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: R98J8

Calculation Name: 2RF4-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2RF4

Chain ID: A

ChEMBL ID:

UniProt ID: P50106

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 175
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1610941.058559
FMO2-HF: Nuclear repulsion 1543043.028649
FMO2-HF: Total energy -67898.02991
FMO2-MP2: Total energy -68097.601911


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:22:LYS)


Summations of interaction energy for fragment #1(A:22:LYS)
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.
-29.364-22.405-0.078-3.732-3.146-0.006
Interaction energy analysis for fragmet #1(A:22:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.964 / q_NPA : 0.968
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].
3A24VAL00.0530.1003.782-5.3031.221-0.073-3.686-2.765-0.006
4A25THR0-0.023-0.0556.707-0.660-0.6600.0000.0000.0000.000
5A26ASN0-0.028-0.0418.7130.1230.1230.0000.0000.0000.000
6A27PRO0-0.0140.00111.2120.7140.7140.0000.0000.0000.000
7A28ILE00.033-0.00614.6760.3690.3690.0000.0000.0000.000
8A29ASP-1-0.981-0.99816.954-14.414-14.4140.0000.0000.0000.000
9A30GLU-1-0.854-0.91420.341-11.229-11.2290.0000.0000.0000.000
10A31LYS10.9050.95223.94910.07710.0770.0000.0000.0000.000
11A32ASN00.0290.00122.5590.6460.6460.0000.0000.0000.000
12A33GLY0-0.044-0.01721.577-0.017-0.0170.0000.0000.0000.000
13A34THR0-0.018-0.01717.744-0.184-0.1840.0000.0000.0000.000
14A35SER0-0.021-0.05212.9330.4270.4270.0000.0000.0000.000
15A36ASN00.0220.03314.251-0.609-0.6090.0000.0000.0000.000
16A37CYS0-0.009-0.00411.363-1.246-1.2460.0000.0000.0000.000
17A38ILE0-0.055-0.01211.159-1.473-1.4730.0000.0000.0000.000
18A39VAL00.0110.0208.9270.7420.7420.0000.0000.0000.000
19A40ARG10.8410.91612.43817.47417.4740.0000.0000.0000.000
20A41VAL00.003-0.0238.632-1.013-1.0130.0000.0000.0000.000
21A42PRO0-0.018-0.00312.0650.6850.6850.0000.0000.0000.000
22A43ILE0-0.025-0.0129.783-2.383-2.3830.0000.0000.0000.000
23A44ALA00.0440.03312.3871.8091.8090.0000.0000.0000.000
24A45LEU0-0.068-0.04913.233-1.526-1.5260.0000.0000.0000.000
25A46TYR00.0220.01615.1841.2611.2610.0000.0000.0000.000
26A47VAL0-0.017-0.01917.507-0.449-0.4490.0000.0000.0000.000
27A48SER00.016-0.00219.6360.6520.6520.0000.0000.0000.000
28A49LEU0-0.044-0.00422.4850.0660.0660.0000.0000.0000.000
29A50ALA00.0200.01725.2600.2240.2240.0000.0000.0000.000
30A51PRO00.0540.00628.2020.0680.0680.0000.0000.0000.000
31A52MET0-0.017-0.02031.6380.1410.1410.0000.0000.0000.000
32A53TYR00.002-0.00727.8230.1040.1040.0000.0000.0000.000
33A54LEU00.0900.05530.017-0.273-0.2730.0000.0000.0000.000
34A55GLU-1-0.976-0.97631.956-8.278-8.2780.0000.0000.0000.000
35A56ASN0-0.019-0.02531.186-0.188-0.1880.0000.0000.0000.000
36A57PRO00.0810.03526.315-0.166-0.1660.0000.0000.0000.000
37A58LEU0-0.0150.01325.570-0.534-0.5340.0000.0000.0000.000
38A59GLN00.051-0.00225.742-0.462-0.4620.0000.0000.0000.000
39A60GLY0-0.0040.00026.682-0.038-0.0380.0000.0000.0000.000
40A61VAL00.0270.00120.402-0.316-0.3160.0000.0000.0000.000
41A62MET00.0420.02521.573-0.532-0.5320.0000.0000.0000.000
42A63LYS10.8460.93523.61610.67610.6760.0000.0000.0000.000
43A64GLN0-0.036-0.01818.5490.3880.3880.0000.0000.0000.000
44A65HIS00.014-0.00715.910-1.000-1.0000.0000.0000.0000.000
45A66LEU00.0080.00919.375-0.382-0.3820.0000.0000.0000.000
46A67ASN00.0530.04320.340-0.762-0.7620.0000.0000.0000.000
47A68PRO0-0.071-0.02319.323-0.381-0.3810.0000.0000.0000.000
48A69LEU00.0100.00214.062-0.696-0.6960.0000.0000.0000.000
49A70VAL00.0420.02816.013-0.480-0.4800.0000.0000.0000.000
50A71MET0-0.028-0.02016.6200.2570.2570.0000.0000.0000.000
51A72LYS10.7950.90215.35215.15615.1560.0000.0000.0000.000
52A73TYR00.0130.0105.363-0.803-0.8030.0000.0000.0000.000
53A74ASN00.0040.0029.572-1.777-1.7770.0000.0000.0000.000
54A75ASN00.0660.0126.762-1.480-1.4800.0000.0000.0000.000
55A76LYS10.9180.9715.19423.14823.238-0.0010.000-0.0890.000
56A77VAL0-0.012-0.0064.878-7.657-7.589-0.001-0.004-0.0630.000
57A78GLY0-0.005-0.0033.8470.6570.782-0.001-0.022-0.1020.000
58A79GLY00.0500.0064.929-0.270-0.272-0.001-0.0020.0070.000
59A80VAL0-0.057-0.0247.8630.7530.7530.0000.0000.0000.000
60A81VAL00.0170.02311.615-0.504-0.5040.0000.0000.0000.000
61A82LEU00.005-0.00613.6291.3321.3320.0000.0000.0000.000
62A83GLY00.0160.00816.5081.1411.1410.0000.0000.0000.000
63A84TYR0-0.023-0.01617.346-0.840-0.8400.0000.0000.0000.000
64A85GLU-1-0.781-0.86218.853-14.236-14.2360.0000.0000.0000.000
65A86GLY00.022-0.00519.923-0.631-0.6310.0000.0000.0000.000
66A87LEU0-0.055-0.01719.794-0.205-0.2050.0000.0000.0000.000
67A88LYS10.8590.91921.18814.80614.8060.0000.0000.0000.000
68A89ILE00.024-0.01121.940-0.515-0.5150.0000.0000.0000.000
69A90LEU00.0280.00423.978-0.121-0.1210.0000.0000.0000.000
70A91ASP-1-0.860-0.87121.123-14.602-14.6020.0000.0000.0000.000
71A92ALA0-0.018-0.05223.089-0.354-0.3540.0000.0000.0000.000
72A93ASP-1-0.925-0.96925.890-9.942-9.9420.0000.0000.0000.000
73A94PRO0-0.0410.01229.412-0.015-0.0150.0000.0000.0000.000
74A112PRO00.013-0.02133.8650.0710.0710.0000.0000.0000.000
75A113PHE0-0.051-0.04829.355-0.096-0.0960.0000.0000.0000.000
76A114GLY00.0160.03327.808-0.208-0.2080.0000.0000.0000.000
77A115PHE0-0.0120.01021.828-0.191-0.1910.0000.0000.0000.000
78A116THR00.0420.01422.4420.6280.6280.0000.0000.0000.000
79A117TRP0-0.0020.01614.941-1.067-1.0670.0000.0000.0000.000
80A118CYS0-0.071-0.01018.7720.5460.5460.0000.0000.0000.000
81A119HIS00.0610.02515.230-1.264-1.2640.0000.0000.0000.000
82A120VAL0-0.022-0.00815.8651.0671.0670.0000.0000.0000.000
83A121ASN00.000-0.00415.291-1.822-1.8220.0000.0000.0000.000
84A122LEU00.0030.01111.7761.2851.2850.0000.0000.0000.000
85A123TYR00.000-0.01914.395-0.893-0.8930.0000.0000.0000.000
86A124VAL0-0.056-0.0418.5990.3810.3810.0000.0000.0000.000
87A125TRP00.0450.04511.221-0.546-0.5460.0000.0000.0000.000
88A126GLN00.011-0.0135.948-4.094-4.0940.0000.0000.0000.000
89A127PRO00.0130.0318.085-0.827-0.8270.0000.0000.0000.000
90A128GLN0-0.016-0.0324.322-0.311-0.157-0.001-0.018-0.1340.000
91A129VAL0-0.008-0.0266.6052.2822.2820.0000.0000.0000.000
92A130GLY0-0.020-0.0068.637-0.800-0.8000.0000.0000.0000.000
93A131ASP-1-0.727-0.8029.706-21.691-21.6910.0000.0000.0000.000
94A132VAL00.0050.00612.3020.8210.8210.0000.0000.0000.000
95A133LEU0-0.0070.00112.661-0.042-0.0420.0000.0000.0000.000
96A134GLU-1-0.787-0.89516.848-11.094-11.0940.0000.0000.0000.000
97A135GLY0-0.044-0.02719.933-0.458-0.4580.0000.0000.0000.000
98A136TYR00.0360.02621.7570.3520.3520.0000.0000.0000.000
99A137ILE00.0140.01224.374-0.382-0.3820.0000.0000.0000.000
100A138PHE0-0.036-0.01224.2640.2050.2050.0000.0000.0000.000
101A139ILE0-0.010-0.01525.0830.3270.3270.0000.0000.0000.000
102A140GLN0-0.0250.00027.188-0.168-0.1680.0000.0000.0000.000
103A141SER00.0140.00228.7230.2230.2230.0000.0000.0000.000
104A142ALA0-0.0230.00429.393-0.194-0.1940.0000.0000.0000.000
105A143SER0-0.118-0.06728.220-0.113-0.1130.0000.0000.0000.000
106A144HIS0-0.029-0.02422.110-0.428-0.4280.0000.0000.0000.000
107A145ILE00.0560.04824.6650.2060.2060.0000.0000.0000.000
108A146GLY00.0290.01422.752-0.466-0.4660.0000.0000.0000.000
109A147LEU0-0.034-0.02720.5250.3010.3010.0000.0000.0000.000
110A148LEU00.0100.02620.899-0.459-0.4590.0000.0000.0000.000
111A149ILE0-0.010-0.01115.5000.1970.1970.0000.0000.0000.000
112A150HIS0-0.027-0.02417.0230.2640.2640.0000.0000.0000.000
113A151ASP-1-0.939-0.97321.016-10.742-10.7420.0000.0000.0000.000
114A152ALA0-0.0080.00620.0700.1950.1950.0000.0000.0000.000
115A153PHE0-0.035-0.01815.856-0.562-0.5620.0000.0000.0000.000
116A154ASN00.0170.00117.7970.1440.1440.0000.0000.0000.000
117A155ALA00.0310.03016.751-0.808-0.8080.0000.0000.0000.000
118A156SER00.0040.01617.9510.7290.7290.0000.0000.0000.000
119A157ILE00.0340.03118.662-0.552-0.5520.0000.0000.0000.000
120A158LYS10.8530.89518.09413.63313.6330.0000.0000.0000.000
121A159LYS11.0241.00522.6078.8558.8550.0000.0000.0000.000
122A160ASN0-0.042-0.03123.0780.0390.0390.0000.0000.0000.000
123A161ASN00.0080.01119.537-0.091-0.0910.0000.0000.0000.000
124A162ILE00.0100.03423.007-0.174-0.1740.0000.0000.0000.000
125A163PRO00.0110.00225.9610.0760.0760.0000.0000.0000.000
126A164VAL0-0.037-0.00228.3940.0960.0960.0000.0000.0000.000
127A165ASP-1-0.811-0.88830.984-8.356-8.3560.0000.0000.0000.000
128A166TRP0-0.0100.00027.2500.0410.0410.0000.0000.0000.000
129A167THR0-0.025-0.01832.8680.0380.0380.0000.0000.0000.000
130A168PHE0-0.004-0.01332.330-0.066-0.0660.0000.0000.0000.000
131A169VAL00.0350.03235.1310.1150.1150.0000.0000.0000.000
132A170HIS00.029-0.00637.125-0.141-0.1410.0000.0000.0000.000
133A171ASN00.032-0.01539.4450.0460.0460.0000.0000.0000.000
134A172ASP-1-0.849-0.89341.809-6.488-6.4880.0000.0000.0000.000
135A210GLY0-0.078-0.04740.735-0.017-0.0170.0000.0000.0000.000
136A211ASN00.0240.02540.9650.0010.0010.0000.0000.0000.000
137A212ARG10.9180.94540.8636.4776.4770.0000.0000.0000.000
138A213SER0-0.053-0.05337.1230.0740.0740.0000.0000.0000.000
139A214LEU00.0300.02737.083-0.180-0.1800.0000.0000.0000.000
140A215GLY0-0.028-0.01235.9830.0810.0810.0000.0000.0000.000
141A216HIS0-0.039-0.02933.779-0.174-0.1740.0000.0000.0000.000
142A217TRP0-0.048-0.03328.597-0.218-0.2180.0000.0000.0000.000
143A218VAL00.0880.07832.772-0.186-0.1860.0000.0000.0000.000
144A219ASP-1-0.822-0.90532.900-8.039-8.0390.0000.0000.0000.000
145A220SER0-0.014-0.02934.1430.2220.2220.0000.0000.0000.000
146A221ASN0-0.142-0.07635.8900.3370.3370.0000.0000.0000.000
147A222GLY0-0.018-0.01637.1890.1980.1980.0000.0000.0000.000
148A223GLU-1-0.894-0.93635.794-7.231-7.2310.0000.0000.0000.000
149A224PRO0-0.067-0.05835.234-0.190-0.1900.0000.0000.0000.000
150A225ILE0-0.082-0.03729.531-0.146-0.1460.0000.0000.0000.000
151A226ASP-1-0.854-0.93729.694-9.296-9.2960.0000.0000.0000.000
152A227GLY00.0750.04229.3770.2120.2120.0000.0000.0000.000
153A228LYS10.7750.88323.51411.10511.1050.0000.0000.0000.000
154A229LEU00.0190.00523.6510.0920.0920.0000.0000.0000.000
155A230ARG10.8860.95820.74711.63511.6350.0000.0000.0000.000
156A231PHE0-0.014-0.01415.5150.1200.1200.0000.0000.0000.000
157A232THR00.0220.01315.572-0.319-0.3190.0000.0000.0000.000
158A233VAL0-0.028-0.02510.1140.4520.4520.0000.0000.0000.000
159A234ARG10.9310.97212.64513.34813.3480.0000.0000.0000.000
160A235ASN0-0.031-0.0409.881-0.958-0.9580.0000.0000.0000.000
161A236VAL0-0.0070.0147.6340.9770.9770.0000.0000.0000.000
162A237HIS0-0.016-0.0169.024-1.647-1.6470.0000.0000.0000.000
163A238THR0-0.003-0.0028.1231.1151.1150.0000.0000.0000.000
164A239THR0-0.002-0.01811.0380.2450.2450.0000.0000.0000.000
165A240GLY00.0020.01714.3900.8960.8960.0000.0000.0000.000
166A241ARG10.8770.94216.85012.69912.6990.0000.0000.0000.000
167A242VAL00.0300.00916.040-0.722-0.7220.0000.0000.0000.000
168A243VAL00.0100.02610.6010.0130.0130.0000.0000.0000.000
169A244SER0-0.045-0.02613.4820.9750.9750.0000.0000.0000.000
170A245VAL00.006-0.00112.082-0.899-0.8990.0000.0000.0000.000
171A246ASP-1-0.796-0.88013.320-13.109-13.1090.0000.0000.0000.000
172A247GLY00.012-0.00214.528-0.670-0.6700.0000.0000.0000.000
173A248THR0-0.081-0.06516.6330.7080.7080.0000.0000.0000.000
174A249LEU00.0310.02019.244-0.328-0.3280.0000.0000.0000.000
175A250ILE0-0.0120.00519.9280.4640.4640.0000.0000.0000.000