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: 72N4K

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 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 222
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2549060.664649
FMO2-HF: Nuclear repulsion 2462556.463119
FMO2-HF: Total energy -86504.201529
FMO2-MP2: Total energy -86754.65088


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.
-11.965-3.3118.87-5.405-12.116-0.016
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 : -0.010 / q_NPA : -0.014
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-1-0.883-0.9363.694-1.8700.983-0.004-1.292-1.5570.001
4A47SER0-0.061-0.0403.137-1.580-0.5810.054-0.365-0.6880.000
5A48PRO00.0500.0054.049-1.520-1.3070.001-0.055-0.1590.000
6A49LEU00.0130.0096.545-0.174-0.1740.0000.0000.0000.000
7A50LEU00.0010.0012.088-2.197-1.0334.168-2.343-2.989-0.006
8A51LEU0-0.017-0.0042.311-2.593-0.9772.853-1.779-2.690-0.010
9A52ALA00.0250.0093.0921.6150.3950.0741.350-0.203-0.001
10A53ALA0-0.0030.0005.1160.1850.1850.0000.0000.0000.000
11A54LYS10.9140.9682.171-0.7570.0791.300-0.420-1.7160.002
12A55GLU-1-0.983-1.0024.959-0.182-0.154-0.001-0.004-0.0230.000
13A56ASN0-0.006-0.0057.5290.0520.0520.0000.0000.0000.000
14A57ASP-1-0.849-0.9199.328-0.192-0.1920.0000.0000.0000.000
15A58VAL00.0610.01311.158-0.013-0.0130.0000.0000.0000.000
16A59GLN0-0.055-0.02913.6340.0300.0300.0000.0000.0000.000
17A60ALA0-0.0070.00610.5790.0270.0270.0000.0000.0000.000
18A61LEU00.0480.0208.2810.0260.0260.0000.0000.0000.000
19A62SER0-0.017-0.01211.6360.0400.0400.0000.0000.0000.000
20A63LYS10.8560.91915.0090.1430.1430.0000.0000.0000.000
21A64LEU0-0.004-0.0039.3920.0330.0330.0000.0000.0000.000
22A65LEU00.005-0.01112.5020.0300.0300.0000.0000.0000.000
23A66LYS10.9020.96414.9930.0750.0750.0000.0000.0000.000
24A67PHE0-0.106-0.03614.7510.0170.0170.0000.0000.0000.000
25A68GLU-1-0.863-0.91217.006-0.019-0.0190.0000.0000.0000.000
26A69GLY0-0.027-0.01215.7420.0200.0200.0000.0000.0000.000
27A70CYS0-0.084-0.04910.1580.0640.0640.0000.0000.0000.000
28A71GLU-1-0.847-0.90611.5710.0440.0440.0000.0000.0000.000
29A72VAL0-0.005-0.02310.615-0.021-0.0210.0000.0000.0000.000
30A73HIS0-0.021-0.02611.248-0.075-0.0750.0000.0000.0000.000
31A74GLN0-0.0120.0376.3430.4240.4240.0000.0000.0000.000
32A75ARG10.7990.8667.2180.0270.0270.0000.0000.0000.000
33A76GLY00.0000.0123.9190.2640.4250.000-0.042-0.1190.000
34A77ALA0-0.001-0.0114.4890.3000.358-0.001-0.008-0.0480.000
35A78MET0-0.064-0.0286.5100.1700.1700.0000.0000.0000.000
36A79GLY00.0390.0178.0120.0460.0460.0000.0000.0000.000
37A80GLU-1-0.850-0.9153.978-2.560-2.0900.005-0.124-0.350-0.001
38A81THR00.0830.0256.607-0.075-0.0750.0000.0000.0000.000
39A82ALA00.0700.0096.222-0.272-0.2720.0000.0000.0000.000
40A83LEU00.0280.0277.277-0.044-0.0440.0000.0000.0000.000
41A84HIS00.0020.0217.838-0.050-0.0500.0000.0000.0000.000
42A85ILE0-0.025-0.0012.875-1.0530.0060.405-0.228-1.236-0.001
43A86ALA00.010-0.0075.7600.1670.1670.0000.0000.0000.000
44A87ALA00.002-0.0038.5030.1080.1080.0000.0000.0000.000
45A88LEU0-0.039-0.0245.3640.0610.0610.0000.0000.0000.000
46A89TYR0-0.047-0.0393.478-0.3110.1060.016-0.095-0.3380.000
47A90ASP-1-0.863-0.9098.458-0.212-0.2120.0000.0000.0000.000
48A91ASN0-0.067-0.0278.3280.1120.1120.0000.0000.0000.000
49A92LEU00.0220.00211.791-0.027-0.0270.0000.0000.0000.000
50A93GLU-1-0.876-0.94014.723-0.240-0.2400.0000.0000.0000.000
51A94ALA00.0220.0089.8230.0040.0040.0000.0000.0000.000
52A95ALA00.0200.01011.954-0.013-0.0130.0000.0000.0000.000
53A96MET0-0.041-0.01713.0760.0270.0270.0000.0000.0000.000
54A97VAL0-0.012-0.00613.6420.0240.0240.0000.0000.0000.000
55A98LEU0-0.010-0.0088.9820.0140.0140.0000.0000.0000.000
56A99MET0-0.031-0.02013.6280.0390.0390.0000.0000.0000.000
57A100GLU-1-0.888-0.91716.674-0.112-0.1120.0000.0000.0000.000
58A101ALA0-0.043-0.01215.7250.0200.0200.0000.0000.0000.000
59A102ALA00.0050.00615.0030.0230.0230.0000.0000.0000.000
60A103PRO00.0310.02116.599-0.027-0.0270.0000.0000.0000.000
61A104GLU-1-0.873-0.93716.981-0.145-0.1450.0000.0000.0000.000
62A105LEU0-0.017-0.01811.933-0.017-0.0170.0000.0000.0000.000
63A106VAL0-0.068-0.02914.800-0.031-0.0310.0000.0000.0000.000
64A107PHE0-0.079-0.04116.984-0.004-0.0040.0000.0000.0000.000
65A108GLU-1-0.885-0.93213.792-0.146-0.1460.0000.0000.0000.000
66A109PRO0-0.0290.00514.380-0.047-0.0470.0000.0000.0000.000
67A110MET0-0.026-0.0027.841-0.014-0.0140.0000.0000.0000.000
68A111THR00.0260.00312.1590.0290.0290.0000.0000.0000.000
69A112SER0-0.0180.00710.9590.0600.0600.0000.0000.0000.000
70A113GLU-1-0.874-0.94713.307-0.054-0.0540.0000.0000.0000.000
71A114LEU0-0.036-0.01812.016-0.001-0.0010.0000.0000.0000.000
72A115TYR0-0.016-0.0239.805-0.006-0.0060.0000.0000.0000.000
73A116GLU-1-0.844-0.89913.339-0.113-0.1130.0000.0000.0000.000
74A117GLY00.0360.01415.9050.0090.0090.0000.0000.0000.000
75A118GLN0-0.072-0.04711.2520.0390.0390.0000.0000.0000.000
76A119THR00.038-0.00413.668-0.034-0.0340.0000.0000.0000.000
77A120ALA00.0580.01512.830-0.017-0.0170.0000.0000.0000.000
78A121LEU00.0140.00613.8100.0060.0060.0000.0000.0000.000
79A122HIS00.0240.02415.466-0.009-0.0090.0000.0000.0000.000
80A123ILE0-0.0010.0099.6980.0090.0090.0000.0000.0000.000
81A124ALA00.0240.01113.6850.0140.0140.0000.0000.0000.000
82A125VAL0-0.034-0.01415.7240.0230.0230.0000.0000.0000.000
83A126ILE0-0.050-0.02414.6090.0200.0200.0000.0000.0000.000
84A127ASN0-0.018-0.00511.6900.0360.0360.0000.0000.0000.000
85A128GLN0-0.049-0.02316.2090.0210.0210.0000.0000.0000.000
86A129ASN00.0040.00915.5180.0310.0310.0000.0000.0000.000
87A130VAL00.0200.00218.503-0.006-0.0060.0000.0000.0000.000
88A131ASN0-0.022-0.01720.1740.0110.0110.0000.0000.0000.000
89A132LEU00.0130.01113.7150.0020.0020.0000.0000.0000.000
90A133VAL00.0340.01218.199-0.002-0.0020.0000.0000.0000.000
91A134ARG10.9230.97020.2250.1240.1240.0000.0000.0000.000
92A135ALA0-0.011-0.00319.3470.0080.0080.0000.0000.0000.000
93A136LEU00.0280.00415.7850.0040.0040.0000.0000.0000.000
94A137LEU0-0.031-0.01520.0370.0100.0100.0000.0000.0000.000
95A138ALA0-0.020-0.00423.4490.0100.0100.0000.0000.0000.000
96A139ARG10.7570.85320.3760.1690.1690.0000.0000.0000.000
97A140GLY00.0130.01323.3870.0020.0020.0000.0000.0000.000
98A141ALA0-0.0100.00020.1650.0030.0030.0000.0000.0000.000
99A142SER00.0010.00021.6140.0130.0130.0000.0000.0000.000
100A143VAL00.0470.01522.193-0.013-0.0130.0000.0000.0000.000
101A144SER0-0.031-0.02024.5540.0030.0030.0000.0000.0000.000
102A145ALA0-0.0290.00519.9830.0060.0060.0000.0000.0000.000
103A146ARG10.8470.88121.7330.0810.0810.0000.0000.0000.000
104A147ALA0-0.017-0.00617.240-0.003-0.0030.0000.0000.0000.000
105A148THR0-0.022-0.03418.8180.0060.0060.0000.0000.0000.000
106A149GLY00.0330.03416.5570.0160.0160.0000.0000.0000.000
107A150SER00.008-0.01717.531-0.005-0.0050.0000.0000.0000.000
108A151VAL0-0.026-0.00813.8810.0130.0130.0000.0000.0000.000
109A152PHE0-0.011-0.00414.1100.0000.0000.0000.0000.0000.000
110A153HIS0-0.075-0.03419.1080.0190.0190.0000.0000.0000.000
111A154TYR00.0120.01922.331-0.002-0.0020.0000.0000.0000.000
112A155ARG10.9390.95722.6410.0690.0690.0000.0000.0000.000
113A156PRO0-0.0020.00824.892-0.004-0.0040.0000.0000.0000.000
114A157HIS00.005-0.00822.135-0.003-0.0030.0000.0000.0000.000
115A158ASN0-0.056-0.02420.021-0.002-0.0020.0000.0000.0000.000
116A159LEU0-0.001-0.00117.6450.0050.0050.0000.0000.0000.000
117A160ILE0-0.0210.00418.4160.0060.0060.0000.0000.0000.000
118A161TYR0-0.071-0.11121.4050.0050.0050.0000.0000.0000.000
119A162TYR00.0550.00919.2190.0030.0030.0000.0000.0000.000
120A163GLY00.0160.01222.9500.0000.0000.0000.0000.0000.000
121A164GLU-1-0.721-0.81321.506-0.094-0.0940.0000.0000.0000.000
122A165HIS00.0400.02721.271-0.016-0.0160.0000.0000.0000.000
123A166PRO00.0590.03220.4400.0000.0000.0000.0000.0000.000
124A167LEU00.0470.02622.0060.0000.0000.0000.0000.0000.000
125A168SER0-0.028-0.01524.3120.0050.0050.0000.0000.0000.000
126A169PHE00.0120.00016.6840.0020.0020.0000.0000.0000.000
127A170ALA00.0210.01521.9860.0010.0010.0000.0000.0000.000
128A171ALA0-0.016-0.02523.6850.0050.0050.0000.0000.0000.000
129A172CYS0-0.067-0.02623.3550.0080.0080.0000.0000.0000.000
130A173VAL0-0.0170.00219.8390.0050.0050.0000.0000.0000.000
131A174GLY0-0.0230.00223.2240.0030.0030.0000.0000.0000.000
132A175SER00.0240.01524.0840.0060.0060.0000.0000.0000.000
133A176GLU-1-0.848-0.93926.131-0.072-0.0720.0000.0000.0000.000
134A177GLU-1-0.938-0.97026.836-0.105-0.1050.0000.0000.0000.000
135A178ILE00.0350.01721.292-0.001-0.0010.0000.0000.0000.000
136A179VAL00.013-0.00525.478-0.001-0.0010.0000.0000.0000.000
137A180ARG10.8850.94127.8510.0790.0790.0000.0000.0000.000
138A181LEU00.0460.02724.8190.0020.0020.0000.0000.0000.000
139A182LEU0-0.013-0.00222.9700.0000.0000.0000.0000.0000.000
140A183ILE0-0.023-0.01027.0770.0030.0030.0000.0000.0000.000
141A184GLU-1-0.972-0.98330.625-0.080-0.0800.0000.0000.0000.000
142A185HIS0-0.094-0.04827.5270.0010.0010.0000.0000.0000.000
143A186GLY00.0080.00729.036-0.003-0.0030.0000.0000.0000.000
144A187ALA0-0.058-0.03027.5140.0010.0010.0000.0000.0000.000
145A188ASP-1-0.848-0.91629.218-0.060-0.0600.0000.0000.0000.000
146A189ILE00.007-0.01830.714-0.003-0.0030.0000.0000.0000.000
147A190ARG10.8410.91132.4820.0490.0490.0000.0000.0000.000
148A191ALA0-0.0010.01929.0480.0030.0030.0000.0000.0000.000
149A192GLN0-0.065-0.05330.6260.0000.0000.0000.0000.0000.000
150A193ASP-1-0.714-0.77526.254-0.075-0.0750.0000.0000.0000.000
151A194SER0-0.029-0.05625.7910.0080.0080.0000.0000.0000.000
152A195LEU0-0.086-0.03728.1390.0070.0070.0000.0000.0000.000
153A196GLY00.0350.02230.7300.0050.0050.0000.0000.0000.000
154A197ASN0-0.050-0.03329.2920.0070.0070.0000.0000.0000.000
155A198THR00.0620.02630.356-0.004-0.0040.0000.0000.0000.000
156A199VAL00.0700.01528.304-0.001-0.0010.0000.0000.0000.000
157A200LEU00.0040.01130.2300.0000.0000.0000.0000.0000.000
158A201HIS0-0.012-0.00732.093-0.001-0.0010.0000.0000.0000.000
159A202ILE00.0210.01826.0730.0010.0010.0000.0000.0000.000
160A203LEU00.0130.00728.894-0.001-0.0010.0000.0000.0000.000
161A204ILE0-0.123-0.03730.5600.0020.0020.0000.0000.0000.000
162A205LEU00.0130.01129.0610.0030.0030.0000.0000.0000.000
163A206GLN0-0.045-0.01525.511-0.006-0.0060.0000.0000.0000.000
164A207PRO00.0390.00426.4110.0050.0050.0000.0000.0000.000
165A208ASN0-0.042-0.01928.3980.0050.0050.0000.0000.0000.000
166A209LYS10.9600.97130.3730.0490.0490.0000.0000.0000.000
167A210THR0-0.0090.00533.1890.0010.0010.0000.0000.0000.000
168A211PHE00.0600.03026.7920.0030.0030.0000.0000.0000.000
169A212ALA00.0280.03031.125-0.001-0.0010.0000.0000.0000.000
170A213CYS0-0.015-0.02032.1980.0010.0010.0000.0000.0000.000
171A214GLN0-0.062-0.03634.1270.0040.0040.0000.0000.0000.000
172A215MET00.0290.04028.3610.0010.0010.0000.0000.0000.000
173A216TYR0-0.058-0.05732.7980.0000.0000.0000.0000.0000.000
174A217ASN0-0.008-0.02434.8970.0030.0030.0000.0000.0000.000
175A218LEU00.0190.02831.8060.0020.0020.0000.0000.0000.000
176A219LEU00.0190.00730.3770.0000.0000.0000.0000.0000.000
177A220LEU0-0.004-0.00734.5160.0010.0010.0000.0000.0000.000
178A221SER0-0.134-0.06837.2020.0020.0020.0000.0000.0000.000
179A222TYR00.023-0.00834.2390.0000.0000.0000.0000.0000.000
180A223ASP-1-0.884-0.92637.892-0.048-0.0480.0000.0000.0000.000
181A224GLY00.0200.01739.5610.0020.0020.0000.0000.0000.000
182A225GLY0-0.057-0.03342.9690.0010.0010.0000.0000.0000.000
183A226ASP-1-0.859-0.91441.367-0.044-0.0440.0000.0000.0000.000
184A227HIS0-0.069-0.04645.0160.0010.0010.0000.0000.0000.000
185A228LEU0-0.033-0.02845.0940.0020.0020.0000.0000.0000.000
186A229LYS10.8930.96142.1250.0350.0350.0000.0000.0000.000
187A230SER00.1510.07142.474-0.002-0.0020.0000.0000.0000.000
188A231LEU00.0550.02534.6180.0010.0010.0000.0000.0000.000
189A232GLU-1-0.829-0.91238.692-0.043-0.0430.0000.0000.0000.000
190A233LEU0-0.080-0.04840.4050.0010.0010.0000.0000.0000.000
191A234VAL0-0.068-0.03037.0330.0030.0030.0000.0000.0000.000
192A235PRO0-0.055-0.02338.346-0.002-0.0020.0000.0000.0000.000
193A236ASN00.0380.02433.9830.0020.0020.0000.0000.0000.000
194A237ASN00.030-0.00733.0870.0030.0030.0000.0000.0000.000
195A238GLN0-0.051-0.01134.5490.0050.0050.0000.0000.0000.000
196A239GLY0-0.025-0.00437.8880.0020.0020.0000.0000.0000.000
197A240LEU0-0.047-0.02137.3480.0020.0020.0000.0000.0000.000
198A241THR00.0190.01838.318-0.002-0.0020.0000.0000.0000.000
199A242PRO00.0930.04036.3120.0010.0010.0000.0000.0000.000
200A243PHE00.0010.00137.8820.0010.0010.0000.0000.0000.000
201A244LYS10.9330.96841.1170.0290.0290.0000.0000.0000.000
202A245LEU00.0300.02133.4780.0010.0010.0000.0000.0000.000
203A246ALA00.0330.01037.4770.0000.0000.0000.0000.0000.000
204A247GLY0-0.046-0.02338.4420.0010.0010.0000.0000.0000.000
205A248VAL0-0.075-0.04537.8390.0010.0010.0000.0000.0000.000
206A249GLU-1-0.896-0.94833.973-0.043-0.0430.0000.0000.0000.000
207A250GLY0-0.0070.02136.8160.0000.0000.0000.0000.0000.000
208A251ASN0-0.044-0.03634.3040.0010.0010.0000.0000.0000.000
209A252ILE00.033-0.00137.6000.0000.0000.0000.0000.0000.000
210A253VAL00.0020.00137.6070.0010.0010.0000.0000.0000.000
211A254MET00.0540.02735.5710.0010.0010.0000.0000.0000.000
212A255PHE00.0040.00238.9050.0010.0010.0000.0000.0000.000
213A256GLN0-0.028-0.03141.7970.0030.0030.0000.0000.0000.000
214A257HIS00.0000.01739.6890.0020.0020.0000.0000.0000.000
215A258LEU00.0190.00538.5820.0010.0010.0000.0000.0000.000
216A259MET0-0.087-0.03043.0240.0020.0020.0000.0000.0000.000
217A260GLN00.028-0.02346.3790.0010.0010.0000.0000.0000.000
218A261LYS10.9200.99741.1410.0450.0450.0000.0000.0000.000
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