FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 6N7QZ

Calculation Name: 3RON-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3RON

Chain ID: A

ChEMBL ID:

UniProt ID: P0A382

Base Structure: X-ray

Registration Date: 2023-06-22

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 201
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2243129.323579
FMO2-HF: Nuclear repulsion 2166035.378134
FMO2-HF: Total energy -77093.945445
FMO2-MP2: Total energy -77319.33808


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:38:ASN)


Summations of interaction energy for fragment #1(A:38:ASN)
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.
-31.283-25.38518.948-10.907-13.938-0.016
Interaction energy analysis for fragmet #1(A:38:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.011 / q_NPA : -0.018
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].
3A40LEU0-0.008-0.0012.041-13.106-9.6525.635-4.416-4.6730.041
4A41LEU00.0050.0013.6730.1620.4090.0220.053-0.3220.001
5A42SER0-0.033-0.0224.259-1.373-1.229-0.001-0.016-0.1280.000
6A43ILE0-0.036-0.0056.706-0.620-0.6200.0000.0000.0000.000
7A44ASN0-0.002-0.0139.194-0.079-0.0790.0000.0000.0000.000
8A45GLU-1-0.825-0.90711.8940.2810.2810.0000.0000.0000.000
9A46ILE0-0.047-0.02911.876-0.043-0.0430.0000.0000.0000.000
10A47ASP-1-0.827-0.91816.4400.0020.0020.0000.0000.0000.000
11A48ASN0-0.036-0.01918.954-0.022-0.0220.0000.0000.0000.000
12A49PRO00.0710.00817.051-0.033-0.0330.0000.0000.0000.000
13A50ASN00.0070.01816.336-0.057-0.0570.0000.0000.0000.000
14A51TYR00.0360.01715.010-0.031-0.0310.0000.0000.0000.000
15A52ILE00.0210.02411.380-0.059-0.0590.0000.0000.0000.000
16A53LEU00.0010.00310.117-0.179-0.1790.0000.0000.0000.000
17A54GLN00.004-0.0079.749-0.223-0.2230.0000.0000.0000.000
18A55ALA00.0430.0139.307-0.175-0.1750.0000.0000.0000.000
19A56ILE00.0110.0045.228-0.228-0.2280.0000.0000.0000.000
20A57MET0-0.048-0.0254.975-1.632-1.571-0.0010.000-0.0590.000
21A58LEU00.0100.0056.617-0.379-0.3790.0000.0000.0000.000
22A59ALA00.0340.0133.088-0.3140.3930.055-0.288-0.4730.000
23A60ASN0-0.019-0.0181.901-18.191-19.28210.862-4.713-5.058-0.049
24A61ALA0-0.0120.0173.2122.9602.4530.0410.606-0.1400.000
25A62PHE00.030-0.0135.3510.5990.5990.0000.0000.0000.000
26A63GLN00.0560.0342.5621.8154.5702.337-2.093-2.999-0.009
27A64ASN0-0.065-0.0414.4320.5210.588-0.001-0.018-0.0480.000
28A65ALA0-0.023-0.0197.535-0.056-0.0560.0000.0000.0000.000
29A66LEU0-0.030-0.0045.0280.0240.0240.0000.0000.0000.000
30A67VAL0-0.016-0.0099.377-0.302-0.3020.0000.0000.0000.000
31A68PRO00.0200.01112.2690.1190.1190.0000.0000.0000.000
32A69THR00.0190.01314.101-0.001-0.0010.0000.0000.0000.000
33A70SER00.0100.00416.799-0.060-0.0600.0000.0000.0000.000
34A71THR00.0540.01120.1000.0160.0160.0000.0000.0000.000
35A72ASP-1-0.887-0.94221.5250.1970.1970.0000.0000.0000.000
36A73PHE0-0.043-0.01317.084-0.013-0.0130.0000.0000.0000.000
37A74GLY00.0290.00219.403-0.004-0.0040.0000.0000.0000.000
38A75ASP-1-0.946-0.95415.2970.2110.2110.0000.0000.0000.000
39A76ALA00.0160.01113.497-0.004-0.0040.0000.0000.0000.000
40A77LEU00.0040.0198.015-0.028-0.0280.0000.0000.0000.000
41A78ARG10.7970.87810.223-0.561-0.5610.0000.0000.0000.000
42A79PHE00.0330.0278.282-0.185-0.1850.0000.0000.0000.000
43A80SER0-0.0040.00010.068-0.205-0.2050.0000.0000.0000.000
44A81MET00.0260.01513.032-0.067-0.0670.0000.0000.0000.000
45A82PRO00.021-0.00514.776-0.068-0.0680.0000.0000.0000.000
46A83LYS10.8750.94612.001-0.227-0.2270.0000.0000.0000.000
47A84GLY00.025-0.00411.306-0.068-0.0680.0000.0000.0000.000
48A85LEU0-0.010-0.01112.306-0.112-0.1120.0000.0000.0000.000
49A86GLU-1-0.886-0.92414.2890.0500.0500.0000.0000.0000.000
50A87ILE0-0.012-0.0018.720-0.058-0.0580.0000.0000.0000.000
51A88ALA00.0190.01212.200-0.105-0.1050.0000.0000.0000.000
52A89ASN0-0.090-0.04813.635-0.032-0.0320.0000.0000.0000.000
53A90THR0-0.080-0.04013.034-0.028-0.0280.0000.0000.0000.000
54A91ILE0-0.035-0.0059.597-0.071-0.0710.0000.0000.0000.000
55A92THR0-0.0130.00613.2030.1100.1100.0000.0000.0000.000
56A93PRO0-0.021-0.02614.594-0.075-0.0750.0000.0000.0000.000
57A94MET00.0190.01716.287-0.024-0.0240.0000.0000.0000.000
58A95GLY00.0340.01416.449-0.006-0.0060.0000.0000.0000.000
59A96ALA0-0.047-0.01617.3760.0170.0170.0000.0000.0000.000
60A97VAL00.005-0.00315.3540.0010.0010.0000.0000.0000.000
61A98VAL0-0.042-0.01517.7480.0020.0020.0000.0000.0000.000
62A99SER0-0.020-0.02418.5610.0040.0040.0000.0000.0000.000
63A100TYR00.019-0.00717.6620.0170.0170.0000.0000.0000.000
64A101VAL0-0.020-0.00317.900-0.030-0.0300.0000.0000.0000.000
65A102ASP-1-0.817-0.90618.0300.4450.4450.0000.0000.0000.000
66A103GLN00.0100.00920.107-0.044-0.0440.0000.0000.0000.000
67A104ASN00.0150.01021.0650.0570.0570.0000.0000.0000.000
68A105VAL0-0.0040.00422.464-0.027-0.0270.0000.0000.0000.000
69A106THR00.0090.00924.0680.0140.0140.0000.0000.0000.000
70A107GLN0-0.018-0.02326.769-0.001-0.0010.0000.0000.0000.000
71A108THR00.0280.00828.8370.0030.0030.0000.0000.0000.000
72A109ASN0-0.019-0.01631.7260.0020.0020.0000.0000.0000.000
73A110ASN00.0160.01730.766-0.006-0.0060.0000.0000.0000.000
74A111GLN00.0060.00029.4020.0120.0120.0000.0000.0000.000
75A112VAL00.0210.01523.4920.0100.0100.0000.0000.0000.000
76A113SER00.0420.01724.7870.0300.0300.0000.0000.0000.000
77A114VAL0-0.0070.01126.0470.0100.0100.0000.0000.0000.000
78A115MET0-0.0380.00021.8870.0100.0100.0000.0000.0000.000
79A116ILE00.0190.01420.8700.0250.0250.0000.0000.0000.000
80A117ASN0-0.013-0.02622.1550.0120.0120.0000.0000.0000.000
81A118LYS10.8320.91624.454-0.236-0.2360.0000.0000.0000.000
82A119VAL00.0100.00217.8910.0020.0020.0000.0000.0000.000
83A120LEU00.0290.02019.7200.0250.0250.0000.0000.0000.000
84A121GLU-1-0.819-0.88821.4310.2340.2340.0000.0000.0000.000
85A122VAL0-0.0210.00919.567-0.015-0.0150.0000.0000.0000.000
86A123LEU00.0210.00215.435-0.004-0.0040.0000.0000.0000.000
87A124LYS10.8440.90418.971-0.260-0.2600.0000.0000.0000.000
88A125THR0-0.074-0.03321.921-0.039-0.0390.0000.0000.0000.000
89A126VAL0-0.0440.00016.221-0.030-0.0300.0000.0000.0000.000
90A127LEU00.0380.01816.084-0.035-0.0350.0000.0000.0000.000
91A128GLY00.0520.03919.369-0.046-0.0460.0000.0000.0000.000
92A129VAL00.002-0.00222.9430.0090.0090.0000.0000.0000.000
93A130ALA00.0220.01025.1390.0070.0070.0000.0000.0000.000
94A131LEU00.0210.02417.467-0.003-0.0030.0000.0000.0000.000
95A132SER00.024-0.00520.8510.0270.0270.0000.0000.0000.000
96A133GLY0-0.016-0.00521.8660.0110.0110.0000.0000.0000.000
97A134SER0-0.078-0.05221.091-0.009-0.0090.0000.0000.0000.000
98A135VAL00.000-0.00117.274-0.007-0.0070.0000.0000.0000.000
99A136ILE00.0210.02919.3050.0500.0500.0000.0000.0000.000
100A137ASP-1-0.870-0.92121.2240.2260.2260.0000.0000.0000.000
101A138GLN00.003-0.01916.3030.0290.0290.0000.0000.0000.000
102A139LEU0-0.017-0.00415.9600.0880.0880.0000.0000.0000.000
103A140THR0-0.010-0.02817.4780.0480.0480.0000.0000.0000.000
104A141ALA0-0.0020.01217.7270.0110.0110.0000.0000.0000.000
105A142ALA00.0080.01013.3000.0240.0240.0000.0000.0000.000
106A143VAL0-0.0010.00515.0300.0650.0650.0000.0000.0000.000
107A144THR0-0.004-0.02617.140-0.029-0.0290.0000.0000.0000.000
108A145ASN0-0.042-0.01115.497-0.077-0.0770.0000.0000.0000.000
109A146THR00.0290.03114.6710.0880.0880.0000.0000.0000.000
110A147PHE0-0.039-0.02015.741-0.017-0.0170.0000.0000.0000.000
111A148THR0-0.038-0.02518.923-0.064-0.0640.0000.0000.0000.000
112A149ASN0-0.016-0.01918.6570.0090.0090.0000.0000.0000.000
113A150LEU00.0510.03216.098-0.003-0.0030.0000.0000.0000.000
114A151ASN00.0360.01217.614-0.019-0.0190.0000.0000.0000.000
115A152THR0-0.080-0.04516.867-0.046-0.0460.0000.0000.0000.000
116A153GLN00.0490.02913.2760.1360.1360.0000.0000.0000.000
117A154LYS10.8460.93713.106-0.108-0.1080.0000.0000.0000.000
118A155ASN00.0160.00812.8560.0290.0290.0000.0000.0000.000
119A156GLU-1-0.917-0.9439.305-0.236-0.2360.0000.0000.0000.000
120A157ALA00.0060.0044.4900.1240.185-0.001-0.022-0.0380.000
121A158TRP00.0150.0176.2310.4220.4220.0000.0000.0000.000
122A159ILE0-0.050-0.0197.4570.1130.1130.0000.0000.0000.000
123A160PHE00.0190.0177.222-0.237-0.2370.0000.0000.0000.000
124A161TRP0-0.024-0.03312.9820.0470.0470.0000.0000.0000.000
125A162GLY00.0140.01216.515-0.011-0.0110.0000.0000.0000.000
126A163LYS10.8090.89518.847-0.222-0.2220.0000.0000.0000.000
127A164GLU-1-0.783-0.88220.6840.2200.2200.0000.0000.0000.000
128A165THR00.001-0.01424.242-0.016-0.0160.0000.0000.0000.000
129A166ALA00.025-0.00428.0610.0040.0040.0000.0000.0000.000
130A167ASN0-0.035-0.02030.133-0.006-0.0060.0000.0000.0000.000
131A168GLN0-0.090-0.03825.056-0.007-0.0070.0000.0000.0000.000
132A169THR00.0160.00020.934-0.014-0.0140.0000.0000.0000.000
133A170ASN0-0.028-0.01220.3460.0080.0080.0000.0000.0000.000
134A171TYR0-0.021-0.03715.162-0.065-0.0650.0000.0000.0000.000
135A172THR00.011-0.01011.896-0.043-0.0430.0000.0000.0000.000
136A173TYR0-0.017-0.03311.1810.0520.0520.0000.0000.0000.000
137A174ASN0-0.019-0.0026.745-0.225-0.2250.0000.0000.0000.000
138A175VAL00.0330.0137.5510.5120.5120.0000.0000.0000.000
139A176LEU00.010-0.0044.818-0.104-0.1040.0000.0000.0000.000
140A177PHE00.0190.0247.964-0.094-0.0940.0000.0000.0000.000
141A178ALA00.0050.0088.786-0.155-0.1550.0000.0000.0000.000
142A179ILE0-0.005-0.00410.824-0.020-0.0200.0000.0000.0000.000
143A180GLN00.0480.00714.637-0.063-0.0630.0000.0000.0000.000
144A181ASN00.0680.03917.138-0.013-0.0130.0000.0000.0000.000
145A182ALA00.0480.01420.606-0.008-0.0080.0000.0000.0000.000
146A183GLN0-0.063-0.02422.574-0.003-0.0030.0000.0000.0000.000
147A184THR0-0.080-0.03517.8070.0170.0170.0000.0000.0000.000
148A185GLY0-0.0100.00021.169-0.014-0.0140.0000.0000.0000.000
149A186GLY00.002-0.00222.152-0.014-0.0140.0000.0000.0000.000
150A187VAL0-0.047-0.03118.443-0.023-0.0230.0000.0000.0000.000
151A188MET0-0.0100.00712.387-0.029-0.0290.0000.0000.0000.000
152A189TYR0-0.001-0.01214.864-0.016-0.0160.0000.0000.0000.000
153A190CYS0-0.020-0.0058.905-0.042-0.0420.0000.0000.0000.000
154A191VAL0-0.012-0.00611.137-0.041-0.0410.0000.0000.0000.000
155A192PRO00.0200.0228.1380.2540.2540.0000.0000.0000.000
156A193VAL0-0.032-0.0079.366-0.385-0.3850.0000.0000.0000.000
157A194GLY00.0270.0289.7540.4790.4790.0000.0000.0000.000
158A195PHE0-0.036-0.01711.471-0.294-0.2940.0000.0000.0000.000
159A196GLU-1-0.836-0.91813.8520.5650.5650.0000.0000.0000.000
160A197ILE0-0.033-0.00616.156-0.078-0.0780.0000.0000.0000.000
161A198LYS10.9050.96319.133-0.283-0.2830.0000.0000.0000.000
162A199VAL00.0240.00522.295-0.005-0.0050.0000.0000.0000.000
163A200SER0-0.023-0.01224.505-0.010-0.0100.0000.0000.0000.000
164A201ALA00.0220.01226.563-0.016-0.0160.0000.0000.0000.000
165A202VAL00.0060.03626.2500.0150.0150.0000.0000.0000.000
166A203LYS10.8600.91918.841-0.198-0.1980.0000.0000.0000.000
167A204GLU-1-0.847-0.94223.7110.1580.1580.0000.0000.0000.000
168A205GLN0-0.041-0.02325.4870.0020.0020.0000.0000.0000.000
169A206VAL00.0070.00920.9920.0080.0080.0000.0000.0000.000
170A207LEU0-0.068-0.02919.6300.0250.0250.0000.0000.0000.000
171A208PHE0-0.053-0.03722.0540.0070.0070.0000.0000.0000.000
172A209PHE0-0.0050.02323.242-0.012-0.0120.0000.0000.0000.000
173A210THR00.009-0.02123.5970.0190.0190.0000.0000.0000.000
174A211ILE00.037-0.00824.0320.0090.0090.0000.0000.0000.000
175A212GLN0-0.003-0.00726.2400.0020.0020.0000.0000.0000.000
176A213ASP-1-0.783-0.84427.5790.1710.1710.0000.0000.0000.000
177A214SER0-0.019-0.03429.2650.0060.0060.0000.0000.0000.000
178A215ALA00.0060.02227.143-0.007-0.0070.0000.0000.0000.000
179A216SER00.009-0.00529.094-0.002-0.0020.0000.0000.0000.000
180A217TYR00.0230.00621.917-0.002-0.0020.0000.0000.0000.000
181A218ASN0-0.086-0.05924.228-0.024-0.0240.0000.0000.0000.000
182A219VAL00.0420.03818.6270.0170.0170.0000.0000.0000.000
183A220ASN0-0.015-0.00318.3210.0200.0200.0000.0000.0000.000
184A221ILE00.010-0.00116.3770.0800.0800.0000.0000.0000.000
185A222GLN00.0090.01314.755-0.041-0.0410.0000.0000.0000.000
186A223SER0-0.018-0.03413.4540.1300.1300.0000.0000.0000.000
187A224LEU0-0.017-0.00512.072-0.112-0.1120.0000.0000.0000.000
188A225LYS10.8800.95113.672-0.097-0.0970.0000.0000.0000.000
189A226PHE00.0320.01412.043-0.052-0.0520.0000.0000.0000.000
190A227ALA00.0090.00114.2650.0220.0220.0000.0000.0000.000
191A228GLN00.0360.01813.332-0.062-0.0620.0000.0000.0000.000
192A229PRO00.0250.01516.3620.0170.0170.0000.0000.0000.000
193A230LEU0-0.0270.00816.944-0.051-0.0510.0000.0000.0000.000
194A231VAL0-0.025-0.02015.8410.0180.0180.0000.0000.0000.000
195A232SER0-0.025-0.01416.726-0.031-0.0310.0000.0000.0000.000
196A233SER0-0.004-0.00715.5190.0070.0070.0000.0000.0000.000
197A234SER0-0.010-0.00517.6800.0390.0390.0000.0000.0000.000
198A235GLN0-0.025-0.02213.339-0.028-0.0280.0000.0000.0000.000
199A236TYR0-0.001-0.00815.084-0.051-0.0510.0000.0000.0000.000
200A237PRO0-0.042-0.00210.2740.0380.0380.0000.0000.0000.000
201A238ILE00.0310.0169.3010.0550.0550.0000.0000.0000.000