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: J3YR9

Calculation Name: 2D13-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2D13

Chain ID: A

ChEMBL ID:

UniProt ID: O58996

Base Structure: X-ray

Registration Date: 2023-03-13

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 217
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2616043.641305
FMO2-HF: Nuclear repulsion 2531755.407373
FMO2-HF: Total energy -84288.233932
FMO2-MP2: Total energy -84539.852866


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:2:VAL)


Summations of interaction energy for fragment #1(A:2:VAL)
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.
-13.02-8.3442.314-2.854-4.1370.009
Interaction energy analysis for fragmet #1(A:2:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.019 / q_NPA : -0.032
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].
3A4LEU0-0.032-0.0013.632-1.0321.472-0.016-1.225-1.2640.001
4A5ALA00.0150.0016.1860.3170.3170.0000.0000.0000.000
5A6ASP-1-0.781-0.8834.3014.7724.965-0.001-0.044-0.1480.000
6A7VAL0-0.043-0.0246.649-0.451-0.4510.0000.0000.0000.000
7A8ALA00.0230.0219.9550.2800.2800.0000.0000.0000.000
8A9VAL0-0.014-0.01812.529-0.134-0.1340.0000.0000.0000.000
9A10LEU00.0110.01315.0280.0170.0170.0000.0000.0000.000
10A11TYR0-0.061-0.07717.600-0.038-0.0380.0000.0000.0000.000
11A12SER00.028-0.00319.6340.0000.0000.0000.0000.0000.000
12A13GLY00.0510.03221.774-0.010-0.0100.0000.0000.0000.000
13A14GLY00.0510.02523.038-0.019-0.0190.0000.0000.0000.000
14A15LYS10.8660.91922.742-0.035-0.0350.0000.0000.0000.000
15A16ASP-1-0.779-0.87122.3300.0540.0540.0000.0000.0000.000
16A17SER0-0.030-0.00619.723-0.006-0.0060.0000.0000.0000.000
17A18ASN0-0.0050.00918.0550.0380.0380.0000.0000.0000.000
18A19TYR0-0.087-0.09217.657-0.020-0.0200.0000.0000.0000.000
19A20ALA00.031-0.00317.496-0.035-0.0350.0000.0000.0000.000
20A21LEU0-0.014-0.00412.336-0.016-0.0160.0000.0000.0000.000
21A22TYR0-0.006-0.01113.031-0.043-0.0430.0000.0000.0000.000
22A23TRP00.003-0.01213.608-0.084-0.0840.0000.0000.0000.000
23A24ALA00.0190.02310.776-0.085-0.0850.0000.0000.0000.000
24A25LEU00.0170.0027.931-0.139-0.1390.0000.0000.0000.000
25A26LYS10.9440.9769.3090.0700.0700.0000.0000.0000.000
26A27SER0-0.138-0.07211.555-0.102-0.1020.0000.0000.0000.000
27A28GLY00.0300.0157.518-0.024-0.0240.0000.0000.0000.000
28A29LEU0-0.0300.0006.501-0.627-0.6270.0000.0000.0000.000
29A30ARG10.8490.9362.224-12.975-11.0712.332-1.583-2.6530.008
30A31VAL00.0090.0005.2020.1670.242-0.001-0.002-0.0720.000
31A32ARG10.8640.9526.077-3.272-3.2720.0000.0000.0000.000
32A33TYR00.018-0.0038.893-0.066-0.0660.0000.0000.0000.000
33A34LEU00.0040.02512.524-0.084-0.0840.0000.0000.0000.000
34A35VAL00.028-0.00315.2540.0190.0190.0000.0000.0000.000
35A36SER0-0.049-0.01518.259-0.056-0.0560.0000.0000.0000.000
36A37MET00.0070.04221.5780.0190.0190.0000.0000.0000.000
37A38VAL0-0.025-0.01524.681-0.018-0.0180.0000.0000.0000.000
38A39SER0-0.002-0.00428.1000.0060.0060.0000.0000.0000.000
39A40GLU-1-0.935-0.93231.5670.1220.1220.0000.0000.0000.000
40A41ASN0-0.0090.00633.444-0.011-0.0110.0000.0000.0000.000
41A51ASN00.0450.00629.219-0.003-0.0030.0000.0000.0000.000
42A52VAL00.1090.04125.7730.0060.0060.0000.0000.0000.000
43A53GLU-1-0.950-0.91425.2840.1890.1890.0000.0000.0000.000
44A54LEU00.0190.01125.7860.0070.0070.0000.0000.0000.000
45A55THR0-0.043-0.08421.4180.0140.0140.0000.0000.0000.000
46A56SER00.007-0.00320.4790.0410.0410.0000.0000.0000.000
47A57LEU0-0.028-0.00320.7540.0230.0230.0000.0000.0000.000
48A58GLN00.0560.02819.2660.0260.0260.0000.0000.0000.000
49A59ALA00.0330.03516.4440.0060.0060.0000.0000.0000.000
50A60ARG10.9260.96616.012-0.183-0.1830.0000.0000.0000.000
51A61ALA0-0.014-0.00817.383-0.001-0.0010.0000.0000.0000.000
52A62LEU00.0070.01113.401-0.046-0.0460.0000.0000.0000.000
53A63GLY0-0.070-0.02012.4970.0160.0160.0000.0000.0000.000
54A64ILE0-0.030-0.0129.9490.1630.1630.0000.0000.0000.000
55A65PRO0-0.017-0.00311.282-0.149-0.1490.0000.0000.0000.000
56A66ILE0-0.006-0.01014.2280.0280.0280.0000.0000.0000.000
57A67ILE0-0.006-0.00115.756-0.023-0.0230.0000.0000.0000.000
58A68LYS10.9030.95519.048-0.327-0.3270.0000.0000.0000.000
59A69GLY00.046-0.00422.7220.0060.0060.0000.0000.0000.000
60A70PHE0-0.035-0.03624.680-0.015-0.0150.0000.0000.0000.000
61A71THR0-0.017-0.04328.465-0.005-0.0050.0000.0000.0000.000
62A72LYS10.8540.95830.855-0.141-0.1410.0000.0000.0000.000
63A73GLY00.022-0.03234.1240.0000.0000.0000.0000.0000.000
64A74GLU-1-0.833-0.88935.0350.1170.1170.0000.0000.0000.000
65A75LYS10.9460.94633.644-0.106-0.1060.0000.0000.0000.000
66A76GLU-1-0.953-0.97733.8900.1050.1050.0000.0000.0000.000
67A77LYS10.9510.99531.498-0.177-0.1770.0000.0000.0000.000
68A78GLU-1-0.884-0.95129.4940.1690.1690.0000.0000.0000.000
69A79VAL0-0.033-0.02327.6680.0150.0150.0000.0000.0000.000
70A80GLU-1-0.908-0.95326.6430.1980.1980.0000.0000.0000.000
71A81ASP-1-0.805-0.90326.3730.2370.2370.0000.0000.0000.000
72A82LEU0-0.056-0.03021.2240.0280.0280.0000.0000.0000.000
73A83LYS10.9190.95022.083-0.181-0.1810.0000.0000.0000.000
74A84ASN00.014-0.01521.9560.0350.0350.0000.0000.0000.000
75A85VAL0-0.0350.00119.2100.0320.0320.0000.0000.0000.000
76A86LEU0-0.065-0.04717.0970.0720.0720.0000.0000.0000.000
77A87GLU-1-0.919-0.94817.1590.3860.3860.0000.0000.0000.000
78A88GLY0-0.0030.01218.3460.0160.0160.0000.0000.0000.000
79A89LEU0-0.094-0.05013.5900.1130.1130.0000.0000.0000.000
80A90LYS10.9300.95810.903-1.066-1.0660.0000.0000.0000.000
81A91VAL0-0.061-0.0259.8030.3810.3810.0000.0000.0000.000
82A92ASP-1-0.813-0.9098.6850.5690.5690.0000.0000.0000.000
83A93GLY00.007-0.01611.676-0.151-0.1510.0000.0000.0000.000
84A94ILE0-0.0160.01112.8960.1210.1210.0000.0000.0000.000
85A95VAL0-0.010-0.01113.048-0.085-0.0850.0000.0000.0000.000
86A96ALA00.015-0.00516.0730.0320.0320.0000.0000.0000.000
87A97GLY00.036-0.01019.712-0.028-0.0280.0000.0000.0000.000
88A98ALA0-0.0360.00121.708-0.013-0.0130.0000.0000.0000.000
89A99LEU00.0290.01724.414-0.009-0.0090.0000.0000.0000.000
90A100ALA00.0720.02526.998-0.009-0.0090.0000.0000.0000.000
91A101SER00.0110.01129.9540.0000.0000.0000.0000.0000.000
92A102ARG11.0251.00829.335-0.025-0.0250.0000.0000.0000.000
93A103TYR00.0410.02030.5190.0090.0090.0000.0000.0000.000
94A104GLN0-0.001-0.01027.9100.0030.0030.0000.0000.0000.000
95A105LYS10.8650.94124.391-0.040-0.0400.0000.0000.0000.000
96A106GLU-1-0.875-0.93426.1580.0790.0790.0000.0000.0000.000
97A107ARG10.9160.96527.701-0.119-0.1190.0000.0000.0000.000
98A108ILE00.005-0.00121.8510.0150.0150.0000.0000.0000.000
99A109GLU-1-0.897-0.95422.9380.0920.0920.0000.0000.0000.000
100A110ASN0-0.005-0.00924.097-0.002-0.0020.0000.0000.0000.000
101A111VAL00.0340.03622.2060.0050.0050.0000.0000.0000.000
102A112ALA00.0300.00019.3960.0180.0180.0000.0000.0000.000
103A113ARG10.8930.95120.722-0.102-0.1020.0000.0000.0000.000
104A114GLU-1-0.919-0.96122.9180.1770.1770.0000.0000.0000.000
105A115LEU0-0.042-0.01019.2870.0090.0090.0000.0000.0000.000
106A116GLY0-0.0290.00718.9190.0300.0300.0000.0000.0000.000
107A117LEU0-0.041-0.00814.4880.0240.0240.0000.0000.0000.000
108A118LYS10.9130.95413.345-0.058-0.0580.0000.0000.0000.000
109A119VAL00.0190.00616.0640.0440.0440.0000.0000.0000.000
110A120TYR00.0000.00211.942-0.086-0.0860.0000.0000.0000.000
111A121THR0-0.013-0.02017.6130.0320.0320.0000.0000.0000.000
112A122PRO00.0130.01217.466-0.019-0.0190.0000.0000.0000.000
113A123ALA00.031-0.01120.018-0.021-0.0210.0000.0000.0000.000
114A124TRP0-0.076-0.04623.2400.0070.0070.0000.0000.0000.000
115A125GLU-1-0.917-0.96125.468-0.027-0.0270.0000.0000.0000.000
116A126LYS10.8671.00123.9410.0580.0580.0000.0000.0000.000
117A127ASP-1-0.835-0.93328.373-0.025-0.0250.0000.0000.0000.000
118A128PRO00.0610.02730.213-0.004-0.0040.0000.0000.0000.000
119A129TYR0-0.031-0.05230.897-0.001-0.0010.0000.0000.0000.000
120A130GLN00.004-0.02629.731-0.009-0.0090.0000.0000.0000.000
121A131TYR0-0.063-0.04223.645-0.010-0.0100.0000.0000.0000.000
122A132MET0-0.018-0.00726.9650.0000.0000.0000.0000.0000.000
123A133LEU00.0190.00028.601-0.003-0.0030.0000.0000.0000.000
124A134GLU-1-0.848-0.85122.446-0.113-0.1130.0000.0000.0000.000
125A135ILE00.011-0.00123.428-0.009-0.0090.0000.0000.0000.000
126A136ILE0-0.021-0.00324.7540.0000.0000.0000.0000.0000.000
127A137LYS10.9120.95225.7590.0870.0870.0000.0000.0000.000
128A138LEU0-0.078-0.02720.067-0.011-0.0110.0000.0000.0000.000
129A139GLY00.0150.00721.506-0.008-0.0080.0000.0000.0000.000
130A140PHE0-0.050-0.02019.0890.0160.0160.0000.0000.0000.000
131A141LYS10.8200.91523.7610.0140.0140.0000.0000.0000.000
132A142VAL00.017-0.00925.2880.0140.0140.0000.0000.0000.000
133A143VAL00.0580.03627.603-0.009-0.0090.0000.0000.0000.000
134A144PHE00.0130.01330.3010.0080.0080.0000.0000.0000.000
135A145VAL00.001-0.00830.256-0.003-0.0030.0000.0000.0000.000
136A146ALA00.0320.01933.2320.0040.0040.0000.0000.0000.000
137A147VAL0-0.056-0.01835.270-0.003-0.0030.0000.0000.0000.000
138A148SER0-0.006-0.01637.9160.0020.0020.0000.0000.0000.000
139A149ALA00.0950.05239.9130.0000.0000.0000.0000.0000.000
140A150TYR00.0060.00841.793-0.002-0.0020.0000.0000.0000.000
141A151GLY00.0450.01244.432-0.002-0.0020.0000.0000.0000.000
142A152LEU0-0.071-0.02438.271-0.003-0.0030.0000.0000.0000.000
143A153ASN00.0400.06942.3650.0040.0040.0000.0000.0000.000
144A154GLU-1-0.816-0.93742.1880.0370.0370.0000.0000.0000.000
145A155SER0-0.139-0.10941.9130.0010.0010.0000.0000.0000.000
146A156TRP00.0230.00736.509-0.002-0.0020.0000.0000.0000.000
147A157LEU0-0.0300.00837.0090.0010.0010.0000.0000.0000.000
148A158GLY00.004-0.01234.729-0.003-0.0030.0000.0000.0000.000
149A159ARG10.7900.92035.097-0.017-0.0170.0000.0000.0000.000
150A160GLU-1-0.916-0.96930.4750.0100.0100.0000.0000.0000.000
151A161LEU0-0.034-0.00428.531-0.006-0.0060.0000.0000.0000.000
152A162ASN00.0590.03930.839-0.007-0.0070.0000.0000.0000.000
153A163TYR00.0760.01030.3950.0010.0010.0000.0000.0000.000
154A164LYS10.9610.98834.6930.0060.0060.0000.0000.0000.000
155A165ASN0-0.039-0.05235.1290.0010.0010.0000.0000.0000.000
156A166LEU00.0220.01932.0650.0030.0030.0000.0000.0000.000
157A167GLU-1-0.831-0.88635.528-0.028-0.0280.0000.0000.0000.000
158A168GLU-1-0.933-0.97438.7160.0030.0030.0000.0000.0000.000
159A169LEU00.0240.01834.6670.0020.0020.0000.0000.0000.000
160A170LYS10.8400.92037.9960.0240.0240.0000.0000.0000.000
161A171LYS10.9210.96439.3740.0170.0170.0000.0000.0000.000
162A172LEU0-0.021-0.02441.5840.0010.0010.0000.0000.0000.000
163A173SER0-0.026-0.01039.1910.0010.0010.0000.0000.0000.000
164A174GLU-1-0.860-0.93141.298-0.014-0.0140.0000.0000.0000.000
165A175LYS10.8360.90943.951-0.002-0.0020.0000.0000.0000.000
166A176TYR0-0.021-0.01244.1900.0000.0000.0000.0000.0000.000
167A177GLY0-0.0090.02043.0050.0020.0020.0000.0000.0000.000
168A178ILE00.0180.03038.3760.0020.0020.0000.0000.0000.000
169A179HIS0-0.0610.00435.152-0.003-0.0030.0000.0000.0000.000
170A180ILE00.010-0.01533.9590.0020.0020.0000.0000.0000.000
171A181ALA0-0.002-0.02229.837-0.001-0.0010.0000.0000.0000.000
172A182GLY00.0000.00630.7470.0070.0070.0000.0000.0000.000
173A183GLU-1-0.844-0.93931.3890.0260.0260.0000.0000.0000.000
174A184GLY00.015-0.00132.862-0.003-0.0030.0000.0000.0000.000
175A185GLY00.0040.01133.9990.0030.0030.0000.0000.0000.000
176A186GLU-1-0.882-0.93534.9530.0350.0350.0000.0000.0000.000
177A187PHE0-0.025-0.01731.164-0.002-0.0020.0000.0000.0000.000
178A188GLU-1-0.940-0.94130.6670.1030.1030.0000.0000.0000.000
179A189THR0-0.045-0.04327.529-0.008-0.0080.0000.0000.0000.000
180A190PHE00.0360.02024.6800.0140.0140.0000.0000.0000.000
181A191VAL0-0.031-0.01121.412-0.017-0.0170.0000.0000.0000.000
182A192LEU00.0230.01423.3490.0180.0180.0000.0000.0000.000
183A193ASP-1-0.780-0.91021.2430.0110.0110.0000.0000.0000.000
184A194MET00.0160.06115.255-0.029-0.0290.0000.0000.0000.000
185A195PRO00.0310.00016.7940.0130.0130.0000.0000.0000.000
186A196PHE00.018-0.01111.203-0.009-0.0090.0000.0000.0000.000
187A197PHE0-0.0610.00914.3240.0570.0570.0000.0000.0000.000
188A198LYS10.9660.96911.683-0.200-0.2000.0000.0000.0000.000
189A199ALA0-0.027-0.01317.269-0.018-0.0180.0000.0000.0000.000
190A200LYS10.8990.95820.7950.0020.0020.0000.0000.0000.000
191A201ILE0-0.004-0.00222.2550.0120.0120.0000.0000.0000.000
192A202VAL00.0070.01025.645-0.008-0.0080.0000.0000.0000.000
193A203ILE0-0.001-0.01329.2800.0090.0090.0000.0000.0000.000
194A204ASP-1-0.902-0.94031.9260.0690.0690.0000.0000.0000.000
195A205ASP-1-0.893-0.96534.5170.0570.0570.0000.0000.0000.000
196A206ALA0-0.022-0.00335.0880.0090.0090.0000.0000.0000.000
197A207GLU-1-0.827-0.87137.1690.0590.0590.0000.0000.0000.000
198A208LYS10.9070.95038.925-0.033-0.0330.0000.0000.0000.000
199A209PHE00.0270.02339.6830.0010.0010.0000.0000.0000.000
200A210TRP00.0530.02341.6970.0020.0020.0000.0000.0000.000
201A211ASP-1-0.816-0.90643.8490.0520.0520.0000.0000.0000.000
202A212GLY00.001-0.01046.205-0.001-0.0010.0000.0000.0000.000
203A213LEU0-0.103-0.05045.997-0.003-0.0030.0000.0000.0000.000
204A214SER0-0.0210.01140.803-0.001-0.0010.0000.0000.0000.000
205A215GLY00.002-0.01140.319-0.001-0.0010.0000.0000.0000.000
206A216LYS10.9290.95236.377-0.082-0.0820.0000.0000.0000.000
207A217PHE00.000-0.00133.614-0.004-0.0040.0000.0000.0000.000
208A218ILE00.0010.00734.2880.0080.0080.0000.0000.0000.000
209A219ILE00.000-0.02729.833-0.005-0.0050.0000.0000.0000.000
210A220LYS10.8230.91133.244-0.064-0.0640.0000.0000.0000.000
211A221ARG10.9450.97432.892-0.069-0.0690.0000.0000.0000.000
212A222ALA00.0180.00229.197-0.007-0.0070.0000.0000.0000.000
213A223HIS10.8180.92027.974-0.059-0.0590.0000.0000.0000.000
214A224LEU0-0.014-0.02521.5550.0000.0000.0000.0000.0000.000
215A225GLU-1-0.908-0.95125.1750.0330.0330.0000.0000.0000.000
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