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: 3QZ4L

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 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 -2618890.620803
FMO2-HF: Nuclear repulsion 2534600.747981
FMO2-HF: Total energy -84289.872821
FMO2-MP2: Total energy -84541.484442


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.
-20.505-20.26111.316-5.024-6.5360.029
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 : 0.005 / q_NPA : -0.006
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].
3A4LEU0-0.036-0.0023.644-1.3081.581-0.017-1.469-1.4030.003
4A5ALA00.0100.0006.2040.4270.4270.0000.0000.0000.000
5A6ASP-1-0.771-0.8674.1333.7353.9680.000-0.070-0.1620.000
6A7VAL0-0.045-0.0256.625-0.223-0.2230.0000.0000.0000.000
7A8ALA00.0300.0239.7710.2260.2260.0000.0000.0000.000
8A9VAL0-0.016-0.02011.886-0.127-0.1270.0000.0000.0000.000
9A10LEU00.0240.02014.5530.0400.0400.0000.0000.0000.000
10A11TYR0-0.053-0.05917.089-0.034-0.0340.0000.0000.0000.000
11A12SER00.0370.00719.2050.0130.0130.0000.0000.0000.000
12A13GLY00.0660.03421.4310.0000.0000.0000.0000.0000.000
13A14GLY00.0320.01822.704-0.016-0.0160.0000.0000.0000.000
14A15LYS10.8230.88322.4440.0270.0270.0000.0000.0000.000
15A16ASP-1-0.758-0.85222.065-0.043-0.0430.0000.0000.0000.000
16A17SER0-0.020-0.00219.328-0.013-0.0130.0000.0000.0000.000
17A18ASN00.0140.02017.7280.0050.0050.0000.0000.0000.000
18A19TYR0-0.047-0.02817.424-0.040-0.0400.0000.0000.0000.000
19A20ALA00.017-0.00217.076-0.049-0.0490.0000.0000.0000.000
20A21LEU00.0020.00111.879-0.047-0.0470.0000.0000.0000.000
21A22TYR00.007-0.01312.792-0.091-0.0910.0000.0000.0000.000
22A23TRP00.012-0.00713.480-0.113-0.1130.0000.0000.0000.000
23A24ALA00.0190.03110.549-0.095-0.0950.0000.0000.0000.000
24A25LEU00.0100.0028.503-0.198-0.1980.0000.0000.0000.000
25A26LYS10.9350.9739.2830.2090.2090.0000.0000.0000.000
26A27SER0-0.117-0.07211.495-0.068-0.0680.0000.0000.0000.000
27A28GLY00.0250.0117.570-0.003-0.0030.0000.0000.0000.000
28A29LEU0-0.034-0.0036.417-0.762-0.7620.0000.0000.0000.000
29A30ARG10.8010.8832.036-19.812-22.78211.334-3.478-4.8870.026
30A31VAL00.002-0.0024.7550.5640.656-0.001-0.007-0.0840.000
31A32ARG10.8640.9536.249-2.918-2.9180.0000.0000.0000.000
32A33TYR00.0250.0048.4290.1000.1000.0000.0000.0000.000
33A34LEU00.0100.02712.028-0.122-0.1220.0000.0000.0000.000
34A35VAL00.025-0.00614.7950.0400.0400.0000.0000.0000.000
35A36SER0-0.057-0.02417.757-0.054-0.0540.0000.0000.0000.000
36A37MET00.0170.03521.1030.0260.0260.0000.0000.0000.000
37A38VAL0-0.024-0.01424.178-0.019-0.0190.0000.0000.0000.000
38A39SER00.0370.01527.6140.0090.0090.0000.0000.0000.000
39A40GLU-1-0.926-0.94731.0670.0990.0990.0000.0000.0000.000
40A41ASN0-0.046-0.01432.650-0.013-0.0130.0000.0000.0000.000
41A51ASN00.012-0.00128.9020.0050.0050.0000.0000.0000.000
42A52VAL00.0690.01925.5920.0020.0020.0000.0000.0000.000
43A53GLU-1-0.937-0.92924.9170.1590.1590.0000.0000.0000.000
44A54LEU00.0280.01225.4890.0090.0090.0000.0000.0000.000
45A55THR0-0.030-0.04020.8720.0140.0140.0000.0000.0000.000
46A56SER00.015-0.00320.1580.0290.0290.0000.0000.0000.000
47A57LEU0-0.0190.00220.4890.0270.0270.0000.0000.0000.000
48A58GLN00.0480.01218.9970.0230.0230.0000.0000.0000.000
49A59ALA00.0400.03716.170-0.003-0.0030.0000.0000.0000.000
50A60ARG10.9280.96715.795-0.172-0.1720.0000.0000.0000.000
51A61ALA00.0010.00117.2680.0080.0080.0000.0000.0000.000
52A62LEU00.0240.02313.218-0.042-0.0420.0000.0000.0000.000
53A63GLY0-0.065-0.01912.3840.0000.0000.0000.0000.0000.000
54A64ILE0-0.020-0.0089.7290.1570.1570.0000.0000.0000.000
55A65PRO0-0.0030.00210.834-0.125-0.1250.0000.0000.0000.000
56A66ILE0-0.012-0.01013.858-0.008-0.0080.0000.0000.0000.000
57A67ILE0-0.006-0.00215.460-0.004-0.0040.0000.0000.0000.000
58A68LYS10.8800.94218.591-0.272-0.2720.0000.0000.0000.000
59A69GLY00.0320.01022.2490.0110.0110.0000.0000.0000.000
60A70PHE0-0.048-0.04724.202-0.017-0.0170.0000.0000.0000.000
61A71THR0-0.019-0.08127.980-0.003-0.0030.0000.0000.0000.000
62A72LYS10.8410.97030.450-0.122-0.1220.0000.0000.0000.000
63A73GLY00.009-0.01433.4340.0010.0010.0000.0000.0000.000
64A74GLU-1-0.838-0.91734.6030.0920.0920.0000.0000.0000.000
65A75LYS10.8490.90833.399-0.068-0.0680.0000.0000.0000.000
66A76GLU-1-0.851-0.90533.9070.0700.0700.0000.0000.0000.000
67A77LYS10.8710.92230.746-0.156-0.1560.0000.0000.0000.000
68A78GLU-1-0.774-0.88229.4330.1080.1080.0000.0000.0000.000
69A79VAL0-0.051-0.02927.6260.0110.0110.0000.0000.0000.000
70A80GLU-1-0.835-0.90326.6140.1550.1550.0000.0000.0000.000
71A81ASP-1-0.781-0.84326.3460.1920.1920.0000.0000.0000.000
72A82LEU0-0.033-0.02521.2770.0250.0250.0000.0000.0000.000
73A83LYS10.8780.92022.053-0.142-0.1420.0000.0000.0000.000
74A84ASN0-0.008-0.03121.9310.0330.0330.0000.0000.0000.000
75A85VAL0-0.040-0.00419.1940.0340.0340.0000.0000.0000.000
76A86LEU0-0.056-0.04016.8520.0620.0620.0000.0000.0000.000
77A87GLU-1-0.882-0.93717.1360.3160.3160.0000.0000.0000.000
78A88GLY0-0.0060.01118.3300.0190.0190.0000.0000.0000.000
79A89LEU0-0.094-0.04913.5150.1150.1150.0000.0000.0000.000
80A90LYS10.9330.95710.964-1.044-1.0440.0000.0000.0000.000
81A91VAL0-0.058-0.0269.6290.3160.3160.0000.0000.0000.000
82A92ASP-1-0.798-0.8928.6030.2050.2050.0000.0000.0000.000
83A93GLY00.010-0.01611.653-0.106-0.1060.0000.0000.0000.000
84A94ILE0-0.0190.01012.8690.0800.0800.0000.0000.0000.000
85A95VAL0-0.019-0.01612.584-0.077-0.0770.0000.0000.0000.000
86A96ALA00.011-0.00115.7500.0430.0430.0000.0000.0000.000
87A97GLY00.035-0.00819.273-0.034-0.0340.0000.0000.0000.000
88A98ALA0-0.051-0.00921.325-0.005-0.0050.0000.0000.0000.000
89A99LEU00.0160.01824.061-0.014-0.0140.0000.0000.0000.000
90A100ALA00.0620.02426.660-0.008-0.0080.0000.0000.0000.000
91A101SER0-0.011-0.00529.4690.0020.0020.0000.0000.0000.000
92A102ARG10.9410.94529.2170.0400.0400.0000.0000.0000.000
93A103TYR00.0560.03630.4910.0060.0060.0000.0000.0000.000
94A104GLN00.0170.00427.471-0.001-0.0010.0000.0000.0000.000
95A105LYS10.8420.92323.9180.0560.0560.0000.0000.0000.000
96A106GLU-1-0.882-0.93926.1310.0150.0150.0000.0000.0000.000
97A107ARG10.8070.88127.677-0.068-0.0680.0000.0000.0000.000
98A108ILE0-0.011-0.00921.8900.0140.0140.0000.0000.0000.000
99A109GLU-1-0.863-0.93122.913-0.007-0.0070.0000.0000.0000.000
100A110ASN00.0180.00924.077-0.002-0.0020.0000.0000.0000.000
101A111VAL00.0220.03321.8580.0080.0080.0000.0000.0000.000
102A112ALA00.019-0.00219.5650.0170.0170.0000.0000.0000.000
103A113ARG10.8950.94120.708-0.028-0.0280.0000.0000.0000.000
104A114GLU-1-0.899-0.93222.9070.1250.1250.0000.0000.0000.000
105A115LEU0-0.050-0.01319.2310.0130.0130.0000.0000.0000.000
106A116GLY0-0.0320.00518.9100.0270.0270.0000.0000.0000.000
107A117LEU0-0.045-0.01314.5240.0090.0090.0000.0000.0000.000
108A118LYS10.9220.95513.0880.1820.1820.0000.0000.0000.000
109A119VAL00.0240.01016.0440.0240.0240.0000.0000.0000.000
110A120TYR0-0.0030.00111.615-0.072-0.0720.0000.0000.0000.000
111A121THR0-0.004-0.01017.5870.0320.0320.0000.0000.0000.000
112A122PRO00.0080.00416.920-0.005-0.0050.0000.0000.0000.000
113A123ALA00.005-0.00119.730-0.014-0.0140.0000.0000.0000.000
114A124TRP0-0.100-0.06122.9550.0150.0150.0000.0000.0000.000
115A125GLU-1-0.801-0.89425.150-0.083-0.0830.0000.0000.0000.000
116A126LYS10.8430.93922.8600.1730.1730.0000.0000.0000.000
117A127ASP-1-0.816-0.93028.139-0.076-0.0760.0000.0000.0000.000
118A128PRO00.0560.02830.012-0.006-0.0060.0000.0000.0000.000
119A129TYR0-0.029-0.03430.691-0.004-0.0040.0000.0000.0000.000
120A130GLN00.015-0.01729.722-0.010-0.0100.0000.0000.0000.000
121A131TYR0-0.039-0.03023.180-0.017-0.0170.0000.0000.0000.000
122A132MET0-0.027-0.01226.806-0.005-0.0050.0000.0000.0000.000
123A133LEU00.007-0.00228.470-0.003-0.0030.0000.0000.0000.000
124A134GLU-1-0.811-0.85522.247-0.220-0.2200.0000.0000.0000.000
125A135ILE0-0.005-0.00923.397-0.012-0.0120.0000.0000.0000.000
126A136ILE0-0.023-0.00724.6680.0000.0000.0000.0000.0000.000
127A137LYS10.8920.94425.9020.1340.1340.0000.0000.0000.000
128A138LEU0-0.067-0.02419.886-0.010-0.0100.0000.0000.0000.000
129A139GLY00.0130.00821.521-0.012-0.0120.0000.0000.0000.000
130A140PHE0-0.046-0.02018.9150.0150.0150.0000.0000.0000.000
131A141LYS10.7730.88823.6780.0680.0680.0000.0000.0000.000
132A142VAL0-0.003-0.02125.0610.0120.0120.0000.0000.0000.000
133A143VAL00.0500.03327.436-0.004-0.0040.0000.0000.0000.000
134A144PHE00.0250.01930.0600.0040.0040.0000.0000.0000.000
135A145VAL0-0.001-0.00929.9840.0010.0010.0000.0000.0000.000
136A146ALA00.0110.01032.9480.0070.0070.0000.0000.0000.000
137A147VAL0-0.045-0.01134.959-0.006-0.0060.0000.0000.0000.000
138A148SER00.0080.00737.5970.0040.0040.0000.0000.0000.000
139A149ALA00.0840.05439.573-0.001-0.0010.0000.0000.0000.000
140A150TYR00.0160.01341.456-0.001-0.0010.0000.0000.0000.000
141A151GLY00.0470.01444.127-0.003-0.0030.0000.0000.0000.000
142A152LEU0-0.081-0.02537.916-0.003-0.0030.0000.0000.0000.000
143A153ASN00.0410.03742.0900.0040.0040.0000.0000.0000.000
144A154GLU-1-0.797-0.91941.9260.0160.0160.0000.0000.0000.000
145A155SER0-0.099-0.06541.6700.0000.0000.0000.0000.0000.000
146A156TRP00.000-0.00736.496-0.003-0.0030.0000.0000.0000.000
147A157LEU0-0.0360.01236.754-0.001-0.0010.0000.0000.0000.000
148A158GLY00.038-0.01034.515-0.001-0.0010.0000.0000.0000.000
149A159ARG10.7430.87434.9250.0130.0130.0000.0000.0000.000
150A160GLU-1-0.832-0.91829.958-0.038-0.0380.0000.0000.0000.000
151A161LEU0-0.043-0.00928.337-0.004-0.0040.0000.0000.0000.000
152A162ASN00.0520.01830.735-0.007-0.0070.0000.0000.0000.000
153A163TYR00.0840.01930.1940.0000.0000.0000.0000.0000.000
154A164LYS10.8660.93434.6270.0300.0300.0000.0000.0000.000
155A165ASN00.016-0.00435.2550.0040.0040.0000.0000.0000.000
156A166LEU00.0310.02331.7960.0030.0030.0000.0000.0000.000
157A167GLU-1-0.782-0.87535.383-0.061-0.0610.0000.0000.0000.000
158A168GLU-1-0.826-0.90138.586-0.023-0.0230.0000.0000.0000.000
159A169LEU00.0160.01834.4230.0030.0030.0000.0000.0000.000
160A170LYS10.8380.92237.7720.0600.0600.0000.0000.0000.000
161A171LYS10.8740.93239.1820.0510.0510.0000.0000.0000.000
162A172LEU0-0.011-0.01741.3610.0020.0020.0000.0000.0000.000
163A173SER0-0.018-0.00738.9280.0020.0020.0000.0000.0000.000
164A174GLU-1-0.883-0.93841.049-0.047-0.0470.0000.0000.0000.000
165A175LYS10.8240.89543.7210.0270.0270.0000.0000.0000.000
166A176TYR0-0.013-0.00843.9430.0010.0010.0000.0000.0000.000
167A177GLY0-0.0040.02542.7130.0020.0020.0000.0000.0000.000
168A178ILE00.0050.03138.4690.0010.0010.0000.0000.0000.000
169A179HIS0-0.041-0.00734.474-0.003-0.0030.0000.0000.0000.000
170A180ILE00.003-0.01633.6400.0020.0020.0000.0000.0000.000
171A181ALA0-0.005-0.01929.499-0.002-0.0020.0000.0000.0000.000
172A182GLY00.0140.01330.4450.0030.0030.0000.0000.0000.000
173A183GLU-1-0.854-0.94330.977-0.031-0.0310.0000.0000.0000.000
174A184GLY00.0210.00032.5080.0000.0000.0000.0000.0000.000
175A185GLY00.0030.01133.6080.0050.0050.0000.0000.0000.000
176A186GLU-1-0.884-0.93234.569-0.002-0.0020.0000.0000.0000.000
177A187PHE0-0.022-0.02630.9490.0000.0000.0000.0000.0000.000
178A188GLU-1-0.849-0.90230.2770.0520.0520.0000.0000.0000.000
179A189THR0-0.027-0.03827.474-0.007-0.0070.0000.0000.0000.000
180A190PHE00.0200.01524.1470.0090.0090.0000.0000.0000.000
181A191VAL0-0.044-0.01121.368-0.014-0.0140.0000.0000.0000.000
182A192LEU00.0390.02823.1520.0160.0160.0000.0000.0000.000
183A193ASP-1-0.744-0.88021.155-0.043-0.0430.0000.0000.0000.000
184A194MET00.0110.04814.964-0.032-0.0320.0000.0000.0000.000
185A195PRO00.0330.00516.7270.0150.0150.0000.0000.0000.000
186A196PHE00.003-0.01311.881-0.012-0.0120.0000.0000.0000.000
187A197PHE0-0.0610.00714.2950.0550.0550.0000.0000.0000.000
188A198LYS10.9200.94011.482-0.227-0.2270.0000.0000.0000.000
189A199ALA0-0.035-0.01117.305-0.005-0.0050.0000.0000.0000.000
190A200LYS10.8750.93320.7910.0370.0370.0000.0000.0000.000
191A201ILE0-0.006-0.00622.0750.0170.0170.0000.0000.0000.000
192A202VAL00.0150.01425.536-0.011-0.0110.0000.0000.0000.000
193A203ILE0-0.008-0.01529.1910.0100.0100.0000.0000.0000.000
194A204ASP-1-0.878-0.93131.7870.0550.0550.0000.0000.0000.000
195A205ASP-1-0.896-0.96834.3880.0440.0440.0000.0000.0000.000
196A206ALA0-0.0180.00634.9400.0070.0070.0000.0000.0000.000
197A207GLU-1-0.844-0.89536.9500.0420.0420.0000.0000.0000.000
198A208LYS10.8430.92638.657-0.011-0.0110.0000.0000.0000.000
199A209PHE00.0180.01539.4980.0020.0020.0000.0000.0000.000
200A210TRP00.0580.01941.382-0.001-0.0010.0000.0000.0000.000
201A211ASP-1-0.806-0.89943.3850.0280.0280.0000.0000.0000.000
202A212GLY0-0.008-0.00745.8550.0000.0000.0000.0000.0000.000
203A213LEU0-0.097-0.04645.624-0.003-0.0030.0000.0000.0000.000
204A214SER0-0.068-0.02939.856-0.001-0.0010.0000.0000.0000.000
205A215GLY00.028-0.00339.9820.0010.0010.0000.0000.0000.000
206A216LYS10.8740.91734.077-0.050-0.0500.0000.0000.0000.000
207A217PHE0-0.019-0.00733.613-0.002-0.0020.0000.0000.0000.000
208A218ILE00.0280.01833.9990.0050.0050.0000.0000.0000.000
209A219ILE0-0.022-0.02729.930-0.004-0.0040.0000.0000.0000.000
210A220LYS10.8690.93232.981-0.046-0.0460.0000.0000.0000.000
211A221ARG10.9220.97032.689-0.055-0.0550.0000.0000.0000.000
212A222ALA00.0120.00428.990-0.009-0.0090.0000.0000.0000.000
213A223HIS10.7440.85127.869-0.040-0.0400.0000.0000.0000.000
214A224LEU0-0.014-0.02521.409-0.004-0.0040.0000.0000.0000.000
215A225GLU-1-0.845-0.90125.1500.0260.0260.0000.0000.0000.000
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