FMODB

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

Last updated: 2024-07-23

All entries: 37478

Number of unique PDB entries: 7783

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FMODB ID: K96L3

Calculation Name: 3IOY-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3IOY

Chain ID: A

ChEMBL ID:

UniProt ID: Q2GA85

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:


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 277
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3519606.508987
FMO2-HF: Nuclear repulsion 3413545.841306
FMO2-HF: Total energy -106060.667681
FMO2-MP2: Total energy -106369.921586


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:1:LEU)


Summations of interaction energy for fragment #1(A:1: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.
-14.916-1.8327.721-5.834-14.963-0.025
Interaction energy analysis for fragmet #1(A:1:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.014 / q_NPA : -0.009
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].
3A3ASP-1-0.863-0.9323.232-1.6990.7920.110-1.100-1.5010.000
4A4PHE00.0740.0212.636-2.663-0.5552.968-1.205-3.870-0.007
5A5ALA00.0430.0274.6290.0010.092-0.001-0.007-0.0820.000
6A6GLY0-0.0070.0037.4980.0800.0800.0000.0000.0000.000
7A7ARG10.8140.9312.812-1.672-0.6601.500-0.470-2.041-0.003
8A8THR00.0100.0006.902-0.040-0.0400.0000.0000.0000.000
9A9ALA00.005-0.0107.273-0.036-0.0360.0000.0000.0000.000
10A10PHE00.0080.0098.7620.0570.0570.0000.0000.0000.000
11A11VAL00.0150.00110.525-0.040-0.0400.0000.0000.0000.000
12A12THR00.0430.02912.7910.0290.0290.0000.0000.0000.000
13A13GLY00.0300.01115.917-0.021-0.0210.0000.0000.0000.000
14A14GLY0-0.005-0.00716.218-0.015-0.0150.0000.0000.0000.000
15A15ALA00.0100.00916.883-0.004-0.0040.0000.0000.0000.000
16A16ASN0-0.062-0.05320.2910.0090.0090.0000.0000.0000.000
17A17GLY00.0810.04819.736-0.009-0.0090.0000.0000.0000.000
18A18VAL00.026-0.01014.979-0.011-0.0110.0000.0000.0000.000
19A19GLY00.0380.02615.163-0.038-0.0380.0000.0000.0000.000
20A20ILE00.0010.01514.983-0.024-0.0240.0000.0000.0000.000
21A21GLY00.0180.01715.495-0.008-0.0080.0000.0000.0000.000
22A22LEU0-0.029-0.02610.109-0.049-0.0490.0000.0000.0000.000
23A23VAL00.0170.00710.946-0.056-0.0560.0000.0000.0000.000
24A24ARG10.8110.86812.5130.2440.2440.0000.0000.0000.000
25A25GLN0-0.078-0.05110.919-0.031-0.0310.0000.0000.0000.000
26A26LEU00.029-0.0016.681-0.088-0.0880.0000.0000.0000.000
27A27LEU00.0100.0209.048-0.014-0.0140.0000.0000.0000.000
28A28ASN0-0.031-0.00712.179-0.036-0.0360.0000.0000.0000.000
29A29GLN0-0.051-0.0136.929-0.244-0.2440.0000.0000.0000.000
30A30GLY0-0.010-0.0088.268-0.016-0.0160.0000.0000.0000.000
31A31CYS0-0.090-0.0307.009-0.016-0.0160.0000.0000.0000.000
32A32LYS10.9070.9529.1510.1840.1840.0000.0000.0000.000
33A33VAL0-0.037-0.02610.232-0.044-0.0440.0000.0000.0000.000
34A34ALA00.0040.00012.4130.0380.0380.0000.0000.0000.000
35A35ILE0-0.021-0.00914.192-0.028-0.0280.0000.0000.0000.000
36A36ALA00.0290.01516.4540.0240.0240.0000.0000.0000.000
37A37ASP-1-0.866-0.97118.153-0.191-0.1910.0000.0000.0000.000
38A38ILE00.0660.05721.1220.0120.0120.0000.0000.0000.000
39A39ARG10.8440.91624.5450.1180.1180.0000.0000.0000.000
40A40GLN00.0470.00325.363-0.009-0.0090.0000.0000.0000.000
41A41ASP-1-0.826-0.89926.611-0.097-0.0970.0000.0000.0000.000
42A42SER0-0.075-0.05124.4280.0010.0010.0000.0000.0000.000
43A43ILE00.0190.02321.477-0.010-0.0100.0000.0000.0000.000
44A44ASP-1-0.820-0.89823.262-0.114-0.1140.0000.0000.0000.000
45A45LYS10.9320.96825.9420.1350.1350.0000.0000.0000.000
46A46ALA0-0.0050.00820.584-0.003-0.0030.0000.0000.0000.000
47A47LEU00.017-0.00119.882-0.008-0.0080.0000.0000.0000.000
48A48ALA0-0.020-0.00422.4990.0010.0010.0000.0000.0000.000
49A49THR0-0.056-0.04423.779-0.001-0.0010.0000.0000.0000.000
50A50LEU00.0460.02217.434-0.006-0.0060.0000.0000.0000.000
51A51GLU-1-0.916-0.96221.160-0.125-0.1250.0000.0000.0000.000
52A52ALA0-0.071-0.02623.5330.0060.0060.0000.0000.0000.000
53A53GLU-1-0.864-0.89919.518-0.225-0.2250.0000.0000.0000.000
54A54GLY0-0.0290.00021.829-0.004-0.0040.0000.0000.0000.000
55A55SER0-0.029-0.02417.261-0.008-0.0080.0000.0000.0000.000
56A56GLY00.0490.02818.401-0.007-0.0070.0000.0000.0000.000
57A57PRO0-0.044-0.02219.2360.0010.0010.0000.0000.0000.000
58A58GLU-1-0.871-0.92514.009-0.150-0.1500.0000.0000.0000.000
59A59VAL0-0.0160.00214.930-0.031-0.0310.0000.0000.0000.000
60A60MET0-0.048-0.01016.8890.0270.0270.0000.0000.0000.000
61A61GLY00.0000.00117.931-0.021-0.0210.0000.0000.0000.000
62A62VAL00.0020.00718.3370.0110.0110.0000.0000.0000.000
63A63GLN0-0.029-0.02620.871-0.008-0.0080.0000.0000.0000.000
64A64LEU0-0.031-0.02818.7010.0040.0040.0000.0000.0000.000
65A65ASP-1-0.828-0.91422.668-0.116-0.1160.0000.0000.0000.000
66A66VAL0-0.032-0.01718.8540.0040.0040.0000.0000.0000.000
67A67ALA00.0230.02021.4570.0000.0000.0000.0000.0000.000
68A68SER00.0200.02124.2690.0110.0110.0000.0000.0000.000
69A69ARG10.8900.93622.9020.0700.0700.0000.0000.0000.000
70A70GLU-1-0.932-0.96023.086-0.052-0.0520.0000.0000.0000.000
71A71GLY00.0420.01624.2910.0010.0010.0000.0000.0000.000
72A72PHE00.001-0.00315.572-0.008-0.0080.0000.0000.0000.000
73A73LYS10.8310.90419.4230.0300.0300.0000.0000.0000.000
74A74MET00.0030.00420.7410.0020.0020.0000.0000.0000.000
75A75ALA00.0630.02819.4400.0010.0010.0000.0000.0000.000
76A76ALA0-0.022-0.01016.500-0.008-0.0080.0000.0000.0000.000
77A77ASP-1-0.793-0.88717.276-0.040-0.0400.0000.0000.0000.000
78A78GLU-1-0.927-0.95119.911-0.088-0.0880.0000.0000.0000.000
79A79VAL00.014-0.01314.2900.0000.0000.0000.0000.0000.000
80A80GLU-1-0.768-0.84113.741-0.055-0.0550.0000.0000.0000.000
81A81ALA0-0.047-0.00616.5450.0160.0160.0000.0000.0000.000
82A82ARG10.9010.94818.9970.1140.1140.0000.0000.0000.000
83A83PHE0-0.036-0.04213.8710.0050.0050.0000.0000.0000.000
84A84GLY00.0240.03713.653-0.004-0.0040.0000.0000.0000.000
85A85PRO0-0.019-0.01711.582-0.026-0.0260.0000.0000.0000.000
86A86VAL0-0.0020.0039.271-0.025-0.0250.0000.0000.0000.000
87A87SER0-0.046-0.0285.744-0.005-0.0050.0000.0000.0000.000
88A88ILE0-0.013-0.0072.827-0.924-0.1390.239-0.158-0.8660.000
89A89LEU0-0.0050.0135.6090.0860.0860.0000.0000.0000.000
90A90CYS0-0.023-0.0028.051-0.099-0.0990.0000.0000.0000.000
91A91ASN0-0.015-0.01910.3070.0780.0780.0000.0000.0000.000
92A92ASN00.019-0.00713.759-0.023-0.0230.0000.0000.0000.000
93A93ALA0-0.0150.01615.4630.0140.0140.0000.0000.0000.000
94A94GLY0-0.003-0.00418.961-0.005-0.0050.0000.0000.0000.000
95A95VAL0-0.038-0.01321.7320.0030.0030.0000.0000.0000.000
96A96ASN00.016-0.01625.4720.0030.0030.0000.0000.0000.000
97A97LEU00.0400.02427.8040.0020.0020.0000.0000.0000.000
98A98PHE0-0.055-0.03231.484-0.002-0.0020.0000.0000.0000.000
99A99GLN00.0640.03233.2780.0020.0020.0000.0000.0000.000
100A100PRO00.0390.03934.260-0.006-0.0060.0000.0000.0000.000
101A101ILE0-0.002-0.01232.2900.0000.0000.0000.0000.0000.000
102A102GLU-1-0.911-0.95136.196-0.064-0.0640.0000.0000.0000.000
103A103GLU-1-0.964-0.98339.056-0.061-0.0610.0000.0000.0000.000
104A104SER0-0.101-0.04835.551-0.003-0.0030.0000.0000.0000.000
105A105SER0-0.043-0.04337.5990.0030.0030.0000.0000.0000.000
106A106TYR00.001-0.03436.277-0.003-0.0030.0000.0000.0000.000
107A107ASP-1-0.865-0.92135.152-0.062-0.0620.0000.0000.0000.000
108A108ASP-1-0.795-0.87233.816-0.080-0.0800.0000.0000.0000.000
109A109TRP0-0.029-0.03430.064-0.010-0.0100.0000.0000.0000.000
110A110ASP-1-0.908-0.95330.268-0.075-0.0750.0000.0000.0000.000
111A111TRP0-0.026-0.00928.732-0.006-0.0060.0000.0000.0000.000
112A112LEU0-0.014-0.02127.374-0.009-0.0090.0000.0000.0000.000
113A113LEU00.0020.00625.763-0.013-0.0130.0000.0000.0000.000
114A114GLY00.0060.01324.965-0.007-0.0070.0000.0000.0000.000
115A115VAL00.003-0.00422.528-0.007-0.0070.0000.0000.0000.000
116A116ASN0-0.026-0.01721.428-0.019-0.0190.0000.0000.0000.000
117A117LEU00.0060.00320.504-0.016-0.0160.0000.0000.0000.000
118A118HIS00.009-0.01420.809-0.008-0.0080.0000.0000.0000.000
119A119GLY00.0680.05120.1740.0010.0010.0000.0000.0000.000
120A120VAL0-0.033-0.01315.235-0.015-0.0150.0000.0000.0000.000
121A121VAL00.0080.00216.734-0.004-0.0040.0000.0000.0000.000
122A122ASN0-0.016-0.00318.6630.0190.0190.0000.0000.0000.000
123A123GLY00.0730.04615.3410.0110.0110.0000.0000.0000.000
124A124VAL0-0.037-0.03613.2640.0030.0030.0000.0000.0000.000
125A125THR0-0.058-0.05414.9470.0260.0260.0000.0000.0000.000
126A126THR0-0.052-0.03116.6320.0260.0260.0000.0000.0000.000
127A127PHE00.0220.00311.8310.0130.0130.0000.0000.0000.000
128A128VAL0-0.0010.01111.2010.0210.0210.0000.0000.0000.000
129A129PRO0-0.015-0.00813.0900.0450.0450.0000.0000.0000.000
130A130ARG10.8700.93214.0950.0820.0820.0000.0000.0000.000
131A131MET0-0.054-0.0097.8030.0410.0410.0000.0000.0000.000
132A132VAL0-0.030-0.02411.5530.0820.0820.0000.0000.0000.000
133A133GLU-1-0.987-0.99013.1940.1130.1130.0000.0000.0000.000
134A134ARG10.8850.90512.2460.0020.0020.0000.0000.0000.000
135A135VAL0-0.071-0.0209.3050.0680.0680.0000.0000.0000.000
136A136LYS10.8540.92512.113-0.129-0.1290.0000.0000.0000.000
137A137ALA00.0030.02115.544-0.001-0.0010.0000.0000.0000.000
138A138GLY0-0.052-0.02113.851-0.006-0.0060.0000.0000.0000.000
139A139GLU-1-0.954-0.97213.7410.1780.1780.0000.0000.0000.000
140A140GLN0-0.030-0.0256.763-0.082-0.0820.0000.0000.0000.000
141A141LYS10.8880.9336.731-0.949-0.9490.0000.0000.0000.000
142A142GLY00.0790.0533.9290.0800.2650.001-0.038-0.1470.000
143A143GLY00.0350.0012.890-1.290-0.4260.133-0.316-0.681-0.002
144A144HIS0-0.018-0.0182.186-3.503-1.8472.168-1.088-2.735-0.007
145A145VAL0-0.0050.0054.2640.1310.2060.001-0.023-0.0520.000
146A146VAL0-0.005-0.0076.375-0.115-0.1150.0000.0000.0000.000
147A147ASN00.0180.0068.8160.0750.0750.0000.0000.0000.000
148A148THR00.013-0.01212.631-0.040-0.0400.0000.0000.0000.000
149A149ALA00.0180.01014.9650.0440.0440.0000.0000.0000.000
150A150SER00.015-0.01617.7400.0100.0100.0000.0000.0000.000
151A151MET00.0490.03720.060-0.010-0.0100.0000.0000.0000.000
152A152ALA00.0350.03122.1520.0130.0130.0000.0000.0000.000
153A153ALA0-0.074-0.03920.2710.0100.0100.0000.0000.0000.000
154A154PHE0-0.048-0.05018.8300.0000.0000.0000.0000.0000.000
155A155LEU00.0070.01624.1890.0110.0110.0000.0000.0000.000
156A156ALA0-0.015-0.00627.158-0.004-0.0040.0000.0000.0000.000
157A157ALA00.0300.01729.2550.0070.0070.0000.0000.0000.000
158A158GLY00.008-0.00332.538-0.001-0.0010.0000.0000.0000.000
159A159SER0-0.0180.01233.4650.0020.0020.0000.0000.0000.000
160A160PRO0-0.052-0.01528.471-0.002-0.0020.0000.0000.0000.000
161A161GLY00.1120.03629.708-0.006-0.0060.0000.0000.0000.000
162A162ILE00.0470.03128.909-0.004-0.0040.0000.0000.0000.000
163A163TYR00.0140.01322.880-0.013-0.0130.0000.0000.0000.000
164A164ASN00.0550.01825.308-0.019-0.0190.0000.0000.0000.000
165A165THR00.0130.00325.470-0.005-0.0050.0000.0000.0000.000
166A166THR0-0.076-0.04323.560-0.006-0.0060.0000.0000.0000.000
167A167LYS10.8590.94019.0750.2160.2160.0000.0000.0000.000
168A168PHE00.0310.01920.606-0.019-0.0190.0000.0000.0000.000
169A169ALA0-0.0240.00521.626-0.004-0.0040.0000.0000.0000.000
170A170VAL00.0220.01216.422-0.004-0.0040.0000.0000.0000.000
171A171ARG10.8750.95116.9790.1520.1520.0000.0000.0000.000
172A172GLY00.0420.03017.450-0.010-0.0100.0000.0000.0000.000
173A173LEU0-0.022-0.00515.6800.0100.0100.0000.0000.0000.000
174A174SER00.014-0.02513.011-0.008-0.0080.0000.0000.0000.000
175A175GLU-1-0.831-0.88113.449-0.225-0.2250.0000.0000.0000.000
176A176SER0-0.034-0.02815.4180.0240.0240.0000.0000.0000.000
177A177LEU0-0.034-0.01911.9290.0320.0320.0000.0000.0000.000
178A178HIS00.0270.0119.1030.1740.1740.0000.0000.0000.000
179A179TYR00.0320.00711.3720.0520.0520.0000.0000.0000.000
180A180SER0-0.124-0.04613.9270.0690.0690.0000.0000.0000.000
181A181LEU00.0370.00010.2120.0790.0790.0000.0000.0000.000
182A182LEU00.0530.0438.8580.0890.0890.0000.0000.0000.000
183A183LYS10.8510.9259.5290.0160.0160.0000.0000.0000.000
184A184TYR0-0.028-0.02310.6880.0520.0520.0000.0000.0000.000
185A185GLU-1-0.917-0.9655.8322.0092.0090.0000.0000.0000.000
186A186ILE0-0.068-0.0155.5310.3130.3130.0000.0000.0000.000
187A187GLY00.0380.0114.769-0.079-0.004-0.001-0.008-0.0660.000
188A188VAL0-0.024-0.0095.6760.1970.1970.0000.0000.0000.000
189A189SER0-0.014-0.0027.563-0.117-0.1170.0000.0000.0000.000
190A190VAL0-0.017-0.0079.2110.0680.0680.0000.0000.0000.000
191A191LEU0-0.012-0.00111.862-0.005-0.0050.0000.0000.0000.000
192A192CYS0-0.053-0.03313.4750.0560.0560.0000.0000.0000.000
193A193PRO00.0080.01916.4520.0120.0120.0000.0000.0000.000
194A194GLY00.0650.02418.8120.0220.0220.0000.0000.0000.000
195A195LEU00.0270.00222.088-0.008-0.0080.0000.0000.0000.000
196A196VAL0-0.0090.01620.154-0.014-0.0140.0000.0000.0000.000
197A197LYS10.8180.92022.7750.1830.1830.0000.0000.0000.000
198A227ALA00.012-0.01336.902-0.001-0.0010.0000.0000.0000.000
199A228GLY00.0340.01535.103-0.001-0.0010.0000.0000.0000.000
200A229VAL00.0160.00330.603-0.005-0.0050.0000.0000.0000.000
201A230HIS0-0.084-0.04629.745-0.008-0.0080.0000.0000.0000.000
202A231GLU-1-0.864-0.92229.102-0.124-0.1240.0000.0000.0000.000
203A232PHE0-0.061-0.03428.539-0.005-0.0050.0000.0000.0000.000
204A233GLY00.0130.01825.467-0.005-0.0050.0000.0000.0000.000
205A234MET0-0.050-0.03619.189-0.015-0.0150.0000.0000.0000.000
206A235GLU-1-0.777-0.88320.577-0.202-0.2020.0000.0000.0000.000
207A236PRO00.0300.00917.897-0.030-0.0300.0000.0000.0000.000
208A237ASP-1-0.766-0.87315.850-0.358-0.3580.0000.0000.0000.000
209A238VAL0-0.044-0.01315.155-0.043-0.0430.0000.0000.0000.000
210A239ILE0-0.019-0.02314.178-0.042-0.0420.0000.0000.0000.000
211A240GLY00.0390.01711.892-0.063-0.0630.0000.0000.0000.000
212A241ALA00.0190.00810.409-0.114-0.1140.0000.0000.0000.000
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