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

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FMODB ID: JQVZ9

Calculation Name: 3K2N-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3K2N

Chain ID: A

ChEMBL ID:

UniProt ID: Q8KG60

Base Structure: X-ray

Registration Date: 2023-09-23

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 OptHSide
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 177
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1827556.945117
FMO2-HF: Nuclear repulsion 1759133.581623
FMO2-HF: Total energy -68423.363494
FMO2-MP2: Total energy -68625.957273


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:-2:SER)


Summations of interaction energy for fragment #1(A:-2: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.
-9.531-3.5840.728-3.165-3.510.026
Interaction energy analysis for fragmet #1(A:-2:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.081 / q_NPA : 0.034
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].
3A0ALA00.0130.0152.477-8.897-3.4710.727-3.051-3.1020.026
4A1ALA00.0790.0313.751-1.189-0.7390.002-0.108-0.3440.000
5A2LEU0-0.002-0.0034.9930.2840.2840.0000.0000.0000.000
6A3LYS10.9690.9746.914-0.020-0.0200.0000.0000.0000.000
7A4LEU0-0.0060.0288.496-0.002-0.0020.0000.0000.0000.000
8A5MET00.0130.0019.564-0.029-0.0290.0000.0000.0000.000
9A6GLN0-0.014-0.01210.9610.0550.0550.0000.0000.0000.000
10A7TYR00.0010.00412.8860.0230.0230.0000.0000.0000.000
11A8ILE0-0.005-0.00213.6030.0080.0080.0000.0000.0000.000
12A9GLY00.0030.00515.4140.0080.0080.0000.0000.0000.000
13A10ASP-1-0.939-0.97517.112-0.045-0.0450.0000.0000.0000.000
14A11ALA00.021-0.00718.6370.0070.0070.0000.0000.0000.000
15A12ILE0-0.034-0.02418.7060.0050.0050.0000.0000.0000.000
16A13GLY0-0.054-0.00421.6780.0040.0040.0000.0000.0000.000
17A14THR0-0.047-0.01422.8510.0020.0020.0000.0000.0000.000
18A15ILE0-0.068-0.03422.4640.0030.0030.0000.0000.0000.000
19A16ARG10.9600.98426.0270.0230.0230.0000.0000.0000.000
20A17ASP-1-0.789-0.90629.283-0.011-0.0110.0000.0000.0000.000
21A18PRO00.014-0.00127.1640.0000.0000.0000.0000.0000.000
22A19GLN00.0060.00326.5520.0020.0020.0000.0000.0000.000
23A20GLU-1-0.927-0.97526.664-0.013-0.0130.0000.0000.0000.000
24A21LEU00.0000.02121.4540.0010.0010.0000.0000.0000.000
25A22PHE00.032-0.01121.7670.0000.0000.0000.0000.0000.000
26A23ARG10.9741.00521.8640.0020.0020.0000.0000.0000.000
27A24THR0-0.0100.00619.5070.0060.0060.0000.0000.0000.000
28A25VAL0-0.013-0.01417.1120.0050.0050.0000.0000.0000.000
29A26THR0-0.019-0.03116.7750.0070.0070.0000.0000.0000.000
30A27ASP-1-0.878-0.94217.5350.0320.0320.0000.0000.0000.000
31A28LYS10.8840.93914.054-0.011-0.0110.0000.0000.0000.000
32A29LEU0-0.0220.00012.8730.0250.0250.0000.0000.0000.000
33A30ARG10.8370.91012.742-0.021-0.0210.0000.0000.0000.000
34A31LEU0-0.061-0.02010.0900.0080.0080.0000.0000.0000.000
35A32LEU0-0.057-0.0285.4230.0450.0450.0000.0000.0000.000
36A33PHE0-0.0080.0039.2760.0170.0170.0000.0000.0000.000
37A34ALA00.0240.01712.365-0.015-0.0150.0000.0000.0000.000
38A35PHE00.010-0.00615.449-0.003-0.0030.0000.0000.0000.000
39A36ASP-1-0.815-0.88718.9160.0450.0450.0000.0000.0000.000
40A37SER0-0.029-0.00922.196-0.006-0.0060.0000.0000.0000.000
41A38ALA00.0030.00520.4110.0040.0040.0000.0000.0000.000
42A39VAL0-0.019-0.00322.450-0.003-0.0030.0000.0000.0000.000
43A40ILE0-0.0010.00721.9290.0010.0010.0000.0000.0000.000
44A41ILE0-0.0070.00324.7910.0000.0000.0000.0000.0000.000
45A42THR00.0160.00526.771-0.002-0.0020.0000.0000.0000.000
46A43ILE0-0.050-0.04228.6840.0020.0020.0000.0000.0000.000
47A44ASP-1-0.839-0.91130.998-0.001-0.0010.0000.0000.0000.000
48A45ARG10.8500.89530.723-0.008-0.0080.0000.0000.0000.000
49A46GLU-1-0.912-0.96934.7580.0060.0060.0000.0000.0000.000
50A47ARG10.8550.93338.161-0.001-0.0010.0000.0000.0000.000
51A48ARG10.7810.87136.613-0.011-0.0110.0000.0000.0000.000
52A49GLU-1-0.873-0.93836.0980.0050.0050.0000.0000.0000.000
53A50ALA0-0.030-0.01331.6940.0000.0000.0000.0000.0000.000
54A51SER00.0500.01332.0860.0010.0010.0000.0000.0000.000
55A52VAL0-0.043-0.01029.6630.0000.0000.0000.0000.0000.000
56A53PHE0-0.019-0.01025.661-0.002-0.0020.0000.0000.0000.000
57A54PHE0-0.012-0.02423.398-0.002-0.0020.0000.0000.0000.000
58A55GLU-1-0.893-0.94826.3540.0120.0120.0000.0000.0000.000
59A56MET0-0.052-0.02422.1860.0000.0000.0000.0000.0000.000
60A57LEU00.0100.00924.9760.0050.0050.0000.0000.0000.000
61A58ARG10.8700.92121.423-0.036-0.0360.0000.0000.0000.000
62A59PHE0-0.0030.00227.4420.0000.0000.0000.0000.0000.000
63A60GLU-1-0.780-0.87631.0730.0090.0090.0000.0000.0000.000
64A61LEU0-0.0380.00333.0160.0010.0010.0000.0000.0000.000
65A62PRO00.0320.00135.636-0.001-0.0010.0000.0000.0000.000
66A63GLU-1-0.884-0.94538.5690.0070.0070.0000.0000.0000.000
67A64GLN00.0760.03240.570-0.001-0.0010.0000.0000.0000.000
68A65LEU0-0.055-0.01236.6070.0000.0000.0000.0000.0000.000
69A66ARG10.8440.88835.256-0.008-0.0080.0000.0000.0000.000
70A67HIS0-0.043-0.00537.415-0.002-0.0020.0000.0000.0000.000
71A68GLN00.0130.01634.4220.0010.0010.0000.0000.0000.000
72A69THR00.0440.01234.8640.0000.0000.0000.0000.0000.000
73A70ARG10.8090.89934.990-0.011-0.0110.0000.0000.0000.000
74A71SER00.0490.02436.9070.0000.0000.0000.0000.0000.000
75A72ILE0-0.017-0.01632.6570.0010.0010.0000.0000.0000.000
76A73ALA00.0130.01436.2280.0010.0010.0000.0000.0000.000
77A74GLY0-0.035-0.01538.0200.0000.0000.0000.0000.0000.000
78A75THR0-0.070-0.03534.7350.0020.0020.0000.0000.0000.000
79A76TRP00.1000.01927.4190.0010.0010.0000.0000.0000.000
80A77LEU0-0.0100.00127.5520.0020.0020.0000.0000.0000.000
81A78GLU-1-0.716-0.81130.0620.0130.0130.0000.0000.0000.000
82A79GLY00.0100.00431.566-0.001-0.0010.0000.0000.0000.000
83A80HIS10.8250.88325.208-0.036-0.0360.0000.0000.0000.000
84A81LEU0-0.0050.01026.699-0.001-0.0010.0000.0000.0000.000
85A82ASP-1-0.829-0.90227.5840.0090.0090.0000.0000.0000.000
86A83ASP-1-0.805-0.87222.6270.0360.0360.0000.0000.0000.000
87A84ARG10.8020.89220.781-0.023-0.0230.0000.0000.0000.000
88A85THR00.0200.01117.586-0.006-0.0060.0000.0000.0000.000
89A86VAL00.001-0.00115.014-0.002-0.0020.0000.0000.0000.000
90A87THR0-0.031-0.00618.0960.0100.0100.0000.0000.0000.000
91A88VAL0-0.032-0.00817.549-0.004-0.0040.0000.0000.0000.000
92A89ALA0-0.0010.00820.8260.0030.0030.0000.0000.0000.000
93A90SER0-0.006-0.02824.435-0.005-0.0050.0000.0000.0000.000
94A91ILE0-0.049-0.04026.660-0.003-0.0030.0000.0000.0000.000
95A92ALA00.0190.01029.285-0.002-0.0020.0000.0000.0000.000
96A93ARG10.8720.93829.475-0.047-0.0470.0000.0000.0000.000
97A94ASP-1-0.798-0.89625.9000.0670.0670.0000.0000.0000.000
98A95ILE0-0.061-0.02228.048-0.001-0.0010.0000.0000.0000.000
99A96PRO00.003-0.01031.311-0.002-0.0020.0000.0000.0000.000
100A97SER0-0.021-0.01734.462-0.001-0.0010.0000.0000.0000.000
101A98PHE0-0.055-0.00933.699-0.002-0.0020.0000.0000.0000.000
102A99GLY00.1120.04435.7340.0000.0000.0000.0000.0000.000
103A100ALA0-0.069-0.03538.7280.0000.0000.0000.0000.0000.000
104A101ASP-1-0.860-0.91940.7370.0210.0210.0000.0000.0000.000
105A102GLY0-0.002-0.00540.264-0.001-0.0010.0000.0000.0000.000
106A103ALA0-0.057-0.03535.0920.0000.0000.0000.0000.0000.000
107A104PRO00.0750.04036.7050.0010.0010.0000.0000.0000.000
108A105LEU00.0020.00332.3360.0000.0000.0000.0000.0000.000
109A106LEU00.0390.01730.1970.0010.0010.0000.0000.0000.000
110A107TRP0-0.0280.00133.3820.0020.0020.0000.0000.0000.000
111A108THR00.007-0.01835.8810.0000.0000.0000.0000.0000.000
112A109LEU0-0.028-0.01129.2440.0000.0000.0000.0000.0000.000
113A110HIS0-0.0010.00531.8490.0030.0030.0000.0000.0000.000
114A111GLU-1-0.854-0.91833.0200.0230.0230.0000.0000.0000.000
115A112LEU0-0.086-0.04332.3940.0000.0000.0000.0000.0000.000
116A113GLY0-0.0350.00131.8420.0000.0000.0000.0000.0000.000
117A114MET0-0.067-0.01626.2410.0030.0030.0000.0000.0000.000
118A115ARG10.8360.89426.546-0.038-0.0380.0000.0000.0000.000
119A116GLN0-0.031-0.00620.2630.0040.0040.0000.0000.0000.000
120A117ILE00.0110.01223.749-0.004-0.0040.0000.0000.0000.000
121A118VAL0-0.014-0.01417.5290.0040.0040.0000.0000.0000.000
122A119LEU0-0.031-0.00921.020-0.009-0.0090.0000.0000.0000.000
123A120SER00.004-0.01416.6710.0090.0090.0000.0000.0000.000
124A121PRO00.0220.01319.229-0.007-0.0070.0000.0000.0000.000
125A122LEU00.0140.01919.876-0.008-0.0080.0000.0000.0000.000
126A123ARG10.8460.91521.4240.0020.0020.0000.0000.0000.000
127A124SER00.0560.02622.824-0.006-0.0060.0000.0000.0000.000
128A125GLY00.0140.00925.3080.0040.0040.0000.0000.0000.000
129A126GLY0-0.014-0.01125.8390.0030.0030.0000.0000.0000.000
130A127ARG10.9340.97226.9850.0160.0160.0000.0000.0000.000
131A128VAL00.0110.00124.752-0.004-0.0040.0000.0000.0000.000
132A129ILE0-0.017-0.01124.6910.0010.0010.0000.0000.0000.000
133A130GLY00.0650.01925.8640.0000.0000.0000.0000.0000.000
134A131PHE0-0.061-0.02222.8750.0000.0000.0000.0000.0000.000
135A132LEU00.0230.02717.082-0.002-0.0020.0000.0000.0000.000
136A133SER0-0.046-0.03420.8600.0050.0050.0000.0000.0000.000
137A134PHE0-0.004-0.00815.383-0.001-0.0010.0000.0000.0000.000
138A135VAL00.0420.01421.2020.0020.0020.0000.0000.0000.000
139A136SER00.003-0.01921.273-0.001-0.0010.0000.0000.0000.000
140A137ALA00.0600.04123.7740.0000.0000.0000.0000.0000.000
141A138GLU-1-0.891-0.92622.2900.0590.0590.0000.0000.0000.000
142A139GLU-1-0.846-0.92322.6210.0710.0710.0000.0000.0000.000
143A140LYS10.8190.91017.164-0.065-0.0650.0000.0000.0000.000
144A141LEU00.0160.00116.2600.0010.0010.0000.0000.0000.000
145A142TRP00.0160.00712.6150.0240.0240.0000.0000.0000.000
146A143SER0-0.038-0.04011.2620.0110.0110.0000.0000.0000.000
147A144ASP-1-0.800-0.91813.2780.1880.1880.0000.0000.0000.000
148A145GLY0-0.0010.0029.162-0.045-0.0450.0000.0000.0000.000
149A146ASP-1-0.775-0.8548.6310.3890.3890.0000.0000.0000.000
150A147LYS10.8970.93310.205-0.243-0.2430.0000.0000.0000.000
151A148SER0-0.035-0.0119.458-0.055-0.0550.0000.0000.0000.000
152A149LEU0-0.010-0.0074.260-0.208-0.137-0.001-0.006-0.0640.000
153A150LEU0-0.0100.0118.586-0.061-0.0610.0000.0000.0000.000
154A151SER00.0140.00311.987-0.017-0.0170.0000.0000.0000.000
155A152GLY0-0.0030.00910.638-0.006-0.0060.0000.0000.0000.000
156A153VAL00.0280.00310.685-0.003-0.0030.0000.0000.0000.000
157A154SER00.0230.00412.2740.0240.0240.0000.0000.0000.000
158A155SER0-0.049-0.00814.8460.0140.0140.0000.0000.0000.000
159A156SER0-0.031-0.02514.163-0.003-0.0030.0000.0000.0000.000
160A157ILE00.0220.01016.5990.0110.0110.0000.0000.0000.000
161A158ALA00.0120.01318.9640.0070.0070.0000.0000.0000.000
162A159ILE0-0.0160.00419.6700.0060.0060.0000.0000.0000.000
163A160ALA00.0380.02420.9810.0060.0060.0000.0000.0000.000
164A161VAL0-0.009-0.01622.8370.0040.0040.0000.0000.0000.000
165A162SER0-0.084-0.05224.5460.0030.0030.0000.0000.0000.000
166A163ASN00.0050.01025.8270.0020.0020.0000.0000.0000.000
167A164ALA00.0150.00427.3450.0020.0020.0000.0000.0000.000
168A165LEU00.028-0.00328.5420.0020.0020.0000.0000.0000.000
169A166ALA0-0.0110.01030.5150.0020.0020.0000.0000.0000.000
170A167TYR0-0.017-0.02230.5540.0010.0010.0000.0000.0000.000
171A168GLU-1-0.822-0.87333.465-0.007-0.0070.0000.0000.0000.000
172A169GLU-1-0.860-0.91234.953-0.007-0.0070.0000.0000.0000.000
173A170LEU0-0.034-0.02135.1480.0010.0010.0000.0000.0000.000
174A171ARG10.8610.91937.3930.0090.0090.0000.0000.0000.000
175A172GLN0-0.081-0.05538.0870.0010.0010.0000.0000.0000.000
176A173ARG10.7880.88340.1370.0070.0070.0000.0000.0000.000
177A174GLU-1-1.015-0.98342.630-0.008-0.0080.0000.0000.0000.000