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: JQ469

Calculation Name: 3M3I-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3M3I

Chain ID: A

ChEMBL ID:

UniProt ID: E9AES8

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 177
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1929923.01134
FMO2-HF: Nuclear repulsion 1858680.602206
FMO2-HF: Total energy -71242.409134
FMO2-MP2: Total energy -71450.050323


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:10:GLN)


Summations of interaction energy for fragment #1(A:10:GLN)
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.
-15.02-11.1771.577-2.017-3.402-0.007
Interaction energy analysis for fragmet #1(A:10:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.013 / q_NPA : -0.014
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].
3A12THR00.0640.0242.823-7.182-4.4330.700-1.632-1.817-0.006
4A13ALA00.0760.0305.2471.3401.432-0.001-0.004-0.0870.000
5A14GLU-1-0.903-0.9499.005-0.870-0.8700.0000.0000.0000.000
6A15PHE0-0.022-0.0157.9610.5130.5130.0000.0000.0000.000
7A16TRP00.027-0.0126.4470.4000.4000.0000.0000.0000.000
8A17ILE00.0240.02711.4750.0690.0690.0000.0000.0000.000
9A18LYS10.9610.97913.266-0.329-0.3290.0000.0000.0000.000
10A19ARG10.8330.92010.693-1.499-1.4990.0000.0000.0000.000
11A20LEU0-0.0110.00413.5240.0600.0600.0000.0000.0000.000
12A21GLN0-0.058-0.02816.588-0.060-0.0600.0000.0000.0000.000
13A22LEU0-0.0540.00414.149-0.039-0.0390.0000.0000.0000.000
14A23VAL0-0.010-0.01118.290-0.042-0.0420.0000.0000.0000.000
15A24PRO00.022-0.00320.067-0.011-0.0110.0000.0000.0000.000
16A25HIS00.0410.03021.0670.0300.0300.0000.0000.0000.000
17A26PRO0-0.012-0.00322.739-0.036-0.0360.0000.0000.0000.000
18A27GLU-1-0.761-0.85021.756-0.258-0.2580.0000.0000.0000.000
19A28GLY00.0040.03020.950-0.041-0.0410.0000.0000.0000.000
20A29GLY00.0050.01116.8430.0420.0420.0000.0000.0000.000
21A30TYR0-0.035-0.04214.8130.0700.0700.0000.0000.0000.000
22A31TYR0-0.025-0.02617.3210.0270.0270.0000.0000.0000.000
23A32SER00.0490.03119.1400.0080.0080.0000.0000.0000.000
24A33GLU-1-0.836-0.90221.3460.0720.0720.0000.0000.0000.000
25A34VAL0-0.0280.00520.6370.0300.0300.0000.0000.0000.000
26A35VAL0-0.031-0.02023.9430.0020.0020.0000.0000.0000.000
27A36ARG10.8600.89927.035-0.087-0.0870.0000.0000.0000.000
28A37SER0-0.0530.00530.0740.0110.0110.0000.0000.0000.000
29A38ALA00.0320.01132.593-0.013-0.0130.0000.0000.0000.000
30A39HIS0-0.0180.00735.873-0.010-0.0100.0000.0000.0000.000
31A40LYS10.9570.96336.395-0.071-0.0710.0000.0000.0000.000
32A41VAL0-0.012-0.01136.3580.0040.0040.0000.0000.0000.000
33A42ASP-1-0.810-0.89939.1990.0320.0320.0000.0000.0000.000
34A43ASN00.005-0.00436.0640.0060.0060.0000.0000.0000.000
35A44GLU-1-0.786-0.88634.7820.0060.0060.0000.0000.0000.000
36A45GLU-1-0.925-0.95537.859-0.044-0.0440.0000.0000.0000.000
37A46GLY0-0.025-0.00140.898-0.002-0.0020.0000.0000.0000.000
38A47ASN0-0.041-0.00739.3420.0070.0070.0000.0000.0000.000
39A48ARG10.8170.89439.733-0.040-0.0400.0000.0000.0000.000
40A49ARG10.8120.87634.6900.0000.0000.0000.0000.0000.000
41A50HIS0-0.018-0.01432.675-0.002-0.0020.0000.0000.0000.000
42A51ALA00.0180.01233.695-0.006-0.0060.0000.0000.0000.000
43A52TYR00.0570.03927.903-0.008-0.0080.0000.0000.0000.000
44A53THR00.0020.00627.2510.0010.0010.0000.0000.0000.000
45A54THR0-0.033-0.01322.925-0.011-0.0110.0000.0000.0000.000
46A55ILE00.0290.01420.246-0.001-0.0010.0000.0000.0000.000
47A56TYR0-0.0050.00815.9590.0680.0680.0000.0000.0000.000
48A57PHE00.0350.00216.030-0.053-0.0530.0000.0000.0000.000
49A58LEU0-0.019-0.0019.9750.0150.0150.0000.0000.0000.000
50A59CYS0-0.0330.01612.278-0.015-0.0150.0000.0000.0000.000
51A60THR00.031-0.01010.846-0.152-0.1520.0000.0000.0000.000
52A61PRO00.0230.00810.5650.1820.1820.0000.0000.0000.000
53A62GLU-1-0.952-0.96613.633-1.090-1.0900.0000.0000.0000.000
54A63SER0-0.075-0.02715.3340.1640.1640.0000.0000.0000.000
55A64PRO00.0370.00916.6970.0160.0160.0000.0000.0000.000
56A65SER0-0.121-0.07418.0880.0550.0550.0000.0000.0000.000
57A66HIS10.8850.91220.3690.4580.4580.0000.0000.0000.000
58A67LEU0-0.023-0.01223.7280.0310.0310.0000.0000.0000.000
59A68HIS10.8840.94822.8710.2370.2370.0000.0000.0000.000
60A69ARG10.8360.90327.9430.1220.1220.0000.0000.0000.000
61A70LEU00.0060.02026.2690.0050.0050.0000.0000.0000.000
62A71CYS0-0.071-0.04630.625-0.003-0.0030.0000.0000.0000.000
63A72SER0-0.020-0.02031.1650.0070.0070.0000.0000.0000.000
64A73ASP-1-0.825-0.91628.450-0.023-0.0230.0000.0000.0000.000
65A74GLU-1-0.854-0.94822.996-0.069-0.0690.0000.0000.0000.000
66A75THR0-0.073-0.03622.063-0.019-0.0190.0000.0000.0000.000
67A76TRP0-0.019-0.03016.9370.0030.0030.0000.0000.0000.000
68A77MET0-0.025-0.02117.224-0.010-0.0100.0000.0000.0000.000
69A78TYR0-0.026-0.0377.2110.3390.3390.0000.0000.0000.000
70A79HIS0-0.059-0.02311.7080.2080.2080.0000.0000.0000.000
71A80ALA0-0.027-0.0236.7230.5680.5680.0000.0000.0000.000
72A81GLY00.0010.0124.127-0.569-0.506-0.001-0.006-0.0560.000
73A82ASP-1-0.724-0.8455.210-4.469-4.421-0.0010.000-0.0460.000
74A83PRO0-0.0110.0097.1310.4850.4850.0000.0000.0000.000
75A84LEU00.0020.01110.789-0.209-0.2090.0000.0000.0000.000
76A85GLN00.0010.01213.2550.1840.1840.0000.0000.0000.000
77A86LEU00.008-0.00216.320-0.015-0.0150.0000.0000.0000.000
78A87HIS00.0000.00218.8910.0660.0660.0000.0000.0000.000
79A88VAL00.0440.00622.5740.0150.0150.0000.0000.0000.000
80A89ILE0-0.004-0.00125.4900.0050.0050.0000.0000.0000.000
81A90LEU0-0.0090.00328.4540.0110.0110.0000.0000.0000.000
82A91LYS10.9500.98031.2400.0710.0710.0000.0000.0000.000
83A92ASP-1-0.789-0.89334.614-0.072-0.0720.0000.0000.0000.000
84A93PRO00.016-0.01433.180-0.003-0.0030.0000.0000.0000.000
85A94GLN00.0520.03732.7850.0000.0000.0000.0000.0000.000
86A95ASP-1-0.774-0.85927.984-0.090-0.0900.0000.0000.0000.000
87A96GLU-1-0.912-0.97230.526-0.038-0.0380.0000.0000.0000.000
88A97ASP-1-0.946-0.96333.324-0.014-0.0140.0000.0000.0000.000
89A98ARG10.8170.92625.8410.0360.0360.0000.0000.0000.000
90A117ARG10.9800.99142.6410.0540.0540.0000.0000.0000.000
91A118PRO0-0.005-0.01841.4340.0010.0010.0000.0000.0000.000
92A119LYS10.8110.89137.7900.0720.0720.0000.0000.0000.000
93A120TYR0-0.046-0.03832.687-0.003-0.0030.0000.0000.0000.000
94A121GLN0-0.018-0.01034.506-0.016-0.0160.0000.0000.0000.000
95A122VAL0-0.0070.00130.546-0.009-0.0090.0000.0000.0000.000
96A123TYR0-0.030-0.01223.1600.0030.0030.0000.0000.0000.000
97A124ARG10.8150.89325.5960.1220.1220.0000.0000.0000.000
98A125ARG10.9160.96716.8470.5640.5640.0000.0000.0000.000
99A126VAL00.004-0.00319.3270.0220.0220.0000.0000.0000.000
100A127LEU0-0.0110.00814.228-0.049-0.0490.0000.0000.0000.000
101A128VAL00.0210.01014.3750.0740.0740.0000.0000.0000.000
102A129GLY00.035-0.00311.966-0.143-0.1430.0000.0000.0000.000
103A130ALA00.010-0.00510.6080.1180.1180.0000.0000.0000.000
104A131ARG10.7960.9168.0831.0561.0560.0000.0000.0000.000
105A132VAL00.0280.00013.675-0.094-0.0940.0000.0000.0000.000
106A133GLU-1-0.900-0.95515.0000.0160.0160.0000.0000.0000.000
107A134ARG10.8510.92912.0290.4530.4530.0000.0000.0000.000
108A135GLY0-0.0060.00317.523-0.062-0.0620.0000.0000.0000.000
109A136GLU-1-0.855-0.91812.200-0.447-0.4470.0000.0000.0000.000
110A137LEU0-0.007-0.00816.4700.0810.0810.0000.0000.0000.000
111A138LEU00.0200.01014.076-0.018-0.0180.0000.0000.0000.000
112A139GLN0-0.038-0.02016.6310.0110.0110.0000.0000.0000.000
113A140TYR00.007-0.01219.476-0.032-0.0320.0000.0000.0000.000
114A141THR00.0000.01321.6410.0120.0120.0000.0000.0000.000
115A142VAL0-0.0140.00022.941-0.014-0.0140.0000.0000.0000.000
116A143PRO00.0360.01725.6620.0120.0120.0000.0000.0000.000
117A144GLY00.0590.03129.439-0.018-0.0180.0000.0000.0000.000
118A145GLY0-0.044-0.02231.4660.0010.0010.0000.0000.0000.000
119A146ALA0-0.0160.00628.426-0.010-0.0100.0000.0000.0000.000
120A147ILE0-0.0180.00428.7530.0010.0010.0000.0000.0000.000
121A148PHE0-0.043-0.01922.781-0.016-0.0160.0000.0000.0000.000
122A149GLY00.0630.03322.3990.0080.0080.0000.0000.0000.000
123A150SER0-0.004-0.00317.132-0.023-0.0230.0000.0000.0000.000
124A151SER00.0320.00516.105-0.016-0.0160.0000.0000.0000.000
125A152VAL00.0170.0099.4950.0610.0610.0000.0000.0000.000
126A153ALA00.0000.00611.9530.0440.0440.0000.0000.0000.000
127A154ALA0-0.005-0.00510.657-0.312-0.3120.0000.0000.0000.000
128A155ASP-1-0.899-0.95110.203-1.811-1.8110.0000.0000.0000.000
129A156GLY00.0280.01211.7010.1420.1420.0000.0000.0000.000
130A157ALA0-0.068-0.05210.279-0.306-0.3060.0000.0000.0000.000
131A158ASP-1-0.897-0.9599.680-1.112-1.1120.0000.0000.0000.000
132A159GLY00.0040.0158.5310.0280.0280.0000.0000.0000.000
133A160GLN0-0.057-0.0265.0360.5930.5930.0000.0000.0000.000
134A161ALA0-0.079-0.0462.407-4.091-3.3240.870-0.512-1.125-0.001
135A162GLY00.0340.0243.2981.1811.0270.0080.227-0.0810.000
136A163TYR0-0.077-0.0433.7821.0351.3130.002-0.090-0.1900.000
137A164SER00.002-0.0017.154-0.219-0.2190.0000.0000.0000.000
138A165LEU0-0.033-0.0119.0490.1000.1000.0000.0000.0000.000
139A166VAL00.0400.01210.8790.1370.1370.0000.0000.0000.000
140A167SER00.0000.00214.0170.0740.0740.0000.0000.0000.000
141A168CYS0-0.0220.00717.465-0.025-0.0250.0000.0000.0000.000
142A169ILE0-0.007-0.02020.5440.0340.0340.0000.0000.0000.000
143A170VAL00.0110.02324.075-0.017-0.0170.0000.0000.0000.000
144A171SER0-0.074-0.04827.1240.0240.0240.0000.0000.0000.000
145A172PRO00.052-0.00430.352-0.003-0.0030.0000.0000.0000.000
146A173GLY0-0.066-0.02230.336-0.008-0.0080.0000.0000.0000.000
147A174PHE00.0320.00727.856-0.013-0.0130.0000.0000.0000.000
148A175ASP-1-0.815-0.89729.9880.0040.0040.0000.0000.0000.000
149A176TYR00.0210.01126.456-0.001-0.0010.0000.0000.0000.000
150A177ARG10.7670.85732.406-0.001-0.0010.0000.0000.0000.000
151A178ASP-1-0.748-0.83933.088-0.028-0.0280.0000.0000.0000.000
152A179PHE0-0.067-0.02326.302-0.008-0.0080.0000.0000.0000.000
153A180GLU-1-0.837-0.89731.382-0.124-0.1240.0000.0000.0000.000
154A181ILE0-0.030-0.01926.938-0.013-0.0130.0000.0000.0000.000
155A182PHE0-0.013-0.00929.7670.0100.0100.0000.0000.0000.000
156A183THR0-0.003-0.01130.300-0.016-0.0160.0000.0000.0000.000
157A184GLN00.024-0.00828.1080.0260.0260.0000.0000.0000.000
158A185ALA00.0160.00832.4290.0100.0100.0000.0000.0000.000
159A186GLN00.0380.03134.7500.0010.0010.0000.0000.0000.000
160A187LEU0-0.003-0.01330.8090.0100.0100.0000.0000.0000.000
161A188MET0-0.042-0.01434.1410.0010.0010.0000.0000.0000.000
162A189GLU-1-0.939-0.95036.354-0.150-0.1500.0000.0000.0000.000
163A190LEU0-0.086-0.03237.5130.0110.0110.0000.0000.0000.000
164A191TYR0-0.062-0.05134.2840.0100.0100.0000.0000.0000.000
165A192PRO00.0950.04634.865-0.016-0.0160.0000.0000.0000.000
166A193GLN0-0.012-0.01134.712-0.011-0.0110.0000.0000.0000.000
167A194HIS0-0.063-0.03630.668-0.021-0.0210.0000.0000.0000.000
168A195GLU-1-0.813-0.89830.627-0.286-0.2860.0000.0000.0000.000
169A196ALA0-0.013-0.00227.811-0.016-0.0160.0000.0000.0000.000
170A197VAL00.0320.01024.797-0.029-0.0290.0000.0000.0000.000
171A198ILE0-0.0040.00426.477-0.020-0.0200.0000.0000.0000.000
172A199LYS10.8670.90228.1970.2790.2790.0000.0000.0000.000
173A200GLN0-0.065-0.00521.300-0.051-0.0510.0000.0000.0000.000
174A201MET0-0.016-0.01219.979-0.053-0.0530.0000.0000.0000.000
175A202ALA0-0.0160.00524.3410.0140.0140.0000.0000.0000.000
176A203TYR0-0.033-0.02624.660-0.038-0.0380.0000.0000.0000.000
177A204GLU-1-0.928-0.96128.057-0.267-0.2670.0000.0000.0000.000