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: 49V1N

Calculation Name: 3K1R-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3K1R

Chain ID: A

ChEMBL ID:

UniProt ID: Q9Y6N9

Base Structure: X-ray

Registration Date: 2023-09-19

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 OptH
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 192
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2048760.647077
FMO2-HF: Nuclear repulsion 1972449.497299
FMO2-HF: Total energy -76311.149779
FMO2-MP2: Total energy -76535.558092


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.
-7.076-3.0680.209-1.656-2.5610.002
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 : 0.006
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].
3A3ARG10.9690.9753.696-4.990-2.719-0.002-1.042-1.2270.002
4A4LYS10.7850.8862.849-1.009-0.0840.185-0.321-0.7890.000
5A5VAL00.0760.0353.219-0.4600.3520.026-0.293-0.5450.000
6A6ALA00.0470.0255.8370.3900.3900.0000.0000.0000.000
7A7ARG10.8990.9556.367-0.820-0.8200.0000.0000.0000.000
8A8GLU-1-0.879-0.9397.814-0.107-0.1070.0000.0000.0000.000
9A9PHE0-0.0090.0019.9400.0190.0190.0000.0000.0000.000
10A10ARG11.0041.00610.638-0.283-0.2830.0000.0000.0000.000
11A11HIS00.0090.00512.642-0.001-0.0010.0000.0000.0000.000
12A12LYS10.9180.95811.7470.0710.0710.0000.0000.0000.000
13A13VAL00.0030.00615.718-0.001-0.0010.0000.0000.0000.000
14A14ASP-1-0.898-0.95717.8270.1100.1100.0000.0000.0000.000
15A15PHE0-0.084-0.03519.300-0.002-0.0020.0000.0000.0000.000
16A16LEU0-0.046-0.02419.324-0.004-0.0040.0000.0000.0000.000
17A17ILE0-0.0160.00821.003-0.005-0.0050.0000.0000.0000.000
18A18GLU-1-0.930-0.96323.4690.0440.0440.0000.0000.0000.000
19A19ASN00.003-0.00825.9910.0050.0050.0000.0000.0000.000
20A20ASP-1-0.841-0.94024.5140.0790.0790.0000.0000.0000.000
21A21ALA0-0.0020.00824.4400.0010.0010.0000.0000.0000.000
22A22GLU-1-0.818-0.89225.1240.0210.0210.0000.0000.0000.000
23A23LYS10.8620.94120.698-0.082-0.0820.0000.0000.0000.000
24A24ASP-1-0.922-0.96220.3320.0690.0690.0000.0000.0000.000
25A25TYR0-0.053-0.03821.323-0.003-0.0030.0000.0000.0000.000
26A26LEU00.0080.00917.682-0.009-0.0090.0000.0000.0000.000
27A27TYR0-0.005-0.03114.360-0.014-0.0140.0000.0000.0000.000
28A28ASP-1-0.894-0.95316.9110.0240.0240.0000.0000.0000.000
29A29VAL00.0710.03619.206-0.007-0.0070.0000.0000.0000.000
30A30LEU0-0.041-0.01813.987-0.013-0.0130.0000.0000.0000.000
31A31ARG10.8630.93614.969-0.055-0.0550.0000.0000.0000.000
32A32MET0-0.0020.00616.021-0.004-0.0040.0000.0000.0000.000
33A33TYR00.0260.02413.728-0.007-0.0070.0000.0000.0000.000
34A34HIS0-0.035-0.01710.887-0.021-0.0210.0000.0000.0000.000
35A35GLN0-0.060-0.02714.421-0.001-0.0010.0000.0000.0000.000
36A36THR0-0.021-0.01317.491-0.002-0.0020.0000.0000.0000.000
37A37MET0-0.082-0.04012.746-0.002-0.0020.0000.0000.0000.000
38A38ASP-1-0.864-0.92318.025-0.033-0.0330.0000.0000.0000.000
39A39VAL0-0.004-0.01818.7210.0010.0010.0000.0000.0000.000
40A40ALA00.0330.00620.1670.0010.0010.0000.0000.0000.000
41A41VAL00.0180.01623.0270.0030.0030.0000.0000.0000.000
42A42LEU00.0010.01716.6100.0020.0020.0000.0000.0000.000
43A43VAL0-0.047-0.02920.8640.0030.0030.0000.0000.0000.000
44A44GLY0-0.017-0.01222.4320.0030.0030.0000.0000.0000.000
45A45ASP-1-0.858-0.92522.874-0.007-0.0070.0000.0000.0000.000
46A46LEU0-0.055-0.03618.3930.0040.0040.0000.0000.0000.000
47A47LYS10.8910.95822.6320.0210.0210.0000.0000.0000.000
48A48LEU0-0.0120.01826.0170.0020.0020.0000.0000.0000.000
49A49VAL00.0150.01222.2010.0030.0030.0000.0000.0000.000
50A50ILE0-0.081-0.01920.6080.0020.0020.0000.0000.0000.000
51A51ASN00.0850.03725.109-0.003-0.0030.0000.0000.0000.000
52A52GLU-1-0.881-0.95028.1000.0140.0140.0000.0000.0000.000
53A53PRO00.005-0.00827.630-0.002-0.0020.0000.0000.0000.000
54A54SER0-0.035-0.01526.617-0.003-0.0030.0000.0000.0000.000
55A55ARG10.8900.91523.805-0.017-0.0170.0000.0000.0000.000
56A56LEU0-0.0070.00322.639-0.005-0.0050.0000.0000.0000.000
57A57PRO0-0.075-0.04520.272-0.006-0.0060.0000.0000.0000.000
58A58LEU00.0560.02917.762-0.009-0.0090.0000.0000.0000.000
59A59PHE00.0510.03017.268-0.013-0.0130.0000.0000.0000.000
60A60ASP-1-0.883-0.93616.764-0.044-0.0440.0000.0000.0000.000
61A61ALA0-0.109-0.06313.788-0.013-0.0130.0000.0000.0000.000
62A62ILE00.0550.02412.502-0.041-0.0410.0000.0000.0000.000
63A63ARG10.9080.97112.5780.0260.0260.0000.0000.0000.000
64A64PRO0-0.088-0.0528.7040.0080.0080.0000.0000.0000.000
65A65LEU0-0.023-0.0078.502-0.033-0.0330.0000.0000.0000.000
66A66ILE0-0.0460.0109.6470.0150.0150.0000.0000.0000.000
67A67PRO00.0460.02310.5710.0240.0240.0000.0000.0000.000
68A68LEU00.048-0.00110.033-0.005-0.0050.0000.0000.0000.000
69A69LYS10.8970.95412.9380.0740.0740.0000.0000.0000.000
70A70HIS00.0580.02315.352-0.002-0.0020.0000.0000.0000.000
71A71GLN0-0.033-0.01311.7970.0070.0070.0000.0000.0000.000
72A72VAL00.0070.01016.6920.0020.0020.0000.0000.0000.000
73A73GLU-1-0.897-0.95920.175-0.042-0.0420.0000.0000.0000.000
74A74TYR00.020-0.01317.3900.0030.0030.0000.0000.0000.000
75A75ASP-1-0.863-0.93519.339-0.046-0.0460.0000.0000.0000.000
76A76GLN0-0.132-0.07221.4390.0040.0040.0000.0000.0000.000
77A77LEU00.0220.02822.7350.0030.0030.0000.0000.0000.000
78A78THR0-0.062-0.02120.6150.0030.0030.0000.0000.0000.000
79A79PRO00.0150.01523.8690.0000.0000.0000.0000.0000.000
80A80ARG10.9670.99023.9850.0330.0330.0000.0000.0000.000
81A81ARG10.9230.98021.2140.0250.0250.0000.0000.0000.000
82A82SER00.009-0.01724.466-0.003-0.0030.0000.0000.0000.000
83A83ARG10.9640.97723.1880.0100.0100.0000.0000.0000.000
84A84LYS10.9020.96325.6290.0290.0290.0000.0000.0000.000
85A85LEU00.0240.01229.2890.0000.0000.0000.0000.0000.000
86A86LYS10.9200.98332.7590.0160.0160.0000.0000.0000.000
87A87GLU-1-0.961-0.97935.158-0.008-0.0080.0000.0000.0000.000
88A88VAL00.0120.02038.846-0.001-0.0010.0000.0000.0000.000
89A89ARG10.9320.95841.8130.0090.0090.0000.0000.0000.000
90A90LEU00.0160.00344.702-0.001-0.0010.0000.0000.0000.000
91A91ASP-1-0.866-0.92347.808-0.007-0.0070.0000.0000.0000.000
92A92ARG10.8840.93151.5240.0040.0040.0000.0000.0000.000
93A93LEU0-0.068-0.03053.2560.0000.0000.0000.0000.0000.000
94A94HIS00.0250.03253.2980.0000.0000.0000.0000.0000.000
95A95PRO00.005-0.00355.2660.0000.0000.0000.0000.0000.000
96A96GLU-1-0.920-0.95653.256-0.009-0.0090.0000.0000.0000.000
97A97GLY0-0.045-0.00552.7720.0000.0000.0000.0000.0000.000
98A98LEU0-0.018-0.03347.5520.0000.0000.0000.0000.0000.000
99A99GLY00.0300.01947.383-0.001-0.0010.0000.0000.0000.000
100A100LEU0-0.010-0.00942.866-0.001-0.0010.0000.0000.0000.000
101A101SER0-0.032-0.00844.5410.0010.0010.0000.0000.0000.000
102A102VAL00.005-0.00842.578-0.001-0.0010.0000.0000.0000.000
103A103ARG10.9260.96240.7130.0010.0010.0000.0000.0000.000
104A104GLY00.0390.01841.3370.0000.0000.0000.0000.0000.000
105A105GLY00.0360.01641.685-0.001-0.0010.0000.0000.0000.000
106A106LEU00.002-0.00841.7660.0010.0010.0000.0000.0000.000
107A107GLU-1-0.824-0.91943.2120.0060.0060.0000.0000.0000.000
108A108PHE0-0.065-0.03542.1920.0000.0000.0000.0000.0000.000
109A109GLY0-0.0010.01439.8600.0000.0000.0000.0000.0000.000
110A110CYS0-0.072-0.02837.1790.0000.0000.0000.0000.0000.000
111A111GLY00.0330.02436.7270.0000.0000.0000.0000.0000.000
112A112LEU00.0070.00138.0320.0000.0000.0000.0000.0000.000
113A113PHE00.0300.00133.369-0.001-0.0010.0000.0000.0000.000
114A114ILE0-0.018-0.00438.3790.0010.0010.0000.0000.0000.000
115A115SER00.017-0.00338.8010.0000.0000.0000.0000.0000.000
116A116HIS00.002-0.00441.0340.0000.0000.0000.0000.0000.000
117A117LEU00.0300.00839.5230.0000.0000.0000.0000.0000.000
118A118ILE0-0.0050.00843.4290.0000.0000.0000.0000.0000.000
119A119LYS10.9550.97343.2730.0140.0140.0000.0000.0000.000
120A120GLY0-0.026-0.01545.1120.0000.0000.0000.0000.0000.000
121A121GLY00.0200.01846.6860.0000.0000.0000.0000.0000.000
122A122GLN00.0320.01446.395-0.001-0.0010.0000.0000.0000.000
123A123ALA00.0170.00643.146-0.001-0.0010.0000.0000.0000.000
124A124ASP-1-0.815-0.90841.457-0.015-0.0150.0000.0000.0000.000
125A125SER0-0.060-0.01741.558-0.001-0.0010.0000.0000.0000.000
126A126VAL0-0.034-0.01041.706-0.001-0.0010.0000.0000.0000.000
127A127GLY0-0.042-0.03238.200-0.001-0.0010.0000.0000.0000.000
128A128LEU0-0.072-0.03337.0290.0000.0000.0000.0000.0000.000
129A129GLN0-0.005-0.01332.156-0.001-0.0010.0000.0000.0000.000
130A130VAL00.0300.02137.1050.0010.0010.0000.0000.0000.000
131A131GLY00.0510.01633.926-0.001-0.0010.0000.0000.0000.000
132A132ASP-1-0.824-0.91733.441-0.013-0.0130.0000.0000.0000.000
133A133GLU-1-0.830-0.90833.2970.0000.0000.0000.0000.0000.000
134A134ILE0-0.011-0.00935.626-0.001-0.0010.0000.0000.0000.000
135A135VAL0-0.014-0.01234.0240.0010.0010.0000.0000.0000.000
136A136ARG10.8380.91137.4930.0020.0020.0000.0000.0000.000
137A137ILE00.0650.04940.494-0.001-0.0010.0000.0000.0000.000
138A138ASN00.0480.02044.0720.0000.0000.0000.0000.0000.000
139A139GLY00.0050.00543.2590.0000.0000.0000.0000.0000.000
140A140TYR00.0110.00343.4110.0010.0010.0000.0000.0000.000
141A141SER0-0.044-0.04240.428-0.001-0.0010.0000.0000.0000.000
142A142ILE00.0530.01640.3980.0000.0000.0000.0000.0000.000
143A143SER0-0.018-0.01338.2630.0000.0000.0000.0000.0000.000
144A144SER0-0.018-0.01140.1820.0010.0010.0000.0000.0000.000
145A145CYS0-0.0250.02043.4720.0000.0000.0000.0000.0000.000
146A146THR00.0460.04144.5060.0000.0000.0000.0000.0000.000
147A147HIS0-0.048-0.04445.329-0.001-0.0010.0000.0000.0000.000
148A148GLU-1-0.936-0.97147.2240.0020.0020.0000.0000.0000.000
149A149GLU-1-0.852-0.92948.7120.0040.0040.0000.0000.0000.000
150A150VAL00.0260.00744.123-0.001-0.0010.0000.0000.0000.000
151A151ILE0-0.041-0.01747.409-0.001-0.0010.0000.0000.0000.000
152A152ASN00.000-0.01949.856-0.001-0.0010.0000.0000.0000.000
153A153LEU0-0.0100.00546.5210.0000.0000.0000.0000.0000.000
154A154ILE0-0.039-0.01645.892-0.001-0.0010.0000.0000.0000.000
155A155ARG10.8980.93549.5950.0010.0010.0000.0000.0000.000
156A156THR0-0.037-0.00351.8450.0000.0000.0000.0000.0000.000
157A157GLU-1-0.889-0.93052.770-0.003-0.0030.0000.0000.0000.000
158A158LYS10.9170.94753.9590.0040.0040.0000.0000.0000.000
159A159THR0-0.046-0.03550.331-0.001-0.0010.0000.0000.0000.000
160A160VAL00.0360.01846.4950.0010.0010.0000.0000.0000.000
161A161SER0-0.030-0.01444.302-0.001-0.0010.0000.0000.0000.000
162A162ILE00.0330.02440.0960.0010.0010.0000.0000.0000.000
163A163LYS10.8870.93736.5380.0080.0080.0000.0000.0000.000
164A164VAL00.0050.00134.9260.0010.0010.0000.0000.0000.000
165A165ARG10.8380.89929.5570.0010.0010.0000.0000.0000.000
166A166HIS0-0.0150.00728.9740.0000.0000.0000.0000.0000.000
167A167ILE0-0.077-0.02829.054-0.001-0.0010.0000.0000.0000.000
168A168GLY00.0210.00328.677-0.001-0.0010.0000.0000.0000.000
169A169LEU0-0.021-0.01128.7170.0000.0000.0000.0000.0000.000
170A170ILE0-0.026-0.01232.4730.0000.0000.0000.0000.0000.000
171A171PRO00.0110.03436.1970.0010.0010.0000.0000.0000.000
172A172VAL00.002-0.01437.767-0.001-0.0010.0000.0000.0000.000
173A173LYS10.9250.96740.135-0.007-0.0070.0000.0000.0000.000
174A174SER0-0.0110.00343.0470.0000.0000.0000.0000.0000.000
175A175SER00.0610.02645.8390.0000.0000.0000.0000.0000.000
176A176PRO0-0.033-0.04546.9760.0000.0000.0000.0000.0000.000
177A177ASP-1-0.875-0.93148.0160.0100.0100.0000.0000.0000.000
178A178GLU-1-1.028-0.98343.4520.0090.0090.0000.0000.0000.000
179A179PRO00.0300.00439.5720.0000.0000.0000.0000.0000.000
180A180LEU0-0.053-0.02037.025-0.001-0.0010.0000.0000.0000.000
181A181THR00.0000.00735.9040.0010.0010.0000.0000.0000.000
182A182TRP00.027-0.01432.533-0.002-0.0020.0000.0000.0000.000
183A183GLN00.0340.02633.634-0.001-0.0010.0000.0000.0000.000
184A184TYR00.006-0.02526.246-0.003-0.0030.0000.0000.0000.000
185A185VAL0-0.012-0.01232.1400.0010.0010.0000.0000.0000.000
186A186ASP-1-0.881-0.93932.028-0.013-0.0130.0000.0000.0000.000
187A187GLN0-0.0140.01834.1950.0000.0000.0000.0000.0000.000
188A188PHE00.004-0.00236.0320.0010.0010.0000.0000.0000.000
189A189VAL0-0.039-0.03237.8780.0000.0000.0000.0000.0000.000
190A190SER0-0.060-0.04237.5410.0000.0000.0000.0000.0000.000
191A191GLU-1-0.907-0.95039.432-0.002-0.0020.0000.0000.0000.000
192A192SER0-0.114-0.04142.0800.0010.0010.0000.0000.0000.000