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: GNKQ1

Calculation Name: 4O8V-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4O8V

Chain ID: A

ChEMBL ID:

UniProt ID: Q88ND3

Base Structure: X-ray

Registration Date: 2023-06-20

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 279
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3855642.195471
FMO2-HF: Nuclear repulsion 3747725.531095
FMO2-HF: Total energy -107916.664377
FMO2-MP2: Total energy -108235.170471


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:79:PRO)


Summations of interaction energy for fragment #1(A:79:PRO)
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.
-10.864-4.7551.004-3.146-3.967-0.008
Interaction energy analysis for fragmet #1(A:79:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.023 / 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].
3A81VAL0-0.029-0.0093.804-1.1871.273-0.033-1.290-1.1380.001
4A82VAL0-0.0030.0127.2400.1700.1700.0000.0000.0000.000
5A83LEU0-0.021-0.01510.170-0.050-0.0500.0000.0000.0000.000
6A84GLY00.0180.00413.6960.0770.0770.0000.0000.0000.000
7A85ARG10.8210.89316.3160.0180.0180.0000.0000.0000.000
8A86ASP-1-0.893-0.95019.641-0.104-0.1040.0000.0000.0000.000
9A87GLN0-0.008-0.01518.621-0.011-0.0110.0000.0000.0000.000
10A88TRP00.0530.03116.441-0.038-0.0380.0000.0000.0000.000
11A89LEU0-0.075-0.01811.562-0.012-0.0120.0000.0000.0000.000
12A90PHE00.015-0.00110.6670.0360.0360.0000.0000.0000.000
13A91SER00.0990.0495.863-0.108-0.1080.0000.0000.0000.000
14A92ASP-1-0.759-0.8933.3502.0553.3150.072-0.717-0.614-0.005
15A93GLU-1-0.890-0.9453.6000.7321.5820.017-0.333-0.534-0.002
16A94GLU-1-0.861-0.9385.943-0.001-0.0010.0000.0000.0000.000
17A95PHE0-0.032-0.0218.307-0.146-0.1460.0000.0000.0000.000
18A96LYS10.8970.9602.722-10.590-9.8830.199-0.323-0.5830.001
19A97PRO00.0320.0258.836-0.091-0.0910.0000.0000.0000.000
20A98THR00.0180.0089.8870.4530.4530.0000.0000.0000.000
21A99ALA0-0.004-0.01311.469-0.212-0.2120.0000.0000.0000.000
22A100GLY0-0.004-0.00413.7460.0140.0140.0000.0000.0000.000
23A101ALA00.0210.00413.983-0.032-0.0320.0000.0000.0000.000
24A102GLU-1-0.894-0.93415.4980.3320.3320.0000.0000.0000.000
25A103GLN00.0490.00218.790-0.016-0.0160.0000.0000.0000.000
26A104LEU0-0.020-0.00712.138-0.032-0.0320.0000.0000.0000.000
27A105MET00.0180.02516.234-0.015-0.0150.0000.0000.0000.000
28A106GLN00.0000.00817.656-0.030-0.0300.0000.0000.0000.000
29A107GLU-1-0.846-0.90017.8260.2300.2300.0000.0000.0000.000
30A108ASN0-0.013-0.04113.556-0.079-0.0790.0000.0000.0000.000
31A109LEU0-0.0010.00517.988-0.038-0.0380.0000.0000.0000.000
32A110ALA0-0.054-0.01621.162-0.031-0.0310.0000.0000.0000.000
33A111LEU00.0130.00218.191-0.024-0.0240.0000.0000.0000.000
34A112ILE0-0.017-0.00518.486-0.024-0.0240.0000.0000.0000.000
35A113ARG10.9220.96422.050-0.171-0.1710.0000.0000.0000.000
36A114GLY00.0630.04024.924-0.014-0.0140.0000.0000.0000.000
37A115VAL0-0.030-0.01621.794-0.015-0.0150.0000.0000.0000.000
38A116ARG10.8250.90125.145-0.093-0.0930.0000.0000.0000.000
39A117ASP-1-0.755-0.82627.5160.0870.0870.0000.0000.0000.000
40A118THR0-0.007-0.00627.704-0.008-0.0080.0000.0000.0000.000
41A119LEU0-0.013-0.00925.869-0.008-0.0080.0000.0000.0000.000
42A120GLN00.0420.04629.955-0.002-0.0020.0000.0000.0000.000
43A121GLN0-0.057-0.03432.887-0.006-0.0060.0000.0000.0000.000
44A122HIS0-0.063-0.02332.440-0.005-0.0050.0000.0000.0000.000
45A123GLY0-0.012-0.00134.579-0.005-0.0050.0000.0000.0000.000
46A124SER0-0.037-0.02630.763-0.003-0.0030.0000.0000.0000.000
47A125GLN0-0.024-0.02631.8260.0110.0110.0000.0000.0000.000
48A126LEU0-0.029-0.00524.241-0.003-0.0030.0000.0000.0000.000
49A127VAL0-0.010-0.00626.3420.0030.0030.0000.0000.0000.000
50A128LEU0-0.040-0.01520.284-0.005-0.0050.0000.0000.0000.000
51A129ALA00.022-0.01021.281-0.003-0.0030.0000.0000.0000.000
52A130ILE0-0.0010.00318.408-0.001-0.0010.0000.0000.0000.000
53A131VAL0-0.013-0.00615.780-0.012-0.0120.0000.0000.0000.000
54A132PRO00.0060.01116.3350.0350.0350.0000.0000.0000.000
55A133ALA00.014-0.00413.349-0.026-0.0260.0000.0000.0000.000
56A134LYS10.7980.90013.3050.2310.2310.0000.0000.0000.000
57A135ALA0-0.046-0.04012.913-0.014-0.0140.0000.0000.0000.000
58A136ARG10.7270.83814.860-0.228-0.2280.0000.0000.0000.000
59A137VAL00.0280.01517.761-0.012-0.0120.0000.0000.0000.000
60A138TYR00.0120.01117.892-0.019-0.0190.0000.0000.0000.000
61A139THR00.0430.02318.719-0.013-0.0130.0000.0000.0000.000
62A140GLU-1-0.799-0.88119.7370.0000.0000.0000.0000.0000.000
63A141TYR0-0.038-0.01918.768-0.009-0.0090.0000.0000.0000.000
64A142LEU00.0200.03215.318-0.022-0.0220.0000.0000.0000.000
65A143GLY00.0320.01816.520-0.013-0.0130.0000.0000.0000.000
66A144LYS10.9290.95417.605-0.036-0.0360.0000.0000.0000.000
67A145GLU-1-0.929-0.96811.7670.2140.2140.0000.0000.0000.000
68A146ARG10.8930.94815.358-0.141-0.1410.0000.0000.0000.000
69A147PRO00.0020.00712.7440.0480.0480.0000.0000.0000.000
70A148ALA00.0090.00812.881-0.050-0.0500.0000.0000.0000.000
71A149SER00.0590.01814.7280.0140.0140.0000.0000.0000.000
72A150LEU0-0.043-0.00912.309-0.021-0.0210.0000.0000.0000.000
73A151HIS0-0.002-0.02110.326-0.157-0.1570.0000.0000.0000.000
74A152ASP-1-0.895-0.92415.3130.2410.2410.0000.0000.0000.000
75A153ASP-1-0.840-0.92318.8530.1600.1600.0000.0000.0000.000
76A154LEU0-0.0100.00913.957-0.013-0.0130.0000.0000.0000.000
77A155TYR0-0.032-0.04418.179-0.014-0.0140.0000.0000.0000.000
78A156ASN0-0.039-0.03619.544-0.026-0.0260.0000.0000.0000.000
79A157GLN00.0120.00320.884-0.014-0.0140.0000.0000.0000.000
80A158PHE0-0.0060.00617.055-0.003-0.0030.0000.0000.0000.000
81A159HIS0-0.004-0.00621.112-0.015-0.0150.0000.0000.0000.000
82A160ALA0-0.037-0.00924.233-0.014-0.0140.0000.0000.0000.000
83A161GLN00.0330.00123.029-0.020-0.0200.0000.0000.0000.000
84A162ALA0-0.0050.00323.761-0.009-0.0090.0000.0000.0000.000
85A163ARG10.9590.97325.451-0.119-0.1190.0000.0000.0000.000
86A164GLN0-0.0160.00728.085-0.005-0.0050.0000.0000.0000.000
87A165ALA0-0.029-0.00426.720-0.006-0.0060.0000.0000.0000.000
88A166ASN0-0.033-0.02528.673-0.004-0.0040.0000.0000.0000.000
89A167VAL00.0090.00924.755-0.009-0.0090.0000.0000.0000.000
90A168PHE00.0120.00528.0990.0030.0030.0000.0000.0000.000
91A169ALA00.0310.00824.344-0.002-0.0020.0000.0000.0000.000
92A170PRO0-0.021-0.00326.1770.0030.0030.0000.0000.0000.000
93A171ASP-1-0.798-0.88225.3400.0840.0840.0000.0000.0000.000
94A172LEU00.0260.00821.161-0.013-0.0130.0000.0000.0000.000
95A173HCS0-0.030-0.00821.824-0.009-0.0090.0000.0000.0000.000
96A174ALA00.0400.02523.570-0.010-0.0100.0000.0000.0000.000
97A175PRO0-0.0020.00526.290-0.009-0.0090.0000.0000.0000.000
98A176MET0-0.026-0.02419.480-0.007-0.0070.0000.0000.0000.000
99A177GLU-1-0.911-0.97123.8060.0410.0410.0000.0000.0000.000
100A178GLN0-0.050-0.01125.641-0.007-0.0070.0000.0000.0000.000
101A179ALA0-0.037-0.02726.286-0.006-0.0060.0000.0000.0000.000
102A180LYS10.8340.89822.964-0.013-0.0130.0000.0000.0000.000
103A181ALA0-0.026-0.00526.559-0.007-0.0070.0000.0000.0000.000
104A182ARG10.9070.95529.1330.0310.0310.0000.0000.0000.000
105A183GLY00.0200.01327.226-0.006-0.0060.0000.0000.0000.000
106A184GLN0-0.083-0.03720.3480.0090.0090.0000.0000.0000.000
107A185VAL00.0300.02820.943-0.007-0.0070.0000.0000.0000.000
108A186PHE00.019-0.00114.9760.0010.0010.0000.0000.0000.000
109A187LEU0-0.0070.00915.8690.0080.0080.0000.0000.0000.000
110A188ARG10.8560.93216.3080.2350.2350.0000.0000.0000.000
111A189THR0-0.087-0.07814.440-0.030-0.0300.0000.0000.0000.000
112A190ASP-1-0.720-0.85211.888-0.545-0.5450.0000.0000.0000.000
113A191THR0-0.038-0.0367.6500.1260.1260.0000.0000.0000.000
114A192HIS10.7650.87310.9270.4450.4450.0000.0000.0000.000
115A193TRP00.0030.00714.0320.0070.0070.0000.0000.0000.000
116A194THR0-0.012-0.02317.627-0.021-0.0210.0000.0000.0000.000
117A195PRO00.0320.00620.3430.0150.0150.0000.0000.0000.000
118A196MET0-0.072-0.01122.9810.0150.0150.0000.0000.0000.000
119A197GLY00.0670.02321.7650.0120.0120.0000.0000.0000.000
120A198ALA00.0050.00120.6760.0160.0160.0000.0000.0000.000
121A199GLU-1-0.905-0.93922.248-0.041-0.0410.0000.0000.0000.000
122A200VAL0-0.0060.00625.2040.0080.0080.0000.0000.0000.000
123A201ALA00.0100.01122.4720.0100.0100.0000.0000.0000.000
124A202ALA00.017-0.00424.5280.0090.0090.0000.0000.0000.000
125A203GLN0-0.008-0.01326.4700.0060.0060.0000.0000.0000.000
126A204ALA00.0100.01726.9720.0040.0040.0000.0000.0000.000
127A205LEU0-0.033-0.02523.5940.0070.0070.0000.0000.0000.000
128A206ALA00.0230.00728.2440.0040.0040.0000.0000.0000.000
129A207GLU-1-0.902-0.94531.3950.0220.0220.0000.0000.0000.000
130A208ALA0-0.045-0.02730.5260.0030.0030.0000.0000.0000.000
131A209VAL00.0180.00230.5460.0030.0030.0000.0000.0000.000
132A210SER0-0.031-0.01133.1950.0010.0010.0000.0000.0000.000
133A211ARG10.8780.93932.401-0.031-0.0310.0000.0000.0000.000
134A212GLN0-0.055-0.02734.0460.0020.0020.0000.0000.0000.000
135A213SER0-0.046-0.00937.0160.0000.0000.0000.0000.0000.000
136A214LEU0-0.036-0.02032.3380.0000.0000.0000.0000.0000.000
137A215LEU0-0.0030.00433.4220.0000.0000.0000.0000.0000.000
138A216ASN0-0.043-0.00737.032-0.001-0.0010.0000.0000.0000.000
139A217GLY00.0390.00939.431-0.001-0.0010.0000.0000.0000.000
140A218ASP-1-0.952-0.97241.545-0.006-0.0060.0000.0000.0000.000
141A219PRO0-0.041-0.02439.468-0.001-0.0010.0000.0000.0000.000
142A220GLN00.0130.01237.088-0.001-0.0010.0000.0000.0000.000
143A221ALA0-0.052-0.02937.4520.0000.0000.0000.0000.0000.000
144A222PHE00.0390.00233.550-0.003-0.0030.0000.0000.0000.000
145A223ILE00.0010.00335.5170.0020.0020.0000.0000.0000.000
146A224THR0-0.0090.00529.702-0.006-0.0060.0000.0000.0000.000
147A225GLU-1-0.897-0.94032.251-0.061-0.0610.0000.0000.0000.000
148A226ALA0-0.026-0.02830.540-0.007-0.0070.0000.0000.0000.000
149A227GLY00.0010.00130.0990.0030.0030.0000.0000.0000.000
150A228ASN0-0.006-0.01330.3640.0060.0060.0000.0000.0000.000
151A229THR00.000-0.00926.274-0.004-0.0040.0000.0000.0000.000
152A230ALA0-0.030-0.00725.5410.0060.0060.0000.0000.0000.000
153A231PRO00.0320.01323.140-0.005-0.0050.0000.0000.0000.000
154A232TYR0-0.020-0.00514.4660.0070.0070.0000.0000.0000.000
155A233LYS10.9010.96113.8040.6170.6170.0000.0000.0000.000
156A234GLY00.0360.02713.970-0.012-0.0120.0000.0000.0000.000
157A235ASP-1-0.789-0.9059.112-0.747-0.7470.0000.0000.0000.000
158A236LEU00.0150.0017.017-0.224-0.2240.0000.0000.0000.000
159A237THR0-0.049-0.0289.227-0.149-0.1490.0000.0000.0000.000
160A238ASN0-0.045-0.0338.7500.1140.1140.0000.0000.0000.000
161A239PHE00.0150.0232.388-0.950-0.1180.749-0.483-1.098-0.003
162A240LEU0-0.031-0.0037.1280.0090.0090.0000.0000.0000.000
163A241PRO0-0.0200.0139.7880.0470.0470.0000.0000.0000.000
164A242DLE10.3600.74812.3150.8030.8030.0000.0000.0000.000
165A243ASP-2-0.449-1.28814.761-1.007-1.0070.0000.0000.0000.000
166A244PRO0-0.761-0.38316.7430.0110.0110.0000.0000.0000.000
167A245LEU0-0.034-0.03218.6530.0330.0330.0000.0000.0000.000
168A246PHE0-0.048-0.03318.1730.0400.0400.0000.0000.0000.000
169A247SER00.014-0.00118.516-0.015-0.0150.0000.0000.0000.000
170A248ASN0-0.028-0.01919.583-0.021-0.0210.0000.0000.0000.000
171A249LEU0-0.019-0.01618.8640.0240.0240.0000.0000.0000.000
172A250LEU0-0.066-0.00914.920-0.020-0.0200.0000.0000.0000.000
173A251PRO0-0.015-0.00115.5570.0430.0430.0000.0000.0000.000
174A252ALA00.0330.01218.599-0.016-0.0160.0000.0000.0000.000
175A253PRO00.0310.01018.872-0.015-0.0150.0000.0000.0000.000
176A254ASP-1-0.743-0.83917.510-0.239-0.2390.0000.0000.0000.000
177A255ASN0-0.006-0.00920.410-0.010-0.0100.0000.0000.0000.000
178A256LEU00.0060.00119.9850.0040.0040.0000.0000.0000.000
179A257GLN00.0010.00223.0680.0060.0060.0000.0000.0000.000
180A258LYS10.9710.98925.0590.1280.1280.0000.0000.0000.000
181A259ARG10.8910.92925.9560.0860.0860.0000.0000.0000.000
182A260THR0-0.0150.00326.677-0.008-0.0080.0000.0000.0000.000
183A261THR00.016-0.00329.2030.0020.0020.0000.0000.0000.000
184A262ARG10.8730.95231.0230.0500.0500.0000.0000.0000.000
185A263PRO00.0540.03034.0360.0030.0030.0000.0000.0000.000
186A264VAL0-0.068-0.04236.634-0.002-0.0020.0000.0000.0000.000
187A265ASP-1-0.958-0.96440.060-0.035-0.0350.0000.0000.0000.000
188A279GLN0-0.047-0.03934.160-0.002-0.0020.0000.0000.0000.000
189A280ILE00.0080.01131.1350.0000.0000.0000.0000.0000.000
190A281PRO00.0110.01533.4480.0030.0030.0000.0000.0000.000
191A282VAL00.0450.01528.2860.0060.0060.0000.0000.0000.000
192A283ALA00.0050.01226.485-0.007-0.0070.0000.0000.0000.000
193A284LEU0-0.013-0.00121.3120.0080.0080.0000.0000.0000.000
194A285VAL00.0110.00619.411-0.008-0.0080.0000.0000.0000.000
195A286GLY00.0480.01417.1810.0150.0150.0000.0000.0000.000
196A287THR0-0.032-0.04111.940-0.029-0.0290.0000.0000.0000.000
197A288SER00.0920.05310.4770.0170.0170.0000.0000.0000.000
198A289TYR0-0.061-0.04111.519-0.014-0.0140.0000.0000.0000.000
199A290SER00.022-0.02715.4070.0040.0040.0000.0000.0000.000
200A291ALA0-0.0270.00015.9380.0000.0000.0000.0000.0000.000
201A292ASN00.0120.01314.6590.0150.0150.0000.0000.0000.000
202A293PRO00.022-0.00517.6360.0150.0150.0000.0000.0000.000
203A294HIS0-0.0120.00317.7480.0330.0330.0000.0000.0000.000
204A295TRP0-0.016-0.01414.7720.0130.0130.0000.0000.0000.000
205A296ASN0-0.041-0.02520.4190.0160.0160.0000.0000.0000.000
206A297PHE00.0490.01820.6300.0130.0130.0000.0000.0000.000
207A298LEU00.0150.01122.7650.0100.0100.0000.0000.0000.000
208A299GLY00.0490.02924.7940.0080.0080.0000.0000.0000.000
209A300ALA0-0.015-0.00825.6570.0070.0070.0000.0000.0000.000
210A301LEU0-0.004-0.00924.1540.0090.0090.0000.0000.0000.000
211A302GLN0-0.0050.01427.9850.0010.0010.0000.0000.0000.000
212A303GLN00.0210.00930.7220.0010.0010.0000.0000.0000.000
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