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

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FMODB ID: ZV3VN

Calculation Name: 3Q48-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3Q48

Chain ID: A

ChEMBL ID:

UniProt ID: Q9HWU3

Base Structure: X-ray

Registration Date: 2023-09-24

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 200
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2101759.245393
FMO2-HF: Nuclear repulsion 2024511.826658
FMO2-HF: Total energy -77247.418735
FMO2-MP2: Total energy -77476.822884


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:31:ILE)


Summations of interaction energy for fragment #1(A:31: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.
-11.834-3.4295.537-4.986-8.955-0.021
Interaction energy analysis for fragmet #1(A:31:ILE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.004 / q_NPA : -0.001
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].
3A33GLN00.0370.0303.890-0.1781.416-0.013-0.861-0.7200.003
4A34GLY0-0.0350.0026.970-0.084-0.0840.0000.0000.0000.000
5A35THR00.0360.0077.382-0.030-0.0300.0000.0000.0000.000
6A36ARG10.8560.9379.521-0.186-0.1860.0000.0000.0000.000
7A37VAL00.0350.01710.7100.0670.0670.0000.0000.0000.000
8A38VAL00.0090.01113.320-0.031-0.0310.0000.0000.0000.000
9A39PHE0-0.013-0.01216.9620.0180.0180.0000.0000.0000.000
10A40PRO00.0260.01718.808-0.015-0.0150.0000.0000.0000.000
11A41ALA0-0.013-0.01522.3450.0000.0000.0000.0000.0000.000
12A42SER0-0.082-0.05325.012-0.006-0.0060.0000.0000.0000.000
13A43GLU-1-0.897-0.91621.3360.1040.1040.0000.0000.0000.000
14A44ARG10.9500.97022.947-0.067-0.0670.0000.0000.0000.000
15A45GLU-1-0.862-0.93817.9040.0760.0760.0000.0000.0000.000
16A46VAL00.0120.01914.7010.0140.0140.0000.0000.0000.000
17A47THR0-0.012-0.00712.671-0.023-0.0230.0000.0000.0000.000
18A48LEU00.0130.0067.1370.0150.0150.0000.0000.0000.000
19A49ARG10.9490.9817.295-0.791-0.7910.0000.0000.0000.000
20A50VAL00.009-0.0022.272-0.506-0.4231.787-0.439-1.4310.006
21A51SER00.008-0.0162.870-2.286-1.0080.311-0.434-1.155-0.001
22A52ASN0-0.025-0.0202.404-3.792-1.2673.238-2.555-3.208-0.029
23A53THR00.010-0.0133.8620.4330.6740.000-0.036-0.2060.000
24A54SER0-0.015-0.0015.5760.1080.1080.0000.0000.0000.000
25A55GLY00.0480.0148.2560.1660.1660.0000.0000.0000.000
26A56THR0-0.011-0.0029.7700.0820.0820.0000.0000.0000.000
27A57PRO0-0.0230.0018.860-0.096-0.0960.0000.0000.0000.000
28A58VAL00.0070.0144.199-0.105-0.020-0.001-0.006-0.0780.000
29A59LEU0-0.014-0.0097.4790.1700.1700.0000.0000.0000.000
30A60ALA0-0.011-0.0163.878-0.378-0.2290.002-0.031-0.1190.000
31A61GLN00.0010.0115.6520.1800.1800.0000.0000.0000.000
32A62ALA0-0.012-0.0047.221-0.102-0.1020.0000.0000.0000.000
33A63TRP00.0470.0128.7400.0150.0150.0000.0000.0000.000
34A64ILE00.002-0.00611.721-0.031-0.0310.0000.0000.0000.000
35A65ASP-1-0.685-0.78214.265-0.233-0.2330.0000.0000.0000.000
36A66ASP-1-0.773-0.89716.681-0.105-0.1050.0000.0000.0000.000
37A67GLY0-0.055-0.03618.1300.0120.0120.0000.0000.0000.000
38A68ARG10.8800.94319.0410.0940.0940.0000.0000.0000.000
39A69GLN0-0.063-0.04114.486-0.052-0.0520.0000.0000.0000.000
40A70ASP-1-0.914-0.96317.975-0.187-0.1870.0000.0000.0000.000
41A71VAL00.0090.00320.1970.0130.0130.0000.0000.0000.000
42A72PRO00.0120.01319.766-0.018-0.0180.0000.0000.0000.000
43A73PRO00.0160.00215.9650.0140.0140.0000.0000.0000.000
44A74GLU-1-0.905-0.95518.911-0.106-0.1060.0000.0000.0000.000
45A75GLU-1-0.948-0.97921.091-0.108-0.1080.0000.0000.0000.000
46A76LEU0-0.091-0.03619.2230.0070.0070.0000.0000.0000.000
47A77GLN0-0.087-0.03623.0150.0170.0170.0000.0000.0000.000
48A78VAL00.0260.02217.9900.0100.0100.0000.0000.0000.000
49A79PRO0-0.026-0.00221.2510.0010.0010.0000.0000.0000.000
50A80PHE0-0.024-0.02616.9740.0150.0150.0000.0000.0000.000
51A81SER00.0290.03016.802-0.011-0.0110.0000.0000.0000.000
52A82VAL0-0.006-0.02110.1360.0180.0180.0000.0000.0000.000
53A83THR0-0.0390.02613.421-0.027-0.0270.0000.0000.0000.000
54A84PRO00.031-0.01210.5030.0390.0390.0000.0000.0000.000
55A85ALA00.0700.02210.5640.0000.0000.0000.0000.0000.000
56A86VAL00.0220.0009.580-0.059-0.0590.0000.0000.0000.000
57A87THR0-0.034-0.0166.5970.0740.0740.0000.0000.0000.000
58A88ARG10.9000.9517.705-0.001-0.0010.0000.0000.0000.000
59A89VAL0-0.035-0.0164.2500.0210.140-0.001-0.013-0.1050.000
60A90GLU-1-0.787-0.8907.260-0.185-0.1850.0000.0000.0000.000
61A91PRO0-0.015-0.0038.0870.0060.0060.0000.0000.0000.000
62A92ASN0-0.026-0.0078.9570.1350.1350.0000.0000.0000.000
63A93GLY00.0620.0418.0870.0150.0150.0000.0000.0000.000
64A94GLY0-0.019-0.0226.0460.3230.3230.0000.0000.0000.000
65A95ALA0-0.0310.0105.899-0.193-0.1930.0000.0000.0000.000
66A96VAL0-0.024-0.0287.1390.1680.1680.0000.0000.0000.000
67A97LEU0-0.0200.0035.733-0.081-0.0810.0000.0000.0000.000
68A98ARG10.8700.8979.782-0.099-0.0990.0000.0000.0000.000
69A99ILE00.0080.00511.223-0.037-0.0370.0000.0000.0000.000
70A100ALA00.0210.01614.8040.0190.0190.0000.0000.0000.000
71A101TYR0-0.0070.00518.575-0.012-0.0120.0000.0000.0000.000
72A102LEU00.002-0.00321.3070.0060.0060.0000.0000.0000.000
73A103LYS10.9380.95524.159-0.013-0.0130.0000.0000.0000.000
74A104ALA00.0420.03325.918-0.003-0.0030.0000.0000.0000.000
75A105PRO0-0.051-0.03627.7590.0040.0040.0000.0000.0000.000
76A106LEU00.0290.02423.476-0.006-0.0060.0000.0000.0000.000
77A107PRO0-0.0100.00126.9000.0050.0050.0000.0000.0000.000
78A108THR00.0270.00928.3190.0020.0020.0000.0000.0000.000
79A109ASP-1-0.822-0.87930.8680.0050.0050.0000.0000.0000.000
80A110ARG10.8410.87927.6790.0090.0090.0000.0000.0000.000
81A111GLU-1-0.775-0.87122.4410.0330.0330.0000.0000.0000.000
82A112SER0-0.045-0.03122.865-0.009-0.0090.0000.0000.0000.000
83A113LEU0-0.027-0.00617.1050.0090.0090.0000.0000.0000.000
84A114PHE00.0250.01516.771-0.004-0.0040.0000.0000.0000.000
85A115TRP0-0.001-0.00813.013-0.005-0.0050.0000.0000.0000.000
86A116LEU00.0250.0168.2420.0090.0090.0000.0000.0000.000
87A117ASN0-0.057-0.0178.802-0.106-0.1060.0000.0000.0000.000
88A118ILE00.011-0.0102.941-0.5330.0810.139-0.119-0.6340.000
89A119LEU0-0.022-0.0085.623-0.247-0.2470.0000.0000.0000.000
90A120GLU-1-0.866-0.9373.860-4.735-3.7710.013-0.299-0.677-0.002
91A121VAL0-0.005-0.0055.6750.1660.1660.0000.0000.0000.000
92A122PRO0-0.025-0.0247.1830.1910.1910.0000.0000.0000.000
93A123PRO0-0.026-0.0499.1470.0740.0740.0000.0000.0000.000
94A124ARG10.9891.04612.8180.5260.5260.0000.0000.0000.000
95A134PHE0-0.042-0.04012.9430.0100.0100.0000.0000.0000.000
96A135SER00.0230.0139.284-0.061-0.0610.0000.0000.0000.000
97A136PHE00.0180.0234.9650.1920.1920.0000.0000.0000.000
98A137ARG10.8800.9375.8770.2790.2790.0000.0000.0000.000
99A138SER00.002-0.0062.767-0.4050.1140.062-0.151-0.4310.002
100A139ARG10.7730.8525.9750.4200.4200.0000.0000.0000.000
101A140PHE0-0.019-0.0103.912-0.1230.1110.000-0.042-0.1910.000
102A141LYS10.8390.9009.9680.1100.1100.0000.0000.0000.000
103A142LEU00.0070.00713.1340.0290.0290.0000.0000.0000.000
104A143PHE00.018-0.00215.003-0.015-0.0150.0000.0000.0000.000
105A144PHE00.0320.02518.4660.0180.0180.0000.0000.0000.000
106A145ARG10.7700.83020.944-0.085-0.0850.0000.0000.0000.000
107A146PRO00.0330.02423.5530.0090.0090.0000.0000.0000.000
108A147SER00.0670.01727.0850.0050.0050.0000.0000.0000.000
109A148GLN0-0.077-0.03628.6010.0090.0090.0000.0000.0000.000
110A149LEU0-0.044-0.00826.706-0.001-0.0010.0000.0000.0000.000
111A150LYS10.9420.95027.347-0.060-0.0600.0000.0000.0000.000
112A151SER00.006-0.00229.1460.0040.0040.0000.0000.0000.000
113A152VAL00.0400.02622.886-0.006-0.0060.0000.0000.0000.000
114A153ASP-1-0.878-0.93624.4720.1090.1090.0000.0000.0000.000
115A154SER0-0.097-0.05526.450-0.003-0.0030.0000.0000.0000.000
116A155ALA0-0.030-0.00426.356-0.006-0.0060.0000.0000.0000.000
117A156ALA00.0570.02625.289-0.006-0.0060.0000.0000.0000.000
118A157GLY00.0130.01227.316-0.005-0.0050.0000.0000.0000.000
119A158LYS10.9200.94730.717-0.040-0.0400.0000.0000.0000.000
120A159LEU0-0.0430.00826.774-0.005-0.0050.0000.0000.0000.000
121A160GLN0-0.0100.00831.4910.0000.0000.0000.0000.0000.000
122A161TRP00.0530.00827.288-0.005-0.0050.0000.0000.0000.000
123A162LYS10.9040.97134.4900.0150.0150.0000.0000.0000.000
124A163PHE00.0590.03235.571-0.003-0.0030.0000.0000.0000.000
125A164LEU0-0.080-0.04635.3000.0010.0010.0000.0000.0000.000
126A165GLU-1-0.874-0.90537.038-0.025-0.0250.0000.0000.0000.000
127A174DVA00.0200.03632.938-0.001-0.0010.0000.0000.0000.000
128A175VAL0-0.001-0.02231.1900.0040.0040.0000.0000.0000.000
129A176GLN0-0.020-0.02231.811-0.001-0.0010.0000.0000.0000.000
130A177VAL0-0.0220.00527.6520.0050.0050.0000.0000.0000.000
131A178ASN0-0.013-0.02831.070-0.006-0.0060.0000.0000.0000.000
132A179ASN00.0250.01226.8000.0120.0120.0000.0000.0000.000
133A180PRO0-0.0080.01830.409-0.003-0.0030.0000.0000.0000.000
134A181THR0-0.053-0.05428.8350.0060.0060.0000.0000.0000.000
135A182PRO00.0550.01529.022-0.004-0.0040.0000.0000.0000.000
136A183TYR00.0360.02124.5500.0010.0010.0000.0000.0000.000
137A184TYR00.0300.00121.157-0.011-0.0110.0000.0000.0000.000
138A185VAL0-0.0040.01122.4580.0130.0130.0000.0000.0000.000
139A186SER0-0.022-0.02517.735-0.024-0.0240.0000.0000.0000.000
140A187PHE00.0470.01119.8330.0180.0180.0000.0000.0000.000
141A188ALA0-0.045-0.03217.731-0.019-0.0190.0000.0000.0000.000
142A189SER0-0.021-0.01518.792-0.013-0.0130.0000.0000.0000.000
143A190VAL00.0040.00722.0620.0090.0090.0000.0000.0000.000
144A191GLU-1-0.920-0.95925.5840.0110.0110.0000.0000.0000.000
145A192LEU00.0060.01228.4790.0040.0040.0000.0000.0000.000
146A193ILE00.0100.00230.3020.0000.0000.0000.0000.0000.000
147A194VAL00.0280.00334.1690.0000.0000.0000.0000.0000.000
148A195ASP-1-0.838-0.90937.8210.0080.0080.0000.0000.0000.000
149A196GLY0-0.003-0.00135.3360.0000.0000.0000.0000.0000.000
150A197ARG10.8120.91234.254-0.002-0.0020.0000.0000.0000.000
151A198VAL00.0410.01928.3990.0000.0000.0000.0000.0000.000
152A199MET0-0.024-0.00630.854-0.004-0.0040.0000.0000.0000.000
153A200SER00.0030.00125.195-0.001-0.0010.0000.0000.0000.000
154A201VAL00.0280.00427.046-0.005-0.0050.0000.0000.0000.000
155A202GLY00.0330.03623.002-0.008-0.0080.0000.0000.0000.000
156A203LYS10.9360.96215.2030.1390.1390.0000.0000.0000.000
157A204GLY0-0.012-0.01019.639-0.011-0.0110.0000.0000.0000.000
158A205MET0-0.0170.04318.4370.0130.0130.0000.0000.0000.000
159A206VAL00.0070.02821.256-0.008-0.0080.0000.0000.0000.000
160A207ALA00.0280.01224.1460.0060.0060.0000.0000.0000.000
161A208PRO00.0040.00224.6980.0030.0030.0000.0000.0000.000
162A209PHE0-0.034-0.01027.848-0.005-0.0050.0000.0000.0000.000
163A210SER0-0.0190.00328.276-0.006-0.0060.0000.0000.0000.000
164A211THR00.0180.00630.4230.0060.0060.0000.0000.0000.000
165A212LYS10.8280.92623.4690.0490.0490.0000.0000.0000.000
166A213GLU-1-0.786-0.88828.557-0.029-0.0290.0000.0000.0000.000
167A214PHE0-0.063-0.04324.135-0.007-0.0070.0000.0000.0000.000
168A215ASP-1-0.872-0.94928.923-0.050-0.0500.0000.0000.0000.000
169A216TRP00.0360.00929.788-0.002-0.0020.0000.0000.0000.000
170A217GLN00.020-0.00532.184-0.002-0.0020.0000.0000.0000.000
171A218GLY0-0.006-0.00634.1300.0010.0010.0000.0000.0000.000
172A219ASN0-0.042-0.03835.6320.0020.0020.0000.0000.0000.000
173A220PRO0-0.0400.00935.7800.0020.0020.0000.0000.0000.000
174A221LYS10.8910.92038.8600.0240.0240.0000.0000.0000.000
175A222ASN0-0.055-0.01841.8690.0010.0010.0000.0000.0000.000
176A223MET0-0.0040.01239.9410.0020.0020.0000.0000.0000.000
177A224GLU-1-0.865-0.95738.585-0.004-0.0040.0000.0000.0000.000
178A225ALA0-0.0040.01641.6840.0010.0010.0000.0000.0000.000
179A226ALA0-0.061-0.02336.2600.0020.0020.0000.0000.0000.000
180A227SER00.0220.02134.3400.0020.0020.0000.0000.0000.000
181A228VAL0-0.036-0.04029.857-0.003-0.0030.0000.0000.0000.000
182A229ARG10.8520.88927.395-0.035-0.0350.0000.0000.0000.000
183A230TYR0-0.029-0.04725.565-0.006-0.0060.0000.0000.0000.000
184A231GLU-1-0.818-0.89220.9920.0930.0930.0000.0000.0000.000
185A232VAL0-0.025-0.02721.055-0.015-0.0150.0000.0000.0000.000
186A233ILE0-0.067-0.03414.6850.0110.0110.0000.0000.0000.000
187A234ASN0-0.0030.00718.0260.0070.0070.0000.0000.0000.000
188A235ASP-1-0.711-0.85017.0720.1130.1130.0000.0000.0000.000
189A236TYR0-0.020-0.01515.0870.0100.0100.0000.0000.0000.000
190A237GLY0-0.063-0.01912.9880.0660.0660.0000.0000.0000.000
191A238GLY00.0150.01713.9960.0060.0060.0000.0000.0000.000
192A239ARG10.8600.90416.663-0.162-0.1620.0000.0000.0000.000
193A240ASN00.0050.00519.3490.0160.0160.0000.0000.0000.000
194A241THR00.0120.00423.106-0.011-0.0110.0000.0000.0000.000
195A242HIS00.0110.00825.684-0.001-0.0010.0000.0000.0000.000
196A243ASP-1-0.731-0.80929.0570.0350.0350.0000.0000.0000.000
197A244ARG10.7860.89932.042-0.035-0.0350.0000.0000.0000.000
198A245ALA00.0830.05434.585-0.002-0.0020.0000.0000.0000.000
199A246LEU0-0.044-0.01234.2800.0000.0000.0000.0000.0000.000
200A247GLY00.0210.00237.654-0.001-0.0010.0000.0000.0000.000