FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2025-04-23

All entries: 37539

Number of unique PDB entries: 7791

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FMODB ID: JQM29

Calculation Name: 3IB6-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3IB6

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-09-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None


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 179
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1995855.13631
FMO2-HF: Nuclear repulsion 1925684.947795
FMO2-HF: Total energy -70170.188515
FMO2-MP2: Total energy -70377.649153


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:LEU)


Summations of interaction energy for fragment #1(A:2: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.
-27.307-11.78917.567-10.394-22.691-0.043
Interaction energy analysis for fragmet #1(A:2:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.052 / q_NPA : -0.035
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].
3A4HIS0-0.007-0.0083.580-0.2662.195-0.013-1.224-1.224-0.002
4A5VAL0-0.009-0.0044.000-1.096-0.6470.002-0.093-0.3590.000
5A6ILE0-0.024-0.0206.0900.2540.2540.0000.0000.0000.000
6A7TRP00.0470.0038.7390.0770.0770.0000.0000.0000.000
7A8ASP-1-0.718-0.82011.472-0.315-0.3150.0000.0000.0000.000
8A9MET0-0.015-0.02414.7010.0090.0090.0000.0000.0000.000
9A10GLY00.0400.01217.8770.0270.0270.0000.0000.0000.000
10A11GLU-1-0.821-0.90418.472-0.156-0.1560.0000.0000.0000.000
11A12THR00.0060.00213.7440.0070.0070.0000.0000.0000.000
12A13LEU0-0.0100.00713.5910.0310.0310.0000.0000.0000.000
13A14ASN0-0.052-0.03816.9970.0090.0090.0000.0000.0000.000
14A15THR00.0030.01120.775-0.006-0.0060.0000.0000.0000.000
15A16VAL0-0.021-0.00123.080-0.015-0.0150.0000.0000.0000.000
16A17PRO00.0050.00125.6240.0100.0100.0000.0000.0000.000
17A18ASN0-0.038-0.03729.3560.0030.0030.0000.0000.0000.000
18A19THR0-0.060-0.03731.2310.0050.0050.0000.0000.0000.000
19A20ARG10.8190.93224.5070.1280.1280.0000.0000.0000.000
20A21TYR00.0380.00226.023-0.012-0.0120.0000.0000.0000.000
21A22ASP-1-0.740-0.84126.266-0.161-0.1610.0000.0000.0000.000
22A23HIS0-0.031-0.02828.945-0.001-0.0010.0000.0000.0000.000
23A24HIS0-0.0170.00331.6660.0050.0050.0000.0000.0000.000
24A25PRO00.0330.00529.874-0.007-0.0070.0000.0000.0000.000
25A26LEU00.0580.03723.5730.0080.0080.0000.0000.0000.000
26A27ASP-1-0.833-0.89927.992-0.126-0.1260.0000.0000.0000.000
27A28THR0-0.095-0.06929.5000.0100.0100.0000.0000.0000.000
28A29TYR00.0040.01529.9590.0060.0060.0000.0000.0000.000
29A30PRO0-0.021-0.01830.514-0.003-0.0030.0000.0000.0000.000
30A31GLU-1-0.811-0.88729.799-0.088-0.0880.0000.0000.0000.000
31A32VAL0-0.036-0.01025.022-0.002-0.0020.0000.0000.0000.000
32A33VAL00.0160.00325.542-0.001-0.0010.0000.0000.0000.000
33A34LEU00.010-0.00320.126-0.006-0.0060.0000.0000.0000.000
34A35ARG10.7650.86617.6220.1300.1300.0000.0000.0000.000
35A36LYS10.7820.85020.4830.0540.0540.0000.0000.0000.000
36A37ASN00.005-0.00317.6730.0050.0050.0000.0000.0000.000
37A38ALA00.0510.06116.453-0.002-0.0020.0000.0000.0000.000
38A39LYS10.9150.95216.0280.0890.0890.0000.0000.0000.000
39A40GLU-1-0.888-0.94817.001-0.068-0.0680.0000.0000.0000.000
40A41THR0-0.022-0.02711.6530.0330.0330.0000.0000.0000.000
41A42LEU00.0000.01212.342-0.004-0.0040.0000.0000.0000.000
42A43GLU-1-0.754-0.82612.874-0.113-0.1130.0000.0000.0000.000
43A44LYS10.8180.89511.380-0.196-0.1960.0000.0000.0000.000
44A45VAL0-0.012-0.0147.1550.0720.0720.0000.0000.0000.000
45A46LYS10.9010.9308.9370.1070.1070.0000.0000.0000.000
46A47GLN0-0.113-0.07111.5670.0530.0530.0000.0000.0000.000
47A48LEU0-0.080-0.0347.8390.0780.0780.0000.0000.0000.000
48A49GLY0-0.026-0.0058.2590.2080.2080.0000.0000.0000.000
49A50PHE0-0.065-0.0242.383-1.418-0.2701.111-0.496-1.762-0.004
50A51LYS10.8850.9396.7600.8720.8720.0000.0000.0000.000
51A52GLN0-0.004-0.0127.029-0.260-0.2600.0000.0000.0000.000
52A53ALA0-0.0060.0079.4550.0830.0830.0000.0000.0000.000
53A54ILE0-0.028-0.00911.6890.0100.0100.0000.0000.0000.000
54A55LEU0-0.004-0.01512.3110.0080.0080.0000.0000.0000.000
55A56SER0-0.040-0.03814.6400.0130.0130.0000.0000.0000.000
56A57ASN00.0160.00517.641-0.030-0.0300.0000.0000.0000.000
57A58THR0-0.028-0.02720.5370.0050.0050.0000.0000.0000.000
58A59ALA0-0.0020.00523.925-0.002-0.0020.0000.0000.0000.000
59A60THR00.0060.00427.551-0.001-0.0010.0000.0000.0000.000
60A61SER0-0.037-0.04025.6370.0060.0060.0000.0000.0000.000
61A62ASP-1-0.827-0.89525.248-0.194-0.1940.0000.0000.0000.000
62A63THR00.0560.00520.982-0.001-0.0010.0000.0000.0000.000
63A64GLU-1-0.799-0.88123.286-0.232-0.2320.0000.0000.0000.000
64A65VAL0-0.079-0.02626.1490.0100.0100.0000.0000.0000.000
65A66ILE00.0330.01420.2180.0070.0070.0000.0000.0000.000
66A67LYS10.8280.89821.8020.2470.2470.0000.0000.0000.000
67A68ARG10.8560.92023.2620.1480.1480.0000.0000.0000.000
68A69VAL00.0160.01523.4930.0110.0110.0000.0000.0000.000
69A70LEU00.0280.00618.7060.0090.0090.0000.0000.0000.000
70A71THR0-0.035-0.03022.2720.0070.0070.0000.0000.0000.000
71A72ASN0-0.025-0.01724.9520.0120.0120.0000.0000.0000.000
72A73PHE0-0.036-0.01621.2560.0110.0110.0000.0000.0000.000
73A74GLY0-0.0090.00423.8530.0100.0100.0000.0000.0000.000
74A75ILE0-0.047-0.04617.7270.0110.0110.0000.0000.0000.000
75A76ILE0-0.0040.00718.454-0.032-0.0320.0000.0000.0000.000
76A77ASP-1-0.918-0.96718.673-0.211-0.2110.0000.0000.0000.000
77A78TYR0-0.118-0.07314.3270.0000.0000.0000.0000.0000.000
78A79PHE0-0.034-0.02012.744-0.063-0.0630.0000.0000.0000.000
79A80ASP-1-0.816-0.89111.794-0.594-0.5940.0000.0000.0000.000
80A81PHE0-0.013-0.01213.0400.0200.0200.0000.0000.0000.000
81A82ILE00.016-0.00214.616-0.012-0.0120.0000.0000.0000.000
82A83TYR0-0.059-0.02116.9330.0340.0340.0000.0000.0000.000
83A84ALA00.0210.01018.004-0.017-0.0170.0000.0000.0000.000
84A85SER00.012-0.00320.7460.0080.0080.0000.0000.0000.000
85A86ASN0-0.044-0.02922.1930.0140.0140.0000.0000.0000.000
86A87SER00.000-0.03924.1940.0010.0010.0000.0000.0000.000
87A88GLU-1-0.879-0.93626.666-0.118-0.1180.0000.0000.0000.000
88A89LEU0-0.066-0.00429.3620.0090.0090.0000.0000.0000.000
89A90GLN0-0.025-0.03330.3090.0030.0030.0000.0000.0000.000
90A91PRO00.023-0.00130.011-0.009-0.0090.0000.0000.0000.000
91A92GLY0-0.015-0.00628.2560.0000.0000.0000.0000.0000.000
92A93LYS10.8290.94024.8180.2070.2070.0000.0000.0000.000
93A94MET0-0.0230.00819.820-0.003-0.0030.0000.0000.0000.000
94A95GLU-1-0.826-0.90619.987-0.219-0.2190.0000.0000.0000.000
95A96LYS10.7410.87714.1850.3810.3810.0000.0000.0000.000
96A97PRO00.0190.01216.3910.0230.0230.0000.0000.0000.000
97A98ASP-1-0.910-0.95516.557-0.271-0.2710.0000.0000.0000.000
98A99LYS10.8360.87315.9480.3540.3540.0000.0000.0000.000
99A100THR00.0230.01516.134-0.046-0.0460.0000.0000.0000.000
100A101ILE00.0260.02415.466-0.018-0.0180.0000.0000.0000.000
101A102PHE00.0260.02910.883-0.045-0.0450.0000.0000.0000.000
102A103ASP-1-0.824-0.89212.740-0.516-0.5160.0000.0000.0000.000
103A104PHE0-0.027-0.01614.769-0.028-0.0280.0000.0000.0000.000
104A105THR00.001-0.01511.0830.0020.0020.0000.0000.0000.000
105A106LEU0-0.019-0.0077.879-0.065-0.0650.0000.0000.0000.000
106A107ASN0-0.009-0.00411.331-0.017-0.0170.0000.0000.0000.000
107A108ALA0-0.041-0.01714.6990.0300.0300.0000.0000.0000.000
108A109LEU0-0.022-0.0129.2340.0350.0350.0000.0000.0000.000
109A110GLN0-0.129-0.06011.262-0.010-0.0100.0000.0000.0000.000
110A111ILE00.0040.0216.161-0.040-0.0400.0000.0000.0000.000
111A112ASP-1-0.775-0.8597.370-0.805-0.8050.0000.0000.0000.000
112A113LYS10.8630.9066.4790.2830.2830.0000.0000.0000.000
113A114THR0-0.065-0.0605.086-0.266-0.2660.0000.0000.0000.000
114A115GLU-1-0.871-0.9252.243-5.658-3.3571.958-2.034-2.225-0.009
115A116ALA00.0120.0142.548-3.921-2.3633.029-1.950-2.638-0.028
116A117VAL0-0.032-0.0252.261-1.253-0.2312.869-0.832-3.058-0.003
117A118MET0-0.0380.0123.7150.0980.1640.009-0.006-0.0690.000
118A119VAL0-0.031-0.0287.0650.0940.0940.0000.0000.0000.000
119A120GLY00.0460.0149.5770.0050.0050.0000.0000.0000.000
120A121ASN00.006-0.01413.2420.0060.0060.0000.0000.0000.000
121A122THR00.0510.03916.2480.0390.0390.0000.0000.0000.000
122A123PHE0-0.024-0.01116.118-0.036-0.0360.0000.0000.0000.000
123A124GLU-1-0.714-0.88516.415-0.181-0.1810.0000.0000.0000.000
124A125SER00.001-0.01016.7200.0030.0030.0000.0000.0000.000
125A126ASP-1-0.774-0.89012.555-0.381-0.3810.0000.0000.0000.000
126A127ILE0-0.030-0.01411.496-0.072-0.0720.0000.0000.0000.000
127A128ILE00.0110.00512.378-0.028-0.0280.0000.0000.0000.000
128A129GLY00.0210.00714.214-0.001-0.0010.0000.0000.0000.000
129A130ALA0-0.0110.0018.475-0.027-0.0270.0000.0000.0000.000
130A131ASN0-0.004-0.00910.383-0.014-0.0140.0000.0000.0000.000
131A132ARG10.9480.97311.6630.2510.2510.0000.0000.0000.000
132A133ALA0-0.036-0.00511.1940.0270.0270.0000.0000.0000.000
133A134GLY0-0.028-0.02110.365-0.055-0.0550.0000.0000.0000.000
134A135ILE0-0.064-0.0205.629-0.095-0.0950.0000.0000.0000.000
135A136HIS00.0140.0132.374-0.2550.3301.087-0.416-1.256-0.002
136A137ALA00.010-0.0035.643-0.187-0.1870.0000.0000.0000.000
137A138ILE0-0.027-0.0114.8740.1690.1690.0000.0000.0000.000
138A139TRP0-0.024-0.0178.713-0.042-0.0420.0000.0000.0000.000
139A140LEU00.0090.01012.5150.0520.0520.0000.0000.0000.000
140A141GLN0-0.021-0.03314.8720.0130.0130.0000.0000.0000.000
141A142ASN0-0.055-0.02917.7140.0110.0110.0000.0000.0000.000
142A143PRO00.012-0.00820.257-0.013-0.0130.0000.0000.0000.000
143A144GLU-1-0.822-0.85722.371-0.068-0.0680.0000.0000.0000.000
144A145VAL0-0.023-0.01618.604-0.005-0.0050.0000.0000.0000.000
145A146CYS0-0.090-0.01117.856-0.014-0.0140.0000.0000.0000.000
146A147LEU00.0240.01019.3950.0130.0130.0000.0000.0000.000
147A148GLN0-0.056-0.05119.552-0.001-0.0010.0000.0000.0000.000
148A149ASP-1-0.941-0.94521.802-0.101-0.1010.0000.0000.0000.000
149A150GLU-1-0.966-1.00223.330-0.082-0.0820.0000.0000.0000.000
150A151ARG10.8810.95321.4880.0350.0350.0000.0000.0000.000
151A152LEU0-0.005-0.00320.1600.0050.0050.0000.0000.0000.000
152A153PRO0-0.032-0.03119.755-0.002-0.0020.0000.0000.0000.000
153A154LEU00.0060.01813.965-0.022-0.0220.0000.0000.0000.000
154A155VAL0-0.046-0.02513.4530.0310.0310.0000.0000.0000.000
155A156ALA00.0140.02812.003-0.020-0.0200.0000.0000.0000.000
156A157PRO0-0.075-0.0259.3800.0430.0430.0000.0000.0000.000
157A158PRO00.0170.0207.3070.0130.0130.0000.0000.0000.000
158A159PHE0-0.004-0.0336.6250.0870.0870.0000.0000.0000.000
159A160VAL00.0400.0177.879-0.111-0.1110.0000.0000.0000.000
160A161ILE0-0.043-0.0227.2560.0860.0860.0000.0000.0000.000
161A162PRO00.0050.01910.068-0.052-0.0520.0000.0000.0000.000
162A163VAL00.000-0.01110.1040.0540.0540.0000.0000.0000.000
163A164TRP00.0340.02613.319-0.033-0.0330.0000.0000.0000.000
164A165ASP-1-0.761-0.86615.648-0.101-0.1010.0000.0000.0000.000
165A166LEU0-0.001-0.01413.4640.0080.0080.0000.0000.0000.000
166A167ALA0-0.014-0.01312.8220.0030.0030.0000.0000.0000.000
167A168ASP-1-0.856-0.92212.8780.0940.0940.0000.0000.0000.000
168A169VAL0-0.0090.0037.7560.0590.0590.0000.0000.0000.000
169A170PRO00.000-0.0067.5270.0580.0580.0000.0000.0000.000
170A171GLU-1-0.764-0.8707.1910.4810.4810.0000.0000.0000.000
171A172ALA00.0130.0167.4140.1830.1830.0000.0000.0000.000
172A173LEU00.0190.0203.188-0.5410.1570.097-0.156-0.6390.000
173A174LEU00.0040.0032.9820.1141.1780.312-0.543-0.833-0.006
174A175LEU0-0.076-0.0275.5350.4010.4010.0000.0000.0000.000
175A176LEU00.0500.0102.385-0.604-0.1691.507-0.422-1.5190.002
176A177LYS10.9070.9562.308-11.874-9.3353.706-1.819-4.4270.007
177A178LYS10.8910.9543.392-0.205-0.6460.0690.686-0.3150.000
178A179ILE0-0.0370.0005.928-0.226-0.2260.0000.0000.0000.000
179A180SER0-0.055-0.0222.2970.3231.9561.824-1.089-2.3670.002