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: 399JL

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 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 220
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2861281.231405
FMO2-HF: Nuclear repulsion 2771864.178648
FMO2-HF: Total energy -89417.052757
FMO2-MP2: Total energy -89680.847248


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.
1.0493.6120-1.269-1.2960.003
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 : 0.069 / q_NPA : 0.032
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].
3A45ASN00.0110.0113.378-0.0842.2240.002-1.229-1.0810.003
4A46PRO00.0290.0354.5290.5770.820-0.001-0.039-0.2040.000
5A47LEU0-0.0220.0035.3460.2260.238-0.001-0.001-0.0110.000
6A48VAL00.004-0.0078.6120.0590.0590.0000.0000.0000.000
7A49SER0-0.044-0.0238.157-0.089-0.0890.0000.0000.0000.000
8A50GLU-1-0.729-0.8789.120-0.261-0.2610.0000.0000.0000.000
9A51ARG10.8420.95910.9690.2400.2400.0000.0000.0000.000
10A52LEU00.0010.00811.320-0.014-0.0140.0000.0000.0000.000
11A53GLU-1-0.812-0.90015.430-0.425-0.4250.0000.0000.0000.000
12A54LEU0-0.022-0.01317.782-0.053-0.0530.0000.0000.0000.000
13A55SER0-0.058-0.04918.699-0.007-0.0070.0000.0000.0000.000
14A56VAL00.0580.01313.9430.0180.0180.0000.0000.0000.000
15A57LEU00.0430.03117.341-0.010-0.0100.0000.0000.0000.000
16A58TYR0-0.034-0.02319.7070.0210.0210.0000.0000.0000.000
17A59LYS10.8130.90217.6510.4080.4080.0000.0000.0000.000
18A60GLU-1-0.792-0.86315.656-0.736-0.7360.0000.0000.0000.000
19A61TYR0-0.110-0.09417.9700.0130.0130.0000.0000.0000.000
20A62ALA0-0.009-0.01520.664-0.002-0.0020.0000.0000.0000.000
21A63GLU-1-0.903-0.94822.814-0.206-0.2060.0000.0000.0000.000
22A64ASP-1-0.929-0.94826.264-0.185-0.1850.0000.0000.0000.000
23A65ASP-1-0.748-0.86424.609-0.297-0.2970.0000.0000.0000.000
24A66ASN0-0.047-0.06128.093-0.014-0.0140.0000.0000.0000.000
25A67ILE0-0.026-0.00530.1060.0020.0020.0000.0000.0000.000
26A68TYR0-0.036-0.03525.7340.0020.0020.0000.0000.0000.000
27A69GLN0-0.004-0.01023.988-0.012-0.0120.0000.0000.0000.000
28A70GLN0-0.042-0.02727.5540.0040.0040.0000.0000.0000.000
29A71LYS10.9370.95727.4470.2150.2150.0000.0000.0000.000
30A72ILE00.0400.03523.1560.0020.0020.0000.0000.0000.000
31A73LYS10.9060.95726.3310.1930.1930.0000.0000.0000.000
32A74ASP-1-0.872-0.91829.016-0.167-0.1670.0000.0000.0000.000
33A75LEU00.0340.02323.4390.0120.0120.0000.0000.0000.000
34A76HIS00.009-0.01225.746-0.005-0.0050.0000.0000.0000.000
35A77LYS10.8120.91527.2480.1680.1680.0000.0000.0000.000
36A78LYS10.7830.88929.0600.1990.1990.0000.0000.0000.000
37A79TYR0-0.056-0.04824.2040.0110.0110.0000.0000.0000.000
38A80SER0-0.0040.00024.0030.0080.0080.0000.0000.0000.000
39A81TYR00.001-0.00518.954-0.002-0.0020.0000.0000.0000.000
40A82ILE0-0.0120.00115.7700.0350.0350.0000.0000.0000.000
41A83ARG10.7750.88812.5940.4430.4430.0000.0000.0000.000
42A84LYS10.8630.92411.5500.9040.9040.0000.0000.0000.000
43A85THR00.0010.00511.571-0.025-0.0250.0000.0000.0000.000
44A86ARG10.8630.9156.6030.5000.5000.0000.0000.0000.000
45A87PRO0-0.0050.01111.2940.1090.1090.0000.0000.0000.000
46A88ASP-1-0.814-0.90813.108-0.291-0.2910.0000.0000.0000.000
47A89GLY00.0390.02215.0940.0600.0600.0000.0000.0000.000
48A90ASN00.008-0.01215.9100.0720.0720.0000.0000.0000.000
49A91SER0-0.006-0.01516.0340.0080.0080.0000.0000.0000.000
50A92PHE0-0.005-0.00116.975-0.008-0.0080.0000.0000.0000.000
51A93TYR0-0.005-0.02519.5430.0060.0060.0000.0000.0000.000
52A94ARG10.7820.85712.4830.2400.2400.0000.0000.0000.000
53A95ALA0-0.007-0.00316.571-0.008-0.0080.0000.0000.0000.000
54A96PHE00.005-0.01117.5900.0110.0110.0000.0000.0000.000
55A97GLY00.0200.01019.2530.0150.0150.0000.0000.0000.000
56A98PHE0-0.019-0.01014.6810.0030.0030.0000.0000.0000.000
57A99SER0-0.008-0.01217.7530.0120.0120.0000.0000.0000.000
58A100HIS00.0230.00920.3070.0040.0040.0000.0000.0000.000
59A101LEU0-0.012-0.00919.9020.0140.0140.0000.0000.0000.000
60A102GLU-1-0.740-0.84718.032-0.289-0.2890.0000.0000.0000.000
61A103ALA00.0030.00020.6970.0100.0100.0000.0000.0000.000
62A104LEU0-0.053-0.02924.2260.0140.0140.0000.0000.0000.000
63A105LEU0-0.048-0.00720.8250.0140.0140.0000.0000.0000.000
64A106ASP-1-0.893-0.93125.355-0.097-0.0970.0000.0000.0000.000
65A107ASP-1-0.885-0.93728.143-0.058-0.0580.0000.0000.0000.000
66A108SER00.0620.00730.3900.0030.0030.0000.0000.0000.000
67A109LYS10.8690.94131.9670.0400.0400.0000.0000.0000.000
68A110GLU-1-0.817-0.91130.277-0.069-0.0690.0000.0000.0000.000
69A111LEU00.0300.03126.9930.0030.0030.0000.0000.0000.000
70A112GLN0-0.035-0.03330.2060.0060.0060.0000.0000.0000.000
71A113ARG10.7840.88432.0310.0630.0630.0000.0000.0000.000
72A114PHE00.0370.01825.4330.0010.0010.0000.0000.0000.000
73A115LYS10.8830.94129.954-0.003-0.0030.0000.0000.0000.000
74A116ALA0-0.019-0.00830.8510.0050.0050.0000.0000.0000.000
75A117VAL0-0.024-0.01232.2990.0040.0040.0000.0000.0000.000
76A118SER00.023-0.00328.5580.0000.0000.0000.0000.0000.000
77A119ALA0-0.0150.01030.5530.0050.0050.0000.0000.0000.000
78A120LYS10.8550.90732.6090.0230.0230.0000.0000.0000.000
79A121SER0-0.017-0.01730.7780.0010.0010.0000.0000.0000.000
80A122LYS10.8020.88631.437-0.028-0.0280.0000.0000.0000.000
81A123GLU-1-0.851-0.93833.0730.0040.0040.0000.0000.0000.000
82A124ASP-1-0.882-0.90535.246-0.027-0.0270.0000.0000.0000.000
83A125LEU00.0300.01830.374-0.001-0.0010.0000.0000.0000.000
84A126VAL00.0010.00334.9480.0000.0000.0000.0000.0000.000
85A127SER0-0.083-0.04137.107-0.001-0.0010.0000.0000.0000.000
86A128GLN0-0.081-0.04636.044-0.002-0.0020.0000.0000.0000.000
87A129GLY0-0.022-0.01338.783-0.002-0.0020.0000.0000.0000.000
88A130PHE0-0.071-0.02731.6910.0020.0020.0000.0000.0000.000
89A131THR00.003-0.01434.0280.0010.0010.0000.0000.0000.000
90A132GLU-1-0.774-0.87133.1970.0240.0240.0000.0000.0000.000
91A133PHE00.0060.00032.2120.0010.0010.0000.0000.0000.000
92A134THR0-0.072-0.03029.7080.0050.0050.0000.0000.0000.000
93A135ILE0-0.001-0.00728.218-0.001-0.0010.0000.0000.0000.000
94A136GLU-1-0.837-0.90228.0950.0390.0390.0000.0000.0000.000
95A137ASP-1-0.868-0.92824.2950.0880.0880.0000.0000.0000.000
96A138PHE0-0.059-0.00921.7640.0020.0020.0000.0000.0000.000
97A139HIS0-0.014-0.00924.242-0.002-0.0020.0000.0000.0000.000
98A140ASN0-0.008-0.01125.172-0.010-0.0100.0000.0000.0000.000
99A141THR0-0.005-0.01919.5760.0090.0090.0000.0000.0000.000
100A142PHE0-0.005-0.00922.077-0.008-0.0080.0000.0000.0000.000
101A143MET0-0.041-0.01623.553-0.011-0.0110.0000.0000.0000.000
102A144ASP-1-0.876-0.91621.9040.0820.0820.0000.0000.0000.000
103A145LEU00.010-0.00217.638-0.005-0.0050.0000.0000.0000.000
104A146ILE0-0.008-0.00721.637-0.013-0.0130.0000.0000.0000.000
105A147GLU-1-0.887-0.92724.8860.0400.0400.0000.0000.0000.000
106A148GLN0-0.025-0.02318.905-0.008-0.0080.0000.0000.0000.000
107A149VAL00.0150.00921.941-0.002-0.0020.0000.0000.0000.000
108A150GLU-1-0.831-0.89024.0030.0010.0010.0000.0000.0000.000
109A151LYS10.7690.86525.691-0.051-0.0510.0000.0000.0000.000
110A152GLN0-0.105-0.04725.0560.0060.0060.0000.0000.0000.000
111A153THR00.0040.01319.0410.0140.0140.0000.0000.0000.000
112A154SER0-0.046-0.05617.985-0.035-0.0350.0000.0000.0000.000
113A155VAL00.0610.00415.9450.0060.0060.0000.0000.0000.000
114A156ALA00.0140.01113.685-0.035-0.0350.0000.0000.0000.000
115A157ASP-1-0.865-0.89113.2730.1260.1260.0000.0000.0000.000
116A158LEU00.0320.02414.8440.0230.0230.0000.0000.0000.000
117A159LEU0-0.027-0.02410.005-0.008-0.0080.0000.0000.0000.000
118A160ALA0-0.0080.00210.351-0.020-0.0200.0000.0000.0000.000
119A161SER0-0.005-0.01511.4370.0690.0690.0000.0000.0000.000
120A162PHE0-0.0030.00012.544-0.001-0.0010.0000.0000.0000.000
121A163ASN0-0.085-0.0647.162-0.327-0.3270.0000.0000.0000.000
122A164ASP-1-0.769-0.8448.3820.5460.5460.0000.0000.0000.000
123A165GLN0-0.018-0.03710.314-0.125-0.1250.0000.0000.0000.000
124A166SER0-0.0020.00511.719-0.072-0.0720.0000.0000.0000.000
125A167THR0-0.011-0.03314.867-0.054-0.0540.0000.0000.0000.000
126A168SER0-0.017-0.01312.267-0.058-0.0580.0000.0000.0000.000
127A169ASP-1-0.814-0.88714.621-0.083-0.0830.0000.0000.0000.000
128A170TYR0-0.024-0.01516.512-0.013-0.0130.0000.0000.0000.000
129A171LEU00.0280.02517.677-0.011-0.0110.0000.0000.0000.000
130A172VAL0-0.025-0.01016.759-0.012-0.0120.0000.0000.0000.000
131A173VAL00.0240.00619.691-0.005-0.0050.0000.0000.0000.000
132A174TYR00.009-0.00922.3680.0000.0000.0000.0000.0000.000
133A175LEU0-0.0060.00220.587-0.004-0.0040.0000.0000.0000.000
134A176ARG10.7930.89220.3770.1180.1180.0000.0000.0000.000
135A177LEU00.0020.00225.3240.0010.0010.0000.0000.0000.000
136A178LEU0-0.0030.00126.4520.0010.0010.0000.0000.0000.000
137A179THR0-0.038-0.03026.769-0.003-0.0030.0000.0000.0000.000
138A180SER0-0.021-0.06129.3180.0000.0000.0000.0000.0000.000
139A181GLY00.0520.02431.1820.0030.0030.0000.0000.0000.000
140A182TYR00.0450.03132.9130.0010.0010.0000.0000.0000.000
141A183LEU0-0.011-0.01231.2320.0010.0010.0000.0000.0000.000
142A184GLN0-0.013-0.01433.5510.0070.0070.0000.0000.0000.000
143A185ARG10.8000.89835.9100.0400.0400.0000.0000.0000.000
144A186GLU-1-0.878-0.92537.995-0.040-0.0400.0000.0000.0000.000
145A187SER00.002-0.00239.514-0.003-0.0030.0000.0000.0000.000
146A188LYS10.8030.86540.4510.0330.0330.0000.0000.0000.000
147A189PHE0-0.050-0.00638.0650.0000.0000.0000.0000.0000.000
148A190PHE00.0610.00035.474-0.003-0.0030.0000.0000.0000.000
149A191GLU-1-0.794-0.88739.085-0.041-0.0410.0000.0000.0000.000
150A192HIS0-0.085-0.02541.578-0.001-0.0010.0000.0000.0000.000
151A193PHE0-0.067-0.02937.407-0.003-0.0030.0000.0000.0000.000
152A194ILE0-0.029-0.00635.579-0.005-0.0050.0000.0000.0000.000
153A195GLU-1-0.946-0.96238.340-0.068-0.0680.0000.0000.0000.000
154A196GLY0-0.015-0.01340.5410.0020.0020.0000.0000.0000.000
155A197GLY0-0.013-0.01641.912-0.001-0.0010.0000.0000.0000.000
156A198ARG10.7680.86232.7680.0650.0650.0000.0000.0000.000
157A199THR0-0.015-0.01639.831-0.002-0.0020.0000.0000.0000.000
158A200VAL00.0190.00636.280-0.001-0.0010.0000.0000.0000.000
159A201LYS10.9100.95335.4240.0190.0190.0000.0000.0000.000
160A202GLU-1-0.859-0.90834.974-0.032-0.0320.0000.0000.0000.000
161A203PHE00.0320.00931.614-0.001-0.0010.0000.0000.0000.000
162A204CYS00.0270.01631.388-0.006-0.0060.0000.0000.0000.000
163A205GLN00.0200.01030.117-0.002-0.0020.0000.0000.0000.000
164A206GLN0-0.032-0.00730.0510.0010.0010.0000.0000.0000.000
165A207GLU-1-0.828-0.87428.211-0.094-0.0940.0000.0000.0000.000
166A208VAL0-0.037-0.01026.910-0.011-0.0110.0000.0000.0000.000
167A209GLU-1-0.777-0.87325.844-0.037-0.0370.0000.0000.0000.000
168A210PRO0-0.057-0.01925.1520.0050.0050.0000.0000.0000.000
169A211MET00.0500.02317.642-0.016-0.0160.0000.0000.0000.000
170A212CYS0-0.111-0.05617.3840.0160.0160.0000.0000.0000.000
171A213LYS10.8300.92820.0480.0790.0790.0000.0000.0000.000
172A214GLU-1-0.748-0.83619.040-0.276-0.2760.0000.0000.0000.000
173A215SER0-0.013-0.02122.3320.0150.0150.0000.0000.0000.000
174A216ASP-1-0.829-0.90624.710-0.140-0.1400.0000.0000.0000.000
175A217HIS00.007-0.02327.8470.0110.0110.0000.0000.0000.000
176A218ILE0-0.0150.00130.3000.0050.0050.0000.0000.0000.000
177A219HIS00.0440.05426.1290.0050.0050.0000.0000.0000.000
178A220ILE0-0.020-0.00326.1850.0050.0050.0000.0000.0000.000
179A221ILE0-0.013-0.00328.3630.0050.0050.0000.0000.0000.000
180A222ALA00.0130.01430.9950.0060.0060.0000.0000.0000.000
181A223LEU0-0.0060.00224.4290.0080.0080.0000.0000.0000.000
182A224ALA00.0010.00329.0080.0050.0050.0000.0000.0000.000
183A225GLN0-0.043-0.03430.4280.0030.0030.0000.0000.0000.000
184A226ALA0-0.044-0.01630.4950.0060.0060.0000.0000.0000.000
185A227LEU00.0080.00726.6900.0070.0070.0000.0000.0000.000
186A228SER0-0.040-0.01230.9380.0040.0040.0000.0000.0000.000
187A229VAL0-0.055-0.01627.7630.0010.0010.0000.0000.0000.000
188A230SER00.0060.00730.265-0.008-0.0080.0000.0000.0000.000
189A231ILE00.0160.00625.849-0.009-0.0090.0000.0000.0000.000
190A232GLN0-0.012-0.01427.6510.0150.0150.0000.0000.0000.000
191A233VAL0-0.012-0.00525.307-0.018-0.0180.0000.0000.0000.000
192A234GLU-1-0.757-0.84225.436-0.178-0.1780.0000.0000.0000.000
193A235TYR00.029-0.01125.747-0.017-0.0170.0000.0000.0000.000
194A236MET00.0110.07422.6750.0050.0050.0000.0000.0000.000
195A246PRO0-0.086-0.06130.4250.0010.0010.0000.0000.0000.000
196A247HIS00.0510.05931.2600.0010.0010.0000.0000.0000.000
197A248ILE00.011-0.00530.987-0.012-0.0120.0000.0000.0000.000
198A249PHE0-0.0170.01429.7780.0070.0070.0000.0000.0000.000
199A250PRO00.0660.01131.751-0.004-0.0040.0000.0000.0000.000
200A251GLU-1-0.859-0.91935.203-0.102-0.1020.0000.0000.0000.000
201A252GLY0-0.050-0.02537.4360.0050.0050.0000.0000.0000.000
202A253SER0-0.066-0.03535.3530.0040.0040.0000.0000.0000.000
203A254GLU-1-0.910-0.96734.825-0.089-0.0890.0000.0000.0000.000
204A255PRO0-0.044-0.00829.7560.0010.0010.0000.0000.0000.000
205A256LYS10.8740.92528.7720.0880.0880.0000.0000.0000.000
206A257VAL00.0170.03422.984-0.007-0.0070.0000.0000.0000.000
207A258TYR0-0.028-0.03723.8570.0070.0070.0000.0000.0000.000
208A259LEU00.0180.01520.487-0.028-0.0280.0000.0000.0000.000
209A260LEU0-0.021-0.01620.2930.0240.0240.0000.0000.0000.000
210A261TYR00.0380.02820.942-0.029-0.0290.0000.0000.0000.000
211A262ARG10.7130.81116.8280.5350.5350.0000.0000.0000.000
212A263PRO00.003-0.01722.2570.0050.0050.0000.0000.0000.000
213A264GLY00.0080.01921.606-0.017-0.0170.0000.0000.0000.000
214A265HIS0-0.040-0.03214.3830.0160.0160.0000.0000.0000.000
215A266TYR0-0.007-0.02417.9430.0370.0370.0000.0000.0000.000
216A267ASP-1-0.783-0.85815.210-0.719-0.7190.0000.0000.0000.000
217A268ILE00.0350.02315.7890.0580.0580.0000.0000.0000.000
218A269LEU0-0.050-0.02218.647-0.039-0.0390.0000.0000.0000.000
219A270TYR0-0.013-0.04917.6180.0080.0080.0000.0000.0000.000
220A271LYS10.8930.95922.9310.1740.1740.0000.0000.0000.000