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

tag_button

FMODB ID: 4JL6N

Calculation Name: 2I9I-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2I9I

Chain ID: A

ChEMBL ID:

UniProt ID: O25234

Base Structure: X-ray

Registration Date: 2023-09-22

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 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 221
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2617723.424667
FMO2-HF: Nuclear repulsion 2528169.618819
FMO2-HF: Total energy -89553.805848
FMO2-MP2: Total energy -89816.936739


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:51:GLU)


Summations of interaction energy for fragment #1(A:51:GLU)
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.
-169.778-175.39144.008-20.249-18.1470.161
Interaction energy analysis for fragmet #1(A:51:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.802 / q_NPA : -0.871
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].
3A53MET00.0120.0123.295-1.7290.4490.003-0.816-1.3650.002
4A54LYS10.9740.9875.614-24.393-24.3930.0000.0000.0000.000
5A55THR0-0.011-0.0119.4141.1831.1830.0000.0000.0000.000
6A56SER0-0.051-0.04511.919-0.610-0.6100.0000.0000.0000.000
7A57SER00.0850.02415.4260.2020.2020.0000.0000.0000.000
8A58GLU-1-0.883-0.88218.33215.05915.0590.0000.0000.0000.000
9A59HIS0-0.002-0.00716.742-1.119-1.1190.0000.0000.0000.000
10A60VAL00.0130.01015.8940.6800.6800.0000.0000.0000.000
11A61THR0-0.053-0.04010.742-0.050-0.0500.0000.0000.0000.000
12A62PRO00.0250.01114.075-0.052-0.0520.0000.0000.0000.000
13A63LEU00.0120.02713.6111.7861.7860.0000.0000.0000.000
14A64ASP-1-0.922-0.95912.67620.91120.9110.0000.0000.0000.000
15A65PHE0-0.058-0.03112.3721.8251.8250.0000.0000.0000.000
16A66ASN00.0460.01113.577-1.991-1.9910.0000.0000.0000.000
17A67TYR00.0180.00710.1473.0383.0380.0000.0000.0000.000
18A68PRO00.006-0.00314.013-1.480-1.4800.0000.0000.0000.000
19A69ILE00.0060.02016.4550.5580.5580.0000.0000.0000.000
20A70HIS0-0.013-0.00317.537-1.525-1.5250.0000.0000.0000.000
21A71ILE0-0.030-0.01820.6920.0070.0070.0000.0000.0000.000
22A72VAL00.0090.00423.525-0.269-0.2690.0000.0000.0000.000
23A73GLN0-0.034-0.02127.1930.2730.2730.0000.0000.0000.000
24A74ALA00.0300.03029.413-0.400-0.4000.0000.0000.0000.000
25A75PRO00.0060.00031.307-0.037-0.0370.0000.0000.0000.000
26A76GLN00.0090.00732.7600.0670.0670.0000.0000.0000.000
27A77ASN00.0210.00331.906-0.411-0.4110.0000.0000.0000.000
28A78HIS0-0.005-0.00336.011-0.006-0.0060.0000.0000.0000.000
29A79HIS10.8030.89334.037-9.056-9.0560.0000.0000.0000.000
30A80VAL00.0050.00333.4760.1490.1490.0000.0000.0000.000
31A81VAL0-0.0100.00227.988-0.145-0.1450.0000.0000.0000.000
32A82GLY00.0270.01130.527-0.111-0.1110.0000.0000.0000.000
33A83ILE0-0.028-0.01824.4210.3760.3760.0000.0000.0000.000
34A84LEU0-0.047-0.01426.739-0.297-0.2970.0000.0000.0000.000
35A85THR0-0.009-0.00425.5180.4990.4990.0000.0000.0000.000
36A86PRO0-0.053-0.02220.904-0.097-0.0970.0000.0000.0000.000
37A87ARG10.8720.92022.606-12.327-12.3270.0000.0000.0000.000
38A88ILE0-0.0040.00416.3970.1400.1400.0000.0000.0000.000
39A89GLN0-0.0010.00119.886-0.572-0.5720.0000.0000.0000.000
40A90VAL0-0.001-0.00916.8070.8520.8520.0000.0000.0000.000
41A91SER00.027-0.00516.415-0.647-0.6470.0000.0000.0000.000
42A92ASP-1-0.822-0.92118.73413.42113.4210.0000.0000.0000.000
43A93ASN0-0.014-0.01315.563-0.065-0.0650.0000.0000.0000.000
44A94LEU00.0170.00013.1580.7530.7530.0000.0000.0000.000
45A95LYS10.8310.91817.254-13.153-13.1530.0000.0000.0000.000
46A96PRO0-0.012-0.00320.005-0.228-0.2280.0000.0000.0000.000
47A97TYR0-0.004-0.00616.5560.2990.2990.0000.0000.0000.000
48A98ILE0-0.018-0.00316.9920.6340.6340.0000.0000.0000.000
49A99ASP-1-0.852-0.92018.82513.89613.8960.0000.0000.0000.000
50A100LYS10.8960.95616.372-18.578-18.5780.0000.0000.0000.000
51A101PHE0-0.030-0.01911.5260.3910.3910.0000.0000.0000.000
52A102GLN00.045-0.00216.9710.5590.5590.0000.0000.0000.000
53A103ASP-1-0.863-0.92919.53713.27013.2700.0000.0000.0000.000
54A104ALA0-0.065-0.02117.269-0.272-0.2720.0000.0000.0000.000
55A105LEU00.0220.00914.235-0.039-0.0390.0000.0000.0000.000
56A106ILE0-0.009-0.00518.148-0.322-0.3220.0000.0000.0000.000
57A107ASN00.0190.01421.636-1.067-1.0670.0000.0000.0000.000
58A108GLN00.0190.01716.5130.6900.6900.0000.0000.0000.000
59A109ILE00.0360.00817.454-0.351-0.3510.0000.0000.0000.000
60A110GLN0-0.0150.00220.762-0.273-0.2730.0000.0000.0000.000
61A111THR0-0.010-0.02321.937-0.304-0.3040.0000.0000.0000.000
62A112ILE0-0.026-0.00718.379-0.284-0.2840.0000.0000.0000.000
63A113PHE00.004-0.00322.896-0.408-0.4080.0000.0000.0000.000
64A114GLU-1-0.816-0.89726.22111.30711.3070.0000.0000.0000.000
65A115LYS10.8640.93224.554-12.302-12.3020.0000.0000.0000.000
66A116ARG10.8780.93320.936-14.481-14.4810.0000.0000.0000.000
67A117GLY0-0.0060.00927.891-0.296-0.2960.0000.0000.0000.000
68A118TYR0-0.073-0.06428.825-0.339-0.3390.0000.0000.0000.000
69A119GLN00.003-0.01030.8070.2040.2040.0000.0000.0000.000
70A120VAL0-0.002-0.00827.4520.1580.1580.0000.0000.0000.000
71A121LEU0-0.0150.00230.703-0.256-0.2560.0000.0000.0000.000
72A122ARG10.8650.91725.473-12.219-12.2190.0000.0000.0000.000
73A123PHE00.0090.00229.807-0.405-0.4050.0000.0000.0000.000
74A124GLN0-0.0040.00029.8350.3440.3440.0000.0000.0000.000
75A125ASP-1-0.821-0.92929.86610.04810.0480.0000.0000.0000.000
76A126GLU-1-0.782-0.88831.3939.1719.1710.0000.0000.0000.000
77A127LYS10.9160.94632.992-9.040-9.0400.0000.0000.0000.000
78A128ALA0-0.0110.01534.205-0.255-0.2550.0000.0000.0000.000
79A129LEU0-0.0350.00932.681-0.111-0.1110.0000.0000.0000.000
80A130ASN00.027-0.00836.832-0.297-0.2970.0000.0000.0000.000
81A131ALA00.011-0.01040.2070.1000.1000.0000.0000.0000.000
82A132GLN00.0260.01142.3390.0030.0030.0000.0000.0000.000
83A133ASP-1-0.819-0.88937.4858.3708.3700.0000.0000.0000.000
84A134LYS10.7890.89435.788-8.805-8.8050.0000.0000.0000.000
85A135ARG10.8740.93738.088-7.301-7.3010.0000.0000.0000.000
86A136LYS10.9210.96539.022-8.006-8.0060.0000.0000.0000.000
87A137ILE0-0.055-0.01933.0700.1040.1040.0000.0000.0000.000
88A138PHE00.0000.00230.982-0.116-0.1160.0000.0000.0000.000
89A139SER00.002-0.02629.8000.0080.0080.0000.0000.0000.000
90A140VAL0-0.0060.00528.6530.0230.0230.0000.0000.0000.000
91A141LEU0-0.0240.00321.4260.1810.1810.0000.0000.0000.000
92A142ASP-1-0.757-0.85624.66212.41512.4150.0000.0000.0000.000
93A143LEU00.0040.00717.5630.4480.4480.0000.0000.0000.000
94A144LYS10.8920.93820.968-13.044-13.0440.0000.0000.0000.000
95A145GLY00.0470.00618.0090.9700.9700.0000.0000.0000.000
96A146TRP0-0.0440.00616.408-1.181-1.1810.0000.0000.0000.000
97A147VAL00.0180.00312.0571.0311.0310.0000.0000.0000.000
98A148GLY00.0490.01313.110-1.270-1.2700.0000.0000.0000.000
99A149ILE0-0.023-0.01010.5052.1042.1040.0000.0000.0000.000
100A150LEU0-0.0130.00612.140-1.535-1.5350.0000.0000.0000.000
101A151GLU-1-0.795-0.89212.70317.67917.6790.0000.0000.0000.000
102A152ASP-1-0.816-0.90415.10814.58214.5820.0000.0000.0000.000
103A153LEU0-0.0060.00911.250-0.969-0.9690.0000.0000.0000.000
104A154LYS10.8940.93514.436-14.056-14.0560.0000.0000.0000.000
105A155MET0-0.039-0.0149.7200.1760.1760.0000.0000.0000.000
106A156ASN00.0430.02014.0670.7210.7210.0000.0000.0000.000
107A157LEU0-0.017-0.01310.8681.2041.2040.0000.0000.0000.000
108A158LYS10.8750.92211.654-17.333-17.3330.0000.0000.0000.000
109A159ASP-1-0.781-0.85713.55216.50816.5080.0000.0000.0000.000
110A160PRO0-0.001-0.01314.690-0.742-0.7420.0000.0000.0000.000
111A161ASN0-0.073-0.04116.671-1.305-1.3050.0000.0000.0000.000
112A162ASN0-0.084-0.04417.126-1.091-1.0910.0000.0000.0000.000
113A163PRO00.0410.02618.0130.4900.4900.0000.0000.0000.000
114A164ASN0-0.009-0.00519.4370.1620.1620.0000.0000.0000.000
115A165LEU0-0.016-0.00615.600-0.187-0.1870.0000.0000.0000.000
116A166ASP-1-0.788-0.87116.03714.68814.6880.0000.0000.0000.000
117A167THR0-0.042-0.04311.2210.4120.4120.0000.0000.0000.000
118A168LEU0-0.0180.02514.309-0.018-0.0180.0000.0000.0000.000
119A169VAL0-0.081-0.0479.7101.0471.0470.0000.0000.0000.000
120A170ASP-1-0.758-0.87910.91619.00619.0060.0000.0000.0000.000
121A171GLN0-0.043-0.0375.7562.9982.9980.0000.0000.0000.000
122A172SER0-0.008-0.0216.909-1.662-1.6620.0000.0000.0000.000
123A173SER0-0.028-0.0188.723-0.531-0.5310.0000.0000.0000.000
124A174GLY00.0630.03710.919-0.493-0.4930.0000.0000.0000.000
125A175SER00.000-0.00411.6241.6931.6930.0000.0000.0000.000
126A176VAL0-0.026-0.01313.358-1.346-1.3460.0000.0000.0000.000
127A177TRP0-0.027-0.02515.6830.2900.2900.0000.0000.0000.000
128A178PHE00.0040.00015.107-0.655-0.6550.0000.0000.0000.000
129A179ASN0-0.066-0.04820.221-0.640-0.6400.0000.0000.0000.000
130A180PHE00.0150.00423.711-0.093-0.0930.0000.0000.0000.000
131A181TYR00.008-0.00926.093-0.117-0.1170.0000.0000.0000.000
132A182GLU-1-0.657-0.79529.6858.7108.7100.0000.0000.0000.000
133A183PRO0-0.042-0.02233.213-0.076-0.0760.0000.0000.0000.000
134A184GLU-1-0.847-0.92134.8037.7157.7150.0000.0000.0000.000
135A185SER0-0.073-0.08436.746-0.014-0.0140.0000.0000.0000.000
136A186ASN0-0.066-0.03333.9240.1690.1690.0000.0000.0000.000
137A187ARG10.9030.96432.516-9.290-9.2900.0000.0000.0000.000
138A188VAL00.0410.02026.5720.0750.0750.0000.0000.0000.000
139A189VAL0-0.035-0.01528.440-0.208-0.2080.0000.0000.0000.000
140A190HIS0-0.036-0.03620.173-0.577-0.5770.0000.0000.0000.000
141A191ASP-1-0.912-0.94922.35113.26513.2650.0000.0000.0000.000
142A192PHE00.0150.00716.2570.3890.3890.0000.0000.0000.000
143A193ALA00.0420.02416.067-0.216-0.2160.0000.0000.0000.000
144A194VAL0-0.041-0.0329.6270.6510.6510.0000.0000.0000.000
145A195GLU-1-0.843-0.91810.05321.64321.6430.0000.0000.0000.000
146A196VAL0-0.004-0.0068.0423.4153.4150.0000.0000.0000.000
147A197GLY00.0150.0327.5891.7661.7660.0000.0000.0000.000
148A198THR0-0.020-0.0053.858-4.045-3.5720.001-0.135-0.3390.000
149A199PHE0-0.040-0.0182.077-8.908-5.4468.209-4.979-6.6920.000
150A200GLN00.001-0.0103.528-6.038-5.3670.006-0.090-0.5880.000
151A201ALA0-0.0060.0005.2783.5453.5450.0000.0000.0000.000
152A202MET0-0.015-0.0157.771-2.623-2.6230.0000.0000.0000.000
153A203THR00.0160.03010.604-0.344-0.3440.0000.0000.0000.000
154A204TYR0-0.004-0.02013.683-0.821-0.8210.0000.0000.0000.000
155A205THR0-0.034-0.01613.2280.1930.1930.0000.0000.0000.000
156A206TYR0-0.011-0.00115.619-0.544-0.5440.0000.0000.0000.000
157A207LYS10.9570.96918.546-11.841-11.8410.0000.0000.0000.000
158A208HIS00.0300.03021.074-0.924-0.9240.0000.0000.0000.000
159A209ASN00.0180.01624.1320.2940.2940.0000.0000.0000.000
160A210ASN00.007-0.01626.5140.3640.3640.0000.0000.0000.000
161A211SER0-0.035-0.01028.191-0.085-0.0850.0000.0000.0000.000
162A212GLY00.0220.02527.807-0.146-0.1460.0000.0000.0000.000
163A213GLY00.0120.00128.886-0.216-0.2160.0000.0000.0000.000
164A214LEU00.0120.00628.3160.3290.3290.0000.0000.0000.000
165A215ASN0-0.030-0.04225.164-0.061-0.0610.0000.0000.0000.000
166A216SER00.0100.00327.4660.1460.1460.0000.0000.0000.000
167A217SER0-0.0130.02421.9310.4240.4240.0000.0000.0000.000
168A218ASN0-0.014-0.03922.5700.2150.2150.0000.0000.0000.000
169A219SER00.0090.01023.633-0.079-0.0790.0000.0000.0000.000
170A220ILE0-0.019-0.00919.6350.1610.1610.0000.0000.0000.000
171A221ILE0-0.0100.00523.056-0.379-0.3790.0000.0000.0000.000
172A222HIS00.0430.01919.8780.6670.6670.0000.0000.0000.000
173A223GLU-1-0.874-0.94122.91011.64811.6480.0000.0000.0000.000
174A224TYR0-0.060-0.02723.635-0.347-0.3470.0000.0000.0000.000
175A225LEU0-0.033-0.01118.2840.4860.4860.0000.0000.0000.000
176A226GLU-1-0.918-0.95118.62613.30013.3000.0000.0000.0000.000
177A227LYS10.8410.89918.812-13.562-13.5620.0000.0000.0000.000
178A228ASN00.0290.01515.1120.2240.2240.0000.0000.0000.000
179A229LYS10.9280.94613.954-13.513-13.5130.0000.0000.0000.000
180A230GLU-1-0.867-0.92114.62717.32917.3290.0000.0000.0000.000
181A231ASP-1-0.713-0.83612.49624.98224.9820.0000.0000.0000.000
182A232ALA0-0.004-0.00410.1212.5662.5660.0000.0000.0000.000
183A233ILE00.0090.01210.0493.0163.0160.0000.0000.0000.000
184A234HIS10.7910.88011.669-18.148-18.1480.0000.0000.0000.000
185A235LYS10.7640.8587.470-25.337-25.3370.0000.0000.0000.000
186A236ILE00.0130.0016.2885.8435.8430.0000.0000.0000.000
187A237LEU00.0000.0097.7172.6772.6770.0000.0000.0000.000
188A238ASN00.010-0.0178.531-0.881-0.8810.0000.0000.0000.000
189A239ARG10.7590.8431.679-134.869-147.47135.791-14.222-8.9670.159
190A240MET00.0070.0035.5190.9240.974-0.0010.000-0.0480.000
191A241TYR0-0.016-0.0237.988-1.656-1.6560.0000.0000.0000.000
192A242ALA0-0.002-0.0016.884-1.609-1.6090.0000.0000.0000.000
193A243VAL0-0.035-0.0164.648-1.795-1.640-0.001-0.007-0.1480.000
194A244VAL00.0150.0177.629-3.830-3.8300.0000.0000.0000.000
195A245MET00.0020.01511.213-2.706-2.7060.0000.0000.0000.000
196A246LYS10.9620.9938.452-33.878-33.8780.0000.0000.0000.000
197A247LYS10.8380.92511.201-23.401-23.4010.0000.0000.0000.000
198A248ALA00.0380.01312.800-1.722-1.7220.0000.0000.0000.000
199A249VAL0-0.027-0.02414.938-1.426-1.4260.0000.0000.0000.000
200A250THR0-0.102-0.05713.670-0.789-0.7890.0000.0000.0000.000
201A251GLU-1-0.790-0.86716.08416.85316.8530.0000.0000.0000.000
202A252LEU0-0.0090.01718.462-1.193-1.1930.0000.0000.0000.000
203A253THR0-0.019-0.02620.577-0.229-0.2290.0000.0000.0000.000
204A254LYS10.8930.94022.737-10.783-10.7830.0000.0000.0000.000
205A255GLU-1-0.838-0.91325.22912.06912.0690.0000.0000.0000.000
206A256ASN0-0.008-0.02821.431-0.887-0.8870.0000.0000.0000.000
207A257ILE0-0.0250.00624.418-0.197-0.1970.0000.0000.0000.000
208A258ASP-1-0.803-0.90227.2869.7159.7150.0000.0000.0000.000
209A259LYS10.8150.93524.769-12.834-12.8340.0000.0000.0000.000
210A260TYR00.0310.01430.423-0.240-0.2400.0000.0000.0000.000
211A261ARG10.8870.93533.467-9.058-9.0580.0000.0000.0000.000
212A262GLU-1-0.870-0.91835.0117.6867.6860.0000.0000.0000.000
213A263ALA00.0490.01737.545-0.204-0.2040.0000.0000.0000.000
214A264ILE00.0040.00833.473-0.196-0.1960.0000.0000.0000.000
215A265ASP-1-0.801-0.87037.8448.4658.4650.0000.0000.0000.000
216A266ARG10.8330.90039.929-7.865-7.8650.0000.0000.0000.000
217A267MET0-0.073-0.02338.298-0.230-0.2300.0000.0000.0000.000
218A268LYS10.8000.89336.677-8.696-8.6960.0000.0000.0000.000
219A269GLY00.0000.01842.225-0.117-0.1170.0000.0000.0000.000
220A270PHE00.0050.01139.814-0.165-0.1650.0000.0000.0000.000
221A271LYS10.8770.93643.105-6.897-6.8970.0000.0000.0000.000