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: N9VMQ

Calculation Name: 5CDD-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5CDD

Chain ID: A

ChEMBL ID:

UniProt ID: D1FK67

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 208
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2238248.992154
FMO2-HF: Nuclear repulsion 2154285.416265
FMO2-HF: Total energy -83963.57589
FMO2-MP2: Total energy -84207.828262


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:1:ILE)


Summations of interaction energy for fragment #1(A:1: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.
-3.1321.470.214-1.762-3.054-0.004
Interaction energy analysis for fragmet #1(A:1:ILE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.010 / q_NPA : -0.012
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].
3A3ILE00.0200.0002.873-3.0260.1000.170-1.322-1.973-0.001
4A4GLY00.0000.0125.0630.1150.245-0.001-0.007-0.1220.000
5A5ASN0-0.026-0.0018.5620.1560.1560.0000.0000.0000.000
6A6LYS10.9850.9968.730-0.117-0.1170.0000.0000.0000.000
7A7THR00.008-0.0038.6690.1320.1320.0000.0000.0000.000
8A8ASN0-0.028-0.02210.064-0.126-0.1260.0000.0000.0000.000
9A9GLU-1-0.899-0.94613.0080.2010.2010.0000.0000.0000.000
10A10ASN0-0.053-0.01716.032-0.050-0.0500.0000.0000.0000.000
11A11VAL0-0.012-0.00514.1920.0600.0600.0000.0000.0000.000
12A12ILE00.0110.00617.359-0.044-0.0440.0000.0000.0000.000
13A13SER0-0.004-0.00419.0580.0470.0470.0000.0000.0000.000
14A14PHE0-0.042-0.02320.605-0.020-0.0200.0000.0000.0000.000
15A15PHE0-0.002-0.01023.4930.0020.0020.0000.0000.0000.000
16A16ASP-1-0.875-0.91225.4040.1330.1330.0000.0000.0000.000
17A17SER0-0.083-0.05723.0030.0090.0090.0000.0000.0000.000
18A18THR0-0.009-0.02823.811-0.010-0.0100.0000.0000.0000.000
19A19ASP-1-0.792-0.84322.5970.0940.0940.0000.0000.0000.000
20A20ALA0-0.028-0.04019.552-0.007-0.0070.0000.0000.0000.000
21A21GLU-1-0.954-0.97818.2720.0920.0920.0000.0000.0000.000
22A22THR0-0.012-0.03121.203-0.012-0.0120.0000.0000.0000.000
23A23GLN00.0140.01624.5450.0010.0010.0000.0000.0000.000
24A24ASN00.0050.00219.192-0.002-0.0020.0000.0000.0000.000
25A25HIS0-0.010-0.00623.214-0.004-0.0040.0000.0000.0000.000
26A26ASP-1-0.830-0.90924.8800.0500.0500.0000.0000.0000.000
27A27VAL00.010-0.00125.566-0.005-0.0050.0000.0000.0000.000
28A28LEU0-0.010-0.00722.166-0.004-0.0040.0000.0000.0000.000
29A29MET0-0.027-0.00826.639-0.010-0.0100.0000.0000.0000.000
30A30LYS10.7950.88529.814-0.055-0.0550.0000.0000.0000.000
31A31GLY0-0.0180.00029.686-0.001-0.0010.0000.0000.0000.000
32A32CYS0-0.122-0.04125.0740.0020.0020.0000.0000.0000.000
33A33GLY00.0130.01128.287-0.005-0.0050.0000.0000.0000.000
34A34GLU-1-0.963-0.97924.918-0.007-0.0070.0000.0000.0000.000
35A35PHE00.014-0.01418.8900.0080.0080.0000.0000.0000.000
36A36ILE0-0.0070.00817.968-0.013-0.0130.0000.0000.0000.000
37A37VAL00.0440.02915.4470.0100.0100.0000.0000.0000.000
38A38ASN0-0.001-0.00813.192-0.029-0.0290.0000.0000.0000.000
39A39LEU00.0950.04411.4540.0030.0030.0000.0000.0000.000
40A40ARG10.9420.96712.9290.2890.2890.0000.0000.0000.000
41A41THR0-0.004-0.01416.7150.0100.0100.0000.0000.0000.000
42A42LEU00.0260.01317.0200.0090.0090.0000.0000.0000.000
43A43LEU0-0.052-0.02615.511-0.001-0.0010.0000.0000.0000.000
44A44ARG10.7770.89219.8640.1480.1480.0000.0000.0000.000
45A45THR0-0.0200.00223.1690.0100.0100.0000.0000.0000.000
46A46PHE00.0260.01024.317-0.006-0.0060.0000.0000.0000.000
47A47ARG10.9120.95423.8780.0420.0420.0000.0000.0000.000
48A48THR00.0360.01526.752-0.006-0.0060.0000.0000.0000.000
49A49ILE0-0.020-0.01425.0590.0010.0010.0000.0000.0000.000
50A50THR00.0280.00027.7030.0030.0030.0000.0000.0000.000
51A51ASP-1-0.851-0.89831.210-0.021-0.0210.0000.0000.0000.000
52A52ASN0-0.043-0.03534.3030.0020.0020.0000.0000.0000.000
53A53TRP00.0160.01734.090-0.002-0.0020.0000.0000.0000.000
54A54ILE00.0250.00736.0630.0000.0000.0000.0000.0000.000
55A55LEU00.0110.01436.749-0.003-0.0030.0000.0000.0000.000
56A56GLN00.0040.00340.5160.0020.0020.0000.0000.0000.000
57A57ALA0-0.012-0.00643.395-0.002-0.0020.0000.0000.0000.000
58A58ASN0-0.015-0.00645.627-0.001-0.0010.0000.0000.0000.000
59A59THR00.0150.00740.3720.0000.0000.0000.0000.0000.000
60A60LYS10.8360.93139.4780.0540.0540.0000.0000.0000.000
61A61THR00.0540.01235.0200.0000.0000.0000.0000.0000.000
62A62PRO00.0250.02632.332-0.001-0.0010.0000.0000.0000.000
63A63ILE0-0.011-0.00227.7920.0020.0020.0000.0000.0000.000
64A64THR00.0330.02526.709-0.002-0.0020.0000.0000.0000.000
65A65ASP-1-0.867-0.93028.436-0.068-0.0680.0000.0000.0000.000
66A66LEU0-0.056-0.02229.1470.0040.0040.0000.0000.0000.000
67A67THR0-0.073-0.05824.125-0.001-0.0010.0000.0000.0000.000
68A68ASN00.013-0.01024.429-0.013-0.0130.0000.0000.0000.000
69A69THR00.0020.01324.173-0.003-0.0030.0000.0000.0000.000
70A70THR00.009-0.00624.3620.0010.0010.0000.0000.0000.000
71A71ASP-1-0.845-0.91420.353-0.139-0.1390.0000.0000.0000.000
72A72ALA0-0.0100.03119.557-0.013-0.0130.0000.0000.0000.000
73A73GLN0-0.0130.00120.1970.0040.0040.0000.0000.0000.000
74A74GLY00.0520.03219.2590.0100.0100.0000.0000.0000.000
75A75ARG10.8100.88419.9130.0370.0370.0000.0000.0000.000
76A76ASP-1-0.751-0.86622.000-0.089-0.0890.0000.0000.0000.000
77A77TYR00.0540.01419.042-0.005-0.0050.0000.0000.0000.000
78A78MET0-0.0410.00117.649-0.017-0.0170.0000.0000.0000.000
79A79SER00.001-0.00317.336-0.022-0.0220.0000.0000.0000.000
80A80TYR0-0.0020.01414.937-0.025-0.0250.0000.0000.0000.000
81A81LEU00.004-0.01613.456-0.015-0.0150.0000.0000.0000.000
82A82SER0-0.077-0.03712.299-0.070-0.0700.0000.0000.0000.000
83A83TYR0-0.022-0.03812.374-0.061-0.0610.0000.0000.0000.000
84A84LEU00.0070.0188.468-0.020-0.0200.0000.0000.0000.000
85A85TYR0-0.047-0.0177.171-0.292-0.2920.0000.0000.0000.000
86A86ARG11.0111.0218.8730.5580.5580.0000.0000.0000.000
87A87PHE0-0.012-0.00710.4980.0830.0830.0000.0000.0000.000
88A88TYR0-0.018-0.03212.748-0.022-0.0220.0000.0000.0000.000
89A89ARG10.8090.88715.4910.2190.2190.0000.0000.0000.000
90A90GLY00.0440.03018.1320.0000.0000.0000.0000.0000.000
91A91GLY00.0350.01921.3720.0000.0000.0000.0000.0000.000
92A92ARG10.8900.94320.2660.1550.1550.0000.0000.0000.000
93A93ARG10.8480.91125.1510.1010.1010.0000.0000.0000.000
94A94TYR00.016-0.00126.308-0.005-0.0050.0000.0000.0000.000
95A95LYS10.8440.91830.0640.0580.0580.0000.0000.0000.000
96A96PHE0-0.014-0.00632.3930.0000.0000.0000.0000.0000.000
97A97PHE00.0260.01033.1110.0010.0010.0000.0000.0000.000
98A98ASN00.0490.02137.7830.0010.0010.0000.0000.0000.000
99A99THR0-0.057-0.04239.6510.0020.0020.0000.0000.0000.000
100A100THR0-0.004-0.00842.4490.0020.0020.0000.0000.0000.000
101A101PRO00.0100.00145.0140.0000.0000.0000.0000.0000.000
102A102LEU0-0.019-0.00146.882-0.001-0.0010.0000.0000.0000.000
103A103LYS10.9280.96450.4680.0200.0200.0000.0000.0000.000
104A104GLN00.0640.02753.790-0.001-0.0010.0000.0000.0000.000
105A105SER0-0.051-0.01756.202-0.001-0.0010.0000.0000.0000.000
106A106GLN00.0160.00051.9530.0000.0000.0000.0000.0000.000
107A107THR00.0370.01751.3620.0010.0010.0000.0000.0000.000
108A108CYS0-0.048-0.00346.328-0.001-0.0010.0000.0000.0000.000
109A109TYR00.0280.00145.0870.0000.0000.0000.0000.0000.000
110A110ILE0-0.011-0.00339.3430.0000.0000.0000.0000.0000.000
111A111ARG10.9120.96241.2380.0460.0460.0000.0000.0000.000
112A112SER00.0040.00935.6800.0000.0000.0000.0000.0000.000
113A113PHE00.010-0.00836.6060.0010.0010.0000.0000.0000.000
114A114LEU00.0290.00931.539-0.004-0.0040.0000.0000.0000.000
115A115MET0-0.037-0.00432.1240.0030.0030.0000.0000.0000.000
116A116PRO00.0120.01930.239-0.006-0.0060.0000.0000.0000.000
117A117ARG10.8420.88523.5960.1510.1510.0000.0000.0000.000
118A118ASN0-0.027-0.03024.7610.0030.0030.0000.0000.0000.000
119A119TYR00.0030.02329.0660.0000.0000.0000.0000.0000.000
120A120SER00.013-0.00532.651-0.001-0.0010.0000.0000.0000.000
121A121ALA00.012-0.01335.5190.0000.0000.0000.0000.0000.000
122A122ASP-1-0.911-0.94537.983-0.056-0.0560.0000.0000.0000.000
123A123GLU-1-0.804-0.87334.796-0.076-0.0760.0000.0000.0000.000
124A124ILE0-0.041-0.02735.993-0.004-0.0040.0000.0000.0000.000
125A125ASN0-0.026-0.00438.7910.0030.0030.0000.0000.0000.000
126A126VAL0-0.017-0.02539.820-0.002-0.0020.0000.0000.0000.000
127A127ASP-1-0.888-0.93941.173-0.051-0.0510.0000.0000.0000.000
128A128GLY0-0.014-0.00538.759-0.003-0.0030.0000.0000.0000.000
129A129PRO0-0.024-0.02835.8110.0030.0030.0000.0000.0000.000
130A130SER0-0.022-0.01438.1970.0010.0010.0000.0000.0000.000
131A131HIS00.0210.02337.2570.0010.0010.0000.0000.0000.000
132A132ILE0-0.026-0.02939.8960.0000.0000.0000.0000.0000.000
133A133THR0-0.034-0.01940.6230.0020.0020.0000.0000.0000.000
134A134TYR00.0710.02343.4480.0000.0000.0000.0000.0000.000
135A135PRO00.0250.01143.1240.0010.0010.0000.0000.0000.000
136A136VAL0-0.019-0.01545.2030.0010.0010.0000.0000.0000.000
137A137ILE0-0.015-0.01047.4440.0010.0010.0000.0000.0000.000
138A138ASN0-0.017-0.01740.7730.0010.0010.0000.0000.0000.000
139A139PRO0-0.0080.00441.927-0.002-0.0020.0000.0000.0000.000
140A140VAL00.0130.02036.436-0.001-0.0010.0000.0000.0000.000
141A141HIS00.0190.04336.1460.0020.0020.0000.0000.0000.000
142A142GLU-1-0.846-0.92734.201-0.051-0.0510.0000.0000.0000.000
143A143VAL0-0.005-0.00532.6410.0000.0000.0000.0000.0000.000
144A144GLU-1-0.787-0.88228.468-0.102-0.1020.0000.0000.0000.000
145A145VAL0-0.029-0.00727.6390.0030.0030.0000.0000.0000.000
146A146PRO00.0290.01127.215-0.010-0.0100.0000.0000.0000.000
147A147PHE00.001-0.01020.573-0.005-0.0050.0000.0000.0000.000
148A148TYR00.0070.00625.615-0.002-0.0020.0000.0000.0000.000
149A149SER00.021-0.01422.6290.0030.0030.0000.0000.0000.000
150A150GLN00.0270.02825.669-0.002-0.0020.0000.0000.0000.000
151A151TYR0-0.0140.00320.774-0.012-0.0120.0000.0000.0000.000
152A152ARG10.9410.96718.0960.2550.2550.0000.0000.0000.000
153A153LYS10.8870.94812.6750.4290.4290.0000.0000.0000.000
154A154ILE00.0330.03817.2970.0020.0020.0000.0000.0000.000
155A155PRO0-0.005-0.01014.829-0.031-0.0310.0000.0000.0000.000
156A156ILE0-0.020-0.02712.2620.0430.0430.0000.0000.0000.000
157A157ALA00.0030.00715.792-0.004-0.0040.0000.0000.0000.000
158A158SER0-0.027-0.00618.5750.0070.0070.0000.0000.0000.000
159A159THR00.0230.00719.2850.0110.0110.0000.0000.0000.000
160A160SER0-0.002-0.00521.3020.0100.0100.0000.0000.0000.000
161A161ASP-1-0.882-0.94922.015-0.165-0.1650.0000.0000.0000.000
162A162LYS10.8430.90623.9270.1000.1000.0000.0000.0000.000
163A163GLY00.0190.00927.6810.0040.0040.0000.0000.0000.000
164A164TYR0-0.073-0.02322.778-0.002-0.0020.0000.0000.0000.000
165A165ASP-1-0.730-0.83423.260-0.168-0.1680.0000.0000.0000.000
166A166SER00.0180.02326.0480.0070.0070.0000.0000.0000.000
167A167SER0-0.006-0.01326.884-0.010-0.0100.0000.0000.0000.000
168A168LEU0-0.0070.00228.8700.0050.0050.0000.0000.0000.000
169A169MET0-0.0170.00431.4930.0000.0000.0000.0000.0000.000
170A170TYR0-0.004-0.03434.7350.0010.0010.0000.0000.0000.000
171A171PHE00.0150.01036.7790.0010.0010.0000.0000.0000.000
172A172SER00.0460.02440.5670.0010.0010.0000.0000.0000.000
173A173ASN00.0290.01343.5000.0000.0000.0000.0000.0000.000
174A174THR0-0.008-0.00346.3420.0020.0020.0000.0000.0000.000
175A175SER0-0.025-0.01744.610-0.001-0.0010.0000.0000.0000.000
176A176THR0-0.052-0.04040.6160.0020.0020.0000.0000.0000.000
177A177THR00.0850.04340.0170.0000.0000.0000.0000.0000.000
178A178GLN0-0.0060.04236.8760.0010.0010.0000.0000.0000.000
179A179ILE00.0470.04733.695-0.001-0.0010.0000.0000.0000.000
180A180VAL0-0.0050.00230.246-0.002-0.0020.0000.0000.0000.000
181A181ALA00.0160.01128.9710.0010.0010.0000.0000.0000.000
182A182ARG10.7080.81821.4620.1080.1080.0000.0000.0000.000
183A183ALA00.0410.00423.4080.0040.0040.0000.0000.0000.000
184A184GLY00.0360.01621.819-0.003-0.0030.0000.0000.0000.000
185A185ASN0-0.030-0.03122.847-0.002-0.0020.0000.0000.0000.000
186A186ASP-1-0.856-0.94123.180-0.119-0.1190.0000.0000.0000.000
187A187ASP-1-0.824-0.88821.828-0.170-0.1700.0000.0000.0000.000
188A188PHE0-0.108-0.02617.688-0.027-0.0270.0000.0000.0000.000
189A189THR0-0.014-0.00214.0270.0090.0090.0000.0000.0000.000
190A190PHE00.0210.01711.7420.0000.0000.0000.0000.0000.000
191A191GLY00.001-0.0089.9360.0000.0000.0000.0000.0000.000
192A192TRP0-0.038-0.0445.7830.1560.1560.0000.0000.0000.000
193A193MET00.0030.0093.776-0.436-0.0020.003-0.065-0.3720.000
194A194ILE0-0.038-0.0173.355-1.326-0.5430.043-0.359-0.468-0.003
195A195GLY00.0010.0084.801-0.206-0.077-0.001-0.009-0.1190.000
196A196PRO00.0020.0015.9080.0140.0140.0000.0000.0000.000
197A197PRO00.0060.0139.2730.0700.0700.0000.0000.0000.000
198A198GLN0-0.013-0.01512.5760.0340.0340.0000.0000.0000.000
199A199LEU0-0.003-0.00314.994-0.033-0.0330.0000.0000.0000.000
200A200GLN0-0.0040.00517.4440.0080.0080.0000.0000.0000.000
201A201GLY00.0100.00821.208-0.002-0.0020.0000.0000.0000.000
202A202GLU-1-0.941-0.97323.5190.0530.0530.0000.0000.0000.000
203A203THR0-0.041-0.03027.2430.0020.0020.0000.0000.0000.000
204A204ARG10.9680.98129.512-0.067-0.0670.0000.0000.0000.000
205A205SER00.0250.02733.1050.0010.0010.0000.0000.0000.000
206A206VAL0-0.071-0.06634.4840.0020.0020.0000.0000.0000.000
207A207VAL0-0.053-0.03837.334-0.003-0.0030.0000.0000.0000.000
208A208PRO00.1220.10038.486-0.001-0.0010.0000.0000.0000.000