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: 2JRGR

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 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 222
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2547780.441963
FMO2-HF: Nuclear repulsion 2461275.205594
FMO2-HF: Total energy -86505.236369
FMO2-MP2: Total energy -86755.618998


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.
-11.386-3.28310.524-5.525-13.104-0.017
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 : 0.012 / q_NPA : -0.013
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-1-0.864-0.9273.331-2.784-0.264-0.003-1.091-1.4260.001
4A47SER0-0.065-0.0523.021-0.6810.4570.091-0.445-0.7840.000
5A48PRO00.0450.0014.056-0.767-0.5530.001-0.055-0.1600.000
6A49LEU00.0290.0206.5360.0910.0910.0000.0000.0000.000
7A50LEU00.0040.0062.133-1.771-0.5254.566-2.545-3.268-0.004
8A51LEU0-0.006-0.0012.443-2.075-0.5812.885-1.582-2.797-0.010
9A52ALA00.008-0.0013.2441.5910.5070.0631.228-0.206-0.001
10A53ALA00.0020.0055.1920.2520.2520.0000.0000.0000.000
11A54LYS10.8520.9352.450-1.237-0.3461.244-0.393-1.7430.000
12A55GLU-1-0.922-0.9665.0000.1960.233-0.001-0.004-0.0320.000
13A56ASN0-0.002-0.0057.5420.0320.0320.0000.0000.0000.000
14A57ASP-1-0.839-0.9099.235-0.281-0.2810.0000.0000.0000.000
15A58VAL00.0700.01611.048-0.057-0.0570.0000.0000.0000.000
16A59GLN0-0.041-0.01913.563-0.006-0.0060.0000.0000.0000.000
17A60ALA0-0.017-0.00510.6440.0050.0050.0000.0000.0000.000
18A61LEU00.0490.0198.204-0.028-0.0280.0000.0000.0000.000
19A62SER0-0.019-0.01911.5880.0170.0170.0000.0000.0000.000
20A63LYS10.8430.92014.9380.2840.2840.0000.0000.0000.000
21A64LEU0-0.015-0.0099.4530.0220.0220.0000.0000.0000.000
22A65LEU00.005-0.00812.4380.0110.0110.0000.0000.0000.000
23A66LYS10.9130.97114.9990.2670.2670.0000.0000.0000.000
24A67PHE0-0.111-0.05114.9040.0400.0400.0000.0000.0000.000
25A68GLU-1-0.875-0.91416.966-0.219-0.2190.0000.0000.0000.000
26A69GLY0-0.026-0.01015.7370.0290.0290.0000.0000.0000.000
27A70CYS0-0.076-0.04010.397-0.076-0.0760.0000.0000.0000.000
28A71GLU-1-0.858-0.91211.533-0.387-0.3870.0000.0000.0000.000
29A72VAL00.017-0.00810.606-0.162-0.1620.0000.0000.0000.000
30A73HIS0-0.010-0.02411.242-0.098-0.0980.0000.0000.0000.000
31A74GLN0-0.070-0.0016.801-0.231-0.2310.0000.0000.0000.000
32A75ARG10.8080.8767.4370.4080.4080.0000.0000.0000.000
33A76GLY0-0.0130.0024.056-0.321-0.1800.000-0.036-0.1050.000
34A77ALA00.000-0.0104.5100.3870.443-0.001-0.006-0.0490.000
35A78MET0-0.065-0.0266.3830.1440.1440.0000.0000.0000.000
36A79GLY00.0420.0298.0600.0320.0320.0000.0000.0000.000
37A80GLU-1-0.850-0.9223.870-2.086-1.5850.006-0.149-0.358-0.001
38A81THR00.0830.0126.595-0.248-0.2480.0000.0000.0000.000
39A82ALA00.0610.0076.024-0.162-0.1620.0000.0000.0000.000
40A83LEU00.0290.0277.0720.0400.0400.0000.0000.0000.000
41A84HIS00.0000.0317.781-0.025-0.0250.0000.0000.0000.000
42A85ILE0-0.022-0.0012.546-0.724-0.2571.644-0.327-1.784-0.002
43A86ALA00.006-0.0105.7940.1960.1960.0000.0000.0000.000
44A87ALA00.002-0.0068.5190.1240.1240.0000.0000.0000.000
45A88LEU0-0.028-0.0135.1690.0750.0750.0000.0000.0000.000
46A89TYR0-0.039-0.0353.305-0.3660.1160.029-0.120-0.3920.000
47A90ASP-1-0.844-0.8898.408-0.130-0.1300.0000.0000.0000.000
48A91ASN0-0.059-0.0268.1900.1080.1080.0000.0000.0000.000
49A92LEU00.0200.00311.772-0.050-0.0500.0000.0000.0000.000
50A93GLU-1-0.870-0.93614.700-0.240-0.2400.0000.0000.0000.000
51A94ALA00.0190.0059.827-0.019-0.0190.0000.0000.0000.000
52A95ALA00.0240.00811.965-0.042-0.0420.0000.0000.0000.000
53A96MET0-0.028-0.01013.1470.0110.0110.0000.0000.0000.000
54A97VAL0-0.019-0.00813.6590.0130.0130.0000.0000.0000.000
55A98LEU0-0.005-0.0069.056-0.010-0.0100.0000.0000.0000.000
56A99MET0-0.023-0.01513.7010.0280.0280.0000.0000.0000.000
57A100GLU-1-0.883-0.91716.773-0.193-0.1930.0000.0000.0000.000
58A101ALA0-0.062-0.02215.7590.0190.0190.0000.0000.0000.000
59A102ALA00.0050.00415.1160.0110.0110.0000.0000.0000.000
60A103PRO00.0220.02316.450-0.025-0.0250.0000.0000.0000.000
61A104GLU-1-0.826-0.91417.052-0.348-0.3480.0000.0000.0000.000
62A105LEU0-0.012-0.01511.591-0.012-0.0120.0000.0000.0000.000
63A106VAL0-0.066-0.02914.653-0.011-0.0110.0000.0000.0000.000
64A107PHE0-0.086-0.04416.8180.0170.0170.0000.0000.0000.000
65A108GLU-1-0.863-0.90213.695-0.322-0.3220.0000.0000.0000.000
66A109PRO0-0.043-0.00614.298-0.024-0.0240.0000.0000.0000.000
67A110MET0-0.0250.0057.599-0.040-0.0400.0000.0000.0000.000
68A111THR00.023-0.00112.0660.0430.0430.0000.0000.0000.000
69A112SER0-0.038-0.01910.7070.0710.0710.0000.0000.0000.000
70A113GLU-1-0.843-0.91913.2390.0280.0280.0000.0000.0000.000
71A114LEU0-0.0070.00512.009-0.001-0.0010.0000.0000.0000.000
72A115TYR00.000-0.0229.700-0.013-0.0130.0000.0000.0000.000
73A116GLU-1-0.836-0.87613.245-0.125-0.1250.0000.0000.0000.000
74A117GLY00.0360.01215.7790.0180.0180.0000.0000.0000.000
75A118GLN0-0.077-0.05310.7880.0260.0260.0000.0000.0000.000
76A119THR00.035-0.01113.507-0.050-0.0500.0000.0000.0000.000
77A120ALA00.0610.01512.6550.0070.0070.0000.0000.0000.000
78A121LEU00.0130.00913.6290.0220.0220.0000.0000.0000.000
79A122HIS00.0170.02515.329-0.004-0.0040.0000.0000.0000.000
80A123ILE00.0030.0119.4310.0180.0180.0000.0000.0000.000
81A124ALA00.0280.01513.5330.0260.0260.0000.0000.0000.000
82A125VAL0-0.044-0.02015.6690.0270.0270.0000.0000.0000.000
83A126ILE0-0.046-0.02314.6820.0220.0220.0000.0000.0000.000
84A127ASN0-0.049-0.02711.6770.0450.0450.0000.0000.0000.000
85A128GLN0-0.056-0.02616.1680.0090.0090.0000.0000.0000.000
86A129ASN0-0.0060.00015.8670.0080.0080.0000.0000.0000.000
87A130VAL00.020-0.00218.477-0.015-0.0150.0000.0000.0000.000
88A131ASN0-0.024-0.01820.1740.0030.0030.0000.0000.0000.000
89A132LEU00.0180.01813.683-0.007-0.0070.0000.0000.0000.000
90A133VAL00.0270.00518.202-0.012-0.0120.0000.0000.0000.000
91A134ARG10.8430.91520.2310.1060.1060.0000.0000.0000.000
92A135ALA0-0.016-0.00219.3730.0020.0020.0000.0000.0000.000
93A136LEU00.0250.00415.792-0.005-0.0050.0000.0000.0000.000
94A137LEU0-0.035-0.01620.0700.0030.0030.0000.0000.0000.000
95A138ALA0-0.021-0.00423.4800.0070.0070.0000.0000.0000.000
96A139ARG10.7670.85819.9890.2390.2390.0000.0000.0000.000
97A140GLY00.0050.00923.200-0.006-0.0060.0000.0000.0000.000
98A141ALA0-0.0100.00019.9760.0010.0010.0000.0000.0000.000
99A142SER0-0.005-0.00121.4760.0220.0220.0000.0000.0000.000
100A143VAL00.0500.01322.016-0.007-0.0070.0000.0000.0000.000
101A144SER0-0.040-0.02524.3790.0080.0080.0000.0000.0000.000
102A145ALA0-0.0260.00519.8350.0060.0060.0000.0000.0000.000
103A146ARG10.8430.88421.5790.0780.0780.0000.0000.0000.000
104A147ALA0-0.023-0.00717.187-0.010-0.0100.0000.0000.0000.000
105A148THR0-0.024-0.05218.6860.0130.0130.0000.0000.0000.000
106A149GLY00.0230.03116.4690.0160.0160.0000.0000.0000.000
107A150SER00.008-0.04317.4680.0070.0070.0000.0000.0000.000
108A151VAL0-0.059-0.01113.7730.0130.0130.0000.0000.0000.000
109A152PHE0-0.013-0.00913.8850.0010.0010.0000.0000.0000.000
110A153HIS0-0.065-0.01119.0270.0150.0150.0000.0000.0000.000
111A154TYR00.0040.01422.2620.0080.0080.0000.0000.0000.000
112A155ARG10.8980.92023.279-0.014-0.0140.0000.0000.0000.000
113A156PRO0-0.0110.00524.8640.0010.0010.0000.0000.0000.000
114A157HIS00.001-0.01222.221-0.004-0.0040.0000.0000.0000.000
115A158ASN0-0.054-0.02519.8240.0240.0240.0000.0000.0000.000
116A159LEU0-0.0030.00017.735-0.003-0.0030.0000.0000.0000.000
117A160ILE0-0.027-0.00318.223-0.004-0.0040.0000.0000.0000.000
118A161TYR0-0.018-0.05121.3500.0030.0030.0000.0000.0000.000
119A162TYR00.0530.00918.8790.0020.0020.0000.0000.0000.000
120A163GLY00.0180.01322.849-0.007-0.0070.0000.0000.0000.000
121A164GLU-1-0.723-0.82321.380-0.061-0.0610.0000.0000.0000.000
122A165HIS00.0430.02921.130-0.021-0.0210.0000.0000.0000.000
123A166PRO00.0620.03420.2690.0090.0090.0000.0000.0000.000
124A167LEU00.0400.02121.8510.0050.0050.0000.0000.0000.000
125A168SER0-0.016-0.00624.1450.0060.0060.0000.0000.0000.000
126A169PHE00.0210.00616.4530.0070.0070.0000.0000.0000.000
127A170ALA00.0330.02121.8570.0070.0070.0000.0000.0000.000
128A171ALA0-0.026-0.02823.5500.0070.0070.0000.0000.0000.000
129A172CYS0-0.082-0.03823.1890.0090.0090.0000.0000.0000.000
130A173VAL0-0.025-0.00119.7060.0090.0090.0000.0000.0000.000
131A174GLY0-0.023-0.00523.1210.0040.0040.0000.0000.0000.000
132A175SER00.0180.01223.9140.0000.0000.0000.0000.0000.000
133A176GLU-1-0.798-0.89526.007-0.045-0.0450.0000.0000.0000.000
134A177GLU-1-0.845-0.91426.831-0.086-0.0860.0000.0000.0000.000
135A178ILE00.0520.02721.247-0.005-0.0050.0000.0000.0000.000
136A179VAL00.011-0.00725.411-0.004-0.0040.0000.0000.0000.000
137A180ARG10.8130.89627.7010.0510.0510.0000.0000.0000.000
138A181LEU00.0390.03124.802-0.002-0.0020.0000.0000.0000.000
139A182LEU0-0.0020.00322.773-0.004-0.0040.0000.0000.0000.000
140A183ILE0-0.024-0.01526.909-0.001-0.0010.0000.0000.0000.000
141A184GLU-1-0.947-0.97530.548-0.077-0.0770.0000.0000.0000.000
142A185HIS0-0.097-0.05127.322-0.006-0.0060.0000.0000.0000.000
143A186GLY00.0080.00728.855-0.006-0.0060.0000.0000.0000.000
144A187ALA0-0.061-0.02727.3130.0010.0010.0000.0000.0000.000
145A188ASP-1-0.831-0.91029.049-0.054-0.0540.0000.0000.0000.000
146A189ILE0-0.006-0.02330.5590.0010.0010.0000.0000.0000.000
147A190ARG10.7900.86832.3300.0440.0440.0000.0000.0000.000
148A191ALA00.0120.02828.9090.0030.0030.0000.0000.0000.000
149A192GLN0-0.071-0.05730.4880.0020.0020.0000.0000.0000.000
150A193ASP-1-0.761-0.83426.143-0.039-0.0390.0000.0000.0000.000
151A194SER0-0.014-0.04725.7840.0030.0030.0000.0000.0000.000
152A195LEU0-0.090-0.03728.1030.0060.0060.0000.0000.0000.000
153A196GLY00.0400.02330.6320.0040.0040.0000.0000.0000.000
154A197ASN0-0.051-0.02529.4270.0030.0030.0000.0000.0000.000
155A198THR00.0780.02830.235-0.005-0.0050.0000.0000.0000.000
156A199VAL00.0740.01628.2400.0030.0030.0000.0000.0000.000
157A200LEU00.0030.00930.1040.0030.0030.0000.0000.0000.000
158A201HIS0-0.022-0.00532.0160.0010.0010.0000.0000.0000.000
159A202ILE00.0180.02025.9840.0040.0040.0000.0000.0000.000
160A203LEU00.0140.01028.8860.0040.0040.0000.0000.0000.000
161A204ILE0-0.129-0.04030.4600.0040.0040.0000.0000.0000.000
162A205LEU00.0060.01129.0380.0040.0040.0000.0000.0000.000
163A206GLN0-0.031-0.00725.4380.0060.0060.0000.0000.0000.000
164A207PRO00.031-0.00426.4690.0000.0000.0000.0000.0000.000
165A208ASN0-0.034-0.01528.4450.0000.0000.0000.0000.0000.000
166A209LYS10.9370.95830.309-0.008-0.0080.0000.0000.0000.000
167A210THR0-0.0260.00233.378-0.003-0.0030.0000.0000.0000.000
168A211PHE00.0720.03426.400-0.001-0.0010.0000.0000.0000.000
169A212ALA00.0370.03330.995-0.004-0.0040.0000.0000.0000.000
170A213CYS0-0.016-0.02132.102-0.003-0.0030.0000.0000.0000.000
171A214GLN0-0.061-0.03734.1960.0010.0010.0000.0000.0000.000
172A215MET00.0320.03928.099-0.003-0.0030.0000.0000.0000.000
173A216TYR0-0.052-0.05432.679-0.003-0.0030.0000.0000.0000.000
174A217ASN0-0.018-0.02434.778-0.001-0.0010.0000.0000.0000.000
175A218LEU00.0240.03031.754-0.001-0.0010.0000.0000.0000.000
176A219LEU00.0220.01130.219-0.002-0.0020.0000.0000.0000.000
177A220LEU0-0.011-0.01034.376-0.001-0.0010.0000.0000.0000.000
178A221SER0-0.127-0.06437.0940.0000.0000.0000.0000.0000.000
179A222TYR00.0320.00034.1720.0000.0000.0000.0000.0000.000
180A223ASP-1-0.863-0.91537.738-0.038-0.0380.0000.0000.0000.000
181A224GLY00.0040.00239.4090.0000.0000.0000.0000.0000.000
182A225GLY0-0.052-0.03242.8170.0020.0020.0000.0000.0000.000
183A226ASP-1-0.867-0.92741.995-0.039-0.0390.0000.0000.0000.000
184A227HIS0-0.058-0.02544.8580.0020.0020.0000.0000.0000.000
185A228LEU0-0.025-0.03144.9050.0020.0020.0000.0000.0000.000
186A229LYS10.8710.95941.8330.0250.0250.0000.0000.0000.000
187A230SER00.1320.07542.149-0.002-0.0020.0000.0000.0000.000
188A231LEU00.0580.02334.4700.0020.0020.0000.0000.0000.000
189A232GLU-1-0.806-0.90238.562-0.020-0.0200.0000.0000.0000.000
190A233LEU0-0.066-0.04340.2800.0020.0020.0000.0000.0000.000
191A234VAL0-0.054-0.02836.8810.0020.0020.0000.0000.0000.000
192A235PRO0-0.053-0.02038.2280.0000.0000.0000.0000.0000.000
193A236ASN00.0390.01733.875-0.001-0.0010.0000.0000.0000.000
194A237ASN00.027-0.00632.8740.0000.0000.0000.0000.0000.000
195A238GLN0-0.054-0.01035.0010.0020.0020.0000.0000.0000.000
196A239GLY0-0.013-0.00237.8030.0020.0020.0000.0000.0000.000
197A240LEU0-0.059-0.02737.3530.0010.0010.0000.0000.0000.000
198A241THR00.0270.02238.217-0.001-0.0010.0000.0000.0000.000
199A242PRO00.0920.04336.1750.0030.0030.0000.0000.0000.000
200A243PHE00.0210.00337.7790.0020.0020.0000.0000.0000.000
201A244LYS10.9350.96941.0200.0040.0040.0000.0000.0000.000
202A245LEU00.0280.01833.3980.0020.0020.0000.0000.0000.000
203A246ALA00.0340.00937.4030.0020.0020.0000.0000.0000.000
204A247GLY0-0.042-0.02538.3640.0020.0020.0000.0000.0000.000
205A248VAL0-0.079-0.05038.0760.0020.0020.0000.0000.0000.000
206A249GLU-1-0.850-0.93033.8520.0080.0080.0000.0000.0000.000
207A250GLY0-0.0100.01936.7670.0020.0020.0000.0000.0000.000
208A251ASN0-0.034-0.03234.2580.0020.0020.0000.0000.0000.000
209A252ILE00.0410.00337.538-0.003-0.0030.0000.0000.0000.000
210A253VAL00.0080.01037.544-0.001-0.0010.0000.0000.0000.000
211A254MET00.0540.03135.426-0.001-0.0010.0000.0000.0000.000
212A255PHE0-0.0010.00438.820-0.001-0.0010.0000.0000.0000.000
213A256GLN0-0.046-0.03941.716-0.001-0.0010.0000.0000.0000.000
214A257HIS0-0.0070.00039.1810.0010.0010.0000.0000.0000.000
215A258LEU00.0160.00738.431-0.001-0.0010.0000.0000.0000.000
216A259MET0-0.104-0.03542.923-0.001-0.0010.0000.0000.0000.000
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