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: JL979

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 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 396
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -6187828.699404
FMO2-HF: Nuclear repulsion 6042836.562808
FMO2-HF: Total energy -144992.136596
FMO2-MP2: Total energy -145419.897387


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.
-41.754-29.28728.467-12.343-28.587-0.036
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 : -0.029
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].
3A5VAL0-0.003-0.0112.393-1.4752.1891.190-1.424-3.4290.004
4A6ALA0-0.009-0.0013.2930.3450.1260.0870.501-0.3680.001
5A7ARG10.8060.8884.726-0.813-0.638-0.001-0.011-0.1620.000
6A8VAL0-0.020-0.0142.591-2.813-0.9041.378-0.926-2.3620.010
7A9ARG10.8210.8665.3520.7930.917-0.001-0.003-0.1190.000
8A10GLY00.0120.0217.2300.0970.0970.0000.0000.0000.000
9A11LEU0-0.059-0.0237.0050.0410.0410.0000.0000.0000.000
10A12HIS0-0.011-0.0077.2860.2350.2350.0000.0000.0000.000
11A13PRO00.008-0.00311.014-0.080-0.0800.0000.0000.0000.000
12A14SER0-0.0010.01214.179-0.015-0.0150.0000.0000.0000.000
13A15LEU00.0060.0088.432-0.050-0.0500.0000.0000.0000.000
14A16GLY0-0.031-0.01812.6450.0020.0020.0000.0000.0000.000
15A17ASP-1-0.896-0.94414.655-0.139-0.1390.0000.0000.0000.000
16A18GLY0-0.028-0.01516.5710.0260.0260.0000.0000.0000.000
17A19TRP0-0.057-0.01516.5140.0010.0010.0000.0000.0000.000
18A20VAL0-0.028-0.01012.921-0.058-0.0580.0000.0000.0000.000
19A21HIS0-0.044-0.04011.2940.0440.0440.0000.0000.0000.000
20A22PHE0-0.040-0.02811.012-0.095-0.0950.0000.0000.0000.000
21A23ASP-1-0.790-0.89713.409-0.031-0.0310.0000.0000.0000.000
22A24ALA00.0250.00710.6780.0330.0330.0000.0000.0000.000
23A25PRO0-0.0120.00012.6530.0430.0430.0000.0000.0000.000
24A26ALA0-0.0180.00215.6880.0100.0100.0000.0000.0000.000
25A27GLY0-0.017-0.00414.9640.0000.0000.0000.0000.0000.000
26A28MET0-0.067-0.0038.6800.0450.0450.0000.0000.0000.000
27A29LEU00.000-0.00310.3490.0180.0180.0000.0000.0000.000
28A30ILE0-0.003-0.00711.1600.0950.0950.0000.0000.0000.000
29A31PRO0-0.039-0.0049.707-0.053-0.0530.0000.0000.0000.000
30A32ASP-1-0.858-0.93411.9470.0490.0490.0000.0000.0000.000
31A33SER00.0210.00312.707-0.013-0.0130.0000.0000.0000.000
32A34VAL00.0090.01713.307-0.033-0.0330.0000.0000.0000.000
33A35ALA00.0540.03315.992-0.028-0.0280.0000.0000.0000.000
34A36THR00.0210.01518.226-0.026-0.0260.0000.0000.0000.000
35A37THR0-0.040-0.03518.121-0.020-0.0200.0000.0000.0000.000
36A38VAL00.0020.01319.883-0.014-0.0140.0000.0000.0000.000
37A39SER0-0.034-0.01222.200-0.016-0.0160.0000.0000.0000.000
38A40THR0-0.086-0.05223.437-0.009-0.0090.0000.0000.0000.000
39A41ALA0-0.004-0.00224.264-0.008-0.0080.0000.0000.0000.000
40A42PHE00.0110.01726.030-0.005-0.0050.0000.0000.0000.000
41A43ARG10.9300.97827.869-0.030-0.0300.0000.0000.0000.000
42A44ARG10.8750.92829.103-0.029-0.0290.0000.0000.0000.000
43A45SER0-0.034-0.02028.362-0.002-0.0020.0000.0000.0000.000
44A46GLY00.0210.01430.969-0.002-0.0020.0000.0000.0000.000
45A47ALA0-0.003-0.01133.6940.0030.0030.0000.0000.0000.000
46A48SER00.0200.00935.2860.0020.0020.0000.0000.0000.000
47A49THR00.0410.01732.6010.0000.0000.0000.0000.0000.000
48A50VAL0-0.0240.00235.240-0.002-0.0020.0000.0000.0000.000
49A51GLY00.0280.00938.9530.0000.0000.0000.0000.0000.000
50A52ALA00.001-0.01039.6000.0010.0010.0000.0000.0000.000
51A53HIS00.0280.04337.3990.0010.0010.0000.0000.0000.000
52A54PRO00.033-0.00335.3690.0020.0020.0000.0000.0000.000
53A55SER00.001-0.01733.4780.0030.0030.0000.0000.0000.000
54A56ALA00.0320.03633.1940.0040.0040.0000.0000.0000.000
55A57ARG10.9890.99032.422-0.020-0.0200.0000.0000.0000.000
56A58ARG10.9190.96026.238-0.042-0.0420.0000.0000.0000.000
57A59SER00.0340.01028.8600.0050.0050.0000.0000.0000.000
58A60ALA00.011-0.00229.3610.0050.0050.0000.0000.0000.000
59A61ALA0-0.0040.00227.6840.0030.0030.0000.0000.0000.000
60A62VAL0-0.0170.01223.5080.0040.0040.0000.0000.0000.000
61A63LEU0-0.023-0.00424.5080.0090.0090.0000.0000.0000.000
62A64ASP-1-0.919-0.96425.7630.0580.0580.0000.0000.0000.000
63A65ALA00.0450.02222.0050.0040.0040.0000.0000.0000.000
64A66ALA0-0.011-0.01520.9870.0130.0130.0000.0000.0000.000
65A67ARG10.7890.85221.203-0.056-0.0560.0000.0000.0000.000
66A68GLU-1-0.898-0.94821.4380.0660.0660.0000.0000.0000.000
67A69ALA0-0.026-0.00517.0290.0030.0030.0000.0000.0000.000
68A70VAL00.027-0.00417.2590.0180.0180.0000.0000.0000.000
69A71ALA0-0.033-0.01118.8310.0070.0070.0000.0000.0000.000
70A72ASP-1-0.769-0.87016.3760.0740.0740.0000.0000.0000.000
71A73LEU0-0.053-0.01312.506-0.002-0.0020.0000.0000.0000.000
72A74VAL0-0.009-0.00815.6490.0120.0120.0000.0000.0000.000
73A75ASN0-0.017-0.00618.346-0.022-0.0220.0000.0000.0000.000
74A76ALA0-0.003-0.00619.986-0.011-0.0110.0000.0000.0000.000
75A77ASP-1-0.837-0.92423.1800.0450.0450.0000.0000.0000.000
76A78PRO00.0640.02424.4120.0060.0060.0000.0000.0000.000
77A79GLY0-0.004-0.00625.5750.0020.0020.0000.0000.0000.000
78A80GLY0-0.013-0.01827.392-0.003-0.0030.0000.0000.0000.000
79A81VAL0-0.044-0.00723.0510.0050.0050.0000.0000.0000.000
80A82VAL0-0.031-0.00725.910-0.006-0.0060.0000.0000.0000.000
81A83LEU0-0.016-0.01622.9570.0110.0110.0000.0000.0000.000
82A84GLY00.0410.00125.548-0.011-0.0110.0000.0000.0000.000
83A85ALA0-0.0010.00125.3770.0090.0090.0000.0000.0000.000
84A86ASP-1-0.759-0.86423.4480.1170.1170.0000.0000.0000.000
85A87ARG10.8160.87921.918-0.132-0.1320.0000.0000.0000.000
86A88ALA0-0.009-0.00924.697-0.008-0.0080.0000.0000.0000.000
87A89VAL0-0.048-0.02327.341-0.008-0.0080.0000.0000.0000.000
88A90LEU0-0.020-0.00225.529-0.006-0.0060.0000.0000.0000.000
89A91LEU00.0660.02126.049-0.006-0.0060.0000.0000.0000.000
90A92SER0-0.056-0.03329.920-0.006-0.0060.0000.0000.0000.000
91A93LEU0-0.0120.00332.418-0.004-0.0040.0000.0000.0000.000
92A94LEU00.0150.00430.225-0.004-0.0040.0000.0000.0000.000
93A95ALA00.0060.01733.576-0.004-0.0040.0000.0000.0000.000
94A96GLU-1-0.967-0.99635.5590.0430.0430.0000.0000.0000.000
95A97ALA0-0.0290.00136.453-0.003-0.0030.0000.0000.0000.000
96A98SER0-0.030-0.02936.088-0.001-0.0010.0000.0000.0000.000
97A99SER0-0.013-0.00738.637-0.003-0.0030.0000.0000.0000.000
98A100SER00.0180.01042.0550.0010.0010.0000.0000.0000.000
99A101ARG10.8700.93338.382-0.045-0.0450.0000.0000.0000.000
100A102ALA0-0.0050.00039.5610.0010.0010.0000.0000.0000.000
101A103GLY00.024-0.00541.397-0.001-0.0010.0000.0000.0000.000
102A104LEU0-0.0050.00045.1940.0010.0010.0000.0000.0000.000
103A105GLY0-0.027-0.00947.953-0.001-0.0010.0000.0000.0000.000
104A106TYR0-0.059-0.03042.9540.0000.0000.0000.0000.0000.000
105A107GLU-1-0.810-0.87141.1510.0380.0380.0000.0000.0000.000
106A108VAL00.0130.00236.3240.0010.0010.0000.0000.0000.000
107A109ILE0-0.016-0.00533.816-0.002-0.0020.0000.0000.0000.000
108A110VAL00.0140.01532.3600.0030.0030.0000.0000.0000.000
109A111SER00.022-0.02327.579-0.004-0.0040.0000.0000.0000.000
110A112ARG10.8380.90829.825-0.049-0.0490.0000.0000.0000.000
111A113LEU00.0250.01423.991-0.002-0.0020.0000.0000.0000.000
112A114ASP-1-0.857-0.89524.9270.1110.1110.0000.0000.0000.000
113A115ASP-1-0.786-0.87422.8130.0990.0990.0000.0000.0000.000
114A116GLU-1-0.696-0.82725.3150.0540.0540.0000.0000.0000.000
115A117ALA0-0.040-0.02425.590-0.004-0.0040.0000.0000.0000.000
116A118ASN0-0.032-0.02526.459-0.007-0.0070.0000.0000.0000.000
117A119ILE00.0160.01628.467-0.004-0.0040.0000.0000.0000.000
118A120ALA00.0120.00331.451-0.005-0.0050.0000.0000.0000.000
119A121PRO0-0.039-0.01831.347-0.005-0.0050.0000.0000.0000.000
120A122TRP00.0430.01330.531-0.007-0.0070.0000.0000.0000.000
121A123LEU0-0.0080.00535.413-0.004-0.0040.0000.0000.0000.000
122A124ARG10.8960.94733.641-0.053-0.0530.0000.0000.0000.000
123A125ALA0-0.024-0.01438.330-0.003-0.0030.0000.0000.0000.000
124A126ALA00.0310.01139.730-0.002-0.0020.0000.0000.0000.000
125A127HIS0-0.030-0.00741.116-0.003-0.0030.0000.0000.0000.000
126A128ARG10.8730.96139.502-0.040-0.0400.0000.0000.0000.000
127A129TYR0-0.028-0.01441.895-0.001-0.0010.0000.0000.0000.000
128A130GLY00.0200.00444.969-0.001-0.0010.0000.0000.0000.000
129A131ALA0-0.0640.00042.111-0.001-0.0010.0000.0000.0000.000
130A132LYS10.9050.95142.375-0.036-0.0360.0000.0000.0000.000
131A133VAL00.0410.01137.6030.0010.0010.0000.0000.0000.000
132A134LYS10.7560.86138.825-0.043-0.0430.0000.0000.0000.000
133A135TRP00.0440.00632.2830.0020.0020.0000.0000.0000.000
134A136ALA00.0150.02631.792-0.002-0.0020.0000.0000.0000.000
135A137GLU-1-0.825-0.91532.3970.0520.0520.0000.0000.0000.000
136A138VAL00.002-0.00228.0980.0030.0030.0000.0000.0000.000
137A139ASP-1-0.831-0.89630.4430.0540.0540.0000.0000.0000.000
138A140ILE0-0.036-0.03230.3820.0030.0030.0000.0000.0000.000
139A141GLU-1-0.884-0.91730.9860.0490.0490.0000.0000.0000.000
140A142THR0-0.033-0.05027.0290.0030.0030.0000.0000.0000.000
141A143GLY00.0030.00825.8200.0070.0070.0000.0000.0000.000
142A144GLU-1-0.878-0.93323.9260.1220.1220.0000.0000.0000.000
143A145LEU0-0.004-0.00526.916-0.009-0.0090.0000.0000.0000.000
144A146PRO00.0020.00728.7540.0040.0040.0000.0000.0000.000
145A147THR00.014-0.00528.792-0.004-0.0040.0000.0000.0000.000
146A148TRP00.0360.00231.307-0.002-0.0020.0000.0000.0000.000
147A149GLN0-0.0010.01131.915-0.007-0.0070.0000.0000.0000.000
148A150TRP00.042-0.00629.706-0.004-0.0040.0000.0000.0000.000
149A151GLU-1-0.919-0.95335.4060.0430.0430.0000.0000.0000.000
150A152SER0-0.0300.00138.523-0.002-0.0020.0000.0000.0000.000
151A153LEU0-0.067-0.03035.294-0.002-0.0020.0000.0000.0000.000
152A154ILE0-0.030-0.00134.519-0.001-0.0010.0000.0000.0000.000
153A155SER00.005-0.02439.018-0.003-0.0030.0000.0000.0000.000
154A156LYS11.0210.99941.930-0.028-0.0280.0000.0000.0000.000
155A157SER0-0.059-0.03444.285-0.001-0.0010.0000.0000.0000.000
156A158THR00.0090.02037.5060.0010.0010.0000.0000.0000.000
157A159ARG10.8840.94739.486-0.037-0.0370.0000.0000.0000.000
158A160LEU00.0000.00835.2710.0010.0010.0000.0000.0000.000
159A161VAL00.0340.01431.296-0.002-0.0020.0000.0000.0000.000
160A162ALA0-0.0260.01629.7970.0030.0030.0000.0000.0000.000
161A163VAL0-0.004-0.01526.348-0.004-0.0040.0000.0000.0000.000
162A164ASN00.0200.02322.3980.0040.0040.0000.0000.0000.000
163A165SER0-0.010-0.04318.533-0.005-0.0050.0000.0000.0000.000
164A166ALA00.0350.00717.9140.0100.0100.0000.0000.0000.000
165A167SER0-0.0040.02419.978-0.008-0.0080.0000.0000.0000.000
166A168GLY00.009-0.00417.7280.0160.0160.0000.0000.0000.000
167A169THR0-0.016-0.00718.710-0.009-0.0090.0000.0000.0000.000
168A170LEU00.0210.00420.306-0.008-0.0080.0000.0000.0000.000
169A171GLY00.0250.02817.437-0.001-0.0010.0000.0000.0000.000
170A172GLY00.0060.00917.8570.0260.0260.0000.0000.0000.000
171A173VAL0-0.035-0.02916.9320.0050.0050.0000.0000.0000.000
172A174THR0-0.0030.00520.086-0.013-0.0130.0000.0000.0000.000
173A175ASP-1-0.794-0.86422.9810.1000.1000.0000.0000.0000.000
174A176LEU00.028-0.01223.765-0.009-0.0090.0000.0000.0000.000
175A177ARG10.8340.89424.389-0.096-0.0960.0000.0000.0000.000
176A178ALA00.0160.00227.651-0.005-0.0050.0000.0000.0000.000
177A179MET0-0.0010.01629.233-0.003-0.0030.0000.0000.0000.000
178A180THR00.0250.00228.301-0.003-0.0030.0000.0000.0000.000
179A181LYS10.8240.90629.898-0.064-0.0640.0000.0000.0000.000
180A182LEU00.0710.04933.679-0.002-0.0020.0000.0000.0000.000
181A183VAL0-0.039-0.02632.894-0.003-0.0030.0000.0000.0000.000
182A184HIS0-0.040-0.04730.766-0.004-0.0040.0000.0000.0000.000
183A185ASP-1-0.907-0.94135.9790.0400.0400.0000.0000.0000.000
184A186VAL0-0.112-0.05138.764-0.003-0.0030.0000.0000.0000.000
185A187GLY0-0.031-0.00539.250-0.001-0.0010.0000.0000.0000.000
186A188ALA0-0.086-0.04336.595-0.001-0.0010.0000.0000.0000.000
187A189LEU0-0.018-0.00733.2840.0000.0000.0000.0000.0000.000
188A190VAL00.001-0.00628.2330.0010.0010.0000.0000.0000.000
189A191VAL0-0.020-0.02327.7190.0020.0020.0000.0000.0000.000
190A192VAL00.0240.00022.5310.0000.0000.0000.0000.0000.000
191A193ASP-1-0.758-0.83922.2590.1530.1530.0000.0000.0000.000
192A194HIS00.0530.04014.884-0.024-0.0240.0000.0000.0000.000
193A195SER0-0.061-0.07517.4120.0380.0380.0000.0000.0000.000
194A196ALA0-0.0120.00416.5070.0260.0260.0000.0000.0000.000
195A197ALA00.0510.01814.6560.0350.0350.0000.0000.0000.000
196A198ALA0-0.0130.00813.0770.0750.0750.0000.0000.0000.000
197A199PRO0-0.029-0.01410.0560.0730.0730.0000.0000.0000.000
198A200TYR0-0.072-0.0528.5060.3790.3790.0000.0000.0000.000
199A201ARG10.9720.9969.476-0.340-0.3400.0000.0000.0000.000
200A202LEU00.0090.01311.455-0.014-0.0140.0000.0000.0000.000
201A203LEU0-0.019-0.00113.726-0.017-0.0170.0000.0000.0000.000
202A204ASP-1-0.724-0.85017.4710.0730.0730.0000.0000.0000.000
203A205ILE0-0.022-0.01619.614-0.008-0.0080.0000.0000.0000.000
204A206ARG10.8000.89922.783-0.071-0.0710.0000.0000.0000.000
205A207GLU-1-0.954-0.96120.0960.0700.0700.0000.0000.0000.000
206A208THR0-0.074-0.06121.694-0.001-0.0010.0000.0000.0000.000
207A209ASP-1-0.793-0.88624.5370.0550.0550.0000.0000.0000.000
208A210ALA00.0200.02425.046-0.003-0.0030.0000.0000.0000.000
209A211ASP-1-0.786-0.87027.0810.0600.0600.0000.0000.0000.000
210A212VAL0-0.042-0.02227.094-0.002-0.0020.0000.0000.0000.000
211A213VAL00.0320.02620.7490.0030.0030.0000.0000.0000.000
212A214THR0-0.038-0.02022.818-0.007-0.0070.0000.0000.0000.000
213A215VAL0-0.001-0.00317.3480.0160.0160.0000.0000.0000.000
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