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

tag_button

FMODB ID: 6N75Z

Calculation Name: 2RFA-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2RFA

Chain ID: A

ChEMBL ID:

UniProt ID: Q91WD2

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 222
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2553886.598834
FMO2-HF: Nuclear repulsion 2467380.969124
FMO2-HF: Total energy -86505.629711
FMO2-MP2: Total energy -86755.949367


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:44:ILE)


Summations of interaction energy for fragment #1(A:44: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.
-10.314-2.2227.356-4.013-11.435-0.011
Interaction energy analysis for fragmet #1(A:44:ILE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.025 / q_NPA : -0.006
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].
3A46GLU-1-0.886-0.9313.639-2.271-0.200-0.009-0.805-1.2570.001
4A47SER0-0.035-0.0313.468-0.1670.4610.012-0.221-0.4190.000
5A48PRO00.023-0.0054.739-0.514-0.417-0.001-0.008-0.0880.000
6A49LEU00.0150.0196.8400.1110.1110.0000.0000.0000.000
7A50LEU00.0160.0062.366-1.726-0.3272.778-1.498-2.679-0.003
8A51LEU00.0010.0042.636-1.654-0.1621.546-0.927-2.110-0.008
9A52ALA00.001-0.0073.3890.7490.4480.0340.440-0.1730.000
10A53ALA0-0.005-0.0015.1710.2210.2210.0000.0000.0000.000
11A54LYS10.8500.9242.323-1.566-0.6091.454-0.442-1.9690.001
12A55GLU-1-0.912-0.9464.7910.3870.441-0.001-0.006-0.0470.000
13A56ASN00.004-0.0137.5780.0190.0190.0000.0000.0000.000
14A57ASP-1-0.811-0.8889.607-0.260-0.2600.0000.0000.0000.000
15A58VAL00.0510.00811.434-0.062-0.0620.0000.0000.0000.000
16A59GLN00.0240.02813.917-0.004-0.0040.0000.0000.0000.000
17A60ALA0-0.032-0.00310.7890.0140.0140.0000.0000.0000.000
18A61LEU00.0430.0168.269-0.014-0.0140.0000.0000.0000.000
19A62SER00.001-0.01211.7810.0160.0160.0000.0000.0000.000
20A63LYS10.7690.86914.9970.2710.2710.0000.0000.0000.000
21A64LEU00.006-0.0099.5300.0270.0270.0000.0000.0000.000
22A65LEU00.0360.01412.3750.0040.0040.0000.0000.0000.000
23A66LYS10.8510.94814.9750.2780.2780.0000.0000.0000.000
24A67PHE0-0.067-0.04515.7280.0490.0490.0000.0000.0000.000
25A68GLU-1-0.912-0.93717.668-0.226-0.2260.0000.0000.0000.000
26A69GLY0-0.0050.00316.4490.0110.0110.0000.0000.0000.000
27A70CYS0-0.092-0.04211.223-0.074-0.0740.0000.0000.0000.000
28A71GLU-1-0.842-0.92011.958-0.452-0.4520.0000.0000.0000.000
29A72VAL00.0390.01911.006-0.153-0.1530.0000.0000.0000.000
30A73HIS0-0.045-0.03411.512-0.096-0.0960.0000.0000.0000.000
31A74GLN0-0.069-0.0136.984-0.250-0.2500.0000.0000.0000.000
32A75ARG10.7870.8617.1930.4740.4740.0000.0000.0000.000
33A76GLY0-0.0080.0084.219-0.357-0.227-0.001-0.029-0.1000.000
34A77ALA0-0.028-0.0204.4380.3730.427-0.001-0.006-0.0470.000
35A78MET0-0.046-0.0216.4380.2450.2450.0000.0000.0000.000
36A79GLY00.0520.0348.3370.0860.0860.0000.0000.0000.000
37A80GLU-1-0.838-0.9144.196-1.672-1.3650.000-0.046-0.2610.000
38A81THR00.0810.0116.547-0.243-0.2430.0000.0000.0000.000
39A82ALA00.0600.0106.404-0.152-0.1520.0000.0000.0000.000
40A83LEU00.0170.0207.4530.0290.0290.0000.0000.0000.000
41A84HIS0-0.0040.0347.925-0.018-0.0180.0000.0000.0000.000
42A85ILE0-0.018-0.0042.518-0.845-0.2521.478-0.297-1.774-0.002
43A86ALA0-0.006-0.0055.8080.2020.2020.0000.0000.0000.000
44A87ALA00.003-0.0108.4900.1190.1190.0000.0000.0000.000
45A88LEU0-0.020-0.0114.8740.0750.0750.0000.0000.0000.000
46A89TYR0-0.048-0.0393.118-0.4850.1260.067-0.168-0.5110.000
47A90ASP-1-0.814-0.8808.189-0.111-0.1110.0000.0000.0000.000
48A91ASN0-0.064-0.0197.9040.1090.1090.0000.0000.0000.000
49A92LEU00.002-0.00611.523-0.057-0.0570.0000.0000.0000.000
50A93GLU-1-0.861-0.92614.838-0.215-0.2150.0000.0000.0000.000
51A94ALA00.0150.0019.981-0.016-0.0160.0000.0000.0000.000
52A95ALA00.0210.00312.138-0.045-0.0450.0000.0000.0000.000
53A96MET0-0.022-0.01113.1290.0090.0090.0000.0000.0000.000
54A97VAL0-0.022-0.00913.6930.0080.0080.0000.0000.0000.000
55A98LEU0-0.012-0.0159.166-0.012-0.0120.0000.0000.0000.000
56A99MET0-0.020-0.01013.7900.0260.0260.0000.0000.0000.000
57A100GLU-1-0.887-0.91416.935-0.185-0.1850.0000.0000.0000.000
58A101ALA0-0.066-0.03315.7170.0170.0170.0000.0000.0000.000
59A102ALA00.0130.01015.1230.0050.0050.0000.0000.0000.000
60A103PRO00.0170.01716.705-0.022-0.0220.0000.0000.0000.000
61A104GLU-1-0.804-0.90417.349-0.338-0.3380.0000.0000.0000.000
62A105LEU0-0.003-0.01311.938-0.007-0.0070.0000.0000.0000.000
63A106VAL0-0.059-0.02914.856-0.014-0.0140.0000.0000.0000.000
64A107PHE0-0.089-0.04117.2050.0220.0220.0000.0000.0000.000
65A108GLU-1-0.850-0.89613.834-0.347-0.3470.0000.0000.0000.000
66A109PRO0-0.051-0.00914.587-0.015-0.0150.0000.0000.0000.000
67A110MET0-0.0200.0138.161-0.047-0.0470.0000.0000.0000.000
68A111THR00.008-0.01512.2870.0420.0420.0000.0000.0000.000
69A112SER0-0.023-0.00811.1170.0630.0630.0000.0000.0000.000
70A113GLU-1-0.850-0.91513.4850.0010.0010.0000.0000.0000.000
71A114LEU00.0130.01412.2620.0030.0030.0000.0000.0000.000
72A115TYR0-0.007-0.0239.9360.0010.0010.0000.0000.0000.000
73A116GLU-1-0.846-0.88113.569-0.148-0.1480.0000.0000.0000.000
74A117GLY00.0330.01216.2160.0200.0200.0000.0000.0000.000
75A118GLN0-0.072-0.05910.7060.0350.0350.0000.0000.0000.000
76A119THR00.022-0.00813.491-0.052-0.0520.0000.0000.0000.000
77A120ALA00.0600.01412.8040.0030.0030.0000.0000.0000.000
78A121LEU00.0170.01413.8040.0210.0210.0000.0000.0000.000
79A122HIS00.0010.01515.352-0.002-0.0020.0000.0000.0000.000
80A123ILE00.0140.0169.4290.0220.0220.0000.0000.0000.000
81A124ALA00.0230.01313.4750.0280.0280.0000.0000.0000.000
82A125VAL0-0.054-0.02815.6340.0260.0260.0000.0000.0000.000
83A126ILE0-0.042-0.01914.3690.0210.0210.0000.0000.0000.000
84A127ASN0-0.063-0.04111.5260.0430.0430.0000.0000.0000.000
85A128GLN0-0.022-0.00615.8580.0110.0110.0000.0000.0000.000
86A129ASN00.0180.01415.9940.0080.0080.0000.0000.0000.000
87A130VAL00.033-0.00718.401-0.017-0.0170.0000.0000.0000.000
88A131ASN0-0.019-0.00820.4660.0020.0020.0000.0000.0000.000
89A132LEU00.0350.02713.660-0.008-0.0080.0000.0000.0000.000
90A133VAL00.0160.00418.143-0.012-0.0120.0000.0000.0000.000
91A134ARG10.8140.89620.2140.0970.0970.0000.0000.0000.000
92A135ALA0-0.017-0.00719.5400.0020.0020.0000.0000.0000.000
93A136LEU00.015-0.00215.902-0.007-0.0070.0000.0000.0000.000
94A137LEU0-0.030-0.01420.1790.0020.0020.0000.0000.0000.000
95A138ALA0-0.021-0.00323.7000.0060.0060.0000.0000.0000.000
96A139ARG10.7630.86320.1920.2320.2320.0000.0000.0000.000
97A140GLY00.0040.00323.357-0.007-0.0070.0000.0000.0000.000
98A141ALA0-0.0070.00120.2580.0010.0010.0000.0000.0000.000
99A142SER00.007-0.00421.6750.0210.0210.0000.0000.0000.000
100A143VAL00.0440.01422.327-0.004-0.0040.0000.0000.0000.000
101A144SER0-0.042-0.01524.6550.0090.0090.0000.0000.0000.000
102A145ALA0-0.0140.00220.0100.0040.0040.0000.0000.0000.000
103A146ARG10.8310.87721.5820.0850.0850.0000.0000.0000.000
104A147ALA0-0.0010.00317.420-0.009-0.0090.0000.0000.0000.000
105A148THR0-0.040-0.06218.9360.0130.0130.0000.0000.0000.000
106A149GLY00.0100.02216.6770.0150.0150.0000.0000.0000.000
107A150SER0-0.022-0.06217.7360.0100.0100.0000.0000.0000.000
108A151VAL0-0.039-0.00813.9370.0170.0170.0000.0000.0000.000
109A152PHE0-0.0010.00213.9940.0070.0070.0000.0000.0000.000
110A153HIS0-0.052-0.00919.2030.0170.0170.0000.0000.0000.000
111A154TYR0-0.037-0.03122.5470.0090.0090.0000.0000.0000.000
112A155ARG10.9040.93523.246-0.001-0.0010.0000.0000.0000.000
113A156PRO0-0.0030.00424.6520.0010.0010.0000.0000.0000.000
114A157HIS0-0.002-0.01122.003-0.001-0.0010.0000.0000.0000.000
115A158ASN0-0.054-0.02319.7710.0230.0230.0000.0000.0000.000
116A159LEU0-0.014-0.01517.822-0.004-0.0040.0000.0000.0000.000
117A160ILE0-0.043-0.00518.220-0.003-0.0030.0000.0000.0000.000
118A161TYR0-0.014-0.04121.5710.0020.0020.0000.0000.0000.000
119A162TYR00.0520.00918.7360.0030.0030.0000.0000.0000.000
120A163GLY00.0120.00722.963-0.007-0.0070.0000.0000.0000.000
121A164GLU-1-0.731-0.82421.502-0.069-0.0690.0000.0000.0000.000
122A165HIS00.0200.01321.293-0.022-0.0220.0000.0000.0000.000
123A166PRO00.0380.02120.2710.0090.0090.0000.0000.0000.000
124A167LEU00.0430.02421.7440.0070.0070.0000.0000.0000.000
125A168SER0-0.019-0.01224.1530.0060.0060.0000.0000.0000.000
126A169PHE00.0230.01116.5500.0090.0090.0000.0000.0000.000
127A170ALA00.0280.01321.8590.0090.0090.0000.0000.0000.000
128A171ALA0-0.013-0.01523.4060.0080.0080.0000.0000.0000.000
129A172CYS0-0.082-0.03823.3240.0090.0090.0000.0000.0000.000
130A173VAL0-0.036-0.00619.7670.0100.0100.0000.0000.0000.000
131A174GLY0-0.017-0.01123.2220.0030.0030.0000.0000.0000.000
132A175SER00.004-0.00123.6380.0000.0000.0000.0000.0000.000
133A176GLU-1-0.801-0.89425.760-0.041-0.0410.0000.0000.0000.000
134A177GLU-1-0.849-0.90526.798-0.078-0.0780.0000.0000.0000.000
135A178ILE00.0440.02721.060-0.005-0.0050.0000.0000.0000.000
136A179VAL00.001-0.01325.213-0.005-0.0050.0000.0000.0000.000
137A180ARG10.8070.90127.5830.0460.0460.0000.0000.0000.000
138A181LEU00.0600.02824.865-0.002-0.0020.0000.0000.0000.000
139A182LEU0-0.0120.00222.748-0.005-0.0050.0000.0000.0000.000
140A183ILE0-0.020-0.00826.864-0.001-0.0010.0000.0000.0000.000
141A184GLU-1-0.948-0.98330.523-0.072-0.0720.0000.0000.0000.000
142A185HIS0-0.079-0.03927.375-0.005-0.0050.0000.0000.0000.000
143A186GLY0-0.0020.00129.113-0.006-0.0060.0000.0000.0000.000
144A187ALA0-0.055-0.03227.3070.0010.0010.0000.0000.0000.000
145A188ASP-1-0.838-0.92029.114-0.054-0.0540.0000.0000.0000.000
146A189ILE0-0.005-0.01430.6050.0000.0000.0000.0000.0000.000
147A190ARG10.7760.84632.4290.0440.0440.0000.0000.0000.000
148A191ALA00.0380.04529.3050.0030.0030.0000.0000.0000.000
149A192GLN0-0.075-0.06030.6540.0030.0030.0000.0000.0000.000
150A193ASP-1-0.713-0.81226.212-0.045-0.0450.0000.0000.0000.000
151A194SER0-0.023-0.04825.8930.0030.0030.0000.0000.0000.000
152A195LEU0-0.090-0.03327.8100.0060.0060.0000.0000.0000.000
153A196GLY00.0380.02030.5600.0040.0040.0000.0000.0000.000
154A197ASN0-0.049-0.02929.5460.0040.0040.0000.0000.0000.000
155A198THR00.0710.00530.091-0.004-0.0040.0000.0000.0000.000
156A199VAL00.0550.01928.1290.0040.0040.0000.0000.0000.000
157A200LEU00.0060.00530.0130.0040.0040.0000.0000.0000.000
158A201HIS0-0.0390.00032.1000.0020.0020.0000.0000.0000.000
159A202ILE00.0340.02625.9670.0050.0050.0000.0000.0000.000
160A203LEU00.0180.02028.7320.0050.0050.0000.0000.0000.000
161A204ILE0-0.143-0.04930.4510.0040.0040.0000.0000.0000.000
162A205LEU00.0210.01228.7830.0040.0040.0000.0000.0000.000
163A206GLN0-0.0120.00025.2030.0070.0070.0000.0000.0000.000
164A207PRO00.032-0.00226.1940.0000.0000.0000.0000.0000.000
165A208ASN0-0.016-0.00928.270-0.001-0.0010.0000.0000.0000.000
166A209LYS10.9290.95230.084-0.010-0.0100.0000.0000.0000.000
167A210THR0-0.0350.00433.213-0.003-0.0030.0000.0000.0000.000
168A211PHE00.0700.03725.982-0.001-0.0010.0000.0000.0000.000
169A212ALA00.0350.03030.594-0.004-0.0040.0000.0000.0000.000
170A213CYS0-0.021-0.02031.776-0.003-0.0030.0000.0000.0000.000
171A214GLN0-0.062-0.03233.9630.0010.0010.0000.0000.0000.000
172A215MET00.0320.03628.010-0.003-0.0030.0000.0000.0000.000
173A216TYR0-0.060-0.05932.490-0.003-0.0030.0000.0000.0000.000
174A217ASN0-0.006-0.01934.469-0.001-0.0010.0000.0000.0000.000
175A218LEU00.0130.02231.996-0.001-0.0010.0000.0000.0000.000
176A219LEU00.0200.01730.139-0.002-0.0020.0000.0000.0000.000
177A220LEU0-0.007-0.01334.311-0.001-0.0010.0000.0000.0000.000
178A221SER0-0.104-0.05537.0650.0000.0000.0000.0000.0000.000
179A222TYR00.0430.01234.1880.0000.0000.0000.0000.0000.000
180A223ASP-1-0.803-0.86637.854-0.037-0.0370.0000.0000.0000.000
181A224GLY0-0.010-0.02039.4680.0000.0000.0000.0000.0000.000
182A225GLY0-0.043-0.02642.6230.0030.0030.0000.0000.0000.000
183A226ASP-1-0.888-0.92342.637-0.038-0.0380.0000.0000.0000.000
184A227HIS0-0.056-0.02144.7840.0020.0020.0000.0000.0000.000
185A228LEU0-0.008-0.02344.9430.0020.0020.0000.0000.0000.000
186A229LYS10.8410.92341.8920.0270.0270.0000.0000.0000.000
187A230SER00.0610.02441.468-0.001-0.0010.0000.0000.0000.000
188A231LEU00.0460.01934.3140.0020.0020.0000.0000.0000.000
189A232GLU-1-0.727-0.85238.639-0.019-0.0190.0000.0000.0000.000
190A233LEU0-0.057-0.02840.2840.0030.0030.0000.0000.0000.000
191A234VAL0-0.0150.00536.8290.0010.0010.0000.0000.0000.000
192A235PRO0-0.045-0.02338.5090.0010.0010.0000.0000.0000.000
193A236ASN00.0370.01433.918-0.001-0.0010.0000.0000.0000.000
194A237ASN00.024-0.00732.8620.0010.0010.0000.0000.0000.000
195A238GLN0-0.047-0.00335.1580.0020.0020.0000.0000.0000.000
196A239GLY00.0010.00237.5350.0020.0020.0000.0000.0000.000
197A240LEU0-0.059-0.03537.3370.0010.0010.0000.0000.0000.000
198A241THR00.0320.03338.035-0.001-0.0010.0000.0000.0000.000
199A242PRO00.0570.03236.0230.0030.0030.0000.0000.0000.000
200A243PHE00.0330.01037.5680.0030.0030.0000.0000.0000.000
201A244LYS10.9340.96940.8330.0050.0050.0000.0000.0000.000
202A245LEU00.0280.01333.2350.0020.0020.0000.0000.0000.000
203A246ALA00.0180.00337.4290.0030.0030.0000.0000.0000.000
204A247GLY0-0.026-0.01538.3620.0020.0020.0000.0000.0000.000
205A248VAL0-0.078-0.04037.9700.0020.0020.0000.0000.0000.000
206A249GLU-1-0.825-0.90033.2340.0070.0070.0000.0000.0000.000
207A250GLY0-0.0010.01136.2630.0020.0020.0000.0000.0000.000
208A251ASN0-0.021-0.01234.3810.0030.0030.0000.0000.0000.000
209A252ILE00.033-0.00937.543-0.003-0.0030.0000.0000.0000.000
210A253VAL00.0080.01937.574-0.001-0.0010.0000.0000.0000.000
211A254MET00.0480.02935.514-0.001-0.0010.0000.0000.0000.000
212A255PHE0-0.0100.00238.918-0.002-0.0020.0000.0000.0000.000
213A256GLN0-0.037-0.03341.758-0.001-0.0010.0000.0000.0000.000
214A257HIS0-0.010-0.00739.2050.0010.0010.0000.0000.0000.000
215A258LEU00.0190.01138.624-0.001-0.0010.0000.0000.0000.000
216A259MET0-0.100-0.03543.130-0.001-0.0010.0000.0000.0000.000
217A260GLN00.041-0.00446.3280.0000.0000.0000.0000.0000.000
218A261LYS10.8430.94240.3750.0190.0190.0000.0000.0000.000
219A262ARG10.9100.95946.3710.0080.0080.0000.0000.0000.000
220A263LYS10.8500.93748.3180.0060.0060.0000.0000.0000.000
221A264HIS0-0.032-0.01149.2740.0000.0000.0000.0000.0000.000
222A265ILE0-0.0140.00947.241-0.001-0.0010.0000.0000.0000.000