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: 2N34R

Calculation Name: 2ERF-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2ERF

Chain ID: A

ChEMBL ID:

UniProt ID: P07996

Base Structure: X-ray

Registration Date: 2023-09-23

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 208
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2423334.725298
FMO2-HF: Nuclear repulsion 2343767.646301
FMO2-HF: Total energy -79567.078997
FMO2-MP2: Total energy -79801.800433


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:7:GLY)


Summations of interaction energy for fragment #1(A:7:GLY)
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.
-7.278-2.6274.483-4.604-4.533-0.036
Interaction energy analysis for fragmet #1(A:7:GLY)
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 : -0.007
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].
3A9ASP-1-0.904-0.9433.797-2.530-1.551-0.011-0.544-0.4240.001
4A10ASN0-0.071-0.0385.9220.0450.0450.0000.0000.0000.000
5A11SER00.0270.0042.610-1.765-0.4611.094-1.268-1.131-0.006
6A12VAL00.0010.0014.4730.0320.187-0.001-0.011-0.1430.000
7A13PHE00.0140.0106.9250.1840.1840.0000.0000.0000.000
8A14ASP-1-0.773-0.87210.621-0.258-0.2580.0000.0000.0000.000
9A15ILE00.0330.00313.2780.0330.0330.0000.0000.0000.000
10A16PHE00.016-0.00716.3250.0300.0300.0000.0000.0000.000
11A17GLU-1-0.995-0.98914.633-0.362-0.3620.0000.0000.0000.000
12A18LEU0-0.003-0.00413.3930.0240.0240.0000.0000.0000.000
13A19THR0-0.052-0.02017.6560.0300.0300.0000.0000.0000.000
14A20GLY00.0250.01520.6800.0210.0210.0000.0000.0000.000
15A21ALA00.0010.00022.5510.0200.0200.0000.0000.0000.000
16A22ALA0-0.0010.00322.7030.0160.0160.0000.0000.0000.000
17A23ARG10.9400.96120.6510.2140.2140.0000.0000.0000.000
18A24LYS10.9791.00426.6340.1200.1200.0000.0000.0000.000
19A25GLY0-0.005-0.01628.8590.0000.0000.0000.0000.0000.000
20A26SER0-0.019-0.01530.9680.0050.0050.0000.0000.0000.000
21A27GLY00.0890.05129.972-0.007-0.0070.0000.0000.0000.000
22A28ARG10.8370.92826.8300.1170.1170.0000.0000.0000.000
23A29ARG11.0021.02330.1060.0630.0630.0000.0000.0000.000
24A30LEU0-0.0240.00125.598-0.003-0.0030.0000.0000.0000.000
25A31VAL0-0.079-0.05027.2260.0110.0110.0000.0000.0000.000
26A32LYS10.9870.98426.4620.0560.0560.0000.0000.0000.000
27A33GLY00.0390.00523.7620.0020.0020.0000.0000.0000.000
28A34PRO0-0.045-0.01921.2250.0020.0020.0000.0000.0000.000
29A35ASP-1-0.696-0.77217.472-0.149-0.1490.0000.0000.0000.000
30A36PRO0-0.029-0.01620.557-0.007-0.0070.0000.0000.0000.000
31A37SER0-0.089-0.06718.549-0.004-0.0040.0000.0000.0000.000
32A38SER00.004-0.01217.992-0.015-0.0150.0000.0000.0000.000
33A39PRO0-0.042-0.01819.9520.0180.0180.0000.0000.0000.000
34A40ALA00.0150.01621.405-0.011-0.0110.0000.0000.0000.000
35A41PHE0-0.002-0.01820.6930.0080.0080.0000.0000.0000.000
36A42ARG10.9480.97425.6130.0650.0650.0000.0000.0000.000
37A43ILE0-0.009-0.01225.411-0.002-0.0020.0000.0000.0000.000
38A44GLU-1-0.965-0.99029.483-0.066-0.0660.0000.0000.0000.000
39A45ASP-1-0.816-0.91431.896-0.070-0.0700.0000.0000.0000.000
40A46ALA00.011-0.00328.056-0.005-0.0050.0000.0000.0000.000
41A47ASN0-0.067-0.04028.830-0.009-0.0090.0000.0000.0000.000
42A48LEU0-0.032-0.01830.739-0.004-0.0040.0000.0000.0000.000
43A49ILE0-0.0340.00124.666-0.004-0.0040.0000.0000.0000.000
44A50PRO0-0.027-0.00524.7350.0040.0040.0000.0000.0000.000
45A51PRO0-0.010-0.00723.458-0.006-0.0060.0000.0000.0000.000
46A52VAL00.008-0.00216.782-0.006-0.0060.0000.0000.0000.000
47A53PRO0-0.0100.00619.1780.0190.0190.0000.0000.0000.000
48A54ASP-1-0.810-0.91019.162-0.181-0.1810.0000.0000.0000.000
49A55ASP-1-0.818-0.90918.236-0.317-0.3170.0000.0000.0000.000
50A56LYS10.8300.90514.3620.4070.4070.0000.0000.0000.000
51A57PHE0-0.001-0.00114.306-0.033-0.0330.0000.0000.0000.000
52A58GLN00.027-0.00815.2570.0120.0120.0000.0000.0000.000
53A59ASP-1-0.851-0.91211.322-0.477-0.4770.0000.0000.0000.000
54A60LEU0-0.037-0.00810.534-0.028-0.0280.0000.0000.0000.000
55A61VAL0-0.050-0.02511.4170.0380.0380.0000.0000.0000.000
56A62ASP-1-0.757-0.85812.243-0.161-0.1610.0000.0000.0000.000
57A63ALA00.0240.0437.2300.0610.0610.0000.0000.0000.000
58A64VAL0-0.0110.0038.9250.1190.1190.0000.0000.0000.000
59A65ARG10.7410.84911.0920.2080.2080.0000.0000.0000.000
60A66THR0-0.106-0.0698.6790.0380.0380.0000.0000.0000.000
61A67GLU-1-0.837-0.9125.9120.5840.5840.0000.0000.0000.000
62A68LYS10.8930.9549.369-0.063-0.0630.0000.0000.0000.000
63A69GLY00.0310.00811.6090.0190.0190.0000.0000.0000.000
64A70PHE00.0250.0049.310-0.041-0.0410.0000.0000.0000.000
65A71LEU00.0070.0267.8670.0770.0770.0000.0000.0000.000
66A72LEU0-0.051-0.0249.959-0.119-0.1190.0000.0000.0000.000
67A73LEU00.0090.0179.8050.0580.0580.0000.0000.0000.000
68A74ALA00.0220.00013.564-0.029-0.0290.0000.0000.0000.000
69A75SER00.0170.03517.0660.0220.0220.0000.0000.0000.000
70A76LEU0-0.034-0.02819.932-0.012-0.0120.0000.0000.0000.000
71A77ARG10.8930.96223.3130.0510.0510.0000.0000.0000.000
72A78GLN00.0120.02526.959-0.005-0.0050.0000.0000.0000.000
73A79MET0-0.026-0.00928.8540.0070.0070.0000.0000.0000.000
74A80LYS10.9750.99232.3140.0190.0190.0000.0000.0000.000
75A81LYS10.9780.99133.9500.0120.0120.0000.0000.0000.000
76A82THR0-0.021-0.00731.876-0.001-0.0010.0000.0000.0000.000
77A83ARG10.8370.90330.4780.0360.0360.0000.0000.0000.000
78A84GLY00.0090.00628.350-0.001-0.0010.0000.0000.0000.000
79A85THR0-0.014-0.01424.5720.0010.0010.0000.0000.0000.000
80A86LEU0-0.025-0.01720.337-0.005-0.0050.0000.0000.0000.000
81A87LEU00.0060.00216.884-0.017-0.0170.0000.0000.0000.000
82A88ALA00.0240.00821.6070.0150.0150.0000.0000.0000.000
83A89LEU0-0.0410.00318.286-0.014-0.0140.0000.0000.0000.000
84A90GLU-1-0.793-0.88322.461-0.088-0.0880.0000.0000.0000.000
85A91ARG10.9950.99525.7730.0580.0580.0000.0000.0000.000
86A92LYS10.7460.84324.7110.1410.1410.0000.0000.0000.000
87A93ASP-1-0.845-0.88629.110-0.068-0.0680.0000.0000.0000.000
88A94HIS0-0.038-0.02831.3430.0050.0050.0000.0000.0000.000
89A95SER0-0.074-0.05132.0330.0040.0040.0000.0000.0000.000
90A96GLY00.0320.01430.8270.0050.0050.0000.0000.0000.000
91A97GLN0-0.037-0.00325.838-0.006-0.0060.0000.0000.0000.000
92A98VAL00.008-0.01322.4030.0080.0080.0000.0000.0000.000
93A99PHE00.0570.01817.7260.0040.0040.0000.0000.0000.000
94A100SER0-0.033-0.02322.337-0.008-0.0080.0000.0000.0000.000
95A101VAL00.0580.05318.5830.0100.0100.0000.0000.0000.000
96A102VAL0-0.020-0.01922.061-0.010-0.0100.0000.0000.0000.000
97A103SER00.0340.01724.3790.0100.0100.0000.0000.0000.000
98A104ASN00.024-0.01925.872-0.003-0.0030.0000.0000.0000.000
99A105GLY00.0500.00929.2850.0050.0050.0000.0000.0000.000
100A106LYS10.7660.86431.4400.0320.0320.0000.0000.0000.000
101A107ALA00.0110.01331.6610.0020.0020.0000.0000.0000.000
102A108GLY0-0.038-0.00830.7270.0030.0030.0000.0000.0000.000
103A109THR00.034-0.00527.7460.0030.0030.0000.0000.0000.000
104A110LEU0-0.027-0.01120.150-0.009-0.0090.0000.0000.0000.000
105A111ASP-1-0.782-0.84124.703-0.014-0.0140.0000.0000.0000.000
106A112LEU0-0.0020.00019.955-0.013-0.0130.0000.0000.0000.000
107A113SER00.0210.01023.3650.0110.0110.0000.0000.0000.000
108A114LEU00.0240.01020.243-0.012-0.0120.0000.0000.0000.000
109A115THR0-0.056-0.03424.3280.0090.0090.0000.0000.0000.000
110A116VAL00.0400.01924.197-0.006-0.0060.0000.0000.0000.000
111A117GLN0-0.016-0.01326.9220.0000.0000.0000.0000.0000.000
112A118GLY0-0.005-0.01029.9100.0040.0040.0000.0000.0000.000
113A119LYS10.9160.97030.6030.0160.0160.0000.0000.0000.000
114A120GLN00.0210.01229.1810.0000.0000.0000.0000.0000.000
115A121HIS10.7960.88126.6780.0150.0150.0000.0000.0000.000
116A122VAL00.001-0.00826.829-0.005-0.0050.0000.0000.0000.000
117A123VAL00.0120.02424.5540.0040.0040.0000.0000.0000.000
118A124SER0-0.006-0.02625.997-0.006-0.0060.0000.0000.0000.000
119A125VAL0-0.022-0.00921.7500.0060.0060.0000.0000.0000.000
120A126GLU-1-0.859-0.95325.2080.0000.0000.0000.0000.0000.000
121A127GLU-1-0.891-0.93827.0600.0310.0310.0000.0000.0000.000
122A128ALA00.0250.02024.5660.0030.0030.0000.0000.0000.000
123A129LEU0-0.024-0.00626.487-0.008-0.0080.0000.0000.0000.000
124A130LEU00.0460.02122.7770.0000.0000.0000.0000.0000.000
125A131ALA0-0.058-0.00926.686-0.005-0.0050.0000.0000.0000.000
126A132THR00.0480.00328.7780.0030.0030.0000.0000.0000.000
127A133GLY0-0.066-0.03530.8240.0030.0030.0000.0000.0000.000
128A134GLN0-0.014-0.02129.627-0.005-0.0050.0000.0000.0000.000
129A135TRP0-0.045-0.02723.075-0.001-0.0010.0000.0000.0000.000
130A136LYS10.9010.96423.4170.0120.0120.0000.0000.0000.000
131A137SER0-0.020-0.00717.954-0.016-0.0160.0000.0000.0000.000
132A138ILE0-0.013-0.00617.6960.0180.0180.0000.0000.0000.000
133A139THR00.0290.00812.293-0.030-0.0300.0000.0000.0000.000
134A140LEU0-0.024-0.01014.3560.0300.0300.0000.0000.0000.000
135A141PHE00.0180.0019.725-0.031-0.0310.0000.0000.0000.000
136A142VAL00.0160.00113.0950.0110.0110.0000.0000.0000.000
137A143GLN00.0010.00610.9220.0060.0060.0000.0000.0000.000
138A144GLU-1-0.852-0.92514.7840.0980.0980.0000.0000.0000.000
139A145ASP-1-0.860-0.92717.3520.0550.0550.0000.0000.0000.000
140A146ARG10.9350.98316.954-0.141-0.1410.0000.0000.0000.000
141A147ALA0-0.0010.00117.579-0.001-0.0010.0000.0000.0000.000
142A148GLN0-0.018-0.01816.3800.0280.0280.0000.0000.0000.000
143A149LEU0-0.036-0.01416.704-0.012-0.0120.0000.0000.0000.000
144A150TYR00.0320.00915.2740.0180.0180.0000.0000.0000.000
145A151ILE0-0.034-0.02618.513-0.023-0.0230.0000.0000.0000.000
146A152ASP-1-0.786-0.89020.375-0.002-0.0020.0000.0000.0000.000
147A153CYS0-0.142-0.05714.382-0.005-0.0050.0000.0000.0000.000
148A154GLU-1-0.915-0.95620.8120.0400.0400.0000.0000.0000.000
149A155LYS10.7350.86222.293-0.028-0.0280.0000.0000.0000.000
150A156MET0-0.006-0.00419.5110.0060.0060.0000.0000.0000.000
151A157GLU-1-0.813-0.86521.5750.0430.0430.0000.0000.0000.000
152A158ASN0-0.011-0.03020.5000.0080.0080.0000.0000.0000.000
153A159ALA0-0.0010.00521.972-0.006-0.0060.0000.0000.0000.000
154A160GLU-1-0.936-0.95822.1990.0610.0610.0000.0000.0000.000
155A161LEU0-0.065-0.04219.489-0.012-0.0120.0000.0000.0000.000
156A162ASP-1-0.819-0.89323.9340.0120.0120.0000.0000.0000.000
157A163VAL0-0.048-0.02823.0520.0000.0000.0000.0000.0000.000
158A164PRO00.0290.02419.395-0.003-0.0030.0000.0000.0000.000
159A165ILE00.0330.03715.249-0.018-0.0180.0000.0000.0000.000
160A166GLN0-0.004-0.04115.414-0.026-0.0260.0000.0000.0000.000
161A167SER0-0.092-0.06117.089-0.011-0.0110.0000.0000.0000.000
162A168VAL0-0.040-0.02019.961-0.005-0.0050.0000.0000.0000.000
163A169PHE0-0.0170.00215.174-0.013-0.0130.0000.0000.0000.000
164A170THR00.026-0.00217.124-0.005-0.0050.0000.0000.0000.000
165A171ARG10.9830.95718.0740.0720.0720.0000.0000.0000.000
166A172ASP-1-0.817-0.87719.223-0.131-0.1310.0000.0000.0000.000
167A173LEU0-0.0320.01018.7370.0040.0040.0000.0000.0000.000
168A174ALA00.0390.01619.1020.0060.0060.0000.0000.0000.000
169A175SER0-0.048-0.03721.1200.0060.0060.0000.0000.0000.000
170A176ILE0-0.034-0.01524.2660.0100.0100.0000.0000.0000.000
171A177ALA0-0.024-0.01322.8920.0100.0100.0000.0000.0000.000
172A178ARG10.9830.99122.1930.1160.1160.0000.0000.0000.000
173A179LEU00.0100.02716.6950.0150.0150.0000.0000.0000.000
174A180ARG10.7820.87920.7840.1140.1140.0000.0000.0000.000
175A181ILE00.0570.01819.3380.0020.0020.0000.0000.0000.000
176A182ALA0-0.046-0.03022.6760.0100.0100.0000.0000.0000.000
177A183LYS10.8500.91725.2040.1010.1010.0000.0000.0000.000
178A184GLY00.018-0.00226.396-0.006-0.0060.0000.0000.0000.000
179A185GLY00.0050.01328.5650.0040.0040.0000.0000.0000.000
180A186VAL0-0.0080.00431.302-0.002-0.0020.0000.0000.0000.000
181A187ASN0-0.043-0.03734.9430.0010.0010.0000.0000.0000.000
182A188ASP-1-0.743-0.82930.518-0.042-0.0420.0000.0000.0000.000
183A189ASN00.0360.01729.343-0.007-0.0070.0000.0000.0000.000
184A190PHE0-0.006-0.00525.6250.0060.0060.0000.0000.0000.000
185A191GLN00.0110.00928.4570.0010.0010.0000.0000.0000.000
186A192GLY00.008-0.00829.2680.0060.0060.0000.0000.0000.000
187A193VAL0-0.094-0.04625.601-0.004-0.0040.0000.0000.0000.000
188A194LEU00.0390.03121.6770.0050.0050.0000.0000.0000.000
189A195GLN00.022-0.01219.2520.0120.0120.0000.0000.0000.000
190A196ASN0-0.020-0.02215.360-0.009-0.0090.0000.0000.0000.000
191A197VAL00.0100.01115.4220.0040.0040.0000.0000.0000.000
192A198ARG10.8400.89910.7710.3350.3350.0000.0000.0000.000
193A199PHE00.0180.0139.9810.0790.0790.0000.0000.0000.000
194A200VAL0-0.033-0.0214.502-0.171-0.148-0.001-0.003-0.0190.000
195A201PHE0-0.013-0.0033.9610.1640.3160.000-0.064-0.0880.000
196A202GLY00.007-0.0172.366-5.669-3.8333.332-2.966-2.203-0.028
197A203THR0-0.052-0.0273.2581.0951.2990.0710.258-0.534-0.003
198A204THR00.003-0.0174.799-0.339-0.341-0.001-0.0060.0090.000
199A205PRO00.0380.0028.591-0.055-0.0550.0000.0000.0000.000
200A206GLU-1-0.868-0.91411.3900.3480.3480.0000.0000.0000.000
201A207ASP-1-0.816-0.8908.1680.9820.9820.0000.0000.0000.000
202A208ILE0-0.0040.0017.567-0.078-0.0780.0000.0000.0000.000
203A209LEU00.0220.00910.704-0.043-0.0430.0000.0000.0000.000
204A210ARG10.8430.91613.667-0.336-0.3360.0000.0000.0000.000
205A211ASN0-0.036-0.0109.713-0.023-0.0230.0000.0000.0000.000
206A212LYS10.8510.91113.698-0.161-0.1610.0000.0000.0000.000
207A213GLY0-0.0020.00413.447-0.031-0.0310.0000.0000.0000.000
208A215SER00.0310.00216.487-0.001-0.0010.0000.0000.0000.000