FMODB

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

Last updated: 2024-07-23

All entries: 37478

Number of unique PDB entries: 7783

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FMODB ID: 3J36L

Calculation Name: 2R3Y-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2R3Y

Chain ID: A

ChEMBL ID:

UniProt ID: P0AEE3

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 285
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3468888.986827
FMO2-HF: Nuclear repulsion 3364091.984343
FMO2-HF: Total energy -104797.002484
FMO2-MP2: Total energy -105106.430285


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:42:MET)


Summations of interaction energy for fragment #1(A:42: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.
0.3812.446-0.017-0.891-1.1560.003
Interaction energy analysis for fragmet #1(A:42:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.033 / q_NPA : 0.001
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].
3A44PRO0-0.0100.0073.806-0.4291.636-0.017-0.891-1.1560.003
4A45ALA00.0530.0355.8450.1020.1020.0000.0000.0000.000
5A46SER0-0.005-0.0178.2480.0680.0680.0000.0000.0000.000
6A47TYR00.1030.05611.256-0.001-0.0010.0000.0000.0000.000
7A48ASN00.0270.00813.7670.0300.0300.0000.0000.0000.000
8A49LEU0-0.0080.00714.5890.0350.0350.0000.0000.0000.000
9A50ALA00.0330.01416.2770.0340.0340.0000.0000.0000.000
10A51VAL00.0200.01318.3910.0240.0240.0000.0000.0000.000
11A52ARG10.8790.91714.5720.4480.4480.0000.0000.0000.000
12A53ARG10.8510.91919.0180.2680.2680.0000.0000.0000.000
13A54ALA00.0470.02522.3550.0160.0160.0000.0000.0000.000
14A55ALA00.0010.01523.3620.0140.0140.0000.0000.0000.000
15A56PRO0-0.013-0.01124.2040.0140.0140.0000.0000.0000.000
16A57ALA00.0020.00927.3420.0110.0110.0000.0000.0000.000
17A58VAL0-0.043-0.00127.8820.0090.0090.0000.0000.0000.000
18A59VAL0-0.033-0.02030.478-0.004-0.0040.0000.0000.0000.000
19A60ASN00.0500.02531.654-0.002-0.0020.0000.0000.0000.000
20A61VAL0-0.010-0.01834.7240.0020.0020.0000.0000.0000.000
21A62TYR0-0.056-0.03435.9930.0000.0000.0000.0000.0000.000
22A63ASN00.0080.01341.1080.0020.0020.0000.0000.0000.000
23A64ARG10.9000.92144.1460.0490.0490.0000.0000.0000.000
24A65GLY00.0290.01847.0730.0000.0000.0000.0000.0000.000
25A66LEU0-0.003-0.03050.7360.0000.0000.0000.0000.0000.000
26A67ASN0-0.040-0.01653.9270.0020.0020.0000.0000.0000.000
27A68THR0-0.0030.00349.5260.0010.0010.0000.0000.0000.000
28A69ASN0-0.026-0.01651.3040.0020.0020.0000.0000.0000.000
29A70SER00.018-0.01754.3150.0000.0000.0000.0000.0000.000
30A71HIS0-0.050-0.00755.7890.0010.0010.0000.0000.0000.000
31A72ASN0-0.026-0.00655.4800.0010.0010.0000.0000.0000.000
32A73GLN0-0.041-0.00751.5370.0010.0010.0000.0000.0000.000
33A74LEU00.002-0.00148.5020.0000.0000.0000.0000.0000.000
34A75GLU-1-0.882-0.94547.104-0.037-0.0370.0000.0000.0000.000
35A76ILE0-0.047-0.02541.6810.0000.0000.0000.0000.0000.000
36A77ARG10.8890.97244.9520.0400.0400.0000.0000.0000.000
37A78THR00.013-0.01341.7720.0010.0010.0000.0000.0000.000
38A79LEU0-0.046-0.01436.655-0.001-0.0010.0000.0000.0000.000
39A80GLY0-0.0090.00036.3970.0020.0020.0000.0000.0000.000
40A81SER0-0.033-0.00932.677-0.006-0.0060.0000.0000.0000.000
41A82GLY00.0450.03034.1070.0060.0060.0000.0000.0000.000
42A83VAL0-0.023-0.00231.416-0.008-0.0080.0000.0000.0000.000
43A84ILE0-0.009-0.00333.2390.0070.0070.0000.0000.0000.000
44A85MET00.0030.00133.418-0.007-0.0070.0000.0000.0000.000
45A86ASP-1-0.745-0.87835.113-0.073-0.0730.0000.0000.0000.000
46A87GLN00.051-0.00635.5240.0000.0000.0000.0000.0000.000
47A88ARG10.8310.93137.9020.0650.0650.0000.0000.0000.000
48A89GLY00.0270.01139.4840.0030.0030.0000.0000.0000.000
49A90TYR0-0.049-0.00840.3180.0020.0020.0000.0000.0000.000
50A91ILE00.006-0.00637.006-0.005-0.0050.0000.0000.0000.000
51A92ILE00.0110.02936.7280.0050.0050.0000.0000.0000.000
52A93THR00.011-0.01737.098-0.003-0.0030.0000.0000.0000.000
53A94ASN00.0270.00838.1370.0000.0000.0000.0000.0000.000
54A95LYS10.8650.92940.4180.0390.0390.0000.0000.0000.000
55A96HIS0-0.110-0.08239.3980.0000.0000.0000.0000.0000.000
56A97VAL0-0.0140.00638.8450.0010.0010.0000.0000.0000.000
57A98ILE0-0.026-0.03042.2630.0000.0000.0000.0000.0000.000
58A99ASN00.0420.02844.9000.0020.0020.0000.0000.0000.000
59A100ASP-1-0.931-0.97148.155-0.035-0.0350.0000.0000.0000.000
60A101ALA0-0.044-0.00447.3910.0000.0000.0000.0000.0000.000
61A102ASP-1-0.805-0.88349.445-0.035-0.0350.0000.0000.0000.000
62A103GLN00.005-0.00546.561-0.001-0.0010.0000.0000.0000.000
63A104ILE0-0.0060.01542.908-0.001-0.0010.0000.0000.0000.000
64A105ILE0-0.0220.00040.1230.0000.0000.0000.0000.0000.000
65A106VAL00.0070.00037.071-0.002-0.0020.0000.0000.0000.000
66A107ALA0-0.008-0.00135.3920.0010.0010.0000.0000.0000.000
67A108LEU0-0.003-0.01332.488-0.004-0.0040.0000.0000.0000.000
68A109GLN00.000-0.00127.1230.0010.0010.0000.0000.0000.000
69A110ASP-1-0.879-0.91529.182-0.111-0.1110.0000.0000.0000.000
70A111GLY00.0180.00830.5330.0030.0030.0000.0000.0000.000
71A112ARG10.7680.86933.3440.1030.1030.0000.0000.0000.000
72A113VAL00.015-0.00236.215-0.002-0.0020.0000.0000.0000.000
73A114PHE0-0.033-0.02237.4310.0020.0020.0000.0000.0000.000
74A115GLU-1-0.859-0.92341.659-0.048-0.0480.0000.0000.0000.000
75A116ALA0-0.062-0.04342.522-0.001-0.0010.0000.0000.0000.000
76A117LEU00.0000.00844.5630.0020.0020.0000.0000.0000.000
77A118LEU00.0140.01245.976-0.003-0.0030.0000.0000.0000.000
78A119VAL0-0.039-0.03245.6080.0020.0020.0000.0000.0000.000
79A120GLY00.0770.02447.1780.0020.0020.0000.0000.0000.000
80A121SER0-0.071-0.03546.148-0.002-0.0020.0000.0000.0000.000
81A122ASP-1-0.716-0.82045.652-0.039-0.0390.0000.0000.0000.000
82A123SER00.000-0.01546.073-0.002-0.0020.0000.0000.0000.000
83A124LEU0-0.019-0.00346.7990.0000.0000.0000.0000.0000.000
84A125THR0-0.029-0.06742.264-0.001-0.0010.0000.0000.0000.000
85A126ASP-1-0.748-0.85941.777-0.050-0.0500.0000.0000.0000.000
86A127LEU0-0.0040.02238.654-0.004-0.0040.0000.0000.0000.000
87A128ALA00.015-0.01041.6300.0040.0040.0000.0000.0000.000
88A129VAL0-0.0060.00441.537-0.004-0.0040.0000.0000.0000.000
89A130LEU0-0.0060.00240.3890.0030.0030.0000.0000.0000.000
90A131LYS10.8860.93742.4550.0570.0570.0000.0000.0000.000
91A132ILE00.0190.03638.4590.0030.0030.0000.0000.0000.000
92A133ASN0-0.019-0.02442.9930.0000.0000.0000.0000.0000.000
93A134ALA00.0050.00139.5460.0000.0000.0000.0000.0000.000
94A135THR0-0.0080.00241.2070.0010.0010.0000.0000.0000.000
95A136GLY00.013-0.01038.688-0.002-0.0020.0000.0000.0000.000
96A137GLY00.0000.02236.168-0.004-0.0040.0000.0000.0000.000
97A138LEU0-0.006-0.00434.8470.0000.0000.0000.0000.0000.000
98A139PRO0-0.0070.01829.909-0.002-0.0020.0000.0000.0000.000
99A140THR0-0.014-0.02030.6000.0060.0060.0000.0000.0000.000
100A141ILE00.0150.00528.356-0.010-0.0100.0000.0000.0000.000
101A142PRO0-0.0120.00224.9700.0070.0070.0000.0000.0000.000
102A143ILE00.0520.02327.8720.0010.0010.0000.0000.0000.000
103A144ASN0-0.039-0.01926.1210.0090.0090.0000.0000.0000.000
104A145ALA00.028-0.00329.4420.0020.0020.0000.0000.0000.000
105A146ARG10.9360.95730.9160.0770.0770.0000.0000.0000.000
106A147ARG10.8100.89923.5370.1310.1310.0000.0000.0000.000
107A148VAL0-0.017-0.00729.2250.0030.0030.0000.0000.0000.000
108A149PRO0-0.023-0.02728.081-0.003-0.0030.0000.0000.0000.000
109A150HIS0-0.0020.00426.3640.0110.0110.0000.0000.0000.000
110A151ILE0-0.002-0.00127.009-0.005-0.0050.0000.0000.0000.000
111A152GLY00.0030.00124.9000.0030.0030.0000.0000.0000.000
112A153ASP-1-0.895-0.93422.729-0.105-0.1050.0000.0000.0000.000
113A154VAL00.001-0.00317.7050.0010.0010.0000.0000.0000.000
114A155VAL0-0.070-0.04520.898-0.008-0.0080.0000.0000.0000.000
115A156LEU0-0.038-0.03218.523-0.008-0.0080.0000.0000.0000.000
116A157ALA00.0200.01422.7290.0070.0070.0000.0000.0000.000
117A158ILE0-0.053-0.02623.596-0.010-0.0100.0000.0000.0000.000
118A159GLY00.017-0.01726.6640.0100.0100.0000.0000.0000.000
119A160ASN00.0300.03428.887-0.012-0.0120.0000.0000.0000.000
120A161PRO00.0190.02628.7260.0080.0080.0000.0000.0000.000
121A162TYR0-0.008-0.03531.9480.0000.0000.0000.0000.0000.000
122A163ASN0-0.016-0.01033.912-0.002-0.0020.0000.0000.0000.000
123A164LEU0-0.0170.00129.0000.0010.0010.0000.0000.0000.000
124A165GLY00.0270.02229.068-0.005-0.0050.0000.0000.0000.000
125A166GLN0-0.041-0.03525.406-0.015-0.0150.0000.0000.0000.000
126A167THR0-0.042-0.01524.559-0.010-0.0100.0000.0000.0000.000
127A168ILE0-0.018-0.02320.429-0.001-0.0010.0000.0000.0000.000
128A169THR0-0.031-0.01922.062-0.006-0.0060.0000.0000.0000.000
129A170GLN0-0.051-0.04117.416-0.006-0.0060.0000.0000.0000.000
130A171GLY00.1100.05821.2600.0120.0120.0000.0000.0000.000
131A172ILE0-0.0060.00421.682-0.016-0.0160.0000.0000.0000.000
132A173ILE0-0.0470.00623.9890.0060.0060.0000.0000.0000.000
133A174SER00.022-0.01827.3210.0050.0050.0000.0000.0000.000
134A175ALA0-0.032-0.01829.4990.0060.0060.0000.0000.0000.000
135A176THR0-0.002-0.00232.284-0.004-0.0040.0000.0000.0000.000
136A177GLY00.003-0.00334.7240.0030.0030.0000.0000.0000.000
137A178ARG10.9290.97636.2480.0370.0370.0000.0000.0000.000
138A179ILE00.0680.03038.921-0.002-0.0020.0000.0000.0000.000
139A180GLY0-0.018-0.00639.160-0.001-0.0010.0000.0000.0000.000
140A181LEU0-0.012-0.01040.0270.0020.0020.0000.0000.0000.000
141A182ASN00.0100.00343.0790.0000.0000.0000.0000.0000.000
142A183PRO0-0.0110.00346.0560.0010.0010.0000.0000.0000.000
143A184THR00.0010.01147.9720.0000.0000.0000.0000.0000.000
144A185GLY00.0400.00346.072-0.001-0.0010.0000.0000.0000.000
145A186ARG10.9650.97944.7070.0250.0250.0000.0000.0000.000
146A187GLN0-0.002-0.00242.7250.0010.0010.0000.0000.0000.000
147A188ASN0-0.035-0.00638.760-0.002-0.0020.0000.0000.0000.000
148A189PHE00.0460.02036.656-0.003-0.0030.0000.0000.0000.000
149A190LEU0-0.053-0.03630.1620.0020.0020.0000.0000.0000.000
150A191GLN00.0190.00432.2080.0020.0020.0000.0000.0000.000
151A192THR0-0.066-0.05226.725-0.005-0.0050.0000.0000.0000.000
152A193ASP-1-0.790-0.88225.340-0.064-0.0640.0000.0000.0000.000
153A194ALA0-0.032-0.00524.768-0.002-0.0020.0000.0000.0000.000
154A195SER0-0.026-0.02825.5400.0050.0050.0000.0000.0000.000
155A196ILE00.0070.02627.383-0.009-0.0090.0000.0000.0000.000
156A197ASN00.0190.01129.7510.0110.0110.0000.0000.0000.000
157A198HIS00.0910.04932.908-0.003-0.0030.0000.0000.0000.000
158A199GLY00.0590.03634.574-0.003-0.0030.0000.0000.0000.000
159A200ASN0-0.013-0.02528.6610.0000.0000.0000.0000.0000.000
160A201SER00.0260.02132.670-0.004-0.0040.0000.0000.0000.000
161A202GLY0-0.0120.00935.697-0.001-0.0010.0000.0000.0000.000
162A203GLY00.0270.01031.618-0.003-0.0030.0000.0000.0000.000
163A204ALA00.007-0.00428.1590.0040.0040.0000.0000.0000.000
164A205LEU00.0190.03725.943-0.006-0.0060.0000.0000.0000.000
165A206VAL0-0.003-0.00522.6240.0050.0050.0000.0000.0000.000
166A207ASN00.0960.05022.336-0.018-0.0180.0000.0000.0000.000
167A208SER00.030-0.00316.952-0.009-0.0090.0000.0000.0000.000
168A209LEU0-0.050-0.03017.962-0.035-0.0350.0000.0000.0000.000
169A210GLY00.010-0.00920.172-0.001-0.0010.0000.0000.0000.000
170A211GLU-1-0.785-0.84722.428-0.128-0.1280.0000.0000.0000.000
171A212LEU00.0030.00525.4300.0000.0000.0000.0000.0000.000
172A213MET0-0.027-0.01526.3540.0080.0080.0000.0000.0000.000
173A214GLY00.0330.00029.2170.0090.0090.0000.0000.0000.000
174A215ILE0-0.0300.00731.130-0.007-0.0070.0000.0000.0000.000
175A216ASN00.023-0.00228.8180.0090.0090.0000.0000.0000.000
176A217THR0-0.021-0.02733.0730.0010.0010.0000.0000.0000.000
177A218LEU00.0400.00535.7100.0020.0020.0000.0000.0000.000
178A219SER00.0350.03933.734-0.002-0.0020.0000.0000.0000.000
179A220PHE0-0.0420.00235.5510.0020.0020.0000.0000.0000.000
180A221ASP-1-0.866-0.97736.291-0.042-0.0420.0000.0000.0000.000
181A222LYS10.8690.92838.1740.0300.0300.0000.0000.0000.000
182A223SER00.0590.05440.7580.0000.0000.0000.0000.0000.000
183A224ASN0-0.132-0.09942.4700.0000.0000.0000.0000.0000.000
184A225ASP-1-0.933-0.97245.238-0.014-0.0140.0000.0000.0000.000
185A226GLY00.0250.03344.8530.0010.0010.0000.0000.0000.000
186A227GLU-1-0.976-0.97639.960-0.013-0.0130.0000.0000.0000.000
187A228THR0-0.002-0.01736.392-0.001-0.0010.0000.0000.0000.000
188A229PRO0-0.053-0.01336.1060.0010.0010.0000.0000.0000.000
189A230GLU-1-0.915-0.95028.745-0.028-0.0280.0000.0000.0000.000
190A231GLY0-0.0010.00129.4150.0010.0010.0000.0000.0000.000
191A232ILE0-0.034-0.01030.0740.0000.0000.0000.0000.0000.000
192A233GLY00.0290.03231.7870.0010.0010.0000.0000.0000.000
193A234PHE0-0.016-0.01432.8070.0000.0000.0000.0000.0000.000
194A235ALA00.0460.01432.028-0.003-0.0030.0000.0000.0000.000
195A236ILE0-0.0090.02534.0380.0030.0030.0000.0000.0000.000
196A237PRO00.0250.01833.778-0.006-0.0060.0000.0000.0000.000
197A238PHE00.005-0.00931.0780.0030.0030.0000.0000.0000.000
198A239GLN00.0080.01134.1850.0040.0040.0000.0000.0000.000
199A240LEU0-0.025-0.00136.6860.0030.0030.0000.0000.0000.000
200A241ALA00.0340.00936.4270.0020.0020.0000.0000.0000.000
201A242THR00.0210.00036.3450.0010.0010.0000.0000.0000.000
202A243LYS10.9450.97938.8780.0510.0510.0000.0000.0000.000
203A244ILE0-0.016-0.00341.8800.0030.0030.0000.0000.0000.000
204A245MET00.0380.01738.8360.0010.0010.0000.0000.0000.000
205A246ASP-1-0.908-0.96242.034-0.058-0.0580.0000.0000.0000.000
206A247LYS10.8170.90244.2910.0440.0440.0000.0000.0000.000
207A248LEU0-0.0220.00744.2910.0020.0020.0000.0000.0000.000
208A249ILE0-0.046-0.01442.6490.0010.0010.0000.0000.0000.000
209A250ARG10.8490.93147.0840.0450.0450.0000.0000.0000.000
210A251ASP-1-0.897-0.95449.900-0.037-0.0370.0000.0000.0000.000
211A252GLY0-0.0020.01550.4430.0010.0010.0000.0000.0000.000
212A253ARG10.8020.85850.5800.0330.0330.0000.0000.0000.000
213A254VAL0-0.038-0.00848.0690.0000.0000.0000.0000.0000.000
214A255ILE0-0.019-0.00850.2630.0010.0010.0000.0000.0000.000
215A256ARG10.8390.92547.0370.0370.0370.0000.0000.0000.000
216A257GLY00.0050.03453.5850.0010.0010.0000.0000.0000.000
217A258TYR00.0010.00156.0820.0000.0000.0000.0000.0000.000
218A259ILE00.000-0.01158.4380.0000.0000.0000.0000.0000.000
219A260GLY00.016-0.00660.8460.0000.0000.0000.0000.0000.000
220A261ILE00.0120.01260.0510.0010.0010.0000.0000.0000.000
221A262GLY00.0440.00658.844-0.001-0.0010.0000.0000.0000.000
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