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: ZNN2N

Calculation Name: 3IC6-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3IC6

Chain ID: A

ChEMBL ID:

UniProt ID: Q5F8U0

Base Structure: X-ray

Registration Date: 2023-09-27

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 217
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2431112.138446
FMO2-HF: Nuclear repulsion 2346734.621482
FMO2-HF: Total energy -84377.516965
FMO2-MP2: Total energy -84619.092741


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:4:LEU)


Summations of interaction energy for fragment #1(A:4:LEU)
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.
-3.173-0.651-0.016-1.239-1.2660.004
Interaction energy analysis for fragmet #1(A:4:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.023 / q_NPA : 0.008
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].
3A6PRO00.0130.0223.836-1.3351.187-0.016-1.239-1.2660.004
4A7ALA0-0.020-0.0146.2340.2760.2760.0000.0000.0000.000
5A8LEU00.008-0.0078.851-0.081-0.0810.0000.0000.0000.000
6A9PRO00.0320.02012.2100.0650.0650.0000.0000.0000.000
7A10ASP-1-0.857-0.92813.873-0.296-0.2960.0000.0000.0000.000
8A11TYR00.0280.00914.8090.0290.0290.0000.0000.0000.000
9A12LEU00.0130.00315.9180.0250.0250.0000.0000.0000.000
10A13GLY0-0.020-0.01619.4160.0220.0220.0000.0000.0000.000
11A14ASN0-0.095-0.02921.5930.0410.0410.0000.0000.0000.000
12A15ILE00.0040.00521.0360.0110.0110.0000.0000.0000.000
13A16ARG10.7980.88024.7210.1390.1390.0000.0000.0000.000
14A17ILE0-0.028-0.02325.580-0.003-0.0030.0000.0000.0000.000
15A18ILE00.0280.00729.1650.0100.0100.0000.0000.0000.000
16A19LEU0-0.026-0.00932.136-0.002-0.0020.0000.0000.0000.000
17A20THR00.0390.01235.2670.0050.0050.0000.0000.0000.000
18A21ARG10.7290.83338.8780.0900.0900.0000.0000.0000.000
19A22THR0-0.0070.00537.4880.0010.0010.0000.0000.0000.000
20A23SER00.0200.00840.3730.0040.0040.0000.0000.0000.000
21A24HIS00.0340.00739.2140.0030.0030.0000.0000.0000.000
22A25PRO00.0880.04638.592-0.007-0.0070.0000.0000.0000.000
23A26ALA00.0350.02636.572-0.006-0.0060.0000.0000.0000.000
24A27ASN0-0.056-0.04734.624-0.014-0.0140.0000.0000.0000.000
25A28ILE00.0190.02733.377-0.011-0.0110.0000.0000.0000.000
26A29GLY00.0580.03132.083-0.009-0.0090.0000.0000.0000.000
27A30SER0-0.063-0.04930.308-0.011-0.0110.0000.0000.0000.000
28A31ALA0-0.0040.00828.670-0.017-0.0170.0000.0000.0000.000
29A32ALA00.0630.03927.533-0.017-0.0170.0000.0000.0000.000
30A33ARG10.9590.97925.7670.1630.1630.0000.0000.0000.000
31A34ALA0-0.044-0.01724.135-0.024-0.0240.0000.0000.0000.000
32A35MET00.0110.00523.107-0.023-0.0230.0000.0000.0000.000
33A36LYS10.8320.90921.0060.1700.1700.0000.0000.0000.000
34A37THR0-0.105-0.06019.602-0.029-0.0290.0000.0000.0000.000
35A38MET0-0.053-0.00418.129-0.071-0.0710.0000.0000.0000.000
36A39GLY00.0030.00117.282-0.026-0.0260.0000.0000.0000.000
37A40LEU0-0.021-0.00718.2330.0130.0130.0000.0000.0000.000
38A41HIS00.019-0.02020.1690.0320.0320.0000.0000.0000.000
39A42ARG10.8770.94623.7130.1780.1780.0000.0000.0000.000
40A43LEU00.0260.02126.742-0.006-0.0060.0000.0000.0000.000
41A44THR00.0080.00629.8420.0050.0050.0000.0000.0000.000
42A45ILE0-0.044-0.02533.344-0.004-0.0040.0000.0000.0000.000
43A46VAL00.0580.02336.3750.0050.0050.0000.0000.0000.000
44A47THR0-0.046-0.02739.3790.0000.0000.0000.0000.0000.000
45A48PRO00.0040.00940.371-0.001-0.0010.0000.0000.0000.000
46A49ASN0-0.062-0.03742.2320.0050.0050.0000.0000.0000.000
47A50LEU0-0.005-0.00140.294-0.001-0.0010.0000.0000.0000.000
48A51MET0-0.031-0.01642.9820.0040.0040.0000.0000.0000.000
49A52ALA00.0200.00745.477-0.002-0.0020.0000.0000.0000.000
50A53THR0-0.074-0.06042.6750.0000.0000.0000.0000.0000.000
51A54PRO00.018-0.01344.6640.0020.0020.0000.0000.0000.000
52A55MET0-0.052-0.01538.5700.0010.0010.0000.0000.0000.000
53A56THR0-0.057-0.04642.6100.0010.0010.0000.0000.0000.000
54A57GLU-1-0.877-0.93845.394-0.054-0.0540.0000.0000.0000.000
55A58ASN0-0.098-0.05348.3890.0020.0020.0000.0000.0000.000
56A59PRO00.0050.01745.794-0.001-0.0010.0000.0000.0000.000
57A60PRO00.0010.01643.1130.0030.0030.0000.0000.0000.000
58A61VAL00.001-0.01646.295-0.002-0.0020.0000.0000.0000.000
59A62PHE0-0.003-0.00242.8110.0000.0000.0000.0000.0000.000
60A63ASN00.023-0.00446.5840.0020.0020.0000.0000.0000.000
61A64PRO0-0.032-0.02146.713-0.001-0.0010.0000.0000.0000.000
62A65ASP-1-0.905-0.94347.467-0.054-0.0540.0000.0000.0000.000
63A66ASP-1-0.899-0.92547.922-0.053-0.0530.0000.0000.0000.000
64A67VAL00.0100.00341.583-0.001-0.0010.0000.0000.0000.000
65A68GLN0-0.067-0.03942.915-0.005-0.0050.0000.0000.0000.000
66A69SER0-0.035-0.03643.5850.0000.0000.0000.0000.0000.000
67A70PHE0-0.078-0.03540.0320.0000.0000.0000.0000.0000.000
68A71ALA00.0340.02440.678-0.003-0.0030.0000.0000.0000.000
69A72LEU0-0.010-0.01535.6510.0010.0010.0000.0000.0000.000
70A73PRO00.0280.00839.6130.0030.0030.0000.0000.0000.000
71A74GLU-1-0.854-0.93438.509-0.081-0.0810.0000.0000.0000.000
72A75GLU-1-0.810-0.87037.823-0.090-0.0900.0000.0000.0000.000
73A76SER0-0.046-0.03935.626-0.004-0.0040.0000.0000.0000.000
74A77PHE00.0390.00133.308-0.010-0.0100.0000.0000.0000.000
75A78ILE0-0.0200.00333.069-0.006-0.0060.0000.0000.0000.000
76A79LEU0-0.040-0.02732.810-0.006-0.0060.0000.0000.0000.000
77A80ALA0-0.0150.01129.729-0.011-0.0110.0000.0000.0000.000
78A81SER0-0.063-0.03527.571-0.016-0.0160.0000.0000.0000.000
79A82GLY0-0.0050.00225.4250.0070.0070.0000.0000.0000.000
80A83ALA0-0.033-0.02025.095-0.010-0.0100.0000.0000.0000.000
81A84ALA00.0390.02026.2860.0010.0010.0000.0000.0000.000
82A85ASP-1-0.804-0.88424.502-0.169-0.1690.0000.0000.0000.000
83A86VAL00.0410.00824.9910.0040.0040.0000.0000.0000.000
84A87LEU0-0.044-0.01927.6740.0030.0030.0000.0000.0000.000
85A88HIS0-0.033-0.01530.9520.0080.0080.0000.0000.0000.000
86A89ASN0-0.100-0.04727.660-0.001-0.0010.0000.0000.0000.000
87A90ALA0-0.0150.01230.661-0.004-0.0040.0000.0000.0000.000
88A91GLU-1-0.841-0.90331.526-0.121-0.1210.0000.0000.0000.000
89A92ILE0-0.002-0.00534.587-0.004-0.0040.0000.0000.0000.000
90A93VAL00.0140.00737.3100.0040.0040.0000.0000.0000.000
91A94ALA00.0440.01740.033-0.001-0.0010.0000.0000.0000.000
92A95THR0-0.062-0.05142.3990.0000.0000.0000.0000.0000.000
93A96LEU00.027-0.00336.994-0.003-0.0030.0000.0000.0000.000
94A97ASP-1-0.788-0.88438.886-0.088-0.0880.0000.0000.0000.000
95A98GLU-1-0.820-0.88839.541-0.082-0.0820.0000.0000.0000.000
96A99ALA0-0.035-0.01435.782-0.003-0.0030.0000.0000.0000.000
97A100LEU0-0.014-0.00334.340-0.008-0.0080.0000.0000.0000.000
98A101ALA00.0360.04935.537-0.004-0.0040.0000.0000.0000.000
99A102ASP-1-0.787-0.87532.278-0.125-0.1250.0000.0000.0000.000
100A103THR0-0.080-0.06130.970-0.009-0.0090.0000.0000.0000.000
101A104THR00.018-0.03329.6750.0060.0060.0000.0000.0000.000
102A105ILE0-0.047-0.01728.0700.0030.0030.0000.0000.0000.000
103A106ALA00.0460.02131.063-0.005-0.0050.0000.0000.0000.000
104A107CYS0-0.052-0.01030.0750.0040.0040.0000.0000.0000.000
105A108ALA00.0550.02232.711-0.001-0.0010.0000.0000.0000.000
106A109LEU0-0.0090.00931.836-0.002-0.0020.0000.0000.0000.000
107A110THR0-0.0350.00434.9490.0080.0080.0000.0000.0000.000
108A111SER00.0700.04236.907-0.005-0.0050.0000.0000.0000.000
109A112ARG10.8800.92339.3670.1080.1080.0000.0000.0000.000
110A113ARG10.8920.95741.9070.1000.1000.0000.0000.0000.000
111A114ARG10.8930.92444.7740.0780.0780.0000.0000.0000.000
112A115GLH00.0900.02639.4780.0000.0000.0000.0000.0000.000
113A116ILE0-0.017-0.11043.6730.0020.0020.0000.0000.0000.000
114A117THR00.0190.07443.8670.0010.0010.0000.0000.0000.000
115A118ALA0-0.0110.05240.8400.0020.0020.0000.0000.0000.000
116A119PRO00.004-0.00437.3110.0010.0010.0000.0000.0000.000
117A120LEU0-0.0080.00136.036-0.001-0.0010.0000.0000.0000.000
118A121GLN00.0320.01731.0420.0060.0060.0000.0000.0000.000
119A122THR0-0.022-0.03628.525-0.005-0.0050.0000.0000.0000.000
120A123PRO00.0400.00126.013-0.003-0.0030.0000.0000.0000.000
121A124ARG10.7940.87222.2050.3100.3100.0000.0000.0000.000
122A125ASP-1-0.848-0.91124.315-0.219-0.2190.0000.0000.0000.000
123A126LEU0-0.039-0.01726.9700.0040.0040.0000.0000.0000.000
124A127VAL00.0140.00821.1600.0060.0060.0000.0000.0000.000
125A128PRO00.0340.02921.555-0.007-0.0070.0000.0000.0000.000
126A129GLU-1-0.821-0.87222.637-0.175-0.1750.0000.0000.0000.000
127A130LEU0-0.001-0.01224.3030.0070.0070.0000.0000.0000.000
128A131LEU00.0240.00917.6820.0060.0060.0000.0000.0000.000
129A132GLN0-0.023-0.01820.9680.0190.0190.0000.0000.0000.000
130A133ALA00.0170.00922.2010.0100.0100.0000.0000.0000.000
131A134ALA00.0200.01821.6590.0110.0110.0000.0000.0000.000
132A135ASN0-0.034-0.03317.972-0.017-0.0170.0000.0000.0000.000
133A136ARG10.8050.89920.6940.1910.1910.0000.0000.0000.000
134A137GLY0-0.017-0.00223.5440.0190.0190.0000.0000.0000.000
135A138GLU-1-0.818-0.85724.850-0.150-0.1500.0000.0000.0000.000
136A139LYS10.8870.94425.9790.1450.1450.0000.0000.0000.000
137A140VAL00.0090.01325.2480.0070.0070.0000.0000.0000.000
138A141ALA00.0260.00827.927-0.006-0.0060.0000.0000.0000.000
139A142LEU0-0.036-0.01026.180-0.001-0.0010.0000.0000.0000.000
140A143VAL00.0200.00930.2700.0030.0030.0000.0000.0000.000
141A144PHE00.007-0.00829.1900.0000.0000.0000.0000.0000.000
142A145GLY00.0250.00035.1880.0050.0050.0000.0000.0000.000
143A146ASN00.0160.01638.617-0.001-0.0010.0000.0000.0000.000
144A147GLU-1-0.753-0.86138.739-0.107-0.1070.0000.0000.0000.000
145A148THR0-0.0310.00040.7330.0010.0010.0000.0000.0000.000
146A149PHE0-0.025-0.03344.1080.0010.0010.0000.0000.0000.000
147A150GLY00.0050.01940.4710.0000.0000.0000.0000.0000.000
148A151LEU0-0.003-0.00137.0990.0040.0040.0000.0000.0000.000
149A152SER0-0.065-0.05541.6130.0010.0010.0000.0000.0000.000
150A153ILE0-0.017-0.02343.750-0.003-0.0030.0000.0000.0000.000
151A154GLU-1-0.862-0.92844.937-0.077-0.0770.0000.0000.0000.000
152A155GLU-1-0.694-0.81040.912-0.097-0.0970.0000.0000.0000.000
153A156VAL0-0.024-0.02140.002-0.004-0.0040.0000.0000.0000.000
154A157ARG10.9010.94140.3020.0740.0740.0000.0000.0000.000
155A158ALA00.0120.02740.5260.0010.0010.0000.0000.0000.000
156A159CYS0-0.0480.00636.132-0.005-0.0050.0000.0000.0000.000
157A160ASN00.0280.00834.171-0.002-0.0020.0000.0000.0000.000
158A161ARG10.8070.86931.4500.1490.1490.0000.0000.0000.000
159A162LEU0-0.016-0.00234.7930.0030.0030.0000.0000.0000.000
160A163MET00.0460.03127.901-0.006-0.0060.0000.0000.0000.000
161A164THR0-0.064-0.06132.8120.0100.0100.0000.0000.0000.000
162A165ILE00.0350.01329.841-0.012-0.0120.0000.0000.0000.000
163A166ASN0-0.017-0.00831.6990.0160.0160.0000.0000.0000.000
164A167GLY00.033-0.00632.224-0.010-0.0100.0000.0000.0000.000
165A168ASN0-0.0100.00334.3190.0060.0060.0000.0000.0000.000
166A169PRO00.0060.00537.1770.0010.0010.0000.0000.0000.000
167A170ASP-1-0.911-0.95040.295-0.086-0.0860.0000.0000.0000.000
168A171TYR0-0.077-0.05038.3290.0050.0050.0000.0000.0000.000
169A172PHE0-0.022-0.00434.116-0.006-0.0060.0000.0000.0000.000
170A173SER0-0.038-0.02036.9890.0040.0040.0000.0000.0000.000
171A174LEU00.0060.02231.047-0.004-0.0040.0000.0000.0000.000
172A175ASN00.0290.00934.225-0.003-0.0030.0000.0000.0000.000
173A176LEU00.0840.03433.983-0.009-0.0090.0000.0000.0000.000
174A177ALA00.0510.02831.606-0.010-0.0100.0000.0000.0000.000
175A178GLN0-0.006-0.00729.800-0.009-0.0090.0000.0000.0000.000
176A179ALA00.0060.01029.109-0.017-0.0170.0000.0000.0000.000
177A180VAL00.0390.01427.734-0.012-0.0120.0000.0000.0000.000
178A181GLN00.0210.00824.015-0.031-0.0310.0000.0000.0000.000
179A182VAL0-0.044-0.02324.651-0.025-0.0250.0000.0000.0000.000
180A183VAL00.005-0.00224.625-0.022-0.0220.0000.0000.0000.000
181A184CYS0-0.027-0.01522.820-0.012-0.0120.0000.0000.0000.000
182A185TYR00.0180.00818.266-0.049-0.0490.0000.0000.0000.000
183A186GLU-1-0.780-0.83319.677-0.392-0.3920.0000.0000.0000.000
184A187ILE00.0230.01419.754-0.031-0.0310.0000.0000.0000.000
185A188PHE00.0100.00612.692-0.050-0.0500.0000.0000.0000.000
186A189SER0-0.127-0.06515.584-0.084-0.0840.0000.0000.0000.000
187A190GLN00.014-0.01315.862-0.024-0.0240.0000.0000.0000.000
188A191THR0-0.062-0.04213.385-0.031-0.0310.0000.0000.0000.000
189A192ASP-1-0.973-0.97310.723-0.948-0.9480.0000.0000.0000.000
190A193SER0-0.027-0.01111.9170.0400.0400.0000.0000.0000.000
191A194PRO0-0.047-0.02013.543-0.007-0.0070.0000.0000.0000.000
192A195MET0-0.010-0.00914.4310.0700.0700.0000.0000.0000.000
193A196THR0-0.058-0.02316.4590.0100.0100.0000.0000.0000.000
194A197HIS00.0110.00915.3560.0160.0160.0000.0000.0000.000
195A198LEU0-0.016-0.02519.8760.0190.0190.0000.0000.0000.000
196A199GLN0-0.051-0.03423.6150.0060.0060.0000.0000.0000.000
197A200GLN00.0970.07124.4020.0050.0050.0000.0000.0000.000
198A201GLU-1-0.972-1.04929.107-0.072-0.0720.0000.0000.0000.000
199A202ASP-1-0.903-0.95330.864-0.111-0.1110.0000.0000.0000.000
200A203HIS0-0.118-0.00730.072-0.003-0.0030.0000.0000.0000.000
201A204ALA0-0.0310.00331.8690.0050.0050.0000.0000.0000.000
202A205ALA0-0.007-0.00333.6160.0010.0010.0000.0000.0000.000
203A206THR00.008-0.00733.747-0.004-0.0040.0000.0000.0000.000
204A207HIS0-0.009-0.01235.7960.0040.0040.0000.0000.0000.000
205A208GLU-1-0.968-0.98837.882-0.077-0.0770.0000.0000.0000.000
206A209GLN00.0170.00837.4520.0020.0020.0000.0000.0000.000
207A210ILE0-0.013-0.00837.3670.0050.0050.0000.0000.0000.000
208A211LYS10.8450.90741.3590.0810.0810.0000.0000.0000.000
209A212GLY00.0090.00743.8920.0040.0040.0000.0000.0000.000
210A213MET00.0060.00340.7240.0030.0030.0000.0000.0000.000
211A214LEU0-0.077-0.02343.9720.0020.0020.0000.0000.0000.000
212A215ALA0-0.072-0.03247.3570.0030.0030.0000.0000.0000.000
213A216HIS0-0.045-0.01349.2740.0030.0030.0000.0000.0000.000
214A217MET0-0.066-0.03248.4500.0030.0030.0000.0000.0000.000
215A218GLU-1-0.893-0.94346.256-0.058-0.0580.0000.0000.0000.000
216A219SER0-0.018-0.01547.2180.0040.0040.0000.0000.0000.000
217A220VAL0-0.029-0.01047.543-0.001-0.0010.0000.0000.0000.000