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: 989Y2

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 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 197
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2220736.753089
FMO2-HF: Nuclear repulsion 2142261.68397
FMO2-HF: Total energy -78475.069119
FMO2-MP2: Total energy -78700.644286


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.
-91.534-85.6865.723-5.536-6.0330.046
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 : -0.845 / q_NPA : -0.930
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].
3A131ILE00.006-0.0073.288-7.997-5.6670.012-0.993-1.3490.003
4A132ASN0-0.003-0.0061.999-35.399-32.2545.713-4.525-4.3320.043
5A133THR0-0.0080.0074.901-3.567-3.363-0.001-0.010-0.1920.000
6A134LEU0-0.0330.0057.352-1.611-1.6110.0000.0000.0000.000
7A135TRP0-0.035-0.02810.5500.3380.3380.0000.0000.0000.000
8A136THR00.0380.01512.696-0.463-0.4630.0000.0000.0000.000
9A137GLY0-0.0490.00113.437-1.015-1.0150.0000.0000.0000.000
10A138VAL00.008-0.01313.211-0.627-0.6270.0000.0000.0000.000
11A139ASN0-0.022-0.01115.808-0.965-0.9650.0000.0000.0000.000
12A140PRO00.0580.04418.808-0.290-0.2900.0000.0000.0000.000
13A141THR00.001-0.01121.032-0.194-0.1940.0000.0000.0000.000
14A142GLU-1-0.899-0.94124.49310.62510.6250.0000.0000.0000.000
15A143ALA0-0.0090.00224.5780.5950.5950.0000.0000.0000.000
16A144ASN00.0010.00520.333-0.724-0.7240.0000.0000.0000.000
17A145CYS0-0.035-0.02223.9980.1340.1340.0000.0000.0000.000
18A146GLN00.0070.02325.923-0.130-0.1300.0000.0000.0000.000
19A147ILE0-0.046-0.03526.0000.0420.0420.0000.0000.0000.000
20A148MET0-0.0390.00529.383-0.190-0.1900.0000.0000.0000.000
21A149ASN00.014-0.01433.1720.1910.1910.0000.0000.0000.000
22A150SER0-0.039-0.01635.389-0.087-0.0870.0000.0000.0000.000
23A151SER0-0.044-0.02333.537-0.282-0.2820.0000.0000.0000.000
24A152GLU-1-0.916-0.95836.0938.2108.2100.0000.0000.0000.000
25A153SER0-0.038-0.02132.856-0.072-0.0720.0000.0000.0000.000
26A154ASN0-0.052-0.01827.361-0.133-0.1330.0000.0000.0000.000
27A155ASP-1-0.758-0.88729.65910.49310.4930.0000.0000.0000.000
28A156CYS0-0.0130.00126.5060.0710.0710.0000.0000.0000.000
29A157LYS10.8750.92622.140-13.035-13.0350.0000.0000.0000.000
30A158LEU00.0120.00120.1390.0110.0110.0000.0000.0000.000
31A159ILE0-0.039-0.00715.8230.5870.5870.0000.0000.0000.000
32A160LEU00.0470.00815.589-0.237-0.2370.0000.0000.0000.000
33A161THR0-0.024-0.0309.6691.3421.3420.0000.0000.0000.000
34A162LEU00.0060.01611.615-0.561-0.5610.0000.0000.0000.000
35A163VAL00.0290.0065.8342.6192.6190.0000.0000.0000.000
36A164LYS10.8280.9367.070-32.693-32.6930.0000.0000.0000.000
37A165THR0-0.009-0.0056.7386.3136.3130.0000.0000.0000.000
38A166GLY00.0350.0249.107-3.280-3.2800.0000.0000.0000.000
39A167ALA00.0150.00011.2100.4010.4010.0000.0000.0000.000
40A168LEU00.0100.00912.953-1.399-1.3990.0000.0000.0000.000
41A169VAL0-0.0100.00611.5752.7992.7990.0000.0000.0000.000
42A170THR0-0.034-0.02210.595-2.906-2.9060.0000.0000.0000.000
43A171ALA0-0.012-0.01111.9691.9051.9050.0000.0000.0000.000
44A172PHE00.0030.01012.963-1.083-1.0830.0000.0000.0000.000
45A173VAL00.004-0.01114.9330.3830.3830.0000.0000.0000.000
46A174TYR0-0.0030.00516.6080.0040.0040.0000.0000.0000.000
47A175VAL00.0140.00920.7940.3050.3050.0000.0000.0000.000
48A176ILE0-0.002-0.00421.069-0.138-0.1380.0000.0000.0000.000
49A177GLY00.0210.00424.9080.0120.0120.0000.0000.0000.000
50A178VAL0-0.036-0.01527.4820.0700.0700.0000.0000.0000.000
51A179SER00.0190.01030.188-0.386-0.3860.0000.0000.0000.000
52A180ASN00.0590.01233.5220.1520.1520.0000.0000.0000.000
53A181ASN00.015-0.00336.397-0.116-0.1160.0000.0000.0000.000
54A182PHE00.0490.03028.458-0.047-0.0470.0000.0000.0000.000
55A183ASN00.0610.02031.4800.3350.3350.0000.0000.0000.000
56A184MET0-0.015-0.00333.775-0.129-0.1290.0000.0000.0000.000
57A185LEU00.0180.01533.130-0.233-0.2330.0000.0000.0000.000
58A186THR0-0.001-0.00233.263-0.154-0.1540.0000.0000.0000.000
59A187THR0-0.031-0.01835.857-0.167-0.1670.0000.0000.0000.000
60A188HIS0-0.059-0.02138.433-0.337-0.3370.0000.0000.0000.000
61A189ARG10.9490.96738.708-7.188-7.1880.0000.0000.0000.000
62A190ASN0-0.086-0.04238.6270.1510.1510.0000.0000.0000.000
63A191ILE00.0140.02433.530-0.076-0.0760.0000.0000.0000.000
64A192ASN0-0.034-0.03033.3090.2550.2550.0000.0000.0000.000
65A193PHE00.0300.02427.326-0.140-0.1400.0000.0000.0000.000
66A194THR00.0380.01928.2180.3240.3240.0000.0000.0000.000
67A195ALA00.0030.01924.278-0.143-0.1430.0000.0000.0000.000
68A196GLU-1-0.888-0.95825.45810.90210.9020.0000.0000.0000.000
69A197LEU0-0.025-0.01220.1760.0780.0780.0000.0000.0000.000
70A198PHE00.0360.00324.0510.0390.0390.0000.0000.0000.000
71A199PHE00.011-0.00118.6200.3920.3920.0000.0000.0000.000
72A200ASP-1-0.703-0.82921.93713.57713.5770.0000.0000.0000.000
73A201SER00.0250.00322.1010.7520.7520.0000.0000.0000.000
74A202THR0-0.077-0.05119.4680.5020.5020.0000.0000.0000.000
75A203GLY00.024-0.00917.6641.0231.0230.0000.0000.0000.000
76A204ASN0-0.065-0.05017.7121.5301.5300.0000.0000.0000.000
77A205LEU0-0.027-0.01019.658-0.533-0.5330.0000.0000.0000.000
78A206LEU00.0440.01921.472-0.286-0.2860.0000.0000.0000.000
79A207THR00.002-0.00323.827-0.450-0.4500.0000.0000.0000.000
80A208ARG10.9170.94526.145-10.643-10.6430.0000.0000.0000.000
81A209LEU00.0060.01328.668-0.357-0.3570.0000.0000.0000.000
82A210SER0-0.0100.01425.3220.0200.0200.0000.0000.0000.000
83A211SER00.0510.03126.185-0.156-0.1560.0000.0000.0000.000
84A212LEU0-0.0200.00519.538-0.110-0.1100.0000.0000.0000.000
85A213LYS10.8960.94224.201-11.165-11.1650.0000.0000.0000.000
86A214THR0-0.025-0.02020.585-0.241-0.2410.0000.0000.0000.000
87A215PRO0-0.005-0.00619.2100.5820.5820.0000.0000.0000.000
88A216LEU00.0380.03414.7430.3490.3490.0000.0000.0000.000
89A217ASN00.0280.00312.6610.9370.9370.0000.0000.0000.000
90A218HIS10.8460.9257.686-29.652-29.6520.0000.0000.0000.000
91A219LYS10.9150.9635.166-42.828-42.659-0.001-0.008-0.1600.000
92A220SER00.0090.0037.8612.0892.0890.0000.0000.0000.000
93A221GLY00.0510.0288.739-2.482-2.4820.0000.0000.0000.000
94A222GLN0-0.003-0.0069.9322.0152.0150.0000.0000.0000.000
95A223ASN00.0580.03512.376-1.211-1.2110.0000.0000.0000.000
96A224MET0-0.0030.00811.8992.2322.2320.0000.0000.0000.000
97A225ALA0-0.026-0.01610.319-0.839-0.8390.0000.0000.0000.000
98A226THR00.005-0.00112.468-1.305-1.3050.0000.0000.0000.000
99A227GLY00.0130.00313.9560.2660.2660.0000.0000.0000.000
100A228ALA00.0380.00713.3900.7560.7560.0000.0000.0000.000
101A229ILE0-0.0140.00612.2271.1501.1500.0000.0000.0000.000
102A230THR0-0.025-0.06613.245-0.348-0.3480.0000.0000.0000.000
103A231ASN00.0480.0397.746-1.867-1.8670.0000.0000.0000.000
104A232ALA0-0.0340.01911.9391.0591.0590.0000.0000.0000.000
105A233LYS10.9760.99713.721-14.750-14.7500.0000.0000.0000.000
106A234GLY00.0180.02512.879-0.375-0.3750.0000.0000.0000.000
107A235PHE0-0.066-0.0577.9201.1921.1920.0000.0000.0000.000
108A236MET0-0.0360.02313.593-0.715-0.7150.0000.0000.0000.000
109A237PRO00.0190.01917.3610.4940.4940.0000.0000.0000.000
110A238SER00.0510.02619.517-0.960-0.9600.0000.0000.0000.000
111A239THR0-0.012-0.01620.980-0.590-0.5900.0000.0000.0000.000
112A240THR0-0.041-0.00823.705-0.661-0.6610.0000.0000.0000.000
113A241ALA0-0.008-0.01222.421-0.480-0.4800.0000.0000.0000.000
114A242TYR0-0.0160.00720.3080.0860.0860.0000.0000.0000.000
115A243PRO00.0690.05425.5690.1590.1590.0000.0000.0000.000
116A244PHE00.032-0.00526.3130.0230.0230.0000.0000.0000.000
117A245ASN0-0.078-0.06830.717-0.171-0.1710.0000.0000.0000.000
118A246ASP-1-0.793-0.87632.7929.0409.0400.0000.0000.0000.000
119A247ASN00.011-0.02034.2460.3030.3030.0000.0000.0000.000
120A248SER0-0.099-0.05636.322-0.026-0.0260.0000.0000.0000.000
121A249ARG10.8690.93127.642-10.900-10.9000.0000.0000.0000.000
122A250GLU-1-0.912-0.94431.4059.3949.3940.0000.0000.0000.000
123A251LYS10.9460.95831.265-8.688-8.6880.0000.0000.0000.000
124A252GLU-1-0.860-0.92427.73511.07811.0780.0000.0000.0000.000
125A253ASN0-0.088-0.05126.5600.2250.2250.0000.0000.0000.000
126A254TYR0-0.020-0.00326.5510.2200.2200.0000.0000.0000.000
127A255ILE0-0.0020.00820.9800.1670.1670.0000.0000.0000.000
128A256TYR0-0.006-0.01225.196-0.236-0.2360.0000.0000.0000.000
129A257GLY0-0.007-0.00624.7980.4520.4520.0000.0000.0000.000
130A258THR00.0050.01425.299-0.440-0.4400.0000.0000.0000.000
131A259CYS0-0.097-0.01723.7230.5800.5800.0000.0000.0000.000
132A260TYR00.043-0.00225.317-0.433-0.4330.0000.0000.0000.000
133A261TYR0-0.060-0.03326.4990.5150.5150.0000.0000.0000.000
134A262THR0-0.062-0.03227.414-0.147-0.1470.0000.0000.0000.000
135A263ALA00.0580.03129.882-0.006-0.0060.0000.0000.0000.000
136A264SER0-0.036-0.04433.4590.0630.0630.0000.0000.0000.000
137A265ASP-1-0.867-0.91535.6778.6968.6960.0000.0000.0000.000
138A266ARG10.8450.90131.835-9.547-9.5470.0000.0000.0000.000
139A267THR0-0.057-0.02432.4030.2990.2990.0000.0000.0000.000
140A268ALA0-0.017-0.01229.3790.1850.1850.0000.0000.0000.000
141A269PHE00.0280.00531.109-0.172-0.1720.0000.0000.0000.000
142A270PRO0-0.014-0.00530.1260.3900.3900.0000.0000.0000.000
143A271ILE0-0.043-0.02628.255-0.270-0.2700.0000.0000.0000.000
144A272ASP-1-0.897-0.94328.42010.45210.4520.0000.0000.0000.000
145A273ILE0-0.026-0.02422.9300.0570.0570.0000.0000.0000.000
146A274SER0-0.037-0.02027.163-0.064-0.0640.0000.0000.0000.000
147A275VAL00.010-0.00421.8750.0690.0690.0000.0000.0000.000
148A276MET0-0.0160.01025.221-0.353-0.3530.0000.0000.0000.000
149A277LEU0-0.022-0.01421.0580.3500.3500.0000.0000.0000.000
150A278ASN0-0.013-0.02823.230-0.322-0.3220.0000.0000.0000.000
151A279ARG10.9200.99426.318-9.969-9.9690.0000.0000.0000.000
152A280ARG10.9490.96429.903-10.130-10.1300.0000.0000.0000.000
153A281ALA00.0590.03230.3000.3310.3310.0000.0000.0000.000
154A282ILE0-0.066-0.02030.825-0.330-0.3300.0000.0000.0000.000
155A283ASN00.020-0.01331.553-0.115-0.1150.0000.0000.0000.000
156A284ASP-1-0.866-0.93931.5349.4669.4660.0000.0000.0000.000
157A285GLU-1-0.998-0.98528.10210.95310.9530.0000.0000.0000.000
158A286THR0-0.058-0.03926.9190.4270.4270.0000.0000.0000.000
159A287SER0-0.0120.00124.147-0.207-0.2070.0000.0000.0000.000
160A288TYR0-0.069-0.04821.3270.2490.2490.0000.0000.0000.000
161A289CYS0-0.062-0.02223.754-0.219-0.2190.0000.0000.0000.000
162A290ILE00.0180.02318.6790.2320.2320.0000.0000.0000.000
163A291ARG10.8020.91323.088-11.158-11.1580.0000.0000.0000.000
164A292ILE00.0160.01520.6200.0350.0350.0000.0000.0000.000
165A293THR00.005-0.01825.093-0.136-0.1360.0000.0000.0000.000
166A294TRP00.0300.01022.5020.2000.2000.0000.0000.0000.000
167A295SER0-0.041-0.03128.771-0.419-0.4190.0000.0000.0000.000
168A296TRP00.0360.01331.2490.3660.3660.0000.0000.0000.000
169A297ASN00.0310.00934.698-0.311-0.3110.0000.0000.0000.000
170A298THR0-0.005-0.00436.870-0.043-0.0430.0000.0000.0000.000
171A299GLY0-0.028-0.02239.738-0.156-0.1560.0000.0000.0000.000
172A300ASP-1-0.897-0.95841.3357.1527.1520.0000.0000.0000.000
173A301ALA0-0.040-0.00139.1670.2230.2230.0000.0000.0000.000
174A302PRO0-0.0260.00234.864-0.103-0.1030.0000.0000.0000.000
175A303GLU-1-0.716-0.78735.5468.8988.8980.0000.0000.0000.000
176A304VAL00.0270.01038.912-0.178-0.1780.0000.0000.0000.000
177A305GLN00.020-0.01340.8740.0440.0440.0000.0000.0000.000
178A306THR0-0.055-0.03741.7660.1100.1100.0000.0000.0000.000
179A307SER0-0.016-0.01439.308-0.071-0.0710.0000.0000.0000.000
180A308ALA00.0090.02236.8670.2430.2430.0000.0000.0000.000
181A309THR00.0040.00133.5820.0610.0610.0000.0000.0000.000
182A310THR0-0.054-0.03328.6080.0480.0480.0000.0000.0000.000
183A311LEU0-0.0120.01429.3470.0740.0740.0000.0000.0000.000
184A312VAL0-0.004-0.00924.2110.3490.3490.0000.0000.0000.000
185A313THR00.0120.00923.967-0.123-0.1230.0000.0000.0000.000
186A314SER00.0390.01322.5080.3130.3130.0000.0000.0000.000
187A315PRO0-0.045-0.02717.310-0.088-0.0880.0000.0000.0000.000
188A316PHE00.0290.03019.406-0.177-0.1770.0000.0000.0000.000
189A317THR0-0.012-0.02314.7701.3471.3470.0000.0000.0000.000
190A318PHE0-0.030-0.00417.071-0.844-0.8440.0000.0000.0000.000
191A319TYR00.0270.00013.5890.8390.8390.0000.0000.0000.000
192A320TYR0-0.039-0.02515.755-1.246-1.2460.0000.0000.0000.000
193A321ILE00.0330.01116.2021.4001.4000.0000.0000.0000.000
194A322ARG10.8580.93411.854-24.587-24.5870.0000.0000.0000.000
195A323GLU-1-0.773-0.87416.33313.96213.9620.0000.0000.0000.000
196A324ASP-1-0.943-0.96415.81819.31319.3130.0000.0000.0000.000
197A325ASP-1-0.900-0.97412.45822.00822.0080.0000.0000.0000.000