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: 767JK

Calculation Name: 3EXV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3EXV

Chain ID: A

ChEMBL ID:

UniProt ID: P35774

Base Structure: X-ray

Registration Date: 2023-09-23

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 197
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2220783.665625
FMO2-HF: Nuclear repulsion 2142308.078885
FMO2-HF: Total energy -78475.58674
FMO2-MP2: Total energy -78701.171032


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:129:ASP)


Summations of interaction energy for fragment #1(A:129:ASP)
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.
-92.909-93.21314.834-7.668-6.8620.057
Interaction energy analysis for fragmet #1(A:129:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.837 / q_NPA : -0.919
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].
3A131ILE00.0230.0063.705-8.291-5.933-0.009-1.072-1.2770.003
4A132ASN0-0.008-0.0151.733-38.585-41.74414.845-6.536-5.1510.054
5A133THR00.0020.0124.152-5.543-5.250-0.001-0.048-0.2440.000
6A134LEU0-0.037-0.0036.568-2.109-2.1090.0000.0000.0000.000
7A135TRP0-0.025-0.0199.8650.0680.0680.0000.0000.0000.000
8A136THR00.0390.00411.831-0.578-0.5780.0000.0000.0000.000
9A137GLY0-0.042-0.00212.496-1.082-1.0820.0000.0000.0000.000
10A138VAL0-0.005-0.01712.586-0.702-0.7020.0000.0000.0000.000
11A139ASN00.000-0.00615.201-0.911-0.9110.0000.0000.0000.000
12A140PRO00.0640.05117.860-0.354-0.3540.0000.0000.0000.000
13A141THR00.019-0.00220.051-0.263-0.2630.0000.0000.0000.000
14A142GLU-1-0.870-0.93923.62710.89710.8970.0000.0000.0000.000
15A143ALA0-0.0110.00923.8850.6080.6080.0000.0000.0000.000
16A144ASN0-0.015-0.00719.548-0.775-0.7750.0000.0000.0000.000
17A145CYS0-0.023-0.01223.2310.2580.2580.0000.0000.0000.000
18A146GLN00.0010.01325.176-0.190-0.1900.0000.0000.0000.000
19A147ILE0-0.054-0.04525.2350.1100.1100.0000.0000.0000.000
20A148MET0-0.0320.01428.782-0.187-0.1870.0000.0000.0000.000
21A149ASN00.012-0.01032.6260.1280.1280.0000.0000.0000.000
22A150SER0-0.0070.00234.789-0.130-0.1300.0000.0000.0000.000
23A151SER0-0.061-0.03333.086-0.275-0.2750.0000.0000.0000.000
24A152GLU-1-0.934-0.96735.5768.3738.3730.0000.0000.0000.000
25A153SER0-0.045-0.02532.303-0.084-0.0840.0000.0000.0000.000
26A154ASN0-0.031-0.02626.752-0.132-0.1320.0000.0000.0000.000
27A155ASP-1-0.765-0.86828.74310.73310.7330.0000.0000.0000.000
28A156CYS0-0.019-0.00525.7050.0410.0410.0000.0000.0000.000
29A157LYS10.8370.91321.478-13.280-13.2800.0000.0000.0000.000
30A158LEU00.0350.01719.6600.1050.1050.0000.0000.0000.000
31A159ILE0-0.059-0.00715.4910.6550.6550.0000.0000.0000.000
32A160LEU00.0610.01515.074-0.220-0.2200.0000.0000.0000.000
33A161THR0-0.045-0.0399.2191.5831.5830.0000.0000.0000.000
34A162LEU00.0180.03511.190-0.693-0.6930.0000.0000.0000.000
35A163VAL00.008-0.0115.4743.1083.1080.0000.0000.0000.000
36A164LYS10.7960.9176.986-32.194-32.1940.0000.0000.0000.000
37A165THR0-0.023-0.0186.8954.6644.6640.0000.0000.0000.000
38A166GLY00.0450.0329.308-3.148-3.1480.0000.0000.0000.000
39A167ALA00.0100.00311.4040.2200.2200.0000.0000.0000.000
40A168LEU0-0.0060.00113.016-1.430-1.4300.0000.0000.0000.000
41A169VAL0-0.0220.00111.2492.5822.5820.0000.0000.0000.000
42A170THR0-0.002-0.01010.139-3.111-3.1110.0000.0000.0000.000
43A171ALA0-0.019-0.01011.4652.0212.0210.0000.0000.0000.000
44A172PHE00.0090.00412.305-1.221-1.2210.0000.0000.0000.000
45A173VAL0-0.004-0.01814.3240.4900.4900.0000.0000.0000.000
46A174TYR0-0.0020.00416.225-0.558-0.5580.0000.0000.0000.000
47A175VAL00.0240.01520.1220.2970.2970.0000.0000.0000.000
48A176ILE00.0160.00520.517-0.156-0.1560.0000.0000.0000.000
49A177GLY00.0150.00324.3920.0460.0460.0000.0000.0000.000
50A178VAL0-0.038-0.02126.8220.0810.0810.0000.0000.0000.000
51A179SER00.0270.01229.607-0.368-0.3680.0000.0000.0000.000
52A180ASN00.022-0.00432.9010.0740.0740.0000.0000.0000.000
53A181ASN00.021-0.00135.853-0.101-0.1010.0000.0000.0000.000
54A182PHE00.0760.03927.898-0.074-0.0740.0000.0000.0000.000
55A183ASN00.0380.01630.8290.2950.2950.0000.0000.0000.000
56A184MET00.0180.01633.206-0.118-0.1180.0000.0000.0000.000
57A185LEU00.0100.02432.856-0.217-0.2170.0000.0000.0000.000
58A186THR00.003-0.01632.933-0.160-0.1600.0000.0000.0000.000
59A187THR0-0.030-0.02135.418-0.173-0.1730.0000.0000.0000.000
60A188HIS0-0.062-0.02737.961-0.269-0.2690.0000.0000.0000.000
61A189ARG10.9250.95238.277-7.231-7.2310.0000.0000.0000.000
62A190ASN0-0.086-0.04637.9930.1540.1540.0000.0000.0000.000
63A191ILE00.0180.02632.808-0.085-0.0850.0000.0000.0000.000
64A192ASN0-0.037-0.02632.5810.2240.2240.0000.0000.0000.000
65A193PHE00.0340.02026.609-0.180-0.1800.0000.0000.0000.000
66A194THR00.014-0.01827.7690.1880.1880.0000.0000.0000.000
67A195ALA00.0210.02023.594-0.148-0.1480.0000.0000.0000.000
68A196GLU-1-0.719-0.83924.98911.05811.0580.0000.0000.0000.000
69A197LEU0-0.032-0.00719.7250.0870.0870.0000.0000.0000.000
70A198PHE00.010-0.00223.474-0.060-0.0600.0000.0000.0000.000
71A199PHE00.003-0.01118.0850.4700.4700.0000.0000.0000.000
72A200ASP-1-0.680-0.81221.67414.13114.1310.0000.0000.0000.000
73A201SER0-0.013-0.00222.1150.5930.5930.0000.0000.0000.000
74A202THR0-0.057-0.06419.3400.4970.4970.0000.0000.0000.000
75A203GLY00.0370.00917.6151.0901.0900.0000.0000.0000.000
76A204ASN0-0.070-0.04217.8981.5471.5470.0000.0000.0000.000
77A205LEU00.0040.00219.470-0.573-0.5730.0000.0000.0000.000
78A206LEU00.0420.02321.210-0.326-0.3260.0000.0000.0000.000
79A207THR0-0.008-0.00223.308-0.539-0.5390.0000.0000.0000.000
80A208ARG10.9250.95225.646-11.038-11.0380.0000.0000.0000.000
81A209LEU00.0020.01228.172-0.382-0.3820.0000.0000.0000.000
82A210SER0-0.035-0.00124.2610.0780.0780.0000.0000.0000.000
83A211SER00.0470.02825.478-0.159-0.1590.0000.0000.0000.000
84A212LEU0-0.019-0.00718.797-0.166-0.1660.0000.0000.0000.000
85A213LYS10.8680.92023.497-11.541-11.5410.0000.0000.0000.000
86A214THR0-0.007-0.00519.670-0.211-0.2110.0000.0000.0000.000
87A215PRO0-0.010-0.01619.0920.5100.5100.0000.0000.0000.000
88A216LEU00.0270.02714.0210.2720.2720.0000.0000.0000.000
89A217ASN00.007-0.01212.6831.1131.1130.0000.0000.0000.000
90A218HIS10.8360.9147.861-30.309-30.3090.0000.0000.0000.000
91A219LYS10.8740.9554.782-43.253-43.049-0.001-0.012-0.1900.000
92A220SER00.0220.0068.0161.1401.1400.0000.0000.0000.000
93A221GLY00.0520.0348.947-2.588-2.5880.0000.0000.0000.000
94A222GLN00.021-0.0039.4325.4125.4120.0000.0000.0000.000
95A223ASN00.0380.02011.884-1.229-1.2290.0000.0000.0000.000
96A224MET0-0.0150.01511.3552.5502.5500.0000.0000.0000.000
97A225ALA0-0.016-0.01210.261-0.968-0.9680.0000.0000.0000.000
98A226THR0-0.004-0.00712.420-1.028-1.0280.0000.0000.0000.000
99A227GLY00.0210.00514.204-0.490-0.4900.0000.0000.0000.000
100A228ALA0-0.0030.01114.8300.3530.3530.0000.0000.0000.000
101A229ILE00.0190.02012.4161.2371.2370.0000.0000.0000.000
102A230THR00.014-0.00612.3711.6231.6230.0000.0000.0000.000
103A231ASN00.0020.0048.006-1.810-1.8100.0000.0000.0000.000
104A232ALA00.0370.01112.0971.5331.5330.0000.0000.0000.000
105A233LYS10.9250.96414.067-15.223-15.2230.0000.0000.0000.000
106A234GLY00.0100.01313.365-0.538-0.5380.0000.0000.0000.000
107A235PHE0-0.045-0.0478.0511.4891.4890.0000.0000.0000.000
108A236MET0-0.0490.02013.363-0.812-0.8120.0000.0000.0000.000
109A237PRO00.0050.00817.1580.4480.4480.0000.0000.0000.000
110A238SER0-0.010-0.03519.252-0.946-0.9460.0000.0000.0000.000
111A239THR0-0.014-0.04220.816-0.619-0.6190.0000.0000.0000.000
112A240THR0-0.0300.00223.694-0.718-0.7180.0000.0000.0000.000
113A241ALA00.000-0.00422.169-0.503-0.5030.0000.0000.0000.000
114A242TYR0-0.0010.00920.0620.0770.0770.0000.0000.0000.000
115A243PRO00.0640.05025.2800.1530.1530.0000.0000.0000.000
116A244PHE00.0530.01026.0840.0560.0560.0000.0000.0000.000
117A245ASN0-0.047-0.04030.424-0.115-0.1150.0000.0000.0000.000
118A246ASP-1-0.780-0.86932.3829.1999.1990.0000.0000.0000.000
119A247ASN00.017-0.00433.9560.3660.3660.0000.0000.0000.000
120A248SER0-0.114-0.05935.735-0.148-0.1480.0000.0000.0000.000
121A249ARG10.8020.85527.142-11.178-11.1780.0000.0000.0000.000
122A250GLU-1-0.849-0.88331.1959.4769.4760.0000.0000.0000.000
123A251LYS10.8650.90630.841-8.811-8.8110.0000.0000.0000.000
124A252GLU-1-0.792-0.85527.20511.34711.3470.0000.0000.0000.000
125A253ASN0-0.103-0.07226.1570.2430.2430.0000.0000.0000.000
126A254TYR0-0.020-0.00426.0120.2360.2360.0000.0000.0000.000
127A255ILE0-0.0090.00320.8660.2280.2280.0000.0000.0000.000
128A256TYR00.002-0.00925.115-0.280-0.2800.0000.0000.0000.000
129A257GLY00.0060.00524.8660.4190.4190.0000.0000.0000.000
130A258THR00.0000.00925.339-0.434-0.4340.0000.0000.0000.000
131A259CYS0-0.090-0.02023.5580.6010.6010.0000.0000.0000.000
132A260TYR00.049-0.00125.099-0.394-0.3940.0000.0000.0000.000
133A261TYR0-0.054-0.03026.2750.5310.5310.0000.0000.0000.000
134A262THR0-0.065-0.03727.221-0.106-0.1060.0000.0000.0000.000
135A263ALA00.0470.02529.6000.0020.0020.0000.0000.0000.000
136A264SER0-0.033-0.04633.2200.0600.0600.0000.0000.0000.000
137A265ASP-1-0.863-0.91335.5878.7828.7820.0000.0000.0000.000
138A266ARG10.8430.91731.677-9.424-9.4240.0000.0000.0000.000
139A267THR0-0.053-0.03731.9900.3140.3140.0000.0000.0000.000
140A268ALA0-0.004-0.00529.0130.1910.1910.0000.0000.0000.000
141A269PHE00.0410.02030.705-0.105-0.1050.0000.0000.0000.000
142A270PRO0-0.020-0.01229.9830.4050.4050.0000.0000.0000.000
143A271ILE0-0.021-0.01628.070-0.257-0.2570.0000.0000.0000.000
144A272ASP-1-0.885-0.93127.95410.57510.5750.0000.0000.0000.000
145A273ILE0-0.031-0.02222.671-0.004-0.0040.0000.0000.0000.000
146A274SER0-0.045-0.02526.369-0.069-0.0690.0000.0000.0000.000
147A275VAL0-0.008-0.00921.4470.1670.1670.0000.0000.0000.000
148A276MET0-0.036-0.00624.686-0.505-0.5050.0000.0000.0000.000
149A277LEU0-0.0080.00120.6400.2790.2790.0000.0000.0000.000
150A278ASN0-0.002-0.02022.843-0.363-0.3630.0000.0000.0000.000
151A279ARG10.8900.94525.911-9.969-9.9690.0000.0000.0000.000
152A280ARG10.8180.88129.508-10.555-10.5550.0000.0000.0000.000
153A281ALA00.0480.03429.8910.3190.3190.0000.0000.0000.000
154A282ILE0-0.069-0.03730.682-0.297-0.2970.0000.0000.0000.000
155A283ASN0-0.017-0.02931.249-0.128-0.1280.0000.0000.0000.000
156A284ASP-1-0.858-0.92731.2119.7389.7380.0000.0000.0000.000
157A285GLU-1-0.905-0.94128.40411.16311.1630.0000.0000.0000.000
158A286THR0-0.042-0.02726.8950.5090.5090.0000.0000.0000.000
159A287SER0-0.038-0.02724.580-0.005-0.0050.0000.0000.0000.000
160A288TYR0-0.044-0.02521.5430.2940.2940.0000.0000.0000.000
161A289CYS0-0.066-0.02723.664-0.444-0.4440.0000.0000.0000.000
162A290ILE00.0000.00818.0220.2530.2530.0000.0000.0000.000
163A291ARG10.7650.88322.348-11.404-11.4040.0000.0000.0000.000
164A292ILE00.0110.00719.6770.1870.1870.0000.0000.0000.000
165A293THR00.0220.01424.270-0.132-0.1320.0000.0000.0000.000
166A294TRP00.0490.03021.7810.2220.2220.0000.0000.0000.000
167A295SER0-0.053-0.04028.047-0.424-0.4240.0000.0000.0000.000
168A296TRP00.0340.00631.0940.3690.3690.0000.0000.0000.000
169A297ASN00.0050.00334.175-0.314-0.3140.0000.0000.0000.000
170A298THR00.010-0.00136.696-0.008-0.0080.0000.0000.0000.000
171A299GLY0-0.020-0.00939.535-0.185-0.1850.0000.0000.0000.000
172A300ASP-1-0.892-0.95141.2077.2037.2030.0000.0000.0000.000
173A301ALA0-0.036-0.00239.0030.2120.2120.0000.0000.0000.000
174A302PRO0-0.0170.00534.505-0.076-0.0760.0000.0000.0000.000
175A303GLU-1-0.721-0.76835.3418.9608.9600.0000.0000.0000.000
176A304VAL00.0310.00938.480-0.188-0.1880.0000.0000.0000.000
177A305GLN00.018-0.00540.5550.0420.0420.0000.0000.0000.000
178A306THR0-0.054-0.02941.7130.0760.0760.0000.0000.0000.000
179A307SER0-0.041-0.04838.905-0.090-0.0900.0000.0000.0000.000
180A308ALA00.0230.01836.3010.2540.2540.0000.0000.0000.000
181A309THR0-0.009-0.00333.6660.0180.0180.0000.0000.0000.000
182A310THR0-0.059-0.04328.4200.1110.1110.0000.0000.0000.000
183A311LEU0-0.0060.02128.9420.0840.0840.0000.0000.0000.000
184A312VAL0-0.015-0.01224.0120.3830.3830.0000.0000.0000.000
185A313THR00.0080.00322.721-0.326-0.3260.0000.0000.0000.000
186A314SER00.001-0.00422.2500.2810.2810.0000.0000.0000.000
187A315PRO0-0.051-0.03216.914-0.028-0.0280.0000.0000.0000.000
188A316PHE00.0510.03918.824-0.524-0.5240.0000.0000.0000.000
189A317THR0-0.040-0.03614.3931.5361.5360.0000.0000.0000.000
190A318PHE0-0.0100.00516.515-0.943-0.9430.0000.0000.0000.000
191A319TYR00.0250.00113.1440.8590.8590.0000.0000.0000.000
192A320TYR0-0.039-0.02615.392-1.342-1.3420.0000.0000.0000.000
193A321ILE00.0360.01216.0441.3841.3840.0000.0000.0000.000
194A322ARG10.7660.86712.095-23.308-23.3080.0000.0000.0000.000
195A323GLU-1-0.717-0.79816.11413.79913.7990.0000.0000.0000.000
196A324ASP-1-0.832-0.89915.59521.02821.0280.0000.0000.0000.000
197A325ASP-1-0.828-0.90512.48223.10423.1040.0000.0000.0000.000