Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

tag_button

FMODB ID: 85QJY

Calculation Name: 4E16-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4E16

Chain ID: A

ChEMBL ID:

UniProt ID: Q180S3

Base Structure: X-ray

Registration Date: 2023-06-22

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 232
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2685108.742852
FMO2-HF: Nuclear repulsion 2594713.3118
FMO2-HF: Total energy -90395.431052
FMO2-MP2: Total energy -90657.270717


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:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-36.078-33.1618.782-6.987-14.715-0.003
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.031 / q_NPA : 0.048
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].
3A3LYS10.7860.8802.046-27.039-28.88512.155-3.340-6.9700.035
4A4VAL00.0570.0204.4700.1460.340-0.001-0.025-0.1690.000
5A5HIS10.8140.8916.831-0.351-0.3510.0000.0000.0000.000
6A6PHE00.0210.01410.017-0.045-0.0450.0000.0000.0000.000
7A7VAL0-0.016-0.02213.0020.0840.0840.0000.0000.0000.000
8A8GLY0-0.0040.00316.124-0.034-0.0340.0000.0000.0000.000
9A9ALA0-0.026-0.03219.6980.0170.0170.0000.0000.0000.000
10A10GLY00.0430.03821.6880.0060.0060.0000.0000.0000.000
11A11PRO0-0.090-0.04724.836-0.011-0.0110.0000.0000.0000.000
12A12GLY00.025-0.01228.264-0.008-0.0080.0000.0000.0000.000
13A13ASP-1-0.837-0.91129.4580.0430.0430.0000.0000.0000.000
14A14LYS10.8290.89127.316-0.036-0.0360.0000.0000.0000.000
15A15GLU-1-0.957-0.97626.0220.0680.0680.0000.0000.0000.000
16A16LEU0-0.049-0.01926.4620.0050.0050.0000.0000.0000.000
17A17ILE0-0.0300.00719.6170.0020.0020.0000.0000.0000.000
18A18THR0-0.002-0.00518.7600.0140.0140.0000.0000.0000.000
19A19LEU00.0340.00918.8260.0080.0080.0000.0000.0000.000
20A20LYS10.9370.96611.847-0.465-0.4650.0000.0000.0000.000
21A21GLY00.0700.03115.0740.0160.0160.0000.0000.0000.000
22A22TYR00.0510.03516.8600.0000.0000.0000.0000.0000.000
23A23LYS10.9460.98714.844-0.203-0.2030.0000.0000.0000.000
24A24LEU0-0.019-0.00810.0840.0120.0120.0000.0000.0000.000
25A25LEU0-0.0110.00013.654-0.010-0.0100.0000.0000.0000.000
26A26SER00.016-0.01916.716-0.007-0.0070.0000.0000.0000.000
27A27ASN0-0.080-0.05113.6070.0020.0020.0000.0000.0000.000
28A28ALA0-0.0120.00913.5070.0340.0340.0000.0000.0000.000
29A29ASP-1-0.816-0.89112.3750.2540.2540.0000.0000.0000.000
30A30VAL0-0.0060.00011.755-0.017-0.0170.0000.0000.0000.000
31A31VAL00.0160.00213.260-0.007-0.0070.0000.0000.0000.000
32A32ILE00.0300.02312.8510.0030.0030.0000.0000.0000.000
33A33TYR00.0340.01716.5780.0020.0020.0000.0000.0000.000
34A34ALA00.0270.02419.868-0.012-0.0120.0000.0000.0000.000
35A35GLY00.0190.00922.4180.0070.0070.0000.0000.0000.000
36A36SER0-0.034-0.02625.2900.0060.0060.0000.0000.0000.000
37A37LEU0-0.021-0.00625.2480.0070.0070.0000.0000.0000.000
38A38VAL0-0.017-0.00522.1780.0050.0050.0000.0000.0000.000
39A39ASN00.002-0.01225.487-0.007-0.0070.0000.0000.0000.000
40A40PRO00.006-0.00825.9510.0040.0040.0000.0000.0000.000
41A41GLU-1-0.796-0.86326.5370.0320.0320.0000.0000.0000.000
42A42LEU0-0.039-0.01422.9370.0070.0070.0000.0000.0000.000
43A43LEU0-0.027-0.02921.1640.0070.0070.0000.0000.0000.000
44A44GLU-1-0.862-0.91623.4090.0390.0390.0000.0000.0000.000
45A45TYR0-0.075-0.05521.4880.0090.0090.0000.0000.0000.000
46A46CYS0-0.081-0.02818.9350.0080.0080.0000.0000.0000.000
47A47LYS10.8450.91714.720-0.218-0.2180.0000.0000.0000.000
48A48GLU-1-0.920-0.95520.7410.0510.0510.0000.0000.0000.000
49A49ASP-1-0.942-0.96520.0880.0740.0740.0000.0000.0000.000
50A50CYS0-0.127-0.05516.681-0.003-0.0030.0000.0000.0000.000
51A51GLN00.0090.00115.497-0.002-0.0020.0000.0000.0000.000
52A52ILE00.0200.00616.793-0.023-0.0230.0000.0000.0000.000
53A53HIS00.0370.02116.257-0.013-0.0130.0000.0000.0000.000
54A54ASN00.017-0.00619.276-0.007-0.0070.0000.0000.0000.000
55A55SER00.053-0.00818.971-0.002-0.0020.0000.0000.0000.000
56A56ALA0-0.071-0.02620.895-0.005-0.0050.0000.0000.0000.000
57A57HIS0-0.085-0.04323.8060.0050.0050.0000.0000.0000.000
58A58MET00.0190.04417.2530.0040.0040.0000.0000.0000.000
59A59ASP-1-0.874-0.93520.635-0.211-0.2110.0000.0000.0000.000
60A60LEU0-0.001-0.00816.370-0.014-0.0140.0000.0000.0000.000
61A61GLN0-0.036-0.02714.797-0.038-0.0380.0000.0000.0000.000
62A62GLU-1-0.858-0.93215.745-0.200-0.2000.0000.0000.0000.000
63A63ILE0-0.027-0.02114.309-0.014-0.0140.0000.0000.0000.000
64A64ILE0-0.018-0.01811.099-0.050-0.0500.0000.0000.0000.000
65A65ASP-1-0.803-0.87410.984-0.522-0.5220.0000.0000.0000.000
66A66VAL00.0090.00911.799-0.017-0.0170.0000.0000.0000.000
67A67MET0-0.075-0.0328.587-0.010-0.0100.0000.0000.0000.000
68A68ARG10.8040.9037.2210.3820.3820.0000.0000.0000.000
69A69GLU-1-0.862-0.9317.445-0.229-0.2290.0000.0000.0000.000
70A70GLY0-0.0120.0009.1210.1600.1600.0000.0000.0000.000
71A71ILE0-0.044-0.0302.300-0.417-0.1571.058-0.255-1.063-0.002
72A72GLU-1-0.883-0.9535.3580.1730.266-0.0010.000-0.0910.000
73A73ASN0-0.108-0.0687.0930.3450.3450.0000.0000.0000.000
74A74ASN0-0.124-0.0616.6940.6670.6670.0000.0000.0000.000
75A75LYS10.9280.9778.045-0.134-0.1340.0000.0000.0000.000
76A76SER0-0.0020.0128.092-0.017-0.0170.0000.0000.0000.000
77A77VAL00.0450.0257.989-0.054-0.0540.0000.0000.0000.000
78A78VAL0-0.030-0.0209.7370.0150.0150.0000.0000.0000.000
79A79ARG10.8070.89712.4790.1340.1340.0000.0000.0000.000
80A80LEU00.0330.02514.3590.0270.0270.0000.0000.0000.000
81A81GLN0-0.008-0.02117.658-0.048-0.0480.0000.0000.0000.000
82A82THR00.001-0.00920.1560.0210.0210.0000.0000.0000.000
83A83GLY0-0.0090.00423.367-0.004-0.0040.0000.0000.0000.000
84A84ASP-1-0.798-0.88920.8310.0670.0670.0000.0000.0000.000
85A85PHE00.027-0.00216.364-0.016-0.0160.0000.0000.0000.000
86A86SER0-0.084-0.05621.047-0.018-0.0180.0000.0000.0000.000
87A87ILE0-0.042-0.02022.367-0.007-0.0070.0000.0000.0000.000
88A88TYR00.011-0.00925.2010.0010.0010.0000.0000.0000.000
89A89GLY00.0460.03221.558-0.003-0.0030.0000.0000.0000.000
90A90SER0-0.023-0.01420.212-0.004-0.0040.0000.0000.0000.000
91A91ILE00.0440.03414.712-0.024-0.0240.0000.0000.0000.000
92A92ARG10.8330.90715.8270.1510.1510.0000.0000.0000.000
93A93GLU-1-0.876-0.94316.413-0.236-0.2360.0000.0000.0000.000
94A94GLN00.0270.00513.665-0.055-0.0550.0000.0000.0000.000
95A95VAL00.0140.00711.275-0.103-0.1030.0000.0000.0000.000
96A96GLU-1-0.866-0.91411.948-0.378-0.3780.0000.0000.0000.000
97A97ASP-1-0.785-0.88313.164-0.575-0.5750.0000.0000.0000.000
98A98LEU00.0120.0047.384-0.068-0.0680.0000.0000.0000.000
99A99ASN0-0.003-0.0018.396-0.379-0.3790.0000.0000.0000.000
100A100LYS10.7720.88210.3740.4290.4290.0000.0000.0000.000
101A101LEU0-0.019-0.0228.5710.0610.0610.0000.0000.0000.000
102A102ASN0-0.098-0.0346.999-0.094-0.0940.0000.0000.0000.000
103A103ILE00.0190.0203.424-1.407-0.9650.016-0.071-0.3870.000
104A104ASP-1-0.814-0.9052.259-7.691-4.0585.556-3.313-5.877-0.036
105A105TYR0-0.027-0.0273.8270.1530.295-0.0010.017-0.1580.000
106A106ASP-1-0.880-0.9266.4771.7871.7870.0000.0000.0000.000
107A107CYS0-0.0100.0008.921-0.251-0.2510.0000.0000.0000.000
108A108THR0-0.035-0.02112.5910.1050.1050.0000.0000.0000.000
109A109PRO00.0460.02214.961-0.038-0.0380.0000.0000.0000.000
110A110GLY00.0150.00718.6820.0140.0140.0000.0000.0000.000
111A111VAL00.0070.00521.790-0.003-0.0030.0000.0000.0000.000
112A112SER00.0390.01325.520-0.010-0.0100.0000.0000.0000.000
113A113SER00.0590.01927.0520.0030.0030.0000.0000.0000.000
114A114PHE00.0410.01228.8610.0020.0020.0000.0000.0000.000
115A115LEU00.0150.02827.8330.0000.0000.0000.0000.0000.000
116A116GLY00.0460.03731.1930.0020.0020.0000.0000.0000.000
117A117ALA00.000-0.01432.4330.0000.0000.0000.0000.0000.000
118A118ALA0-0.030-0.01135.184-0.001-0.0010.0000.0000.0000.000
119A119SER00.004-0.00933.3920.0020.0020.0000.0000.0000.000
120A120SER0-0.047-0.03935.8920.0000.0000.0000.0000.0000.000
121A121LEU0-0.062-0.05237.905-0.002-0.0020.0000.0000.0000.000
122A122GLY0-0.0230.01639.425-0.001-0.0010.0000.0000.0000.000
123A123VAL0-0.078-0.03539.493-0.001-0.0010.0000.0000.0000.000
124A124GLU-1-0.881-0.94438.3680.0320.0320.0000.0000.0000.000
125A125TYR0-0.062-0.07234.458-0.004-0.0040.0000.0000.0000.000
126A126THR0-0.058-0.00737.699-0.002-0.0020.0000.0000.0000.000
127A127VAL00.0570.03540.1010.0020.0020.0000.0000.0000.000
128A128PRO00.0560.01642.865-0.002-0.0020.0000.0000.0000.000
129A129GLU-1-0.955-0.97845.3620.0130.0130.0000.0000.0000.000
130A130ILE0-0.064-0.00246.196-0.002-0.0020.0000.0000.0000.000
131A131SER0-0.036-0.04042.539-0.001-0.0010.0000.0000.0000.000
132A132GLN00.0440.02240.4550.0020.0020.0000.0000.0000.000
133A133SER0-0.036-0.02637.9510.0000.0000.0000.0000.0000.000
134A134VAL00.0170.01735.344-0.001-0.0010.0000.0000.0000.000
135A135ILE0-0.0250.00435.7600.0000.0000.0000.0000.0000.000
136A136ILE00.0010.00431.2160.0000.0000.0000.0000.0000.000
137A137THR00.0160.00933.540-0.004-0.0040.0000.0000.0000.000
138A138ARG10.8020.87028.4880.0540.0540.0000.0000.0000.000
139A139MET0-0.045-0.01435.1270.0000.0000.0000.0000.0000.000
140A140GLU-1-0.786-0.85432.761-0.049-0.0490.0000.0000.0000.000
141A141GLY0-0.007-0.00536.9910.0030.0030.0000.0000.0000.000
142A142ARG10.7680.85239.8110.0270.0270.0000.0000.0000.000
143A143THR00.0160.01637.102-0.003-0.0030.0000.0000.0000.000
144A144PRO0-0.0160.00039.5350.0030.0030.0000.0000.0000.000
145A145VAL00.0570.02337.513-0.003-0.0030.0000.0000.0000.000
146A146PRO0-0.0060.00537.3670.0020.0020.0000.0000.0000.000
147A147GLU-1-0.766-0.88240.463-0.022-0.0220.0000.0000.0000.000
148A148LYS10.9100.95439.2800.0330.0330.0000.0000.0000.000
149A149GLU-1-0.944-0.96134.428-0.035-0.0350.0000.0000.0000.000
150A150SER0-0.028-0.01238.7090.0010.0010.0000.0000.0000.000
151A151ILE00.021-0.01039.1240.0020.0020.0000.0000.0000.000
152A152GLN0-0.009-0.02342.1340.0010.0010.0000.0000.0000.000
153A153SER0-0.065-0.02742.2620.0030.0030.0000.0000.0000.000
154A154TYR00.018-0.00735.7550.0030.0030.0000.0000.0000.000
155A155ALA00.0410.01442.1030.0020.0020.0000.0000.0000.000
156A156LYS10.8560.94245.0780.0140.0140.0000.0000.0000.000
157A157HIS0-0.022-0.00342.7310.0020.0020.0000.0000.0000.000
158A158GLN0-0.063-0.04545.4870.0030.0030.0000.0000.0000.000
159A159THR00.0070.00441.0160.0020.0020.0000.0000.0000.000
160A160SER0-0.053-0.03139.917-0.002-0.0020.0000.0000.0000.000
161A161MET0-0.035-0.00839.143-0.001-0.0010.0000.0000.0000.000
162A162VAL0-0.006-0.00334.7000.0020.0020.0000.0000.0000.000
163A163ILE0-0.018-0.00736.573-0.003-0.0030.0000.0000.0000.000
164A164PHE00.0370.01729.8830.0010.0010.0000.0000.0000.000
165A165LEU00.0100.00135.169-0.003-0.0030.0000.0000.0000.000
166A166SER00.0480.00836.6250.0010.0010.0000.0000.0000.000
167A167VAL00.0300.03638.3120.0000.0000.0000.0000.0000.000
168A168GLN00.0200.00441.4600.0000.0000.0000.0000.0000.000
169A169GLU-1-0.827-0.91241.566-0.027-0.0270.0000.0000.0000.000
170A170ILE00.0380.01644.0580.0000.0000.0000.0000.0000.000
171A171GLU-1-0.820-0.90145.285-0.012-0.0120.0000.0000.0000.000
172A172LYS10.9020.97944.7260.0220.0220.0000.0000.0000.000
173A173VAL00.0630.03141.8720.0000.0000.0000.0000.0000.000
174A174VAL00.0090.00544.7320.0010.0010.0000.0000.0000.000
175A175SER0-0.048-0.04347.8550.0000.0000.0000.0000.0000.000
176A176LYS10.8980.94244.5130.0220.0220.0000.0000.0000.000
177A177LEU00.0130.01143.6490.0000.0000.0000.0000.0000.000
178A178LEU0-0.037-0.02047.3870.0010.0010.0000.0000.0000.000
179A179GLU-1-0.884-0.93749.463-0.017-0.0170.0000.0000.0000.000
180A180GLY0-0.011-0.01247.9730.0000.0000.0000.0000.0000.000
181A181GLY0-0.0040.00748.8190.0000.0000.0000.0000.0000.000
182A182TYR0-0.071-0.01144.3560.0000.0000.0000.0000.0000.000
183A183PRO00.0290.01750.731-0.001-0.0010.0000.0000.0000.000
184A184LYS10.8760.92852.9430.0060.0060.0000.0000.0000.000
185A185ASP-1-0.806-0.88254.0990.0010.0010.0000.0000.0000.000
186A186THR0-0.033-0.02248.4100.0010.0010.0000.0000.0000.000
187A187PRO0-0.024-0.00548.365-0.001-0.0010.0000.0000.0000.000
188A188ILE0-0.005-0.00844.5140.0000.0000.0000.0000.0000.000
189A189ALA0-0.018-0.00942.6490.0010.0010.0000.0000.0000.000
190A190VAL0-0.026-0.01741.231-0.002-0.0020.0000.0000.0000.000
191A191ILE00.0240.00737.5660.0010.0010.0000.0000.0000.000
192A192TYR0-0.012-0.02737.488-0.002-0.0020.0000.0000.0000.000
193A193LYS10.8030.88132.9310.0030.0030.0000.0000.0000.000
194A194ALA00.0580.02733.6280.0020.0020.0000.0000.0000.000
195A195THR0-0.011-0.00931.6730.0020.0020.0000.0000.0000.000
196A196TRP0-0.0080.02929.0200.0020.0020.0000.0000.0000.000
197A197ALA00.0390.01533.8950.0000.0000.0000.0000.0000.000
198A198ASP-1-0.839-0.90235.9490.0020.0020.0000.0000.0000.000
199A199GLU-1-0.876-0.90036.6020.0150.0150.0000.0000.0000.000
200A200LYS10.8720.91938.275-0.001-0.0010.0000.0000.0000.000
201A201ILE00.0280.02141.017-0.002-0.0020.0000.0000.0000.000
202A202VAL0-0.021-0.00943.0320.0000.0000.0000.0000.0000.000
203A203LYS10.9360.95445.182-0.010-0.0100.0000.0000.0000.000
204A204GLY0-0.018-0.01247.6810.0000.0000.0000.0000.0000.000
205A205THR00.0180.01449.8210.0000.0000.0000.0000.0000.000
206A206LEU00.0380.00847.751-0.001-0.0010.0000.0000.0000.000
207A207SER0-0.096-0.05251.139-0.001-0.0010.0000.0000.0000.000
208A208ASP-1-0.719-0.82952.699-0.001-0.0010.0000.0000.0000.000
209A209ILE00.0370.02046.3460.0000.0000.0000.0000.0000.000
210A210ALA00.0350.00848.911-0.001-0.0010.0000.0000.0000.000
211A211VAL0-0.041-0.01549.994-0.001-0.0010.0000.0000.0000.000
212A212LYS10.8610.92649.744-0.001-0.0010.0000.0000.0000.000
213A213VAL00.0140.01045.1510.0000.0000.0000.0000.0000.000
214A214LYS10.8180.89747.6200.0110.0110.0000.0000.0000.000
215A215GLU-1-0.914-0.96149.799-0.003-0.0030.0000.0000.0000.000
216A216ASN0-0.014-0.00946.9910.0020.0020.0000.0000.0000.000
217A217ASN0-0.051-0.00747.6690.0000.0000.0000.0000.0000.000
218A218ILE0-0.014-0.00341.460-0.002-0.0020.0000.0000.0000.000
219A219ASN00.0140.01341.189-0.003-0.0030.0000.0000.0000.000
220A220LYS10.9660.97236.1320.0180.0180.0000.0000.0000.000
221A221THR0-0.002-0.00832.9300.0010.0010.0000.0000.0000.000
222A222ALA0-0.0070.00536.1620.0020.0020.0000.0000.0000.000
223A223LEU00.0000.01532.787-0.003-0.0030.0000.0000.0000.000
224A224ILE0-0.024-0.00936.7060.0010.0010.0000.0000.0000.000
225A225MET0-0.0050.00838.2630.0000.0000.0000.0000.0000.000
226A226VAL00.023-0.00440.7290.0000.0000.0000.0000.0000.000
227A227GLY00.1090.04943.0690.0000.0000.0000.0000.0000.000
228A228ARG10.8700.88945.601-0.003-0.0030.0000.0000.0000.000
229A229PHE00.0750.04940.2570.0000.0000.0000.0000.0000.000
230A230LEU0-0.022-0.00542.6090.0010.0010.0000.0000.0000.000
231A231GLY0-0.064-0.03445.6380.0000.0000.0000.0000.0000.000
232A232GLU-1-0.947-0.95345.0560.0150.0150.0000.0000.0000.000