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: Z6VQN

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 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 175
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1611228.671786
FMO2-HF: Nuclear repulsion 1543332.481323
FMO2-HF: Total energy -67896.190463
FMO2-MP2: Total energy -68095.995037


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.
-34.901-28.108-0.082-3.699-3.013-0.011
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 : 0.957 / q_NPA : 0.952
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].
3A24VAL00.0630.1093.782-5.6470.861-0.079-3.657-2.772-0.011
4A25THR0-0.027-0.0466.714-0.894-0.8940.0000.0000.0000.000
5A26ASN0-0.008-0.0168.340-0.339-0.3390.0000.0000.0000.000
6A27PRO0-0.037-0.00810.9690.7740.7740.0000.0000.0000.000
7A28ILE00.0620.00914.6080.4180.4180.0000.0000.0000.000
8A29ASP-1-0.975-0.99016.697-14.747-14.7470.0000.0000.0000.000
9A30GLU-1-0.757-0.89920.033-11.355-11.3550.0000.0000.0000.000
10A31LYS10.7860.94123.61110.01110.0110.0000.0000.0000.000
11A32ASN00.040-0.01622.1270.5950.5950.0000.0000.0000.000
12A33GLY0-0.043-0.02721.316-0.001-0.0010.0000.0000.0000.000
13A34THR0-0.009-0.01417.158-0.100-0.1000.0000.0000.0000.000
14A35SER00.0430.01613.0950.4340.4340.0000.0000.0000.000
15A36ASN00.0250.03413.871-1.084-1.0840.0000.0000.0000.000
16A37CYS0-0.003-0.01010.833-1.231-1.2310.0000.0000.0000.000
17A38ILE0-0.044-0.00911.071-1.435-1.4350.0000.0000.0000.000
18A39VAL00.0050.0199.1180.7290.7290.0000.0000.0000.000
19A40ARG10.8830.95712.51517.71717.7170.0000.0000.0000.000
20A41VAL0-0.011-0.0249.092-0.915-0.9150.0000.0000.0000.000
21A42PRO0-0.018-0.00712.2520.6600.6600.0000.0000.0000.000
22A43ILE0-0.047-0.02110.363-2.316-2.3160.0000.0000.0000.000
23A44ALA00.0650.04312.7241.6951.6950.0000.0000.0000.000
24A45LEU0-0.077-0.05113.653-1.446-1.4460.0000.0000.0000.000
25A46TYR00.0140.00915.6651.2481.2480.0000.0000.0000.000
26A47VAL0-0.025-0.01718.057-0.464-0.4640.0000.0000.0000.000
27A48SER00.023-0.00920.1970.6170.6170.0000.0000.0000.000
28A49LEU0-0.0440.00223.0710.0790.0790.0000.0000.0000.000
29A50ALA00.0250.01025.8380.2180.2180.0000.0000.0000.000
30A51PRO00.0390.01228.8040.0610.0610.0000.0000.0000.000
31A52MET0-0.013-0.02632.2940.1390.1390.0000.0000.0000.000
32A53TYR00.0010.01628.6320.1410.1410.0000.0000.0000.000
33A54LEU00.0740.04930.599-0.262-0.2620.0000.0000.0000.000
34A55GLU-1-0.976-0.97432.501-8.188-8.1880.0000.0000.0000.000
35A56ASN0-0.018-0.02631.553-0.252-0.2520.0000.0000.0000.000
36A57PRO00.0810.03626.875-0.153-0.1530.0000.0000.0000.000
37A58LEU00.0030.01325.835-0.520-0.5200.0000.0000.0000.000
38A59GLN00.0660.00526.261-0.570-0.5700.0000.0000.0000.000
39A60GLY0-0.012-0.00127.250-0.041-0.0410.0000.0000.0000.000
40A61VAL00.0290.00321.064-0.294-0.2940.0000.0000.0000.000
41A62MET00.0460.02522.140-0.544-0.5440.0000.0000.0000.000
42A63LYS10.8380.91423.95610.47710.4770.0000.0000.0000.000
43A64GLN0-0.037-0.02119.3830.4650.4650.0000.0000.0000.000
44A65HIS00.027-0.00316.675-0.965-0.9650.0000.0000.0000.000
45A66LEU00.0090.01019.591-0.389-0.3890.0000.0000.0000.000
46A67ASN00.0170.02520.444-0.582-0.5820.0000.0000.0000.000
47A68PRO0-0.102-0.05019.699-0.313-0.3130.0000.0000.0000.000
48A69LEU00.008-0.00314.063-0.628-0.6280.0000.0000.0000.000
49A70VAL00.0410.03016.170-0.487-0.4870.0000.0000.0000.000
50A71MET0-0.030-0.01516.9420.2560.2560.0000.0000.0000.000
51A72LYS10.8470.94415.53214.29714.2970.0000.0000.0000.000
52A73TYR00.0200.0065.498-1.107-1.1070.0000.0000.0000.000
53A74ASN00.0180.0139.508-1.795-1.7950.0000.0000.0000.000
54A75ASN00.0370.0006.589-1.806-1.8060.0000.0000.0000.000
55A76LYS10.9080.9655.52222.15222.1520.0000.0000.0000.000
56A77VAL0-0.010-0.0045.257-6.688-6.6880.0000.0000.0000.000
57A78GLY0-0.008-0.0054.0110.4070.506-0.001-0.020-0.0790.000
58A79GLY00.0530.0135.073-0.240-0.248-0.001-0.0020.0110.000
59A80VAL0-0.046-0.0218.2290.7640.7640.0000.0000.0000.000
60A81VAL00.0160.02011.956-0.516-0.5160.0000.0000.0000.000
61A82LEU00.007-0.00313.9051.2941.2940.0000.0000.0000.000
62A83GLY00.0190.00916.8471.1191.1190.0000.0000.0000.000
63A84TYR0-0.024-0.01917.417-0.792-0.7920.0000.0000.0000.000
64A85GLU-1-0.856-0.94719.005-13.844-13.8440.0000.0000.0000.000
65A86GLY00.014-0.01220.245-0.603-0.6030.0000.0000.0000.000
66A87LEU0-0.045-0.01020.407-0.189-0.1890.0000.0000.0000.000
67A88LYS10.9620.98921.56913.37513.3750.0000.0000.0000.000
68A89ILE00.037-0.00322.328-0.486-0.4860.0000.0000.0000.000
69A90LEU00.001-0.01824.402-0.111-0.1110.0000.0000.0000.000
70A91ASP-1-0.886-0.90320.580-14.967-14.9670.0000.0000.0000.000
71A92ALA0-0.038-0.06523.460-0.290-0.2900.0000.0000.0000.000
72A93ASP-1-0.952-0.98226.259-9.918-9.9180.0000.0000.0000.000
73A94PRO0-0.0210.02029.7540.0070.0070.0000.0000.0000.000
74A112PRO00.012-0.02234.4300.0680.0680.0000.0000.0000.000
75A113PHE0-0.030-0.04330.027-0.112-0.1120.0000.0000.0000.000
76A114GLY0-0.0040.03028.355-0.186-0.1860.0000.0000.0000.000
77A115PHE0-0.0180.01322.733-0.167-0.1670.0000.0000.0000.000
78A116THR00.0340.00722.9620.6070.6070.0000.0000.0000.000
79A117TRP0-0.0020.02315.632-1.108-1.1080.0000.0000.0000.000
80A118CYS0-0.086-0.02119.2050.5670.5670.0000.0000.0000.000
81A119HIS00.0830.04715.170-1.211-1.2110.0000.0000.0000.000
82A120VAL0-0.024-0.01616.1671.0501.0500.0000.0000.0000.000
83A121ASN0-0.008-0.00315.582-2.014-2.0140.0000.0000.0000.000
84A122LEU00.0130.01212.1381.2861.2860.0000.0000.0000.000
85A123TYR00.0220.01914.461-0.822-0.8220.0000.0000.0000.000
86A124VAL0-0.033-0.0319.0050.4260.4260.0000.0000.0000.000
87A125TRP00.0410.04711.438-0.511-0.5110.0000.0000.0000.000
88A126GLN00.000-0.0166.011-4.410-4.4100.0000.0000.0000.000
89A127PRO0-0.0150.0147.744-0.890-0.8900.0000.0000.0000.000
90A128GLN0-0.021-0.0504.0890.3360.530-0.001-0.020-0.1730.000
91A129VAL00.006-0.0176.6912.1592.1590.0000.0000.0000.000
92A130GLY0-0.022-0.0048.793-0.797-0.7970.0000.0000.0000.000
93A131ASP-1-0.790-0.8799.057-22.153-22.1530.0000.0000.0000.000
94A132VAL00.0060.01112.1990.8720.8720.0000.0000.0000.000
95A133LEU0-0.010-0.00312.443-0.094-0.0940.0000.0000.0000.000
96A134GLU-1-0.880-0.96116.614-11.057-11.0570.0000.0000.0000.000
97A135GLY0-0.045-0.03019.633-0.447-0.4470.0000.0000.0000.000
98A136TYR00.0260.02321.4980.3770.3770.0000.0000.0000.000
99A137ILE00.0050.00724.151-0.373-0.3730.0000.0000.0000.000
100A138PHE0-0.036-0.00624.2490.1910.1910.0000.0000.0000.000
101A139ILE00.000-0.01524.9780.3320.3320.0000.0000.0000.000
102A140GLN0-0.0030.00127.126-0.162-0.1620.0000.0000.0000.000
103A141SER00.000-0.00928.9090.2130.2130.0000.0000.0000.000
104A142ALA00.0050.01429.463-0.179-0.1790.0000.0000.0000.000
105A143SER0-0.164-0.08128.257-0.090-0.0900.0000.0000.0000.000
106A144HIS0-0.020-0.02522.505-0.393-0.3930.0000.0000.0000.000
107A145ILE00.0570.04724.6900.2160.2160.0000.0000.0000.000
108A146GLY00.0230.01122.689-0.450-0.4500.0000.0000.0000.000
109A147LEU0-0.036-0.02720.4150.2950.2950.0000.0000.0000.000
110A148LEU0-0.0030.02020.641-0.443-0.4430.0000.0000.0000.000
111A149ILE0-0.002-0.00915.2790.2020.2020.0000.0000.0000.000
112A150HIS0-0.031-0.02216.4180.2590.2590.0000.0000.0000.000
113A151ASP-1-0.950-0.98520.736-10.689-10.6890.0000.0000.0000.000
114A152ALA00.0030.01320.0440.1820.1820.0000.0000.0000.000
115A153PHE0-0.033-0.01215.592-0.523-0.5230.0000.0000.0000.000
116A154ASN00.004-0.00917.6010.0840.0840.0000.0000.0000.000
117A155ALA00.0360.03716.598-0.745-0.7450.0000.0000.0000.000
118A156SER0-0.0320.00117.9170.7160.7160.0000.0000.0000.000
119A157ILE00.0490.03518.718-0.530-0.5300.0000.0000.0000.000
120A158LYS10.9470.95819.21712.91612.9160.0000.0000.0000.000
121A159LYS11.0260.99822.7888.7958.7950.0000.0000.0000.000
122A160ASN0-0.054-0.02623.3300.0920.0920.0000.0000.0000.000
123A161ASN0-0.017-0.01720.055-0.008-0.0080.0000.0000.0000.000
124A162ILE00.0180.04223.228-0.172-0.1720.0000.0000.0000.000
125A163PRO00.0320.00326.1150.0760.0760.0000.0000.0000.000
126A164VAL0-0.0260.00428.5470.1020.1020.0000.0000.0000.000
127A165ASP-1-0.865-0.92531.189-8.288-8.2880.0000.0000.0000.000
128A166TRP0-0.013-0.00427.6140.0190.0190.0000.0000.0000.000
129A167THR0-0.040-0.02332.9720.0450.0450.0000.0000.0000.000
130A168PHE0-0.019-0.02532.990-0.061-0.0610.0000.0000.0000.000
131A169VAL00.0490.03935.2080.1100.1100.0000.0000.0000.000
132A170HIS00.012-0.01437.252-0.099-0.0990.0000.0000.0000.000
133A171ASN00.0650.02339.4740.0450.0450.0000.0000.0000.000
134A172ASP-1-0.856-0.91841.786-6.396-6.3960.0000.0000.0000.000
135A210GLY0-0.093-0.06140.686-0.021-0.0210.0000.0000.0000.000
136A211ASN00.0330.03341.028-0.027-0.0270.0000.0000.0000.000
137A212ARG10.9210.94240.7376.4366.4360.0000.0000.0000.000
138A213SER0-0.065-0.06037.1150.0780.0780.0000.0000.0000.000
139A214LEU00.0180.03337.023-0.182-0.1820.0000.0000.0000.000
140A215GLY0-0.0050.00036.0030.0770.0770.0000.0000.0000.000
141A216HIS0-0.060-0.03933.721-0.158-0.1580.0000.0000.0000.000
142A217TRP0-0.026-0.00828.701-0.163-0.1630.0000.0000.0000.000
143A218VAL00.0920.07132.752-0.182-0.1820.0000.0000.0000.000
144A219ASP-1-0.864-0.94432.735-8.050-8.0500.0000.0000.0000.000
145A220SER00.0030.00634.1740.2380.2380.0000.0000.0000.000
146A221ASN0-0.092-0.04436.4080.3250.3250.0000.0000.0000.000
147A222GLY0-0.016-0.00937.1940.1950.1950.0000.0000.0000.000
148A223GLU-1-0.904-0.93835.644-7.223-7.2230.0000.0000.0000.000
149A224PRO0-0.071-0.06235.177-0.189-0.1890.0000.0000.0000.000
150A225ILE0-0.083-0.03629.484-0.145-0.1450.0000.0000.0000.000
151A226ASP-1-0.821-0.91829.311-9.307-9.3070.0000.0000.0000.000
152A227GLY00.0620.03729.1910.2120.2120.0000.0000.0000.000
153A228LYS10.8000.90823.42310.90710.9070.0000.0000.0000.000
154A229LEU00.0190.00823.4080.0750.0750.0000.0000.0000.000
155A230ARG10.9441.00221.06411.47111.4710.0000.0000.0000.000
156A231PHE0-0.020-0.01615.6530.1400.1400.0000.0000.0000.000
157A232THR00.0320.02015.593-0.336-0.3360.0000.0000.0000.000
158A233VAL0-0.023-0.02210.1600.5000.5000.0000.0000.0000.000
159A234ARG10.9290.97612.78613.14213.1420.0000.0000.0000.000
160A235ASN0-0.040-0.04210.132-0.924-0.9240.0000.0000.0000.000
161A236VAL00.0130.0277.5910.8940.8940.0000.0000.0000.000
162A237HIS0-0.010-0.0029.129-1.363-1.3630.0000.0000.0000.000
163A238THR00.0040.0018.0581.0371.0370.0000.0000.0000.000
164A239THR0-0.014-0.02310.9970.2400.2400.0000.0000.0000.000
165A240GLY00.0100.02114.3930.8700.8700.0000.0000.0000.000
166A241ARG10.8750.94116.82512.64312.6430.0000.0000.0000.000
167A242VAL00.0330.01516.145-0.718-0.7180.0000.0000.0000.000
168A243VAL00.0030.02110.756-0.014-0.0140.0000.0000.0000.000
169A244SER0-0.018-0.01413.3830.7490.7490.0000.0000.0000.000
170A245VAL00.0070.00111.778-0.910-0.9100.0000.0000.0000.000
171A246ASP-1-0.907-0.96013.370-13.120-13.1200.0000.0000.0000.000
172A247GLY00.028-0.00714.653-0.648-0.6480.0000.0000.0000.000
173A248THR0-0.050-0.03616.7010.7000.7000.0000.0000.0000.000
174A249LEU00.0280.01619.376-0.324-0.3240.0000.0000.0000.000
175A250ILE0-0.0110.00120.0870.4810.4810.0000.0000.0000.000