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

tag_button

FMODB ID: 396QL

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 OptAll
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 -2780156.299032
FMO2-HF: Nuclear repulsion 2690246.961188
FMO2-HF: Total energy -89909.337844
FMO2-MP2: Total energy -90171.968873


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.
-4.426-0.9260.013-1.506-2.0070
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 : -0.056 / q_NPA : -0.042
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-1-0.809-0.9073.181-0.0642.365-0.009-1.228-1.191-0.001
4A648VAL00.0200.0175.2761.4531.491-0.001-0.002-0.0350.000
5A649ALA00.0210.0138.3610.3950.3950.0000.0000.0000.000
6A650GLU-1-0.773-0.8765.0803.5433.632-0.001-0.003-0.0850.000
7A651VAL0-0.0070.0034.5170.3490.464-0.001-0.022-0.0930.000
8A652LEU0-0.009-0.0146.808-0.418-0.4180.0000.0000.0000.000
9A653ASN0-0.039-0.0209.335-0.538-0.5380.0000.0000.0000.000
10A654ARG10.8490.9153.185-8.079-7.6200.015-0.145-0.3290.001
11A655CYS0-0.059-0.0249.271-0.373-0.3730.0000.0000.0000.000
12A656ALA0-0.047-0.02711.609-0.243-0.2430.0000.0000.0000.000
13A657SER0-0.018-0.00513.063-0.224-0.2240.0000.0000.0000.000
14A658SER00.0360.01214.814-0.035-0.0350.0000.0000.0000.000
15A659ASN0-0.023-0.00714.082-0.172-0.1720.0000.0000.0000.000
16A660TRP00.0640.01214.5970.1360.1360.0000.0000.0000.000
17A661SER00.0220.01312.302-0.004-0.0040.0000.0000.0000.000
18A662GLU-1-0.839-0.89910.0961.8761.8760.0000.0000.0000.000
19A663ARG10.7790.8669.726-0.541-0.5410.0000.0000.0000.000
20A664LYS10.7980.8818.940-1.671-1.6710.0000.0000.0000.000
21A665GLU-1-0.777-0.8835.9402.0952.0950.0000.0000.0000.000
22A666GLY0-0.006-0.0096.1500.4610.4610.0000.0000.0000.000
23A667LEU0-0.011-0.0217.673-0.280-0.2800.0000.0000.0000.000
24A668LEU0-0.0030.0046.884-0.282-0.2820.0000.0000.0000.000
25A669GLY00.0260.0184.494-0.475-0.413-0.001-0.018-0.0420.000
26A670LEU0-0.004-0.0065.086-0.949-0.949-0.001-0.0010.0020.000
27A671GLN0-0.027-0.0308.491-0.291-0.2910.0000.0000.0000.000
28A672ASN0-0.0030.0033.2900.1820.4900.012-0.087-0.2340.000
29A673LEU0-0.019-0.0066.312-0.248-0.2480.0000.0000.0000.000
30A674LEU0-0.005-0.0058.1820.0110.0110.0000.0000.0000.000
31A675LYS10.8230.9059.8980.1170.1170.0000.0000.0000.000
32A676ASN0-0.079-0.0407.577-0.021-0.0210.0000.0000.0000.000
33A677GLN00.0000.00110.668-0.034-0.0340.0000.0000.0000.000
34A678ARG10.8580.9397.2701.5751.5750.0000.0000.0000.000
35A679THR0-0.013-0.01011.8600.0920.0920.0000.0000.0000.000
36A680LEU0-0.0140.00112.052-0.042-0.0420.0000.0000.0000.000
37A681SER0-0.007-0.03914.8350.0120.0120.0000.0000.0000.000
38A682ARG10.8610.87417.2100.0900.0900.0000.0000.0000.000
39A683ILE00.0140.00117.3440.0330.0330.0000.0000.0000.000
40A684GLU-1-0.816-0.87312.1380.0530.0530.0000.0000.0000.000
41A685LEU00.0460.02715.7590.0810.0810.0000.0000.0000.000
42A686LYS10.8930.94017.622-0.148-0.1480.0000.0000.0000.000
43A687ARG10.9360.96812.892-0.768-0.7680.0000.0000.0000.000
44A688LEU00.0070.01213.1530.0750.0750.0000.0000.0000.000
45A689CYS00.0130.01215.9400.0140.0140.0000.0000.0000.000
46A690GLU-1-0.844-0.89219.5410.2760.2760.0000.0000.0000.000
47A691ILE0-0.069-0.03413.7330.0030.0030.0000.0000.0000.000
48A692PHE00.047-0.00114.1910.0130.0130.0000.0000.0000.000
49A693THR0-0.044-0.03718.624-0.033-0.0330.0000.0000.0000.000
50A694ARG10.9120.96317.906-0.547-0.5470.0000.0000.0000.000
51A695MET0-0.0170.01713.815-0.020-0.0200.0000.0000.0000.000
52A696PHE00.0470.02119.546-0.007-0.0070.0000.0000.0000.000
53A697ALA0-0.056-0.03722.792-0.028-0.0280.0000.0000.0000.000
54A698ASP-1-0.792-0.87017.9230.6580.6580.0000.0000.0000.000
55A699PRO0-0.0030.00221.418-0.027-0.0270.0000.0000.0000.000
56A700HIS00.0120.01118.920-0.025-0.0250.0000.0000.0000.000
57A701GLY00.0520.02320.0790.0140.0140.0000.0000.0000.000
58A702LYS10.8570.93415.508-0.500-0.5000.0000.0000.0000.000
59A703VAL00.0580.02614.5890.0090.0090.0000.0000.0000.000
60A704PHE00.0590.02516.671-0.025-0.0250.0000.0000.0000.000
61A705SER0-0.044-0.03919.240-0.051-0.0510.0000.0000.0000.000
62A706MET0-0.0010.00711.409-0.055-0.0550.0000.0000.0000.000
63A707PHE00.0350.03015.345-0.021-0.0210.0000.0000.0000.000
64A708LEU0-0.007-0.00116.679-0.050-0.0500.0000.0000.0000.000
65A709GLU-1-0.855-0.93216.4880.3240.3240.0000.0000.0000.000
66A710THR00.014-0.00512.603-0.033-0.0330.0000.0000.0000.000
67A711LEU0-0.041-0.00915.547-0.053-0.0530.0000.0000.0000.000
68A712VAL00.0160.01618.722-0.038-0.0380.0000.0000.0000.000
69A713ASP-1-0.819-0.88714.003-0.045-0.0450.0000.0000.0000.000
70A714PHE0-0.015-0.02315.789-0.029-0.0290.0000.0000.0000.000
71A715ILE00.007-0.00417.194-0.024-0.0240.0000.0000.0000.000
72A716GLN0-0.041-0.03819.677-0.030-0.0300.0000.0000.0000.000
73A717VAL0-0.038-0.01015.640-0.019-0.0190.0000.0000.0000.000
74A718HIS00.0070.00015.150-0.007-0.0070.0000.0000.0000.000
75A719LYS10.8580.92620.5300.0920.0920.0000.0000.0000.000
76A720ASP-1-0.832-0.90124.016-0.067-0.0670.0000.0000.0000.000
77A721ASP-1-0.814-0.86622.604-0.048-0.0480.0000.0000.0000.000
78A722LEU0-0.037-0.01420.2210.0260.0260.0000.0000.0000.000
79A723GLN0-0.048-0.03324.2570.0230.0230.0000.0000.0000.000
80A724ASP-1-0.893-0.94127.3550.0560.0560.0000.0000.0000.000
81A725TRP0-0.045-0.03820.7860.0170.0170.0000.0000.0000.000
82A726LEU00.0220.01626.0760.0180.0180.0000.0000.0000.000
83A727PHE00.0470.01627.9600.0050.0050.0000.0000.0000.000
84A728VAL0-0.0130.00725.0730.0060.0060.0000.0000.0000.000
85A729LEU00.0050.00822.9910.0130.0130.0000.0000.0000.000
86A730LEU00.0560.02525.8000.0080.0080.0000.0000.0000.000
87A731THR0-0.041-0.04129.1240.0080.0080.0000.0000.0000.000
88A732GLN0-0.011-0.00626.282-0.001-0.0010.0000.0000.0000.000
89A733LEU0-0.0130.00624.0700.0130.0130.0000.0000.0000.000
90A734LEU00.0080.00427.706-0.001-0.0010.0000.0000.0000.000
91A735LYS10.8610.94230.229-0.160-0.1600.0000.0000.0000.000
92A736LYS10.8430.93024.856-0.292-0.2920.0000.0000.0000.000
93A737MET0-0.0160.00229.2770.0060.0060.0000.0000.0000.000
94A738GLY0-0.019-0.01431.302-0.007-0.0070.0000.0000.0000.000
95A739ALA0-0.054-0.03230.805-0.004-0.0040.0000.0000.0000.000
96A740ASP-1-0.855-0.92332.7660.1400.1400.0000.0000.0000.000
97A741LEU00.0130.02626.8430.0070.0070.0000.0000.0000.000
98A742LEU00.0750.03627.700-0.014-0.0140.0000.0000.0000.000
99A743GLY00.0690.03529.0670.0040.0040.0000.0000.0000.000
100A744SER0-0.003-0.00425.502-0.006-0.0060.0000.0000.0000.000
101A745VAL0-0.005-0.01024.2070.0060.0060.0000.0000.0000.000
102A746GLN0-0.006-0.01426.065-0.010-0.0100.0000.0000.0000.000
103A747ALA00.0190.00927.048-0.008-0.0080.0000.0000.0000.000
104A748LYS10.8180.91520.197-0.268-0.2680.0000.0000.0000.000
105A749VAL00.0160.00624.427-0.004-0.0040.0000.0000.0000.000
106A750GLN0-0.030-0.02526.223-0.005-0.0050.0000.0000.0000.000
107A751LYS10.9070.95823.973-0.042-0.0420.0000.0000.0000.000
108A752ALA00.0350.01723.048-0.013-0.0130.0000.0000.0000.000
109A753LEU0-0.023-0.00724.648-0.010-0.0100.0000.0000.0000.000
110A754ASP-1-0.797-0.88028.1550.0550.0550.0000.0000.0000.000
111A755ILE0-0.0090.00122.489-0.010-0.0100.0000.0000.0000.000
112A756THR0-0.034-0.03525.931-0.009-0.0090.0000.0000.0000.000
113A757ARG10.8160.89027.317-0.054-0.0540.0000.0000.0000.000
114A758GLU-1-0.866-0.91826.9970.0080.0080.0000.0000.0000.000
115A759SER0-0.041-0.02225.564-0.019-0.0190.0000.0000.0000.000
116A760PHE0-0.006-0.01224.570-0.004-0.0040.0000.0000.0000.000
117A761PRO00.0470.03329.9840.0020.0020.0000.0000.0000.000
118A762ASN00.0410.02433.6680.0120.0120.0000.0000.0000.000
119A763ASP-1-0.795-0.90036.2570.0200.0200.0000.0000.0000.000
120A764LEU0-0.0010.00732.6240.0080.0080.0000.0000.0000.000
121A765GLN00.0090.01232.0270.0190.0190.0000.0000.0000.000
122A766PHE00.0520.00634.5110.0090.0090.0000.0000.0000.000
123A767ASN0-0.019-0.01837.5560.0070.0070.0000.0000.0000.000
124A768ILE0-0.0140.00831.6390.0060.0060.0000.0000.0000.000
125A769LEU0-0.017-0.00434.8590.0070.0070.0000.0000.0000.000
126A770MET0-0.0360.01437.3580.0020.0020.0000.0000.0000.000
127A771ARG10.8810.91437.239-0.053-0.0530.0000.0000.0000.000
128A772PHE0-0.014-0.01234.1240.0070.0070.0000.0000.0000.000
129A773THR0-0.038-0.03337.7840.0040.0040.0000.0000.0000.000
130A774VAL0-0.038-0.02140.8730.0000.0000.0000.0000.0000.000
131A775ASP-1-0.832-0.88737.2130.1100.1100.0000.0000.0000.000
132A776GLN00.0140.00940.766-0.001-0.0010.0000.0000.0000.000
133A777THR0-0.103-0.05137.5350.0040.0040.0000.0000.0000.000
134A778GLN00.0360.01835.6810.0200.0200.0000.0000.0000.000
135A779THR0-0.010-0.02139.044-0.009-0.0090.0000.0000.0000.000
136A780PRO0-0.0140.01738.4740.0060.0060.0000.0000.0000.000
137A781SER00.0610.02837.269-0.008-0.0080.0000.0000.0000.000
138A782LEU00.017-0.00839.906-0.003-0.0030.0000.0000.0000.000
139A783LYS10.8840.93336.803-0.125-0.1250.0000.0000.0000.000
140A784VAL00.0350.02734.788-0.001-0.0010.0000.0000.0000.000
141A785LYS10.7910.91936.975-0.085-0.0850.0000.0000.0000.000
142A786VAL0-0.004-0.00938.280-0.005-0.0050.0000.0000.0000.000
143A787ALA00.0020.01034.095-0.005-0.0050.0000.0000.0000.000
144A788ILE00.007-0.00136.175-0.005-0.0050.0000.0000.0000.000
145A789LEU0-0.020-0.00937.402-0.006-0.0060.0000.0000.0000.000
146A790LYS11.0091.00037.589-0.083-0.0830.0000.0000.0000.000
147A791TYR0-0.025-0.00630.904-0.002-0.0020.0000.0000.0000.000
148A792ILE00.010-0.00536.367-0.006-0.0060.0000.0000.0000.000
149A793GLU-1-0.837-0.87539.3060.0380.0380.0000.0000.0000.000
150A794THR0-0.019-0.03635.593-0.006-0.0060.0000.0000.0000.000
151A795LEU0-0.043-0.01635.231-0.005-0.0050.0000.0000.0000.000
152A796ALA00.0380.00037.917-0.006-0.0060.0000.0000.0000.000
153A797LYS10.7910.89039.720-0.033-0.0330.0000.0000.0000.000
154A798GLN0-0.069-0.04033.569-0.001-0.0010.0000.0000.0000.000
155A799MET0-0.083-0.02038.888-0.002-0.0020.0000.0000.0000.000
156A800ASP-1-0.829-0.89940.592-0.008-0.0080.0000.0000.0000.000
157A801PRO00.030-0.00242.9760.0040.0040.0000.0000.0000.000
158A802ARG10.7610.86545.737-0.006-0.0060.0000.0000.0000.000
159A803ASP-1-0.768-0.89240.3060.0080.0080.0000.0000.0000.000
160A804PHE0-0.045-0.01042.7820.0060.0060.0000.0000.0000.000
161A805THR00.007-0.01345.383-0.003-0.0030.0000.0000.0000.000
162A806ASN00.0280.02347.6600.0060.0060.0000.0000.0000.000
163A807SER00.005-0.00246.0020.0010.0010.0000.0000.0000.000
164A808SER00.021-0.00748.5340.0010.0010.0000.0000.0000.000
165A809GLU-1-0.821-0.90242.4820.0570.0570.0000.0000.0000.000
166A810THR00.0350.02344.5670.0030.0030.0000.0000.0000.000
167A811ARG10.9050.95446.153-0.030-0.0300.0000.0000.0000.000
168A812LEU0-0.0120.01046.5350.0010.0010.0000.0000.0000.000
169A813ALA00.014-0.00643.8360.0030.0030.0000.0000.0000.000
170A814VAL00.0250.00545.6600.0020.0020.0000.0000.0000.000
171A815SER0-0.012-0.01748.0400.0000.0000.0000.0000.0000.000
172A816ARG10.7910.89142.878-0.077-0.0770.0000.0000.0000.000
173A817VAL00.0510.03744.6850.0020.0020.0000.0000.0000.000
174A818ILE00.0190.02547.3460.0000.0000.0000.0000.0000.000
175A819THR0-0.054-0.02949.6990.0010.0010.0000.0000.0000.000
176A820TRP00.032-0.00142.1630.0020.0020.0000.0000.0000.000
177A821THR00.011-0.00948.5340.0010.0010.0000.0000.0000.000
178A822THR0-0.062-0.04550.446-0.002-0.0020.0000.0000.0000.000
179A823GLU-1-0.790-0.86846.8430.0760.0760.0000.0000.0000.000
180A824PRO00.0540.03350.3080.0000.0000.0000.0000.0000.000
181A825LYS10.8260.88847.188-0.078-0.0780.0000.0000.0000.000
182A826SER0-0.013-0.02644.8510.0030.0030.0000.0000.0000.000
183A827SER00.0320.01047.198-0.004-0.0040.0000.0000.0000.000
184A828ASP-1-0.862-0.90842.7250.0760.0760.0000.0000.0000.000
185A829VAL0-0.028-0.01843.028-0.002-0.0020.0000.0000.0000.000
186A830ARG10.8640.93944.841-0.062-0.0620.0000.0000.0000.000
187A831LYS10.9110.94346.683-0.048-0.0480.0000.0000.0000.000
188A832ALA00.0380.02742.280-0.003-0.0030.0000.0000.0000.000
189A833ALA0-0.0020.00944.351-0.002-0.0020.0000.0000.0000.000
190A834GLN00.0450.02046.534-0.002-0.0020.0000.0000.0000.000
191A835SER0-0.014-0.02043.820-0.002-0.0020.0000.0000.0000.000
192A836VAL0-0.0020.02042.665-0.003-0.0030.0000.0000.0000.000
193A837LEU0-0.030-0.02145.325-0.003-0.0030.0000.0000.0000.000
194A838ILE00.0010.00548.974-0.002-0.0020.0000.0000.0000.000
195A839SER00.001-0.01744.844-0.002-0.0020.0000.0000.0000.000
196A840LEU00.005-0.00743.537-0.003-0.0030.0000.0000.0000.000
197A841PHE0-0.025-0.00947.233-0.003-0.0030.0000.0000.0000.000
198A842GLU-1-0.924-0.97148.4760.0180.0180.0000.0000.0000.000
199A843LEU0-0.0450.00143.865-0.002-0.0020.0000.0000.0000.000
200A844ASN0-0.026-0.04047.660-0.004-0.0040.0000.0000.0000.000
201A845THR00.0520.03150.2350.0010.0010.0000.0000.0000.000
202A846PRO00.0000.00853.4230.0020.0020.0000.0000.0000.000
203A847GLU-1-0.780-0.86049.7640.0170.0170.0000.0000.0000.000
204A848PHE00.014-0.00548.6050.0030.0030.0000.0000.0000.000
205A849THR0-0.008-0.01852.6530.0020.0020.0000.0000.0000.000
206A850MET0-0.039-0.01854.0410.0010.0010.0000.0000.0000.000
207A851LEU0-0.049-0.01249.6440.0010.0010.0000.0000.0000.000
208A852LEU0-0.002-0.00853.7040.0020.0020.0000.0000.0000.000
209A853GLY00.0090.01456.1140.0010.0010.0000.0000.0000.000
210A854ALA0-0.053-0.01455.6240.0000.0000.0000.0000.0000.000
211A855LEU0-0.004-0.00452.9210.0020.0020.0000.0000.0000.000
212A856PRO0-0.010-0.00756.810-0.002-0.0020.0000.0000.0000.000
213A857LYS11.0200.98859.151-0.026-0.0260.0000.0000.0000.000
214A858THR00.0110.01858.786-0.001-0.0010.0000.0000.0000.000
215A859PHE00.0220.00253.1100.0010.0010.0000.0000.0000.000
216A860GLN0-0.030-0.00656.631-0.001-0.0010.0000.0000.0000.000
217A861ASP-1-0.824-0.89758.8800.0300.0300.0000.0000.0000.000
218A862GLY00.000-0.00157.1310.0000.0000.0000.0000.0000.000
219A863ALA00.0240.00254.9170.0000.0000.0000.0000.0000.000
220A864THR0-0.009-0.01255.980-0.002-0.0020.0000.0000.0000.000
221A865LYS10.8440.90359.293-0.034-0.0340.0000.0000.0000.000
222A866LEU0-0.081-0.02953.0420.0010.0010.0000.0000.0000.000
223A867LEU0-0.0030.00552.4350.0000.0000.0000.0000.0000.000
224A868HIS0-0.058-0.02456.150-0.004-0.0040.0000.0000.0000.000
225A869ASN0-0.025-0.00357.1800.0010.0010.0000.0000.0000.000