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: 43VVN

Calculation Name: 1N81-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1N81

Chain ID: A

ChEMBL ID:

UniProt ID: Q8IEU2

Base Structure: X-ray

Registration Date: 2023-06-20

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 186
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2243790.766111
FMO2-HF: Nuclear repulsion 2165508.835795
FMO2-HF: Total energy -78281.930316
FMO2-MP2: Total energy -78512.542345


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:21:TYR)


Summations of interaction energy for fragment #1(A:21: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.
-7.632-1.9462.732-2.525-5.8930.012
Interaction energy analysis for fragmet #1(A:21:TYR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.008 / q_NPA : -0.017
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].
3A23TYR00.0490.0442.516-4.6490.6622.683-2.435-5.5590.010
4A24GLU-1-0.892-0.9344.118-0.803-0.4280.049-0.090-0.3340.002
5A25HIS10.8040.9226.1800.2860.2860.0000.0000.0000.000
6A26GLU-1-0.905-1.0167.314-1.872-1.8720.0000.0000.0000.000
7A27THR0-0.0080.0068.7990.2060.2060.0000.0000.0000.000
8A28HIS0-0.035-0.00310.762-0.045-0.0450.0000.0000.0000.000
9A29ALA00.0430.02514.147-0.042-0.0420.0000.0000.0000.000
10A30PRO0-0.009-0.01515.336-0.008-0.0080.0000.0000.0000.000
11A31LEU00.0450.04618.9790.0340.0340.0000.0000.0000.000
12A32SER00.0210.01220.266-0.016-0.0160.0000.0000.0000.000
13A33PRO00.018-0.01523.465-0.007-0.0070.0000.0000.0000.000
14A34ARG10.8010.90626.308-0.056-0.0560.0000.0000.0000.000
15A35ILE00.0240.00924.070-0.001-0.0010.0000.0000.0000.000
16A36ARG11.0061.00924.0700.0820.0820.0000.0000.0000.000
17A37LYS10.9160.96426.7990.0190.0190.0000.0000.0000.000
18A38VAL0-0.026-0.01030.358-0.002-0.0020.0000.0000.0000.000
19A39GLY00.0410.02528.8900.0010.0010.0000.0000.0000.000
20A40ASP-1-0.873-0.94029.456-0.043-0.0430.0000.0000.0000.000
21A41ILE0-0.090-0.04631.4910.0000.0000.0000.0000.0000.000
22A42GLU-1-0.754-0.85433.1290.0310.0310.0000.0000.0000.000
23A43PHE00.0520.01129.6900.0010.0010.0000.0000.0000.000
24A44HIS00.0510.05331.5880.0010.0010.0000.0000.0000.000
25A45ALA0-0.0150.00335.8600.0000.0000.0000.0000.0000.000
26A46CYS0-0.054-0.02336.2790.0020.0020.0000.0000.0000.000
27A47SER0-0.017-0.02136.0930.0000.0000.0000.0000.0000.000
28A48ASP-1-0.813-0.90338.119-0.021-0.0210.0000.0000.0000.000
29A49TYR0-0.066-0.06741.1860.0000.0000.0000.0000.0000.000
30A50ILE00.0270.00538.4820.0010.0010.0000.0000.0000.000
31A51TYR00.0220.01642.3740.0000.0000.0000.0000.0000.000
32A52LEU0-0.035-0.01143.8830.0000.0000.0000.0000.0000.000
33A53LEU00.0120.00744.1240.0000.0000.0000.0000.0000.000
34A54MET00.0210.02445.2530.0010.0010.0000.0000.0000.000
35A55THR0-0.079-0.04047.2690.0000.0000.0000.0000.0000.000
36A56LEU0-0.041-0.02550.0010.0010.0010.0000.0000.0000.000
37A57SER0-0.012-0.01149.5940.0010.0010.0000.0000.0000.000
38A58LYS10.8550.93351.5820.0130.0130.0000.0000.0000.000
39A59ASP-1-0.832-0.89354.622-0.003-0.0030.0000.0000.0000.000
40A60PRO00.0780.02754.8340.0010.0010.0000.0000.0000.000
41A61GLU-1-0.853-0.92955.7670.0060.0060.0000.0000.0000.000
42A62LYS10.7980.88254.8520.0040.0040.0000.0000.0000.000
43A63PHE0-0.0070.01047.4140.0010.0010.0000.0000.0000.000
44A64ASN0-0.040-0.02750.7940.0020.0020.0000.0000.0000.000
45A65TYR0-0.028-0.00651.6200.0020.0020.0000.0000.0000.000
46A66ALA00.019-0.00149.0800.0010.0010.0000.0000.0000.000
47A67LEU00.0130.03546.0140.0010.0010.0000.0000.0000.000
48A68LYS10.8900.93444.240-0.023-0.0230.0000.0000.0000.000
49A69ASP-1-0.774-0.83948.4790.0100.0100.0000.0000.0000.000
50A70ARG10.8960.90944.009-0.030-0.0300.0000.0000.0000.000
51A71VAL0-0.042-0.00247.0180.0000.0000.0000.0000.0000.000
52A72SER0-0.010-0.05648.366-0.002-0.0020.0000.0000.0000.000
53A73ILE00.0290.03542.526-0.002-0.0020.0000.0000.0000.000
54A74ARG10.8900.93143.637-0.024-0.0240.0000.0000.0000.000
55A75ARG10.8610.93544.353-0.003-0.0030.0000.0000.0000.000
56A76TYR00.0130.00842.333-0.002-0.0020.0000.0000.0000.000
57A77VAL00.0170.01338.823-0.003-0.0030.0000.0000.0000.000
58A78ARG10.9550.97840.432-0.013-0.0130.0000.0000.0000.000
59A79LYS10.8900.93842.2730.0170.0170.0000.0000.0000.000
60A80ASN0-0.014-0.01637.552-0.007-0.0070.0000.0000.0000.000
61A81GLN00.0680.03637.847-0.002-0.0020.0000.0000.0000.000
62A82ASN0-0.048-0.02838.836-0.004-0.0040.0000.0000.0000.000
63A83ARG10.9671.00635.6560.0350.0350.0000.0000.0000.000
64A84TYR0-0.052-0.04633.149-0.007-0.0070.0000.0000.0000.000
65A85ASN0-0.060-0.03235.2490.0020.0020.0000.0000.0000.000
66A86TYR00.012-0.01032.8030.0010.0010.0000.0000.0000.000
67A87PHE00.0260.00036.5110.0020.0020.0000.0000.0000.000
68A88LEU0-0.0350.00035.1660.0020.0020.0000.0000.0000.000
69A89ILE0-0.018-0.01035.6020.0050.0050.0000.0000.0000.000
70A90GLU-1-0.846-0.91036.4330.0510.0510.0000.0000.0000.000
71A91GLU-1-0.898-0.95339.7610.0320.0320.0000.0000.0000.000
72A92ARG10.8740.92435.463-0.069-0.0690.0000.0000.0000.000
73A93VAL00.0040.00434.8840.0010.0010.0000.0000.0000.000
74A94GLN0-0.006-0.02137.706-0.002-0.0020.0000.0000.0000.000
75A95ASP-1-0.852-0.92439.8630.0320.0320.0000.0000.0000.000
76A96ASN0-0.049-0.05736.459-0.004-0.0040.0000.0000.0000.000
77A97ILE0-0.0250.01935.413-0.001-0.0010.0000.0000.0000.000
78A98VAL0-0.011-0.01337.644-0.003-0.0030.0000.0000.0000.000
79A99ASN0-0.0260.00439.716-0.006-0.0060.0000.0000.0000.000
80A100ARG10.8220.89633.645-0.048-0.0480.0000.0000.0000.000
81A101ILE0-0.017-0.01137.671-0.002-0.0020.0000.0000.0000.000
82A102SER00.0110.00739.051-0.001-0.0010.0000.0000.0000.000
83A103ASP-1-0.901-0.96639.0170.0330.0330.0000.0000.0000.000
84A104ARG10.7490.84932.340-0.024-0.0240.0000.0000.0000.000
85A105LEU0-0.048-0.01038.549-0.003-0.0030.0000.0000.0000.000
86A106ILE00.0120.00141.894-0.002-0.0020.0000.0000.0000.000
87A107SER0-0.0040.00638.123-0.001-0.0010.0000.0000.0000.000
88A108TYR00.002-0.01533.4550.0010.0010.0000.0000.0000.000
89A109CYS0-0.045-0.02140.023-0.005-0.0050.0000.0000.0000.000
90A110THR0-0.0150.01043.539-0.001-0.0010.0000.0000.0000.000
91A111ASP-1-0.888-0.94444.4610.0130.0130.0000.0000.0000.000
92A112LYS10.8880.94640.4130.0000.0000.0000.0000.0000.000
93A113GLU-1-0.842-0.90845.971-0.011-0.0110.0000.0000.0000.000
94A114VAL00.0010.00343.968-0.002-0.0020.0000.0000.0000.000
95A115THR00.018-0.00345.248-0.001-0.0010.0000.0000.0000.000
96A116GLU-1-0.917-0.97443.938-0.031-0.0310.0000.0000.0000.000
97A117ASP-1-0.882-0.94741.638-0.034-0.0340.0000.0000.0000.000
98A118TYR0-0.113-0.06640.169-0.001-0.0010.0000.0000.0000.000
99A119ILE00.024-0.00239.3290.0010.0010.0000.0000.0000.000
100A120LYS10.8740.93936.6850.0410.0410.0000.0000.0000.000
101A121LYS10.9871.01235.2280.0130.0130.0000.0000.0000.000
102A122ILE0-0.060-0.03134.7370.0020.0020.0000.0000.0000.000
103A123ASP-1-0.776-0.86733.858-0.029-0.0290.0000.0000.0000.000
104A124ASP-1-0.864-0.94630.714-0.051-0.0510.0000.0000.0000.000
105A125TYR0-0.060-0.03929.8590.0000.0000.0000.0000.0000.000
106A126LEU0-0.037-0.02030.5240.0070.0070.0000.0000.0000.000
107A127TRP00.0130.01122.7020.0030.0030.0000.0000.0000.000
108A128VAL00.0060.00925.7090.0000.0000.0000.0000.0000.000
109A129GLU-1-0.770-0.86625.5980.0360.0360.0000.0000.0000.000
110A130GLN0-0.053-0.02826.2670.0110.0110.0000.0000.0000.000
111A131ARG10.9050.94417.2270.0940.0940.0000.0000.0000.000
112A132VAL0-0.018-0.00921.7090.0100.0100.0000.0000.0000.000
113A133ILE0-0.036-0.01322.0570.0210.0210.0000.0000.0000.000
114A134GLU-1-0.899-0.95721.211-0.018-0.0180.0000.0000.0000.000
115A135GLU-1-0.748-0.84415.722-0.014-0.0140.0000.0000.0000.000
116A136VAL0-0.014-0.01017.8870.0410.0410.0000.0000.0000.000
117A137SER0-0.050-0.05219.7810.0270.0270.0000.0000.0000.000
118A138ILE00.0350.02714.6740.0180.0180.0000.0000.0000.000
119A139ASN0-0.045-0.02614.9430.0940.0940.0000.0000.0000.000
120A140VAL0-0.038-0.02116.5280.0470.0470.0000.0000.0000.000
121A141ASP-1-0.846-0.89218.5430.1700.1700.0000.0000.0000.000
122A142HIS0-0.052-0.03712.193-0.068-0.0680.0000.0000.0000.000
123A143ALA0-0.0260.01115.4410.0870.0870.0000.0000.0000.000
124A144ARG10.9280.95915.851-0.608-0.6080.0000.0000.0000.000
125A145GLU-1-0.871-0.94518.4690.3550.3550.0000.0000.0000.000
126A146VAL00.0700.02021.735-0.005-0.0050.0000.0000.0000.000
127A147LYS10.9450.97224.551-0.282-0.2820.0000.0000.0000.000
128A148GLU-1-0.776-0.86418.1830.3740.3740.0000.0000.0000.000
129A149LYS10.8530.94220.076-0.298-0.2980.0000.0000.0000.000
130A150LYS11.0060.99822.218-0.175-0.1750.0000.0000.0000.000
131A151ARG10.7550.83818.397-0.354-0.3540.0000.0000.0000.000
132A152ILE00.0140.00117.587-0.017-0.0170.0000.0000.0000.000
133A153MET0-0.0100.02121.419-0.020-0.0200.0000.0000.0000.000
134A154ASN0-0.090-0.04224.467-0.032-0.0320.0000.0000.0000.000
135A155ASP-1-0.822-0.88720.1560.2430.2430.0000.0000.0000.000
136A156LYS11.0010.97923.144-0.131-0.1310.0000.0000.0000.000
137A157LYS10.9050.96118.903-0.236-0.2360.0000.0000.0000.000
138A158LEU00.0090.00316.944-0.009-0.0090.0000.0000.0000.000
139A159ILE00.0220.00720.230-0.019-0.0190.0000.0000.0000.000
140A160ARG10.7500.86223.107-0.071-0.0710.0000.0000.0000.000
141A161MET00.0280.02817.668-0.002-0.0020.0000.0000.0000.000
142A162LEU00.0100.00216.901-0.021-0.0210.0000.0000.0000.000
143A163PHE0-0.002-0.02520.339-0.024-0.0240.0000.0000.0000.000
144A164ASP-1-0.841-0.90222.1080.0480.0480.0000.0000.0000.000
145A165THR0-0.046-0.01817.809-0.016-0.0160.0000.0000.0000.000
146A166TYR0-0.038-0.05817.680-0.031-0.0310.0000.0000.0000.000
147A167GLU-1-0.774-0.86423.0910.0130.0130.0000.0000.0000.000
148A168TYR0-0.0060.00321.770-0.005-0.0050.0000.0000.0000.000
149A169VAL0-0.047-0.02320.577-0.010-0.0100.0000.0000.0000.000
150A170LYS10.8230.92823.9580.0610.0610.0000.0000.0000.000
151A171ASP-1-0.933-0.94427.156-0.043-0.0430.0000.0000.0000.000
152A172VAL0-0.037-0.01329.0670.0050.0050.0000.0000.0000.000
153A173LYS10.9290.95229.899-0.021-0.0210.0000.0000.0000.000
154A174PHE0-0.056-0.01030.0720.0010.0010.0000.0000.0000.000
155A175THR00.009-0.00333.0990.0030.0030.0000.0000.0000.000
156A176ASP-1-0.859-0.95533.6590.0400.0400.0000.0000.0000.000
157A177ASP-1-0.857-0.91534.7160.0470.0470.0000.0000.0000.000
158A178GLN00.001-0.00435.0050.0020.0020.0000.0000.0000.000
159A179TYR00.0040.00827.2230.0040.0040.0000.0000.0000.000
160A180LYS10.8430.91731.332-0.045-0.0450.0000.0000.0000.000
161A181ASP-1-0.891-0.95833.1120.0490.0490.0000.0000.0000.000
162A182ALA0-0.008-0.01030.5740.0030.0030.0000.0000.0000.000
163A183ALA00.0120.00328.5890.0040.0040.0000.0000.0000.000
164A184ALA0-0.031-0.01029.4680.0090.0090.0000.0000.0000.000
165A185ARG10.8630.92832.068-0.030-0.0300.0000.0000.0000.000
166A186ILE00.0340.03225.4850.0010.0010.0000.0000.0000.000
167A187SER0-0.014-0.02627.1150.0040.0040.0000.0000.0000.000
168A188GLN0-0.036-0.01028.7290.0010.0010.0000.0000.0000.000
169A189PHE00.009-0.00527.9690.0000.0000.0000.0000.0000.000
170A190LEU00.004-0.00224.1350.0020.0020.0000.0000.0000.000
171A191ILE0-0.043-0.03027.7750.0050.0050.0000.0000.0000.000
172A192ASP-1-0.788-0.85930.0220.0680.0680.0000.0000.0000.000
173A193VAL0-0.052-0.01629.099-0.005-0.0050.0000.0000.0000.000
174A194VAL00.0010.01224.574-0.004-0.0040.0000.0000.0000.000
175A195ASP-1-0.909-0.97927.4090.0730.0730.0000.0000.0000.000
176A196SER0-0.043-0.05322.9880.0040.0040.0000.0000.0000.000
177A197TYR0-0.022-0.01124.2810.0140.0140.0000.0000.0000.000
178A198ILE0-0.065-0.02325.7390.0050.0050.0000.0000.0000.000
179A199ILE00.0270.02126.999-0.006-0.0060.0000.0000.0000.000
180A200LYS10.9270.96230.804-0.076-0.0760.0000.0000.0000.000
181A201PRO00.0020.00134.5570.0020.0020.0000.0000.0000.000
182A202ILE00.0330.01935.425-0.005-0.0050.0000.0000.0000.000
183A203PRO0-0.019-0.01338.0160.0000.0000.0000.0000.0000.000
184A204ALA00.0120.01241.3550.0000.0000.0000.0000.0000.000
185A205LEU00.0520.02944.482-0.003-0.0030.0000.0000.0000.000
186A206PRO0-0.050-0.02446.809-0.004-0.0040.0000.0000.0000.000