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: V58Q1

Calculation Name: 3OFV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3OFV

Chain ID: A

ChEMBL ID:

UniProt ID: D6J9H8

Base Structure: X-ray

Registration Date: 2023-06-21

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 190
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1982528.151941
FMO2-HF: Nuclear repulsion 1911057.016615
FMO2-HF: Total energy -71471.135326
FMO2-MP2: Total energy -71682.735971


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:1:THR)


Summations of interaction energy for fragment #1(A:1:THR)
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.
-8.034-2.4320.459-2.438-3.6180.004
Interaction energy analysis for fragmet #1(A:1:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.040 / 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].
3A3LYS10.8850.9472.384-3.0100.8590.375-1.897-2.3460.007
4A4LEU0-0.023-0.0085.1720.8070.891-0.001-0.003-0.0790.000
5A5ILE00.0100.0098.700-0.353-0.3530.0000.0000.0000.000
6A6VAL0-0.021-0.01511.1050.1780.1780.0000.0000.0000.000
7A7GLY00.0360.01414.475-0.017-0.0170.0000.0000.0000.000
8A8LEU0-0.043-0.03617.3870.0320.0320.0000.0000.0000.000
9A9ALA00.0190.00320.0110.0350.0350.0000.0000.0000.000
10A10ASN0-0.0310.00423.702-0.032-0.0320.0000.0000.0000.000
11A11PRO00.0400.03126.4380.0130.0130.0000.0000.0000.000
12A12GLY00.0620.02028.0640.0040.0040.0000.0000.0000.000
13A13ALA00.005-0.01231.205-0.001-0.0010.0000.0000.0000.000
14A14GLU-1-0.911-0.93733.549-0.122-0.1220.0000.0000.0000.000
15A15TYR0-0.013-0.02429.911-0.004-0.0040.0000.0000.0000.000
16A16ALA0-0.0180.00728.562-0.006-0.0060.0000.0000.0000.000
17A17ALA0-0.011-0.00728.287-0.001-0.0010.0000.0000.0000.000
18A18THR0-0.060-0.03829.6130.0010.0010.0000.0000.0000.000
19A19ARG10.8860.92027.4120.1070.1070.0000.0000.0000.000
20A20HIS0-0.053-0.05225.296-0.019-0.0190.0000.0000.0000.000
21A21ASN0-0.011-0.00723.948-0.044-0.0440.0000.0000.0000.000
22A22ALA00.0380.03622.112-0.001-0.0010.0000.0000.0000.000
23A23GLY00.0200.00618.6760.0060.0060.0000.0000.0000.000
24A24ALA0-0.021-0.01818.6190.0000.0000.0000.0000.0000.000
25A25TRP00.0060.00820.3700.0230.0230.0000.0000.0000.000
26A26PHE0-0.0030.00212.4900.0160.0160.0000.0000.0000.000
27A27VAL00.0090.00014.7300.0330.0330.0000.0000.0000.000
28A28ASP-1-0.912-0.96416.901-0.088-0.0880.0000.0000.0000.000
29A29LEU0-0.0120.01119.0500.0390.0390.0000.0000.0000.000
30A30LEU0-0.009-0.01412.6400.0440.0440.0000.0000.0000.000
31A31ALA0-0.013-0.01516.5280.0590.0590.0000.0000.0000.000
32A32GLU-1-0.984-0.98018.0680.0860.0860.0000.0000.0000.000
33A33ARG10.8470.89718.229-0.104-0.1040.0000.0000.0000.000
34A34LEU0-0.047-0.02713.3110.0480.0480.0000.0000.0000.000
35A35ARG10.8880.95317.701-0.190-0.1900.0000.0000.0000.000
36A36ALA00.0110.01217.3400.0000.0000.0000.0000.0000.000
37A37PRO00.0090.03118.709-0.032-0.0320.0000.0000.0000.000
38A38LEU00.0290.00417.5170.0010.0010.0000.0000.0000.000
39A39ARG10.8790.95020.6570.0500.0500.0000.0000.0000.000
40A40GLU-1-0.934-0.97021.877-0.164-0.1640.0000.0000.0000.000
41A41GLU-1-0.778-0.86718.743-0.234-0.2340.0000.0000.0000.000
42A42ALA00.0540.01722.131-0.035-0.0350.0000.0000.0000.000
43A43LYS10.8050.90119.4900.2290.2290.0000.0000.0000.000
44A44PHE00.0100.00316.977-0.045-0.0450.0000.0000.0000.000
45A45PHE0-0.001-0.02420.285-0.029-0.0290.0000.0000.0000.000
46A46GLY00.0800.03520.929-0.018-0.0180.0000.0000.0000.000
47A47TYR0-0.0380.01321.1430.0260.0260.0000.0000.0000.000
48A48THR0-0.002-0.03516.754-0.030-0.0300.0000.0000.0000.000
49A49SER0-0.008-0.02916.0910.0590.0590.0000.0000.0000.000
50A50ARG10.8270.89812.689-0.414-0.4140.0000.0000.0000.000
51A51VAL00.0270.02211.3030.0260.0260.0000.0000.0000.000
52A52THR0-0.027-0.02210.946-0.036-0.0360.0000.0000.0000.000
53A53LEU00.0080.0048.322-0.161-0.1610.0000.0000.0000.000
54A54GLY00.0180.0187.9260.5180.5180.0000.0000.0000.000
55A55GLY0-0.058-0.0358.7340.2480.2480.0000.0000.0000.000
56A56GLU-1-0.804-0.8934.6982.1262.247-0.001-0.005-0.1140.000
57A57ASP-1-0.812-0.8858.0450.0870.0870.0000.0000.0000.000
58A58VAL0-0.0240.0046.251-0.022-0.0220.0000.0000.0000.000
59A59ARG10.8400.9178.4920.2410.2410.0000.0000.0000.000
60A60LEU0-0.0060.01111.007-0.183-0.1830.0000.0000.0000.000
61A61LEU00.016-0.00513.7030.0270.0270.0000.0000.0000.000
62A62VAL00.0360.02516.066-0.041-0.0410.0000.0000.0000.000
63A63PRO0-0.044-0.00818.7600.0280.0280.0000.0000.0000.000
64A64THR00.034-0.00321.1550.0200.0200.0000.0000.0000.000
65A65THR0-0.028-0.02223.1140.0090.0090.0000.0000.0000.000
66A66PHE00.0410.02025.5960.0110.0110.0000.0000.0000.000
67A67MET00.0170.03023.061-0.044-0.0440.0000.0000.0000.000
68A68ASN0-0.012-0.01324.143-0.034-0.0340.0000.0000.0000.000
69A69LEU0-0.034-0.01625.206-0.014-0.0140.0000.0000.0000.000
70A70SER0-0.014-0.01220.304-0.014-0.0140.0000.0000.0000.000
71A71GLY00.0380.01119.544-0.042-0.0420.0000.0000.0000.000
72A72LYS10.8470.95119.4390.2680.2680.0000.0000.0000.000
73A73ALA00.0180.01819.321-0.014-0.0140.0000.0000.0000.000
74A74VAL00.0330.00814.164-0.033-0.0330.0000.0000.0000.000
75A75ALA00.0140.00315.162-0.096-0.0960.0000.0000.0000.000
76A76ALA0-0.031-0.01316.406-0.037-0.0370.0000.0000.0000.000
77A77MET0-0.0110.00013.610-0.016-0.0160.0000.0000.0000.000
78A78ALA00.0460.01911.770-0.008-0.0080.0000.0000.0000.000
79A79SER0-0.0010.01012.309-0.098-0.0980.0000.0000.0000.000
80A80PHE0-0.065-0.03415.0440.0620.0620.0000.0000.0000.000
81A81PHE0-0.037-0.03310.7090.1200.1200.0000.0000.0000.000
82A82ARG10.8670.94110.5730.6050.6050.0000.0000.0000.000
83A83ILE00.0080.0216.674-0.082-0.0820.0000.0000.0000.000
84A84ASN0-0.030-0.0216.2541.0601.0600.0000.0000.0000.000
85A85PRO00.037-0.0067.775-0.502-0.5020.0000.0000.0000.000
86A86ASP-1-0.910-0.9445.816-3.827-3.8270.0000.0000.0000.000
87A87GLU-1-0.820-0.9052.913-9.633-8.3360.089-0.518-0.868-0.003
88A88ILE0-0.032-0.0185.3320.9260.956-0.001-0.007-0.0220.000
89A89LEU0-0.012-0.0107.826-0.024-0.0240.0000.0000.0000.000
90A90VAL0-0.031-0.0299.4390.2540.2540.0000.0000.0000.000
91A91ALA00.0120.01813.0910.0460.0460.0000.0000.0000.000
92A92HIS0-0.058-0.05215.436-0.023-0.0230.0000.0000.0000.000
93A93ASP-1-0.730-0.82818.737-0.260-0.2600.0000.0000.0000.000
94A94GLU-1-0.815-0.89920.245-0.357-0.3570.0000.0000.0000.000
95A95LEU00.0260.00122.3500.0290.0290.0000.0000.0000.000
96A96ASP-1-0.915-0.94022.892-0.200-0.2000.0000.0000.0000.000
97A97LEU0-0.0230.00619.3990.0130.0130.0000.0000.0000.000
98A98PRO00.011-0.00223.973-0.006-0.0060.0000.0000.0000.000
99A99PRO00.0270.00424.977-0.003-0.0030.0000.0000.0000.000
100A100GLY00.0260.02425.1000.0100.0100.0000.0000.0000.000
101A101VAL0-0.080-0.03121.1030.0150.0150.0000.0000.0000.000
102A102ALA00.0530.02217.583-0.023-0.0230.0000.0000.0000.000
103A103LYS10.8970.95115.9020.1500.1500.0000.0000.0000.000
104A104PHE00.0840.04810.407-0.047-0.0470.0000.0000.0000.000
105A105LYS10.8570.94111.4200.6370.6370.0000.0000.0000.000
106A106LEU00.0700.0477.159-0.128-0.1280.0000.0000.0000.000
107A107GLY00.0310.02110.4090.1740.1740.0000.0000.0000.000
108A108GLY0-0.002-0.00713.2030.1000.1000.0000.0000.0000.000
109A109GLY0-0.003-0.01116.781-0.028-0.0280.0000.0000.0000.000
110A110HIS00.0470.01818.806-0.026-0.0260.0000.0000.0000.000
111A111GLY00.0400.01620.6000.0150.0150.0000.0000.0000.000
112A112GLY0-0.040-0.01222.9810.0240.0240.0000.0000.0000.000
113A113HIS00.003-0.01221.616-0.009-0.0090.0000.0000.0000.000
114A114ASN00.038-0.01922.732-0.045-0.0450.0000.0000.0000.000
115A115GLY00.0470.04321.870-0.012-0.0120.0000.0000.0000.000
116A116LEU0-0.011-0.00316.575-0.055-0.0550.0000.0000.0000.000
117A117LYS10.9260.96719.5790.2760.2760.0000.0000.0000.000
118A118ASP-1-0.771-0.88421.726-0.464-0.4640.0000.0000.0000.000
119A119ILE00.0350.01715.696-0.008-0.0080.0000.0000.0000.000
120A120ILE0-0.0070.00217.314-0.056-0.0560.0000.0000.0000.000
121A121SER0-0.053-0.00818.605-0.017-0.0170.0000.0000.0000.000
122A122LYS10.8150.88320.0360.4270.4270.0000.0000.0000.000
123A123LEU0-0.0450.00113.542-0.009-0.0090.0000.0000.0000.000
124A124GLY0-0.0040.00216.606-0.061-0.0610.0000.0000.0000.000
125A125ASN0-0.080-0.05119.271-0.003-0.0030.0000.0000.0000.000
126A126ASN00.0930.04913.1440.0100.0100.0000.0000.0000.000
127A127PRO00.003-0.00215.508-0.062-0.0620.0000.0000.0000.000
128A128ASN0-0.045-0.01611.0460.0620.0620.0000.0000.0000.000
129A129PHE00.0620.0349.150-0.229-0.2290.0000.0000.0000.000
130A130HIS00.001-0.0064.3821.3941.461-0.001-0.005-0.0600.000
131A131ARG10.7890.9029.1230.9860.9860.0000.0000.0000.000
132A132LEU0-0.010-0.00311.9870.0300.0300.0000.0000.0000.000
133A133ARG10.7310.82213.7650.3450.3450.0000.0000.0000.000
134A134ILE00.0530.01517.2310.0520.0520.0000.0000.0000.000
135A135GLY0-0.008-0.00119.815-0.009-0.0090.0000.0000.0000.000
136A136ILE0-0.027-0.01622.9710.0230.0230.0000.0000.0000.000
137A137GLY00.0160.01726.1670.0170.0170.0000.0000.0000.000
138A138HIS00.0520.00928.460-0.014-0.0140.0000.0000.0000.000
139A139PRO0-0.0140.00530.9520.0100.0100.0000.0000.0000.000
140A140GLY00.0170.01934.0820.0080.0080.0000.0000.0000.000
141A141ASP-1-0.788-0.88236.098-0.103-0.1030.0000.0000.0000.000
142A142LYS10.8650.90730.5080.1670.1670.0000.0000.0000.000
143A143ASN0-0.0100.00035.574-0.010-0.0100.0000.0000.0000.000
144A144LYS10.8690.92537.0830.0870.0870.0000.0000.0000.000
145A145VAL00.0100.00130.8460.0000.0000.0000.0000.0000.000
146A146VAL00.0400.02732.359-0.005-0.0050.0000.0000.0000.000
147A147GLY00.0380.01033.129-0.002-0.0020.0000.0000.0000.000
148A148PHE0-0.0030.00229.2440.0050.0050.0000.0000.0000.000
149A149VAL00.0400.00127.9160.0040.0040.0000.0000.0000.000
150A150LEU0-0.058-0.02229.595-0.005-0.0050.0000.0000.0000.000
151A151GLY00.0430.03332.0310.0100.0100.0000.0000.0000.000
152A152LYS10.9550.97231.7320.0540.0540.0000.0000.0000.000
153A153PRO0-0.0200.00929.4770.0040.0040.0000.0000.0000.000
154A154PRO00.0130.00632.7320.0070.0070.0000.0000.0000.000
155A155VAL00.0570.01433.517-0.001-0.0010.0000.0000.0000.000
156A156SER00.0020.00332.9540.0010.0010.0000.0000.0000.000
157A157GLU-1-0.805-0.89730.463-0.086-0.0860.0000.0000.0000.000
158A158GLN0-0.079-0.04927.357-0.008-0.0080.0000.0000.0000.000
159A159LYS10.8530.91128.172-0.008-0.0080.0000.0000.0000.000
160A160LEU0-0.019-0.00627.9070.0080.0080.0000.0000.0000.000
161A161ILE0-0.019-0.02223.6970.0010.0010.0000.0000.0000.000
162A162ASP-1-0.816-0.90323.373-0.051-0.0510.0000.0000.0000.000
163A163GLU-1-0.822-0.89723.1480.0290.0290.0000.0000.0000.000
164A164ALA0-0.023-0.00321.1500.0170.0170.0000.0000.0000.000
165A165ILE0-0.015-0.00419.035-0.003-0.0030.0000.0000.0000.000
166A166ASP-1-0.775-0.84318.3110.1250.1250.0000.0000.0000.000
167A167GLU-1-0.866-0.92317.6940.2130.2130.0000.0000.0000.000
168A168ALA0-0.017-0.01315.1250.0380.0380.0000.0000.0000.000
169A169ALA0-0.0030.00013.8670.0290.0290.0000.0000.0000.000
170A170ARG10.9210.92914.272-0.102-0.1020.0000.0000.0000.000
171A171CYS0-0.093-0.05812.4850.1060.1060.0000.0000.0000.000
172A172THR0-0.046-0.0259.1420.0890.0890.0000.0000.0000.000
173A173GLU-1-0.934-0.9709.7070.5880.5880.0000.0000.0000.000
174A174MET0-0.043-0.01611.3830.1800.1800.0000.0000.0000.000
175A175TRP0-0.031-0.0096.3010.0000.0000.0000.0000.0000.000
176A176PHE0-0.0010.0005.0790.1350.269-0.001-0.003-0.1290.000
177A177THR0-0.0380.0058.279-0.063-0.0630.0000.0000.0000.000
178A178ASP-1-0.744-0.86511.1371.0421.0420.0000.0000.0000.000
179A179GLY0-0.016-0.02012.507-0.133-0.1330.0000.0000.0000.000
180A180LEU00.0200.01515.834-0.103-0.1030.0000.0000.0000.000
181A181THR00.0120.00514.173-0.076-0.0760.0000.0000.0000.000
182A182LYS10.8930.92314.889-0.712-0.7120.0000.0000.0000.000
183A183ALA0-0.052-0.02817.252-0.076-0.0760.0000.0000.0000.000
184A184THR0-0.005-0.00819.226-0.060-0.0600.0000.0000.0000.000
185A185ASN00.012-0.00117.420-0.059-0.0590.0000.0000.0000.000
186A186ARG10.8980.94120.067-0.475-0.4750.0000.0000.0000.000
187A187LEU0-0.022-0.00523.564-0.033-0.0330.0000.0000.0000.000
188A188HIS0-0.0010.00222.417-0.040-0.0400.0000.0000.0000.000
189A189ALA0-0.071-0.02624.066-0.015-0.0150.0000.0000.0000.000
190A190PHE0-0.0080.01425.857-0.021-0.0210.0000.0000.0000.000