FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: LZGG9

Calculation Name: 2IM5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2IM5

Chain ID: A

ChEMBL ID:

UniProt ID: Q7MXV0

Base Structure: X-ray

Registration Date: 2023-06-22

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 389
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -7248448.119627
FMO2-HF: Nuclear repulsion 7091303.742338
FMO2-HF: Total energy -157144.377289
FMO2-MP2: Total energy -157605.030877


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:3:ILE)


Summations of interaction energy for fragment #1(A:3:ILE)
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.
-43.436-32.14321.871-12.706-20.458-0.107
Interaction energy analysis for fragmet #1(A:3:ILE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.075 / q_NPA : -0.036
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].
3A5ARG10.9250.9523.417-9.688-6.5370.018-1.501-1.6680.012
4A6SER00.0260.0056.120-0.269-0.2690.0000.0000.0000.000
5A7ILE00.0230.0168.584-0.199-0.1990.0000.0000.0000.000
6A8LEU0-0.008-0.01111.028-0.119-0.1190.0000.0000.0000.000
7A9ASP-1-0.783-0.8625.368-0.446-0.4460.0000.0000.0000.000
8A10THR00.031-0.0207.803-0.182-0.1820.0000.0000.0000.000
9A11ASP-1-0.747-0.83810.284-0.222-0.2220.0000.0000.0000.000
10A12LEU00.0430.02213.5280.0060.0060.0000.0000.0000.000
11A13TYR0-0.046-0.05215.6130.0100.0100.0000.0000.0000.000
12A14LYS10.7520.89213.3180.2700.2700.0000.0000.0000.000
13A15PHE00.0520.02413.6310.0030.0030.0000.0000.0000.000
14A16THR00.0470.02318.3180.0050.0050.0000.0000.0000.000
15A17THR0-0.045-0.04220.3830.0090.0090.0000.0000.0000.000
16A18GLY00.0320.03019.8430.0000.0000.0000.0000.0000.000
17A19TYR00.014-0.00720.7340.0080.0080.0000.0000.0000.000
18A20ALA00.0190.01023.6170.0050.0050.0000.0000.0000.000
19A21TYR0-0.071-0.07421.0980.0090.0090.0000.0000.0000.000
20A22ALA00.0010.00123.8550.0040.0040.0000.0000.0000.000
21A23LYS10.8400.94225.7840.0310.0310.0000.0000.0000.000
22A24LEU0-0.033-0.01928.9220.0030.0030.0000.0000.0000.000
23A25PHE0-0.070-0.03127.805-0.001-0.0010.0000.0000.0000.000
24A26PRO00.0370.02227.121-0.010-0.0100.0000.0000.0000.000
25A27ARG10.9040.94327.7570.0420.0420.0000.0000.0000.000
26A28ALA00.0360.03327.001-0.003-0.0030.0000.0000.0000.000
27A29TYR0-0.036-0.00625.1180.0010.0010.0000.0000.0000.000
28A30GLY00.018-0.00123.2160.0070.0070.0000.0000.0000.000
29A31GLU-1-0.764-0.87221.305-0.225-0.2250.0000.0000.0000.000
30A32PHE0-0.026-0.00917.1940.0130.0130.0000.0000.0000.000
31A33ARG10.8700.92218.3490.2070.2070.0000.0000.0000.000
32A34PHE0-0.001-0.00211.8370.0050.0050.0000.0000.0000.000
33A35ILE0-0.023-0.02516.0390.0390.0390.0000.0000.0000.000
34A36ASP-1-0.708-0.85315.390-0.393-0.3930.0000.0000.0000.000
35A37ARG10.7960.88117.0370.2850.2850.0000.0000.0000.000
36A38ASN0-0.0170.00417.5580.0450.0450.0000.0000.0000.000
37A39ARG10.8300.91619.6000.2410.2410.0000.0000.0000.000
38A40GLN00.0490.02514.3710.0350.0350.0000.0000.0000.000
39A41GLY0-0.0160.00417.723-0.010-0.0100.0000.0000.0000.000
40A42PHE0-0.026-0.01611.150-0.027-0.0270.0000.0000.0000.000
41A43THR00.0470.02014.3310.0150.0150.0000.0000.0000.000
42A44GLU-1-0.755-0.89013.892-0.490-0.4900.0000.0000.0000.000
43A45GLU-1-0.922-0.95312.419-0.417-0.4170.0000.0000.0000.000
44A46PHE00.0030.0147.422-0.113-0.1130.0000.0000.0000.000
45A47ALA00.0200.0079.087-0.181-0.1810.0000.0000.0000.000
46A48GLU-1-0.768-0.86210.478-0.672-0.6720.0000.0000.0000.000
47A49LEU0-0.0160.0006.169-0.100-0.1000.0000.0000.0000.000
48A50VAL00.004-0.0016.049-0.527-0.5270.0000.0000.0000.000
49A51ARG10.7100.8147.0960.3200.3200.0000.0000.0000.000
50A52GLY0-0.014-0.0068.2870.1250.1250.0000.0000.0000.000
51A53GLU-1-0.818-0.9231.923-24.171-23.02715.003-7.913-8.234-0.102
52A54ILE0-0.031-0.0185.1080.4030.423-0.001-0.001-0.0170.000
53A55ARG10.8280.8897.8470.9020.9020.0000.0000.0000.000
54A56ALA00.0000.0124.3970.3100.373-0.001-0.002-0.0590.000
55A57MET0-0.0090.0005.4060.4910.4910.0000.0000.0000.000
56A58ALA0-0.0200.0007.0580.1800.1800.0000.0000.0000.000
57A59ALA0-0.057-0.0258.5810.0230.0230.0000.0000.0000.000
58A60LEU0-0.071-0.0146.7360.1030.1030.0000.0000.0000.000
59A61SER0-0.018-0.02510.091-0.152-0.1520.0000.0000.0000.000
60A62LEU0-0.040-0.00213.6480.0720.0720.0000.0000.0000.000
61A63THR0-0.009-0.03314.376-0.017-0.0170.0000.0000.0000.000
62A64ARG10.8160.85117.072-0.262-0.2620.0000.0000.0000.000
63A65ASP-1-0.838-0.91918.4870.2800.2800.0000.0000.0000.000
64A66GLU-1-0.789-0.84813.2340.4060.4060.0000.0000.0000.000
65A67LYS10.7780.88118.061-0.160-0.1600.0000.0000.0000.000
66A68GLU-1-0.835-0.91020.8220.1390.1390.0000.0000.0000.000
67A69PHE00.0180.01217.967-0.020-0.0200.0000.0000.0000.000
68A70LEU0-0.016-0.00817.637-0.024-0.0240.0000.0000.0000.000
69A71GLN0-0.054-0.03421.248-0.009-0.0090.0000.0000.0000.000
70A72ARG10.7890.88624.410-0.137-0.1370.0000.0000.0000.000
71A73GLU-1-0.911-0.95921.8370.0540.0540.0000.0000.0000.000
72A74LEU0-0.105-0.03518.854-0.015-0.0150.0000.0000.0000.000
73A75PRO00.0460.02123.362-0.003-0.0030.0000.0000.0000.000
74A76TYR00.0100.00822.284-0.005-0.0050.0000.0000.0000.000
75A77LEU0-0.058-0.02120.405-0.011-0.0110.0000.0000.0000.000
76A78PRO00.0190.00324.9390.0100.0100.0000.0000.0000.000
77A79PRO00.0590.01126.0540.0020.0020.0000.0000.0000.000
78A80ILE00.0180.01726.6030.0050.0050.0000.0000.0000.000
79A81TYR00.0380.01419.719-0.001-0.0010.0000.0000.0000.000
80A82ILE00.0120.00921.9630.0050.0050.0000.0000.0000.000
81A83ASP-1-0.844-0.91622.2220.0930.0930.0000.0000.0000.000
82A84PHE0-0.056-0.02819.4170.0060.0060.0000.0000.0000.000
83A85LEU00.007-0.01216.8120.0010.0010.0000.0000.0000.000
84A86ASP-1-0.752-0.84217.8580.2000.2000.0000.0000.0000.000
85A87GLY0-0.0190.00219.0790.0300.0300.0000.0000.0000.000
86A88PHE0-0.053-0.01513.808-0.008-0.0080.0000.0000.0000.000
87A89ARG10.8900.94214.233-0.156-0.1560.0000.0000.0000.000
88A90PHE00.0060.00010.626-0.056-0.0560.0000.0000.0000.000
89A91ASP-1-0.841-0.92813.164-0.125-0.1250.0000.0000.0000.000
90A92PRO0-0.023-0.02711.173-0.043-0.0430.0000.0000.0000.000
91A93GLU-1-0.964-0.95513.383-0.202-0.2020.0000.0000.0000.000
92A94GLU-1-0.810-0.87016.353-0.202-0.2020.0000.0000.0000.000
93A95VAL0-0.063-0.04712.371-0.009-0.0090.0000.0000.0000.000
94A96THR0-0.0080.00915.3910.0110.0110.0000.0000.0000.000
95A97VAL0-0.013-0.01411.062-0.005-0.0050.0000.0000.0000.000
96A98SER0-0.019-0.00714.3580.0520.0520.0000.0000.0000.000
97A99ILE00.0050.01814.457-0.030-0.0300.0000.0000.0000.000
98A100ASP-1-0.810-0.90517.771-0.240-0.2400.0000.0000.0000.000
99A101ALA00.009-0.00521.0200.0030.0030.0000.0000.0000.000
100A102GLN0-0.098-0.05323.1780.0270.0270.0000.0000.0000.000
101A103GLY00.0100.01420.4940.0030.0030.0000.0000.0000.000
102A104HIS0-0.012-0.01518.145-0.002-0.0020.0000.0000.0000.000
103A105LEU0-0.0010.01310.6850.0010.0010.0000.0000.0000.000
104A106ASP-1-0.829-0.87515.318-0.321-0.3210.0000.0000.0000.000
105A107ILE00.0460.00210.728-0.038-0.0380.0000.0000.0000.000
106A108ARG10.7970.85915.0520.3250.3250.0000.0000.0000.000
107A109ALA00.0370.04315.025-0.016-0.0160.0000.0000.0000.000
108A110GLN0-0.073-0.05717.0500.0460.0460.0000.0000.0000.000
109A111GLY00.0860.04020.3670.0000.0000.0000.0000.0000.000
110A112LEU0-0.011-0.00122.1190.0040.0040.0000.0000.0000.000
111A113LEU00.0000.00021.290-0.015-0.0150.0000.0000.0000.000
112A114TYR0-0.020-0.02020.603-0.014-0.0140.0000.0000.0000.000
113A115ARG10.7980.89116.5400.1330.1330.0000.0000.0000.000
114A116VAL00.009-0.00216.751-0.021-0.0210.0000.0000.0000.000
115A117THR0-0.031-0.02816.094-0.049-0.0490.0000.0000.0000.000
116A118LEU0-0.017-0.01713.804-0.026-0.0260.0000.0000.0000.000
117A119TRP00.013-0.0049.186-0.063-0.0630.0000.0000.0000.000
118A120GLU-1-0.818-0.85610.606-0.425-0.4250.0000.0000.0000.000
119A121THR0-0.019-0.0449.106-0.075-0.0750.0000.0000.0000.000
120A122PRO00.0400.0236.402-0.081-0.0810.0000.0000.0000.000
121A123ILE00.0500.0295.757-0.303-0.3030.0000.0000.0000.000
122A124LEU0-0.055-0.0297.305-0.123-0.1230.0000.0000.0000.000
123A125ALA00.0120.0095.187-0.031-0.0310.0000.0000.0000.000
124A126VAL0-0.0070.0012.547-1.823-0.2100.831-0.543-1.9010.001
125A127ILE0-0.013-0.0083.644-0.537-0.1230.010-0.019-0.406-0.001
126A128SER0-0.029-0.0286.4220.1560.1560.0000.0000.0000.000
127A129GLU-1-0.782-0.8802.411-4.429-1.5791.396-1.451-2.796-0.013
128A130LEU0-0.033-0.0262.291-0.511-0.1062.250-0.459-2.196-0.001
129A131TYR00.0110.0014.1120.1500.2240.006-0.016-0.0650.000
130A132TYR00.005-0.0207.2330.1100.1100.0000.0000.0000.000
131A133ARG10.9000.9472.624-1.917-0.7622.358-0.728-2.785-0.003
132A134PHE0-0.049-0.0217.0260.0890.0890.0000.0000.0000.000
133A135ILE0-0.065-0.0278.7310.0680.0680.0000.0000.0000.000
134A136GLY0-0.024-0.00910.5200.0480.0480.0000.0000.0000.000
135A137ALA0-0.045-0.01111.1740.0470.0470.0000.0000.0000.000
136A138GLU-1-0.900-0.96810.919-0.069-0.0690.0000.0000.0000.000
137A139PRO0-0.056-0.02111.367-0.009-0.0090.0000.0000.0000.000
138A140ASP-1-0.834-0.92114.1820.0050.0050.0000.0000.0000.000
139A141TRP00.003-0.02911.269-0.013-0.0130.0000.0000.0000.000
140A142LYS10.9180.98317.4020.0060.0060.0000.0000.0000.000
141A143GLN00.0270.02119.6700.0050.0050.0000.0000.0000.000
142A144VAL00.0000.00514.857-0.003-0.0030.0000.0000.0000.000
143A145GLU-1-0.780-0.85218.0650.0640.0640.0000.0000.0000.000
144A146GLU-1-0.903-0.96120.185-0.003-0.0030.0000.0000.0000.000
145A147VAL0-0.008-0.01020.2190.0010.0010.0000.0000.0000.000
146A148THR0-0.035-0.02218.217-0.010-0.0100.0000.0000.0000.000
147A149ARG10.8860.93620.840-0.017-0.0170.0000.0000.0000.000
148A150SER0-0.049-0.02723.7920.0010.0010.0000.0000.0000.000
149A151LYS10.7790.87919.8120.0950.0950.0000.0000.0000.000
150A152GLY00.0440.02123.866-0.001-0.0010.0000.0000.0000.000
151A153GLU-1-0.778-0.86424.8220.0130.0130.0000.0000.0000.000
152A154LEU00.0050.01927.9160.0000.0000.0000.0000.0000.000
153A155MET0-0.0210.00325.128-0.002-0.0020.0000.0000.0000.000
154A156ARG10.8070.89528.333-0.007-0.0070.0000.0000.0000.000
155A157GLU-1-0.913-0.94529.986-0.016-0.0160.0000.0000.0000.000
156A158HIS10.7540.86231.6940.0250.0250.0000.0000.0000.000
157A159ARG10.8630.92831.890-0.002-0.0020.0000.0000.0000.000
158A160ALA0-0.0050.00529.109-0.002-0.0020.0000.0000.0000.000
159A161THR00.003-0.00627.354-0.001-0.0010.0000.0000.0000.000
160A162PHE0-0.013-0.01520.765-0.008-0.0080.0000.0000.0000.000
161A163SER00.0260.03220.3990.0140.0140.0000.0000.0000.000
162A164ILE00.0230.01615.057-0.014-0.0140.0000.0000.0000.000
163A165PHE0-0.014-0.02715.9520.0000.0000.0000.0000.0000.000
164A166GLY00.016-0.00113.891-0.017-0.0170.0000.0000.0000.000
165A167MET00.0370.0746.403-0.003-0.0030.0000.0000.0000.000
166A168ARG10.8290.9148.8980.2400.2400.0000.0000.0000.000
167A169ARG10.8250.9249.3770.2870.2870.0000.0000.0000.000
168A170ARG10.7940.8893.6070.4800.6600.001-0.035-0.1450.000
169A171PHE00.0170.0208.128-0.138-0.1380.0000.0000.0000.000
170A172SER00.0830.0175.286-0.118-0.1180.0000.0000.0000.000
171A173LEU0-0.027-0.0133.8220.0520.2760.000-0.038-0.1860.000
172A174GLU-1-0.899-0.9575.6880.4370.4370.0000.0000.0000.000
173A175VAL00.0170.0168.1650.0450.0450.0000.0000.0000.000
174A176GLU-1-0.826-0.9229.039-0.229-0.2290.0000.0000.0000.000
175A177ASP-1-0.818-0.8839.6540.3270.3270.0000.0000.0000.000
176A178ARG10.8150.86311.401-0.079-0.0790.0000.0000.0000.000
177A179VAL00.0090.00513.5020.0030.0030.0000.0000.0000.000
178A180THR0-0.046-0.04313.624-0.005-0.0050.0000.0000.0000.000
179A181ASP-1-0.920-0.94215.7540.1320.1320.0000.0000.0000.000
180A182ILE0-0.0030.00117.414-0.004-0.0040.0000.0000.0000.000
181A183LEU0-0.009-0.02018.084-0.004-0.0040.0000.0000.0000.000
182A184LYS10.8600.92720.147-0.106-0.1060.0000.0000.0000.000
183A185GLN0-0.050-0.00721.939-0.004-0.0040.0000.0000.0000.000
184A186TYR0-0.009-0.01823.394-0.005-0.0050.0000.0000.0000.000
185A187ALA00.0180.01224.022-0.005-0.0050.0000.0000.0000.000
186A188GLY0-0.0020.01325.927-0.004-0.0040.0000.0000.0000.000
187A189GLU-1-0.858-0.93227.0060.0100.0100.0000.0000.0000.000
188A190SER0-0.099-0.05227.323-0.005-0.0050.0000.0000.0000.000
189A191LEU00.0210.02720.438-0.009-0.0090.0000.0000.0000.000
190A192PHE0-0.033-0.02123.3940.0100.0100.0000.0000.0000.000
191A193GLY00.0490.02221.1520.0120.0120.0000.0000.0000.000
192A194THR00.0050.00114.890-0.025-0.0250.0000.0000.0000.000
193A195SER0-0.004-0.02014.8810.0200.0200.0000.0000.0000.000
194A196ASN0-0.034-0.0168.8660.0590.0590.0000.0000.0000.000
195A197VAL00.0340.00212.9610.0370.0370.0000.0000.0000.000
196A198HIS00.0500.0409.1520.0470.0470.0000.0000.0000.000
197A199LEU0-0.005-0.00410.1210.0480.0480.0000.0000.0000.000
198A200ALA0-0.037-0.00913.3670.0090.0090.0000.0000.0000.000
199A201HIS00.0090.00715.295-0.015-0.0150.0000.0000.0000.000
200A202LYS10.8040.88812.263-0.334-0.3340.0000.0000.0000.000
201A203HIS0-0.054-0.03214.1700.0020.0020.0000.0000.0000.000
202A204GLY00.0070.02618.284-0.018-0.0180.0000.0000.0000.000
203A205LEU0-0.083-0.03818.125-0.018-0.0180.0000.0000.0000.000
204A206ARG10.9440.96620.605-0.010-0.0100.0000.0000.0000.000
205A207VAL00.0430.02217.553-0.008-0.0080.0000.0000.0000.000
206A208SER0-0.074-0.06118.977-0.001-0.0010.0000.0000.0000.000
207A209GLY00.0380.00819.058-0.016-0.0160.0000.0000.0000.000
208A210THR0-0.027-0.00220.8410.0090.0090.0000.0000.0000.000
209A211HIS00.0330.02821.641-0.005-0.0050.0000.0000.0000.000
210A212PRO00.0230.02119.985-0.002-0.0020.0000.0000.0000.000
211A213HIS0-0.003-0.03722.092-0.001-0.0010.0000.0000.0000.000
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213A215TRP00.0600.03723.1700.0060.0060.0000.0000.0000.000
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