1710.0000.0000.0000.000
153A185ASP-1-0.752-0.83324.832-0.163-0.1630.0000.0000.0000.000
154A186LEU0-0.006-0.01122.6960.0080.0080.0000.0000.0000.000
155A187GLY0-0.0090.00226.4490.0070.0070.0000.0000.0000.000
156A188TRP0-0.044-0.03924.604-0.014-0.0140.0000.0000.0000.000
157A189MET0-0.020-0.00423.1240.0040.0040.0000.0000.0000.000
158A190LEU00.0050.00223.960-0.003-0.0030.0000.0000.0000.000
159A191HIS0-0.032-0.02515.996-0.007-0.0070.0000.0000.0000.000
160A192ASP-1-0.738-0.86119.034-0.275-0.2750.0000.0000.0000.000
161A193ILE0-0.018-0.01121.6580.0170.0170.0000.0000.0000.000
162A194ASP-1-0.827-0.87322.174-0.153-0.1530.0000.0000.0000.000
163A195PHE0-0.008-0.03524.4640.0090.0090.0000.0000.0000.000
164A196GLU-1-0.924-0.95824.524-0.095-0.0950.0000.0000.0000.000
165A197HIS0-0.032-0.00727.7020.0050.0050.0000.0000.0000.000
166A198GLY00.009-0.00630.5680.0050.0050.0000.0000.0000.000
167A199ASN0-0.048-0.03329.429-0.010-0.0100.0000.0000.0000.000
168A200THR0-0.0070.01426.6530.0090.0090.0000.0000.0000.000
169A201PRO0-0.035-0.02226.065-0.011-0.0110.0000.0000.0000.000
170A202HIS00.0430.04320.6200.0180.0180.0000.0000.0000.000
171A203PHE0-0.019-0.01923.734-0.015-0.0150.0000.0000.0000.000
172A204PHE00.006-0.00518.395-0.004-0.0040.0000.0000.0000.000
173A205ARG10.7970.87322.1280.1480.1480.0000.0000.0000.000
174A206ALA00.0000.01820.827-0.017-0.0170.0000.0000.0000.000
175A207GLU-1-0.770-0.88920.548-0.177-0.1770.0000.0000.0000.000
176A208LEU0-0.056-0.00820.025-0.033-0.0330.0000.0000.0000.000
177A209LYS10.8360.88618.3980.2450.2450.0000.0000.0000.000
178A210ASN00.001-0.00519.077-0.017-0.0170.0000.0000.0000.000
179A211GLY00.0500.03019.841-0.019-0.0190.0000.0000.0000.000
180A212VAL0-0.064-0.03714.094-0.031-0.0310.0000.0000.0000.000
181A213ILE00.0090.02216.8940.0390.0390.0000.0000.0000.000
182A214ASP-1-0.800-0.88212.438-0.658-0.6580.0000.0000.0000.000
183A215VAL0-0.030-0.02012.9650.0820.0820.0000.0000.0000.000
184A216PRO0-0.0020.01212.776-0.049-0.0490.0000.0000.0000.000
185A217PRO00.025-0.01112.168-0.021-0.0210.0000.0000.0000.000
186A218PHE0-0.0510.00114.2200.0260.0260.0000.0000.0000.000
187A219TYR0-0.046-0.04416.7560.0200.0200.0000.0000.0000.000
188A220ALA00.0080.01017.8340.0030.0030.0000.0000.0000.000