FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 3J3KL

Calculation Name: 2B1E-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2B1E

Chain ID: A

ChEMBL ID:

UniProt ID: P19658

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 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 545
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -9670800.081895
FMO2-HF: Nuclear repulsion 9451184.079513
FMO2-HF: Total energy -219616.002382
FMO2-MP2: Total energy -220257.666246


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:67:THR)


Summations of interaction energy for fragment #1(A:67:THR)
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.
-0.8851.976-0.002-0.905-1.9550.005
Interaction energy analysis for fragmet #1(A:67:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.026 / q_NPA : -0.021
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].
3A69ASN00.018-0.0233.652-0.2241.795-0.004-0.740-1.2750.005
4A70SER00.0020.0015.366-0.372-0.280-0.001-0.005-0.0860.000
5A71VAL0-0.016-0.0035.883-0.328-0.3280.0000.0000.0000.000
6A72ALA00.0000.0284.055-0.378-0.251-0.001-0.018-0.1080.000
7A73SER00.0420.0136.185-0.194-0.1940.0000.0000.0000.000
8A74VAL00.0870.0417.9720.1170.1170.0000.0000.0000.000
9A75LYS10.9890.99510.0900.1320.1320.0000.0000.0000.000
10A76ASP-1-0.925-0.9715.512-0.373-0.3730.0000.0000.0000.000
11A77LEU00.0010.0044.516-0.157-0.043-0.001-0.006-0.1070.000
12A78ALA00.0530.0276.7390.0010.0010.0000.0000.0000.000
13A79ASN0-0.046-0.0267.7670.0280.0280.0000.0000.0000.000
14A80GLU-1-0.902-0.9663.680-1.863-1.3540.005-0.136-0.3790.000
15A81ALA00.0630.0296.832-0.038-0.0380.0000.0000.0000.000
16A82SER0-0.015-0.0099.766-0.118-0.1180.0000.0000.0000.000
17A83LYS10.8160.9146.0980.8030.8030.0000.0000.0000.000
18A84TYR00.0190.0045.139-0.422-0.4220.0000.0000.0000.000
19A85GLU-1-0.780-0.88111.3970.1570.1570.0000.0000.0000.000
20A86ILE0-0.021-0.00714.246-0.039-0.0390.0000.0000.0000.000
21A87ILE0-0.075-0.04411.688-0.033-0.0330.0000.0000.0000.000
22A88LEU00.0330.01314.892-0.023-0.0230.0000.0000.0000.000
23A89GLN0-0.031-0.00717.251-0.004-0.0040.0000.0000.0000.000
24A90LYS10.8540.94216.7720.0390.0390.0000.0000.0000.000
25A91GLY0-0.0010.00920.893-0.009-0.0090.0000.0000.0000.000
26A92ILE00.0360.01121.813-0.008-0.0080.0000.0000.0000.000
27A93ASN0-0.0010.01422.900-0.004-0.0040.0000.0000.0000.000
28A94GLN0-0.023-0.00721.893-0.019-0.0190.0000.0000.0000.000
29A95VAL0-0.0330.00017.222-0.015-0.0150.0000.0000.0000.000
30A96GLY00.0440.03719.522-0.013-0.0130.0000.0000.0000.000
31A97LEU00.0210.00120.0220.0130.0130.0000.0000.0000.000
32A98LYS10.9550.98419.271-0.010-0.0100.0000.0000.0000.000
33A99GLN00.0180.00116.0230.0300.0300.0000.0000.0000.000
34A100TYR00.0190.00915.4200.0350.0350.0000.0000.0000.000
35A101THR00.0140.01016.5400.0300.0300.0000.0000.0000.000
36A102GLN0-0.0180.00211.9390.0870.0870.0000.0000.0000.000
37A103VAL0-0.025-0.01311.6380.0710.0710.0000.0000.0000.000
38A104VAL00.000-0.00812.2940.1020.1020.0000.0000.0000.000
39A105HIS00.0770.04113.1630.0630.0630.0000.0000.0000.000
40A106LYS10.9060.9715.227-0.687-0.6870.0000.0000.0000.000
41A107LEU0-0.051-0.0259.5040.2410.2410.0000.0000.0000.000
42A108ASP-1-0.832-0.93111.4010.5040.5040.0000.0000.0000.000
43A109ASP-1-0.899-0.94310.0350.6420.6420.0000.0000.0000.000
44A110MET0-0.101-0.0415.601-0.027-0.0270.0000.0000.0000.000
45A111LEU0-0.021-0.0289.258-0.027-0.0270.0000.0000.0000.000
46A112GLU-1-0.904-0.94612.7400.4280.4280.0000.0000.0000.000
47A113ASP-1-0.873-0.9338.8691.2451.2450.0000.0000.0000.000
48A114ILE0-0.161-0.0829.382-0.027-0.0270.0000.0000.0000.000
49A115GLN00.0340.01011.838-0.092-0.0920.0000.0000.0000.000
50A116SER00.0570.04114.932-0.053-0.0530.0000.0000.0000.000
51A117GLY00.0070.00616.6770.0020.0020.0000.0000.0000.000
52A118GLN0-0.149-0.09018.037-0.039-0.0390.0000.0000.0000.000
53A119ALA0-0.0040.01413.354-0.013-0.0130.0000.0000.0000.000
54A120ASN0-0.028-0.02715.2570.0110.0110.0000.0000.0000.000
55A121ARG10.8500.9388.285-0.947-0.9470.0000.0000.0000.000
56A122GLU-1-0.928-0.95615.7030.2190.2190.0000.0000.0000.000
57A123GLU-1-0.846-0.90418.1850.3070.3070.0000.0000.0000.000
58A124ASN0-0.021-0.01017.746-0.018-0.0180.0000.0000.0000.000
59A125SER00.025-0.01019.5590.0220.0220.0000.0000.0000.000
60A126GLU-1-0.946-0.97114.6090.2730.2730.0000.0000.0000.000
61A127PHE00.0360.01113.7690.0390.0390.0000.0000.0000.000
62A128HIS0-0.028-0.04115.9770.0170.0170.0000.0000.0000.000
63A129GLY00.0000.00717.932-0.003-0.0030.0000.0000.0000.000
64A130ILE0-0.013-0.0119.989-0.007-0.0070.0000.0000.0000.000
65A131LEU0-0.0030.01814.5340.0360.0360.0000.0000.0000.000
66A132THR00.0370.02516.073-0.018-0.0180.0000.0000.0000.000
67A133HIS0-0.144-0.07814.1110.0120.0120.0000.0000.0000.000
68A134LEU00.010-0.00510.780-0.022-0.0220.0000.0000.0000.000
69A135GLU-1-0.852-0.91514.9390.2970.2970.0000.0000.0000.000
70A136GLN0-0.053-0.04618.208-0.037-0.0370.0000.0000.0000.000
71A137LEU0-0.035-0.01114.028-0.041-0.0410.0000.0000.0000.000
72A138ILE00.0790.06114.555-0.039-0.0390.0000.0000.0000.000
73A139LYS10.9270.97118.064-0.239-0.2390.0000.0000.0000.000
74A140ARG10.8280.90419.222-0.216-0.2160.0000.0000.0000.000
75A141SER00.002-0.00818.340-0.030-0.0300.0000.0000.0000.000
76A142GLU-1-0.796-0.85920.2940.2280.2280.0000.0000.0000.000
77A143ALA0-0.043-0.03022.586-0.020-0.0200.0000.0000.0000.000
78A144GLN0-0.039-0.02323.233-0.025-0.0250.0000.0000.0000.000
79A145LEU00.0340.01720.820-0.017-0.0170.0000.0000.0000.000
80A146ARG10.8890.93425.087-0.162-0.1620.0000.0000.0000.000
81A147VAL0-0.024-0.00228.303-0.010-0.0100.0000.0000.0000.000
82A148TYR0-0.039-0.05127.128-0.010-0.0100.0000.0000.0000.000
83A149PHE00.0120.00628.787-0.008-0.0080.0000.0000.0000.000
84A150ILE00.0350.00830.344-0.007-0.0070.0000.0000.0000.000
85A151SER0-0.051-0.01632.215-0.008-0.0080.0000.0000.0000.000
86A152ILE00.0320.02229.835-0.006-0.0060.0000.0000.0000.000
87A153LEU00.0190.05034.041-0.005-0.0050.0000.0000.0000.000
88A154ASN0-0.100-0.03836.343-0.007-0.0070.0000.0000.0000.000
89A155SER0-0.059-0.04836.882-0.004-0.0040.0000.0000.0000.000
90A156ILE0-0.0080.01438.842-0.004-0.0040.0000.0000.0000.000
91A157LYS10.8470.91240.256-0.028-0.0280.0000.0000.0000.000
92A158PRO00.001-0.02344.776-0.001-0.0010.0000.0000.0000.000
93A159PHE0-0.011-0.00947.202-0.001-0.0010.0000.0000.0000.000
94A160ASP-1-0.800-0.90650.6170.0190.0190.0000.0000.0000.000
95A161PRO00.032-0.00852.166-0.001-0.0010.0000.0000.0000.000
96A162GLN00.0240.00754.066-0.001-0.0010.0000.0000.0000.000
97A163ILE0-0.0190.00255.157-0.001-0.0010.0000.0000.0000.000
98A164ASN0-0.026-0.01650.8970.0000.0000.0000.0000.0000.000
99A165ILE00.0570.04054.751-0.001-0.0010.0000.0000.0000.000
100A166THR0-0.051-0.01657.353-0.001-0.0010.0000.0000.0000.000
101A167LYS10.8360.90356.556-0.010-0.0100.0000.0000.0000.000
102A168LYS10.9330.97856.987-0.010-0.0100.0000.0000.0000.000
103A169MET0-0.050-0.02352.160-0.001-0.0010.0000.0000.0000.000
104A170PRO00.0300.00748.6720.0010.0010.0000.0000.0000.000
105A171PHE0-0.035-0.01347.673-0.001-0.0010.0000.0000.0000.000
106A172PRO0-0.009-0.00544.606-0.001-0.0010.0000.0000.0000.000
107A173TYR0-0.052-0.05639.1350.0030.0030.0000.0000.0000.000
108A174TYR0-0.068-0.05236.3920.0000.0000.0000.0000.0000.000
109A175GLU-1-0.915-0.94434.7910.0140.0140.0000.0000.0000.000
110A176ASP-1-0.827-0.93334.3230.0190.0190.0000.0000.0000.000
111A177GLN0-0.017-0.02130.8860.0060.0060.0000.0000.0000.000
112A178GLN00.0010.00130.5260.0050.0050.0000.0000.0000.000
113A179LEU00.0310.02331.5980.0070.0070.0000.0000.0000.000
114A180GLY00.0230.02129.3450.0050.0050.0000.0000.0000.000
115A181ALA0-0.046-0.03426.9350.0080.0080.0000.0000.0000.000
116A182LEU0-0.016-0.01527.4260.0100.0100.0000.0000.0000.000
117A183SER00.0370.00128.9210.0060.0060.0000.0000.0000.000
118A184TRP0-0.013-0.02018.935-0.002-0.0020.0000.0000.0000.000
119A185ILE0-0.027-0.01524.0210.0140.0140.0000.0000.0000.000
120A186LEU0-0.010-0.00225.6450.0120.0120.0000.0000.0000.000
121A187ASP-1-0.888-0.94424.0050.1010.1010.0000.0000.0000.000
122A188TYR0-0.095-0.09118.0210.0130.0130.0000.0000.0000.000
123A189PHE0-0.014-0.02822.3750.0140.0140.0000.0000.0000.000
124A190HIS0-0.094-0.04524.7920.0010.0010.0000.0000.0000.000
125A191GLY0-0.031-0.00921.9750.0010.0010.0000.0000.0000.000
126A192ASN00.0080.01418.8530.0350.0350.0000.0000.0000.000
127A193SER0-0.023-0.00722.240-0.005-0.0050.0000.0000.0000.000
128A194GLU-1-0.801-0.89224.8790.1650.1650.0000.0000.0000.000
129A195GLY00.0200.00327.393-0.010-0.0100.0000.0000.0000.000
130A196SER00.004-0.00829.396-0.005-0.0050.0000.0000.0000.000
131A197ILE00.0290.02928.754-0.008-0.0080.0000.0000.0000.000
132A198ILE0-0.019-0.00528.657-0.008-0.0080.0000.0000.0000.000
133A199GLN00.0310.01430.925-0.013-0.0130.0000.0000.0000.000
134A200ASP-1-0.883-0.94533.8430.0770.0770.0000.0000.0000.000
135A201ILE0-0.048-0.01531.413-0.006-0.0060.0000.0000.0000.000
136A202LEU00.0000.00434.072-0.006-0.0060.0000.0000.0000.000
137A203VAL00.020-0.00135.721-0.006-0.0060.0000.0000.0000.000
138A204GLY00.0080.00638.535-0.005-0.0050.0000.0000.0000.000
139A205GLU-1-0.867-0.94836.5180.0510.0510.0000.0000.0000.000
140A206ARG10.8240.89138.695-0.044-0.0440.0000.0000.0000.000
141A207SER0-0.002-0.00341.222-0.004-0.0040.0000.0000.0000.000
142A208LYS10.8450.92740.719-0.052-0.0520.0000.0000.0000.000
143A209LEU0-0.023-0.00541.865-0.003-0.0030.0000.0000.0000.000
144A210ILE00.0600.02144.434-0.003-0.0030.0000.0000.0000.000
145A211LEU0-0.0040.00547.202-0.002-0.0020.0000.0000.0000.000
146A212LYS10.9000.95345.684-0.036-0.0360.0000.0000.0000.000
147A213CYS0-0.0530.01547.945-0.002-0.0020.0000.0000.0000.000
148A214MET00.001-0.00550.907-0.002-0.0020.0000.0000.0000.000
149A215ALA0-0.0080.00252.840-0.001-0.0010.0000.0000.0000.000
150A216PHE0-0.048-0.02251.730-0.001-0.0010.0000.0000.0000.000
151A217LEU0-0.056-0.02856.173-0.001-0.0010.0000.0000.0000.000
152A218GLU-1-0.967-0.97357.3290.0240.0240.0000.0000.0000.000
153A219PRO0-0.019-0.00558.8980.0000.0000.0000.0000.0000.000
154A220PHE0-0.045-0.01961.323-0.001-0.0010.0000.0000.0000.000
155A221ALA00.0050.01761.533-0.001-0.0010.0000.0000.0000.000
156A234LYS10.8730.92372.903-0.011-0.0110.0000.0000.0000.000
157A235GLY00.002-0.00469.6190.0000.0000.0000.0000.0000.000
158A236SER0-0.047-0.02269.2510.0000.0000.0000.0000.0000.000
159A237SER0-0.032-0.00767.3120.0000.0000.0000.0000.0000.000
160A238GLY00.0950.04864.3910.0000.0000.0000.0000.0000.000
161A239MET0-0.020-0.01660.4620.0010.0010.0000.0000.0000.000
162A240ASN0-0.0060.00561.8710.0010.0010.0000.0000.0000.000
163A241SER00.0750.04259.9780.0000.0000.0000.0000.0000.000
164A242TYR00.0410.02655.9620.0010.0010.0000.0000.0000.000
165A243THR00.0330.01956.8480.0010.0010.0000.0000.0000.000
166A244GLU-1-0.892-0.95256.6250.0160.0160.0000.0000.0000.000
167A245ALA0-0.010-0.01554.0730.0000.0000.0000.0000.0000.000
168A246LEU0-0.015-0.00951.7010.0010.0010.0000.0000.0000.000
169A247LEU0-0.009-0.00751.8940.0010.0010.0000.0000.0000.000
170A248GLY00.0230.02351.2110.0000.0000.0000.0000.0000.000
171A249PHE0-0.001-0.02647.0920.0010.0010.0000.0000.0000.000
172A250ILE0-0.019-0.00147.0150.0020.0020.0000.0000.0000.000
173A251ALA0-0.020-0.01247.0410.0010.0010.0000.0000.0000.000
174A252ASN00.022-0.00444.8820.0000.0000.0000.0000.0000.000
175A253GLU-1-0.739-0.84742.0510.0410.0410.0000.0000.0000.000
176A254LYN0-0.059-0.02241.8250.0020.0020.0000.0000.0000.000
177A255SER0-0.006-0.00341.7190.0010.0010.0000.0000.0000.000
178A256LEU00.0550.03937.2040.0010.0010.0000.0000.0000.000
179A257VAL0-0.042-0.02437.3390.0030.0030.0000.0000.0000.000
180A258ASP-1-0.901-0.97636.7150.0410.0410.0000.0000.0000.000
181A259ASP-1-0.866-0.90636.0910.0300.0300.0000.0000.0000.000
182A260LEU0-0.087-0.04132.6800.0020.0020.0000.0000.0000.000
183A261TYR0-0.0070.01731.6880.0080.0080.0000.0000.0000.000
184A262SER00.0470.02530.063-0.005-0.0050.0000.0000.0000.000
185A263GLN0-0.005-0.02632.630-0.001-0.0010.0000.0000.0000.000
186A264TYR0-0.040-0.03535.103-0.002-0.0020.0000.0000.0000.000
187A265THR0-0.0100.01132.8310.0040.0040.0000.0000.0000.000
188A266GLU-1-0.895-0.96434.6030.0740.0740.0000.0000.0000.000
189A267SER00.0670.04833.873-0.004-0.0040.0000.0000.0000.000
190A268LYS10.8570.94636.330-0.048-0.0480.0000.0000.0000.000
191A269PRO0-0.025-0.01938.293-0.002-0.0020.0000.0000.0000.000
192A270HIS00.0630.04538.333-0.004-0.0040.0000.0000.0000.000
193A271VAL00.0090.00236.122-0.001-0.0010.0000.0000.0000.000
194A272LEU00.0210.00239.435-0.002-0.0020.0000.0000.0000.000
195A273SER00.0120.00942.343-0.003-0.0030.0000.0000.0000.000
196A274GLN00.0080.00239.710-0.001-0.0010.0000.0000.0000.000
197A275ILE0-0.0290.00539.463-0.001-0.0010.0000.0000.0000.000
198A276LEU00.010-0.00743.779-0.003-0.0030.0000.0000.0000.000
199A277SER0-0.010-0.01146.998-0.003-0.0030.0000.0000.0000.000
200A278PRO00.000-0.00446.283-0.002-0.0020.0000.0000.0000.000
201A279LEU00.0330.01547.475-0.002-0.0020.0000.0000.0000.000
202A280ILE0-0.0040.00350.997-0.002-0.0020.0000.0000.0000.000
203A281SER0-0.022-0.00652.591-0.002-0.0020.0000.0000.0000.000
204A282ALA0-0.016-0.01053.596-0.001-0.0010.0000.0000.0000.000
205A283TYR00.004-0.02455.241-0.001-0.0010.0000.0000.0000.000
206A284ALA00.029-0.00157.016-0.001-0.0010.0000.0000.0000.000
207A285LYS10.9440.97958.347-0.030-0.0300.0000.0000.0000.000
208A286LEU00.0180.01759.358-0.001-0.0010.0000.0000.0000.000
209A287PHE00.0120.00061.155-0.001-0.0010.0000.0000.0000.000
210A288GLY00.0500.01662.858-0.001-0.0010.0000.0000.0000.000
211A289ALA0-0.061-0.02964.336-0.001-0.0010.0000.0000.0000.000
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