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

tag_button

FMODB ID: J3YJ9

Calculation Name: 2OZV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2OZV

Chain ID: A

ChEMBL ID:

UniProt ID: Q7D120

Base Structure: X-ray

Registration Date: 2023-03-13

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 -2296017.364374
FMO2-HF: Nuclear repulsion 2216223.207142
FMO2-HF: Total energy -79794.157233
FMO2-MP2: Total energy -80023.554763


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:31:MET)


Summations of interaction energy for fragment #1(A:31:MET)
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.
-9.574-4.1554.79-2.183-8.027-0.003
Interaction energy analysis for fragmet #1(A:31:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.044 / q_NPA : 0.012
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].
3A33ALA00.0090.0063.491-1.281-0.0220.003-0.405-0.8570.002
4A34MET00.0560.0343.5430.2750.8660.010-0.114-0.4880.000
5A35LEU0-0.007-0.0122.4760.4611.3871.581-0.448-2.059-0.001
6A36LEU0-0.0080.0105.5590.8160.8160.0000.0000.0000.000
7A37ALA00.0400.0177.9420.3010.3010.0000.0000.0000.000
8A38SER0-0.049-0.0278.5150.3150.3150.0000.0000.0000.000
9A39LEU0-0.016-0.0139.7860.2030.2030.0000.0000.0000.000
10A40VAL00.0100.02512.2480.1200.1200.0000.0000.0000.000
11A41ALA0-0.0030.00215.210-0.062-0.0620.0000.0000.0000.000
12A42ASP-1-0.820-0.91617.217-0.180-0.1800.0000.0000.0000.000
13A43ASP-1-0.903-0.94019.985-0.406-0.4060.0000.0000.0000.000
14A44ARG10.8670.93222.1360.1930.1930.0000.0000.0000.000
15A45ALA00.0120.01123.323-0.019-0.0190.0000.0000.0000.000
16A46CYS0-0.084-0.03521.4250.0090.0090.0000.0000.0000.000
17A47ARG10.9170.96622.8020.0950.0950.0000.0000.0000.000
18A48ILE0-0.014-0.02216.4570.0070.0070.0000.0000.0000.000
19A49ALA00.0220.02719.2850.0040.0040.0000.0000.0000.000
20A50ASP-1-0.806-0.92912.771-0.212-0.2120.0000.0000.0000.000
21A51LEU0-0.055-0.04116.0790.0310.0310.0000.0000.0000.000
22A52GLY00.0860.08314.0940.0430.0430.0000.0000.0000.000
23A53ALA0-0.035-0.05112.933-0.033-0.0330.0000.0000.0000.000
24A54GLY0-0.029-0.03010.9860.0550.0550.0000.0000.0000.000
25A55ALA00.0440.03211.522-0.031-0.0310.0000.0000.0000.000
26A56GLY00.0920.03412.655-0.052-0.0520.0000.0000.0000.000
27A57ALA0-0.021-0.0067.196-0.081-0.0810.0000.0000.0000.000
28A58ALA0-0.007-0.0048.572-0.256-0.2560.0000.0000.0000.000
29A59GLY00.0830.0289.374-0.090-0.0900.0000.0000.0000.000
30A60MET0-0.031-0.01211.1670.0100.0100.0000.0000.0000.000
31A61ALA00.0140.0108.374-0.027-0.0270.0000.0000.0000.000
32A62VAL0-0.052-0.02510.5030.0090.0090.0000.0000.0000.000
33A63ALA00.0220.01413.3450.0400.0400.0000.0000.0000.000
34A64ALA0-0.0390.00112.7630.0480.0480.0000.0000.0000.000
35A65ARG10.8400.92012.1050.8300.8300.0000.0000.0000.000
36A66LEU0-0.027-0.00315.2560.0530.0530.0000.0000.0000.000
37A67GLU-1-0.856-0.93818.190-0.264-0.2640.0000.0000.0000.000
38A68LYS10.8370.90721.0260.3180.3180.0000.0000.0000.000
39A69ALA0-0.0200.00318.8060.0270.0270.0000.0000.0000.000
40A70GLU-1-0.912-0.95020.793-0.151-0.1510.0000.0000.0000.000
41A71VAL0-0.024-0.02215.8480.0030.0030.0000.0000.0000.000
42A72THR00.0200.01919.2930.0120.0120.0000.0000.0000.000
43A73LEU0-0.023-0.01014.630-0.006-0.0060.0000.0000.0000.000
44A74TYR0-0.005-0.03817.9140.0100.0100.0000.0000.0000.000
45A75GLU-1-0.855-0.93016.0280.1130.1130.0000.0000.0000.000
46A76ARG10.8500.92119.730-0.184-0.1840.0000.0000.0000.000
47A77SER0-0.025-0.01621.592-0.014-0.0140.0000.0000.0000.000
48A78GLN00.1000.04422.4640.0020.0020.0000.0000.0000.000
49A79GLU-1-0.979-0.98121.3920.1490.1490.0000.0000.0000.000
50A80MET0-0.020-0.00215.3510.0170.0170.0000.0000.0000.000
51A81ALA00.0550.02618.585-0.020-0.0200.0000.0000.0000.000
52A82GLU-1-0.837-0.90820.544-0.037-0.0370.0000.0000.0000.000
53A83PHE0-0.046-0.02013.962-0.015-0.0150.0000.0000.0000.000
54A84ALA00.0180.00316.090-0.023-0.0230.0000.0000.0000.000
55A85ARG10.7480.83617.082-0.021-0.0210.0000.0000.0000.000
56A86ARG10.8150.87919.7290.0260.0260.0000.0000.0000.000
57A87SER0-0.029-0.00513.628-0.033-0.0330.0000.0000.0000.000
58A88LEU0-0.001-0.01615.967-0.050-0.0500.0000.0000.0000.000
59A89GLU-1-0.870-0.90018.058-0.090-0.0900.0000.0000.0000.000
60A90LEU0-0.048-0.01215.7660.0060.0060.0000.0000.0000.000
61A91PRO0-0.003-0.02119.242-0.025-0.0250.0000.0000.0000.000
62A92ASP-1-0.948-0.97214.396-0.466-0.4660.0000.0000.0000.000
63A93ASN0-0.019-0.01214.141-0.119-0.1190.0000.0000.0000.000
64A94ALA0-0.004-0.00716.9830.0060.0060.0000.0000.0000.000
65A95ALA0-0.053-0.01818.3790.0150.0150.0000.0000.0000.000
66A96PHE00.017-0.00913.5980.0080.0080.0000.0000.0000.000
67A97SER00.0320.02818.8480.0130.0130.0000.0000.0000.000
68A98ALA00.0030.00219.7150.0190.0190.0000.0000.0000.000
69A99ARG10.7870.89218.6760.3700.3700.0000.0000.0000.000
70A100ILE0-0.043-0.01615.707-0.014-0.0140.0000.0000.0000.000
71A101GLU-1-0.912-0.94419.952-0.069-0.0690.0000.0000.0000.000
72A102VAL0-0.034-0.00618.480-0.002-0.0020.0000.0000.0000.000
73A103LEU00.0000.00321.0420.0110.0110.0000.0000.0000.000
74A104GLU-1-0.814-0.89922.1770.0310.0310.0000.0000.0000.000
75A105ALA00.0190.00023.435-0.005-0.0050.0000.0000.0000.000
76A106ASP-1-0.800-0.87123.2040.1530.1530.0000.0000.0000.000
77A107VAL00.0480.01919.987-0.008-0.0080.0000.0000.0000.000
78A108THR0-0.085-0.05223.0080.0020.0020.0000.0000.0000.000
79A109LEU0-0.0130.00525.117-0.001-0.0010.0000.0000.0000.000
80A110ARG10.8980.93828.058-0.116-0.1160.0000.0000.0000.000
81A111ALA0-0.006-0.01530.730-0.004-0.0040.0000.0000.0000.000
82A112LYS10.9990.99732.852-0.027-0.0270.0000.0000.0000.000
83A113ALA00.0660.05632.718-0.004-0.0040.0000.0000.0000.000
84A114ARG10.8390.90827.082-0.033-0.0330.0000.0000.0000.000
85A115VAL00.0260.00929.673-0.005-0.0050.0000.0000.0000.000
86A116GLU-1-0.958-0.98731.6930.0200.0200.0000.0000.0000.000
87A117ALA0-0.041-0.01428.328-0.002-0.0020.0000.0000.0000.000
88A118GLY00.0400.03027.922-0.001-0.0010.0000.0000.0000.000
89A119LEU0-0.067-0.00923.200-0.009-0.0090.0000.0000.0000.000
90A120PRO0-0.003-0.00426.6610.0090.0090.0000.0000.0000.000
91A121ASP-1-0.820-0.91528.2910.0080.0080.0000.0000.0000.000
92A122GLU-1-0.964-0.97728.540-0.022-0.0220.0000.0000.0000.000
93A123HIS00.0300.01726.071-0.003-0.0030.0000.0000.0000.000
94A124PHE00.0200.00622.397-0.012-0.0120.0000.0000.0000.000
95A125HIS00.0320.01722.8850.0090.0090.0000.0000.0000.000
96A126HIS0-0.022-0.03517.741-0.008-0.0080.0000.0000.0000.000
97A127VAL0-0.0090.00117.9320.0070.0070.0000.0000.0000.000
98A128ILE0-0.021-0.01112.1710.0040.0040.0000.0000.0000.000
99A129MET0-0.024-0.00613.0000.0610.0610.0000.0000.0000.000
100A130ASN00.011-0.0197.7630.0090.0090.0000.0000.0000.000
101A131PRO00.0070.02811.0270.0750.0750.0000.0000.0000.000
102A132PRO0-0.0030.00812.5860.1230.1230.0000.0000.0000.000
103A133TYR0-0.003-0.0148.2700.0610.0610.0000.0000.0000.000
104A155GLY00.0330.01920.0610.0140.0140.0000.0000.0000.000
105A156LEU0-0.017-0.02217.917-0.035-0.0350.0000.0000.0000.000
106A157PHE00.0290.00813.132-0.031-0.0310.0000.0000.0000.000
107A158GLU-1-0.760-0.84619.2110.1040.1040.0000.0000.0000.000
108A159ASP-1-0.812-0.90422.8920.1380.1380.0000.0000.0000.000
109A160TRP00.0400.01515.307-0.010-0.0100.0000.0000.0000.000
110A161ILE00.013-0.00217.450-0.031-0.0310.0000.0000.0000.000
111A162ARG10.7240.85620.991-0.144-0.1440.0000.0000.0000.000
112A163THR0-0.029-0.03822.918-0.020-0.0200.0000.0000.0000.000
113A164ALA00.0270.00919.976-0.018-0.0180.0000.0000.0000.000
114A165SER0-0.027-0.02122.010-0.024-0.0240.0000.0000.0000.000
115A166ALA0-0.041-0.02024.753-0.011-0.0110.0000.0000.0000.000
116A167ILE00.0540.03821.920-0.006-0.0060.0000.0000.0000.000
117A168MET0-0.0630.03819.928-0.023-0.0230.0000.0000.0000.000
118A169VAL0-0.0040.00925.1080.0120.0120.0000.0000.0000.000
119A170SER00.010-0.01426.5280.0040.0040.0000.0000.0000.000
120A171GLY0-0.011-0.00426.393-0.009-0.0090.0000.0000.0000.000
121A172GLY00.0280.01523.640-0.013-0.0130.0000.0000.0000.000
122A173GLN0-0.042-0.03515.6580.0430.0430.0000.0000.0000.000
123A174LEU0-0.0050.00416.623-0.015-0.0150.0000.0000.0000.000
124A175SER00.004-0.01312.688-0.013-0.0130.0000.0000.0000.000
125A176LEU00.0110.00811.5050.0060.0060.0000.0000.0000.000
126A177ILE0-0.0160.0034.270-0.164-0.033-0.001-0.019-0.1110.000
127A178SER0-0.002-0.0098.5990.0100.0100.0000.0000.0000.000
128A179ARG10.9680.9898.574-0.670-0.6700.0000.0000.0000.000
129A180PRO00.0630.0319.555-0.225-0.2250.0000.0000.0000.000
130A181GLN00.0240.00012.577-0.049-0.0490.0000.0000.0000.000
131A182SER0-0.0140.00514.013-0.033-0.0330.0000.0000.0000.000
132A183VAL00.0130.01215.938-0.072-0.0720.0000.0000.0000.000
133A184ALA00.0190.00317.020-0.052-0.0520.0000.0000.0000.000
134A185GLU-1-0.853-0.93018.5710.3550.3550.0000.0000.0000.000
135A186ILE00.0170.00714.049-0.038-0.0380.0000.0000.0000.000
136A187ILE00.0090.00318.474-0.045-0.0450.0000.0000.0000.000
137A188ALA0-0.028-0.01421.079-0.029-0.0290.0000.0000.0000.000
138A189ALA0-0.0090.01020.564-0.023-0.0230.0000.0000.0000.000
139A190CYS0-0.033-0.00519.947-0.028-0.0280.0000.0000.0000.000
140A191GLY00.0520.03422.738-0.021-0.0210.0000.0000.0000.000
141A192SER0-0.069-0.04926.348-0.003-0.0030.0000.0000.0000.000
142A193ARG10.7600.85824.416-0.123-0.1230.0000.0000.0000.000
143A194PHE00.0170.00021.690-0.014-0.0140.0000.0000.0000.000
144A195GLY00.0520.03323.7610.0190.0190.0000.0000.0000.000
145A196GLY0-0.035-0.03122.541-0.015-0.0150.0000.0000.0000.000
146A197LEU00.0110.01518.781-0.014-0.0140.0000.0000.0000.000
147A198GLU-1-0.809-0.89416.644-0.060-0.0600.0000.0000.0000.000
148A199ILE00.000-0.00713.9910.0020.0020.0000.0000.0000.000
149A200THR00.0160.01210.955-0.066-0.0660.0000.0000.0000.000
150A201LEU0-0.0010.00910.3130.1200.1200.0000.0000.0000.000
151A202ILE00.0370.0244.173-0.608-0.2410.031-0.093-0.3060.001
152A203HIS00.001-0.0227.5770.3400.3400.0000.0000.0000.000
153A204PRO00.0030.0145.021-0.130-0.1300.0000.0000.0000.000
154A205ARG10.8890.9136.056-0.558-0.5580.0000.0000.0000.000
155A206PRO00.0160.0009.3710.1100.1100.0000.0000.0000.000
156A207GLY0-0.018-0.00212.943-0.008-0.0080.0000.0000.0000.000
157A208GLU-1-0.829-0.8859.5550.4890.4890.0000.0000.0000.000
158A209ASP-1-0.881-0.93011.9560.6060.6060.0000.0000.0000.000
159A210ALA0-0.062-0.0339.6160.1440.1440.0000.0000.0000.000
160A211VAL00.013-0.0094.9010.0010.0010.0000.0000.0000.000
161A212ARG10.7810.8624.118-3.592-3.1540.016-0.064-0.3890.000
162A213MET0-0.047-0.0137.047-0.324-0.3240.0000.0000.0000.000
163A214LEU00.0480.0326.219-0.044-0.0440.0000.0000.0000.000
164A215VAL0-0.018-0.0209.6970.0280.0280.0000.0000.0000.000
165A216THR00.0700.05013.305-0.057-0.0570.0000.0000.0000.000
166A217ALA0-0.036-0.02315.6360.0400.0400.0000.0000.0000.000
167A218ILE00.0030.01219.367-0.022-0.0220.0000.0000.0000.000
168A219LYS10.8220.90422.5390.0290.0290.0000.0000.0000.000
169A220GLY00.005-0.00224.964-0.010-0.0100.0000.0000.0000.000
170A221SER0-0.053-0.01525.1890.0030.0030.0000.0000.0000.000
171A222ARG11.0000.97927.3010.0000.0000.0000.0000.0000.000
172A223ALA0-0.0420.00325.5690.0080.0080.0000.0000.0000.000
173A224ARG10.9820.98925.005-0.057-0.0570.0000.0000.0000.000
174A225LEU00.0260.02120.657-0.012-0.0120.0000.0000.0000.000
175A226THR0-0.077-0.04420.490-0.011-0.0110.0000.0000.0000.000
176A227PHE00.0510.02116.1740.0040.0040.0000.0000.0000.000
177A228ARG10.8050.90314.9610.0790.0790.0000.0000.0000.000
178A229ALA00.008-0.00116.0100.0510.0510.0000.0000.0000.000
179A230PRO0-0.0060.00311.835-0.019-0.0190.0000.0000.0000.000
180A231LEU00.0280.0207.879-0.100-0.1000.0000.0000.0000.000
181A232ILE0-0.0070.0018.3830.3320.3320.0000.0000.0000.000
182A233MET0-0.020-0.0102.986-0.653-0.5292.474-0.468-2.131-0.002
183A234HIS10.8330.9144.4170.4570.540-0.001-0.003-0.0780.000
184A235GLU-1-0.826-0.9158.363-0.083-0.0830.0000.0000.0000.000
185A236THR00.008-0.02911.7630.0050.0050.0000.0000.0000.000
186A237GLY0-0.021-0.00113.689-0.022-0.0220.0000.0000.0000.000
187A238SER0-0.0210.00512.219-0.035-0.0350.0000.0000.0000.000
188A239HIS00.0350.00210.500-0.022-0.0220.0000.0000.0000.000
189A240ALA0-0.0080.0079.189-0.147-0.1470.0000.0000.0000.000
190A241PHE0-0.0020.0002.505-0.885-0.2750.631-0.226-1.0150.000
191A242THR00.0070.0117.6120.0450.0450.0000.0000.0000.000
192A243PRO00.0500.0129.296-0.180-0.1800.0000.0000.0000.000
193A244PHE00.0320.02411.381-0.100-0.1000.0000.0000.0000.000
194A245VAL00.0330.0054.688-0.180-0.107-0.001-0.002-0.0700.000
195A246ASP-1-0.827-0.9097.046-2.041-2.0410.0000.0000.0000.000
196A247ASP-1-0.826-0.8938.584-1.026-1.0260.0000.0000.0000.000
197A248LEU0-0.070-0.0247.156-0.051-0.0510.0000.0000.0000.000
198A249ASN0-0.066-0.0393.241-2.621-1.8040.047-0.341-0.523-0.003
199A250ASN0-0.085-0.0565.726-0.112-0.1120.0000.0000.0000.000
200A251GLY00.0050.0198.6940.2500.2500.0000.0000.0000.000
201A252ARG10.7550.84510.5991.2601.2600.0000.0000.0000.000
202A253ALA0-0.018-0.00311.9480.1490.1490.0000.0000.0000.000
203A254ALA00.0030.00811.782-0.155-0.1550.0000.0000.0000.000
204A255TYR0-0.037-0.04410.9110.0580.0580.0000.0000.0000.000
205A256ALA00.0230.01812.9590.0340.0340.0000.0000.0000.000
206A257ARG10.8540.92016.4650.0920.0920.0000.0000.0000.000
207A258ASN0-0.059-0.04118.214-0.020-0.0200.0000.0000.0000.000
208A259VAL0-0.0250.00120.999-0.005-0.0050.0000.0000.0000.000