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: JL139

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 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 225
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2770932.287939
FMO2-HF: Nuclear repulsion 2681023.37278
FMO2-HF: Total energy -89908.915159
FMO2-MP2: Total energy -90171.529125


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.
-6.492-2.3740.035-1.805-2.3470
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 : -0.053 / q_NPA : -0.035
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-1-0.820-0.9083.006-0.0712.8350.005-1.496-1.414-0.001
4A648VAL00.0250.0145.0601.3651.418-0.001-0.003-0.0480.000
5A649ALA00.0210.0068.2460.3270.3270.0000.0000.0000.000
6A650GLU-1-0.781-0.8804.6564.4664.601-0.001-0.013-0.1220.000
7A651VAL0-0.0040.0044.3750.0860.219-0.001-0.025-0.1080.000
8A652LEU0-0.005-0.0096.546-0.461-0.4610.0000.0000.0000.000
9A653ASN0-0.023-0.0209.243-0.643-0.6430.0000.0000.0000.000
10A654ARG10.8420.9163.106-10.199-9.5060.035-0.237-0.4910.001
11A655CYS0-0.058-0.0209.220-0.415-0.4150.0000.0000.0000.000
12A656ALA0-0.056-0.03011.531-0.243-0.2430.0000.0000.0000.000
13A657SER0-0.005-0.00112.525-0.240-0.2400.0000.0000.0000.000
14A658SER00.0250.01114.400-0.066-0.0660.0000.0000.0000.000
15A659ASN00.008-0.00114.416-0.203-0.2030.0000.0000.0000.000
16A660TRP00.0660.01314.3840.1430.1430.0000.0000.0000.000
17A661SER00.0150.00812.299-0.016-0.0160.0000.0000.0000.000
18A662GLU-1-0.869-0.91510.0842.1162.1160.0000.0000.0000.000
19A663ARG10.7600.8589.580-0.539-0.5390.0000.0000.0000.000
20A664LYS10.7820.8779.443-1.350-1.3500.0000.0000.0000.000
21A665GLU-1-0.793-0.8946.2141.6941.6940.0000.0000.0000.000
22A666GLY00.0110.0006.2190.3630.3630.0000.0000.0000.000
23A667LEU0-0.004-0.0147.523-0.283-0.2830.0000.0000.0000.000
24A668LEU0-0.0140.0016.767-0.307-0.3070.0000.0000.0000.000
25A669GLY00.0230.0184.638-0.511-0.452-0.001-0.015-0.0420.000
26A670LEU0-0.001-0.0115.267-0.791-0.782-0.0010.000-0.0080.000
27A671GLN0-0.026-0.0298.532-0.308-0.3080.0000.0000.0000.000
28A672ASN00.0040.0053.8070.1700.3000.000-0.016-0.1140.000
29A673LEU0-0.0130.0006.457-0.220-0.2200.0000.0000.0000.000
30A674LEU0-0.0040.0038.3740.0130.0130.0000.0000.0000.000
31A675LYS10.8260.90410.1960.1610.1610.0000.0000.0000.000
32A676ASN0-0.097-0.0507.621-0.003-0.0030.0000.0000.0000.000
33A677GLN00.0040.00410.697-0.018-0.0180.0000.0000.0000.000
34A678ARG10.8680.9387.0671.1931.1930.0000.0000.0000.000
35A679THR0-0.023-0.01511.5260.1150.1150.0000.0000.0000.000
36A680LEU0-0.026-0.00411.9820.0070.0070.0000.0000.0000.000
37A681SER0-0.007-0.03615.077-0.014-0.0140.0000.0000.0000.000
38A682ARG10.9090.93017.4450.0000.0000.0000.0000.0000.000
39A683ILE00.021-0.00817.5860.0230.0230.0000.0000.0000.000
40A684GLU-1-0.821-0.87312.4140.2880.2880.0000.0000.0000.000
41A685LEU00.0410.02915.9710.0830.0830.0000.0000.0000.000
42A686LYS10.9120.94917.701-0.236-0.2360.0000.0000.0000.000
43A687ARG10.9460.97612.776-0.976-0.9760.0000.0000.0000.000
44A688LEU0-0.0040.00013.0970.0650.0650.0000.0000.0000.000
45A689CYS00.0120.01115.9860.0010.0010.0000.0000.0000.000
46A690GLU-1-0.869-0.90519.5220.3610.3610.0000.0000.0000.000
47A691ILE0-0.079-0.04513.598-0.001-0.0010.0000.0000.0000.000
48A692PHE00.037-0.00214.1650.0140.0140.0000.0000.0000.000
49A693THR0-0.041-0.03218.544-0.039-0.0390.0000.0000.0000.000
50A694ARG10.9370.96917.898-0.625-0.6250.0000.0000.0000.000
51A695MET0-0.0170.02413.830-0.020-0.0200.0000.0000.0000.000
52A696PHE00.0470.02019.500-0.017-0.0170.0000.0000.0000.000
53A697ALA0-0.088-0.04622.837-0.035-0.0350.0000.0000.0000.000
54A698ASP-1-0.747-0.84817.7870.6800.6800.0000.0000.0000.000
55A699PRO0-0.0100.00021.001-0.029-0.0290.0000.0000.0000.000
56A700HIS00.0120.01218.917-0.028-0.0280.0000.0000.0000.000
57A701GLY00.0650.02420.2660.0070.0070.0000.0000.0000.000
58A702LYS10.9060.95515.388-0.442-0.4420.0000.0000.0000.000
59A703VAL00.0380.01214.599-0.006-0.0060.0000.0000.0000.000
60A704PHE00.0480.02716.679-0.019-0.0190.0000.0000.0000.000
61A705SER0-0.017-0.02019.470-0.047-0.0470.0000.0000.0000.000
62A706MET00.0080.00711.525-0.047-0.0470.0000.0000.0000.000
63A707PHE00.0230.02115.552-0.019-0.0190.0000.0000.0000.000
64A708LEU0-0.014-0.01316.677-0.046-0.0460.0000.0000.0000.000
65A709GLU-1-0.889-0.94016.6020.2090.2090.0000.0000.0000.000
66A710THR00.009-0.00812.754-0.032-0.0320.0000.0000.0000.000
67A711LEU0-0.025-0.00315.639-0.046-0.0460.0000.0000.0000.000
68A712VAL00.0170.02318.651-0.030-0.0300.0000.0000.0000.000
69A713ASP-1-0.826-0.90015.072-0.078-0.0780.0000.0000.0000.000
70A714PHE0-0.017-0.01315.831-0.023-0.0230.0000.0000.0000.000
71A715ILE0-0.006-0.01517.404-0.016-0.0160.0000.0000.0000.000
72A716GLN0-0.029-0.03019.656-0.021-0.0210.0000.0000.0000.000
73A717VAL0-0.043-0.00515.742-0.017-0.0170.0000.0000.0000.000
74A718HIS00.005-0.00215.267-0.002-0.0020.0000.0000.0000.000
75A719LYS10.8710.94220.6480.0710.0710.0000.0000.0000.000
76A720ASP-1-0.851-0.91824.130-0.038-0.0380.0000.0000.0000.000
77A721ASP-1-0.843-0.92022.7130.0130.0130.0000.0000.0000.000
78A722LEU0-0.040-0.02120.4870.0320.0320.0000.0000.0000.000
79A723GLN0-0.025-0.01724.6010.0160.0160.0000.0000.0000.000
80A724ASP-1-0.903-0.94227.1570.0990.0990.0000.0000.0000.000
81A725TRP0-0.052-0.04120.8830.0180.0180.0000.0000.0000.000
82A726LEU00.0250.02225.9770.0150.0150.0000.0000.0000.000
83A727PHE00.0400.01027.9810.0030.0030.0000.0000.0000.000
84A728VAL0-0.0040.00925.1800.0020.0020.0000.0000.0000.000
85A729LEU00.0080.01222.9500.0110.0110.0000.0000.0000.000
86A730LEU00.0550.02225.8110.0040.0040.0000.0000.0000.000
87A731THR0-0.029-0.03929.1150.0040.0040.0000.0000.0000.000
88A732GLN0-0.036-0.01426.0730.0030.0030.0000.0000.0000.000
89A733LEU00.0060.01024.1540.0100.0100.0000.0000.0000.000
90A734LEU00.0080.00827.775-0.005-0.0050.0000.0000.0000.000
91A735LYS10.8650.94030.177-0.181-0.1810.0000.0000.0000.000
92A736LYS10.8690.93625.502-0.281-0.2810.0000.0000.0000.000
93A737MET0-0.0090.01029.1360.0020.0020.0000.0000.0000.000
94A738GLY0-0.031-0.01331.232-0.009-0.0090.0000.0000.0000.000
95A739ALA0-0.079-0.04530.722-0.004-0.0040.0000.0000.0000.000
96A740ASP-1-0.860-0.91132.8860.1280.1280.0000.0000.0000.000
97A741LEU00.0130.02126.8490.0080.0080.0000.0000.0000.000
98A742LEU00.0670.03027.978-0.015-0.0150.0000.0000.0000.000
99A743GLY00.0610.02629.1500.0030.0030.0000.0000.0000.000
100A744SER0-0.005-0.00825.393-0.003-0.0030.0000.0000.0000.000
101A745VAL00.0140.00024.1610.0010.0010.0000.0000.0000.000
102A746GLN00.009-0.01725.858-0.006-0.0060.0000.0000.0000.000
103A747ALA00.0160.01426.783-0.007-0.0070.0000.0000.0000.000
104A748LYS10.8320.91720.116-0.204-0.2040.0000.0000.0000.000
105A749VAL0-0.0010.01024.2650.0010.0010.0000.0000.0000.000
106A750GLN0-0.007-0.01426.333-0.001-0.0010.0000.0000.0000.000
107A751LYS10.9580.99524.035-0.031-0.0310.0000.0000.0000.000
108A752ALA00.0340.01223.194-0.013-0.0130.0000.0000.0000.000
109A753LEU0-0.027-0.01124.798-0.008-0.0080.0000.0000.0000.000
110A754ASP-1-0.811-0.89328.3450.0490.0490.0000.0000.0000.000
111A755ILE0-0.036-0.00622.848-0.008-0.0080.0000.0000.0000.000
112A756THR0-0.030-0.03126.101-0.005-0.0050.0000.0000.0000.000
113A757ARG10.8210.89927.410-0.055-0.0550.0000.0000.0000.000
114A758GLU-1-0.908-0.93927.566-0.003-0.0030.0000.0000.0000.000
115A759SER0-0.042-0.02825.928-0.016-0.0160.0000.0000.0000.000
116A760PHE0-0.028-0.02024.7650.0000.0000.0000.0000.0000.000
117A761PRO00.0550.03730.318-0.002-0.0020.0000.0000.0000.000
118A762ASN00.0800.04233.9210.0120.0120.0000.0000.0000.000
119A763ASP-1-0.787-0.89136.4420.0380.0380.0000.0000.0000.000
120A764LEU0-0.008-0.00132.9690.0090.0090.0000.0000.0000.000
121A765GLN0-0.002-0.00232.0480.0180.0180.0000.0000.0000.000
122A766PHE00.0610.00634.5120.0080.0080.0000.0000.0000.000
123A767ASN0-0.054-0.04537.8370.0060.0060.0000.0000.0000.000
124A768ILE0-0.0260.00231.7840.0060.0060.0000.0000.0000.000
125A769LEU0-0.0090.00434.8680.0070.0070.0000.0000.0000.000
126A770MET0-0.0520.00737.4570.0010.0010.0000.0000.0000.000
127A771ARG10.9220.93636.734-0.077-0.0770.0000.0000.0000.000
128A772PHE00.001-0.00633.9410.0070.0070.0000.0000.0000.000
129A773THR0-0.042-0.02637.7670.0030.0030.0000.0000.0000.000
130A774VAL0-0.038-0.03740.8420.0000.0000.0000.0000.0000.000
131A775ASP-1-0.888-0.90636.8870.1300.1300.0000.0000.0000.000
132A776GLN00.022-0.00240.3410.0010.0010.0000.0000.0000.000
133A777THR0-0.110-0.05637.7060.0030.0030.0000.0000.0000.000
134A778GLN00.0330.01135.5120.0220.0220.0000.0000.0000.000
135A779THR0-0.012-0.01139.164-0.008-0.0080.0000.0000.0000.000
136A780PRO0-0.0050.01538.4380.0040.0040.0000.0000.0000.000
137A781SER00.0540.02437.548-0.009-0.0090.0000.0000.0000.000
138A782LEU00.024-0.01440.196-0.003-0.0030.0000.0000.0000.000
139A783LYS10.8770.92837.047-0.118-0.1180.0000.0000.0000.000
140A784VAL00.0380.02734.748-0.001-0.0010.0000.0000.0000.000
141A785LYS10.8390.95036.994-0.088-0.0880.0000.0000.0000.000
142A786VAL0-0.003-0.00538.783-0.005-0.0050.0000.0000.0000.000
143A787ALA00.0050.01234.292-0.006-0.0060.0000.0000.0000.000
144A788ILE0-0.002-0.00536.220-0.004-0.0040.0000.0000.0000.000
145A789LEU0-0.017-0.01037.334-0.005-0.0050.0000.0000.0000.000
146A790LYS10.9980.99337.542-0.078-0.0780.0000.0000.0000.000
147A791TYR0-0.014-0.00531.031-0.003-0.0030.0000.0000.0000.000
148A792ILE0-0.005-0.00736.435-0.006-0.0060.0000.0000.0000.000
149A793GLU-1-0.823-0.87139.3240.0350.0350.0000.0000.0000.000
150A794THR0-0.034-0.03935.841-0.006-0.0060.0000.0000.0000.000
151A795LEU0-0.032-0.01335.235-0.005-0.0050.0000.0000.0000.000
152A796ALA00.024-0.00737.980-0.005-0.0050.0000.0000.0000.000
153A797LYS10.8010.89140.095-0.032-0.0320.0000.0000.0000.000
154A798GLN0-0.068-0.03333.875-0.004-0.0040.0000.0000.0000.000
155A799MET0-0.085-0.01939.282-0.001-0.0010.0000.0000.0000.000
156A800ASP-1-0.841-0.91140.839-0.003-0.0030.0000.0000.0000.000
157A801PRO00.020-0.00343.3400.0050.0050.0000.0000.0000.000
158A802ARG10.7690.87646.090-0.016-0.0160.0000.0000.0000.000
159A803ASP-1-0.777-0.88740.6970.0200.0200.0000.0000.0000.000
160A804PHE0-0.056-0.02443.0430.0060.0060.0000.0000.0000.000
161A805THR0-0.007-0.02245.503-0.002-0.0020.0000.0000.0000.000
162A806ASN00.0110.00747.8710.0070.0070.0000.0000.0000.000
163A807SER00.0190.01646.4080.0000.0000.0000.0000.0000.000
164A808SER00.015-0.01648.7620.0000.0000.0000.0000.0000.000
165A809GLU-1-0.808-0.89742.3110.0750.0750.0000.0000.0000.000
166A810THR00.0320.01444.5730.0020.0020.0000.0000.0000.000
167A811ARG10.9290.96746.320-0.042-0.0420.0000.0000.0000.000
168A812LEU0-0.031-0.00846.1890.0000.0000.0000.0000.0000.000
169A813ALA00.002-0.00344.0380.0020.0020.0000.0000.0000.000
170A814VAL00.0420.01045.8770.0010.0010.0000.0000.0000.000
171A815SER0-0.022-0.01848.294-0.001-0.0010.0000.0000.0000.000
172A816ARG10.8650.93742.836-0.089-0.0890.0000.0000.0000.000
173A817VAL00.0380.03044.9240.0010.0010.0000.0000.0000.000
174A818ILE00.0230.02847.586-0.001-0.0010.0000.0000.0000.000
175A819THR0-0.042-0.01150.0680.0000.0000.0000.0000.0000.000
176A820TRP00.022-0.00342.3780.0020.0020.0000.0000.0000.000
177A821THR00.014-0.00548.7640.0000.0000.0000.0000.0000.000
178A822THR0-0.073-0.04450.660-0.002-0.0020.0000.0000.0000.000
179A823GLU-1-0.832-0.89747.2730.0770.0770.0000.0000.0000.000
180A824PRO00.0430.03050.717-0.001-0.0010.0000.0000.0000.000
181A825LYS10.8610.91347.618-0.079-0.0790.0000.0000.0000.000
182A826SER00.0130.00945.0400.0020.0020.0000.0000.0000.000
183A827SER00.0470.01647.488-0.003-0.0030.0000.0000.0000.000
184A828ASP-1-0.904-0.95342.9960.0700.0700.0000.0000.0000.000
185A829VAL0-0.020-0.01943.487-0.001-0.0010.0000.0000.0000.000
186A830ARG10.8660.93845.341-0.059-0.0590.0000.0000.0000.000
187A831LYS10.9150.93846.589-0.045-0.0450.0000.0000.0000.000
188A832ALA00.0210.02442.561-0.003-0.0030.0000.0000.0000.000
189A833ALA00.0140.00644.570-0.001-0.0010.0000.0000.0000.000
190A834GLN00.0430.02646.628-0.001-0.0010.0000.0000.0000.000
191A835SER00.001-0.00544.031-0.002-0.0020.0000.0000.0000.000
192A836VAL00.0060.02042.777-0.003-0.0030.0000.0000.0000.000
193A837LEU0-0.030-0.02445.455-0.002-0.0020.0000.0000.0000.000
194A838ILE0-0.010-0.00448.978-0.002-0.0020.0000.0000.0000.000
195A839SER0-0.010-0.02145.019-0.002-0.0020.0000.0000.0000.000
196A840LEU00.004-0.00843.875-0.002-0.0020.0000.0000.0000.000
197A841PHE0-0.027-0.00947.487-0.002-0.0020.0000.0000.0000.000
198A842GLU-1-0.922-0.98149.2440.0170.0170.0000.0000.0000.000
199A843LEU0-0.0570.00944.166-0.002-0.0020.0000.0000.0000.000
200A844ASN0-0.034-0.04048.048-0.004-0.0040.0000.0000.0000.000
201A845THR00.0640.03550.4550.0010.0010.0000.0000.0000.000
202A846PRO00.0150.01453.8490.0020.0020.0000.0000.0000.000
203A847GLU-1-0.792-0.87350.0070.0260.0260.0000.0000.0000.000
204A848PHE00.0170.00349.0730.0030.0030.0000.0000.0000.000
205A849THR0-0.022-0.02652.8430.0020.0020.0000.0000.0000.000
206A850MET0-0.030-0.01454.4040.0010.0010.0000.0000.0000.000
207A851LEU0-0.050-0.00849.8620.0020.0020.0000.0000.0000.000
208A852LEU00.003-0.00754.0080.0020.0020.0000.0000.0000.000
209A853GLY00.0130.01256.2510.0010.0010.0000.0000.0000.000
210A854ALA0-0.061-0.02055.7940.0000.0000.0000.0000.0000.000
211A855LEU0-0.023-0.00852.9670.0030.0030.0000.0000.0000.000
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