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

tag_button

FMODB ID: JLLQ9

Calculation Name: 4I6L-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4I6L

Chain ID: A

ChEMBL ID:

UniProt ID: Q96FW1

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 220
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2855484.894309
FMO2-HF: Nuclear repulsion 2766068.274114
FMO2-HF: Total energy -89416.620194
FMO2-MP2: Total energy -89680.42663


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:43:GLY)


Summations of interaction energy for fragment #1(A:43:GLY)
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.
-0.4431.2930.003-0.765-0.9730.002
Interaction energy analysis for fragmet #1(A:43:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.027 / q_NPA : -0.003
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].
3A45ASN00.0050.0003.462-0.4191.0070.003-0.690-0.7380.002
4A46PRO00.0230.0303.9670.4600.7540.001-0.072-0.2230.000
5A47LEU0-0.0120.0065.0420.3030.319-0.001-0.003-0.0120.000
6A48VAL00.0180.0048.3940.1510.1510.0000.0000.0000.000
7A49SER0-0.0210.0017.988-0.186-0.1860.0000.0000.0000.000
8A50GLU-1-0.757-0.9088.802-0.533-0.5330.0000.0000.0000.000
9A51ARG10.8510.95110.4300.3250.3250.0000.0000.0000.000
10A52LEU00.0090.00510.9020.0110.0110.0000.0000.0000.000
11A53GLU-1-0.868-0.94514.822-0.226-0.2260.0000.0000.0000.000
12A54LEU00.018-0.00717.217-0.019-0.0190.0000.0000.0000.000
13A55SER00.0000.00318.7480.0060.0060.0000.0000.0000.000
14A56VAL0-0.012-0.02413.5520.0350.0350.0000.0000.0000.000
15A57LEU00.0210.01616.799-0.017-0.0170.0000.0000.0000.000
16A58TYR0-0.005-0.00619.3900.0180.0180.0000.0000.0000.000
17A59LYS10.9360.97817.5190.1140.1140.0000.0000.0000.000
18A60GLU-1-0.874-0.92115.688-0.360-0.3600.0000.0000.0000.000
19A61TYR0-0.173-0.11418.023-0.001-0.0010.0000.0000.0000.000
20A62ALA00.0310.01620.5000.0080.0080.0000.0000.0000.000
21A63GLU-1-0.925-0.96622.617-0.008-0.0080.0000.0000.0000.000
22A64ASP-1-0.927-0.94326.220-0.050-0.0500.0000.0000.0000.000
23A65ASP-1-0.774-0.89224.443-0.091-0.0910.0000.0000.0000.000
24A66ASN0-0.053-0.06727.919-0.014-0.0140.0000.0000.0000.000
25A67ILE0-0.0300.00129.932-0.003-0.0030.0000.0000.0000.000
26A68TYR0-0.035-0.03925.690-0.006-0.0060.0000.0000.0000.000
27A69GLN0-0.0120.00324.306-0.018-0.0180.0000.0000.0000.000
28A70GLN0-0.037-0.03327.6320.0010.0010.0000.0000.0000.000
29A71LYS10.9880.98627.2610.1120.1120.0000.0000.0000.000
30A72ILE00.0670.04923.021-0.005-0.0050.0000.0000.0000.000
31A73LYS10.9280.97926.0670.0760.0760.0000.0000.0000.000
32A74ASP-1-0.885-0.92428.664-0.091-0.0910.0000.0000.0000.000
33A75LEU00.0470.01923.5660.0020.0020.0000.0000.0000.000
34A76HIS0-0.010-0.01324.960-0.007-0.0070.0000.0000.0000.000
35A77LYS10.8070.91126.7020.0970.0970.0000.0000.0000.000
36A78LYS10.7750.88728.4350.1360.1360.0000.0000.0000.000
37A79TYR0-0.079-0.06523.759-0.001-0.0010.0000.0000.0000.000
38A80SER00.0060.01023.6050.0090.0090.0000.0000.0000.000
39A81TYR0-0.006-0.00918.5330.0040.0040.0000.0000.0000.000
40A82ILE0-0.016-0.00115.6510.0210.0210.0000.0000.0000.000
41A83ARG10.7950.91012.3480.5500.5500.0000.0000.0000.000
42A84LYS10.8800.92811.2000.6520.6520.0000.0000.0000.000
43A85THR00.0010.01011.365-0.090-0.0900.0000.0000.0000.000
44A86ARG10.8310.9106.1590.7410.7410.0000.0000.0000.000
45A87PRO0-0.0100.00610.7220.0840.0840.0000.0000.0000.000
46A88ASP-1-0.803-0.90612.790-0.338-0.3380.0000.0000.0000.000
47A89GLY00.0200.01214.7710.0400.0400.0000.0000.0000.000
48A90ASN0-0.014-0.01815.3490.0590.0590.0000.0000.0000.000
49A91SER0-0.025-0.02415.700-0.008-0.0080.0000.0000.0000.000
50A92PHE00.0230.01616.687-0.017-0.0170.0000.0000.0000.000
51A93TYR00.015-0.01719.357-0.002-0.0020.0000.0000.0000.000
52A94ARG10.7880.87012.2950.4190.4190.0000.0000.0000.000
53A95ALA0-0.009-0.00316.407-0.026-0.0260.0000.0000.0000.000
54A96PHE0-0.002-0.01417.4670.0070.0070.0000.0000.0000.000
55A97GLY00.0110.00419.4380.0110.0110.0000.0000.0000.000
56A98PHE0-0.029-0.01415.101-0.001-0.0010.0000.0000.0000.000
57A99SER0-0.009-0.00317.8950.0230.0230.0000.0000.0000.000
58A100HIS00.0370.01220.3350.0120.0120.0000.0000.0000.000
59A101LEU0-0.006-0.00919.9620.0160.0160.0000.0000.0000.000
60A102GLU-1-0.726-0.83617.904-0.361-0.3610.0000.0000.0000.000
61A103ALA0-0.007-0.00221.1320.0130.0130.0000.0000.0000.000
62A104LEU0-0.075-0.03324.5380.0180.0180.0000.0000.0000.000
63A105LEU0-0.0300.00121.1150.0120.0120.0000.0000.0000.000
64A106ASP-1-0.912-0.93825.711-0.155-0.1550.0000.0000.0000.000
65A107ASP-1-0.886-0.94728.279-0.100-0.1000.0000.0000.0000.000
66A108SER00.0430.00930.6360.0000.0000.0000.0000.0000.000
67A109LYS10.9100.95532.1980.0820.0820.0000.0000.0000.000
68A110GLU-1-0.836-0.91330.569-0.112-0.1120.0000.0000.0000.000
69A111LEU00.0460.03927.0330.0000.0000.0000.0000.0000.000
70A112GLN0-0.051-0.04130.2750.0040.0040.0000.0000.0000.000
71A113ARG10.8250.91031.9730.1130.1130.0000.0000.0000.000
72A114PHE00.0340.02125.4090.0020.0020.0000.0000.0000.000
73A115LYS10.8710.92329.9240.0980.0980.0000.0000.0000.000
74A116ALA0-0.028-0.01730.8400.0040.0040.0000.0000.0000.000
75A117VAL0-0.032-0.01831.9130.0050.0050.0000.0000.0000.000
76A118SER00.023-0.00128.4390.0000.0000.0000.0000.0000.000
77A119ALA0-0.0070.01930.4570.0010.0010.0000.0000.0000.000
78A120LYS10.8440.91232.4610.0770.0770.0000.0000.0000.000
79A121SER0-0.017-0.02130.6790.0020.0020.0000.0000.0000.000
80A122LYS10.8640.93031.0100.0720.0720.0000.0000.0000.000
81A123GLU-1-0.868-0.95132.794-0.055-0.0550.0000.0000.0000.000
82A124ASP-1-0.884-0.92635.184-0.071-0.0710.0000.0000.0000.000
83A125LEU00.0230.01130.2130.0020.0020.0000.0000.0000.000
84A126VAL0-0.016-0.00534.7650.0030.0030.0000.0000.0000.000
85A127SER0-0.064-0.01936.7860.0040.0040.0000.0000.0000.000
86A128GLN0-0.098-0.05536.1380.0000.0000.0000.0000.0000.000
87A129GLY0-0.031-0.02038.391-0.001-0.0010.0000.0000.0000.000
88A130PHE0-0.061-0.01631.3360.0010.0010.0000.0000.0000.000
89A131THR00.0100.00133.8170.0030.0030.0000.0000.0000.000
90A132GLU-1-0.775-0.88032.975-0.063-0.0630.0000.0000.0000.000
91A133PHE00.005-0.01032.243-0.003-0.0030.0000.0000.0000.000
92A134THR0-0.065-0.02729.3620.0010.0010.0000.0000.0000.000
93A135ILE00.000-0.00728.045-0.005-0.0050.0000.0000.0000.000
94A136GLU-1-0.895-0.94227.985-0.069-0.0690.0000.0000.0000.000
95A137ASP-1-0.858-0.93224.597-0.082-0.0820.0000.0000.0000.000
96A138PHE0-0.070-0.02221.513-0.011-0.0110.0000.0000.0000.000
97A139HIS0-0.016-0.01023.948-0.010-0.0100.0000.0000.0000.000
98A140ASN00.000-0.00425.593-0.003-0.0030.0000.0000.0000.000
99A141THR00.008-0.00119.527-0.004-0.0040.0000.0000.0000.000
100A142PHE0-0.017-0.01522.035-0.015-0.0150.0000.0000.0000.000
101A143MET0-0.044-0.02323.415-0.007-0.0070.0000.0000.0000.000
102A144ASP-1-0.879-0.92021.897-0.149-0.1490.0000.0000.0000.000
103A145LEU00.006-0.00117.811-0.009-0.0090.0000.0000.0000.000
104A146ILE0-0.018-0.01321.792-0.004-0.0040.0000.0000.0000.000
105A147GLU-1-0.862-0.90925.013-0.098-0.0980.0000.0000.0000.000
106A148GLN0-0.037-0.03219.284-0.017-0.0170.0000.0000.0000.000
107A149VAL00.012-0.00122.0890.0000.0000.0000.0000.0000.000
108A150GLU-1-0.829-0.88724.218-0.095-0.0950.0000.0000.0000.000
109A151LYS10.7450.86126.2330.1120.1120.0000.0000.0000.000
110A152GLN0-0.091-0.04825.3960.0020.0020.0000.0000.0000.000
111A153THR00.0090.02119.5100.0050.0050.0000.0000.0000.000
112A154SER0-0.042-0.05817.856-0.015-0.0150.0000.0000.0000.000
113A155VAL00.0700.00616.077-0.016-0.0160.0000.0000.0000.000
114A156ALA0-0.006-0.00213.849-0.052-0.0520.0000.0000.0000.000
115A157ASP-1-0.864-0.89713.515-0.310-0.3100.0000.0000.0000.000
116A158LEU00.0170.01915.341-0.014-0.0140.0000.0000.0000.000
117A159LEU0-0.032-0.0249.930-0.012-0.0120.0000.0000.0000.000
118A160ALA0-0.0060.00010.555-0.105-0.1050.0000.0000.0000.000
119A161SER00.0220.01711.369-0.004-0.0040.0000.0000.0000.000
120A162PHE00.0000.00012.5490.0230.0230.0000.0000.0000.000
121A163ASN0-0.077-0.0537.267-0.239-0.2390.0000.0000.0000.000
122A164ASP-1-0.789-0.8588.502-0.209-0.2090.0000.0000.0000.000
123A165GLN0-0.025-0.0289.915-0.029-0.0290.0000.0000.0000.000
124A166SER00.0120.00511.7730.0120.0120.0000.0000.0000.000
125A167THR0-0.002-0.02514.8510.0160.0160.0000.0000.0000.000
126A168SER0-0.048-0.04112.2860.0220.0220.0000.0000.0000.000
127A169ASP-1-0.801-0.88414.307-0.282-0.2820.0000.0000.0000.000
128A170TYR0-0.022-0.01016.2340.0210.0210.0000.0000.0000.000
129A171LEU00.0150.02117.5010.0150.0150.0000.0000.0000.000
130A172VAL0-0.018-0.01516.5610.0150.0150.0000.0000.0000.000
131A173VAL00.0210.00719.5350.0160.0160.0000.0000.0000.000
132A174TYR00.019-0.00621.9960.0150.0150.0000.0000.0000.000
133A175LEU0-0.007-0.00120.5230.0090.0090.0000.0000.0000.000
134A176ARG10.8010.90019.8370.1830.1830.0000.0000.0000.000
135A177LEU00.0060.00225.1100.0110.0110.0000.0000.0000.000
136A178LEU0-0.0120.00626.4910.0090.0090.0000.0000.0000.000
137A179THR0-0.038-0.02826.6130.0060.0060.0000.0000.0000.000
138A180SER0-0.035-0.07429.1150.0090.0090.0000.0000.0000.000
139A181GLY00.0460.01330.9910.0070.0070.0000.0000.0000.000
140A182TYR00.0310.01832.6370.0050.0050.0000.0000.0000.000
141A183LEU00.0040.00231.1140.0050.0050.0000.0000.0000.000
142A184GLN0-0.007-0.01333.4730.0100.0100.0000.0000.0000.000
143A185ARG10.8370.93336.4240.0800.0800.0000.0000.0000.000
144A186GLU-1-0.914-0.94737.776-0.065-0.0650.0000.0000.0000.000
145A187SER00.007-0.01139.4180.0000.0000.0000.0000.0000.000
146A188LYS10.8060.87340.3640.0490.0490.0000.0000.0000.000
147A189PHE0-0.0240.00337.8260.0020.0020.0000.0000.0000.000
148A190PHE00.057-0.00335.343-0.001-0.0010.0000.0000.0000.000
149A191GLU-1-0.799-0.88738.628-0.052-0.0520.0000.0000.0000.000
150A192HIS0-0.072-0.01940.9920.0020.0020.0000.0000.0000.000
151A193PHE0-0.072-0.02937.2220.0000.0000.0000.0000.0000.000
152A194ILE0-0.056-0.01335.467-0.003-0.0030.0000.0000.0000.000
153A195GLU-1-0.941-0.96038.258-0.053-0.0530.0000.0000.0000.000
154A196GLY0-0.002-0.00440.1460.0000.0000.0000.0000.0000.000
155A197GLY0-0.016-0.01841.4180.0000.0000.0000.0000.0000.000
156A198ARG10.7640.85932.5180.0670.0670.0000.0000.0000.000
157A199THR0-0.023-0.01839.5900.0000.0000.0000.0000.0000.000
158A200VAL00.0450.01335.896-0.002-0.0020.0000.0000.0000.000
159A201LYS10.9230.96435.3270.0560.0560.0000.0000.0000.000
160A202GLU-1-0.851-0.90934.566-0.050-0.0500.0000.0000.0000.000
161A203PHE00.0350.01331.439-0.002-0.0020.0000.0000.0000.000
162A204CYS00.0010.01431.108-0.006-0.0060.0000.0000.0000.000
163A205GLN00.0070.00729.737-0.005-0.0050.0000.0000.0000.000
164A206GLN0-0.028-0.00229.7780.0010.0010.0000.0000.0000.000
165A207GLU-1-0.807-0.87327.740-0.088-0.0880.0000.0000.0000.000
166A208VAL0-0.057-0.01926.560-0.010-0.0100.0000.0000.0000.000
167A209GLU-1-0.787-0.88025.359-0.093-0.0930.0000.0000.0000.000
168A210PRO0-0.053-0.00624.672-0.005-0.0050.0000.0000.0000.000
169A211MET00.0590.02817.210-0.008-0.0080.0000.0000.0000.000
170A212CYS0-0.098-0.05718.3190.0120.0120.0000.0000.0000.000
171A213LYS10.8320.93019.5260.0950.0950.0000.0000.0000.000
172A214GLU-1-0.742-0.83518.855-0.263-0.2630.0000.0000.0000.000
173A215SER0-0.013-0.02822.0870.0120.0120.0000.0000.0000.000
174A216ASP-1-0.830-0.91724.380-0.120-0.1200.0000.0000.0000.000
175A217HIS00.006-0.01927.4120.0020.0020.0000.0000.0000.000
176A218ILE0-0.020-0.00630.1510.0010.0010.0000.0000.0000.000
177A219HIS00.0360.05625.678-0.007-0.0070.0000.0000.0000.000
178A220ILE0-0.005-0.00325.826-0.001-0.0010.0000.0000.0000.000
179A221ILE0-0.0150.00028.1500.0010.0010.0000.0000.0000.000
180A222ALA00.0090.00730.6260.0040.0040.0000.0000.0000.000
181A223LEU00.0080.00924.3660.0030.0030.0000.0000.0000.000
182A224ALA0-0.011-0.00328.9080.0000.0000.0000.0000.0000.000
183A225GLN0-0.029-0.01830.3820.0020.0020.0000.0000.0000.000
184A226ALA0-0.054-0.01530.6320.0050.0050.0000.0000.0000.000
185A227LEU0-0.010-0.00826.6720.0030.0030.0000.0000.0000.000
186A228SER0-0.040-0.01330.8740.0000.0000.0000.0000.0000.000
187A229VAL0-0.050-0.01827.3730.0010.0010.0000.0000.0000.000
188A230SER0-0.0010.00030.296-0.004-0.0040.0000.0000.0000.000
189A231ILE00.004-0.00525.719-0.012-0.0120.0000.0000.0000.000
190A232GLN00.007-0.00427.6160.0150.0150.0000.0000.0000.000
191A233VAL0-0.017-0.00224.867-0.016-0.0160.0000.0000.0000.000
192A234GLU-1-0.766-0.85125.359-0.125-0.1250.0000.0000.0000.000
193A235TYR00.0360.00825.161-0.016-0.0160.0000.0000.0000.000
194A236MET0-0.0070.03422.8430.0030.0030.0000.0000.0000.000
195A246PRO0-0.085-0.05530.5530.0020.0020.0000.0000.0000.000
196A247HIS00.0560.06030.9140.0010.0010.0000.0000.0000.000
197A248ILE00.018-0.00230.958-0.010-0.0100.0000.0000.0000.000
198A249PHE0-0.0330.02329.4710.0080.0080.0000.0000.0000.000
199A250PRO00.0560.00231.765-0.007-0.0070.0000.0000.0000.000
200A251GLU-1-0.864-0.93735.122-0.088-0.0880.0000.0000.0000.000
201A252GLY0-0.032-0.00837.6150.0030.0030.0000.0000.0000.000
202A253SER0-0.058-0.02935.0540.0000.0000.0000.0000.0000.000
203A254GLU-1-0.915-0.97034.791-0.095-0.0950.0000.0000.0000.000
204A255PRO0-0.022-0.00629.710-0.003-0.0030.0000.0000.0000.000
205A256LYS10.8880.93628.6260.1210.1210.0000.0000.0000.000
206A257VAL00.0040.02223.032-0.011-0.0110.0000.0000.0000.000
207A258TYR0-0.017-0.02524.1650.0150.0150.0000.0000.0000.000
208A259LEU00.0270.01520.251-0.025-0.0250.0000.0000.0000.000
209A260LEU0-0.026-0.01119.8010.0270.0270.0000.0000.0000.000
210A261TYR00.0130.00420.754-0.015-0.0150.0000.0000.0000.000
211A262ARG10.7480.85316.4210.3340.3340.0000.0000.0000.000
212A263PRO00.004-0.01621.427-0.008-0.0080.0000.0000.0000.000
213A264GLY00.0060.00921.204-0.006-0.0060.0000.0000.0000.000
214A265HIS0-0.037-0.02514.2170.0150.0150.0000.0000.0000.000
215A266TYR0-0.009-0.02517.9930.0290.0290.0000.0000.0000.000
216A267ASP-1-0.798-0.87914.927-0.547-0.5470.0000.0000.0000.000
217A268ILE00.0320.02015.8320.0470.0470.0000.0000.0000.000
218A269LEU0-0.042-0.01018.478-0.016-0.0160.0000.0000.0000.000
219A270TYR0-0.029-0.05517.322-0.003-0.0030.0000.0000.0000.000
220A271LYS10.8880.95122.4830.1550.1550.0000.0000.0000.000