FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 39V8L

Calculation Name: 3CAI-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3CAI

Chain ID: A

ChEMBL ID:

UniProt ID: P9WQ67

Base Structure: X-ray

Registration Date: 2023-09-19

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 396
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -6198767.018734
FMO2-HF: Nuclear repulsion 6053774.487283
FMO2-HF: Total energy -144992.531451
FMO2-MP2: Total energy -145420.174278


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:3:TYR)


Summations of interaction energy for fragment #1(A:3:TYR)
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.
-44.931-31.05431.787-13.904-31.76-0.059
Interaction energy analysis for fragmet #1(A:3:TYR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.007 / q_NPA : -0.027
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].
3A5VAL00.0150.0022.419-2.0731.6521.315-1.517-3.5240.002
4A6ALA0-0.0180.0023.2380.3500.1040.0980.507-0.3590.001
5A7ARG10.7960.8774.630-0.550-0.337-0.001-0.026-0.1850.000
6A8VAL0-0.024-0.0152.677-2.539-0.4240.770-0.870-2.0150.009
7A9ARG10.8060.8705.3710.9211.026-0.001-0.002-0.1010.000
8A10GLY0-0.0050.0147.5550.1860.1860.0000.0000.0000.000
9A11LEU0-0.045-0.0146.7750.1010.1010.0000.0000.0000.000
10A12HIS0-0.0090.0017.2310.1950.1950.0000.0000.0000.000
11A13PRO00.016-0.00511.009-0.068-0.0680.0000.0000.0000.000
12A14SER00.0360.03314.013-0.009-0.0090.0000.0000.0000.000
13A15LEU00.0300.0288.519-0.022-0.0220.0000.0000.0000.000
14A16GLY0-0.069-0.05912.364-0.084-0.0840.0000.0000.0000.000
15A17ASP-1-0.911-0.95215.215-0.163-0.1630.0000.0000.0000.000
16A18GLY0-0.0050.00117.1500.0260.0260.0000.0000.0000.000
17A19TRP0-0.071-0.02016.5190.0130.0130.0000.0000.0000.000
18A20VAL0-0.028-0.00913.451-0.059-0.0590.0000.0000.0000.000
19A21HIS0-0.048-0.04711.1850.0340.0340.0000.0000.0000.000
20A22PHE0-0.010-0.01610.946-0.085-0.0850.0000.0000.0000.000
21A23ASP-1-0.801-0.89213.392-0.055-0.0550.0000.0000.0000.000
22A24ALA00.0290.01610.7310.0290.0290.0000.0000.0000.000
23A25PRO0-0.004-0.00212.6160.0430.0430.0000.0000.0000.000
24A26ALA0-0.0170.00315.3660.0080.0080.0000.0000.0000.000
25A27GLY0-0.021-0.00714.802-0.004-0.0040.0000.0000.0000.000
26A28MET0-0.0540.0118.5470.0270.0270.0000.0000.0000.000
27A29LEU0-0.002-0.00410.4200.0210.0210.0000.0000.0000.000
28A30ILE0-0.006-0.00910.8640.0660.0660.0000.0000.0000.000
29A31PRO0-0.0130.0089.722-0.056-0.0560.0000.0000.0000.000
30A32ASP-1-0.850-0.91511.844-0.037-0.0370.0000.0000.0000.000
31A33SER00.0280.00412.6730.0040.0040.0000.0000.0000.000
32A34VAL0-0.0050.02113.441-0.010-0.0100.0000.0000.0000.000
33A35ALA00.0550.03316.055-0.013-0.0130.0000.0000.0000.000
34A36THR0-0.007-0.00318.203-0.008-0.0080.0000.0000.0000.000
35A37THR0-0.031-0.02418.083-0.011-0.0110.0000.0000.0000.000
36A38VAL0-0.0080.00419.733-0.006-0.0060.0000.0000.0000.000
37A39SER0-0.040-0.02722.082-0.007-0.0070.0000.0000.0000.000
38A40THR0-0.099-0.05623.225-0.004-0.0040.0000.0000.0000.000
39A41ALA0-0.024-0.01124.157-0.003-0.0030.0000.0000.0000.000
40A42PHE00.0480.02925.874-0.002-0.0020.0000.0000.0000.000
41A43ARG10.9300.98027.7730.0070.0070.0000.0000.0000.000
42A44ARG10.8610.91229.1080.0040.0040.0000.0000.0000.000
43A45SER0-0.0050.00028.5780.0000.0000.0000.0000.0000.000
44A46GLY0-0.0060.00631.101-0.002-0.0020.0000.0000.0000.000
45A47ALA00.009-0.00733.7650.0020.0020.0000.0000.0000.000
46A48SER00.0230.01535.1970.0020.0020.0000.0000.0000.000
47A49THR00.0370.01632.309-0.001-0.0010.0000.0000.0000.000
48A50VAL0-0.0210.00234.890-0.001-0.0010.0000.0000.0000.000
49A51GLY00.0330.00338.6410.0000.0000.0000.0000.0000.000
50A52ALA0-0.002-0.00139.4260.0000.0000.0000.0000.0000.000
51A53HIS00.0310.04537.291-0.001-0.0010.0000.0000.0000.000
52A54PRO00.011-0.01635.0860.0010.0010.0000.0000.0000.000
53A55SER00.014-0.00533.2220.0010.0010.0000.0000.0000.000
54A56ALA00.0370.02732.9420.0020.0020.0000.0000.0000.000
55A57ARG10.9920.99332.6270.0080.0080.0000.0000.0000.000
56A58ARG10.9270.96825.808-0.003-0.0030.0000.0000.0000.000
57A59SER00.007-0.01128.7490.0030.0030.0000.0000.0000.000
58A60ALA00.008-0.00529.5300.0040.0040.0000.0000.0000.000
59A61ALA00.0000.00327.6490.0020.0020.0000.0000.0000.000
60A62VAL0-0.025-0.00723.5090.0020.0020.0000.0000.0000.000
61A63LEU0-0.019-0.00324.3600.0070.0070.0000.0000.0000.000
62A64ASP-1-0.914-0.95425.6230.0260.0260.0000.0000.0000.000
63A65ALA00.0460.01921.8250.0030.0030.0000.0000.0000.000
64A66ALA0-0.013-0.01220.7640.0100.0100.0000.0000.0000.000
65A67ARG10.7800.85121.032-0.029-0.0290.0000.0000.0000.000
66A68GLU-1-0.892-0.93220.9800.0180.0180.0000.0000.0000.000
67A69ALA0-0.0020.00216.6240.0030.0030.0000.0000.0000.000
68A70VAL00.016-0.00716.8600.0190.0190.0000.0000.0000.000
69A71ALA0-0.0060.00318.7870.0070.0070.0000.0000.0000.000
70A72ASP-1-0.788-0.87716.1220.0190.0190.0000.0000.0000.000
71A73LEU0-0.046-0.01712.379-0.005-0.0050.0000.0000.0000.000
72A74VAL0-0.006-0.00415.3290.0210.0210.0000.0000.0000.000
73A75ASN0-0.035-0.01018.010-0.019-0.0190.0000.0000.0000.000
74A76ALA00.002-0.00219.831-0.006-0.0060.0000.0000.0000.000
75A77ASP-1-0.827-0.91822.8360.0150.0150.0000.0000.0000.000
76A78PRO00.0480.01824.1430.0070.0070.0000.0000.0000.000
77A79GLY00.013-0.00525.5640.0020.0020.0000.0000.0000.000
78A80GLY0-0.007-0.01527.282-0.002-0.0020.0000.0000.0000.000
79A81VAL0-0.029-0.00422.8570.0070.0070.0000.0000.0000.000
80A82VAL0-0.024-0.00425.744-0.006-0.0060.0000.0000.0000.000
81A83LEU0-0.015-0.01622.8090.0100.0100.0000.0000.0000.000
82A84GLY00.0290.00125.366-0.009-0.0090.0000.0000.0000.000
83A85ALA00.0040.00024.9930.0080.0080.0000.0000.0000.000
84A86ASP-1-0.754-0.85923.1430.0960.0960.0000.0000.0000.000
85A87ARG10.8000.86421.788-0.116-0.1160.0000.0000.0000.000
86A88ALA0-0.005-0.00424.719-0.006-0.0060.0000.0000.0000.000
87A89VAL0-0.052-0.02327.258-0.006-0.0060.0000.0000.0000.000
88A90LEU0-0.036-0.00925.488-0.005-0.0050.0000.0000.0000.000
89A91LEU00.0740.02525.819-0.004-0.0040.0000.0000.0000.000
90A92SER0-0.053-0.04529.810-0.004-0.0040.0000.0000.0000.000
91A93LEU0-0.0040.01132.364-0.003-0.0030.0000.0000.0000.000
92A94LEU00.0180.01029.889-0.003-0.0030.0000.0000.0000.000
93A95ALA00.0120.02533.350-0.003-0.0030.0000.0000.0000.000
94A96GLU-1-0.951-0.96735.3950.0330.0330.0000.0000.0000.000
95A97ALA0-0.022-0.00236.344-0.003-0.0030.0000.0000.0000.000
96A98SER0-0.026-0.03935.596-0.001-0.0010.0000.0000.0000.000
97A99SER0-0.026-0.00538.241-0.002-0.0020.0000.0000.0000.000
98A100SER00.0020.00441.6080.0010.0010.0000.0000.0000.000
99A101ARG10.8180.89438.076-0.037-0.0370.0000.0000.0000.000
100A102ALA00.0230.00939.4560.0020.0020.0000.0000.0000.000
101A103GLY00.015-0.00541.335-0.001-0.0010.0000.0000.0000.000
102A104LEU0-0.010-0.00945.1960.0010.0010.0000.0000.0000.000
103A105GLY0-0.0090.00147.701-0.001-0.0010.0000.0000.0000.000
104A106TYR0-0.056-0.02342.7820.0000.0000.0000.0000.0000.000
105A107GLU-1-0.805-0.86140.8720.0360.0360.0000.0000.0000.000
106A108VAL00.0120.00536.3010.0000.0000.0000.0000.0000.000
107A109ILE0-0.025-0.00733.561-0.001-0.0010.0000.0000.0000.000
108A110VAL00.0250.03131.8400.0020.0020.0000.0000.0000.000
109A111SER00.028-0.02827.518-0.001-0.0010.0000.0000.0000.000
110A112ARG10.8180.89729.910-0.054-0.0540.0000.0000.0000.000
111A113LEU00.0400.02323.883-0.001-0.0010.0000.0000.0000.000
112A114ASP-1-0.846-0.87724.4590.1070.1070.0000.0000.0000.000
113A115ASP-1-0.751-0.85022.7750.0910.0910.0000.0000.0000.000
114A116GLU-1-0.719-0.84025.0970.0490.0490.0000.0000.0000.000
115A117ALA0-0.039-0.02625.425-0.006-0.0060.0000.0000.0000.000
116A118ASN0-0.039-0.03226.193-0.008-0.0080.0000.0000.0000.000
117A119ILE00.0050.01228.231-0.003-0.0030.0000.0000.0000.000
118A120ALA00.0140.00131.332-0.005-0.0050.0000.0000.0000.000
119A121PRO0-0.040-0.01030.843-0.005-0.0050.0000.0000.0000.000
120A122TRP00.0460.01030.145-0.007-0.0070.0000.0000.0000.000
121A123LEU0-0.020-0.00335.315-0.004-0.0040.0000.0000.0000.000
122A124ARG10.8940.93432.975-0.045-0.0450.0000.0000.0000.000
123A125ALA0-0.021-0.00237.953-0.003-0.0030.0000.0000.0000.000
124A126ALA00.0320.01039.406-0.002-0.0020.0000.0000.0000.000
125A127HIS0-0.017-0.01640.631-0.003-0.0030.0000.0000.0000.000
126A128ARG10.8550.94839.391-0.033-0.0330.0000.0000.0000.000
127A129TYR0-0.024-0.00541.665-0.001-0.0010.0000.0000.0000.000
128A130GLY00.0150.01144.917-0.001-0.0010.0000.0000.0000.000
129A131ALA0-0.0520.00242.0210.0000.0000.0000.0000.0000.000
130A132LYS10.8930.93342.229-0.035-0.0350.0000.0000.0000.000
131A133VAL00.0490.02137.5500.0010.0010.0000.0000.0000.000
132A134LYS10.7330.85438.345-0.042-0.0420.0000.0000.0000.000
133A135TRP00.0540.00432.0300.0010.0010.0000.0000.0000.000
134A136ALA00.0180.02531.326-0.002-0.0020.0000.0000.0000.000
135A137GLU-1-0.828-0.91831.8720.0560.0560.0000.0000.0000.000
136A138VAL00.008-0.00628.0930.0040.0040.0000.0000.0000.000
137A139ASP-1-0.821-0.88830.4350.0670.0670.0000.0000.0000.000
138A140ILE0-0.046-0.03330.2270.0040.0040.0000.0000.0000.000
139A141GLU-1-0.839-0.89030.6930.0710.0710.0000.0000.0000.000
140A142THR0-0.042-0.05426.8290.0040.0040.0000.0000.0000.000
141A143GLY00.0030.00925.6270.0080.0080.0000.0000.0000.000
142A144GLU-1-0.813-0.90623.4610.1430.1430.0000.0000.0000.000
143A145LEU0-0.010-0.01326.471-0.011-0.0110.0000.0000.0000.000
144A146PRO0-0.0110.00228.5790.0030.0030.0000.0000.0000.000
145A147THR00.017-0.00128.647-0.005-0.0050.0000.0000.0000.000
146A148TRP00.0430.00831.137-0.003-0.0030.0000.0000.0000.000
147A149GLN00.0000.00931.732-0.008-0.0080.0000.0000.0000.000
148A150TRP00.0700.01429.293-0.006-0.0060.0000.0000.0000.000
149A151GLU-1-0.927-0.96035.1260.0440.0440.0000.0000.0000.000
150A152SER0-0.077-0.03138.153-0.003-0.0030.0000.0000.0000.000
151A153LEU0-0.048-0.02034.887-0.002-0.0020.0000.0000.0000.000
152A154ILE0-0.0100.01134.234-0.002-0.0020.0000.0000.0000.000
153A155SER0-0.017-0.03838.758-0.003-0.0030.0000.0000.0000.000
154A156LYS11.0150.98941.839-0.027-0.0270.0000.0000.0000.000
155A157SER0-0.070-0.02944.064-0.002-0.0020.0000.0000.0000.000
156A158THR00.0120.00837.3930.0010.0010.0000.0000.0000.000
157A159ARG10.8520.92439.215-0.033-0.0330.0000.0000.0000.000
158A160LEU0-0.0060.00734.9630.0000.0000.0000.0000.0000.000
159A161VAL00.0260.00631.140-0.002-0.0020.0000.0000.0000.000
160A162ALA0-0.0050.02429.5990.0030.0030.0000.0000.0000.000
161A163VAL0-0.020-0.01325.916-0.002-0.0020.0000.0000.0000.000
162A164ASN00.0230.01521.9840.0010.0010.0000.0000.0000.000
163A165SER0-0.002-0.02818.188-0.005-0.0050.0000.0000.0000.000
164A166ALA00.0360.01217.6260.0080.0080.0000.0000.0000.000
165A167SER0-0.0340.00419.755-0.006-0.0060.0000.0000.0000.000
166A168GLY00.007-0.00917.8610.0160.0160.0000.0000.0000.000
167A169THR0-0.016-0.01418.588-0.005-0.0050.0000.0000.0000.000
168A170LEU00.0310.01920.480-0.007-0.0070.0000.0000.0000.000
169A171GLY00.0310.03117.2570.0050.0050.0000.0000.0000.000
170A172GLY00.0220.01317.8780.0250.0250.0000.0000.0000.000
171A173VAL0-0.031-0.02017.0910.0010.0010.0000.0000.0000.000
172A174THR0-0.023-0.01220.279-0.013-0.0130.0000.0000.0000.000
173A175ASP-1-0.785-0.86322.8640.1010.1010.0000.0000.0000.000
174A176LEU00.031-0.00723.219-0.010-0.0100.0000.0000.0000.000
175A177ARG10.8170.89023.961-0.101-0.1010.0000.0000.0000.000
176A178ALA00.0190.00827.151-0.006-0.0060.0000.0000.0000.000
177A179MET0-0.0050.00729.069-0.004-0.0040.0000.0000.0000.000
178A180THR00.025-0.01227.980-0.003-0.0030.0000.0000.0000.000
179A181LYS10.8090.90829.694-0.056-0.0560.0000.0000.0000.000
180A182LEU00.0820.05133.530-0.002-0.0020.0000.0000.0000.000
181A183VAL0-0.030-0.01632.516-0.003-0.0030.0000.0000.0000.000
182A184HIS0-0.037-0.03930.590-0.004-0.0040.0000.0000.0000.000
183A185ASP-1-0.899-0.94535.9380.0370.0370.0000.0000.0000.000
184A186VAL0-0.100-0.04738.510-0.003-0.0030.0000.0000.0000.000
185A187GLY0-0.0180.00039.000-0.001-0.0010.0000.0000.0000.000
186A188ALA0-0.078-0.02536.392-0.001-0.0010.0000.0000.0000.000
187A189LEU0-0.003-0.00432.990-0.001-0.0010.0000.0000.0000.000
188A190VAL0-0.0020.00227.6910.0010.0010.0000.0000.0000.000
189A191VAL0-0.022-0.02127.6640.0000.0000.0000.0000.0000.000
190A192VAL00.0370.00622.1700.0010.0010.0000.0000.0000.000
191A193ASP-1-0.759-0.83221.7000.1420.1420.0000.0000.0000.000
192A194HIS00.0650.03814.497-0.019-0.0190.0000.0000.0000.000
193A195SER0-0.068-0.06916.9890.0410.0410.0000.0000.0000.000
194A196ALA00.0070.01316.0640.0210.0210.0000.0000.0000.000
195A197ALA00.0290.00714.0870.0360.0360.0000.0000.0000.000
196A198ALA0-0.0140.00112.6480.0810.0810.0000.0000.0000.000
197A199PRO0-0.022-0.00910.1920.0740.0740.0000.0000.0000.000
198A200TYR0-0.056-0.0368.2590.4120.4120.0000.0000.0000.000
199A201ARG10.9190.9498.718-0.343-0.3430.0000.0000.0000.000
200A202LEU00.0160.01311.157-0.026-0.0260.0000.0000.0000.000
201A203LEU0-0.008-0.00413.320-0.002-0.0020.0000.0000.0000.000
202A204ASP-1-0.727-0.84117.1420.0370.0370.0000.0000.0000.000
203A205ILE0-0.0010.00319.255-0.001-0.0010.0000.0000.0000.000
204A206ARG10.7870.88222.508-0.048-0.0480.0000.0000.0000.000
205A207GLU-1-0.958-0.97219.6330.0520.0520.0000.0000.0000.000
206A208THR0-0.073-0.06821.1000.0010.0010.0000.0000.0000.000
207A209ASP-1-0.829-0.89023.9300.0460.0460.0000.0000.0000.000
208A210ALA00.0630.03625.028-0.003-0.0030.0000.0000.0000.000
209A211ASP-1-0.805-0.87627.0230.0480.0480.0000.0000.0000.000
210A212VAL0-0.042-0.02426.870-0.003-0.0030.0000.0000.0000.000
211A213VAL00.0340.02620.6120.0040.0040.0000.0000.0000.000
212A214THR0-0.036-0.02422.435-0.009-0.0090.0000.0000.0000.000
213A215VAL00.0050.00217.0780.0180.0180.0000.0000.0000.000
214A216ASN00.034-0.01917.738-0.030-0.0300.0000.0000.0000.000
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