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: 4JR8N

Calculation Name: 2IU5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2IU5

Chain ID: A

ChEMBL ID:

UniProt ID: Q9CIV9

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 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
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2072360.413509
FMO2-HF: Nuclear repulsion 1997294.357339
FMO2-HF: Total energy -75066.05617
FMO2-MP2: Total energy -75287.460303


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:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-59.065-51.93518.819-13.025-12.925-0.121
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.036 / q_NPA : -0.021
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].
3A3LYS10.9310.9473.783-5.193-2.929-0.032-1.150-1.0830.005
4A4SER0-0.054-0.0253.757-1.293-0.4560.075-0.299-0.6130.001
5A5ILE00.0190.0102.451-1.3070.0231.072-0.442-1.9600.000
6A6ILE00.0520.0415.588-0.858-0.8580.0000.0000.0000.000
7A7THR0-0.016-0.0218.001-0.273-0.2730.0000.0000.0000.000
8A8GLN00.0690.0337.422-0.073-0.0730.0000.0000.0000.000
9A9LYS10.8910.9553.1045.1125.7710.008-0.267-0.4000.001
10A10ILE0-0.030-0.0058.8520.0380.0380.0000.0000.0000.000
11A11ILE0-0.026-0.01812.3920.0240.0240.0000.0000.0000.000
12A12ALA00.0430.02010.4720.0380.0380.0000.0000.0000.000
13A13LYS10.8480.92211.7410.6840.6840.0000.0000.0000.000
14A14ALA00.0240.01213.2400.0720.0720.0000.0000.0000.000
15A15PHE00.001-0.01315.4970.0620.0620.0000.0000.0000.000
16A16LYS10.8650.9189.9901.7291.7290.0000.0000.0000.000
17A17ASP-1-0.838-0.90816.415-0.493-0.4930.0000.0000.0000.000
18A18LEU0-0.062-0.02618.7170.0490.0490.0000.0000.0000.000
19A19MET00.0140.01119.0430.0650.0650.0000.0000.0000.000
20A20GLN0-0.0030.01820.6720.0530.0530.0000.0000.0000.000
21A21SER0-0.038-0.02822.3310.0230.0230.0000.0000.0000.000
22A22ASN0-0.0210.00324.5270.0550.0550.0000.0000.0000.000
23A23ALA00.0120.01725.126-0.035-0.0350.0000.0000.0000.000
24A24TYR00.1180.03620.0790.0030.0030.0000.0000.0000.000
25A25HIS0-0.0010.00523.950-0.010-0.0100.0000.0000.0000.000
26A26GLN0-0.087-0.05226.2040.0160.0160.0000.0000.0000.000
27A27ILE00.0240.04921.2660.0120.0120.0000.0000.0000.000
28A28SER0-0.028-0.00423.340-0.006-0.0060.0000.0000.0000.000
29A29VAL00.0670.01419.928-0.013-0.0130.0000.0000.0000.000
30A30SER0-0.055-0.03721.6660.0100.0100.0000.0000.0000.000
31A31ASP-1-0.774-0.87123.777-0.198-0.1980.0000.0000.0000.000
32A32ILE00.0150.00217.1640.0020.0020.0000.0000.0000.000
33A33MET0-0.043-0.01017.192-0.021-0.0210.0000.0000.0000.000
34A34GLN0-0.050-0.02820.5090.0180.0180.0000.0000.0000.000
35A35THR0-0.019-0.00619.4280.0210.0210.0000.0000.0000.000
36A36ALA00.0170.00716.8940.0000.0000.0000.0000.0000.000
37A37LYS10.8700.95418.4580.1260.1260.0000.0000.0000.000
38A38ILE00.0070.01315.3280.0520.0520.0000.0000.0000.000
39A39ARG10.9490.96519.758-0.128-0.1280.0000.0000.0000.000
40A40ARG11.0290.99320.7350.1020.1020.0000.0000.0000.000
41A41GLN00.0220.00520.783-0.030-0.0300.0000.0000.0000.000
42A42THR0-0.011-0.00616.2780.0180.0180.0000.0000.0000.000
43A43PHE00.0460.02316.2720.0260.0260.0000.0000.0000.000
44A44TYR0-0.017-0.01515.996-0.018-0.0180.0000.0000.0000.000
45A45ASN0-0.077-0.02315.4030.0270.0270.0000.0000.0000.000
46A46TYR0-0.097-0.05011.0330.0580.0580.0000.0000.0000.000
47A47PHE00.0580.0359.769-0.040-0.0400.0000.0000.0000.000
48A48GLN0-0.029-0.01415.0040.0400.0400.0000.0000.0000.000
49A49ASN0-0.017-0.02817.631-0.015-0.0150.0000.0000.0000.000
50A50GLN00.048-0.00617.212-0.028-0.0280.0000.0000.0000.000
51A51GLU-1-0.919-0.93517.183-0.413-0.4130.0000.0000.0000.000
52A52GLU-1-0.839-0.92914.403-0.318-0.3180.0000.0000.0000.000
53A53LEU0-0.056-0.01811.821-0.097-0.0970.0000.0000.0000.000
54A54LEU00.001-0.01012.431-0.194-0.1940.0000.0000.0000.000
55A55SER00.0160.01112.867-0.142-0.1420.0000.0000.0000.000
56A56TRP00.0420.0154.671-0.329-0.219-0.001-0.006-0.1030.000
57A57ILE0-0.034-0.0238.414-0.493-0.4930.0000.0000.0000.000
58A58PHE0-0.025-0.0089.932-0.311-0.3110.0000.0000.0000.000
59A59GLU-1-0.929-0.9747.492-1.514-1.5140.0000.0000.0000.000
60A60ASN0-0.067-0.0303.972-2.317-2.1480.001-0.043-0.1270.000
61A61ASP-1-0.736-0.8336.087-3.663-3.6630.0000.0000.0000.000
62A62PHE0-0.015-0.0198.1850.0940.0940.0000.0000.0000.000
63A63ALA00.0390.0285.3100.2680.2680.0000.0000.0000.000
64A64GLU-1-0.836-0.9342.136-19.134-17.0193.421-2.889-2.646-0.040
65A65LEU0-0.064-0.0285.4591.1791.1790.0000.0000.0000.000
66A66ILE0-0.040-0.0178.8390.5040.5040.0000.0000.0000.000
67A67ASN0-0.050-0.0447.6430.3460.3460.0000.0000.0000.000
68A68ASP-1-0.900-0.9111.769-30.593-31.01814.276-7.926-5.926-0.088
69A69ASN00.007-0.0045.0500.9411.012-0.001-0.003-0.0670.000
70A70SER0-0.032-0.0277.3980.0860.0860.0000.0000.0000.000
71A71ASP-1-0.967-0.96610.383-0.302-0.3020.0000.0000.0000.000
72A72TYR0-0.050-0.02813.149-0.043-0.0430.0000.0000.0000.000
73A73TYR0-0.076-0.09116.312-0.012-0.0120.0000.0000.0000.000
74A74GLY00.0620.04114.1380.0430.0430.0000.0000.0000.000
75A75TRP00.0190.01914.998-0.046-0.0460.0000.0000.0000.000
76A76GLN0-0.030-0.01116.402-0.030-0.0300.0000.0000.0000.000
77A77ASN00.0150.01414.9350.0160.0160.0000.0000.0000.000
78A78GLU-1-0.742-0.87511.152-1.001-1.0010.0000.0000.0000.000
79A79LEU0-0.0080.00613.704-0.069-0.0690.0000.0000.0000.000
80A80LEU0-0.037-0.01316.748-0.005-0.0050.0000.0000.0000.000
81A81LEU0-0.002-0.01311.7120.0290.0290.0000.0000.0000.000
82A82LEU00.0390.03212.942-0.049-0.0490.0000.0000.0000.000
83A83LEU0-0.034-0.03014.4150.0380.0380.0000.0000.0000.000
84A84ARG10.8710.91815.8770.5050.5050.0000.0000.0000.000
85A85TYR0-0.0240.00111.4380.0940.0940.0000.0000.0000.000
86A86LEU0-0.011-0.01314.6420.0410.0410.0000.0000.0000.000
87A87ASP-1-0.743-0.87217.382-0.452-0.4520.0000.0000.0000.000
88A88GLU-1-1.003-0.98015.598-0.676-0.6760.0000.0000.0000.000
89A89ASN0-0.106-0.06014.1530.0600.0600.0000.0000.0000.000
90A90GLN00.0880.05017.854-0.002-0.0020.0000.0000.0000.000
91A91ILE0-0.029-0.01521.0920.0140.0140.0000.0000.0000.000
92A92PHE0-0.003-0.00415.5540.0410.0410.0000.0000.0000.000
93A93TYR00.063-0.01013.5910.0350.0350.0000.0000.0000.000
94A94GLN0-0.074-0.03620.3260.0370.0370.0000.0000.0000.000
95A95LYS10.7870.87022.8180.4320.4320.0000.0000.0000.000
96A96ILE00.0130.01718.4150.0390.0390.0000.0000.0000.000
97A97PHE0-0.012-0.01221.5170.0220.0220.0000.0000.0000.000
98A98VAL0-0.082-0.02624.1000.0360.0360.0000.0000.0000.000
99A99ILE0-0.065-0.03322.8130.0280.0280.0000.0000.0000.000
100A100ASP-1-0.825-0.91219.613-0.528-0.5280.0000.0000.0000.000
101A101LYS10.9200.95823.1070.3240.3240.0000.0000.0000.000
102A102ASN0-0.053-0.04521.1700.0340.0340.0000.0000.0000.000
103A103PHE00.0560.04115.944-0.027-0.0270.0000.0000.0000.000
104A104GLU-1-0.957-0.97819.652-0.460-0.4600.0000.0000.0000.000
105A105HIS0-0.002-0.01121.205-0.022-0.0220.0000.0000.0000.000
106A106PHE00.0350.03111.7700.0240.0240.0000.0000.0000.000
107A107PHE0-0.010-0.00816.572-0.082-0.0820.0000.0000.0000.000
108A108LEU00.021-0.01117.970-0.039-0.0390.0000.0000.0000.000
109A109ILE00.0180.01615.055-0.005-0.0050.0000.0000.0000.000
110A110GLN0-0.025-0.00312.122-0.250-0.2500.0000.0000.0000.000
111A111TRP00.020-0.00215.070-0.058-0.0580.0000.0000.0000.000
112A112GLU-1-0.950-0.99217.993-0.485-0.4850.0000.0000.0000.000
113A113ASN00.0220.02512.2020.1620.1620.0000.0000.0000.000
114A114LEU0-0.030-0.01014.8460.0120.0120.0000.0000.0000.000
115A115LEU0-0.045-0.04216.1070.0740.0740.0000.0000.0000.000
116A116ASP-1-0.865-0.92416.534-0.524-0.5240.0000.0000.0000.000
117A117LYS10.7870.89712.0130.9790.9790.0000.0000.0000.000
118A118VAL0-0.013-0.01416.3230.0770.0770.0000.0000.0000.000
119A119ILE0-0.010-0.00319.2990.0670.0670.0000.0000.0000.000
120A120PHE0-0.021-0.00714.6730.0550.0550.0000.0000.0000.000
121A121ASP-1-0.780-0.91316.204-0.551-0.5510.0000.0000.0000.000
122A122GLN0-0.0160.00119.0190.0320.0320.0000.0000.0000.000
123A123GLU-1-0.826-0.90322.463-0.197-0.1970.0000.0000.0000.000
124A124LYS10.8910.97415.9640.3530.3530.0000.0000.0000.000
125A125LYS10.7950.91322.2700.2330.2330.0000.0000.0000.000
126A126SER0-0.024-0.02124.4820.0270.0270.0000.0000.0000.000
127A127ASP-1-0.881-0.92027.149-0.118-0.1180.0000.0000.0000.000
128A128TYR0-0.029-0.02126.317-0.013-0.0130.0000.0000.0000.000
129A129HIS0-0.056-0.03030.5050.0040.0040.0000.0000.0000.000
130A130TRP0-0.073-0.03925.318-0.003-0.0030.0000.0000.0000.000
131A131SER00.001-0.01530.4390.0000.0000.0000.0000.0000.000
132A132ASP-1-0.855-0.94827.357-0.199-0.1990.0000.0000.0000.000
133A133LEU0-0.064-0.02827.942-0.021-0.0210.0000.0000.0000.000
134A134GLU-1-0.857-0.93029.709-0.185-0.1850.0000.0000.0000.000
135A135LYS10.9690.99824.6570.2050.2050.0000.0000.0000.000
136A136SER00.0240.02724.905-0.029-0.0290.0000.0000.0000.000
137A137PHE0-0.044-0.02625.936-0.022-0.0220.0000.0000.0000.000
138A138ILE00.0290.01425.460-0.015-0.0150.0000.0000.0000.000
139A139CYS00.0220.01321.988-0.025-0.0250.0000.0000.0000.000
140A140ARG10.9580.96823.4950.2790.2790.0000.0000.0000.000
141A141TYR0-0.065-0.01725.038-0.001-0.0010.0000.0000.0000.000
142A142ASN0-0.011-0.03824.7910.0010.0010.0000.0000.0000.000
143A143ALA00.0360.04321.250-0.017-0.0170.0000.0000.0000.000
144A144ALA00.0070.00322.697-0.021-0.0210.0000.0000.0000.000
145A145ALA0-0.011-0.00225.4450.0040.0040.0000.0000.0000.000
146A146ILE00.0200.00121.3850.0070.0070.0000.0000.0000.000
147A147CYS00.0040.03122.058-0.028-0.0280.0000.0000.0000.000
148A148ALA0-0.030-0.01023.0300.0010.0010.0000.0000.0000.000
149A149ILE00.0180.01225.8740.0120.0120.0000.0000.0000.000
150A150THR0-0.013-0.02721.223-0.004-0.0040.0000.0000.0000.000
151A151ARG10.9981.00923.6520.4000.4000.0000.0000.0000.000
152A152GLU-1-0.973-0.98224.515-0.293-0.2930.0000.0000.0000.000
153A153SER0-0.038-0.02724.9570.0270.0270.0000.0000.0000.000
154A154ILE00.0180.01220.2580.0190.0190.0000.0000.0000.000
155A155ILE0-0.041-0.02224.3680.0230.0230.0000.0000.0000.000
156A156ARG10.8860.94727.2620.3040.3040.0000.0000.0000.000
157A157GLY0-0.0270.01526.7520.0230.0230.0000.0000.0000.000
158A158ASN0-0.132-0.07127.3520.0280.0280.0000.0000.0000.000
159A159SER0-0.0010.00124.380-0.015-0.0150.0000.0000.0000.000
160A160LEU00.040-0.01920.1220.0240.0240.0000.0000.0000.000
161A161GLU-1-0.807-0.88220.854-0.429-0.4290.0000.0000.0000.000
162A162LYS10.8730.93522.6850.3210.3210.0000.0000.0000.000
163A163LEU0-0.016-0.00924.8850.0290.0290.0000.0000.0000.000
164A164TYR0-0.031-0.02619.5910.0280.0280.0000.0000.0000.000
165A165SER00.0200.00323.9170.0000.0000.0000.0000.0000.000
166A166GLN0-0.022-0.01926.6380.0040.0040.0000.0000.0000.000
167A167ILE00.0420.02523.0420.0120.0120.0000.0000.0000.000
168A168VAL00.0440.02322.1900.0020.0020.0000.0000.0000.000
169A169ASN0-0.013-0.01324.7680.0120.0120.0000.0000.0000.000
170A170LEU0-0.029-0.01228.3260.0180.0180.0000.0000.0000.000
171A171LEU00.0070.01622.3090.0110.0110.0000.0000.0000.000
172A172LEU00.008-0.00224.7200.0170.0170.0000.0000.0000.000
173A173ALA0-0.052-0.02227.4590.0200.0200.0000.0000.0000.000
174A174GLN0-0.050-0.02428.4920.0190.0190.0000.0000.0000.000
175A175ILE00.0250.00724.0480.0120.0120.0000.0000.0000.000
176A176LYS10.9300.96828.4840.1870.1870.0000.0000.0000.000
177A177ILE0-0.043-0.01431.2750.0150.0150.0000.0000.0000.000
178A178PHE00.0050.01230.4230.0070.0070.0000.0000.0000.000
179A179GLU-1-0.984-0.97730.745-0.153-0.1530.0000.0000.0000.000