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: 52V1Z

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 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 192
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2050815.084196
FMO2-HF: Nuclear repulsion 1974503.199099
FMO2-HF: Total energy -76311.885096
FMO2-MP2: Total energy -76536.392761


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.
-6.426-2.4470.262-1.601-2.6390.001
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 : 0.023 / q_NPA : -0.004
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].
3A3ARG10.9730.9783.671-4.591-2.3150.000-1.014-1.2610.001
4A4LYS10.7740.8712.765-1.186-0.2650.245-0.317-0.8490.000
5A5VAL00.0620.0243.341-0.3940.3880.017-0.270-0.5290.000
6A6ALA00.0510.0285.9290.3850.3850.0000.0000.0000.000
7A7ARG10.8950.9576.740-0.704-0.7040.0000.0000.0000.000
8A8GLU-1-0.846-0.9167.6930.1500.1500.0000.0000.0000.000
9A9PHE0-0.0060.00210.0240.0170.0170.0000.0000.0000.000
10A10ARG11.0151.00811.080-0.274-0.2740.0000.0000.0000.000
11A11HIS0-0.0030.00013.203-0.005-0.0050.0000.0000.0000.000
12A12LYS10.9120.95711.475-0.027-0.0270.0000.0000.0000.000
13A13VAL00.0020.00515.793-0.004-0.0040.0000.0000.0000.000
14A14ASP-1-0.874-0.94517.8340.1210.1210.0000.0000.0000.000
15A15PHE0-0.095-0.03619.314-0.003-0.0030.0000.0000.0000.000
16A16LEU0-0.044-0.02519.562-0.005-0.0050.0000.0000.0000.000
17A17ILE0-0.0080.00921.203-0.006-0.0060.0000.0000.0000.000
18A18GLU-1-0.916-0.95323.4770.0570.0570.0000.0000.0000.000
19A19ASN0-0.008-0.01425.9920.0050.0050.0000.0000.0000.000
20A20ASP-1-0.793-0.91624.2360.0850.0850.0000.0000.0000.000
21A21ALA00.0150.01524.3770.0000.0000.0000.0000.0000.000
22A22GLU-1-0.812-0.88425.0330.0320.0320.0000.0000.0000.000
23A23LYS10.8070.91020.557-0.094-0.0940.0000.0000.0000.000
24A24ASP-1-0.924-0.96420.2750.0710.0710.0000.0000.0000.000
25A25TYR0-0.067-0.04621.293-0.005-0.0050.0000.0000.0000.000
26A26LEU00.0090.00917.632-0.008-0.0080.0000.0000.0000.000
27A27TYR0-0.001-0.02814.473-0.011-0.0110.0000.0000.0000.000
28A28ASP-1-0.833-0.88316.9000.0190.0190.0000.0000.0000.000
29A29VAL00.0700.03119.231-0.008-0.0080.0000.0000.0000.000
30A30LEU0-0.043-0.01614.023-0.011-0.0110.0000.0000.0000.000
31A31ARG10.7840.86814.984-0.045-0.0450.0000.0000.0000.000
32A32MET00.0250.01316.045-0.008-0.0080.0000.0000.0000.000
33A33TYR00.0250.02813.673-0.005-0.0050.0000.0000.0000.000
34A34HIS0-0.032-0.01510.501-0.008-0.0080.0000.0000.0000.000
35A35GLN0-0.051-0.02714.478-0.003-0.0030.0000.0000.0000.000
36A36THR0-0.025-0.02017.569-0.003-0.0030.0000.0000.0000.000
37A37MET0-0.099-0.04812.6640.0000.0000.0000.0000.0000.000
38A38ASP-1-0.851-0.91318.081-0.026-0.0260.0000.0000.0000.000
39A39VAL0-0.003-0.02018.3140.0030.0030.0000.0000.0000.000
40A40ALA00.0210.00620.1750.0040.0040.0000.0000.0000.000
41A41VAL00.0070.00323.2820.0030.0030.0000.0000.0000.000
42A42LEU00.0010.02016.6070.0030.0030.0000.0000.0000.000
43A43VAL0-0.042-0.03020.7670.0040.0040.0000.0000.0000.000
44A44GLY0-0.017-0.01022.3970.0030.0030.0000.0000.0000.000
45A45ASP-1-0.863-0.92822.779-0.001-0.0010.0000.0000.0000.000
46A46LEU0-0.046-0.03118.2490.0050.0050.0000.0000.0000.000
47A47LYS10.8910.96122.5800.0050.0050.0000.0000.0000.000
48A48LEU0-0.0140.01725.9550.0020.0020.0000.0000.0000.000
49A49VAL00.0150.01322.1620.0030.0030.0000.0000.0000.000
50A50ILE0-0.066-0.01220.4440.0030.0030.0000.0000.0000.000
51A51ASN00.0390.01925.020-0.002-0.0020.0000.0000.0000.000
52A52GLU-1-0.780-0.87728.0200.0290.0290.0000.0000.0000.000
53A53PRO00.001-0.01127.7210.0000.0000.0000.0000.0000.000
54A54SER0-0.084-0.05726.7030.0000.0000.0000.0000.0000.000
55A55ARG10.8420.88523.904-0.030-0.0300.0000.0000.0000.000
56A56LEU0-0.013-0.00222.720-0.002-0.0020.0000.0000.0000.000
57A57PRO0-0.061-0.03620.333-0.003-0.0030.0000.0000.0000.000
58A58LEU00.0300.02318.212-0.002-0.0020.0000.0000.0000.000
59A59PHE00.0670.03417.202-0.007-0.0070.0000.0000.0000.000
60A60ASP-1-0.815-0.86516.9510.0110.0110.0000.0000.0000.000
61A61ALA0-0.094-0.05013.8770.0010.0010.0000.0000.0000.000
62A62ILE00.0570.02212.561-0.025-0.0250.0000.0000.0000.000
63A63ARG10.8670.93912.504-0.027-0.0270.0000.0000.0000.000
64A64PRO0-0.081-0.0488.8050.0140.0140.0000.0000.0000.000
65A65LEU0-0.031-0.0078.5340.0200.0200.0000.0000.0000.000
66A66ILE0-0.0360.0159.598-0.001-0.0010.0000.0000.0000.000
67A67PRO00.0430.03010.4280.0440.0440.0000.0000.0000.000
68A68LEU00.059-0.0019.565-0.014-0.0140.0000.0000.0000.000
69A69LYS10.8980.95512.7680.0720.0720.0000.0000.0000.000
70A70HIS00.0570.02615.199-0.005-0.0050.0000.0000.0000.000
71A71GLN0-0.054-0.03111.225-0.006-0.0060.0000.0000.0000.000
72A72VAL0-0.0050.00116.4600.0020.0020.0000.0000.0000.000
73A73GLU-1-0.877-0.95319.944-0.032-0.0320.0000.0000.0000.000
74A74TYR00.027-0.01217.2410.0020.0020.0000.0000.0000.000
75A75ASP-1-0.845-0.90519.005-0.003-0.0030.0000.0000.0000.000
76A76GLN0-0.137-0.07621.3460.0010.0010.0000.0000.0000.000
77A77LEU00.0160.03222.4800.0010.0010.0000.0000.0000.000
78A78THR0-0.037-0.01620.5990.0030.0030.0000.0000.0000.000
79A79PRO00.0110.01523.802-0.001-0.0010.0000.0000.0000.000
80A80ARG10.9520.97423.3490.0130.0130.0000.0000.0000.000
81A81ARG10.8470.90121.170-0.012-0.0120.0000.0000.0000.000
82A82SER0-0.003-0.01624.5290.0000.0000.0000.0000.0000.000
83A83ARG10.9660.97522.947-0.025-0.0250.0000.0000.0000.000
84A84LYS10.8970.96125.9820.0010.0010.0000.0000.0000.000
85A85LEU00.0320.01629.302-0.001-0.0010.0000.0000.0000.000
86A86LYS10.8590.93932.7810.0020.0020.0000.0000.0000.000
87A87GLU-1-0.861-0.91135.1900.0040.0040.0000.0000.0000.000
88A88VAL00.0000.00538.872-0.001-0.0010.0000.0000.0000.000
89A89ARG10.9230.95641.8500.0000.0000.0000.0000.0000.000
90A90LEU00.0150.00644.891-0.001-0.0010.0000.0000.0000.000
91A91ASP-1-0.852-0.92547.8570.0000.0000.0000.0000.0000.000
92A92ARG10.8700.92451.441-0.003-0.0030.0000.0000.0000.000
93A93LEU0-0.074-0.03353.3140.0000.0000.0000.0000.0000.000
94A94HIS00.0240.03452.8730.0000.0000.0000.0000.0000.000
95A95PRO00.000-0.00655.3310.0000.0000.0000.0000.0000.000
96A96GLU-1-0.921-0.95853.525-0.004-0.0040.0000.0000.0000.000
97A97GLY0-0.036-0.00252.8580.0000.0000.0000.0000.0000.000
98A98LEU0-0.020-0.03147.6160.0000.0000.0000.0000.0000.000
99A99GLY00.0290.01847.4620.0000.0000.0000.0000.0000.000
100A100LEU0-0.009-0.01043.0090.0000.0000.0000.0000.0000.000
101A101SER0-0.026-0.00544.6380.0000.0000.0000.0000.0000.000
102A102VAL0-0.006-0.01542.5970.0000.0000.0000.0000.0000.000
103A103ARG10.9370.97240.639-0.007-0.0070.0000.0000.0000.000
104A104GLY00.0400.01741.4220.0000.0000.0000.0000.0000.000
105A105GLY00.0240.00841.762-0.001-0.0010.0000.0000.0000.000
106A106LEU0-0.001-0.00841.9220.0010.0010.0000.0000.0000.000
107A107GLU-1-0.802-0.90843.2750.0140.0140.0000.0000.0000.000
108A108PHE0-0.057-0.02842.2330.0000.0000.0000.0000.0000.000
109A109GLY0-0.0090.01039.9390.0010.0010.0000.0000.0000.000
110A110CYS0-0.076-0.03037.2690.0010.0010.0000.0000.0000.000
111A111GLY00.0310.02136.8020.0000.0000.0000.0000.0000.000
112A112LEU00.0130.00738.102-0.001-0.0010.0000.0000.0000.000
113A113PHE00.0300.00233.4970.0000.0000.0000.0000.0000.000
114A114ILE0-0.012-0.00338.4720.0000.0000.0000.0000.0000.000
115A115SER00.014-0.00638.8740.0000.0000.0000.0000.0000.000
116A116HIS0-0.005-0.00741.0230.0000.0000.0000.0000.0000.000
117A117LEU00.0270.02639.5790.0000.0000.0000.0000.0000.000
118A118ILE00.0030.00643.3940.0000.0000.0000.0000.0000.000
119A119LYS10.9530.97543.2060.0080.0080.0000.0000.0000.000
120A120GLY0-0.033-0.02344.9090.0000.0000.0000.0000.0000.000
121A121GLY00.0220.01946.6080.0000.0000.0000.0000.0000.000
122A122GLN00.0320.00546.3740.0000.0000.0000.0000.0000.000
123A123ALA00.0200.01043.2490.0000.0000.0000.0000.0000.000
124A124ASP-1-0.807-0.90141.423-0.006-0.0060.0000.0000.0000.000
125A125SER0-0.064-0.02141.496-0.001-0.0010.0000.0000.0000.000
126A126VAL0-0.020-0.00141.711-0.001-0.0010.0000.0000.0000.000
127A127GLY0-0.012-0.00638.2440.0000.0000.0000.0000.0000.000
128A128LEU0-0.057-0.02537.1000.0010.0010.0000.0000.0000.000
129A129GLN0-0.019-0.03232.138-0.002-0.0020.0000.0000.0000.000
130A130VAL00.0230.01637.0540.0010.0010.0000.0000.0000.000
131A131GLY00.0570.02033.959-0.001-0.0010.0000.0000.0000.000
132A132ASP-1-0.804-0.90133.5330.0030.0030.0000.0000.0000.000
133A133GLU-1-0.819-0.89633.0560.0160.0160.0000.0000.0000.000
134A134ILE0-0.003-0.00635.6970.0000.0000.0000.0000.0000.000
135A135VAL0-0.009-0.00934.0600.0010.0010.0000.0000.0000.000
136A136ARG10.8100.90137.532-0.012-0.0120.0000.0000.0000.000
137A137ILE00.0770.05240.523-0.001-0.0010.0000.0000.0000.000
138A138ASN00.0640.03044.1040.0000.0000.0000.0000.0000.000
139A139GLY00.0080.00743.2640.0000.0000.0000.0000.0000.000
140A140TYR00.0030.00243.4140.0010.0010.0000.0000.0000.000
141A141SER0-0.042-0.04240.5500.0000.0000.0000.0000.0000.000
142A142ILE00.0480.01240.6490.0000.0000.0000.0000.0000.000
143A143SER0-0.012-0.00438.3730.0000.0000.0000.0000.0000.000
144A144SER0-0.025-0.01740.2180.0010.0010.0000.0000.0000.000
145A145CYS0-0.0400.00643.5090.0000.0000.0000.0000.0000.000
146A146THR00.013-0.00344.5620.0000.0000.0000.0000.0000.000
147A147HIS0-0.042-0.04045.516-0.001-0.0010.0000.0000.0000.000
148A148GLU-1-0.881-0.94147.2960.0080.0080.0000.0000.0000.000
149A149GLU-1-0.816-0.88048.6780.0120.0120.0000.0000.0000.000
150A150VAL00.0080.00044.309-0.001-0.0010.0000.0000.0000.000
151A151ILE0-0.035-0.01547.464-0.001-0.0010.0000.0000.0000.000
152A152ASN0-0.046-0.04849.921-0.001-0.0010.0000.0000.0000.000
153A153LEU0-0.0070.00846.555-0.001-0.0010.0000.0000.0000.000
154A154ILE0-0.032-0.00945.910-0.001-0.0010.0000.0000.0000.000
155A155ARG10.9020.94049.645-0.005-0.0050.0000.0000.0000.000
156A156THR0-0.042-0.01551.8180.0000.0000.0000.0000.0000.000
157A157GLU-1-0.862-0.92752.6910.0030.0030.0000.0000.0000.000
158A158LYS10.9070.96054.001-0.001-0.0010.0000.0000.0000.000
159A159THR0-0.045-0.02850.617-0.001-0.0010.0000.0000.0000.000
160A160VAL00.0260.01046.5690.0010.0010.0000.0000.0000.000
161A161SER0-0.079-0.03343.859-0.001-0.0010.0000.0000.0000.000
162A162ILE00.0560.03040.3350.0010.0010.0000.0000.0000.000
163A163LYS10.8380.89637.001-0.006-0.0060.0000.0000.0000.000
164A164VAL00.001-0.00234.9860.0010.0010.0000.0000.0000.000
165A165ARG10.8300.89129.667-0.017-0.0170.0000.0000.0000.000
166A166HIS0-0.043-0.01429.1510.0000.0000.0000.0000.0000.000
167A167ILE0-0.067-0.02529.1290.0010.0010.0000.0000.0000.000
168A168GLY00.0300.00928.7780.0000.0000.0000.0000.0000.000
169A169LEU0-0.030-0.01328.773-0.001-0.0010.0000.0000.0000.000
170A170ILE0-0.034-0.02032.4170.0000.0000.0000.0000.0000.000
171A171PRO00.0110.03236.1370.0000.0000.0000.0000.0000.000
172A172VAL0-0.012-0.02037.760-0.001-0.0010.0000.0000.0000.000
173A173LYS10.8140.88640.040-0.014-0.0140.0000.0000.0000.000
174A174SER0-0.072-0.04742.951-0.001-0.0010.0000.0000.0000.000
175A175SER00.0650.03345.7520.0000.0000.0000.0000.0000.000
176A176PRO00.045-0.00346.8780.0010.0010.0000.0000.0000.000
177A177ASP-1-0.909-0.94947.9190.0140.0140.0000.0000.0000.000
178A178GLU-1-0.915-0.90443.3720.0130.0130.0000.0000.0000.000
179A179PRO00.0290.02439.4050.0000.0000.0000.0000.0000.000
180A180LEU0-0.038-0.01737.125-0.001-0.0010.0000.0000.0000.000
181A181THR00.0070.00635.8060.0010.0010.0000.0000.0000.000
182A182TRP00.028-0.01432.410-0.001-0.0010.0000.0000.0000.000
183A183GLN0-0.002-0.00133.5500.0000.0000.0000.0000.0000.000
184A184TYR0-0.018-0.04226.169-0.001-0.0010.0000.0000.0000.000
185A185VAL00.002-0.00332.0630.0000.0000.0000.0000.0000.000
186A186ASP-1-0.878-0.94631.679-0.002-0.0020.0000.0000.0000.000
187A187GLN0-0.030-0.00734.2200.0000.0000.0000.0000.0000.000
188A188PHE00.0230.00935.9740.0000.0000.0000.0000.0000.000
189A189VAL0-0.028-0.02837.8100.0000.0000.0000.0000.0000.000
190A190SER0-0.046-0.03137.526-0.001-0.0010.0000.0000.0000.000
191A191GLU-1-0.859-0.90739.0190.0040.0040.0000.0000.0000.000
192A192SER0-0.126-0.04342.0250.0000.0000.0000.0000.0000.000