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: KGKR3

Calculation Name: 3R3H-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3R3H

Chain ID: A

ChEMBL ID:

UniProt ID: Q5ZT85

Base Structure: X-ray

Registration Date: 2023-09-22

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 217
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2661191.834465
FMO2-HF: Nuclear repulsion 2575246.120352
FMO2-HF: Total energy -85945.714113
FMO2-MP2: Total energy -86197.778732


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:LYS)


Summations of interaction energy for fragment #1(A:4:LYS)
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.
-76.439-70.1292.272-4.16-4.421-0.04
Interaction energy analysis for fragmet #1(A:4:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.968 / q_NPA : 0.984
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].
3A6LEU0-0.022-0.0222.202-35.852-30.0322.263-4.069-4.014-0.040
4A7SER00.0230.0183.3019.3879.8260.010-0.090-0.3580.000
5A8LEU0-0.0090.0034.985-0.0320.019-0.001-0.001-0.0490.000
6A9THR00.014-0.0097.2981.2481.2480.0000.0000.0000.000
7A10PRO00.0450.0049.7801.1411.1410.0000.0000.0000.000
8A11GLU-1-0.807-0.89911.441-23.807-23.8070.0000.0000.0000.000
9A12LEU00.0050.0147.7680.8120.8120.0000.0000.0000.000
10A13TYR0-0.029-0.02911.7371.1651.1650.0000.0000.0000.000
11A14LYS10.8850.93013.83319.89419.8940.0000.0000.0000.000
12A15TYR00.0160.01912.9780.6440.6440.0000.0000.0000.000
13A16LEU00.0050.00512.6670.8380.8380.0000.0000.0000.000
14A17LEU0-0.008-0.01315.4371.1121.1120.0000.0000.0000.000
15A18ASP-1-0.946-0.95818.714-14.176-14.1760.0000.0000.0000.000
16A19ILE0-0.022-0.00115.7010.6880.6880.0000.0000.0000.000
17A20SER0-0.099-0.05718.4220.3990.3990.0000.0000.0000.000
18A21LEU0-0.052-0.00720.7080.7000.7000.0000.0000.0000.000
19A22ARG10.9140.95022.67512.54212.5420.0000.0000.0000.000
20A23GLU-1-0.738-0.81526.261-11.777-11.7770.0000.0000.0000.000
21A24HIS00.0760.03827.9240.1250.1250.0000.0000.0000.000
22A25PRO00.0380.00131.691-0.141-0.1410.0000.0000.0000.000
23A26ALA00.0760.04933.644-0.051-0.0510.0000.0000.0000.000
24A27LEU0-0.038-0.00729.2000.0210.0210.0000.0000.0000.000
25A28ALA00.0040.01529.256-0.100-0.1000.0000.0000.0000.000
26A29ALA0-0.043-0.02130.261-0.095-0.0950.0000.0000.0000.000
27A30LEU0-0.0010.00832.1200.0510.0510.0000.0000.0000.000
28A31ARG10.8270.87925.15912.43912.4390.0000.0000.0000.000
29A32LYS10.9670.97329.7149.7879.7870.0000.0000.0000.000
30A33GLU-1-0.900-0.93830.603-8.617-8.6170.0000.0000.0000.000
31A34THR0-0.061-0.05331.5950.1880.1880.0000.0000.0000.000
32A35SER0-0.035-0.02027.669-0.278-0.2780.0000.0000.0000.000
33A36THR0-0.025-0.01628.506-0.234-0.2340.0000.0000.0000.000
34A37MET0-0.0230.01330.8520.0360.0360.0000.0000.0000.000
35A38GLU-1-0.841-0.92329.522-11.039-11.0390.0000.0000.0000.000
36A39LEU0-0.039-0.02229.246-0.301-0.3010.0000.0000.0000.000
37A40ALA0-0.015-0.01226.947-0.215-0.2150.0000.0000.0000.000
38A41ASN0-0.047-0.01624.597-0.871-0.8710.0000.0000.0000.000
39A42MET0-0.026-0.00524.506-0.501-0.5010.0000.0000.0000.000
40A43GLN0-0.0040.01326.5130.3940.3940.0000.0000.0000.000
41A44VAL00.0530.03323.164-0.519-0.5190.0000.0000.0000.000
42A45ALA00.0180.01520.0470.1940.1940.0000.0000.0000.000
43A46PRO00.0380.00121.2420.2000.2000.0000.0000.0000.000
44A47GLU-1-0.782-0.90117.587-16.973-16.9730.0000.0000.0000.000
45A48GLN00.0150.01317.636-0.313-0.3130.0000.0000.0000.000
46A49ALA00.0240.01021.3710.4310.4310.0000.0000.0000.000
47A50GLN0-0.021-0.01422.7370.6230.6230.0000.0000.0000.000
48A51PHE0-0.018-0.00820.6560.2900.2900.0000.0000.0000.000
49A52MET00.0420.01322.7900.4010.4010.0000.0000.0000.000
50A53GLN0-0.050-0.02325.8520.3150.3150.0000.0000.0000.000
51A54MET0-0.033-0.01524.1800.5480.5480.0000.0000.0000.000
52A55LEU00.0200.01123.6450.4280.4280.0000.0000.0000.000
53A56ILE00.0490.05727.3350.3730.3730.0000.0000.0000.000
54A57ARG10.9060.95726.95611.68011.6800.0000.0000.0000.000
55A58LEU0-0.062-0.04625.3530.3160.3160.0000.0000.0000.000
56A59THR0-0.049-0.02529.6640.1750.1750.0000.0000.0000.000
57A60ARG10.8300.92131.5429.8329.8320.0000.0000.0000.000
58A61ALA0-0.0090.00233.9080.2800.2800.0000.0000.0000.000
59A62LYS10.8460.92735.7528.1298.1290.0000.0000.0000.000
60A63LYS10.8810.95138.4127.7617.7610.0000.0000.0000.000
61A64VAL0-0.029-0.01832.976-0.179-0.1790.0000.0000.0000.000
62A65LEU0-0.0020.00934.6270.2610.2610.0000.0000.0000.000
63A66GLU-1-0.762-0.84131.379-10.524-10.5240.0000.0000.0000.000
64A67LEU0-0.008-0.01532.0890.3910.3910.0000.0000.0000.000
65A68GLY00.0700.02731.376-0.410-0.4100.0000.0000.0000.000
66A69THR0-0.0010.01330.9370.3390.3390.0000.0000.0000.000
67A70PHE0-0.016-0.01529.508-0.338-0.3380.0000.0000.0000.000
68A71THR00.0310.01431.1950.2440.2440.0000.0000.0000.000
69A72GLY00.018-0.00633.1010.3090.3090.0000.0000.0000.000
70A73TYR0-0.044-0.05126.2670.0590.0590.0000.0000.0000.000
71A74SER00.018-0.02828.500-0.048-0.0480.0000.0000.0000.000
72A75ALA00.0750.04430.0600.0360.0360.0000.0000.0000.000
73A76LEU0-0.043-0.01133.2900.2170.2170.0000.0000.0000.000
74A77ALA00.0260.00928.9340.1120.1120.0000.0000.0000.000
75A78MET00.0200.01629.2290.1060.1060.0000.0000.0000.000
76A79SER0-0.004-0.00632.1720.1960.1960.0000.0000.0000.000
77A80LEU0-0.020-0.01332.7750.1730.1730.0000.0000.0000.000
78A81ALA0-0.087-0.02430.8790.0100.0100.0000.0000.0000.000
79A82LEU0-0.0150.00032.9550.0030.0030.0000.0000.0000.000
80A83PRO0-0.026-0.00736.1720.0620.0620.0000.0000.0000.000
81A84ASP-1-0.929-0.97039.346-7.682-7.6820.0000.0000.0000.000
82A85ASP-1-0.877-0.95142.569-7.567-7.5670.0000.0000.0000.000
83A86GLY0-0.039-0.01539.9280.0390.0390.0000.0000.0000.000
84A87GLN0-0.032-0.02639.8950.1080.1080.0000.0000.0000.000
85A88VAL0-0.009-0.00534.818-0.168-0.1680.0000.0000.0000.000
86A89ILE0-0.043-0.01537.8560.2220.2220.0000.0000.0000.000
87A90THR0-0.040-0.03734.730-0.126-0.1260.0000.0000.0000.000
88A91CYS0-0.044-0.03136.0970.3830.3830.0000.0000.0000.000
89A92ASP-1-0.815-0.92435.982-9.228-9.2280.0000.0000.0000.000
90A93ILE0-0.019-0.02133.9910.2430.2430.0000.0000.0000.000
91A94ASN0-0.019-0.00435.5620.1220.1220.0000.0000.0000.000
92A95GLU-1-0.962-0.96637.306-7.611-7.6110.0000.0000.0000.000
93A96GLY0-0.0230.00138.4080.1700.1700.0000.0000.0000.000
94A97TRP0-0.051-0.03737.7860.1570.1570.0000.0000.0000.000
95A98THR00.0280.00636.985-0.225-0.2250.0000.0000.0000.000
96A99LYS10.8190.90436.4968.8988.8980.0000.0000.0000.000
97A100HIS00.0140.01038.662-0.264-0.2640.0000.0000.0000.000
98A101ALA00.0720.03837.063-0.015-0.0150.0000.0000.0000.000
99A102HIS00.025-0.00538.742-0.076-0.0760.0000.0000.0000.000
100A103PRO0-0.026-0.00740.7650.0890.0890.0000.0000.0000.000
101A104TYR00.0930.04136.8340.0630.0630.0000.0000.0000.000
102A105TRP0-0.005-0.01336.0550.1150.1150.0000.0000.0000.000
103A106ARG10.9440.98539.5987.1487.1480.0000.0000.0000.000
104A107GLU-1-0.948-0.96138.081-8.483-8.4830.0000.0000.0000.000
105A108ALA0-0.027-0.02037.211-0.004-0.0040.0000.0000.0000.000
106A109LYS10.8850.94539.1837.2807.2800.0000.0000.0000.000
107A110GLN00.0480.00237.143-0.026-0.0260.0000.0000.0000.000
108A111GLU-1-0.889-0.95240.556-7.405-7.4050.0000.0000.0000.000
109A112HIS0-0.050-0.02142.7120.1550.1550.0000.0000.0000.000
110A113LYS10.8520.94338.0858.4558.4550.0000.0000.0000.000
111A114ILE0-0.039-0.01237.478-0.102-0.1020.0000.0000.0000.000
112A115LYS10.9290.96740.5077.3307.3300.0000.0000.0000.000
113A116LEU0-0.007-0.00739.089-0.112-0.1120.0000.0000.0000.000
114A117ARG10.8610.92440.5427.6007.6000.0000.0000.0000.000
115A118LEU00.0320.01340.666-0.163-0.1630.0000.0000.0000.000
116A119GLY00.0370.03141.2230.1980.1980.0000.0000.0000.000
117A120PRO00.0230.00139.914-0.225-0.2250.0000.0000.0000.000
118A121ALA00.0630.02036.6800.1260.1260.0000.0000.0000.000
119A122LEU0-0.0060.01138.6260.0540.0540.0000.0000.0000.000
120A123ASP-1-0.839-0.92140.265-7.271-7.2710.0000.0000.0000.000
121A124THR0-0.018-0.01940.6550.2150.2150.0000.0000.0000.000
122A125LEU00.0230.00636.3690.0670.0670.0000.0000.0000.000
123A126HIS0-0.028-0.01541.0980.0820.0820.0000.0000.0000.000
124A127SER0-0.0360.00543.8750.1170.1170.0000.0000.0000.000
125A128LEU00.006-0.01140.5860.1250.1250.0000.0000.0000.000
126A129LEU0-0.0120.00940.7860.0330.0330.0000.0000.0000.000
127A130ASN0-0.067-0.03244.2680.0350.0350.0000.0000.0000.000
128A131GLU-1-0.977-0.99147.696-6.350-6.3500.0000.0000.0000.000
129A132GLY0-0.028-0.01145.8640.1000.1000.0000.0000.0000.000
130A133GLY00.0030.01345.635-0.024-0.0240.0000.0000.0000.000
131A134GLU-1-0.903-0.97341.296-7.639-7.6390.0000.0000.0000.000
132A135HIS0-0.063-0.02038.974-0.111-0.1110.0000.0000.0000.000
133A136GLN0-0.035-0.00539.9560.1040.1040.0000.0000.0000.000
134A137PHE0-0.003-0.00436.0630.0220.0220.0000.0000.0000.000
135A138ASP-1-0.728-0.86235.068-8.700-8.7000.0000.0000.0000.000
136A139PHE0-0.002-0.01127.192-0.329-0.3290.0000.0000.0000.000
137A140ILE00.0000.01631.1960.2630.2630.0000.0000.0000.000
138A141PHE00.001-0.00524.986-0.322-0.3220.0000.0000.0000.000
139A142ILE0-0.026-0.03228.3600.4120.4120.0000.0000.0000.000
140A143ASP-1-0.818-0.91326.739-12.681-12.6810.0000.0000.0000.000
141A144ALA0-0.0220.00828.5230.1510.1510.0000.0000.0000.000
142A145ASP-1-0.791-0.88030.291-9.587-9.5870.0000.0000.0000.000
143A146LYS10.8890.91126.03112.20212.2020.0000.0000.0000.000
144A147THR0-0.055-0.02530.268-0.105-0.1050.0000.0000.0000.000
145A148ASN0-0.019-0.01233.2000.4150.4150.0000.0000.0000.000
146A149TYR0-0.019-0.02525.9440.3070.3070.0000.0000.0000.000
147A150LEU0-0.0120.00530.257-0.095-0.0950.0000.0000.0000.000
148A151ASN00.009-0.00332.436-0.044-0.0440.0000.0000.0000.000
149A152TYR0-0.033-0.05732.5300.2510.2510.0000.0000.0000.000
150A153TYR0-0.038-0.02527.610-0.095-0.0950.0000.0000.0000.000
151A154GLU-1-0.772-0.86731.731-8.965-8.9650.0000.0000.0000.000
152A155LEU0-0.052-0.02734.7050.1710.1710.0000.0000.0000.000
153A156ALA00.0160.00932.4640.1490.1490.0000.0000.0000.000
154A157LEU0-0.011-0.00930.6140.0160.0160.0000.0000.0000.000
155A158LYS10.8550.95034.3417.9597.9590.0000.0000.0000.000
156A159LEU00.004-0.01336.8580.1350.1350.0000.0000.0000.000
157A160VAL0-0.0280.00632.2050.0210.0210.0000.0000.0000.000
158A161THR0-0.029-0.01335.6120.2420.2420.0000.0000.0000.000
159A162PRO00.0240.00634.457-0.248-0.2480.0000.0000.0000.000
160A163LYS10.9410.95832.8528.4688.4680.0000.0000.0000.000
161A164GLY00.0050.00431.837-0.237-0.2370.0000.0000.0000.000
162A165LEU0-0.051-0.03025.333-0.182-0.1820.0000.0000.0000.000
163A166ILE00.0350.01128.0130.2130.2130.0000.0000.0000.000
164A167ALA0-0.005-0.00325.055-0.466-0.4660.0000.0000.0000.000
165A168ILE0-0.037-0.01424.4720.4610.4610.0000.0000.0000.000
166A169ASP-1-0.762-0.89621.487-15.599-15.5990.0000.0000.0000.000
167A170ASN0-0.039-0.02921.0031.1291.1290.0000.0000.0000.000
168A171ILE0-0.057-0.01019.3120.3680.3680.0000.0000.0000.000
169A172PHE0-0.030-0.04014.7430.1140.1140.0000.0000.0000.000
170A173TRP00.0100.01119.011-0.232-0.2320.0000.0000.0000.000
171A174ASP-1-0.853-0.93517.962-16.719-16.7190.0000.0000.0000.000
172A175GLY0-0.042-0.01217.091-0.642-0.6420.0000.0000.0000.000
173A176LYS10.8310.89517.80813.90013.9000.0000.0000.0000.000
174A177VAL0-0.042-0.02318.8470.7240.7240.0000.0000.0000.000
175A178ILE0-0.030-0.02215.8250.3280.3280.0000.0000.0000.000
176A179ASP-1-0.768-0.86419.097-13.701-13.7010.0000.0000.0000.000
177A180PRO0-0.053-0.04121.4040.5580.5580.0000.0000.0000.000
178A181ASN0-0.048-0.02323.9420.9140.9140.0000.0000.0000.000
179A182ASP-1-0.812-0.87925.208-11.685-11.6850.0000.0000.0000.000
180A183THR00.000-0.01527.1360.1760.1760.0000.0000.0000.000
181A184SER0-0.038-0.00528.5330.3750.3750.0000.0000.0000.000
182A185GLY00.021-0.02630.140-0.194-0.1940.0000.0000.0000.000
183A186GLN00.0480.02028.613-0.211-0.2110.0000.0000.0000.000
184A187THR00.0390.03224.887-0.307-0.3070.0000.0000.0000.000
185A188ARG10.9240.97026.2489.3009.3000.0000.0000.0000.000
186A189GLU-1-0.810-0.89928.928-9.609-9.6090.0000.0000.0000.000
187A190ILE00.0190.04423.3070.0480.0480.0000.0000.0000.000
188A191LYS10.8240.92022.99412.70512.7050.0000.0000.0000.000
189A192LYS10.7920.88924.8879.4629.4620.0000.0000.0000.000
190A193LEU00.0350.01626.2480.1510.1510.0000.0000.0000.000
191A194ASN0-0.004-0.01921.0690.2120.2120.0000.0000.0000.000
192A195GLN0-0.036-0.01322.864-0.211-0.2110.0000.0000.0000.000
193A196VAL0-0.012-0.00925.1420.1450.1450.0000.0000.0000.000
194A197ILE00.0430.02723.2650.1600.1600.0000.0000.0000.000
195A198LYS10.8490.94520.89912.28612.2860.0000.0000.0000.000
196A199ASN0-0.061-0.04323.371-0.197-0.1970.0000.0000.0000.000
197A200ASP-1-0.744-0.81826.419-9.405-9.4050.0000.0000.0000.000
198A201SER0-0.041-0.02227.144-0.212-0.2120.0000.0000.0000.000
199A202ARG10.7250.79329.4319.3229.3220.0000.0000.0000.000
200A203VAL0-0.008-0.00526.5580.1590.1590.0000.0000.0000.000
201A204PHE00.0030.00124.682-0.204-0.2040.0000.0000.0000.000
202A205VAL00.017-0.00720.528-0.033-0.0330.0000.0000.0000.000
203A206SER0-0.035-0.01018.092-0.442-0.4420.0000.0000.0000.000
204A207LEU0-0.0140.00315.8190.3570.3570.0000.0000.0000.000
205A208LEU0-0.0050.00115.002-1.162-1.1620.0000.0000.0000.000
206A209ALA0-0.008-0.01011.7810.6990.6990.0000.0000.0000.000
207A210ILE0-0.055-0.03412.302-2.014-2.0140.0000.0000.0000.000
208A211ALA00.0470.02914.652-0.311-0.3110.0000.0000.0000.000
209A212ASP-1-0.751-0.84915.843-17.413-17.4130.0000.0000.0000.000
210A213GLY0-0.014-0.01016.8380.3210.3210.0000.0000.0000.000
211A214MET00.0020.00117.6670.9560.9560.0000.0000.0000.000
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