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: N941Q

Calculation Name: 3WOZ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3WOZ

Chain ID: A

ChEMBL ID:

UniProt ID: Q8BRT1

Base Structure: X-ray

Registration Date: 2023-09-20

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 225
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2769618.516023
FMO2-HF: Nuclear repulsion 2679711.144232
FMO2-HF: Total energy -89907.371791
FMO2-MP2: Total energy -90169.958847


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:645:THR)


Summations of interaction energy for fragment #1(A:645: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.
-5.712-1.3750.015-1.958-2.3950.001
Interaction energy analysis for fragmet #1(A:645: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 : -0.024
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].
3A647ASP-1-0.878-0.9373.199-2.2740.948-0.001-1.710-1.5120.001
4A648VAL00.0380.0114.955-0.590-0.548-0.001-0.003-0.0380.000
5A649ALA00.0150.0027.702-0.046-0.0460.0000.0000.0000.000
6A650GLU-1-0.880-0.9423.6850.9651.1710.001-0.033-0.1740.000
7A651VAL0-0.0140.0014.110-0.152-0.017-0.001-0.024-0.1110.000
8A652LEU0-0.011-0.0196.0090.1030.1030.0000.0000.0000.000
9A653ASN0-0.009-0.0128.230-0.116-0.1160.0000.0000.0000.000
10A654ARG10.9430.9853.444-4.748-4.1830.020-0.167-0.4180.000
11A655CYS0-0.046-0.0148.957-0.045-0.0450.0000.0000.0000.000
12A656ALA0-0.059-0.02911.511-0.038-0.0380.0000.0000.0000.000
13A657SER00.0370.04111.985-0.048-0.0480.0000.0000.0000.000
14A658SER00.0210.00013.883-0.024-0.0240.0000.0000.0000.000
15A659ASN00.0300.00414.046-0.083-0.0830.0000.0000.0000.000
16A660TRP00.0560.01314.3860.0440.0440.0000.0000.0000.000
17A661SER0-0.010-0.00712.442-0.028-0.0280.0000.0000.0000.000
18A662GLU-1-0.930-0.9679.5331.1321.1320.0000.0000.0000.000
19A663ARG10.7980.9029.580-0.205-0.2050.0000.0000.0000.000
20A664LYS10.9220.95810.839-0.443-0.4430.0000.0000.0000.000
21A665GLU-1-0.916-0.9645.7811.2881.2880.0000.0000.0000.000
22A666GLY00.006-0.0056.2130.0130.0130.0000.0000.0000.000
23A667LEU0-0.013-0.0217.505-0.254-0.2540.0000.0000.0000.000
24A668LEU0-0.0170.0066.560-0.157-0.1570.0000.0000.0000.000
25A669GLY00.0350.0224.548-0.341-0.274-0.001-0.017-0.0490.000
26A670LEU0-0.008-0.0115.246-0.411-0.400-0.0010.000-0.0100.000
27A671GLN0-0.018-0.0318.507-0.076-0.0760.0000.0000.0000.000
28A672ASN0-0.0060.0044.3470.4060.495-0.001-0.004-0.0830.000
29A673LEU0-0.037-0.0176.0380.0090.0090.0000.0000.0000.000
30A674LEU00.0000.0048.2820.1190.1190.0000.0000.0000.000
31A675LYS10.9160.96310.1430.4150.4150.0000.0000.0000.000
32A676ASN0-0.056-0.0246.7970.2060.2060.0000.0000.0000.000
33A677GLN00.0010.00110.6450.0320.0320.0000.0000.0000.000
34A678ARG10.8920.9627.8090.3790.3790.0000.0000.0000.000
35A679THR0-0.014-0.01311.4640.0260.0260.0000.0000.0000.000
36A680LEU0-0.028-0.00811.9570.0140.0140.0000.0000.0000.000
37A681SER00.0320.00314.8900.0080.0080.0000.0000.0000.000
38A682ARG11.0340.99917.1690.0130.0130.0000.0000.0000.000
39A683ILE00.016-0.01116.8140.0000.0000.0000.0000.0000.000
40A684GLU-1-0.866-0.91212.3150.0480.0480.0000.0000.0000.000
41A685LEU00.0570.03715.3240.0060.0060.0000.0000.0000.000
42A686LYS10.9450.98117.309-0.042-0.0420.0000.0000.0000.000
43A687ARG10.9590.98411.945-0.248-0.2480.0000.0000.0000.000
44A688LEU0-0.0020.00013.1390.0180.0180.0000.0000.0000.000
45A689CYS00.0210.01715.7130.0020.0020.0000.0000.0000.000
46A690GLU-1-0.927-0.95019.0150.0950.0950.0000.0000.0000.000
47A691ILE0-0.077-0.04113.0590.0140.0140.0000.0000.0000.000
48A692PHE00.033-0.00414.3330.0110.0110.0000.0000.0000.000
49A693THR0-0.048-0.03218.525-0.003-0.0030.0000.0000.0000.000
50A694ARG10.9470.97017.124-0.156-0.1560.0000.0000.0000.000
51A695MET0-0.0240.02113.891-0.005-0.0050.0000.0000.0000.000
52A696PHE00.0470.01619.491-0.004-0.0040.0000.0000.0000.000
53A697ALA0-0.091-0.05222.816-0.006-0.0060.0000.0000.0000.000
54A698ASP-1-0.748-0.86917.9390.1980.1980.0000.0000.0000.000
55A699PRO0-0.0050.00320.810-0.010-0.0100.0000.0000.0000.000
56A700HIS00.0030.00518.745-0.009-0.0090.0000.0000.0000.000
57A701GLY00.0650.02320.261-0.005-0.0050.0000.0000.0000.000
58A702LYS10.8860.94215.069-0.120-0.1200.0000.0000.0000.000
59A703VAL00.0170.00714.826-0.011-0.0110.0000.0000.0000.000
60A704PHE00.0460.02616.673-0.026-0.0260.0000.0000.0000.000
61A705SER0-0.001-0.01319.460-0.025-0.0250.0000.0000.0000.000
62A706MET00.0140.01911.271-0.003-0.0030.0000.0000.0000.000
63A707PHE00.0200.02515.488-0.033-0.0330.0000.0000.0000.000
64A708LEU0-0.021-0.01716.661-0.026-0.0260.0000.0000.0000.000
65A709GLU-1-0.941-0.97816.471-0.037-0.0370.0000.0000.0000.000
66A710THR0-0.007-0.02012.637-0.030-0.0300.0000.0000.0000.000
67A711LEU0-0.019-0.00415.458-0.026-0.0260.0000.0000.0000.000
68A712VAL00.0000.01818.628-0.005-0.0050.0000.0000.0000.000
69A713ASP-1-0.887-0.95315.109-0.237-0.2370.0000.0000.0000.000
70A714PHE0-0.019-0.01515.806-0.009-0.0090.0000.0000.0000.000
71A715ILE0-0.012-0.01617.3280.0040.0040.0000.0000.0000.000
72A716GLN0-0.025-0.02719.5130.0170.0170.0000.0000.0000.000
73A717VAL0-0.041-0.00915.6670.0000.0000.0000.0000.0000.000
74A718HIS00.0230.01015.2820.0230.0230.0000.0000.0000.000
75A719LYS10.9320.97820.5490.1180.1180.0000.0000.0000.000
76A720ASP-1-0.919-0.95224.029-0.080-0.0800.0000.0000.0000.000
77A721ASP-1-0.967-0.97322.377-0.068-0.0680.0000.0000.0000.000
78A722LEU0-0.065-0.04220.5630.0140.0140.0000.0000.0000.000
79A723GLN00.016-0.00524.5740.0120.0120.0000.0000.0000.000
80A724ASP-1-0.911-0.94627.002-0.002-0.0020.0000.0000.0000.000
81A725TRP0-0.056-0.04220.9280.0040.0040.0000.0000.0000.000
82A726LEU00.0290.02125.9530.0040.0040.0000.0000.0000.000
83A727PHE00.0380.01027.9560.0010.0010.0000.0000.0000.000
84A728VAL0-0.0040.01624.8820.0030.0030.0000.0000.0000.000
85A729LEU00.0100.01222.8580.0040.0040.0000.0000.0000.000
86A730LEU00.0500.02025.7890.0020.0020.0000.0000.0000.000
87A731THR0-0.032-0.04329.0930.0040.0040.0000.0000.0000.000
88A732GLN0-0.039-0.02026.0910.0070.0070.0000.0000.0000.000
89A733LEU00.0210.01624.0520.0050.0050.0000.0000.0000.000
90A734LEU00.0110.01127.7550.0010.0010.0000.0000.0000.000
91A735LYS10.8610.93530.207-0.032-0.0320.0000.0000.0000.000
92A736LYS10.8890.95725.718-0.053-0.0530.0000.0000.0000.000
93A737MET0-0.0140.00929.1210.0020.0020.0000.0000.0000.000
94A738GLY0-0.040-0.02031.213-0.001-0.0010.0000.0000.0000.000
95A739ALA0-0.084-0.04830.7210.0020.0020.0000.0000.0000.000
96A740ASP-1-0.985-0.98732.8730.0260.0260.0000.0000.0000.000
97A741LEU00.0260.03026.8550.0040.0040.0000.0000.0000.000
98A742LEU00.0720.02527.926-0.005-0.0050.0000.0000.0000.000
99A743GLY00.0610.02828.996-0.002-0.0020.0000.0000.0000.000
100A744SER0-0.015-0.01425.340-0.003-0.0030.0000.0000.0000.000
101A745VAL00.0120.00024.078-0.005-0.0050.0000.0000.0000.000
102A746GLN00.019-0.00625.699-0.008-0.0080.0000.0000.0000.000
103A747ALA00.0150.01326.612-0.004-0.0040.0000.0000.0000.000
104A748LYS10.9010.95920.290-0.003-0.0030.0000.0000.0000.000
105A749VAL00.0050.01524.089-0.005-0.0050.0000.0000.0000.000
106A750GLN0-0.005-0.01426.1620.0010.0010.0000.0000.0000.000
107A751LYS10.9681.00123.3320.0800.0800.0000.0000.0000.000
108A752ALA00.0450.01823.100-0.008-0.0080.0000.0000.0000.000
109A753LEU0-0.036-0.01724.626-0.003-0.0030.0000.0000.0000.000
110A754ASP-1-0.822-0.89828.115-0.038-0.0380.0000.0000.0000.000
111A755ILE0-0.0040.00322.762-0.002-0.0020.0000.0000.0000.000
112A756THR0-0.023-0.01326.099-0.002-0.0020.0000.0000.0000.000
113A757ARG10.8280.90327.3790.0330.0330.0000.0000.0000.000
114A758GLU-1-0.952-0.95227.298-0.076-0.0760.0000.0000.0000.000
115A759SER0-0.056-0.05225.856-0.010-0.0100.0000.0000.0000.000
116A760PHE0-0.019-0.01724.816-0.001-0.0010.0000.0000.0000.000
117A761PRO00.0470.03030.2140.0010.0010.0000.0000.0000.000
118A762ASN00.1000.04333.8180.0020.0020.0000.0000.0000.000
119A763ASP-1-0.795-0.88336.365-0.021-0.0210.0000.0000.0000.000
120A764LEU0-0.040-0.03232.7540.0040.0040.0000.0000.0000.000
121A765GLN00.0040.00432.0980.0080.0080.0000.0000.0000.000
122A766PHE00.0650.01334.4860.0040.0040.0000.0000.0000.000
123A767ASN00.012-0.00337.7290.0040.0040.0000.0000.0000.000
124A768ILE0-0.054-0.01531.8060.0040.0040.0000.0000.0000.000
125A769LEU0-0.0160.00234.7350.0040.0040.0000.0000.0000.000
126A770MET0-0.0300.01437.4340.0030.0030.0000.0000.0000.000
127A771ARG10.9510.97036.1680.0000.0000.0000.0000.0000.000
128A772PHE00.0220.00033.9440.0030.0030.0000.0000.0000.000
129A773THR0-0.059-0.03437.7460.0020.0020.0000.0000.0000.000
130A774VAL0-0.062-0.05340.8210.0010.0010.0000.0000.0000.000
131A775ASP-1-0.893-0.92137.0730.0240.0240.0000.0000.0000.000
132A776GLN0-0.006-0.00940.3220.0010.0010.0000.0000.0000.000
133A777THR0-0.095-0.04037.8160.0020.0020.0000.0000.0000.000
134A778GLN00.014-0.00135.4750.0060.0060.0000.0000.0000.000
135A779THR0-0.007-0.00739.148-0.002-0.0020.0000.0000.0000.000
136A780PRO0-0.0060.01738.5070.0020.0020.0000.0000.0000.000
137A781SER00.0640.02437.461-0.002-0.0020.0000.0000.0000.000
138A782LEU00.017-0.02040.181-0.002-0.0020.0000.0000.0000.000
139A783LYS10.9880.99637.041-0.018-0.0180.0000.0000.0000.000
140A784VAL00.0500.03434.769-0.002-0.0020.0000.0000.0000.000
141A785LYS10.9060.97536.977-0.016-0.0160.0000.0000.0000.000
142A786VAL0-0.0030.00138.624-0.002-0.0020.0000.0000.0000.000
143A787ALA00.0110.01134.270-0.003-0.0030.0000.0000.0000.000
144A788ILE0-0.001-0.00236.199-0.003-0.0030.0000.0000.0000.000
145A789LEU0-0.021-0.01437.314-0.002-0.0020.0000.0000.0000.000
146A790LYS11.0020.99237.4480.0040.0040.0000.0000.0000.000
147A791TYR0-0.025-0.01131.073-0.003-0.0030.0000.0000.0000.000
148A792ILE0-0.007-0.00536.412-0.003-0.0030.0000.0000.0000.000
149A793GLU-1-0.858-0.93539.300-0.018-0.0180.0000.0000.0000.000
150A794THR0-0.040-0.03435.643-0.002-0.0020.0000.0000.0000.000
151A795LEU0-0.042-0.01635.089-0.003-0.0030.0000.0000.0000.000
152A796ALA00.024-0.00637.872-0.002-0.0020.0000.0000.0000.000
153A797LYS10.8180.90839.9970.0200.0200.0000.0000.0000.000
154A798GLN0-0.075-0.03833.651-0.003-0.0030.0000.0000.0000.000
155A799MET0-0.086-0.02139.181-0.001-0.0010.0000.0000.0000.000
156A800ASP-1-0.832-0.89540.714-0.032-0.0320.0000.0000.0000.000
157A801PRO00.022-0.01343.2380.0020.0020.0000.0000.0000.000
158A802ARG10.8300.93845.9700.0160.0160.0000.0000.0000.000
159A803ASP-1-0.780-0.88840.707-0.025-0.0250.0000.0000.0000.000
160A804PHE0-0.058-0.02343.0160.0020.0020.0000.0000.0000.000
161A805THR0-0.011-0.02645.4770.0010.0010.0000.0000.0000.000
162A806ASN00.0200.00747.8450.0020.0020.0000.0000.0000.000
163A807SER00.0150.01346.5340.0010.0010.0000.0000.0000.000
164A808SER0-0.003-0.03148.6710.0000.0000.0000.0000.0000.000
165A809GLU-1-0.858-0.93642.5390.0050.0050.0000.0000.0000.000
166A810THR00.0450.01845.1920.0000.0000.0000.0000.0000.000
167A811ARG10.9210.97346.2960.0000.0000.0000.0000.0000.000
168A812LEU0-0.037-0.01145.8620.0000.0000.0000.0000.0000.000
169A813ALA00.009-0.00244.0210.0010.0010.0000.0000.0000.000
170A814VAL00.0430.01245.8540.0000.0000.0000.0000.0000.000
171A815SER0-0.021-0.02248.2710.0000.0000.0000.0000.0000.000
172A816ARG10.9120.97143.573-0.012-0.0120.0000.0000.0000.000
173A817VAL00.0330.02744.8840.0010.0010.0000.0000.0000.000
174A818ILE00.0270.03747.5650.0000.0000.0000.0000.0000.000
175A819THR0-0.037-0.01150.0210.0000.0000.0000.0000.0000.000
176A820TRP0-0.015-0.01042.4070.0010.0010.0000.0000.0000.000
177A821THR00.013-0.01348.7450.0000.0000.0000.0000.0000.000
178A822THR0-0.066-0.04050.6400.0000.0000.0000.0000.0000.000
179A823GLU-1-0.907-0.94847.3090.0120.0120.0000.0000.0000.000
180A824PRO00.0240.03350.700-0.001-0.0010.0000.0000.0000.000
181A825LYS10.9180.95547.846-0.014-0.0140.0000.0000.0000.000
182A826SER00.0280.01144.2920.0000.0000.0000.0000.0000.000
183A827SER00.0470.01147.472-0.001-0.0010.0000.0000.0000.000
184A828ASP-1-0.907-0.95142.8170.0010.0010.0000.0000.0000.000
185A829VAL0-0.048-0.02943.572-0.001-0.0010.0000.0000.0000.000
186A830ARG10.8400.92745.323-0.005-0.0050.0000.0000.0000.000
187A831LYS10.9550.96146.2810.0020.0020.0000.0000.0000.000
188A832ALA00.0170.02242.550-0.001-0.0010.0000.0000.0000.000
189A833ALA00.0230.01144.498-0.001-0.0010.0000.0000.0000.000
190A834GLN00.022-0.00546.6070.0000.0000.0000.0000.0000.000
191A835SER00.0320.04443.9510.0000.0000.0000.0000.0000.000
192A836VAL00.0050.01942.779-0.001-0.0010.0000.0000.0000.000
193A837LEU0-0.021-0.02045.433-0.001-0.0010.0000.0000.0000.000
194A838ILE0-0.0070.00148.9540.0000.0000.0000.0000.0000.000
195A839SER0-0.020-0.02944.880-0.001-0.0010.0000.0000.0000.000
196A840LEU00.003-0.00843.857-0.001-0.0010.0000.0000.0000.000
197A841PHE0-0.028-0.00747.4630.0000.0000.0000.0000.0000.000
198A842GLU-1-0.929-0.99149.273-0.016-0.0160.0000.0000.0000.000
199A843LEU0-0.0550.01444.258-0.001-0.0010.0000.0000.0000.000
200A844ASN0-0.053-0.06247.9430.0000.0000.0000.0000.0000.000
201A845THR00.0630.03950.3490.0010.0010.0000.0000.0000.000
202A846PRO00.0090.01453.8020.0010.0010.0000.0000.0000.000
203A847GLU-1-0.824-0.90350.067-0.008-0.0080.0000.0000.0000.000
204A848PHE00.0150.00649.5560.0020.0020.0000.0000.0000.000
205A849THR0-0.022-0.03552.8180.0010.0010.0000.0000.0000.000
206A850MET0-0.025-0.01054.4650.0010.0010.0000.0000.0000.000
207A851LEU0-0.053-0.01149.7120.0010.0010.0000.0000.0000.000
208A852LEU0-0.009-0.01753.9830.0010.0010.0000.0000.0000.000
209A853GLY00.0270.02556.2280.0010.0010.0000.0000.0000.000
210A854ALA0-0.081-0.02955.7470.0010.0010.0000.0000.0000.000
211A855LEU0-0.026-0.01052.9500.0010.0010.0000.0000.0000.000
212A856PRO0-0.014-0.01256.7900.0000.0000.0000.0000.0000.000
213A857LYS10.9850.96959.377-0.002-0.0020.0000.0000.0000.000
214A858THR00.0090.02158.300-0.001-0.0010.0000.0000.0000.000
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