Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: KGRV3

Calculation Name: 3M65-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3M65

Chain ID: A

ChEMBL ID:

UniProt ID: P37945

Base Structure: X-ray

Registration Date: 2023-09-20

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 206
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2131522.730084
FMO2-HF: Nuclear repulsion 2048504.488499
FMO2-HF: Total energy -83018.241585
FMO2-MP2: Total energy -83260.052547


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:4:GLU)


Summations of interaction energy for fragment #1(A:4:GLU)
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.
-57.951-55.24226.883-14.125-15.4690.161
Interaction energy analysis for fragmet #1(A:4:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.823 / q_NPA : -0.918
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].
3A6LYS10.8580.9331.742-105.982-110.41817.311-6.939-5.9370.073
4A7ARG10.9430.9635.581-27.860-27.8600.0000.0000.0000.000
5A8SER0-0.039-0.0199.139-0.082-0.0820.0000.0000.0000.000
6A9ILE0-0.0230.0038.5110.2500.2500.0000.0000.0000.000
7A10PRO00.0190.02311.975-1.022-1.0220.0000.0000.0000.000
8A11LEU00.0120.00615.0801.1971.1970.0000.0000.0000.000
9A12LEU0-0.020-0.01816.759-1.098-1.0980.0000.0000.0000.000
10A13PRO00.0310.01519.0290.4610.4610.0000.0000.0000.000
11A14LEU0-0.029-0.00419.216-0.614-0.6140.0000.0000.0000.000
12A15ARG10.8260.89722.656-11.158-11.1580.0000.0000.0000.000
13A16GLY00.0110.00826.032-0.171-0.1710.0000.0000.0000.000
14A17LEU00.0400.02121.956-0.126-0.1260.0000.0000.0000.000
15A18LEU00.0100.01018.1600.4190.4190.0000.0000.0000.000
16A19VAL00.0020.01116.374-0.280-0.2800.0000.0000.0000.000
17A20TYR00.020-0.00615.7481.1931.1930.0000.0000.0000.000
18A21PRO00.001-0.01011.527-0.336-0.3360.0000.0000.0000.000
19A22THR0-0.067-0.04613.480-1.689-1.6890.0000.0000.0000.000
20A23MET00.0300.05315.433-1.089-1.0890.0000.0000.0000.000
21A24VAL0-0.019-0.02117.5120.9400.9400.0000.0000.0000.000
22A25LEU00.0170.02019.839-0.795-0.7950.0000.0000.0000.000
23A26HIS0-0.012-0.01721.7910.3130.3130.0000.0000.0000.000
24A27LEU00.0100.00820.715-0.033-0.0330.0000.0000.0000.000
25A28ASP-1-0.871-0.94524.67611.13411.1340.0000.0000.0000.000
26A29VAL0-0.036-0.02622.971-0.022-0.0220.0000.0000.0000.000
27A30GLY00.0330.00226.442-0.249-0.2490.0000.0000.0000.000
28A31ARG10.8780.95224.438-12.704-12.7040.0000.0000.0000.000
29A32ASP-1-0.838-0.91126.96310.86410.8640.0000.0000.0000.000
30A33LYS10.9430.96624.094-11.702-11.7020.0000.0000.0000.000
31A34SER0-0.066-0.03222.6070.5450.5450.0000.0000.0000.000
32A35VAL0-0.016-0.02022.4130.6700.6700.0000.0000.0000.000
33A36GLN00.0410.02323.5010.5060.5060.0000.0000.0000.000
34A37ALA00.0110.02018.7650.5250.5250.0000.0000.0000.000
35A38LEU0-0.021-0.01918.7330.9360.9360.0000.0000.0000.000
36A39GLU-1-0.844-0.93819.49612.79112.7910.0000.0000.0000.000
37A40GLN00.0420.01817.760-0.171-0.1710.0000.0000.0000.000
38A41ALA00.0320.02215.2760.6820.6820.0000.0000.0000.000
39A42MET0-0.081-0.05716.2561.1021.1020.0000.0000.0000.000
40A43MET0-0.064-0.00518.749-0.667-0.6670.0000.0000.0000.000
41A44HIS0-0.049-0.03414.4210.0660.0660.0000.0000.0000.000
42A45ASP-1-0.857-0.9259.61029.15429.1540.0000.0000.0000.000
43A46HIS10.7820.87612.528-17.917-17.9170.0000.0000.0000.000
44A47MET0-0.0450.0017.926-1.124-1.1240.0000.0000.0000.000
45A48ILE00.0410.01911.834-1.300-1.3000.0000.0000.0000.000
46A49PHE0-0.016-0.01110.5932.2892.2890.0000.0000.0000.000
47A50LEU00.0260.01813.304-1.701-1.7010.0000.0000.0000.000
48A51ALA00.0290.01415.3910.9620.9620.0000.0000.0000.000
49A52THR0-0.047-0.02717.252-0.429-0.4290.0000.0000.0000.000
50A53GLN00.0180.00120.6320.3560.3560.0000.0000.0000.000
51A54GLN0-0.073-0.04621.6210.2060.2060.0000.0000.0000.000
52A55ASP-1-0.845-0.92924.84410.89010.8900.0000.0000.0000.000
53A56ILE0-0.052-0.04128.2180.1030.1030.0000.0000.0000.000
54A57SER0-0.025-0.02229.3710.0400.0400.0000.0000.0000.000
55A58ILE00.0350.04628.364-0.348-0.3480.0000.0000.0000.000
56A59ASP-1-0.823-0.91829.26110.43910.4390.0000.0000.0000.000
57A60GLU-1-0.985-1.00027.38211.06111.0610.0000.0000.0000.000
58A61PRO0-0.063-0.02423.804-0.140-0.1400.0000.0000.0000.000
59A62GLY00.0650.04123.8630.3380.3380.0000.0000.0000.000
60A63GLU-1-0.938-0.99816.46816.64416.6440.0000.0000.0000.000
61A64ASP-1-0.941-0.96720.38112.54512.5450.0000.0000.0000.000
62A65GLU-1-0.855-0.92422.75311.28611.2860.0000.0000.0000.000
63A66ILE0-0.094-0.03118.2220.0390.0390.0000.0000.0000.000
64A67PHE00.0110.01317.523-0.003-0.0030.0000.0000.0000.000
65A68THR00.0640.02213.7210.6580.6580.0000.0000.0000.000
66A69VAL0-0.027-0.00811.7021.6991.6990.0000.0000.0000.000
67A70GLY00.0190.00912.159-1.605-1.6050.0000.0000.0000.000
68A71THR0-0.042-0.03311.5272.3642.3640.0000.0000.0000.000
69A72TYR00.0130.0175.3032.5962.5960.0000.0000.0000.000
70A73THR00.010-0.0259.806-0.091-0.0910.0000.0000.0000.000
71A74LYS10.9190.96511.252-25.417-25.4170.0000.0000.0000.000
72A75ILE0-0.0070.00613.156-1.455-1.4550.0000.0000.0000.000
73A76LYS10.7540.85115.755-19.359-19.3590.0000.0000.0000.000
74A77GLN0-0.019-0.01218.483-0.515-0.5150.0000.0000.0000.000
75A78MET00.0190.02121.5330.3350.3350.0000.0000.0000.000
76A79LEU0-0.0260.00223.407-0.314-0.3140.0000.0000.0000.000
77A80LYS10.8850.95127.148-11.225-11.2250.0000.0000.0000.000
78A81LEU0-0.003-0.00429.128-0.335-0.3350.0000.0000.0000.000
79A82PRO0-0.010-0.02132.138-0.045-0.0450.0000.0000.0000.000
80A83ASN00.006-0.00733.8870.0850.0850.0000.0000.0000.000
81A84GLY00.0410.03932.397-0.074-0.0740.0000.0000.0000.000
82A85THR0-0.0260.00029.7280.2910.2910.0000.0000.0000.000
83A86ILE0-0.038-0.02424.171-0.057-0.0570.0000.0000.0000.000
84A87ARG10.9490.99526.519-11.316-11.3160.0000.0000.0000.000
85A88VAL0-0.028-0.02220.2310.1110.1110.0000.0000.0000.000
86A89LEU0-0.0050.00620.760-0.229-0.2290.0000.0000.0000.000
87A90VAL0-0.004-0.01216.8510.7250.7250.0000.0000.0000.000
88A91GLU-1-0.767-0.88014.07920.62920.6290.0000.0000.0000.000
89A92GLY00.0400.03413.4901.7181.7180.0000.0000.0000.000
90A93LEU0-0.065-0.0218.6680.1410.1410.0000.0000.0000.000
91A94LYS10.9330.9672.061-112.906-109.6845.123-4.352-3.9930.060
92A95ARG10.8950.9398.295-25.051-25.0510.0000.0000.0000.000
93A96ALA0-0.016-0.0117.0024.8644.8640.0000.0000.0000.000
94A97HIS0-0.007-0.0076.646-4.044-4.0440.0000.0000.0000.000
95A98ILE00.0210.0108.6852.0922.0920.0000.0000.0000.000
96A99VAL0-0.061-0.0297.991-0.718-0.7180.0000.0000.0000.000
97A100LYS10.7850.85310.693-20.579-20.5790.0000.0000.0000.000
98A101TYR00.0470.02913.5011.3251.3250.0000.0000.0000.000
99A102ASN0-0.074-0.02613.838-1.189-1.1890.0000.0000.0000.000
100A103GLU-1-0.813-0.89818.00813.43613.4360.0000.0000.0000.000
101A104HIS0-0.052-0.02418.5620.4130.4130.0000.0000.0000.000
102A105GLU-1-0.945-0.97922.67710.48310.4830.0000.0000.0000.000
103A106ASP-1-0.828-0.91224.42011.93311.9330.0000.0000.0000.000
104A107TYR0-0.055-0.04017.5060.4550.4550.0000.0000.0000.000
105A108THR00.0260.02318.134-0.218-0.2180.0000.0000.0000.000
106A109SER0-0.016-0.00515.1011.1771.1770.0000.0000.0000.000
107A110VAL00.0070.00411.895-0.537-0.5370.0000.0000.0000.000
108A111ASP-1-0.830-0.8949.64624.78924.7890.0000.0000.0000.000
109A112ILE00.0400.0196.595-0.615-0.6150.0000.0000.0000.000
110A113GLN0-0.009-0.0123.5481.5651.9840.002-0.123-0.2980.000
111A114LEU0-0.072-0.0442.254-3.708-0.8234.443-2.454-4.8750.030
112A115ILE0-0.014-0.0073.642-3.223-2.6040.004-0.257-0.366-0.002
113A116HIS0-0.129-0.0666.3333.1233.1230.0000.0000.0000.000
114A117GLU-1-0.822-0.8977.97026.02426.0240.0000.0000.0000.000
115A118ASP-1-0.871-0.96110.77725.83525.8350.0000.0000.0000.000
116A119ASP-1-1.004-0.97212.98417.64717.6470.0000.0000.0000.000
117A120SER00.0180.01516.061-1.023-1.0230.0000.0000.0000.000
118A121LYS10.7460.86717.072-12.923-12.9230.0000.0000.0000.000
119A122ASP-1-0.864-0.94019.52213.77413.7740.0000.0000.0000.000
120A123THR0-0.043-0.04622.634-0.136-0.1360.0000.0000.0000.000
121A124GLU-1-0.922-0.96324.82911.30411.3040.0000.0000.0000.000
122A125ASP-1-0.740-0.85320.46914.81514.8150.0000.0000.0000.000
123A126GLU-1-0.887-0.93623.52111.87811.8780.0000.0000.0000.000
124A127ALA0-0.072-0.03425.985-0.377-0.3770.0000.0000.0000.000
125A128LEU00.0660.03124.120-0.352-0.3520.0000.0000.0000.000
126A129MET00.0040.00823.080-0.013-0.0130.0000.0000.0000.000
127A130ARG10.8980.95226.219-10.367-10.3670.0000.0000.0000.000
128A131THR0-0.015-0.01329.618-0.393-0.3930.0000.0000.0000.000
129A132LEU0-0.0070.00524.469-0.252-0.2520.0000.0000.0000.000
130A133LEU0-0.008-0.01627.591-0.222-0.2220.0000.0000.0000.000
131A134ASP-1-0.839-0.89030.2148.6018.6010.0000.0000.0000.000
132A135HIS0-0.035-0.03431.805-0.208-0.2080.0000.0000.0000.000
133A136PHE00.0190.01329.581-0.194-0.1940.0000.0000.0000.000
134A137ASP-1-0.814-0.89732.1098.4648.4640.0000.0000.0000.000
135A138GLN0-0.091-0.06234.961-0.443-0.4430.0000.0000.0000.000
136A139TYR00.0150.01133.125-0.188-0.1880.0000.0000.0000.000
137A140ILE00.0140.01032.410-0.231-0.2310.0000.0000.0000.000
138A141LYS10.7900.87436.586-8.467-8.4670.0000.0000.0000.000
139A142ILE0-0.001-0.00339.547-0.263-0.2630.0000.0000.0000.000
140A143SER00.0280.01837.833-0.190-0.1900.0000.0000.0000.000
141A144LYS10.9390.98540.461-7.792-7.7920.0000.0000.0000.000
142A145LYS10.7830.87442.184-6.923-6.9230.0000.0000.0000.000
143A146ILE00.0440.02442.604-0.174-0.1740.0000.0000.0000.000
144A147SER0-0.012-0.01143.178-0.170-0.1700.0000.0000.0000.000
145A148ALA0-0.0090.00045.321-0.136-0.1360.0000.0000.0000.000
146A149GLU-1-0.809-0.89547.9106.4556.4550.0000.0000.0000.000
147A150THR0-0.031-0.01447.721-0.129-0.1290.0000.0000.0000.000
148A151TYR0-0.009-0.01048.884-0.091-0.0910.0000.0000.0000.000
149A152ALA0-0.0160.00250.682-0.117-0.1170.0000.0000.0000.000
150A153ALA00.0030.00853.204-0.121-0.1210.0000.0000.0000.000
151A154VAL0-0.013-0.02551.593-0.104-0.1040.0000.0000.0000.000
152A155THR0-0.070-0.04854.210-0.062-0.0620.0000.0000.0000.000
153A156ASP-1-0.943-0.94856.4035.3975.3970.0000.0000.0000.000
154A157ILE0-0.120-0.05256.076-0.079-0.0790.0000.0000.0000.000
155A158GLU-1-0.898-0.94859.8595.0895.0890.0000.0000.0000.000
156A159GLU-1-0.879-0.93562.0235.2075.2070.0000.0000.0000.000
157A160PRO00.0290.00359.6930.1010.1010.0000.0000.0000.000
158A161GLY00.0100.00258.2480.1050.1050.0000.0000.0000.000
159A162ARG10.9170.94957.623-5.336-5.3360.0000.0000.0000.000
160A163MET00.0070.00454.9330.1320.1320.0000.0000.0000.000
161A164ALA0-0.006-0.00553.7730.1420.1420.0000.0000.0000.000
162A165ASP-1-0.787-0.87252.5805.9645.9640.0000.0000.0000.000
163A166ILE0-0.024-0.00851.9600.1420.1420.0000.0000.0000.000
164A167VAL00.0390.03249.0980.1480.1480.0000.0000.0000.000
165A168ALA00.0250.01348.1580.1910.1910.0000.0000.0000.000
166A169SER0-0.125-0.08247.1570.1610.1610.0000.0000.0000.000
167A170HIS00.004-0.01046.1480.2000.2000.0000.0000.0000.000
168A171LEU00.0050.02743.6470.1940.1940.0000.0000.0000.000
169A172PRO00.0010.00538.571-0.094-0.0940.0000.0000.0000.000
170A173LEU0-0.0030.00939.8510.1260.1260.0000.0000.0000.000
171A174LYS10.9170.94137.931-8.231-8.2310.0000.0000.0000.000
172A175LEU00.0740.01841.130-0.168-0.1680.0000.0000.0000.000
173A176LYS10.8860.93240.983-7.846-7.8460.0000.0000.0000.000
174A177ASP-1-0.767-0.86442.3727.5897.5890.0000.0000.0000.000
175A178LYS10.8670.94744.150-7.407-7.4070.0000.0000.0000.000
176A179GLN0-0.073-0.05047.542-0.102-0.1020.0000.0000.0000.000
177A180ASP-1-0.815-0.88948.6576.3336.3330.0000.0000.0000.000
178A181ILE0-0.026-0.00549.391-0.161-0.1610.0000.0000.0000.000
179A182LEU0-0.025-0.01051.935-0.151-0.1510.0000.0000.0000.000
180A183GLU-1-0.917-0.94052.8536.0446.0440.0000.0000.0000.000
181A184THR0-0.054-0.01653.843-0.064-0.0640.0000.0000.0000.000
182A185ALA00.011-0.00256.374-0.032-0.0320.0000.0000.0000.000
183A186ASP-1-0.861-0.93259.8995.2665.2660.0000.0000.0000.000
184A187VAL00.0400.00658.9810.0930.0930.0000.0000.0000.000
185A188LYS10.9490.97558.496-5.219-5.2190.0000.0000.0000.000
186A189ASP-1-0.876-0.92356.6375.7325.7320.0000.0000.0000.000
187A190ARG10.7450.85554.264-5.590-5.5900.0000.0000.0000.000
188A191LEU0-0.008-0.01753.5700.1230.1230.0000.0000.0000.000
189A192ASN0-0.078-0.05253.1610.1370.1370.0000.0000.0000.000
190A193LYS10.8810.93250.476-6.156-6.1560.0000.0000.0000.000
191A194VAL0-0.010-0.00249.0040.1800.1800.0000.0000.0000.000
192A195ILE0-0.001-0.00548.3160.1520.1520.0000.0000.0000.000
193A196ASP-1-0.880-0.93847.4676.7916.7910.0000.0000.0000.000
194A197PHE0-0.047-0.02944.0150.2240.2240.0000.0000.0000.000
195A198ILE0-0.0050.00343.5580.2080.2080.0000.0000.0000.000
196A199ASN0-0.026-0.01143.2660.2430.2430.0000.0000.0000.000
197A200ASN0-0.008-0.00640.7290.2960.2960.0000.0000.0000.000
198A201GLU-1-0.915-0.96238.8728.5598.5590.0000.0000.0000.000
199A202LYS10.7430.86238.572-7.431-7.4310.0000.0000.0000.000
200A203GLU-1-0.824-0.92438.4528.0908.0900.0000.0000.0000.000
201A204VAL0-0.023-0.01333.9320.2600.2600.0000.0000.0000.000
202A205LEU00.0130.00733.8090.2970.2970.0000.0000.0000.000
203A206GLU-1-0.883-0.91833.6309.1149.1140.0000.0000.0000.000
204A207ILE0-0.039-0.01431.2840.2310.2310.0000.0000.0000.000
205A208GLU-1-1.009-0.97429.31210.99410.9940.0000.0000.0000.000
206A209LYS10.7330.84329.287-9.191-9.1910.0000.0000.0000.000