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: 174KZ

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 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 206
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2074496.19153
FMO2-HF: Nuclear repulsion 1992545.034055
FMO2-HF: Total energy -81951.157475
FMO2-MP2: Total energy -82193.044974


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.
-34.737-13.40713.87-10.298-24.906-0.027
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 : 0.000 / q_NPA : -0.007
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].
3A18LEU00.004-0.0182.416-1.9881.1341.747-1.319-3.5500.005
4A19SER0-0.068-0.0204.719-0.650-0.3680.001-0.039-0.2440.000
5A20THR0-0.034-0.0347.085-0.267-0.2670.0000.0000.0000.000
6A21ALA0-0.052-0.0092.998-1.127-0.2480.317-0.341-0.8550.002
7A22THR00.0140.0124.673-0.448-0.336-0.001-0.013-0.0990.000
8A23THR0-0.034-0.0335.378-0.325-0.3250.0000.0000.0000.000
9A24LEU0-0.016-0.0056.9660.0550.0550.0000.0000.0000.000
10A25PHE00.0430.0158.9980.0430.0430.0000.0000.0000.000
11A26TRP0-0.025-0.0279.907-0.024-0.0240.0000.0000.0000.000
12A27ARG10.9600.98912.2900.1020.1020.0000.0000.0000.000
13A28PRO0-0.0050.01215.374-0.010-0.0100.0000.0000.0000.000
14A29VAL0-0.009-0.00216.8200.0030.0030.0000.0000.0000.000
15A30PRO00.0590.05619.429-0.005-0.0050.0000.0000.0000.000
16A31VAL0-0.052-0.03818.646-0.003-0.0030.0000.0000.0000.000
17A32HIS00.0120.00622.0890.0030.0030.0000.0000.0000.000
18A33VAL0-0.027-0.00921.957-0.006-0.0060.0000.0000.0000.000
19A34LYS10.8330.88823.7590.0990.0990.0000.0000.0000.000
20A35GLN00.0310.02524.450-0.009-0.0090.0000.0000.0000.000
21A36GLN0-0.003-0.00426.2240.0110.0110.0000.0000.0000.000
22A37ASP-1-0.902-0.96228.368-0.088-0.0880.0000.0000.0000.000
23A38ARG10.7350.86723.8960.1160.1160.0000.0000.0000.000
24A39GLU-1-0.882-0.93129.834-0.075-0.0750.0000.0000.0000.000
25A40ASP-1-0.824-0.89028.676-0.095-0.0950.0000.0000.0000.000
26A41VAL0-0.028-0.02126.0530.0050.0050.0000.0000.0000.000
27A42LEU0-0.048-0.01224.981-0.005-0.0050.0000.0000.0000.000
28A43GLU-1-0.816-0.91222.373-0.114-0.1140.0000.0000.0000.000
29A44GLU-1-0.871-0.94721.044-0.096-0.0960.0000.0000.0000.000
30A45LEU0-0.029-0.01916.970-0.005-0.0050.0000.0000.0000.000
31A46THR0-0.045-0.04012.6890.0060.0060.0000.0000.0000.000
32A47PHE00.0240.01412.209-0.018-0.0180.0000.0000.0000.000
33A48ARG10.8050.8667.1640.1350.1350.0000.0000.0000.000
34A49ILE00.0020.0116.9020.0360.0360.0000.0000.0000.000
35A50LEU00.002-0.0082.477-1.366-0.2570.788-0.462-1.4340.000
36A51THR00.0100.0113.029-0.7920.2580.178-0.289-0.938-0.002
37A52GLY00.0300.0132.440-0.5040.5851.927-1.000-2.017-0.001
38A53VAL00.0150.0193.042-0.476-1.0150.0041.250-0.716-0.001
39A54ALA00.0480.0322.674-1.9070.8201.491-2.081-2.138-0.011
40A55LYS10.8490.9063.108-6.811-5.3130.133-0.681-0.9500.010
41A56GLN00.0210.0063.9760.9671.4120.011-0.089-0.3680.000
42A57ASN00.0280.0086.856-0.745-0.7450.0000.0000.0000.000
43A58HIS00.0080.0057.388-0.238-0.2380.0000.0000.0000.000
44A59ASN0-0.021-0.0088.481-0.259-0.2590.0000.0000.0000.000
45A60LEU0-0.0340.0026.886-0.142-0.1420.0000.0000.0000.000
46A61ARG10.9230.9625.2880.6480.6480.0000.0000.0000.000
47A62ILE0-0.029-0.0162.148-2.406-0.8444.283-1.351-4.494-0.001
48A63LEU0-0.0040.0062.903-3.157-1.3820.283-1.059-0.999-0.012
49A64ARG10.8390.9102.763-1.9710.6671.352-0.929-3.0600.009
50A65ILE0-0.009-0.0054.886-0.615-0.493-0.001-0.011-0.1100.000
51A66HIS0-0.001-0.0074.116-0.1310.044-0.001-0.009-0.1660.000
52A67ILE00.0110.0178.7340.0100.0100.0000.0000.0000.000
53A68SER00.0230.00012.439-0.026-0.0260.0000.0000.0000.000
54A69SER00.0600.02814.1580.0170.0170.0000.0000.0000.000
55A70ASP-1-0.870-0.91616.420-0.134-0.1340.0000.0000.0000.000
56A71SER0-0.039-0.02318.6080.0120.0120.0000.0000.0000.000
57A72ASP-1-0.839-0.92820.016-0.140-0.1400.0000.0000.0000.000
58A73LEU0-0.011-0.00617.519-0.013-0.0130.0000.0000.0000.000
59A74PHE0-0.035-0.02316.900-0.021-0.0210.0000.0000.0000.000
60A75PHE0-0.0170.01016.525-0.024-0.0240.0000.0000.0000.000
61A76LEU0-0.014-0.0179.993-0.011-0.0110.0000.0000.0000.000
62A77HIS00.0030.01312.900-0.023-0.0230.0000.0000.0000.000
63A78THR0-0.092-0.0408.425-0.046-0.0460.0000.0000.0000.000
64A79LEU00.0440.0358.992-0.049-0.0490.0000.0000.0000.000
65A80GLU-1-0.872-0.9492.479-9.657-6.3731.358-1.875-2.768-0.025
66A81VAL00.0160.0286.630-0.136-0.1360.0000.0000.0000.000
67A82SER0-0.016-0.0426.434-0.182-0.1820.0000.0000.0000.000
68A83GLU-1-0.902-0.9747.402-0.142-0.1420.0000.0000.0000.000
69A84GLU-1-0.881-0.9239.689-0.028-0.0280.0000.0000.0000.000
70A85ASP-1-0.892-0.94910.217-0.434-0.4340.0000.0000.0000.000
71A86PHE00.007-0.00510.9910.0390.0390.0000.0000.0000.000
72A87GLN0-0.033-0.01612.7700.0300.0300.0000.0000.0000.000
73A88SER0-0.028-0.02415.8000.0270.0270.0000.0000.0000.000
74A89LEU00.0230.00812.4190.0180.0180.0000.0000.0000.000
75A90LYS10.7650.87016.1460.1530.1530.0000.0000.0000.000
76A91ASN00.0250.01417.7990.0200.0200.0000.0000.0000.000
77A92ASP-1-0.862-0.91619.146-0.156-0.1560.0000.0000.0000.000
78A93GLN0-0.060-0.04918.6140.0030.0030.0000.0000.0000.000
79A94GLY0-0.0040.01421.2160.0070.0070.0000.0000.0000.000
80A95ILE0-0.067-0.01516.2530.0090.0090.0000.0000.0000.000
81A96LEU00.0440.02219.913-0.002-0.0020.0000.0000.0000.000
82A97VAL0-0.016-0.00116.4030.0050.0050.0000.0000.0000.000
83A98ASP-1-0.759-0.85614.761-0.169-0.1690.0000.0000.0000.000
84A99PHE00.0300.0066.3830.0090.0090.0000.0000.0000.000
85A100ALA00.0050.00210.681-0.055-0.0550.0000.0000.0000.000
86A101SER0-0.033-0.05211.8280.0000.0000.0000.0000.0000.000
87A102PHE0-0.049-0.01710.8270.0150.0150.0000.0000.0000.000
88A103PRO00.0320.0109.2490.0210.0210.0000.0000.0000.000
89A104GLY00.0460.02911.4010.0220.0220.0000.0000.0000.000
90A105LYS10.8960.96014.5770.1510.1510.0000.0000.0000.000
91A106ILE0-0.007-0.00812.3090.0130.0130.0000.0000.0000.000
92A107ILE00.0010.00711.1460.0100.0100.0000.0000.0000.000
93A108SER00.0230.01214.8420.0130.0130.0000.0000.0000.000
94A109LEU0-0.067-0.03617.8850.0110.0110.0000.0000.0000.000
95A110LEU00.0340.01613.7030.0060.0060.0000.0000.0000.000
96A111GLU-1-0.920-0.97017.702-0.095-0.0950.0000.0000.0000.000
97A112LYS10.8500.93019.9600.0940.0940.0000.0000.0000.000
98A113CYS0-0.070-0.02820.7560.0040.0040.0000.0000.0000.000
99A114ILE0-0.037-0.02118.3060.0040.0040.0000.0000.0000.000
100A115LEU0-0.042-0.02022.6620.0050.0050.0000.0000.0000.000
101A116ALA0-0.0270.02025.6690.0040.0040.0000.0000.0000.000
102A117GLN0-0.042-0.03327.6660.0020.0020.0000.0000.0000.000
103A118PRO0-0.047-0.05331.136-0.001-0.0010.0000.0000.0000.000
104A119GLY0-0.015-0.01533.6840.0000.0000.0000.0000.0000.000
105A120ASP-1-0.840-0.88331.042-0.054-0.0540.0000.0000.0000.000
106A121SER0-0.038-0.04633.896-0.003-0.0030.0000.0000.0000.000
107A122PRO0-0.009-0.00531.1720.0030.0030.0000.0000.0000.000
108A123ARG10.8710.94429.3250.0660.0660.0000.0000.0000.000
109A124PHE00.0310.00723.947-0.003-0.0030.0000.0000.0000.000
110A125GLN00.0390.01524.8820.0050.0050.0000.0000.0000.000
111A126ALA00.0620.03420.006-0.004-0.0040.0000.0000.0000.000
112A127VAL0-0.054-0.02721.5760.0060.0060.0000.0000.0000.000
113A128LEU00.0140.01217.426-0.007-0.0070.0000.0000.0000.000
114A129THR0-0.0020.00120.9200.0090.0090.0000.0000.0000.000
115A130ILE00.0210.00920.095-0.011-0.0110.0000.0000.0000.000
116A131ARG10.8130.89122.3730.1310.1310.0000.0000.0000.000
117A132GLY00.0350.02822.3080.0110.0110.0000.0000.0000.000
118A133GLY0-0.027-0.01119.6840.0030.0030.0000.0000.0000.000
119A134GLU-1-0.837-0.93916.751-0.305-0.3050.0000.0000.0000.000
120A135SER0-0.096-0.07517.0740.0290.0290.0000.0000.0000.000
121A136VAL00.0300.01618.284-0.013-0.0130.0000.0000.0000.000
122A137PHE00.0150.02015.9070.0140.0140.0000.0000.0000.000
123A138LYS10.9090.95218.6480.1020.1020.0000.0000.0000.000
124A139ILE00.0060.01317.4250.0040.0040.0000.0000.0000.000
125A140VAL0-0.070-0.03821.4900.0000.0000.0000.0000.0000.000
126A141GLU-1-0.806-0.88625.179-0.072-0.0720.0000.0000.0000.000
127A142ILE0-0.015-0.02727.770-0.001-0.0010.0000.0000.0000.000
128A143ASN00.0150.00631.1800.0010.0010.0000.0000.0000.000
129A144ASP-1-0.847-0.90234.386-0.048-0.0480.0000.0000.0000.000
130A145GLU-1-0.913-0.94235.663-0.054-0.0540.0000.0000.0000.000
131A146LYS10.8340.91932.1050.0660.0660.0000.0000.0000.000
132A147GLN00.0760.03628.691-0.007-0.0070.0000.0000.0000.000
133A148LEU0-0.027-0.02328.0430.0010.0010.0000.0000.0000.000
134A149PRO0-0.002-0.00224.036-0.001-0.0010.0000.0000.0000.000
135A150HIS0-0.014-0.01122.173-0.002-0.0020.0000.0000.0000.000
136A151ILE0-0.024-0.01816.733-0.005-0.0050.0000.0000.0000.000
137A152THR0-0.047-0.03319.7470.0100.0100.0000.0000.0000.000
138A153LEU00.0020.00613.558-0.007-0.0070.0000.0000.0000.000
139A154ALA00.0430.03215.1500.0140.0140.0000.0000.0000.000
140A155PHE0-0.001-0.01810.977-0.020-0.0200.0000.0000.0000.000
141A156ARG10.9561.0079.6280.5930.5930.0000.0000.0000.000
142A157PRO00.0220.01613.237-0.027-0.0270.0000.0000.0000.000
143A158GLY0-0.030-0.01312.844-0.052-0.0520.0000.0000.0000.000
144A159ASN00.0280.00412.9240.0380.0380.0000.0000.0000.000
145A160ASP-1-0.785-0.90014.216-0.263-0.2630.0000.0000.0000.000
146A161SER0-0.045-0.02713.2510.0060.0060.0000.0000.0000.000
147A162VAL0-0.0050.0009.238-0.061-0.0610.0000.0000.0000.000
148A163VAL00.0610.03310.344-0.032-0.0320.0000.0000.0000.000
149A164LYS10.9210.97312.9390.3320.3320.0000.0000.0000.000
150A165GLN0-0.068-0.0478.081-0.122-0.1220.0000.0000.0000.000
151A166PHE00.0260.0168.0440.0270.0270.0000.0000.0000.000
152A167LEU00.0270.0129.8630.0580.0580.0000.0000.0000.000
153A168ALA0-0.018-0.00412.0650.0410.0410.0000.0000.0000.000
154A169PHE0-0.0150.0017.5670.0320.0320.0000.0000.0000.000
155A170ARG10.9020.95110.6900.1970.1970.0000.0000.0000.000
156A171LEU00.0000.00712.4460.0320.0320.0000.0000.0000.000
157A172SER0-0.097-0.06212.4740.0310.0310.0000.0000.0000.000
158A173GLU-1-0.743-0.84810.669-0.077-0.0770.0000.0000.0000.000
159A174VAL00.0030.00113.8100.0130.0130.0000.0000.0000.000
160A175LYS10.9510.97116.9490.0420.0420.0000.0000.0000.000
161A176GLY00.0140.02217.2900.0070.0070.0000.0000.0000.000
162A177THR00.001-0.00316.791-0.001-0.0010.0000.0000.0000.000
163A178CYS0-0.074-0.05019.523-0.002-0.0020.0000.0000.0000.000
164A179HIS0-0.064-0.02821.876-0.002-0.0020.0000.0000.0000.000
165A180ASP-1-0.868-0.93920.0290.0210.0210.0000.0000.0000.000
166A181LEU0-0.011-0.01722.598-0.001-0.0010.0000.0000.0000.000
167A182SER0-0.039-0.00825.554-0.002-0.0020.0000.0000.0000.000
168A183ASP-1-0.864-0.92027.0770.0190.0190.0000.0000.0000.000
169A184ASP-1-0.864-0.93326.9910.0060.0060.0000.0000.0000.000
170A185LEU0-0.091-0.02929.428-0.001-0.0010.0000.0000.0000.000
171A186SER0-0.026-0.02231.474-0.001-0.0010.0000.0000.0000.000
172A187ARG10.8090.88832.212-0.010-0.0100.0000.0000.0000.000
173A188THR0-0.012-0.02732.460-0.001-0.0010.0000.0000.0000.000
174A189ARG10.8330.91734.2520.0050.0050.0000.0000.0000.000
175A190ASP-1-0.787-0.89236.4700.0090.0090.0000.0000.0000.000
176A191ASP-1-0.829-0.89937.7020.0070.0070.0000.0000.0000.000
177A192ARG10.7830.87539.3470.0020.0020.0000.0000.0000.000
178A193ASP-1-0.792-0.87541.191-0.001-0.0010.0000.0000.0000.000
179A194SER0-0.014-0.00642.8400.0000.0000.0000.0000.0000.000
180A195MET0-0.007-0.00941.9430.0000.0000.0000.0000.0000.000
181A196VAL0-0.023-0.00745.347-0.001-0.0010.0000.0000.0000.000
182A197ALA00.0180.01247.4030.0000.0000.0000.0000.0000.000
183A198GLN00.0190.00945.8100.0000.0000.0000.0000.0000.000
184A199LEU0-0.022-0.00149.3290.0000.0000.0000.0000.0000.000
185A200ALA0-0.012-0.01251.0660.0000.0000.0000.0000.0000.000
186A201GLN00.0220.01252.6440.0000.0000.0000.0000.0000.000
187A202CYS00.0030.01253.4680.0000.0000.0000.0000.0000.000
188A203ARG10.9290.95153.0650.0020.0020.0000.0000.0000.000
189A204GLN0-0.008-0.00257.1260.0000.0000.0000.0000.0000.000
190A205GLN0-0.011-0.01255.9150.0000.0000.0000.0000.0000.000
191A206LEU0-0.0040.00059.0840.0000.0000.0000.0000.0000.000
192A207ALA0-0.047-0.02461.1170.0000.0000.0000.0000.0000.000
193A208GLN00.0180.00262.5760.0000.0000.0000.0000.0000.000
194A209LEU00.0250.01663.1100.0000.0000.0000.0000.0000.000
195A210ARG10.9230.97162.8040.0010.0010.0000.0000.0000.000
196A211GLU-1-0.872-0.92667.2250.0010.0010.0000.0000.0000.000
197A212GLN0-0.040-0.03566.8790.0000.0000.0000.0000.0000.000
198A213TYR0-0.042-0.01169.0050.0000.0000.0000.0000.0000.000
199A214ASP-1-0.863-0.95370.639-0.001-0.0010.0000.0000.0000.000
200A215LYS10.8090.89773.042-0.001-0.0010.0000.0000.0000.000
201A216HIS0-0.040-0.02073.7960.0000.0000.0000.0000.0000.000
202A217LEU0-0.001-0.00773.4720.0000.0000.0000.0000.0000.000
203A218LEU0-0.042-0.00776.8900.0000.0000.0000.0000.0000.000
204A219GLU-1-0.821-0.89578.6370.0010.0010.0000.0000.0000.000
205A220VAL0-0.094-0.03379.5560.0000.0000.0000.0000.0000.000
206A221GLN0-0.066-0.02980.1880.0000.0000.0000.0000.0000.000