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: R8R88

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 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 200
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2102793.124743
FMO2-HF: Nuclear repulsion 2025544.715827
FMO2-HF: Total energy -77248.408916
FMO2-MP2: Total energy -77477.729287


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.
-15.816-4.3044.64-5.94-10.212-0.026
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 : -0.009 / q_NPA : -0.005
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].
3A33GLN0-0.0090.0323.8811.0432.625-0.014-0.831-0.7370.003
4A34GLY00.0090.0066.987-0.348-0.3480.0000.0000.0000.000
5A35THR00.012-0.0087.157-0.033-0.0330.0000.0000.0000.000
6A36ARG10.8320.9269.665-0.433-0.4330.0000.0000.0000.000
7A37VAL00.0180.01411.2910.0950.0950.0000.0000.0000.000
8A38VAL00.0180.01913.966-0.052-0.0520.0000.0000.0000.000
9A39PHE0-0.008-0.01117.2210.0230.0230.0000.0000.0000.000
10A40PRO00.0270.01319.471-0.022-0.0220.0000.0000.0000.000
11A41ALA0-0.020-0.00923.071-0.002-0.0020.0000.0000.0000.000
12A42SER0-0.073-0.05625.519-0.011-0.0110.0000.0000.0000.000
13A43GLU-1-0.892-0.90621.5020.1580.1580.0000.0000.0000.000
14A44ARG10.9170.94023.112-0.111-0.1110.0000.0000.0000.000
15A45GLU-1-0.847-0.91718.3160.1230.1230.0000.0000.0000.000
16A46VAL00.0190.02614.6480.0170.0170.0000.0000.0000.000
17A47THR0-0.020-0.01912.659-0.032-0.0320.0000.0000.0000.000
18A48LEU0-0.0010.0017.1100.0370.0370.0000.0000.0000.000
19A49ARG10.9380.9767.719-0.988-0.9880.0000.0000.0000.000
20A50VAL00.0220.0012.486-0.4470.1320.446-0.215-0.8100.002
21A51SER00.001-0.0342.481-2.537-1.2600.424-0.578-1.1230.002
22A52ASN0-0.020-0.0112.459-3.873-1.1072.209-2.276-2.700-0.024
23A53THR00.006-0.0094.1400.4420.591-0.001-0.020-0.1270.000
24A54SER0-0.010-0.0036.0290.1040.1040.0000.0000.0000.000
25A55GLY00.0350.0058.6190.1750.1750.0000.0000.0000.000
26A56THR0-0.0020.0019.5290.1050.1050.0000.0000.0000.000
27A57PRO0-0.033-0.0018.899-0.128-0.1280.0000.0000.0000.000
28A58VAL00.0160.0164.200-0.100-0.014-0.001-0.006-0.0790.000
29A59LEU0-0.017-0.0087.5120.2620.2620.0000.0000.0000.000
30A60ALA00.008-0.0043.308-0.688-0.4110.026-0.073-0.2300.000
31A61GLN00.0150.0175.1020.2470.267-0.001-0.001-0.0180.000
32A62ALA0-0.026-0.0216.941-0.105-0.1050.0000.0000.0000.000
33A63TRP00.0390.0158.8230.0130.0130.0000.0000.0000.000
34A64ILE0-0.004-0.01311.530-0.010-0.0100.0000.0000.0000.000
35A65ASP-1-0.695-0.80014.216-0.200-0.2000.0000.0000.0000.000
36A66ASP-1-0.755-0.88116.720-0.067-0.0670.0000.0000.0000.000
37A67GLY0-0.066-0.03217.9620.0140.0140.0000.0000.0000.000
38A68ARG10.8620.92418.5900.0690.0690.0000.0000.0000.000
39A69GLN0-0.044-0.03114.370-0.061-0.0610.0000.0000.0000.000
40A70ASP-1-0.884-0.94017.660-0.179-0.1790.0000.0000.0000.000
41A71VAL00.0130.01320.3570.0080.0080.0000.0000.0000.000
42A72PRO00.0020.00419.420-0.017-0.0170.0000.0000.0000.000
43A73PRO00.007-0.00515.7900.0160.0160.0000.0000.0000.000
44A74GLU-1-0.893-0.95218.582-0.099-0.0990.0000.0000.0000.000
45A75GLU-1-0.926-0.96521.164-0.107-0.1070.0000.0000.0000.000
46A76LEU0-0.094-0.03518.6360.0090.0090.0000.0000.0000.000
47A77GLN0-0.081-0.04122.7030.0200.0200.0000.0000.0000.000
48A78VAL00.0180.02318.0340.0120.0120.0000.0000.0000.000
49A79PRO0-0.0150.00321.5000.0010.0010.0000.0000.0000.000
50A80PHE0-0.035-0.03517.4080.0200.0200.0000.0000.0000.000
51A81SER00.0160.02216.899-0.015-0.0150.0000.0000.0000.000
52A82VAL00.001-0.01410.2830.0300.0300.0000.0000.0000.000
53A83THR0-0.0430.01013.347-0.037-0.0370.0000.0000.0000.000
54A84PRO00.020-0.01210.5510.0570.0570.0000.0000.0000.000
55A85ALA00.0820.02810.8820.0070.0070.0000.0000.0000.000
56A86VAL0-0.004-0.0109.221-0.075-0.0750.0000.0000.0000.000
57A87THR0-0.039-0.0136.5390.0930.0930.0000.0000.0000.000
58A88ARG10.8930.9387.6980.0710.0710.0000.0000.0000.000
59A89VAL0-0.013-0.0044.0470.0320.1860.000-0.022-0.1320.000
60A90GLU-1-0.768-0.8727.061-0.363-0.3630.0000.0000.0000.000
61A91PRO0-0.0170.0008.1580.0360.0360.0000.0000.0000.000
62A92ASN0-0.039-0.0229.2110.1330.1330.0000.0000.0000.000
63A93GLY00.0510.0428.4180.1100.1100.0000.0000.0000.000
64A94GLY0-0.018-0.0276.4270.3370.3370.0000.0000.0000.000
65A95ALA0-0.0230.0096.446-0.265-0.2650.0000.0000.0000.000
66A96VAL0-0.037-0.0337.4130.2620.2620.0000.0000.0000.000
67A97LEU00.0170.0326.316-0.112-0.1120.0000.0000.0000.000
68A98ARG10.8870.9219.882-0.139-0.1390.0000.0000.0000.000
69A99ILE00.0100.00811.257-0.043-0.0430.0000.0000.0000.000
70A100ALA00.0100.00314.9480.0230.0230.0000.0000.0000.000
71A101TYR00.0270.02218.769-0.016-0.0160.0000.0000.0000.000
72A102LEU00.0070.00921.7200.0040.0040.0000.0000.0000.000
73A103LYS10.9050.93824.443-0.045-0.0450.0000.0000.0000.000
74A104ALA00.0410.03726.292-0.005-0.0050.0000.0000.0000.000
75A105PRO0-0.055-0.03728.1900.0080.0080.0000.0000.0000.000
76A106LEU00.0240.00723.853-0.005-0.0050.0000.0000.0000.000
77A107PRO00.0030.00127.0380.0030.0030.0000.0000.0000.000
78A108THR00.0240.01228.5510.0050.0050.0000.0000.0000.000
79A109ASP-1-0.829-0.89131.0710.0390.0390.0000.0000.0000.000
80A110ARG10.8510.89427.865-0.022-0.0220.0000.0000.0000.000
81A111GLU-1-0.768-0.87522.7350.1120.1120.0000.0000.0000.000
82A112SER0-0.053-0.03323.409-0.014-0.0140.0000.0000.0000.000
83A113LEU0-0.040-0.01617.0030.0130.0130.0000.0000.0000.000
84A114PHE00.0230.01717.137-0.011-0.0110.0000.0000.0000.000
85A115TRP0-0.015-0.02312.9930.0160.0160.0000.0000.0000.000
86A116LEU00.0290.0248.613-0.001-0.0010.0000.0000.0000.000
87A117ASN0-0.060-0.0298.377-0.089-0.0890.0000.0000.0000.000
88A118ILE00.019-0.0022.640-0.6420.0190.519-0.175-1.0060.000
89A119LEU0-0.013-0.0075.067-0.404-0.305-0.001-0.003-0.0940.000
90A120GLU-1-0.875-0.9422.832-8.761-5.9380.340-1.278-1.885-0.011
91A121VAL0-0.015-0.0334.8990.2350.274-0.001-0.006-0.0320.000
92A122PRO00.008-0.0027.0200.2110.2110.0000.0000.0000.000
93A123PRO0-0.0140.0008.7460.1500.1500.0000.0000.0000.000
94A124ARG10.9100.96712.5130.7060.7060.0000.0000.0000.000
95A134PHE00.008-0.01112.3070.0060.0060.0000.0000.0000.000
96A135SER00.0210.0128.823-0.011-0.0110.0000.0000.0000.000
97A136PHE0-0.0060.0124.7460.1760.276-0.001-0.003-0.0960.000
98A137ARG10.8550.9155.7690.3100.3100.0000.0000.0000.000
99A138SER00.0260.0262.170-0.5460.0910.698-0.409-0.9260.002
100A139ARG10.7760.8505.3960.2690.316-0.001-0.001-0.0450.000
101A140PHE0-0.020-0.0064.029-0.0870.129-0.001-0.043-0.1720.000
102A141LYS10.8610.9039.864-0.039-0.0390.0000.0000.0000.000
103A142LEU00.0140.00713.4350.0510.0510.0000.0000.0000.000
104A143PHE00.002-0.00915.447-0.026-0.0260.0000.0000.0000.000
105A144PHE00.0470.03118.9790.0200.0200.0000.0000.0000.000
106A145ARG10.7500.82321.381-0.173-0.1730.0000.0000.0000.000
107A146PRO00.0260.02424.2170.0090.0090.0000.0000.0000.000
108A147SER00.0710.02927.8070.0030.0030.0000.0000.0000.000
109A148GLN0-0.028-0.01828.8650.0120.0120.0000.0000.0000.000
110A149LEU0-0.051-0.00727.223-0.001-0.0010.0000.0000.0000.000
111A150LYS10.9070.94027.722-0.103-0.1030.0000.0000.0000.000
112A151SER00.001-0.01528.831-0.001-0.0010.0000.0000.0000.000
113A152VAL00.0410.02922.722-0.009-0.0090.0000.0000.0000.000
114A153ASP-1-0.899-0.94724.6910.1720.1720.0000.0000.0000.000
115A154SER0-0.063-0.04326.264-0.008-0.0080.0000.0000.0000.000
116A155ALA0-0.034-0.00326.190-0.009-0.0090.0000.0000.0000.000
117A156ALA00.0490.01125.169-0.009-0.0090.0000.0000.0000.000
118A157GLY0-0.0120.00527.225-0.006-0.0060.0000.0000.0000.000
119A158LYS10.9370.97030.585-0.084-0.0840.0000.0000.0000.000
120A159LEU0-0.0320.01326.591-0.006-0.0060.0000.0000.0000.000
121A160GLN0-0.0160.00631.269-0.002-0.0020.0000.0000.0000.000
122A161TRP00.0640.01827.293-0.005-0.0050.0000.0000.0000.000
123A162LYS10.8910.96334.490-0.007-0.0070.0000.0000.0000.000
124A163PHE00.0650.02235.736-0.002-0.0020.0000.0000.0000.000
125A164LEU0-0.086-0.04935.4790.0000.0000.0000.0000.0000.000
126A165GLU-1-0.869-0.90037.393-0.013-0.0130.0000.0000.0000.000
127A174DVA00.0170.02632.850-0.002-0.0020.0000.0000.0000.000
128A175VAL0-0.001-0.01131.4850.0030.0030.0000.0000.0000.000
129A176GLN0-0.029-0.03231.706-0.002-0.0020.0000.0000.0000.000
130A177VAL0-0.0290.00627.7420.0050.0050.0000.0000.0000.000
131A178ASN00.015-0.02231.229-0.006-0.0060.0000.0000.0000.000
132A179ASN00.0210.00727.0240.0120.0120.0000.0000.0000.000
133A180PRO0-0.0120.01830.542-0.002-0.0020.0000.0000.0000.000
134A181THR0-0.059-0.06128.9700.0070.0070.0000.0000.0000.000
135A182PRO00.0440.02429.543-0.004-0.0040.0000.0000.0000.000
136A183TYR00.0510.01624.8090.0040.0040.0000.0000.0000.000
137A184TYR00.010-0.01021.226-0.016-0.0160.0000.0000.0000.000
138A185VAL00.0090.01022.3980.0170.0170.0000.0000.0000.000
139A186SER0-0.002-0.00617.478-0.024-0.0240.0000.0000.0000.000
140A187PHE00.0260.00619.5920.0220.0220.0000.0000.0000.000
141A188ALA0-0.036-0.02717.787-0.010-0.0100.0000.0000.0000.000
142A189SER0-0.044-0.03918.755-0.020-0.0200.0000.0000.0000.000
143A190VAL00.0190.01222.0050.0100.0100.0000.0000.0000.000
144A191GLU-1-0.918-0.96325.5390.0420.0420.0000.0000.0000.000
145A192LEU00.0130.01628.6040.0040.0040.0000.0000.0000.000
146A193ILE0-0.002-0.00930.3170.0000.0000.0000.0000.0000.000
147A194VAL00.0270.00734.3160.0010.0010.0000.0000.0000.000
148A195ASP-1-0.841-0.90338.0440.0210.0210.0000.0000.0000.000
149A196GLY0-0.019-0.00535.6640.0000.0000.0000.0000.0000.000
150A197ARG10.8490.91234.636-0.015-0.0150.0000.0000.0000.000
151A198VAL00.0140.01028.9690.0000.0000.0000.0000.0000.000
152A199MET0-0.0240.00130.674-0.006-0.0060.0000.0000.0000.000
153A200SER0-0.005-0.00325.1400.0000.0000.0000.0000.0000.000
154A201VAL00.0230.00526.969-0.007-0.0070.0000.0000.0000.000
155A202GLY00.0210.02523.183-0.006-0.0060.0000.0000.0000.000
156A203LYS10.9320.95815.4160.0510.0510.0000.0000.0000.000
157A204GLY0-0.001-0.00619.058-0.018-0.0180.0000.0000.0000.000
158A205MET0-0.0450.02518.7570.0240.0240.0000.0000.0000.000
159A206VAL00.0110.03321.264-0.012-0.0120.0000.0000.0000.000
160A207ALA00.0340.01323.9840.0100.0100.0000.0000.0000.000
161A208PRO00.0180.01624.7120.0010.0010.0000.0000.0000.000
162A209PHE0-0.053-0.01327.856-0.007-0.0070.0000.0000.0000.000
163A210SER0-0.0070.00928.359-0.008-0.0080.0000.0000.0000.000
164A211THR0-0.032-0.03330.4000.0060.0060.0000.0000.0000.000
165A212LYS10.8700.93023.6170.0130.0130.0000.0000.0000.000
166A213GLU-1-0.782-0.86428.532-0.002-0.0020.0000.0000.0000.000
167A214PHE0-0.036-0.02424.280-0.004-0.0040.0000.0000.0000.000
168A215ASP-1-0.877-0.94828.701-0.028-0.0280.0000.0000.0000.000
169A216TRP00.0310.00029.6900.0000.0000.0000.0000.0000.000
170A217GLN00.015-0.00632.106-0.003-0.0030.0000.0000.0000.000
171A218GLY00.0060.00434.4450.0010.0010.0000.0000.0000.000
172A219ASN0-0.043-0.03735.9090.0030.0030.0000.0000.0000.000
173A220PRO0-0.0340.00835.5500.0010.0010.0000.0000.0000.000
174A221LYS10.8930.92138.7020.0110.0110.0000.0000.0000.000
175A222ASN0-0.057-0.02841.7050.0000.0000.0000.0000.0000.000
176A223MET0-0.0090.01439.5020.0020.0020.0000.0000.0000.000
177A224GLU-1-0.873-0.94738.6500.0120.0120.0000.0000.0000.000
178A225ALA00.0200.02141.3590.0010.0010.0000.0000.0000.000
179A226ALA0-0.063-0.02736.4470.0030.0030.0000.0000.0000.000
180A227SER0-0.012-0.00333.9520.0020.0020.0000.0000.0000.000
181A228VAL0-0.019-0.01729.940-0.003-0.0030.0000.0000.0000.000
182A229ARG10.8530.89327.485-0.067-0.0670.0000.0000.0000.000
183A230TYR0-0.016-0.03025.403-0.007-0.0070.0000.0000.0000.000
184A231GLU-1-0.806-0.86821.1230.1570.1570.0000.0000.0000.000
185A232VAL0-0.016-0.02221.141-0.014-0.0140.0000.0000.0000.000
186A233ILE0-0.049-0.02714.7400.0170.0170.0000.0000.0000.000
187A234ASN00.0220.00917.9350.0180.0180.0000.0000.0000.000
188A235ASP-1-0.719-0.85016.8500.2330.2330.0000.0000.0000.000
189A236TYR0-0.012-0.01015.2110.0280.0280.0000.0000.0000.000
190A237GLY0-0.056-0.01812.8280.0990.0990.0000.0000.0000.000
191A238GLY0-0.0050.01013.8610.0050.0050.0000.0000.0000.000
192A239ARG10.8710.90616.527-0.239-0.2390.0000.0000.0000.000
193A240ASN00.0140.01419.1030.0180.0180.0000.0000.0000.000
194A241THR0-0.026-0.01822.881-0.010-0.0100.0000.0000.0000.000
195A242HIS00.0480.02125.589-0.005-0.0050.0000.0000.0000.000
196A243ASP-1-0.737-0.81229.0580.0670.0670.0000.0000.0000.000
197A244ARG10.7670.86931.597-0.069-0.0690.0000.0000.0000.000
198A245ALA00.0800.05134.703-0.002-0.0020.0000.0000.0000.000
199A246LEU0-0.036-0.00233.9640.0010.0010.0000.0000.0000.000
200A247GLY00.0200.00337.598-0.003-0.0030.0000.0000.0000.000