FMODB

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

Last updated: 2024-07-23

All entries: 37478

Number of unique PDB entries: 7783

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FMODB ID: LNQ99

Calculation Name: 3NT8-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3NT8

Chain ID: A

ChEMBL ID:

UniProt ID: O76744

Base Structure: X-ray

Registration Date: 2023-09-22

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None


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 391
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -6439056.788624
FMO2-HF: Nuclear repulsion 6280553.187441
FMO2-HF: Total energy -158503.601184
FMO2-MP2: Total energy -158944.432351


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:24:SER)


Summations of interaction energy for fragment #1(A:24:SER)
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.
-1.5540.648-0.009-1.046-1.147-0.001
Interaction energy analysis for fragmet #1(A:24:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.025 / q_NPA : -0.005
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].
3A26GLY00.0180.0103.3770.3562.333-0.006-1.032-0.939-0.001
4A27CYS0-0.039-0.0144.5791.1911.327-0.002-0.013-0.1210.000
5A28SER00.0540.0198.086-0.155-0.1550.0000.0000.0000.000
6A29ASN0-0.070-0.02910.5790.1970.1970.0000.0000.0000.000
7A30SER00.0240.01111.362-0.205-0.2050.0000.0000.0000.000
8A31GLY0-0.036-0.01113.7820.0540.0540.0000.0000.0000.000
9A32ILE0-0.066-0.02811.0830.0940.0940.0000.0000.0000.000
10A33THR00.010-0.01810.625-0.157-0.1570.0000.0000.0000.000
11A34ASP-1-0.796-0.9115.160-4.031-4.0310.0000.0000.0000.000
12A35SER00.0230.0146.7950.0410.0410.0000.0000.0000.000
13A36ASP-1-0.770-0.8589.178-0.603-0.6030.0000.0000.0000.000
14A37ARG10.7240.8246.6182.3142.3140.0000.0000.0000.000
15A38GLN0-0.035-0.0354.900-0.353-0.264-0.001-0.001-0.0870.000
16A39ALA00.0080.0127.5780.2480.2480.0000.0000.0000.000
17A40PHE00.032-0.01511.1820.1440.1440.0000.0000.0000.000
18A41LEU0-0.0190.0046.7710.1440.1440.0000.0000.0000.000
19A42ASP-1-0.833-0.9129.454-0.219-0.2190.0000.0000.0000.000
20A43PHE0-0.0200.00911.5340.0640.0640.0000.0000.0000.000
21A44HIS00.0310.00714.0690.0610.0610.0000.0000.0000.000
22A45ASN00.0160.00310.7420.0330.0330.0000.0000.0000.000
23A46ASN0-0.022-0.02313.3240.0570.0570.0000.0000.0000.000
24A47ALA00.0110.02016.5020.0140.0140.0000.0000.0000.000
25A48ARG10.8050.87416.688-0.018-0.0180.0000.0000.0000.000
26A49ARG10.8770.93914.153-0.090-0.0900.0000.0000.0000.000
27A50ARG10.8550.90819.5560.0580.0580.0000.0000.0000.000
28A51VAL0-0.0030.00122.4040.0030.0030.0000.0000.0000.000
29A52ALA00.0240.01421.8650.0040.0040.0000.0000.0000.000
30A53LYS10.7860.86721.295-0.045-0.0450.0000.0000.0000.000
31A54GLY00.0270.02725.523-0.001-0.0010.0000.0000.0000.000
32A55LEU0-0.034-0.01824.097-0.005-0.0050.0000.0000.0000.000
33A56GLU-1-0.803-0.86124.531-0.071-0.0710.0000.0000.0000.000
34A57ASP-1-0.816-0.87626.636-0.041-0.0410.0000.0000.0000.000
35A58SER00.013-0.00429.237-0.004-0.0040.0000.0000.0000.000
36A59ASN0-0.010-0.01432.0520.0020.0020.0000.0000.0000.000
37A60SER0-0.011-0.00434.8140.0000.0000.0000.0000.0000.000
38A61GLY00.0050.00834.9230.0040.0040.0000.0000.0000.000
39A62LYS10.7860.89128.9540.0240.0240.0000.0000.0000.000
40A63LEU0-0.021-0.01227.0110.0010.0010.0000.0000.0000.000
41A64ASN0-0.030-0.02230.1370.0040.0040.0000.0000.0000.000
42A65PRO00.0160.01827.702-0.001-0.0010.0000.0000.0000.000
43A66ALA0-0.010-0.00624.7570.0000.0000.0000.0000.0000.000
44A67LYS10.8630.93525.234-0.043-0.0430.0000.0000.0000.000
45A68ASN0-0.029-0.05623.9800.0050.0050.0000.0000.0000.000
46A69MET00.0010.01820.257-0.002-0.0020.0000.0000.0000.000
47A70TYR0-0.049-0.03417.8170.0090.0090.0000.0000.0000.000
48A71LYS10.8100.8959.570-0.545-0.5450.0000.0000.0000.000
49A72LEU0-0.042-0.01313.1780.0200.0200.0000.0000.0000.000
50A73SER00.0080.0029.7780.1180.1180.0000.0000.0000.000
51A74TRP00.027-0.0217.205-0.058-0.0580.0000.0000.0000.000
52A75ASP-1-0.793-0.8859.1740.0280.0280.0000.0000.0000.000
53A77ALA00.0180.01911.373-0.021-0.0210.0000.0000.0000.000
54A78MET0-0.092-0.04614.3260.0350.0350.0000.0000.0000.000
55A79GLU-1-0.711-0.82310.098-1.242-1.2420.0000.0000.0000.000
56A80GLN0-0.047-0.03113.971-0.066-0.0660.0000.0000.0000.000
57A81GLN00.0620.04015.9980.0580.0580.0000.0000.0000.000
58A82LEU0-0.015-0.00616.9900.0330.0330.0000.0000.0000.000
59A83GLN0-0.003-0.01316.333-0.038-0.0380.0000.0000.0000.000
60A84ASP-1-0.844-0.91318.491-0.326-0.3260.0000.0000.0000.000
61A85ALA0-0.019-0.00821.4930.0230.0230.0000.0000.0000.000
62A86ILE0-0.037-0.01319.3080.0240.0240.0000.0000.0000.000
63A87GLN0-0.001-0.00720.4740.0110.0110.0000.0000.0000.000
64A88SER00.0030.00324.3790.0000.0000.0000.0000.0000.000
65A89CYS0-0.091-0.04624.0450.0030.0030.0000.0000.0000.000
66A90PRO00.0450.04425.9000.0140.0140.0000.0000.0000.000
67A91SER0-0.014-0.01528.426-0.007-0.0070.0000.0000.0000.000
68A92GLY00.0130.00929.5790.0080.0080.0000.0000.0000.000
69A93PHE0-0.046-0.03025.942-0.010-0.0100.0000.0000.0000.000
70A94ALA00.007-0.00824.2680.0050.0050.0000.0000.0000.000
71A95GLY0-0.0050.00626.3960.0020.0020.0000.0000.0000.000
72A96ILE0-0.035-0.00720.9110.0060.0060.0000.0000.0000.000
73A97GLN00.0160.00523.5330.0270.0270.0000.0000.0000.000
74A98GLY00.0190.00222.864-0.009-0.0090.0000.0000.0000.000
75A99VAL0-0.076-0.03719.5070.0120.0120.0000.0000.0000.000
76A100ALA00.0340.03822.3170.0000.0000.0000.0000.0000.000
77A101GLN00.026-0.01421.6160.0020.0020.0000.0000.0000.000
78A102ASN0-0.0170.01620.9330.0260.0260.0000.0000.0000.000
79A103THR00.0100.00621.739-0.031-0.0310.0000.0000.0000.000
80A104MET00.0340.04223.3190.0210.0210.0000.0000.0000.000
81A105SER00.018-0.00124.613-0.018-0.0180.0000.0000.0000.000
82A106TRP00.0280.02123.1500.0260.0260.0000.0000.0000.000
83A107SER0-0.023-0.03727.7060.0010.0010.0000.0000.0000.000
84A108SER0-0.0180.00929.6790.0070.0070.0000.0000.0000.000
85A109SER00.0230.00631.525-0.006-0.0060.0000.0000.0000.000
86A110GLY00.0210.02032.3490.0040.0040.0000.0000.0000.000
87A111GLY0-0.027-0.00529.472-0.007-0.0070.0000.0000.0000.000
88A112TYR0-0.041-0.06024.0240.0050.0050.0000.0000.0000.000
89A113PRO00.0060.00624.221-0.019-0.0190.0000.0000.0000.000
90A114ASP-1-0.791-0.87119.204-0.413-0.4130.0000.0000.0000.000
91A115PRO0-0.012-0.01218.2740.0270.0270.0000.0000.0000.000
92A116SER00.007-0.00615.5910.0120.0120.0000.0000.0000.000
93A117VAL0-0.009-0.00617.2980.0140.0140.0000.0000.0000.000
94A118LYS10.8640.93819.8780.2360.2360.0000.0000.0000.000
95A119ILE0-0.0050.02313.8650.0310.0310.0000.0000.0000.000
96A120GLU-1-0.830-0.90017.842-0.170-0.1700.0000.0000.0000.000
97A121PRO00.0280.02319.0330.0220.0220.0000.0000.0000.000
98A122THR0-0.067-0.04120.2020.0240.0240.0000.0000.0000.000
99A123LEU0-0.016-0.00115.7510.0200.0200.0000.0000.0000.000
100A124SER00.002-0.03220.1610.0280.0280.0000.0000.0000.000
101A125GLY00.0050.00722.5910.0190.0190.0000.0000.0000.000
102A126TRP0-0.043-0.04418.6400.0140.0140.0000.0000.0000.000
103A127TRP00.019-0.01921.2980.0120.0120.0000.0000.0000.000
104A128SER0-0.073-0.04324.1370.0160.0160.0000.0000.0000.000
105A129GLY00.0360.02427.3650.0060.0060.0000.0000.0000.000
106A130ALA00.0490.02527.9230.0060.0060.0000.0000.0000.000
107A131LYS10.8320.89729.0660.0620.0620.0000.0000.0000.000
108A132LYS10.8780.93429.9030.0910.0910.0000.0000.0000.000
109A133ASN0-0.021-0.01932.4320.0040.0040.0000.0000.0000.000
110A134GLY00.0020.03033.4030.0040.0040.0000.0000.0000.000
111A135VAL0-0.032-0.03330.121-0.003-0.0030.0000.0000.0000.000
112A136GLY00.0230.02333.6170.0020.0020.0000.0000.0000.000
113A137PRO00.0210.00234.8210.0010.0010.0000.0000.0000.000
114A138ASP-1-0.828-0.90435.6200.0030.0030.0000.0000.0000.000
115A139ASN0-0.031-0.03030.128-0.001-0.0010.0000.0000.0000.000
116A140LYS10.8460.92431.196-0.001-0.0010.0000.0000.0000.000
117A141TYR00.0380.03830.294-0.007-0.0070.0000.0000.0000.000
118A142THR00.022-0.00332.6870.0010.0010.0000.0000.0000.000
119A143GLY00.0270.02033.955-0.001-0.0010.0000.0000.0000.000
120A144GLY0-0.001-0.00633.412-0.004-0.0040.0000.0000.0000.000
121A145GLY00.0200.01533.031-0.001-0.0010.0000.0000.0000.000
122A146LEU0-0.021-0.01029.728-0.006-0.0060.0000.0000.0000.000
123A147PHE0-0.0160.00126.5090.0000.0000.0000.0000.0000.000
124A148ALA00.0350.03524.4110.0020.0020.0000.0000.0000.000
125A149PHE00.0690.02623.701-0.001-0.0010.0000.0000.0000.000
126A150SER0-0.011-0.02623.9130.0080.0080.0000.0000.0000.000
127A151ASN0-0.012-0.02422.0220.0230.0230.0000.0000.0000.000
128A152MET0-0.099-0.01718.8010.0080.0080.0000.0000.0000.000
129A153VAL00.0050.00919.6180.0140.0140.0000.0000.0000.000
130A154TYR0-0.045-0.03322.2610.0110.0110.0000.0000.0000.000
131A155SER00.0370.02221.5920.0040.0040.0000.0000.0000.000
132A156GLU-1-0.812-0.89221.4490.0610.0610.0000.0000.0000.000
133A157THR0-0.0170.00217.7630.0130.0130.0000.0000.0000.000
134A158THR00.0110.00216.3850.0120.0120.0000.0000.0000.000
135A159LYS10.8350.90513.424-0.016-0.0160.0000.0000.0000.000
136A160LEU00.0090.00911.752-0.028-0.0280.0000.0000.0000.000
137A161GLY00.0320.02412.064-0.014-0.0140.0000.0000.0000.000
138A162CYS0-0.074-0.01812.8240.0250.0250.0000.0000.0000.000
139A163ALA00.0590.03313.531-0.101-0.1010.0000.0000.0000.000
140A164TYR0-0.022-0.02814.7810.0920.0920.0000.0000.0000.000
141A165LYS10.8730.93618.6300.2700.2700.0000.0000.0000.000
142A166VAL00.0500.02821.5540.0270.0270.0000.0000.0000.000
143A168GLY00.0370.01927.5710.0160.0160.0000.0000.0000.000
144A169THR00.0260.01328.914-0.009-0.0090.0000.0000.0000.000
145A170LYS10.8610.92528.2580.1740.1740.0000.0000.0000.000
146A171LEU0-0.0040.00221.154-0.013-0.0130.0000.0000.0000.000
147A172ALA0-0.0110.01723.7320.0150.0150.0000.0000.0000.000
148A173VAL00.0350.00018.469-0.035-0.0350.0000.0000.0000.000
149A174SER0-0.054-0.04518.9950.0390.0390.0000.0000.0000.000
150A176ILE00.0140.00717.0060.0310.0310.0000.0000.0000.000
151A177TYR00.019-0.02116.814-0.010-0.0100.0000.0000.0000.000
152A178ASN00.0480.02818.109-0.006-0.0060.0000.0000.0000.000
153A179GLY00.014-0.00219.8300.0220.0220.0000.0000.0000.000
154A180VAL0-0.018-0.00722.699-0.016-0.0160.0000.0000.0000.000
155A181GLY00.0590.03425.4720.0090.0090.0000.0000.0000.000
156A182TYR0-0.034-0.02026.2360.0020.0020.0000.0000.0000.000
157A183ILE0-0.024-0.00929.719-0.002-0.0020.0000.0000.0000.000
158A184THR00.017-0.01432.1630.0010.0010.0000.0000.0000.000
159A185ASN0-0.046-0.03135.4340.0020.0020.0000.0000.0000.000
160A186GLN00.0010.01328.5090.0080.0080.0000.0000.0000.000
161A187PRO0-0.016-0.00331.048-0.005-0.0050.0000.0000.0000.000
162A188MET0-0.026-0.02126.963-0.002-0.0020.0000.0000.0000.000
163A189TRP00.024-0.01225.6790.0000.0000.0000.0000.0000.000
164A190GLU-1-0.768-0.85027.4780.0460.0460.0000.0000.0000.000
165A191THR00.0310.01229.0220.0030.0030.0000.0000.0000.000
166A192GLY0-0.036-0.02130.2560.0030.0030.0000.0000.0000.000
167A193GLN0-0.043-0.01528.363-0.006-0.0060.0000.0000.0000.000
168A194ALA00.0260.03023.6600.0060.0060.0000.0000.0000.000
169A195CYS0-0.082-0.02718.594-0.024-0.0240.0000.0000.0000.000
170A196GLN0-0.037-0.03423.629-0.004-0.0040.0000.0000.0000.000
171A197THR0-0.059-0.03423.0860.0130.0130.0000.0000.0000.000
172A198GLY00.036-0.00122.0230.0000.0000.0000.0000.0000.000
173A199ALA0-0.013-0.00222.737-0.003-0.0030.0000.0000.0000.000
174A200ASP-1-0.813-0.89125.3670.1000.1000.0000.0000.0000.000
175A201CYS0-0.052-0.00818.1390.0160.0160.0000.0000.0000.000
176A202SER00.0600.03424.5840.0060.0060.0000.0000.0000.000
177A203THR0-0.044-0.01523.9410.0000.0000.0000.0000.0000.000
178A204TYR0-0.019-0.01921.238-0.005-0.0050.0000.0000.0000.000
179A205LYS10.9550.98123.212-0.090-0.0900.0000.0000.0000.000
180A206ASN0-0.002-0.00521.6920.0010.0010.0000.0000.0000.000
181A207SER00.0120.01319.6680.0310.0310.0000.0000.0000.000
182A208GLY00.0110.00618.198-0.006-0.0060.0000.0000.0000.000
183A210GLU-1-0.768-0.86312.2490.4360.4360.0000.0000.0000.000
184A211ASP-1-0.808-0.88116.8320.0410.0410.0000.0000.0000.000
185A212GLY00.0390.01619.322-0.021-0.0210.0000.0000.0000.000
186A213LEU00.003-0.00615.321-0.010-0.0100.0000.0000.0000.000
187A215THR00.003-0.00714.4690.0010.0010.0000.0000.0000.000
188A216LYS10.8210.89615.848-0.214-0.2140.0000.0000.0000.000
189A217GLY00.0550.04215.2980.0620.0620.0000.0000.0000.000
190A218PRO0-0.023-0.03714.636-0.020-0.0200.0000.0000.0000.000
191A219ASP-1-0.851-0.90316.4960.1630.1630.0000.0000.0000.000
192A220VAL00.0070.01219.0930.0110.0110.0000.0000.0000.000
193A221PRO0-0.018-0.02021.890-0.013-0.0130.0000.0000.0000.000
194A222GLU-1-0.772-0.83123.8820.0690.0690.0000.0000.0000.000
195A223THR0-0.048-0.04526.7170.0020.0020.0000.0000.0000.000
196A224ASN00.015-0.00230.288-0.005-0.0050.0000.0000.0000.000
197A225GLN0-0.014-0.01233.878-0.003-0.0030.0000.0000.0000.000
198A226GLN0-0.076-0.05035.380-0.006-0.0060.0000.0000.0000.000
199A227CYS00.007-0.00337.819-0.004-0.0040.0000.0000.0000.000
200A228PRO00.0340.01937.995-0.003-0.0030.0000.0000.0000.000
201A229SER0-0.024-0.00939.077-0.001-0.0010.0000.0000.0000.000
202A230ASN0-0.062-0.02639.139-0.005-0.0050.0000.0000.0000.000
203A231THR00.011-0.00635.2350.0030.0030.0000.0000.0000.000
204A232GLY00.0170.00633.972-0.004-0.0040.0000.0000.0000.000
205A233MET0-0.093-0.02133.401-0.003-0.0030.0000.0000.0000.000
206A234THR0-0.009-0.02129.211-0.003-0.0030.0000.0000.0000.000
207A235ASP-1-0.717-0.83731.8080.0570.0570.0000.0000.0000.000
208A236SER0-0.011-0.02427.727-0.004-0.0040.0000.0000.0000.000
209A237VAL00.0290.01829.862-0.003-0.0030.0000.0000.0000.000
210A238ARG10.7350.84531.910-0.043-0.0430.0000.0000.0000.000
211A239ASP-1-0.800-0.89532.7090.0580.0580.0000.0000.0000.000
212A240THR0-0.073-0.02230.5220.0010.0010.0000.0000.0000.000
213A241PHE0-0.012-0.01132.903-0.004-0.0040.0000.0000.0000.000
214A242LEU00.0040.00436.248-0.003-0.0030.0000.0000.0000.000
215A243SER0-0.033-0.02834.448-0.002-0.0020.0000.0000.0000.000
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