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: LNZJ9

Calculation Name: 2O8V-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2O8V

Chain ID: A

ChEMBL ID:

UniProt ID: P17854

Base Structure: X-ray

Registration Date: 2023-09-21

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 229
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2844938.113008
FMO2-HF: Nuclear repulsion 2754809.029366
FMO2-HF: Total energy -90129.083642
FMO2-MP2: Total energy -90398.457442


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:2:SER)


Summations of interaction energy for fragment #1(A:2:SER)
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.
1.0212.278-0.009-0.504-0.7440.002
Interaction energy analysis for fragmet #1(A:2:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.029 / q_NPA : -0.021
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].
3A4LEU00.0230.0113.8110.0921.349-0.009-0.504-0.7440.002
4A5ASP-1-0.814-0.9086.0561.7561.7560.0000.0000.0000.000
5A6LEU0-0.025-0.0248.260-0.349-0.3490.0000.0000.0000.000
6A7ASN0-0.052-0.03311.855-0.130-0.1300.0000.0000.0000.000
7A8ALA00.0780.04810.394-0.061-0.0610.0000.0000.0000.000
8A9LEU0-0.020-0.0139.995-0.125-0.1250.0000.0000.0000.000
9A10ASN0-0.084-0.05113.177-0.121-0.1210.0000.0000.0000.000
10A11GLU-1-0.956-0.95115.4500.2420.2420.0000.0000.0000.000
11A12LEU00.0050.00513.080-0.041-0.0410.0000.0000.0000.000
12A13PRO00.0150.01217.2320.0090.0090.0000.0000.0000.000
13A14LYS10.9560.96818.9160.0220.0220.0000.0000.0000.000
14A15VAL00.006-0.00920.365-0.015-0.0150.0000.0000.0000.000
15A16ASP-1-0.775-0.90116.907-0.108-0.1080.0000.0000.0000.000
16A17ARG10.8880.96515.296-0.108-0.1080.0000.0000.0000.000
17A18ILE0-0.058-0.03615.554-0.044-0.0440.0000.0000.0000.000
18A19LEU0-0.0010.00117.394-0.029-0.0290.0000.0000.0000.000
19A20ALA00.0480.02811.968-0.049-0.0490.0000.0000.0000.000
20A21LEU0-0.009-0.02112.223-0.097-0.0970.0000.0000.0000.000
21A22ALA0-0.0260.00113.522-0.045-0.0450.0000.0000.0000.000
22A23GLU-1-0.926-0.95712.080-0.662-0.6620.0000.0000.0000.000
23A24THR0-0.016-0.0039.483-0.131-0.1310.0000.0000.0000.000
24A25ASN0-0.013-0.03311.4940.0470.0470.0000.0000.0000.000
25A26ALA00.0120.01714.9090.0350.0350.0000.0000.0000.000
26A27GLU-1-0.860-0.91811.873-0.617-0.6170.0000.0000.0000.000
27A28LEU0-0.003-0.00111.8540.0530.0530.0000.0000.0000.000
28A29GLU-1-0.845-0.89415.226-0.170-0.1700.0000.0000.0000.000
29A30LYS10.7970.88915.9970.5620.5620.0000.0000.0000.000
30A31LEU0-0.0380.00413.6930.0150.0150.0000.0000.0000.000
31A32ASP-1-0.818-0.90718.331-0.205-0.2050.0000.0000.0000.000
32A33ALA0-0.036-0.03419.324-0.012-0.0120.0000.0000.0000.000
33A34GLU-1-0.850-0.94819.841-0.107-0.1070.0000.0000.0000.000
34A35GLY00.0330.02216.9700.0060.0060.0000.0000.0000.000
35A36ARG10.7500.83615.1460.1980.1980.0000.0000.0000.000
36A37VAL0-0.016-0.00814.9340.0100.0100.0000.0000.0000.000
37A38ALA00.0140.00915.0680.0430.0430.0000.0000.0000.000
38A39TRP00.0050.0007.9940.1630.1630.0000.0000.0000.000
39A40ALA0-0.001-0.01110.5520.0110.0110.0000.0000.0000.000
40A41LEU0-0.045-0.02912.1100.1210.1210.0000.0000.0000.000
41A42ASP-1-0.857-0.9008.5411.1841.1840.0000.0000.0000.000
42A43ASN0-0.034-0.0226.100-0.523-0.5230.0000.0000.0000.000
43A44LEU0-0.051-0.0156.960-0.045-0.0450.0000.0000.0000.000
44A45PRO00.014-0.0039.4090.1230.1230.0000.0000.0000.000
45A46GLY00.014-0.00311.090-0.162-0.1620.0000.0000.0000.000
46A47GLU-1-0.826-0.90914.3480.3000.3000.0000.0000.0000.000
47A48TYR00.0360.02311.806-0.040-0.0400.0000.0000.0000.000
48A49VAL0-0.0050.00418.428-0.022-0.0220.0000.0000.0000.000
49A50LEU00.0100.00721.592-0.019-0.0190.0000.0000.0000.000
50A51SER0-0.0130.01724.1150.0000.0000.0000.0000.0000.000
51A52SER0-0.0130.00026.810-0.017-0.0170.0000.0000.0000.000
52A53SER0-0.018-0.01329.7070.0050.0050.0000.0000.0000.000
53A54PHE00.030-0.00331.972-0.001-0.0010.0000.0000.0000.000
54A55GLY00.0440.02534.4780.0000.0000.0000.0000.0000.000
55A56ILE00.009-0.01636.4480.0010.0010.0000.0000.0000.000
56A57GLN00.0680.02831.795-0.003-0.0030.0000.0000.0000.000
57A58ALA0-0.0130.01831.338-0.003-0.0030.0000.0000.0000.000
58A59ALA00.0540.02130.7780.0010.0010.0000.0000.0000.000
59A60VAL00.0080.01828.1490.0000.0000.0000.0000.0000.000
60A61SER00.0250.00525.946-0.001-0.0010.0000.0000.0000.000
61A62LEU0-0.0090.00326.0560.0040.0040.0000.0000.0000.000
62A63HIS00.0390.01527.3500.0120.0120.0000.0000.0000.000
63A64LEU0-0.035-0.00222.5400.0040.0040.0000.0000.0000.000
64A65VAL00.018-0.01521.219-0.001-0.0010.0000.0000.0000.000
65A66ASN0-0.0100.00122.8280.0230.0230.0000.0000.0000.000
66A67GLN0-0.054-0.01424.8320.0080.0080.0000.0000.0000.000
67A68ILE0-0.060-0.02718.8340.0010.0010.0000.0000.0000.000
68A69ARG10.8830.94116.953-0.243-0.2430.0000.0000.0000.000
69A70PRO00.0360.01221.6610.0040.0040.0000.0000.0000.000
70A71ASP-1-0.892-0.94024.2180.1160.1160.0000.0000.0000.000
71A72ILE0-0.0190.01520.8380.0230.0230.0000.0000.0000.000
72A73PRO00.011-0.01922.710-0.017-0.0170.0000.0000.0000.000
73A74VAL00.0240.02525.286-0.003-0.0030.0000.0000.0000.000
74A75ILE0-0.040-0.02025.012-0.001-0.0010.0000.0000.0000.000
75A76LEU00.0130.00228.950-0.011-0.0110.0000.0000.0000.000
76A77THR0-0.026-0.01631.1880.0040.0040.0000.0000.0000.000
77A78ASP-1-0.855-0.90733.8360.0430.0430.0000.0000.0000.000
78A79THR0-0.024-0.05237.5410.0030.0030.0000.0000.0000.000
79A80GLY00.0150.02339.4510.0010.0010.0000.0000.0000.000
80A81TYR0-0.104-0.06942.657-0.002-0.0020.0000.0000.0000.000
81A82LEU00.0130.01037.956-0.004-0.0040.0000.0000.0000.000
82A83PHE00.009-0.00442.631-0.001-0.0010.0000.0000.0000.000
83A84PRO00.0390.01943.7640.0020.0020.0000.0000.0000.000
84A85GLU-1-0.813-0.92545.0070.0160.0160.0000.0000.0000.000
85A86THR0-0.035-0.00839.045-0.003-0.0030.0000.0000.0000.000
86A87TYR0-0.018-0.02440.157-0.001-0.0010.0000.0000.0000.000
87A88ARG10.9500.96840.963-0.017-0.0170.0000.0000.0000.000
88A89PHE00.0440.02636.436-0.001-0.0010.0000.0000.0000.000
89A90ILE0-0.023-0.01735.795-0.001-0.0010.0000.0000.0000.000
90A91ASP-1-0.924-0.96237.2460.0430.0430.0000.0000.0000.000
91A92GLU-1-0.983-0.96739.6740.0100.0100.0000.0000.0000.000
92A93LEU0-0.025-0.02934.414-0.002-0.0020.0000.0000.0000.000
93A94THR0-0.052-0.03933.6470.0010.0010.0000.0000.0000.000
94A95ASP-1-0.870-0.90834.9090.0400.0400.0000.0000.0000.000
95A96LYS10.9380.97436.240-0.001-0.0010.0000.0000.0000.000
96A97LEU0-0.095-0.07631.068-0.003-0.0030.0000.0000.0000.000
97A98LYS10.8400.92831.281-0.030-0.0300.0000.0000.0000.000
98A99LEU00.0010.00829.0300.0030.0030.0000.0000.0000.000
99A100ASN00.0380.03226.416-0.003-0.0030.0000.0000.0000.000
100A101LEU0-0.018-0.01929.0130.0070.0070.0000.0000.0000.000
101A102LYS10.8430.92427.775-0.126-0.1260.0000.0000.0000.000
102A103VAL00.0220.00931.236-0.004-0.0040.0000.0000.0000.000
103A104TYR0-0.074-0.06629.5930.0050.0050.0000.0000.0000.000
104A105ARG10.9881.00534.087-0.082-0.0820.0000.0000.0000.000
105A106ALA00.0210.00236.7330.0060.0060.0000.0000.0000.000
106A107THR0-0.0050.00438.4060.0030.0030.0000.0000.0000.000
107A108GLU-1-0.785-0.87839.8070.0650.0650.0000.0000.0000.000
108A109SER00.020-0.00842.633-0.001-0.0010.0000.0000.0000.000
109A110ALA00.0820.03844.945-0.001-0.0010.0000.0000.0000.000
110A111ALA00.0450.02046.695-0.001-0.0010.0000.0000.0000.000
111A112TRP0-0.018-0.00845.7690.0000.0000.0000.0000.0000.000
112A113GLN00.004-0.00841.920-0.003-0.0030.0000.0000.0000.000
113A114GLU-1-0.822-0.89847.0640.0290.0290.0000.0000.0000.000
114A115ALA0-0.0220.00750.281-0.002-0.0020.0000.0000.0000.000
115A116ARG10.7890.90243.274-0.061-0.0610.0000.0000.0000.000
116A117TYR0-0.072-0.05643.7770.0000.0000.0000.0000.0000.000
117A118GLY00.0400.02349.384-0.002-0.0020.0000.0000.0000.000
118A119LYS10.9010.95049.057-0.021-0.0210.0000.0000.0000.000
119A120LEU0-0.009-0.00543.914-0.002-0.0020.0000.0000.0000.000
120A121TRP0-0.030-0.01746.0780.0000.0000.0000.0000.0000.000
121A122GLU-1-0.883-0.95247.2200.0170.0170.0000.0000.0000.000
122A123GLN0-0.086-0.03448.4920.0000.0000.0000.0000.0000.000
123A124GLY00.0320.02248.0280.0010.0010.0000.0000.0000.000
124A125VAL00.024-0.00342.9070.0010.0010.0000.0000.0000.000
125A126GLU-1-0.776-0.88642.7370.0240.0240.0000.0000.0000.000
126A127GLY0-0.0020.01343.0680.0040.0040.0000.0000.0000.000
127A128ILE0-0.009-0.02140.9900.0030.0030.0000.0000.0000.000
128A129GLU-1-0.957-0.97138.5270.0280.0280.0000.0000.0000.000
129A130LYS10.8740.95038.725-0.051-0.0510.0000.0000.0000.000
130A131TYR0-0.020-0.03240.1930.0050.0050.0000.0000.0000.000
131A132ASN00.037-0.01236.3980.0050.0050.0000.0000.0000.000
132A133ASP-1-0.914-0.95135.2140.0720.0720.0000.0000.0000.000
133A134ILE00.0010.00235.3480.0070.0070.0000.0000.0000.000
134A135ASN0-0.066-0.03637.5520.0050.0050.0000.0000.0000.000
135A136LYS10.8500.93433.559-0.034-0.0340.0000.0000.0000.000
136A137VAL0-0.034-0.02130.3980.0070.0070.0000.0000.0000.000
137A138GLU-1-0.769-0.84830.6470.1160.1160.0000.0000.0000.000
138A139PRO00.0470.02031.3150.0110.0110.0000.0000.0000.000
139A140MET0-0.0090.00526.8760.0130.0130.0000.0000.0000.000
140A141ASN0-0.128-0.08426.6800.0230.0230.0000.0000.0000.000
141A142ARG10.8110.89526.850-0.091-0.0910.0000.0000.0000.000
142A143ALA00.0340.02227.6520.0140.0140.0000.0000.0000.000
143A144LEU0-0.044-0.03321.7140.0130.0130.0000.0000.0000.000
144A145LYS10.9450.97222.835-0.187-0.1870.0000.0000.0000.000
145A146GLU-1-0.845-0.89624.3460.1730.1730.0000.0000.0000.000
146A147LEU0-0.044-0.02723.7050.0060.0060.0000.0000.0000.000
147A148ASN0-0.062-0.02820.1240.0350.0350.0000.0000.0000.000
148A149ALA0-0.0110.00918.8110.0470.0470.0000.0000.0000.000
149A150GLN0-0.061-0.02914.1390.0120.0120.0000.0000.0000.000
150A151THR0-0.0210.01014.034-0.057-0.0570.0000.0000.0000.000
151A152TRP0-0.021-0.04216.281-0.002-0.0020.0000.0000.0000.000
152A153PHE00.0240.02116.258-0.033-0.0330.0000.0000.0000.000
153A154ALA00.001-0.01420.8550.0120.0120.0000.0000.0000.000
154A155GLY00.009-0.00723.690-0.018-0.0180.0000.0000.0000.000
155A156LEU0-0.077-0.03225.2470.0020.0020.0000.0000.0000.000
156A157ARG10.8640.91425.8020.0450.0450.0000.0000.0000.000
157A158ARG10.7300.83021.4590.1760.1760.0000.0000.0000.000
158A159GLU-1-0.818-0.89328.508-0.065-0.0650.0000.0000.0000.000
159A160GLN0-0.038-0.00630.2520.0010.0010.0000.0000.0000.000
160A161SER0-0.0290.00132.8270.0040.0040.0000.0000.0000.000
161A162GLY00.0640.00132.305-0.003-0.0030.0000.0000.0000.000
162A163SER0-0.009-0.00626.8970.0070.0070.0000.0000.0000.000
163A164ARG11.0211.01627.1780.0980.0980.0000.0000.0000.000
164A165ALA00.0620.03024.9630.0020.0020.0000.0000.0000.000
165A166ASN0-0.053-0.02624.395-0.015-0.0150.0000.0000.0000.000
166A167LEU0-0.062-0.03223.1700.0120.0120.0000.0000.0000.000
167A168PRO0-0.026-0.00618.100-0.005-0.0050.0000.0000.0000.000
168A169VAL00.0640.03716.9900.0310.0310.0000.0000.0000.000
169A170LEU00.0060.02611.7400.0360.0360.0000.0000.0000.000
170A171ALA0-0.002-0.02316.267-0.013-0.0130.0000.0000.0000.000
171A172ILE00.0360.03813.4750.0230.0230.0000.0000.0000.000
172A173GLN0-0.054-0.00717.801-0.016-0.0160.0000.0000.0000.000
173A174ARG10.9390.96321.427-0.101-0.1010.0000.0000.0000.000
174A175GLY00.0220.01917.9850.0170.0170.0000.0000.0000.000
175A176VAL0-0.009-0.00316.8560.0430.0430.0000.0000.0000.000
176A177PHE00.047-0.00310.241-0.083-0.0830.0000.0000.0000.000
177A178LYS10.8020.91715.686-0.011-0.0110.0000.0000.0000.000
178A179VAL00.0500.00815.482-0.041-0.0410.0000.0000.0000.000
179A180LEU0-0.071-0.04218.1870.0320.0320.0000.0000.0000.000
180A181PRO00.0790.04119.691-0.024-0.0240.0000.0000.0000.000
181A182ILE0-0.0230.01120.821-0.018-0.0180.0000.0000.0000.000
182A183ILE00.003-0.01121.3000.0130.0130.0000.0000.0000.000
183A184ASP-1-0.829-0.89123.422-0.167-0.1670.0000.0000.0000.000
184A185TRP0-0.011-0.00124.7340.0150.0150.0000.0000.0000.000
185A186ASP-1-0.744-0.85928.138-0.079-0.0790.0000.0000.0000.000
186A187ASN0-0.018-0.03331.8720.0070.0070.0000.0000.0000.000
187A188ARG10.9030.97634.9200.0770.0770.0000.0000.0000.000
188A189THR00.014-0.01328.9060.0020.0020.0000.0000.0000.000
189A190ILE0-0.031-0.00829.7900.0030.0030.0000.0000.0000.000
190A191TYR0-0.0100.00532.6150.0060.0060.0000.0000.0000.000
191A192GLN00.011-0.01534.0630.0030.0030.0000.0000.0000.000
192A193TYR0-0.0010.01127.7540.0000.0000.0000.0000.0000.000
193A194LEU0-0.005-0.01832.6640.0050.0050.0000.0000.0000.000
194A195GLN0-0.028-0.00835.2850.0010.0010.0000.0000.0000.000
195A196LYS10.9270.96430.3200.0850.0850.0000.0000.0000.000
196A197HIS00.0290.02129.0730.0060.0060.0000.0000.0000.000
197A198GLY0-0.0100.01434.4410.0060.0060.0000.0000.0000.000
198A199LEU0-0.100-0.04032.0970.0060.0060.0000.0000.0000.000
199A200LYS10.9520.96136.8250.0120.0120.0000.0000.0000.000
200A201TYR00.0430.01436.8860.0000.0000.0000.0000.0000.000
201A202HIS0-0.0060.00438.7960.0000.0000.0000.0000.0000.000
202A203PRO00.035-0.00340.423-0.002-0.0020.0000.0000.0000.000
203A204LEU00.0050.00943.507-0.001-0.0010.0000.0000.0000.000
204A205TRP0-0.062-0.03240.805-0.002-0.0020.0000.0000.0000.000
205A206ASP-1-0.952-0.96943.447-0.018-0.0180.0000.0000.0000.000
206A207GLU-1-0.913-0.95846.3100.0020.0020.0000.0000.0000.000
207A208GLY0-0.024-0.02147.1970.0000.0000.0000.0000.0000.000
208A209TYR0-0.101-0.04544.478-0.001-0.0010.0000.0000.0000.000
209A210LEU00.0460.03941.763-0.001-0.0010.0000.0000.0000.000
210A211SER0-0.015-0.03738.641-0.003-0.0030.0000.0000.0000.000
211A212VAL00.0470.03639.6280.0020.0020.0000.0000.0000.000
212A213GLY0-0.021-0.03739.004-0.001-0.0010.0000.0000.0000.000
213A214ASP-1-0.736-0.80739.9800.0330.0330.0000.0000.0000.000
214A215THR00.0330.00542.515-0.003-0.0030.0000.0000.0000.000
215A216HIS10.8170.89143.490-0.029-0.0290.0000.0000.0000.000
216A217THR00.0480.03947.3430.0010.0010.0000.0000.0000.000
217A218THR0-0.062-0.02242.1110.0010.0010.0000.0000.0000.000
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