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: YZ6V2

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 OptH
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 -1980735.261163
FMO2-HF: Nuclear repulsion 1909265.384122
FMO2-HF: Total energy -71469.87704
FMO2-MP2: Total energy -71681.527845


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.
-6.806-2.5620.993-1.916-3.3190.003
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 : 0.030 / q_NPA : -0.002
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].
3A3LYS10.9570.9852.195-1.6431.4130.967-1.581-2.4410.005
4A4LEU0-0.022-0.0085.0220.6050.691-0.001-0.005-0.0800.000
5A5ILE00.0070.0118.495-0.172-0.1720.0000.0000.0000.000
6A6VAL0-0.022-0.01510.8620.0440.0440.0000.0000.0000.000
7A7GLY00.0340.00614.2230.0350.0350.0000.0000.0000.000
8A8LEU0-0.043-0.03617.373-0.016-0.0160.0000.0000.0000.000
9A9ALA00.0170.00120.1220.0300.0300.0000.0000.0000.000
10A10ASN0-0.0340.00923.622-0.036-0.0360.0000.0000.0000.000
11A11PRO00.0450.03326.0350.0150.0150.0000.0000.0000.000
12A12GLY00.0620.02227.834-0.003-0.0030.0000.0000.0000.000
13A13ALA00.008-0.01030.9720.0050.0050.0000.0000.0000.000
14A14GLU-1-0.959-0.98733.322-0.010-0.0100.0000.0000.0000.000
15A15TYR00.0280.02429.9080.0010.0010.0000.0000.0000.000
16A16ALA0-0.0090.02028.5460.0060.0060.0000.0000.0000.000
17A17ALA0-0.018-0.00728.2740.0100.0100.0000.0000.0000.000
18A18THR0-0.069-0.05229.5970.0040.0040.0000.0000.0000.000
19A19ARG10.9200.95427.592-0.040-0.0400.0000.0000.0000.000
20A20HIS0-0.064-0.05125.714-0.010-0.0100.0000.0000.0000.000
21A21ASN0-0.003-0.00924.181-0.021-0.0210.0000.0000.0000.000
22A22ALA00.0390.03422.3390.0110.0110.0000.0000.0000.000
23A23GLY00.0250.01018.6780.0270.0270.0000.0000.0000.000
24A24ALA0-0.026-0.02218.6060.0250.0250.0000.0000.0000.000
25A25TRP00.0190.01620.3560.0270.0270.0000.0000.0000.000
26A26PHE0-0.0180.00312.7140.0160.0160.0000.0000.0000.000
27A27VAL00.0140.00514.8430.0410.0410.0000.0000.0000.000
28A28ASP-1-0.918-0.96716.8860.1330.1330.0000.0000.0000.000
29A29LEU0-0.0020.01319.0320.0170.0170.0000.0000.0000.000
30A30LEU0-0.002-0.01212.3100.0320.0320.0000.0000.0000.000
31A31ALA0-0.018-0.01716.5140.0280.0280.0000.0000.0000.000
32A32GLU-1-0.987-0.98218.0500.2220.2220.0000.0000.0000.000
33A33ARG10.8760.93218.124-0.372-0.3720.0000.0000.0000.000
34A34LEU0-0.032-0.01713.2590.0290.0290.0000.0000.0000.000
35A35ARG10.8880.95417.648-0.295-0.2950.0000.0000.0000.000
36A36ALA00.0090.00617.265-0.020-0.0200.0000.0000.0000.000
37A37PRO00.0020.02618.590-0.005-0.0050.0000.0000.0000.000
38A38LEU00.035-0.00417.208-0.012-0.0120.0000.0000.0000.000
39A39ARG10.8740.94520.508-0.088-0.0880.0000.0000.0000.000
40A40GLU-1-0.930-0.97221.743-0.045-0.0450.0000.0000.0000.000
41A41GLU-1-0.853-0.89518.659-0.102-0.1020.0000.0000.0000.000
42A42ALA00.0550.01721.996-0.026-0.0260.0000.0000.0000.000
43A43LYS10.8800.95219.9760.1480.1480.0000.0000.0000.000
44A44PHE00.0150.00517.063-0.046-0.0460.0000.0000.0000.000
45A45PHE0-0.010-0.02520.112-0.014-0.0140.0000.0000.0000.000
46A46GLY00.0790.03320.737-0.004-0.0040.0000.0000.0000.000
47A47TYR0-0.0400.01620.9300.0060.0060.0000.0000.0000.000
48A48THR0-0.005-0.05516.5630.0010.0010.0000.0000.0000.000
49A49SER0-0.020-0.02115.9530.0310.0310.0000.0000.0000.000
50A50ARG10.8560.91512.492-0.425-0.4250.0000.0000.0000.000
51A51VAL00.0280.02611.146-0.007-0.0070.0000.0000.0000.000
52A52THR0-0.016-0.01610.909-0.049-0.0490.0000.0000.0000.000
53A53LEU0-0.008-0.0078.380-0.146-0.1460.0000.0000.0000.000
54A54GLY00.0040.0097.9140.4450.4450.0000.0000.0000.000
55A55GLY0-0.060-0.0348.8130.1080.1080.0000.0000.0000.000
56A56GLU-1-0.877-0.9345.4921.4731.4730.0000.0000.0000.000
57A57ASP-1-0.893-0.9388.0820.3460.3460.0000.0000.0000.000
58A58VAL0-0.0280.0006.2000.1050.1050.0000.0000.0000.000
59A59ARG10.9230.9598.4130.0270.0270.0000.0000.0000.000
60A60LEU0-0.0050.01610.829-0.088-0.0880.0000.0000.0000.000
61A61LEU00.015-0.00813.525-0.031-0.0310.0000.0000.0000.000
62A62VAL00.0350.02815.8660.0020.0020.0000.0000.0000.000
63A63PRO0-0.030-0.00618.5340.0000.0000.0000.0000.0000.000
64A64THR00.019-0.00520.9340.0180.0180.0000.0000.0000.000
65A65THR0-0.025-0.02522.835-0.001-0.0010.0000.0000.0000.000
66A66PHE00.0330.01725.3750.0020.0020.0000.0000.0000.000
67A67MET0-0.0010.02023.205-0.033-0.0330.0000.0000.0000.000
68A68ASN00.001-0.01924.159-0.018-0.0180.0000.0000.0000.000
69A69LEU0-0.047-0.02024.971-0.015-0.0150.0000.0000.0000.000
70A70SER00.0140.01020.037-0.013-0.0130.0000.0000.0000.000
71A71GLY00.0350.00919.303-0.030-0.0300.0000.0000.0000.000
72A72LYS10.8710.95519.2300.1500.1500.0000.0000.0000.000
73A73ALA00.0160.01719.024-0.023-0.0230.0000.0000.0000.000
74A74VAL00.0270.00813.951-0.031-0.0310.0000.0000.0000.000
75A75ALA00.0080.00214.976-0.089-0.0890.0000.0000.0000.000
76A76ALA0-0.029-0.00416.260-0.053-0.0530.0000.0000.0000.000
77A77MET0-0.007-0.00113.215-0.021-0.0210.0000.0000.0000.000
78A78ALA00.0390.01911.647-0.021-0.0210.0000.0000.0000.000
79A79SER0-0.002-0.00812.219-0.133-0.1330.0000.0000.0000.000
80A80PHE0-0.091-0.04214.9600.0280.0280.0000.0000.0000.000
81A81PHE0-0.054-0.03810.6570.1040.1040.0000.0000.0000.000
82A82ARG10.9000.95810.5820.5840.5840.0000.0000.0000.000
83A83ILE00.0150.0306.761-0.099-0.0990.0000.0000.0000.000
84A84ASN00.0020.0026.1941.1171.1170.0000.0000.0000.000
85A85PRO00.017-0.0187.833-0.379-0.3790.0000.0000.0000.000
86A86ASP-1-0.918-0.9475.520-3.739-3.7390.0000.0000.0000.000
87A87GLU-1-0.840-0.9243.195-7.822-6.8060.029-0.319-0.725-0.002
88A88ILE0-0.036-0.0155.2220.9941.024-0.001-0.008-0.0210.000
89A89LEU0-0.007-0.0078.2580.1830.1830.0000.0000.0000.000
90A90VAL0-0.042-0.0349.7830.0640.0640.0000.0000.0000.000
91A91ALA00.0010.01213.4280.0580.0580.0000.0000.0000.000
92A92HIS0-0.049-0.05815.726-0.045-0.0450.0000.0000.0000.000
93A93ASP-1-0.726-0.83619.2600.0290.0290.0000.0000.0000.000
94A94GLU-1-0.826-0.91320.999-0.006-0.0060.0000.0000.0000.000
95A95LEU00.005-0.01323.0530.0130.0130.0000.0000.0000.000
96A96ASP-1-0.945-0.97223.8630.0310.0310.0000.0000.0000.000
97A97LEU0-0.119-0.03920.3060.0150.0150.0000.0000.0000.000
98A98PRO00.0190.00124.880-0.010-0.0100.0000.0000.0000.000
99A99PRO00.0340.00825.5240.0160.0160.0000.0000.0000.000
100A100GLY00.0300.02625.258-0.002-0.0020.0000.0000.0000.000
101A101VAL0-0.068-0.02521.7760.0220.0220.0000.0000.0000.000
102A102ALA00.0500.01917.827-0.020-0.0200.0000.0000.0000.000
103A103LYS10.9040.95116.677-0.204-0.2040.0000.0000.0000.000
104A104PHE00.0860.05211.141-0.024-0.0240.0000.0000.0000.000
105A105LYS10.8360.93212.2450.0180.0180.0000.0000.0000.000
106A106LEU00.0920.0507.6800.0170.0170.0000.0000.0000.000
107A107GLY00.0050.01610.8290.0040.0040.0000.0000.0000.000
108A108GLY0-0.025-0.01813.3290.0910.0910.0000.0000.0000.000
109A109GLY00.000-0.01616.983-0.030-0.0300.0000.0000.0000.000
110A110HIS00.0400.01819.0970.0170.0170.0000.0000.0000.000
111A111GLY00.0560.02520.8040.0120.0120.0000.0000.0000.000
112A112GLY0-0.038-0.01123.3520.0150.0150.0000.0000.0000.000
113A113HIS00.0190.00421.940-0.024-0.0240.0000.0000.0000.000
114A114ASN00.048-0.01322.902-0.034-0.0340.0000.0000.0000.000
115A115GLY00.0300.03422.009-0.019-0.0190.0000.0000.0000.000
116A116LEU0-0.012-0.00216.966-0.042-0.0420.0000.0000.0000.000
117A117LYS10.9200.96619.5660.1150.1150.0000.0000.0000.000
118A118ASP-1-0.774-0.88521.534-0.276-0.2760.0000.0000.0000.000
119A119ILE00.0300.01115.595-0.025-0.0250.0000.0000.0000.000
120A120ILE0-0.0100.00317.272-0.054-0.0540.0000.0000.0000.000
121A121SER0-0.069-0.01818.304-0.042-0.0420.0000.0000.0000.000
122A122LYS10.8480.90320.0560.2420.2420.0000.0000.0000.000
123A123LEU0-0.0300.00613.238-0.025-0.0250.0000.0000.0000.000
124A124GLY0-0.0100.00016.623-0.063-0.0630.0000.0000.0000.000
125A125ASN0-0.100-0.05919.275-0.005-0.0050.0000.0000.0000.000
126A126ASN00.0910.05313.1100.0190.0190.0000.0000.0000.000
127A127PRO00.016-0.00515.244-0.024-0.0240.0000.0000.0000.000
128A128ASN0-0.033-0.01410.6270.1920.1920.0000.0000.0000.000
129A129PHE00.0490.0298.987-0.231-0.2310.0000.0000.0000.000
130A130HIS00.0110.0014.5550.7340.790-0.001-0.003-0.0520.000
131A131ARG10.8240.9329.5130.1850.1850.0000.0000.0000.000
132A132LEU00.001-0.00112.7680.1210.1210.0000.0000.0000.000
133A133ARG10.8300.90514.395-0.142-0.1420.0000.0000.0000.000
134A134ILE00.0530.01417.8940.0390.0390.0000.0000.0000.000
135A135GLY0-0.0090.00020.265-0.031-0.0310.0000.0000.0000.000
136A136ILE0-0.034-0.01823.5860.0060.0060.0000.0000.0000.000
137A137GLY00.0200.01826.702-0.003-0.0030.0000.0000.0000.000
138A138HIS00.0560.00429.228-0.017-0.0170.0000.0000.0000.000
139A139PRO0-0.0110.00331.7070.0040.0040.0000.0000.0000.000
140A140GLY00.0200.01734.7990.0000.0000.0000.0000.0000.000
141A141ASP-1-0.804-0.90536.773-0.001-0.0010.0000.0000.0000.000
142A142LYS10.8710.92731.2650.0140.0140.0000.0000.0000.000
143A143ASN00.0240.02136.086-0.008-0.0080.0000.0000.0000.000
144A144LYS10.8660.93837.545-0.010-0.0100.0000.0000.0000.000
145A145VAL00.0230.00031.3890.0040.0040.0000.0000.0000.000
146A146VAL00.0320.02232.8710.0030.0030.0000.0000.0000.000
147A147GLY00.0390.01233.5860.0020.0020.0000.0000.0000.000
148A148PHE00.0000.00430.0830.0030.0030.0000.0000.0000.000
149A149VAL00.0340.00528.3900.0080.0080.0000.0000.0000.000
150A150LEU0-0.050-0.02229.9690.0030.0030.0000.0000.0000.000
151A151GLY00.0370.03232.4000.0000.0000.0000.0000.0000.000
152A152LYS10.9650.97831.923-0.057-0.0570.0000.0000.0000.000
153A153PRO0-0.026-0.00129.596-0.004-0.0040.0000.0000.0000.000
154A154PRO00.0270.01132.8200.0020.0020.0000.0000.0000.000
155A155VAL00.0580.01333.5100.0060.0060.0000.0000.0000.000
156A156SER00.0100.00332.9460.0070.0070.0000.0000.0000.000
157A157GLU-1-0.895-0.95430.7370.0750.0750.0000.0000.0000.000
158A158GLN0-0.066-0.02127.406-0.005-0.0050.0000.0000.0000.000
159A159LYS10.9740.98128.164-0.128-0.1280.0000.0000.0000.000
160A160LEU00.0040.00427.9110.0130.0130.0000.0000.0000.000
161A161ILE0-0.015-0.01623.6500.0170.0170.0000.0000.0000.000
162A162ASP-1-0.845-0.93423.3660.1680.1680.0000.0000.0000.000
163A163GLU-1-0.926-0.96123.1410.2080.2080.0000.0000.0000.000
164A164ALA0-0.018-0.00321.1650.0320.0320.0000.0000.0000.000
165A165ILE0-0.012-0.00519.0360.0440.0440.0000.0000.0000.000
166A166ASP-1-0.812-0.87918.3040.3810.3810.0000.0000.0000.000
167A167GLU-1-0.881-0.94317.8080.5180.5180.0000.0000.0000.000
168A168ALA0-0.023-0.01215.0730.0760.0760.0000.0000.0000.000
169A169ALA0-0.0030.00713.8610.1150.1150.0000.0000.0000.000
170A170ARG10.8910.91314.263-0.295-0.2950.0000.0000.0000.000
171A171CYS0-0.063-0.02912.4940.0830.0830.0000.0000.0000.000
172A172THR0-0.045-0.0379.1170.1600.1600.0000.0000.0000.000
173A173GLU-1-0.930-0.9739.7000.8530.8530.0000.0000.0000.000
174A174MET0-0.048-0.03111.3770.0540.0540.0000.0000.0000.000
175A175TRP0-0.040-0.0106.2700.1010.1010.0000.0000.0000.000
176A176PHE0-0.013-0.0025.2920.1310.1310.0000.0000.0000.000
177A177THR0-0.0350.0018.276-0.216-0.2160.0000.0000.0000.000
178A178ASP-1-0.752-0.87911.1410.7700.7700.0000.0000.0000.000
179A179GLY0-0.024-0.02412.471-0.093-0.0930.0000.0000.0000.000
180A180LEU00.0210.02015.794-0.064-0.0640.0000.0000.0000.000
181A181THR00.0210.02214.080-0.026-0.0260.0000.0000.0000.000
182A182LYS10.9220.95815.253-0.740-0.7400.0000.0000.0000.000
183A183ALA0-0.060-0.03917.254-0.047-0.0470.0000.0000.0000.000
184A184THR0-0.015-0.01019.067-0.049-0.0490.0000.0000.0000.000
185A185ASN00.0220.00217.331-0.056-0.0560.0000.0000.0000.000
186A186ARG10.8940.94120.092-0.447-0.4470.0000.0000.0000.000
187A187LEU0-0.020-0.00523.564-0.025-0.0250.0000.0000.0000.000
188A188HIS00.0090.00522.585-0.030-0.0300.0000.0000.0000.000
189A189ALA0-0.070-0.02824.098-0.010-0.0100.0000.0000.0000.000
190A190PHE0-0.0110.01425.854-0.016-0.0160.0000.0000.0000.000