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: 3JJYL

Calculation Name: 2IQI-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2IQI

Chain ID: A

ChEMBL ID:

UniProt ID: Q8PCT0

Base Structure: X-ray

Registration Date: 2023-09-21

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 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 178
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1736916.754994
FMO2-HF: Nuclear repulsion 1671013.676934
FMO2-HF: Total energy -65903.078059
FMO2-MP2: Total energy -66099.681981


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:32:ALA)


Summations of interaction energy for fragment #1(A:32:ALA)
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.
-4.654-0.8143.233-3.181-3.891-0.02
Interaction energy analysis for fragmet #1(A:32:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.012 / q_NPA : 0.005
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].
3A34ILE0-0.023-0.0043.218-0.1661.7290.036-0.844-1.0870.004
4A35TYR00.002-0.0195.8990.3250.3250.0000.0000.0000.000
5A36ALA00.010-0.0248.9800.1180.1180.0000.0000.0000.000
6A37PRO0-0.017-0.00112.2250.0450.0450.0000.0000.0000.000
7A38THR0-0.031-0.01215.3160.0240.0240.0000.0000.0000.000
8A39VAL0-0.026-0.01018.4850.0370.0370.0000.0000.0000.000
9A40ARG10.9030.95120.8770.2760.2760.0000.0000.0000.000
10A41VAL00.0080.00424.6000.0040.0040.0000.0000.0000.000
11A42THR0-0.006-0.00427.5790.0010.0010.0000.0000.0000.000
12A43PRO00.0210.01830.9650.0070.0070.0000.0000.0000.000
13A44ASN00.0080.01333.7410.0070.0070.0000.0000.0000.000
14A45PRO00.023-0.00936.0670.0040.0040.0000.0000.0000.000
15A46ALA00.0090.00639.6500.0030.0030.0000.0000.0000.000
16A47TRP00.0020.02231.3380.0030.0030.0000.0000.0000.000
17A48PRO00.0210.02739.0740.0000.0000.0000.0000.0000.000
18A49GLN0-0.047-0.02939.726-0.001-0.0010.0000.0000.0000.000
19A50VAL0-0.040-0.01839.1070.0050.0050.0000.0000.0000.000
20A51SER00.006-0.01141.462-0.003-0.0030.0000.0000.0000.000
21A52TRP0-0.035-0.00236.8290.0000.0000.0000.0000.0000.000
22A53GLN0-0.004-0.01538.409-0.001-0.0010.0000.0000.0000.000
23A54LEU0-0.023-0.00532.7350.0050.0050.0000.0000.0000.000
24A55LEU0-0.0090.00431.221-0.006-0.0060.0000.0000.0000.000
25A56VAL0-0.005-0.00727.0990.0030.0030.0000.0000.0000.000
26A57ALA0-0.039-0.02928.334-0.002-0.0020.0000.0000.0000.000
27A58LYS10.8490.91619.8340.1340.1340.0000.0000.0000.000
28A59PRO0-0.054-0.01421.9290.0140.0140.0000.0000.0000.000
29A60SER0-0.041-0.03422.5220.0010.0010.0000.0000.0000.000
30A61ALA00.0460.01019.594-0.010-0.0100.0000.0000.0000.000
31A62ALA00.0330.02720.1390.0140.0140.0000.0000.0000.000
32A63ARG10.9940.97017.290-0.087-0.0870.0000.0000.0000.000
33A64ILE0-0.0140.01214.3480.0120.0120.0000.0000.0000.000
34A65ILE0-0.0020.01313.912-0.012-0.0120.0000.0000.0000.000
35A66ASP-1-0.891-0.91314.981-0.091-0.0910.0000.0000.0000.000
36A67SER0-0.043-0.02711.7120.0420.0420.0000.0000.0000.000
37A68PRO00.0280.0178.024-0.014-0.0140.0000.0000.0000.000
38A69ARG10.9660.9807.297-0.628-0.6280.0000.0000.0000.000
39A70ILE00.0120.0267.041-0.027-0.0270.0000.0000.0000.000
40A71ASN0-0.016-0.0229.4120.1400.1400.0000.0000.0000.000
41A72VAL00.0010.00212.362-0.065-0.0650.0000.0000.0000.000
42A73ARG10.8110.89714.5240.0240.0240.0000.0000.0000.000
43A74PRO0-0.0070.00516.583-0.022-0.0220.0000.0000.0000.000
44A75THR0-0.003-0.02318.865-0.014-0.0140.0000.0000.0000.000
45A76PRO00.0460.00022.0080.0010.0010.0000.0000.0000.000
46A77GLY0-0.0100.00523.988-0.007-0.0070.0000.0000.0000.000
47A78GLU-1-0.866-0.89419.2790.1680.1680.0000.0000.0000.000
48A79LEU0-0.039-0.03616.497-0.022-0.0220.0000.0000.0000.000
49A80GLN0-0.050-0.02413.5030.0740.0740.0000.0000.0000.000
50A81VAL0-0.023-0.0248.894-0.055-0.0550.0000.0000.0000.000
51A82TYR00.018-0.0107.7240.0930.0930.0000.0000.0000.000
52A83HIS00.0150.0046.0460.1840.1840.0000.0000.0000.000
53A84GLY00.0050.0062.892-0.473-0.1330.319-0.216-0.4420.001
54A85ALA0-0.034-0.0142.488-4.574-3.1082.873-2.211-2.129-0.025
55A86GLY00.0070.0013.4720.7490.9170.0060.092-0.2650.000
56A87TRP0-0.027-0.0025.105-0.361-0.390-0.001-0.0020.0320.000
57A88ALA00.006-0.0108.2940.0090.0090.0000.0000.0000.000
58A89GLN0-0.049-0.02110.0670.0770.0770.0000.0000.0000.000
59A90PRO00.0290.00311.893-0.030-0.0300.0000.0000.0000.000
60A91ALA00.0540.02913.490-0.021-0.0210.0000.0000.0000.000
61A92THR0-0.013-0.03314.998-0.012-0.0120.0000.0000.0000.000
62A93ASP-1-0.812-0.90116.229-0.176-0.1760.0000.0000.0000.000
63A94MET0-0.0190.00413.004-0.011-0.0110.0000.0000.0000.000
64A95LEU00.0030.02517.0650.0030.0030.0000.0000.0000.000
65A96GLU-1-0.856-0.95320.274-0.132-0.1320.0000.0000.0000.000
66A97ASP-1-0.774-0.88619.572-0.265-0.2650.0000.0000.0000.000
67A98SER0-0.046-0.02719.628-0.006-0.0060.0000.0000.0000.000
68A99VAL0-0.016-0.02022.1640.0120.0120.0000.0000.0000.000
69A100VAL0-0.023-0.00625.0370.0100.0100.0000.0000.0000.000
70A101ARG10.9040.94819.5460.2930.2930.0000.0000.0000.000
71A102ALA0-0.0130.00525.9780.0060.0060.0000.0000.0000.000
72A103PHE0-0.019-0.01527.6520.0130.0130.0000.0000.0000.000
73A104GLU-1-0.828-0.88726.844-0.171-0.1710.0000.0000.0000.000
74A105ASP-1-0.871-0.94427.410-0.205-0.2050.0000.0000.0000.000
75A106SER0-0.093-0.05530.5800.0090.0090.0000.0000.0000.000
76A107GLY00.0210.00733.1310.0050.0050.0000.0000.0000.000
77A108LYS10.7800.88435.7940.1020.1020.0000.0000.0000.000
78A109ILE00.0420.01434.4940.0070.0070.0000.0000.0000.000
79A110ALA00.0080.01436.046-0.005-0.0050.0000.0000.0000.000
80A111ALA0-0.023-0.01136.485-0.001-0.0010.0000.0000.0000.000
81A112VAL00.0250.01230.7450.0040.0040.0000.0000.0000.000
82A113ALA00.0150.01631.132-0.003-0.0030.0000.0000.0000.000
83A114ARG10.8550.91523.5960.1850.1850.0000.0000.0000.000
84A115ILE00.018-0.01027.3940.0060.0060.0000.0000.0000.000
85A116GLY0-0.040-0.01327.4920.0070.0070.0000.0000.0000.000
86A117ALA0-0.034-0.01828.467-0.005-0.0050.0000.0000.0000.000
87A118GLY00.0290.01630.399-0.002-0.0020.0000.0000.0000.000
88A119ILE0-0.034-0.01433.6750.0030.0030.0000.0000.0000.000
89A120ARG10.8440.90037.3110.0590.0590.0000.0000.0000.000
90A121SER0-0.019-0.00536.535-0.005-0.0050.0000.0000.0000.000
91A122ASP-1-0.783-0.85938.676-0.053-0.0530.0000.0000.0000.000
92A123TYR0-0.078-0.04237.4530.0030.0030.0000.0000.0000.000
93A124LYS10.9930.99432.5930.0450.0450.0000.0000.0000.000
94A125LEU00.0070.01729.2840.0050.0050.0000.0000.0000.000
95A126ALA0-0.011-0.01229.206-0.003-0.0030.0000.0000.0000.000
96A127ILE00.007-0.01325.2360.0020.0020.0000.0000.0000.000
97A128ASP-1-0.866-0.88325.302-0.033-0.0330.0000.0000.0000.000
98A129VAL00.005-0.01619.765-0.005-0.0050.0000.0000.0000.000
99A130ARG10.8810.93121.8800.0460.0460.0000.0000.0000.000
100A131ARG10.7800.85419.8980.0550.0550.0000.0000.0000.000
101A132PHE00.0500.01113.812-0.009-0.0090.0000.0000.0000.000
102A133GLU-1-0.795-0.86314.981-0.016-0.0160.0000.0000.0000.000
103A134SER00.0360.01814.090-0.030-0.0300.0000.0000.0000.000
104A135ASP-1-0.817-0.91015.9220.0030.0030.0000.0000.0000.000
105A136TYR00.0420.00915.433-0.017-0.0170.0000.0000.0000.000
106A137ALA0-0.025-0.00320.7450.0000.0000.0000.0000.0000.000
107A138GLY0-0.028-0.00524.1870.0000.0000.0000.0000.0000.000
108A139GLN0-0.019-0.01024.078-0.001-0.0010.0000.0000.0000.000
109A140SER0-0.021-0.01623.2670.0090.0090.0000.0000.0000.000
110A141LEU0-0.036-0.00919.783-0.001-0.0010.0000.0000.0000.000
111A142PRO0-0.0110.01716.4780.0070.0070.0000.0000.0000.000
112A143ALA00.0170.00219.549-0.023-0.0230.0000.0000.0000.000
113A144ALA0-0.0160.01816.5660.0150.0150.0000.0000.0000.000
114A145THR0-0.039-0.03717.8940.0050.0050.0000.0000.0000.000
115A146ILE0-0.0080.00118.4340.0000.0000.0000.0000.0000.000
116A147GLU-1-0.854-0.90420.887-0.035-0.0350.0000.0000.0000.000
117A148LEU00.0150.01323.0190.0050.0050.0000.0000.0000.000
118A149ASN0-0.042-0.03325.4890.0050.0050.0000.0000.0000.000
119A150ALA00.0480.04828.7770.0000.0000.0000.0000.0000.000
120A151LYS10.8950.93630.2630.0470.0470.0000.0000.0000.000
121A152LEU00.0400.03633.082-0.005-0.0050.0000.0000.0000.000
122A153LEU0-0.011-0.00935.1490.0050.0050.0000.0000.0000.000
123A154HIS00.0530.03537.834-0.003-0.0030.0000.0000.0000.000
124A155SER0-0.052-0.06339.0160.0020.0020.0000.0000.0000.000
125A156SER0-0.049-0.02640.4960.0020.0020.0000.0000.0000.000
126A157ASP-1-0.802-0.91643.732-0.032-0.0320.0000.0000.0000.000
127A158GLN0-0.107-0.04639.1920.0010.0010.0000.0000.0000.000
128A159ARG10.8230.89840.3840.0400.0400.0000.0000.0000.000
129A160VAL0-0.017-0.02437.893-0.004-0.0040.0000.0000.0000.000
130A161VAL0-0.0280.00939.2880.0020.0020.0000.0000.0000.000
131A162ALA00.0120.00138.1300.0010.0010.0000.0000.0000.000
132A163SER0-0.055-0.04833.4810.0000.0000.0000.0000.0000.000
133A164ARG10.9460.98832.3400.0720.0720.0000.0000.0000.000
134A165THR0-0.021-0.00529.348-0.002-0.0020.0000.0000.0000.000
135A166PHE0-0.0060.00027.3460.0010.0010.0000.0000.0000.000
136A167THR0-0.004-0.02425.8680.0050.0050.0000.0000.0000.000
137A168VAL0-0.0110.02223.2790.0020.0020.0000.0000.0000.000
138A169ALA00.0350.01722.228-0.006-0.0060.0000.0000.0000.000
139A170ARG10.8370.91020.7150.1840.1840.0000.0000.0000.000
140A171PRO00.0070.00520.549-0.010-0.0100.0000.0000.0000.000
141A172SER00.005-0.02016.910-0.038-0.0380.0000.0000.0000.000
142A173SER0-0.020-0.01819.1650.0190.0190.0000.0000.0000.000
143A174SER0-0.014-0.04815.9680.0100.0100.0000.0000.0000.000
144A175THR00.0680.03215.393-0.009-0.0090.0000.0000.0000.000
145A176ASP-1-0.896-0.88912.186-0.238-0.2380.0000.0000.0000.000
146A177THR00.019-0.0017.473-0.111-0.1110.0000.0000.0000.000
147A178ALA00.0270.02410.360-0.055-0.0550.0000.0000.0000.000
148A179ALA00.0080.01911.8970.0260.0260.0000.0000.0000.000
149A180VAL00.0380.01212.3590.0230.0230.0000.0000.0000.000
150A181ALA0-0.003-0.00710.8910.0310.0310.0000.0000.0000.000
151A182ALA00.0430.02112.9830.0340.0340.0000.0000.0000.000
152A183ALA0-0.0200.00416.4320.0470.0470.0000.0000.0000.000
153A184PHE00.028-0.01713.2760.0310.0310.0000.0000.0000.000
154A185GLU-1-0.871-0.91116.493-0.451-0.4510.0000.0000.0000.000
155A186GLN00.0100.01917.9120.0640.0640.0000.0000.0000.000
156A187ALA00.0060.00419.2100.0250.0250.0000.0000.0000.000
157A188LEU00.0240.00516.1560.0260.0260.0000.0000.0000.000
158A189THR00.0190.01420.5520.0220.0220.0000.0000.0000.000
159A190GLN0-0.034-0.00523.2290.0100.0100.0000.0000.0000.000
160A191VAL00.0280.00822.6450.0140.0140.0000.0000.0000.000
161A192THR0-0.008-0.01723.0330.0140.0140.0000.0000.0000.000
162A193THR0-0.031-0.03025.7130.0110.0110.0000.0000.0000.000
163A194GLU-1-0.893-0.94628.554-0.104-0.1040.0000.0000.0000.000
164A195LEU0-0.008-0.00625.7800.0110.0110.0000.0000.0000.000
165A196VAL00.0310.03028.6780.0100.0100.0000.0000.0000.000
166A197GLY00.0270.00631.2240.0080.0080.0000.0000.0000.000
167A198TRP0-0.019-0.02232.6310.0060.0060.0000.0000.0000.000
168A199THR0-0.001-0.00932.1500.0080.0080.0000.0000.0000.000
169A200LEU0-0.0050.00234.8030.0060.0060.0000.0000.0000.000
170A201ILE0-0.018-0.01737.0880.0050.0050.0000.0000.0000.000
171A202THR0-0.024-0.02837.5030.0050.0050.0000.0000.0000.000
172A203GLY00.0340.01338.6450.0040.0040.0000.0000.0000.000
173A204GLN0-0.030-0.01539.9650.0010.0010.0000.0000.0000.000
174A205GLN0-0.029-0.02442.6440.0030.0030.0000.0000.0000.000
175A206ASP-1-0.725-0.80842.741-0.042-0.0420.0000.0000.0000.000
176A207SER0-0.013-0.00143.6960.0020.0020.0000.0000.0000.000
177A208GLN0-0.0400.00245.553-0.002-0.0020.0000.0000.0000.000
178A209THR0-0.070-0.02947.6090.0030.0030.0000.0000.0000.000