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: 6YVZZ

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 OptAll
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 -2423529.957969
FMO2-HF: Nuclear repulsion 2343962.418065
FMO2-HF: Total energy -79567.539904
FMO2-MP2: Total energy -79802.23322


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.
-9.572-7.689.125-5.166-5.852-0.042
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 : -0.006 / q_NPA : -0.009
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-1-0.912-0.9343.866-1.660-0.228-0.012-0.815-0.6060.001
4A10ASN0-0.093-0.0526.059-0.223-0.2230.0000.0000.0000.000
5A11SER00.0260.0072.075-3.392-4.3344.990-1.920-2.129-0.018
6A12VAL0-0.002-0.0104.127-0.1360.110-0.001-0.030-0.2140.000
7A13PHE00.0130.0026.2990.1530.1530.0000.0000.0000.000
8A14ASP-1-0.782-0.87010.0780.0340.0340.0000.0000.0000.000
9A15ILE00.0620.02012.956-0.007-0.0070.0000.0000.0000.000
10A16PHE00.0020.01015.9560.0040.0040.0000.0000.0000.000
11A17GLU-1-0.920-0.95115.2510.0140.0140.0000.0000.0000.000
12A18LEU00.0020.00512.253-0.001-0.0010.0000.0000.0000.000
13A19THR0-0.058-0.04316.7020.0040.0040.0000.0000.0000.000
14A20GLY00.0250.01519.7190.0080.0080.0000.0000.0000.000
15A21ALA00.0120.01421.6440.0120.0120.0000.0000.0000.000
16A22ALA00.0100.00521.5590.0080.0080.0000.0000.0000.000
17A23ARG10.8600.91519.3660.0140.0140.0000.0000.0000.000
18A24LYS10.9610.98425.7470.0360.0360.0000.0000.0000.000
19A25GLY00.0200.01527.8870.0010.0010.0000.0000.0000.000
20A26SER0-0.052-0.04629.445-0.001-0.0010.0000.0000.0000.000
21A27GLY00.0850.05129.105-0.002-0.0020.0000.0000.0000.000
22A28ARG10.8380.91525.9920.0140.0140.0000.0000.0000.000
23A29ARG10.9651.00429.318-0.007-0.0070.0000.0000.0000.000
24A30LEU0-0.0070.00625.1710.0010.0010.0000.0000.0000.000
25A31VAL0-0.078-0.04526.8760.0010.0010.0000.0000.0000.000
26A32LYS10.9910.99126.119-0.044-0.0440.0000.0000.0000.000
27A33GLY00.037-0.00423.688-0.008-0.0080.0000.0000.0000.000
28A34PRO0-0.023-0.00521.1930.0020.0020.0000.0000.0000.000
29A35ASP-1-0.723-0.77517.8220.1560.1560.0000.0000.0000.000
30A36PRO0-0.034-0.02020.687-0.015-0.0150.0000.0000.0000.000
31A37SER0-0.084-0.06418.724-0.003-0.0030.0000.0000.0000.000
32A38SER00.006-0.01418.120-0.013-0.0130.0000.0000.0000.000
33A39PRO0-0.046-0.02019.993-0.004-0.0040.0000.0000.0000.000
34A40ALA00.0240.02121.338-0.001-0.0010.0000.0000.0000.000
35A41PHE0-0.004-0.02220.359-0.005-0.0050.0000.0000.0000.000
36A42ARG10.9380.97525.221-0.012-0.0120.0000.0000.0000.000
37A43ILE0-0.001-0.00124.966-0.003-0.0030.0000.0000.0000.000
38A44GLU-1-0.966-0.99628.9900.0000.0000.0000.0000.0000.000
39A45ASP-1-0.816-0.91731.256-0.029-0.0290.0000.0000.0000.000
40A46ALA00.0160.01027.262-0.002-0.0020.0000.0000.0000.000
41A47ASN0-0.075-0.04828.049-0.010-0.0100.0000.0000.0000.000
42A48LEU0-0.007-0.00529.993-0.004-0.0040.0000.0000.0000.000
43A49ILE0-0.0430.00223.9970.0020.0020.0000.0000.0000.000
44A50PRO0-0.018-0.00323.633-0.003-0.0030.0000.0000.0000.000
45A51PRO00.0060.00622.8560.0000.0000.0000.0000.0000.000
46A52VAL0-0.008-0.00516.3390.0040.0040.0000.0000.0000.000
47A53PRO0-0.0060.00318.5580.0020.0020.0000.0000.0000.000
48A54ASP-1-0.731-0.84618.917-0.141-0.1410.0000.0000.0000.000
49A55ASP-1-0.806-0.89517.990-0.218-0.2180.0000.0000.0000.000
50A56LYS10.8360.89213.7620.2560.2560.0000.0000.0000.000
51A57PHE0-0.024-0.00614.277-0.036-0.0360.0000.0000.0000.000
52A58GLN00.030-0.01215.6360.0030.0030.0000.0000.0000.000
53A59ASP-1-0.828-0.89811.449-0.447-0.4470.0000.0000.0000.000
54A60LEU0-0.0230.00110.818-0.072-0.0720.0000.0000.0000.000
55A61VAL0-0.048-0.01612.074-0.013-0.0130.0000.0000.0000.000
56A62ASP-1-0.741-0.84712.906-0.305-0.3050.0000.0000.0000.000
57A63ALA00.0270.0438.034-0.007-0.0070.0000.0000.0000.000
58A64VAL0-0.0170.0009.5690.0290.0290.0000.0000.0000.000
59A65ARG10.7340.83311.7300.3350.3350.0000.0000.0000.000
60A66THR0-0.095-0.0578.8730.0550.0550.0000.0000.0000.000
61A67GLU-1-0.824-0.9185.819-0.358-0.3580.0000.0000.0000.000
62A68LYS10.8710.9519.4420.2870.2870.0000.0000.0000.000
63A69GLY00.0500.01112.0580.0530.0530.0000.0000.0000.000
64A70PHE00.016-0.0019.394-0.063-0.0630.0000.0000.0000.000
65A71LEU00.0170.0327.6310.1060.1060.0000.0000.0000.000
66A72LEU0-0.050-0.0319.605-0.078-0.0780.0000.0000.0000.000
67A73LEU00.0130.0199.3940.0460.0460.0000.0000.0000.000
68A74ALA00.0260.00513.155-0.025-0.0250.0000.0000.0000.000
69A75SER00.0270.04016.6050.0210.0210.0000.0000.0000.000
70A76LEU0-0.029-0.02719.690-0.012-0.0120.0000.0000.0000.000
71A77ARG10.8860.94823.049-0.026-0.0260.0000.0000.0000.000
72A78GLN0-0.0060.01926.834-0.002-0.0020.0000.0000.0000.000
73A79MET0-0.019-0.00928.7070.0030.0030.0000.0000.0000.000
74A80LYS10.9780.99132.299-0.019-0.0190.0000.0000.0000.000
75A81LYS10.9520.98733.809-0.006-0.0060.0000.0000.0000.000
76A82THR0-0.0160.00531.637-0.003-0.0030.0000.0000.0000.000
77A83ARG10.8360.88330.3600.0250.0250.0000.0000.0000.000
78A84GLY00.0150.01027.989-0.001-0.0010.0000.0000.0000.000
79A85THR0-0.022-0.02624.2710.0000.0000.0000.0000.0000.000
80A86LEU0-0.018-0.00220.2570.0010.0010.0000.0000.0000.000
81A87LEU00.004-0.00216.492-0.002-0.0020.0000.0000.0000.000
82A88ALA00.0170.00421.2120.0040.0040.0000.0000.0000.000
83A89LEU0-0.0240.01218.438-0.007-0.0070.0000.0000.0000.000
84A90GLU-1-0.774-0.86222.544-0.064-0.0640.0000.0000.0000.000
85A91ARG10.9210.94125.6960.0750.0750.0000.0000.0000.000
86A92LYS10.7370.85024.6620.1250.1250.0000.0000.0000.000
87A93ASP-1-0.793-0.85729.337-0.070-0.0700.0000.0000.0000.000
88A94HIS0-0.024-0.02331.3610.0060.0060.0000.0000.0000.000
89A95SER0-0.086-0.05332.5660.0030.0030.0000.0000.0000.000
90A96GLY00.0290.00731.0640.0030.0030.0000.0000.0000.000
91A97GLN0-0.0110.01726.050-0.007-0.0070.0000.0000.0000.000
92A98VAL0-0.003-0.00822.9490.0040.0040.0000.0000.0000.000
93A99PHE00.0720.02517.327-0.005-0.0050.0000.0000.0000.000
94A100SER0-0.054-0.02922.0640.0030.0030.0000.0000.0000.000
95A101VAL00.0620.04918.4250.0020.0020.0000.0000.0000.000
96A102VAL0-0.021-0.02121.9030.0030.0030.0000.0000.0000.000
97A103SER00.0440.01524.2710.0050.0050.0000.0000.0000.000
98A104ASN00.000-0.02325.8160.0040.0040.0000.0000.0000.000
99A105GLY00.0770.02029.3030.0030.0030.0000.0000.0000.000
100A106LYS10.7700.87331.2920.0120.0120.0000.0000.0000.000
101A107ALA0-0.0030.00731.7480.0010.0010.0000.0000.0000.000
102A108GLY0-0.042-0.01631.0460.0020.0020.0000.0000.0000.000
103A109THR00.036-0.00427.6950.0030.0030.0000.0000.0000.000
104A110LEU0-0.034-0.01420.106-0.001-0.0010.0000.0000.0000.000
105A111ASP-1-0.775-0.83624.350-0.024-0.0240.0000.0000.0000.000
106A112LEU0-0.011-0.00220.089-0.007-0.0070.0000.0000.0000.000
107A113SER0-0.008-0.00223.4770.0060.0060.0000.0000.0000.000
108A114LEU00.0520.02120.706-0.010-0.0100.0000.0000.0000.000
109A115THR0-0.063-0.04324.8110.0090.0090.0000.0000.0000.000
110A116VAL00.0350.01624.379-0.007-0.0070.0000.0000.0000.000
111A117GLN00.0210.00027.3870.0040.0040.0000.0000.0000.000
112A118GLY0-0.011-0.00330.4170.0050.0050.0000.0000.0000.000
113A119LYS10.9170.96531.0780.0590.0590.0000.0000.0000.000
114A120GLN00.000-0.00429.081-0.003-0.0030.0000.0000.0000.000
115A121HIS10.7900.88126.7710.0660.0660.0000.0000.0000.000
116A122VAL0-0.015-0.01827.010-0.005-0.0050.0000.0000.0000.000
117A123VAL00.0280.03224.4670.0030.0030.0000.0000.0000.000
118A124SER0-0.005-0.02425.985-0.004-0.0040.0000.0000.0000.000
119A125VAL0-0.032-0.01721.7760.0020.0020.0000.0000.0000.000
120A126GLU-1-0.834-0.94325.222-0.002-0.0020.0000.0000.0000.000
121A127GLU-1-0.882-0.93426.8110.0230.0230.0000.0000.0000.000
122A128ALA00.0080.02224.4240.0050.0050.0000.0000.0000.000
123A129LEU0-0.035-0.00426.204-0.004-0.0040.0000.0000.0000.000
124A130LEU00.012-0.00422.4900.0050.0050.0000.0000.0000.000
125A131ALA0-0.0350.00426.3720.0030.0030.0000.0000.0000.000
126A132THR00.0510.00628.430-0.001-0.0010.0000.0000.0000.000
127A133GLY0-0.070-0.03330.5870.0000.0000.0000.0000.0000.000
128A134GLN0-0.019-0.02429.6210.0030.0030.0000.0000.0000.000
129A135TRP0-0.040-0.02122.934-0.003-0.0030.0000.0000.0000.000
130A136LYS10.8430.93223.525-0.050-0.0500.0000.0000.0000.000
131A137SER0-0.034-0.02817.8220.0030.0030.0000.0000.0000.000
132A138ILE0-0.007-0.00317.232-0.002-0.0020.0000.0000.0000.000
133A139THR00.0230.00812.1160.0130.0130.0000.0000.0000.000
134A140LEU0-0.0200.00114.6840.0070.0070.0000.0000.0000.000
135A141PHE0-0.004-0.01110.087-0.011-0.0110.0000.0000.0000.000
136A142VAL00.0120.00113.1620.0200.0200.0000.0000.0000.000
137A143GLN0-0.014-0.00211.023-0.046-0.0460.0000.0000.0000.000
138A144GLU-1-0.824-0.90614.891-0.105-0.1050.0000.0000.0000.000
139A145ASP-1-0.821-0.90417.566-0.062-0.0620.0000.0000.0000.000
140A146ARG10.8750.94317.2220.0560.0560.0000.0000.0000.000
141A147ALA00.002-0.00417.779-0.013-0.0130.0000.0000.0000.000
142A148GLN00.0080.00816.5750.0200.0200.0000.0000.0000.000
143A149LEU0-0.009-0.01416.968-0.010-0.0100.0000.0000.0000.000
144A150TYR00.0160.00015.5870.0140.0140.0000.0000.0000.000
145A151ILE0-0.041-0.02618.296-0.006-0.0060.0000.0000.0000.000
146A152ASP-1-0.828-0.92920.0170.0710.0710.0000.0000.0000.000
147A153CYS0-0.126-0.04214.425-0.009-0.0090.0000.0000.0000.000
148A154GLU-1-0.860-0.91520.9980.0750.0750.0000.0000.0000.000
149A155LYS10.8160.91222.612-0.035-0.0350.0000.0000.0000.000
150A156MET0-0.018-0.00519.4640.0100.0100.0000.0000.0000.000
151A157GLU-1-0.815-0.89321.8130.0260.0260.0000.0000.0000.000
152A158ASN0-0.012-0.02621.078-0.003-0.0030.0000.0000.0000.000
153A159ALA0-0.011-0.00322.0770.0000.0000.0000.0000.0000.000
154A160GLU-1-0.920-0.95322.308-0.028-0.0280.0000.0000.0000.000
155A161LEU0-0.062-0.03319.773-0.001-0.0010.0000.0000.0000.000
156A162ASP-1-0.838-0.90324.103-0.051-0.0510.0000.0000.0000.000
157A163VAL0-0.042-0.02523.635-0.001-0.0010.0000.0000.0000.000
158A164PRO00.0230.02119.645-0.002-0.0020.0000.0000.0000.000
159A165ILE00.0310.03915.606-0.008-0.0080.0000.0000.0000.000
160A166GLN00.011-0.03415.603-0.011-0.0110.0000.0000.0000.000
161A167SER0-0.082-0.05617.393-0.004-0.0040.0000.0000.0000.000
162A168VAL0-0.021-0.01020.2620.0070.0070.0000.0000.0000.000
163A169PHE0-0.033-0.00216.009-0.001-0.0010.0000.0000.0000.000
164A170THR00.034-0.00417.552-0.024-0.0240.0000.0000.0000.000
165A171ARG10.9610.95518.4190.1650.1650.0000.0000.0000.000
166A172ASP-1-0.826-0.88419.694-0.150-0.1500.0000.0000.0000.000
167A173LEU0-0.0310.01519.4410.0150.0150.0000.0000.0000.000
168A174ALA00.0410.01819.4130.0160.0160.0000.0000.0000.000
169A175SER0-0.039-0.02921.5400.0150.0150.0000.0000.0000.000
170A176ILE00.000-0.00225.0020.0130.0130.0000.0000.0000.000
171A177ALA0-0.018-0.00523.3340.0110.0110.0000.0000.0000.000
172A178ARG10.8530.88621.9570.0950.0950.0000.0000.0000.000
173A179LEU00.0120.03116.3150.0090.0090.0000.0000.0000.000
174A180ARG10.7700.86220.4710.0750.0750.0000.0000.0000.000
175A181ILE00.0570.01418.728-0.005-0.0050.0000.0000.0000.000
176A182ALA0-0.028-0.02222.0660.0060.0060.0000.0000.0000.000
177A183LYS10.8500.91924.9510.0630.0630.0000.0000.0000.000
178A184GLY00.008-0.01426.029-0.008-0.0080.0000.0000.0000.000
179A185GLY0-0.0180.00128.4100.0050.0050.0000.0000.0000.000
180A186VAL0-0.012-0.00931.078-0.001-0.0010.0000.0000.0000.000
181A187ASN0-0.004-0.01434.2320.0030.0030.0000.0000.0000.000
182A188ASP-1-0.779-0.82630.227-0.026-0.0260.0000.0000.0000.000
183A189ASN00.0730.03828.898-0.007-0.0070.0000.0000.0000.000
184A190PHE0-0.049-0.02825.5520.0050.0050.0000.0000.0000.000
185A191GLN00.0350.01227.9420.0020.0020.0000.0000.0000.000
186A192GLY00.012-0.00828.5380.0040.0040.0000.0000.0000.000
187A193VAL0-0.090-0.02725.485-0.003-0.0030.0000.0000.0000.000
188A194LEU00.0320.02321.3460.0020.0020.0000.0000.0000.000
189A195GLN00.013-0.02319.1880.0010.0010.0000.0000.0000.000
190A196ASN0-0.012-0.02815.014-0.013-0.0130.0000.0000.0000.000
191A197VAL0-0.0080.01014.6360.0020.0020.0000.0000.0000.000
192A198ARG10.8500.90610.359-0.098-0.0980.0000.0000.0000.000
193A199PHE00.0330.0269.8370.0450.0450.0000.0000.0000.000
194A200VAL0-0.040-0.0274.401-0.0180.020-0.001-0.004-0.0330.000
195A201PHE0-0.019-0.0014.0730.2160.356-0.001-0.053-0.0860.000
196A202GLY00.008-0.0122.235-5.012-4.2144.125-2.636-2.287-0.023
197A203THR0-0.079-0.0383.2970.4710.6640.0260.295-0.514-0.002
198A204THR0-0.017-0.0315.300-0.249-0.262-0.001-0.0030.0170.000
199A205PRO00.0400.0039.0040.0500.0500.0000.0000.0000.000
200A206GLU-1-0.852-0.89711.9040.2520.2520.0000.0000.0000.000
201A207ASP-1-0.767-0.8558.1910.6910.6910.0000.0000.0000.000
202A208ILE00.0110.0137.4920.0340.0340.0000.0000.0000.000
203A209LEU00.0180.01210.949-0.017-0.0170.0000.0000.0000.000
204A210ARG10.8150.89013.790-0.286-0.2860.0000.0000.0000.000
205A211ASN0-0.074-0.03910.451-0.034-0.0340.0000.0000.0000.000
206A212LYS10.8550.91113.704-0.219-0.2190.0000.0000.0000.000
207A213GLY00.0310.01613.429-0.019-0.0190.0000.0000.0000.000
208A215SER00.0230.00416.412-0.010-0.0100.0000.0000.0000.000