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: 6Y9YZ

Calculation Name: 3Q48-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3Q48

Chain ID: A

ChEMBL ID:

UniProt ID: Q9HWU3

Base Structure: X-ray

Registration Date: 2023-09-24

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 200
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2100077.288072
FMO2-HF: Nuclear repulsion 2022831.295261
FMO2-HF: Total energy -77245.992812
FMO2-MP2: Total energy -77475.538071


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:31:ILE)


Summations of interaction energy for fragment #1(A:31:ILE)
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.
-8.914-1.4195.649-4.641-8.503-0.02
Interaction energy analysis for fragmet #1(A:31:ILE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.004 / 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].
3A33GLN00.0440.0173.890-0.4731.043-0.012-0.832-0.6730.003
4A34GLY0-0.045-0.0026.9640.0290.0290.0000.0000.0000.000
5A35THR00.0470.0037.268-0.104-0.1040.0000.0000.0000.000
6A36ARG10.8520.9409.4400.0250.0250.0000.0000.0000.000
7A37VAL00.0470.02510.5600.0560.0560.0000.0000.0000.000
8A38VAL00.0070.01113.223-0.019-0.0190.0000.0000.0000.000
9A39PHE0-0.017-0.01416.8130.0190.0190.0000.0000.0000.000
10A40PRO00.0310.02418.705-0.011-0.0110.0000.0000.0000.000
11A41ALA0-0.004-0.01222.2400.0020.0020.0000.0000.0000.000
12A42SER0-0.068-0.03024.908-0.001-0.0010.0000.0000.0000.000
13A43GLU-1-0.931-0.95020.9760.0670.0670.0000.0000.0000.000
14A44ARG10.9640.96622.940-0.036-0.0360.0000.0000.0000.000
15A45GLU-1-0.878-0.94017.8330.0460.0460.0000.0000.0000.000
16A46VAL00.0150.02314.3440.0140.0140.0000.0000.0000.000
17A47THR0-0.043-0.02312.706-0.014-0.0140.0000.0000.0000.000
18A48LEU00.0420.0216.621-0.002-0.0020.0000.0000.0000.000
19A49ARG10.9460.9787.335-0.713-0.7130.0000.0000.0000.000
20A50VAL00.0190.0042.252-0.571-0.6001.928-0.443-1.4560.005
21A51SER00.009-0.0022.880-2.109-0.8390.292-0.441-1.121-0.001
22A52ASN0-0.054-0.0402.403-2.900-0.4003.164-2.526-3.138-0.028
23A53THR00.010-0.0164.0600.1970.4070.000-0.029-0.1800.000
24A54SER0-0.0020.0105.671-0.133-0.1330.0000.0000.0000.000
25A55GLY00.0580.0198.3120.1400.1400.0000.0000.0000.000
26A56THR0-0.009-0.0019.7630.0200.0200.0000.0000.0000.000
27A57PRO0-0.035-0.0058.878-0.036-0.0360.0000.0000.0000.000
28A58VAL00.0190.0204.147-0.138-0.049-0.001-0.007-0.0810.000
29A59LEU0-0.016-0.0167.4870.1410.1410.0000.0000.0000.000
30A60ALA0-0.010-0.0113.896-0.330-0.1910.001-0.027-0.1120.000
31A61GLN00.0060.0135.6350.1370.1370.0000.0000.0000.000
32A62ALA0-0.009-0.0077.255-0.126-0.1260.0000.0000.0000.000
33A63TRP00.0240.0028.7240.0290.0290.0000.0000.0000.000
34A64ILE00.0130.00011.675-0.050-0.0500.0000.0000.0000.000
35A65ASP-1-0.720-0.81814.210-0.285-0.2850.0000.0000.0000.000
36A66ASP-1-0.822-0.93816.641-0.152-0.1520.0000.0000.0000.000
37A67GLY0-0.063-0.03718.0910.0120.0120.0000.0000.0000.000
38A68ARG10.9440.98619.0160.1230.1230.0000.0000.0000.000
39A69GLN0-0.047-0.03914.799-0.044-0.0440.0000.0000.0000.000
40A70ASP-1-0.952-0.98717.892-0.201-0.2010.0000.0000.0000.000
41A71VAL00.0160.01920.0950.0160.0160.0000.0000.0000.000
42A72PRO00.0180.01019.710-0.020-0.0200.0000.0000.0000.000
43A73PRO00.0140.00516.0270.0120.0120.0000.0000.0000.000
44A74GLU-1-0.923-0.96718.895-0.116-0.1160.0000.0000.0000.000
45A75GLU-1-0.973-0.98921.075-0.115-0.1150.0000.0000.0000.000
46A76LEU0-0.101-0.04519.4920.0060.0060.0000.0000.0000.000
47A77GLN0-0.056-0.01323.0180.0150.0150.0000.0000.0000.000
48A78VAL00.0310.02517.9920.0080.0080.0000.0000.0000.000
49A79PRO0-0.0210.00321.1240.0030.0030.0000.0000.0000.000
50A80PHE0-0.031-0.03516.9560.0120.0120.0000.0000.0000.000
51A81SER00.0250.03016.805-0.010-0.0100.0000.0000.0000.000
52A82VAL00.000-0.01910.1140.0080.0080.0000.0000.0000.000
53A83THR0-0.0460.02413.407-0.015-0.0150.0000.0000.0000.000
54A84PRO00.031-0.01410.7150.0260.0260.0000.0000.0000.000
55A85ALA00.0660.02410.548-0.005-0.0050.0000.0000.0000.000
56A86VAL00.0200.0009.576-0.060-0.0600.0000.0000.0000.000
57A87THR0-0.043-0.0256.7240.0620.0620.0000.0000.0000.000
58A88ARG10.9590.9947.691-0.097-0.0970.0000.0000.0000.000
59A89VAL0-0.047-0.0164.258-0.0180.103-0.001-0.013-0.1070.000
60A90GLU-1-0.811-0.9157.3160.0260.0260.0000.0000.0000.000
61A91PRO0-0.017-0.0148.1540.0770.0770.0000.0000.0000.000
62A92ASN0-0.0240.0059.0350.1000.1000.0000.0000.0000.000
63A93GLY00.0560.0378.174-0.055-0.0550.0000.0000.0000.000
64A94GLY0-0.018-0.0206.0280.4130.4130.0000.0000.0000.000
65A95ALA0-0.0290.0085.899-0.203-0.2030.0000.0000.0000.000
66A96VAL0-0.019-0.0217.1540.1190.1190.0000.0000.0000.000
67A97LEU0-0.019-0.0026.212-0.067-0.0670.0000.0000.0000.000
68A98ARG10.8640.9049.774-0.078-0.0780.0000.0000.0000.000
69A99ILE00.0150.00611.129-0.033-0.0330.0000.0000.0000.000
70A100ALA00.0370.02614.7950.0190.0190.0000.0000.0000.000
71A101TYR0-0.012-0.00218.565-0.012-0.0120.0000.0000.0000.000
72A102LEU00.003-0.00421.2970.0100.0100.0000.0000.0000.000
73A103LYS10.9280.95324.1480.0140.0140.0000.0000.0000.000
74A104ALA00.0320.02725.874-0.001-0.0010.0000.0000.0000.000
75A105PRO0-0.041-0.03827.6730.0020.0020.0000.0000.0000.000
76A106LEU00.0330.03123.410-0.007-0.0070.0000.0000.0000.000
77A107PRO0-0.0160.00126.7990.0070.0070.0000.0000.0000.000
78A108THR00.0090.00428.2340.0000.0000.0000.0000.0000.000
79A109ASP-1-0.810-0.89130.781-0.028-0.0280.0000.0000.0000.000
80A110ARG10.8480.89527.6190.0430.0430.0000.0000.0000.000
81A111GLU-1-0.793-0.86822.351-0.037-0.0370.0000.0000.0000.000
82A112SER0-0.026-0.02022.770-0.005-0.0050.0000.0000.0000.000
83A113LEU0-0.040-0.01216.9730.0010.0010.0000.0000.0000.000
84A114PHE00.0290.02016.6750.0030.0030.0000.0000.0000.000
85A115TRP0-0.005-0.01012.635-0.024-0.0240.0000.0000.0000.000
86A116LEU00.0270.0208.1550.0200.0200.0000.0000.0000.000
87A117ASN0-0.045-0.0128.757-0.142-0.1420.0000.0000.0000.000
88A118ILE00.0190.0002.807-0.6240.0490.252-0.140-0.7850.000
89A119LEU0-0.026-0.0095.530-0.254-0.2540.0000.0000.0000.000
90A120GLU-1-0.858-0.9403.789-2.394-2.0350.000-0.034-0.3250.000
91A121VAL00.003-0.0055.7190.1140.1140.0000.0000.0000.000
92A122PRO0-0.028-0.0087.3480.1460.1460.0000.0000.0000.000
93A123PRO0-0.038-0.0329.0970.0630.0630.0000.0000.0000.000
94A124ARG10.9751.01312.7730.4180.4180.0000.0000.0000.000
95A134PHE0-0.029-0.04012.9850.0100.0100.0000.0000.0000.000
96A135SER00.0030.0069.302-0.027-0.0270.0000.0000.0000.000
97A136PHE00.0280.0324.9740.1400.1400.0000.0000.0000.000
98A137ARG10.9200.9515.8710.3530.3530.0000.0000.0000.000
99A138SER00.001-0.0052.955-0.1980.2260.026-0.111-0.3400.001
100A139ARG10.7670.8665.8720.5420.5420.0000.0000.0000.000
101A140PHE0-0.016-0.0083.860-0.1270.0960.000-0.038-0.1850.000
102A141LYS10.9000.9699.8440.2630.2630.0000.0000.0000.000
103A142LEU00.0200.00713.0590.0100.0100.0000.0000.0000.000
104A143PHE00.015-0.00114.924-0.006-0.0060.0000.0000.0000.000
105A144PHE00.0430.03018.3830.0180.0180.0000.0000.0000.000
106A145ARG10.7630.80120.814-0.006-0.0060.0000.0000.0000.000
107A146PRO00.0360.02923.4590.0100.0100.0000.0000.0000.000
108A147SER00.0650.01426.9880.0030.0030.0000.0000.0000.000
109A148GLN0-0.093-0.04628.4980.0070.0070.0000.0000.0000.000
110A149LEU0-0.042-0.00426.8050.0000.0000.0000.0000.0000.000
111A150LYS10.9560.96227.252-0.025-0.0250.0000.0000.0000.000
112A151SER0-0.009-0.00929.0530.0050.0050.0000.0000.0000.000
113A152VAL00.0450.03122.902-0.004-0.0040.0000.0000.0000.000
114A153ASP-1-0.869-0.93224.0210.0490.0490.0000.0000.0000.000
115A154SER0-0.107-0.06026.3340.0000.0000.0000.0000.0000.000
116A155ALA0-0.025-0.00426.327-0.003-0.0030.0000.0000.0000.000
117A156ALA00.0680.03325.253-0.004-0.0040.0000.0000.0000.000
118A157GLY00.0070.03527.238-0.003-0.0030.0000.0000.0000.000
119A158LYS10.9160.94630.634-0.002-0.0020.0000.0000.0000.000
120A159LEU0-0.0310.01426.789-0.004-0.0040.0000.0000.0000.000
121A160GLN0-0.010-0.00231.4070.0020.0020.0000.0000.0000.000
122A161TRP00.0570.01127.265-0.006-0.0060.0000.0000.0000.000
123A162LYS10.9390.98734.4150.0400.0400.0000.0000.0000.000
124A163PHE00.0560.03435.499-0.005-0.0050.0000.0000.0000.000
125A164LEU0-0.069-0.04535.2580.0010.0010.0000.0000.0000.000
126A165GLU-1-0.858-0.89337.433-0.043-0.0430.0000.0000.0000.000
127A174DVA00.0450.01433.026-0.001-0.0010.0000.0000.0000.000
128A175VAL00.0190.01231.1780.0050.0050.0000.0000.0000.000
129A176GLN0-0.050-0.04631.727-0.001-0.0010.0000.0000.0000.000
130A177VAL0-0.0370.00027.6560.0050.0050.0000.0000.0000.000
131A178ASN00.003-0.01430.979-0.009-0.0090.0000.0000.0000.000
132A179ASN00.0340.03026.6510.0130.0130.0000.0000.0000.000
133A180PRO0-0.0140.01230.311-0.003-0.0030.0000.0000.0000.000
134A181THR0-0.065-0.06528.5930.0050.0050.0000.0000.0000.000
135A182PRO00.0540.01028.890-0.005-0.0050.0000.0000.0000.000
136A183TYR00.0360.02224.4360.0000.0000.0000.0000.0000.000
137A184TYR00.0420.01721.000-0.006-0.0060.0000.0000.0000.000
138A185VAL0-0.0110.00922.3980.0110.0110.0000.0000.0000.000
139A186SER0-0.040-0.03917.617-0.025-0.0250.0000.0000.0000.000
140A187PHE00.0540.01619.7470.0150.0150.0000.0000.0000.000
141A188ALA0-0.045-0.03617.599-0.025-0.0250.0000.0000.0000.000
142A189SER0-0.015-0.01318.743-0.011-0.0110.0000.0000.0000.000
143A190VAL00.0160.01722.0210.0090.0090.0000.0000.0000.000
144A191GLU-1-0.932-0.96625.536-0.030-0.0300.0000.0000.0000.000
145A192LEU00.0060.01528.4420.0040.0040.0000.0000.0000.000
146A193ILE00.0170.00430.4300.0000.0000.0000.0000.0000.000
147A194VAL00.0330.00234.1180.0010.0010.0000.0000.0000.000
148A195ASP-1-0.919-0.95437.772-0.007-0.0070.0000.0000.0000.000
149A196GLY0-0.015-0.01135.2810.0010.0010.0000.0000.0000.000
150A197ARG10.9010.96834.2080.0170.0170.0000.0000.0000.000
151A198VAL00.0370.01828.350-0.001-0.0010.0000.0000.0000.000
152A199MET0-0.027-0.01830.900-0.002-0.0020.0000.0000.0000.000
153A200SER0-0.0010.00324.934-0.003-0.0030.0000.0000.0000.000
154A201VAL00.0450.01127.005-0.003-0.0030.0000.0000.0000.000
155A202GLY00.0350.03922.960-0.008-0.0080.0000.0000.0000.000
156A203LYS10.9400.96914.8190.2250.2250.0000.0000.0000.000
157A204GLY0-0.039-0.02919.555-0.007-0.0070.0000.0000.0000.000
158A205MET0-0.055-0.01218.3350.0030.0030.0000.0000.0000.000
159A206VAL00.0110.02521.163-0.005-0.0050.0000.0000.0000.000
160A207ALA00.0340.01324.0430.0020.0020.0000.0000.0000.000
161A208PRO00.0140.00624.6430.0050.0050.0000.0000.0000.000
162A209PHE0-0.044-0.02127.735-0.003-0.0030.0000.0000.0000.000
163A210SER0-0.0180.00128.204-0.004-0.0040.0000.0000.0000.000
164A211THR00.0450.02230.3150.0050.0050.0000.0000.0000.000
165A212LYS10.8370.93323.0550.1060.1060.0000.0000.0000.000
166A213GLU-1-0.815-0.90128.467-0.057-0.0570.0000.0000.0000.000
167A214PHE0-0.071-0.04624.297-0.009-0.0090.0000.0000.0000.000
168A215ASP-1-0.900-0.95428.836-0.077-0.0770.0000.0000.0000.000
169A216TRP00.0310.02129.739-0.003-0.0030.0000.0000.0000.000
170A217GLN00.003-0.01732.1410.0000.0000.0000.0000.0000.000
171A218GLY00.0090.00134.1280.0030.0030.0000.0000.0000.000
172A219ASN0-0.049-0.03835.6190.0020.0020.0000.0000.0000.000
173A220PRO0-0.0380.00335.5850.0030.0030.0000.0000.0000.000
174A221LYS10.8840.91338.6460.0410.0410.0000.0000.0000.000
175A222ASN0-0.057-0.01841.7540.0010.0010.0000.0000.0000.000
176A223MET00.0260.02739.3750.0030.0030.0000.0000.0000.000
177A224GLU-1-0.893-0.97338.543-0.022-0.0220.0000.0000.0000.000
178A225ALA0-0.0180.01341.6410.0000.0000.0000.0000.0000.000
179A226ALA0-0.065-0.02536.2470.0020.0020.0000.0000.0000.000
180A227SER00.0360.02934.2910.0020.0020.0000.0000.0000.000
181A228VAL0-0.044-0.04029.786-0.003-0.0030.0000.0000.0000.000
182A229ARG10.8750.92127.2960.0000.0000.0000.0000.0000.000
183A230TYR0-0.054-0.07725.490-0.007-0.0070.0000.0000.0000.000
184A231GLU-1-0.856-0.91920.7490.0200.0200.0000.0000.0000.000
185A232VAL0-0.026-0.03020.988-0.018-0.0180.0000.0000.0000.000
186A233ILE0-0.060-0.03114.7720.0070.0070.0000.0000.0000.000
187A234ASN00.0340.03117.559-0.006-0.0060.0000.0000.0000.000
188A235ASP-1-0.714-0.85016.9610.0110.0110.0000.0000.0000.000
189A236TYR0-0.028-0.01814.943-0.005-0.0050.0000.0000.0000.000
190A237GLY0-0.056-0.01712.8680.0460.0460.0000.0000.0000.000
191A238GLY0-0.0010.00713.8790.0070.0070.0000.0000.0000.000
192A239ARG10.8600.91616.435-0.073-0.0730.0000.0000.0000.000
193A240ASN0-0.0010.00119.2450.0140.0140.0000.0000.0000.000
194A241THR00.0110.00423.001-0.012-0.0120.0000.0000.0000.000
195A242HIS00.0020.00625.5900.0050.0050.0000.0000.0000.000
196A243ASP-1-0.728-0.83228.967-0.001-0.0010.0000.0000.0000.000
197A244ARG10.7940.89131.9590.0010.0010.0000.0000.0000.000
198A245ALA00.0870.05534.506-0.002-0.0020.0000.0000.0000.000
199A246LEU0-0.059-0.01934.256-0.002-0.0020.0000.0000.0000.000
200A247GLY00.0160.00237.5920.0000.0000.0000.0000.0000.000