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: V5RL1

Calculation Name: 3Q0X-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3Q0X

Chain ID: A

ChEMBL ID:

UniProt ID: A9CQL4

Base Structure: X-ray

Registration Date: 2023-06-21

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 206
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2067949.065772
FMO2-HF: Nuclear repulsion 1985998.619685
FMO2-HF: Total energy -81950.446087
FMO2-MP2: Total energy -82192.383187


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:16:PHE)


Summations of interaction energy for fragment #1(A:16:PHE)
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.
-27.161-9.06513.477-8.95-22.623-0.03
Interaction energy analysis for fragmet #1(A:16:PHE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.020 / q_NPA : -0.018
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].
3A18LEU00.0270.0062.473-1.3651.8511.627-1.300-3.5440.008
4A19SER0-0.054-0.0185.041-0.463-0.216-0.001-0.025-0.2220.000
5A20THR0-0.049-0.0446.953-0.085-0.0850.0000.0000.0000.000
6A21ALA0-0.050-0.0013.516-0.778-0.1810.042-0.178-0.4610.001
7A22THR00.0240.0144.399-0.183-0.068-0.001-0.009-0.1040.000
8A23THR0-0.033-0.0205.583-0.227-0.2270.0000.0000.0000.000
9A24LEU0-0.032-0.0187.4020.0390.0390.0000.0000.0000.000
10A25PHE00.0460.0129.4980.0450.0450.0000.0000.0000.000
11A26TRP00.002-0.02210.266-0.025-0.0250.0000.0000.0000.000
12A27ARG10.9560.99212.7060.1140.1140.0000.0000.0000.000
13A28PRO0-0.0060.00315.812-0.007-0.0070.0000.0000.0000.000
14A29VAL0-0.0100.00417.0240.0030.0030.0000.0000.0000.000
15A30PRO00.0580.04819.638-0.002-0.0020.0000.0000.0000.000
16A31VAL0-0.062-0.04218.714-0.002-0.0020.0000.0000.0000.000
17A32HIS0-0.007-0.00222.1600.0050.0050.0000.0000.0000.000
18A33VAL0-0.026-0.01821.975-0.004-0.0040.0000.0000.0000.000
19A34LYS10.8430.89524.0040.0760.0760.0000.0000.0000.000
20A35GLN00.0350.02224.481-0.008-0.0080.0000.0000.0000.000
21A36GLN0-0.017-0.00926.4310.0060.0060.0000.0000.0000.000
22A37ASP-1-0.920-0.96628.714-0.058-0.0580.0000.0000.0000.000
23A38ARG10.8340.93523.8230.0870.0870.0000.0000.0000.000
24A39GLU-1-0.892-0.94030.681-0.055-0.0550.0000.0000.0000.000
25A40ASP-1-0.842-0.89728.782-0.072-0.0720.0000.0000.0000.000
26A41VAL0-0.026-0.02426.0140.0030.0030.0000.0000.0000.000
27A42LEU0-0.041-0.00625.348-0.004-0.0040.0000.0000.0000.000
28A43GLU-1-0.886-0.95422.640-0.088-0.0880.0000.0000.0000.000
29A44GLU-1-0.865-0.94221.105-0.088-0.0880.0000.0000.0000.000
30A45LEU0-0.034-0.01916.965-0.004-0.0040.0000.0000.0000.000
31A46THR0-0.045-0.02512.8150.0010.0010.0000.0000.0000.000
32A47PHE00.0200.01212.316-0.009-0.0090.0000.0000.0000.000
33A48ARG10.8010.8727.5170.1740.1740.0000.0000.0000.000
34A49ILE0-0.0120.0017.3030.0330.0330.0000.0000.0000.000
35A50LEU00.0140.0092.718-1.006-0.0970.215-0.204-0.920-0.001
36A51THR00.001-0.0073.293-0.7530.2310.080-0.292-0.772-0.002
37A52GLY00.0390.0082.290-0.1860.3712.134-0.796-1.895-0.002
38A53VAL00.0220.0202.8720.170-0.4460.2431.493-1.120-0.002
39A54ALA00.0440.0352.169-4.136-1.9344.705-3.578-3.328-0.027
40A55LYS10.8520.9253.201-4.881-3.8390.093-0.192-0.9420.006
41A56GLN00.026-0.0024.1390.7781.1670.004-0.058-0.3360.000
42A57ASN00.0570.0286.622-0.604-0.6040.0000.0000.0000.000
43A58HIS00.0230.0116.902-0.305-0.3050.0000.0000.0000.000
44A59ASN0-0.039-0.0268.460-0.260-0.2600.0000.0000.0000.000
45A60LEU0-0.0220.0106.571-0.093-0.0930.0000.0000.0000.000
46A61ARG10.9390.9805.0730.6240.6240.0000.0000.0000.000
47A62ILE0-0.025-0.0132.263-2.471-0.3183.057-1.204-4.0060.004
48A63LEU0-0.013-0.0012.943-2.473-1.0230.282-0.803-0.929-0.008
49A64ARG10.8490.9162.970-1.4870.7930.610-0.715-2.1750.005
50A65ILE00.0030.0015.137-0.562-0.473-0.001-0.007-0.0800.000
51A66HIS0-0.024-0.0204.548-0.0600.061-0.001-0.002-0.1190.000
52A67ILE00.0280.0249.0050.0000.0000.0000.0000.0000.000
53A68SER00.019-0.00712.715-0.017-0.0170.0000.0000.0000.000
54A69SER00.0450.02114.4440.0100.0100.0000.0000.0000.000
55A70ASP-1-0.889-0.94217.565-0.116-0.1160.0000.0000.0000.000
56A71SER0-0.048-0.02219.3860.0080.0080.0000.0000.0000.000
57A72ASP-1-0.829-0.91820.589-0.104-0.1040.0000.0000.0000.000
58A73LEU0-0.011-0.01718.017-0.010-0.0100.0000.0000.0000.000
59A74PHE0-0.040-0.03017.221-0.013-0.0130.0000.0000.0000.000
60A75PHE0-0.0390.01016.584-0.018-0.0180.0000.0000.0000.000
61A76LEU0-0.001-0.01310.053-0.013-0.0130.0000.0000.0000.000
62A77HIS00.0080.02212.943-0.010-0.0100.0000.0000.0000.000
63A78THR0-0.060-0.0178.236-0.037-0.0370.0000.0000.0000.000
64A79LEU00.0370.0268.877-0.033-0.0330.0000.0000.0000.000
65A80GLU-1-0.880-0.9552.799-5.841-3.4800.389-1.080-1.670-0.012
66A81VAL00.0320.0387.297-0.148-0.1480.0000.0000.0000.000
67A82SER00.0470.0126.552-0.067-0.0670.0000.0000.0000.000
68A83GLU-1-0.911-0.9897.455-0.318-0.3180.0000.0000.0000.000
69A84GLU-1-0.998-0.9959.856-0.025-0.0250.0000.0000.0000.000
70A85ASP-1-0.910-0.96210.298-0.286-0.2860.0000.0000.0000.000
71A86PHE00.0010.00711.5420.0330.0330.0000.0000.0000.000
72A87GLN0-0.023-0.02313.2230.0180.0180.0000.0000.0000.000
73A88SER00.0080.00816.1860.0210.0210.0000.0000.0000.000
74A89LEU00.0270.01912.9830.0150.0150.0000.0000.0000.000
75A90LYS10.8120.89716.7020.1620.1620.0000.0000.0000.000
76A91ASN00.0260.01118.3110.0120.0120.0000.0000.0000.000
77A92ASP-1-0.892-0.93319.677-0.113-0.1130.0000.0000.0000.000
78A93GLN0-0.092-0.07519.047-0.001-0.0010.0000.0000.0000.000
79A94GLY00.0160.02722.0420.0070.0070.0000.0000.0000.000
80A95ILE0-0.092-0.03716.8360.0040.0040.0000.0000.0000.000
81A96LEU00.0460.01720.432-0.003-0.0030.0000.0000.0000.000
82A97VAL0-0.0100.00216.8770.0010.0010.0000.0000.0000.000
83A98ASP-1-0.792-0.87315.073-0.213-0.2130.0000.0000.0000.000
84A99PHE00.0340.0126.4460.0090.0090.0000.0000.0000.000
85A100ALA00.0190.00211.127-0.032-0.0320.0000.0000.0000.000
86A101SER0-0.037-0.04812.173-0.003-0.0030.0000.0000.0000.000
87A102PHE0-0.051-0.01511.0950.0210.0210.0000.0000.0000.000
88A103PRO00.0360.0119.3750.0270.0270.0000.0000.0000.000
89A104GLY00.0530.03011.5080.0230.0230.0000.0000.0000.000
90A105LYS10.8960.95614.7830.1490.1490.0000.0000.0000.000
91A106ILE0-0.009-0.01112.6440.0170.0170.0000.0000.0000.000
92A107ILE0-0.0010.00311.6900.0110.0110.0000.0000.0000.000
93A108SER00.0170.02015.3570.0150.0150.0000.0000.0000.000
94A109LEU0-0.056-0.02818.3630.0120.0120.0000.0000.0000.000
95A110LEU00.0310.00614.0870.0080.0080.0000.0000.0000.000
96A111GLU-1-0.927-0.96618.310-0.117-0.1170.0000.0000.0000.000
97A112LYS10.8970.96020.4740.0980.0980.0000.0000.0000.000
98A113CYS0-0.070-0.03421.2800.0050.0050.0000.0000.0000.000
99A114ILE0-0.030-0.01818.6710.0040.0040.0000.0000.0000.000
100A115LEU0-0.046-0.02522.9410.0050.0050.0000.0000.0000.000
101A116ALA0-0.0290.01826.0120.0050.0050.0000.0000.0000.000
102A117GLN0-0.028-0.01528.0920.0020.0020.0000.0000.0000.000
103A118PRO0-0.041-0.04631.5270.0000.0000.0000.0000.0000.000
104A119GLY0-0.013-0.01234.0020.0000.0000.0000.0000.0000.000
105A120ASP-1-0.844-0.89731.254-0.057-0.0570.0000.0000.0000.000
106A121SER0-0.015-0.02134.111-0.001-0.0010.0000.0000.0000.000
107A122PRO0-0.030-0.00231.1400.0020.0020.0000.0000.0000.000
108A123ARG10.8740.94129.7980.0600.0600.0000.0000.0000.000
109A124PHE00.000-0.00624.236-0.003-0.0030.0000.0000.0000.000
110A125GLN00.0280.00925.5070.0020.0020.0000.0000.0000.000
111A126ALA00.0580.03320.334-0.003-0.0030.0000.0000.0000.000
112A127VAL0-0.045-0.02921.9160.0050.0050.0000.0000.0000.000
113A128LEU00.0210.02617.585-0.006-0.0060.0000.0000.0000.000
114A129THR0-0.021-0.00220.9550.0080.0080.0000.0000.0000.000
115A130ILE00.013-0.01320.408-0.008-0.0080.0000.0000.0000.000
116A131ARG10.8750.92422.6900.0920.0920.0000.0000.0000.000
117A132GLY00.0200.03022.6110.0070.0070.0000.0000.0000.000
118A133GLY0-0.022-0.01819.7110.0030.0030.0000.0000.0000.000
119A134GLU-1-0.878-0.94717.227-0.195-0.1950.0000.0000.0000.000
120A135SER0-0.095-0.06517.0260.0140.0140.0000.0000.0000.000
121A136VAL00.0270.01518.144-0.008-0.0080.0000.0000.0000.000
122A137PHE00.0150.01016.3670.0070.0070.0000.0000.0000.000
123A138LYS10.9190.96418.7020.0810.0810.0000.0000.0000.000
124A139ILE00.0150.01917.9720.0030.0030.0000.0000.0000.000
125A140VAL0-0.070-0.04922.0490.0000.0000.0000.0000.0000.000
126A141GLU-1-0.827-0.89125.778-0.072-0.0720.0000.0000.0000.000
127A142ILE0-0.028-0.02928.4310.0010.0010.0000.0000.0000.000
128A143ASN00.0290.00731.730-0.001-0.0010.0000.0000.0000.000
129A144ASP-1-0.885-0.93534.940-0.045-0.0450.0000.0000.0000.000
130A145GLU-1-0.943-0.95736.394-0.046-0.0460.0000.0000.0000.000
131A146LYS10.8800.94132.1070.0600.0600.0000.0000.0000.000
132A147GLN00.0960.03929.234-0.005-0.0050.0000.0000.0000.000
133A148LEU0-0.040-0.02928.3840.0010.0010.0000.0000.0000.000
134A149PRO00.007-0.00324.687-0.002-0.0020.0000.0000.0000.000
135A150HIS0-0.037-0.02122.494-0.005-0.0050.0000.0000.0000.000
136A151ILE0-0.024-0.02416.921-0.007-0.0070.0000.0000.0000.000
137A152THR0-0.001-0.00319.7130.0090.0090.0000.0000.0000.000
138A153LEU0-0.022-0.00313.639-0.007-0.0070.0000.0000.0000.000
139A154ALA00.0510.02715.7180.0110.0110.0000.0000.0000.000
140A155PHE0-0.006-0.01011.048-0.015-0.0150.0000.0000.0000.000
141A156ARG10.9700.9949.7220.4020.4020.0000.0000.0000.000
142A157PRO0-0.0050.00413.152-0.023-0.0230.0000.0000.0000.000
143A158GLY0-0.034-0.03512.890-0.025-0.0250.0000.0000.0000.000
144A159ASN00.0340.01212.9800.0230.0230.0000.0000.0000.000
145A160ASP-1-0.789-0.90614.509-0.157-0.1570.0000.0000.0000.000
146A161SER0-0.069-0.03912.369-0.006-0.0060.0000.0000.0000.000
147A162VAL0-0.030-0.0079.257-0.045-0.0450.0000.0000.0000.000
148A163VAL00.0760.04510.410-0.047-0.0470.0000.0000.0000.000
149A164LYS10.9530.98513.0330.1590.1590.0000.0000.0000.000
150A165GLN0-0.074-0.0577.925-0.093-0.0930.0000.0000.0000.000
151A166PHE00.0280.0208.2570.0110.0110.0000.0000.0000.000
152A167LEU00.0480.02010.0320.0390.0390.0000.0000.0000.000
153A168ALA0-0.029-0.00412.2480.0350.0350.0000.0000.0000.000
154A169PHE0-0.032-0.0127.6450.0220.0220.0000.0000.0000.000
155A170ARG10.9300.95010.8070.1800.1800.0000.0000.0000.000
156A171LEU00.0120.01812.6160.0250.0250.0000.0000.0000.000
157A172SER0-0.083-0.04412.8890.0220.0220.0000.0000.0000.000
158A173GLU-1-0.735-0.82910.684-0.117-0.1170.0000.0000.0000.000
159A174VAL00.001-0.00714.0270.0080.0080.0000.0000.0000.000
160A175LYS10.9450.95117.1910.0300.0300.0000.0000.0000.000
161A176GLY00.0110.01817.6610.0070.0070.0000.0000.0000.000
162A177THR00.0180.01316.8570.0010.0010.0000.0000.0000.000
163A178CYS0-0.072-0.04119.5960.0000.0000.0000.0000.0000.000
164A179HIS0-0.087-0.04022.0320.0020.0020.0000.0000.0000.000
165A180ASP-1-0.838-0.92820.411-0.014-0.0140.0000.0000.0000.000
166A181LEU0-0.015-0.00922.9200.0000.0000.0000.0000.0000.000
167A182SER0-0.052-0.02225.7030.0010.0010.0000.0000.0000.000
168A183ASP-1-0.862-0.92426.9740.0000.0000.0000.0000.0000.000
169A184ASP-1-0.871-0.92726.971-0.019-0.0190.0000.0000.0000.000
170A185LEU0-0.083-0.03129.6990.0010.0010.0000.0000.0000.000
171A186SER0-0.003-0.00231.7080.0010.0010.0000.0000.0000.000
172A187ARG10.8730.92332.4940.0070.0070.0000.0000.0000.000
173A188THR0-0.021-0.02932.6930.0000.0000.0000.0000.0000.000
174A189ARG10.8500.92534.7930.0140.0140.0000.0000.0000.000
175A190ASP-1-0.834-0.91836.801-0.004-0.0040.0000.0000.0000.000
176A191ASP-1-0.865-0.91637.788-0.009-0.0090.0000.0000.0000.000
177A192ARG10.7720.85739.4490.0110.0110.0000.0000.0000.000
178A193ASP-1-0.804-0.88641.331-0.008-0.0080.0000.0000.0000.000
179A194SER00.0050.01042.9730.0010.0010.0000.0000.0000.000
180A195MET0-0.015-0.01042.3050.0000.0000.0000.0000.0000.000
181A196VAL0-0.0160.00045.5880.0000.0000.0000.0000.0000.000
182A197ALA00.0210.02147.7530.0000.0000.0000.0000.0000.000
183A198GLN00.011-0.00346.2080.0000.0000.0000.0000.0000.000
184A199LEU0-0.027-0.00849.5680.0000.0000.0000.0000.0000.000
185A200ALA00.001-0.01051.3050.0000.0000.0000.0000.0000.000
186A201GLN00.0090.00952.7490.0000.0000.0000.0000.0000.000
187A202CYS0-0.0120.00353.7200.0000.0000.0000.0000.0000.000
188A203ARG10.9520.96053.1700.0090.0090.0000.0000.0000.000
189A204GLN0-0.018-0.00457.3890.0000.0000.0000.0000.0000.000
190A205GLN0-0.001-0.00756.0710.0000.0000.0000.0000.0000.000
191A206LEU0-0.016-0.00159.0650.0000.0000.0000.0000.0000.000
192A207ALA0-0.039-0.02861.2860.0000.0000.0000.0000.0000.000
193A208GLN00.0200.00962.5920.0000.0000.0000.0000.0000.000
194A209LEU00.0060.01663.5960.0000.0000.0000.0000.0000.000
195A210ARG10.9400.96562.8830.0060.0060.0000.0000.0000.000
196A211GLU-1-0.889-0.93467.466-0.004-0.0040.0000.0000.0000.000
197A212GLN0-0.032-0.02967.5060.0000.0000.0000.0000.0000.000
198A213TYR0-0.072-0.02269.5180.0000.0000.0000.0000.0000.000
199A214ASP-1-0.844-0.94771.106-0.005-0.0050.0000.0000.0000.000
200A215LYS10.8200.89973.4520.0030.0030.0000.0000.0000.000
201A216HIS0-0.042-0.01673.6440.0000.0000.0000.0000.0000.000
202A217LEU00.0050.00073.6950.0000.0000.0000.0000.0000.000
203A218LEU0-0.045-0.01177.2180.0000.0000.0000.0000.0000.000
204A219GLU-1-0.821-0.90379.139-0.003-0.0030.0000.0000.0000.000
205A220VAL0-0.079-0.02079.5000.0000.0000.0000.0000.0000.000
206A221GLN0-0.073-0.03180.6150.0000.0000.0000.0000.0000.000