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: 89JNY

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 OptH
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 -1991799.231652
FMO2-HF: Nuclear repulsion 1921630.433839
FMO2-HF: Total energy -70168.797813
FMO2-MP2: Total energy -70376.182833


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.
-18.65-2.3359.326-7.845-17.798-0.032
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 : -0.061 / q_NPA : -0.029
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].
3A4HIS0-0.0040.0093.518-2.8400.510-0.039-1.630-1.6820.000
4A5VAL00.0050.0004.324-1.096-0.780-0.001-0.034-0.2810.000
5A6ILE0-0.037-0.0316.3130.3200.3200.0000.0000.0000.000
6A7TRP0-0.013-0.0438.835-0.053-0.0530.0000.0000.0000.000
7A8ASP-1-0.764-0.88411.596-0.216-0.2160.0000.0000.0000.000
8A9MET0-0.086-0.05114.6100.0030.0030.0000.0000.0000.000
9A10GLY00.036-0.00917.8340.0050.0050.0000.0000.0000.000
10A11GLU-1-0.927-0.96119.154-0.158-0.1580.0000.0000.0000.000
11A12THR00.0100.01013.549-0.022-0.0220.0000.0000.0000.000
12A13LEU0-0.0020.00714.1340.0170.0170.0000.0000.0000.000
13A14ASN0-0.064-0.05917.1590.0110.0110.0000.0000.0000.000
14A15THR0-0.0520.03720.856-0.012-0.0120.0000.0000.0000.000
15A16VAL00.0320.02023.188-0.002-0.0020.0000.0000.0000.000
16A17PRO00.0200.01225.6100.0050.0050.0000.0000.0000.000
17A18ASN00.0240.01929.251-0.005-0.0050.0000.0000.0000.000
18A19THR0-0.069-0.04131.4160.0010.0010.0000.0000.0000.000
19A20ARG10.9100.97525.3110.1200.1200.0000.0000.0000.000
20A21TYR00.0380.00026.752-0.010-0.0100.0000.0000.0000.000
21A22ASP-1-0.739-0.83726.739-0.096-0.0960.0000.0000.0000.000
22A23HIS00.0380.01129.1960.0000.0000.0000.0000.0000.000
23A24HIS0-0.025-0.01132.1680.0060.0060.0000.0000.0000.000
24A25PRO00.0440.01530.187-0.006-0.0060.0000.0000.0000.000
25A26LEU00.0550.03024.0670.0020.0020.0000.0000.0000.000
26A27ASP-1-0.858-0.92728.288-0.066-0.0660.0000.0000.0000.000
27A28THR0-0.092-0.06429.7580.0050.0050.0000.0000.0000.000
28A29TYR00.0050.01729.9290.0030.0030.0000.0000.0000.000
29A30PRO0-0.026-0.02230.503-0.004-0.0040.0000.0000.0000.000
30A31GLU-1-0.866-0.93730.053-0.076-0.0760.0000.0000.0000.000
31A32VAL0-0.003-0.01125.149-0.007-0.0070.0000.0000.0000.000
32A33VAL0-0.002-0.01525.6130.0030.0030.0000.0000.0000.000
33A34LEU00.007-0.00620.300-0.010-0.0100.0000.0000.0000.000
34A35ARG10.8210.90617.9090.1950.1950.0000.0000.0000.000
35A36LYS10.8200.87720.7730.1280.1280.0000.0000.0000.000
36A37ASN00.0260.01517.528-0.002-0.0020.0000.0000.0000.000
37A38ALA00.0200.04416.527-0.014-0.0140.0000.0000.0000.000
38A39LYS10.9720.97516.1420.0790.0790.0000.0000.0000.000
39A40GLU-1-0.894-0.94517.228-0.121-0.1210.0000.0000.0000.000
40A41THR0-0.023-0.02811.688-0.001-0.0010.0000.0000.0000.000
41A42LEU00.0060.01512.349-0.027-0.0270.0000.0000.0000.000
42A43GLU-1-0.822-0.87613.250-0.101-0.1010.0000.0000.0000.000
43A44LYS10.9300.95611.5810.1330.1330.0000.0000.0000.000
44A45VAL00.007-0.0027.5510.0100.0100.0000.0000.0000.000
45A46LYS10.9900.9989.2180.0560.0560.0000.0000.0000.000
46A47GLN0-0.108-0.05211.7080.0440.0440.0000.0000.0000.000
47A48LEU0-0.126-0.0597.7700.0410.0410.0000.0000.0000.000
48A49GLY0-0.028-0.0168.2310.0100.0100.0000.0000.0000.000
49A50PHE0-0.061-0.0142.204-0.744-0.2581.343-0.306-1.522-0.001
50A51LYS10.9320.9616.7880.1050.1050.0000.0000.0000.000
51A52GLN00.0320.0287.397-0.286-0.2860.0000.0000.0000.000
52A53ALA00.0230.0209.8510.1120.1120.0000.0000.0000.000
53A54ILE0-0.0090.00811.846-0.062-0.0620.0000.0000.0000.000
54A55LEU00.0110.00512.8910.0400.0400.0000.0000.0000.000
55A56SER0-0.0070.00814.989-0.024-0.0240.0000.0000.0000.000
56A57ASN00.0710.02717.9040.0080.0080.0000.0000.0000.000
57A58THR0-0.055-0.03220.735-0.003-0.0030.0000.0000.0000.000
58A59ALA00.0030.01324.0590.0010.0010.0000.0000.0000.000
59A60THR00.0220.01427.6440.0060.0060.0000.0000.0000.000
60A61SER0-0.056-0.04625.9020.0070.0070.0000.0000.0000.000
61A62ASP-1-0.846-0.91725.637-0.073-0.0730.0000.0000.0000.000
62A63THR00.042-0.00721.549-0.007-0.0070.0000.0000.0000.000
63A64GLU-1-0.873-0.94123.722-0.057-0.0570.0000.0000.0000.000
64A65VAL0-0.048-0.01126.4670.0010.0010.0000.0000.0000.000
65A66ILE00.0440.01920.6760.0000.0000.0000.0000.0000.000
66A67LYS10.9040.95621.8920.0530.0530.0000.0000.0000.000
67A68ARG10.8910.93723.5820.0590.0590.0000.0000.0000.000
68A69VAL00.0040.01123.4290.0020.0020.0000.0000.0000.000
69A70LEU00.0200.00618.807-0.001-0.0010.0000.0000.0000.000
70A71THR0-0.027-0.02122.4810.0020.0020.0000.0000.0000.000
71A72ASN0-0.008-0.00224.9570.0080.0080.0000.0000.0000.000
72A73PHE0-0.044-0.01221.5610.0030.0030.0000.0000.0000.000
73A74GLY0-0.043-0.02423.602-0.002-0.0020.0000.0000.0000.000
74A75ILE0-0.049-0.03317.8080.0000.0000.0000.0000.0000.000
75A76ILE00.0050.01018.414-0.017-0.0170.0000.0000.0000.000
76A77ASP-1-0.912-0.96418.520-0.066-0.0660.0000.0000.0000.000
77A78TYR0-0.156-0.10214.1650.0080.0080.0000.0000.0000.000
78A79PHE0-0.051-0.02213.128-0.036-0.0360.0000.0000.0000.000
79A80ASP-1-0.855-0.92612.550-0.008-0.0080.0000.0000.0000.000
80A81PHE0-0.044-0.02913.4750.0350.0350.0000.0000.0000.000
81A82ILE00.006-0.00214.812-0.044-0.0440.0000.0000.0000.000
82A83TYR0-0.067-0.03117.1440.0310.0310.0000.0000.0000.000
83A84ALA00.0390.02018.326-0.024-0.0240.0000.0000.0000.000
84A85SER00.000-0.01220.8700.0090.0090.0000.0000.0000.000
85A86ASN0-0.047-0.02122.2760.0130.0130.0000.0000.0000.000
86A87SER00.002-0.01924.4760.0070.0070.0000.0000.0000.000
87A88GLU-1-0.943-0.96726.781-0.069-0.0690.0000.0000.0000.000
88A89LEU0-0.105-0.02429.5460.0060.0060.0000.0000.0000.000
89A90GLN0-0.050-0.04630.6080.0070.0070.0000.0000.0000.000
90A91PRO00.0320.00530.325-0.005-0.0050.0000.0000.0000.000
91A92GLY00.001-0.00328.5820.0030.0030.0000.0000.0000.000
92A93LYS10.8730.96525.5140.0700.0700.0000.0000.0000.000
93A94MET0-0.0160.00320.429-0.004-0.0040.0000.0000.0000.000
94A95GLU-1-0.849-0.94220.248-0.121-0.1210.0000.0000.0000.000
95A96LYS10.7460.89114.6220.2870.2870.0000.0000.0000.000
96A97PRO00.0420.01616.5350.0100.0100.0000.0000.0000.000
97A98ASP-1-0.911-0.95216.919-0.136-0.1360.0000.0000.0000.000
98A99LYS10.9390.94616.4380.0580.0580.0000.0000.0000.000
99A100THR00.0010.00316.585-0.004-0.0040.0000.0000.0000.000
100A101ILE00.0330.03315.5670.0110.0110.0000.0000.0000.000
101A102PHE00.0130.02811.023-0.006-0.0060.0000.0000.0000.000
102A103ASP-1-0.882-0.94713.039-0.085-0.0850.0000.0000.0000.000
103A104PHE0-0.063-0.03714.6570.0310.0310.0000.0000.0000.000
104A105THR0-0.021-0.03211.2340.0170.0170.0000.0000.0000.000
105A106LEU0-0.0170.0008.242-0.009-0.0090.0000.0000.0000.000
106A107ASN00.0260.00811.3830.1080.1080.0000.0000.0000.000
107A108ALA0-0.048-0.01914.5340.0450.0450.0000.0000.0000.000
108A109LEU0-0.028-0.0149.661-0.005-0.0050.0000.0000.0000.000
109A110GLN0-0.126-0.05211.3230.1170.1170.0000.0000.0000.000
110A111ILE0-0.0160.0056.0940.1000.1000.0000.0000.0000.000
111A112ASP-1-0.821-0.9087.4440.0360.0360.0000.0000.0000.000
112A113LYS10.9330.9626.7100.0020.0020.0000.0000.0000.000
113A114THR0-0.104-0.0665.266-0.218-0.2180.0000.0000.0000.000
114A115GLU-1-0.896-0.9492.406-0.4381.2190.872-1.041-1.488-0.006
115A116ALA00.0000.0052.789-3.980-1.6291.131-1.603-1.879-0.020
116A117VAL0-0.042-0.0222.324-2.512-0.7011.556-0.819-2.549-0.006
117A118MET0-0.065-0.0023.6940.2920.3510.0090.001-0.0700.000
118A119VAL0-0.007-0.0107.4640.0180.0180.0000.0000.0000.000
119A120GLY00.0350.0069.6600.0510.0510.0000.0000.0000.000
120A121ASN00.0370.00613.267-0.023-0.0230.0000.0000.0000.000
121A122THR00.0350.03416.3430.0310.0310.0000.0000.0000.000
122A123PHE0-0.031-0.02516.174-0.029-0.0290.0000.0000.0000.000
123A124GLU-1-0.731-0.88716.714-0.189-0.1890.0000.0000.0000.000
124A125SER00.0180.00917.4730.0090.0090.0000.0000.0000.000
125A126ASP-1-0.776-0.90912.652-0.344-0.3440.0000.0000.0000.000
126A127ILE0-0.036-0.01611.459-0.058-0.0580.0000.0000.0000.000
127A128ILE00.002-0.00712.504-0.022-0.0220.0000.0000.0000.000
128A129GLY00.0170.00414.3480.0130.0130.0000.0000.0000.000
129A130ALA00.0090.0118.6000.0110.0110.0000.0000.0000.000
130A131ASN00.000-0.00210.4850.0490.0490.0000.0000.0000.000
131A132ARG10.9390.96411.7770.2010.2010.0000.0000.0000.000
132A133ALA0-0.0290.00211.4110.0480.0480.0000.0000.0000.000
133A134GLY0-0.057-0.03910.3650.0170.0170.0000.0000.0000.000
134A135ILE0-0.0150.0065.566-0.022-0.0220.0000.0000.0000.000
135A136HIS00.014-0.0022.493-0.4050.2620.498-0.269-0.897-0.001
136A137ALA00.0260.0125.778-0.162-0.1620.0000.0000.0000.000
137A138ILE0-0.028-0.0115.1690.0690.0690.0000.0000.0000.000
138A139TRP0-0.029-0.0228.8060.0010.0010.0000.0000.0000.000
139A140LEU0-0.0030.00412.5920.0300.0300.0000.0000.0000.000
140A141GLN0-0.056-0.04814.9410.0330.0330.0000.0000.0000.000
141A142ASN0-0.046-0.02617.9640.0280.0280.0000.0000.0000.000
142A143PRO0-0.003-0.00320.365-0.005-0.0050.0000.0000.0000.000
143A144GLU-1-0.858-0.90322.807-0.120-0.1200.0000.0000.0000.000
144A145VAL0-0.015-0.01918.5450.0020.0020.0000.0000.0000.000
145A146CYS0-0.092-0.00218.003-0.004-0.0040.0000.0000.0000.000
146A147LEU00.011-0.00119.5770.0200.0200.0000.0000.0000.000
147A148GLN0-0.033-0.03719.790-0.012-0.0120.0000.0000.0000.000
148A149ASP-1-0.926-0.94321.913-0.114-0.1140.0000.0000.0000.000
149A150GLU-1-0.975-0.99923.505-0.092-0.0920.0000.0000.0000.000
150A151ARG10.8720.94421.6790.1060.1060.0000.0000.0000.000
151A152LEU00.0000.00420.2120.0070.0070.0000.0000.0000.000
152A153PRO0-0.027-0.02519.918-0.011-0.0110.0000.0000.0000.000
153A154LEU00.0150.02013.857-0.010-0.0100.0000.0000.0000.000
154A155VAL0-0.065-0.03413.5730.0310.0310.0000.0000.0000.000
155A156ALA0-0.0130.03112.316-0.039-0.0390.0000.0000.0000.000
156A157PRO0-0.059-0.0329.3000.0350.0350.0000.0000.0000.000
157A158PRO00.0110.0057.7310.0460.0460.0000.0000.0000.000
158A159PHE00.002-0.0177.0480.0970.0970.0000.0000.0000.000
159A160VAL00.0490.0238.375-0.099-0.0990.0000.0000.0000.000
160A161ILE0-0.050-0.0267.2300.0710.0710.0000.0000.0000.000
161A162PRO00.0040.01810.325-0.030-0.0300.0000.0000.0000.000
162A163VAL00.0130.00510.3920.0170.0170.0000.0000.0000.000
163A164TRP00.0300.02313.4820.0010.0010.0000.0000.0000.000
164A165ASP-1-0.717-0.85815.589-0.191-0.1910.0000.0000.0000.000
165A166LEU0-0.001-0.01613.417-0.021-0.0210.0000.0000.0000.000
166A167ALA0-0.021-0.00513.066-0.016-0.0160.0000.0000.0000.000
167A168ASP-1-0.871-0.94513.066-0.166-0.1660.0000.0000.0000.000
168A169VAL0-0.0260.0007.887-0.014-0.0140.0000.0000.0000.000
169A170PRO00.003-0.0137.838-0.041-0.0410.0000.0000.0000.000
170A171GLU-1-0.848-0.9347.691-0.111-0.1110.0000.0000.0000.000
171A172ALA0-0.0020.0047.6900.0500.0500.0000.0000.0000.000
172A173LEU00.0040.0163.197-0.570-0.0410.046-0.105-0.4700.000
173A174LEU0-0.0080.0003.284-0.1010.7130.103-0.365-0.551-0.003
174A175LEU0-0.037-0.0085.5850.0810.0810.0000.0000.0000.000
175A176LEU00.0330.0002.512-0.871-0.1860.818-0.317-1.1860.001
176A177LYS10.9200.9692.485-2.734-0.4231.961-1.212-3.0600.003
177A178LYS10.8600.9253.423-0.068-0.5400.0600.720-0.3090.000
178A179ILE0-0.040-0.0095.881-0.024-0.0240.0000.0000.0000.000
179A180SER0-0.0050.0112.427-2.021-0.2700.969-0.865-1.8540.001