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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: R13K8

Calculation Name: 1N81-A-Xray315

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: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 186
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2241068.234336
FMO2-HF: Nuclear repulsion 2162788.399901
FMO2-HF: Total energy -78279.834435
FMO2-MP2: Total energy -78510.457372


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.
-6.641-1.252.326-2.261-5.4560.011
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 : -0.007 / q_NPA : -0.018
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].
3A23TYR 00.0370.0352.608-3.7351.3012.274-2.179-5.1310.009
4A24GLU -1-0.888-0.9414.096-0.832-0.4770.052-0.082-0.3250.002
5A25HIS 10.7940.9276.3300.4610.4610.0000.0000.0000.000
6A26GLU -1-0.890-1.0017.504-2.013-2.0130.0000.0000.0000.000
7A27THR 00.0210.0138.8220.1820.1820.0000.0000.0000.000
8A28HIS 0-0.024-0.00210.834-0.050-0.0500.0000.0000.0000.000
9A29ALA 00.0470.02714.465-0.046-0.0460.0000.0000.0000.000
10A30PRO 0-0.018-0.01915.431-0.009-0.0090.0000.0000.0000.000
11A31LEU 00.0410.04619.0510.0310.0310.0000.0000.0000.000
12A32SER 00.0340.01820.376-0.017-0.0170.0000.0000.0000.000
13A33PRO 00.015-0.02223.594-0.006-0.0060.0000.0000.0000.000
14A34ARG 10.8320.92626.408-0.057-0.0570.0000.0000.0000.000
15A35ILE 00.0280.01724.1590.0000.0000.0000.0000.0000.000
16A36ARG 11.0121.01123.6130.0770.0770.0000.0000.0000.000
17A37LYS 10.9660.98526.9000.0170.0170.0000.0000.0000.000
18A38VAL 0-0.021-0.00530.484-0.001-0.0010.0000.0000.0000.000
19A39GLY 00.0320.02029.0110.0010.0010.0000.0000.0000.000
20A40ASP -1-0.855-0.93329.604-0.036-0.0360.0000.0000.0000.000
21A41ILE 0-0.096-0.04531.5790.0000.0000.0000.0000.0000.000
22A42GLU -1-0.744-0.84733.2230.0360.0360.0000.0000.0000.000
23A43PHE 00.025-0.00630.0300.0010.0010.0000.0000.0000.000
24A44HIS 00.0530.04131.8520.0010.0010.0000.0000.0000.000
25A45ALA 0-0.0150.00335.9390.0000.0000.0000.0000.0000.000
26A46CYS 0-0.060-0.03036.3900.0020.0020.0000.0000.0000.000
27A47SER 0-0.020-0.02036.1760.0000.0000.0000.0000.0000.000
28A48ASP -1-0.872-0.95038.199-0.018-0.0180.0000.0000.0000.000
29A49TYR 0-0.078-0.06741.2600.0000.0000.0000.0000.0000.000
30A50ILE 00.0380.01038.5820.0010.0010.0000.0000.0000.000
31A51TYR 00.0090.01042.4460.0000.0000.0000.0000.0000.000
32A52LEU 0-0.030-0.00843.9480.0000.0000.0000.0000.0000.000
33A53LEU 0-0.001-0.00244.2200.0000.0000.0000.0000.0000.000
34A54MET 00.0230.02045.2980.0000.0000.0000.0000.0000.000
35A55THR 0-0.103-0.05147.3400.0000.0000.0000.0000.0000.000
36A56LEU 0-0.051-0.03350.0770.0000.0000.0000.0000.0000.000
37A57SER 0-0.0100.00249.6470.0010.0010.0000.0000.0000.000
38A58LYS 10.9260.96251.6620.0100.0100.0000.0000.0000.000
39A59ASP -1-0.867-0.94454.7030.0000.0000.0000.0000.0000.000
40A60PRO 00.0610.01254.9410.0010.0010.0000.0000.0000.000
41A61GLU -1-0.862-0.91855.8940.0090.0090.0000.0000.0000.000
42A62LYS 10.8350.93254.9110.0020.0020.0000.0000.0000.000
43A63PHE 0-0.0050.01147.4600.0010.0010.0000.0000.0000.000
44A64ASN 00.006-0.00950.9160.0020.0020.0000.0000.0000.000
45A65TYR 0-0.047-0.01951.7350.0020.0020.0000.0000.0000.000
46A66ALA 00.0270.00149.1440.0010.0010.0000.0000.0000.000
47A67LEU 00.0090.03246.1370.0010.0010.0000.0000.0000.000
48A68LYS 10.9580.96846.418-0.026-0.0260.0000.0000.0000.000
49A69ASP -1-0.776-0.83248.5800.0120.0120.0000.0000.0000.000
50A70ARG 10.9010.91043.834-0.033-0.0330.0000.0000.0000.000
51A71VAL 0-0.0400.00147.1390.0000.0000.0000.0000.0000.000
52A72SER 0-0.050-0.09048.499-0.002-0.0020.0000.0000.0000.000
53A73ILE 00.0430.04142.612-0.002-0.0020.0000.0000.0000.000
54A74ARG 10.8820.93443.763-0.026-0.0260.0000.0000.0000.000
55A75ARG 10.8720.94544.480-0.005-0.0050.0000.0000.0000.000
56A76TYR 00.0200.00942.385-0.003-0.0030.0000.0000.0000.000
57A77VAL 00.0220.01739.117-0.003-0.0030.0000.0000.0000.000
58A78ARG 10.9530.97740.541-0.013-0.0130.0000.0000.0000.000
59A79LYS 10.9710.99142.3710.0130.0130.0000.0000.0000.000
60A80ASN 00.000-0.00337.594-0.007-0.0070.0000.0000.0000.000
61A81GLN 00.0510.02737.949-0.003-0.0030.0000.0000.0000.000
62A82ASN 0-0.059-0.03638.921-0.005-0.0050.0000.0000.0000.000
63A83ARG 10.9751.00335.8680.0340.0340.0000.0000.0000.000
64A84TYR 0-0.059-0.03132.643-0.007-0.0070.0000.0000.0000.000
65A85ASN 0-0.067-0.02835.3170.0020.0020.0000.0000.0000.000
66A86TYR 0-0.002-0.01632.5900.0020.0020.0000.0000.0000.000
67A87PHE 00.026-0.00136.6080.0030.0030.0000.0000.0000.000
68A88LEU 0-0.0270.00434.9010.0020.0020.0000.0000.0000.000
69A89ILE 0-0.033-0.02335.6720.0050.0050.0000.0000.0000.000
70A90GLU -1-0.916-0.95636.7400.0520.0520.0000.0000.0000.000
71A91GLU -1-0.887-0.94939.8870.0350.0350.0000.0000.0000.000
72A92ARG 10.9080.96035.194-0.070-0.0700.0000.0000.0000.000
73A93VAL 00.0060.00935.2520.0010.0010.0000.0000.0000.000
74A94GLN 00.010-0.01437.841-0.001-0.0010.0000.0000.0000.000
75A95ASP -1-0.858-0.92939.9800.0340.0340.0000.0000.0000.000
76A96ASN 0-0.072-0.07836.607-0.004-0.0040.0000.0000.0000.000
77A97ILE 0-0.0240.01935.566-0.001-0.0010.0000.0000.0000.000
78A98VAL 0-0.024-0.02037.756-0.003-0.0030.0000.0000.0000.000
79A99ASN 0-0.0130.00739.958-0.005-0.0050.0000.0000.0000.000
80A100ARG 10.8310.90733.765-0.051-0.0510.0000.0000.0000.000
81A101ILE 0-0.011-0.01037.797-0.002-0.0020.0000.0000.0000.000
82A102SER 0-0.029-0.01539.162-0.001-0.0010.0000.0000.0000.000
83A103ASP -1-0.901-0.96238.8970.0400.0400.0000.0000.0000.000
84A104ARG 10.7140.82532.453-0.031-0.0310.0000.0000.0000.000
85A105LEU 0-0.045-0.01138.644-0.003-0.0030.0000.0000.0000.000
86A106ILE 00.002-0.00242.019-0.002-0.0020.0000.0000.0000.000
87A107SER 0-0.0050.00638.123-0.001-0.0010.0000.0000.0000.000
88A108TYR 00.014-0.01133.4610.0010.0010.0000.0000.0000.000
89A109CYS 0-0.047-0.02240.146-0.005-0.0050.0000.0000.0000.000
90A110THR 0-0.0160.00643.654-0.002-0.0020.0000.0000.0000.000
91A111ASP -1-0.871-0.92844.2900.0190.0190.0000.0000.0000.000
92A112LYS 10.8750.93040.089-0.006-0.0060.0000.0000.0000.000
93A113GLU -1-0.901-0.92946.066-0.006-0.0060.0000.0000.0000.000
94A114VAL 00.0210.01144.188-0.002-0.0020.0000.0000.0000.000
95A115THR 00.006-0.00745.174-0.002-0.0020.0000.0000.0000.000
96A116GLU -1-0.923-0.97443.953-0.026-0.0260.0000.0000.0000.000
97A117ASP -1-0.860-0.93941.638-0.029-0.0290.0000.0000.0000.000
98A118TYR 0-0.150-0.08840.2040.0000.0000.0000.0000.0000.000
99A119ILE 00.029-0.00539.3880.0010.0010.0000.0000.0000.000
100A120LYS 10.9740.99437.0020.0380.0380.0000.0000.0000.000
101A121LYS 10.9781.00935.6130.0040.0040.0000.0000.0000.000
102A122ILE 0-0.058-0.02734.8000.0020.0020.0000.0000.0000.000
103A123ASP -1-0.819-0.90033.937-0.021-0.0210.0000.0000.0000.000
104A124ASP -1-0.881-0.94830.700-0.039-0.0390.0000.0000.0000.000
105A125TYR 0-0.061-0.03329.9360.0020.0020.0000.0000.0000.000
106A126LEU 0-0.048-0.02430.6320.0080.0080.0000.0000.0000.000
107A127TRP 00.0200.01422.5720.0030.0030.0000.0000.0000.000
108A128VAL 0-0.009-0.00125.8540.0020.0020.0000.0000.0000.000
109A129GLU -1-0.762-0.85625.7190.0470.0470.0000.0000.0000.000
110A130GLN 0-0.025-0.02026.4770.0090.0090.0000.0000.0000.000
111A131ARG 10.9280.96318.1180.0700.0700.0000.0000.0000.000
112A132VAL 0-0.004-0.00621.8390.0120.0120.0000.0000.0000.000
113A133ILE 0-0.027-0.00822.1680.0210.0210.0000.0000.0000.000
114A134GLU -1-0.919-0.97221.317-0.006-0.0060.0000.0000.0000.000
115A135GLU -1-0.846-0.90615.4680.0580.0580.0000.0000.0000.000
116A136VAL 0-0.019-0.02218.0140.0420.0420.0000.0000.0000.000
117A137SER 0-0.076-0.06119.8230.0260.0260.0000.0000.0000.000
118A138ILE 00.0490.03514.7710.0120.0120.0000.0000.0000.000
119A139ASN 0-0.041-0.02514.5230.0960.0960.0000.0000.0000.000
120A140VAL 0-0.048-0.02816.4190.0430.0430.0000.0000.0000.000
121A141ASP -1-0.874-0.93818.4110.1630.1630.0000.0000.0000.000
122A142HIS 0-0.055-0.03212.472-0.058-0.0580.0000.0000.0000.000
123A143ALA 0-0.0210.01615.2860.0810.0810.0000.0000.0000.000
124A144ARG 10.9430.96116.194-0.602-0.6020.0000.0000.0000.000
125A145GLU -1-0.900-0.95718.4850.3410.3410.0000.0000.0000.000
126A146VAL 00.0780.02821.752-0.004-0.0040.0000.0000.0000.000
127A147LYS 10.9420.96924.419-0.285-0.2850.0000.0000.0000.000
128A148GLU -1-0.785-0.87817.9480.3930.3930.0000.0000.0000.000
129A149LYS 10.8900.96819.958-0.291-0.2910.0000.0000.0000.000
130A150LYS 10.9960.99622.110-0.176-0.1760.0000.0000.0000.000
131A151ARG 10.7520.84418.181-0.364-0.3640.0000.0000.0000.000
132A152ILE 00.007-0.00217.539-0.015-0.0150.0000.0000.0000.000
133A153MET 0-0.0110.02221.344-0.019-0.0190.0000.0000.0000.000
134A154ASN 0-0.056-0.01024.363-0.031-0.0310.0000.0000.0000.000
135A155ASP -1-0.818-0.89820.1980.2590.2590.0000.0000.0000.000
136A156LYS 10.9920.97423.099-0.135-0.1350.0000.0000.0000.000
137A157LYS 10.9290.99119.388-0.260-0.2600.0000.0000.0000.000
138A158LEU 00.0100.00816.933-0.006-0.0060.0000.0000.0000.000
139A159ILE 00.0220.00820.192-0.018-0.0180.0000.0000.0000.000
140A160ARG 10.8260.91723.137-0.092-0.0920.0000.0000.0000.000
141A161MET 00.002-0.00718.102-0.003-0.0030.0000.0000.0000.000
142A162LEU 00.0210.00717.143-0.020-0.0200.0000.0000.0000.000
143A163PHE 0-0.001-0.02520.443-0.025-0.0250.0000.0000.0000.000
144A164ASP -1-0.845-0.90122.2610.0680.0680.0000.0000.0000.000
145A165THR 0-0.045-0.01617.954-0.016-0.0160.0000.0000.0000.000
146A166TYR 0-0.012-0.02717.953-0.037-0.0370.0000.0000.0000.000
147A167GLU -1-0.807-0.89523.1760.0240.0240.0000.0000.0000.000
148A168TYR 0-0.015-0.00222.126-0.007-0.0070.0000.0000.0000.000
149A169VAL 0-0.050-0.02420.692-0.012-0.0120.0000.0000.0000.000
150A170LYS 10.8410.92423.9850.0530.0530.0000.0000.0000.000
151A171ASP -1-0.945-0.94427.189-0.031-0.0310.0000.0000.0000.000
152A172VAL 0-0.0240.00029.0900.0040.0040.0000.0000.0000.000
153A173LYS 10.9000.93429.980-0.030-0.0300.0000.0000.0000.000
154A174PHE 0-0.067-0.01630.1360.0000.0000.0000.0000.0000.000
155A175THR 00.000-0.00733.1720.0030.0030.0000.0000.0000.000
156A176ASP -1-0.868-0.95534.0190.0550.0550.0000.0000.0000.000
157A177ASP -1-0.925-0.95734.8460.0520.0520.0000.0000.0000.000
158A178GLN 00.0110.00335.0660.0020.0020.0000.0000.0000.000
159A179TYR 00.0020.01127.0690.0050.0050.0000.0000.0000.000
160A180LYS 10.9570.97031.464-0.066-0.0660.0000.0000.0000.000
161A181ASP -1-0.928-0.96633.1230.0580.0580.0000.0000.0000.000
162A182ALA 0-0.014-0.01530.6180.0020.0020.0000.0000.0000.000
163A183ALA 0-0.001-0.00228.5480.0040.0040.0000.0000.0000.000
164A184ALA 0-0.027-0.01029.4480.0090.0090.0000.0000.0000.000
165A185ARG 10.8990.95232.027-0.039-0.0390.0000.0000.0000.000
166A186ILE 00.0370.03025.7650.0010.0010.0000.0000.0000.000
167A187SER 0-0.014-0.02627.0430.0040.0040.0000.0000.0000.000
168A188GLN 0-0.029-0.00928.618-0.001-0.0010.0000.0000.0000.000
169A189PHE 0-0.009-0.01227.877-0.001-0.0010.0000.0000.0000.000
170A190LEU 0-0.003-0.00524.1880.0010.0010.0000.0000.0000.000
171A191ILE 0-0.034-0.02727.8110.0040.0040.0000.0000.0000.000
172A192ASP -1-0.809-0.88029.8770.0710.0710.0000.0000.0000.000
173A193VAL 0-0.053-0.02429.164-0.006-0.0060.0000.0000.0000.000
174A194VAL 00.0040.02224.601-0.006-0.0060.0000.0000.0000.000
175A195ASP -1-0.905-0.96927.4750.0730.0730.0000.0000.0000.000
176A196SER 0-0.032-0.02922.8190.0060.0060.0000.0000.0000.000
177A197TYR 0-0.026-0.01124.1520.0120.0120.0000.0000.0000.000
178A198ILE 0-0.045-0.01425.5950.0040.0040.0000.0000.0000.000
179A199ILE 00.0180.01627.003-0.006-0.0060.0000.0000.0000.000
180A200LYS 10.9150.95330.819-0.073-0.0730.0000.0000.0000.000
181A201PRO 0-0.007-0.01034.5720.0010.0010.0000.0000.0000.000
182A202ILE 00.0230.02135.313-0.004-0.0040.0000.0000.0000.000
183A203PRO 0-0.025-0.01338.0350.0000.0000.0000.0000.0000.000
184A204ALA 00.003-0.00141.3720.0000.0000.0000.0000.0000.000
185A205LEU 0-0.025-0.02044.501-0.002-0.0020.0000.0000.0000.000
186A206PRO -1-0.939-0.95346.5890.0300.0300.0000.0000.0000.000