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: V2191

Calculation Name: 2D13-A-Xray310

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: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 220
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2634811.859601
FMO2-HF: Nuclear repulsion 2550201.208263
FMO2-HF: Total energy -84610.651339
FMO2-MP2: Total energy -84863.210047


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:1:ACE )


Summations of interaction energy for fragment #1(A:1:ACE )
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.
-0.682-0.4482.731-1.114-1.8510.005
Interaction energy analysis for fragmet #1(A:1:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.009 / q_NPA : -0.025
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].
3A3GLY 00.0540.0343.8540.7711.555-0.005-0.342-0.437-0.001
4A4LEU 0-0.032-0.0017.0730.0320.0320.0000.0000.0000.000
5A5ALA 00.0140.0009.2290.0470.0470.0000.0000.0000.000
6A6ASP -1-0.784-0.8856.874-1.285-1.2850.0000.0000.0000.000
7A7VAL 0-0.039-0.0238.6140.0990.0990.0000.0000.0000.000
8A8ALA 00.0180.0209.8300.0890.0890.0000.0000.0000.000
9A9VAL 0-0.008-0.01612.145-0.029-0.0290.0000.0000.0000.000
10A10LEU 00.0060.01114.4760.0260.0260.0000.0000.0000.000
11A11TYR 0-0.060-0.07516.5190.0040.0040.0000.0000.0000.000
12A12SER 00.026-0.00518.621-0.003-0.0030.0000.0000.0000.000
13A13GLY 00.0520.03020.705-0.001-0.0010.0000.0000.0000.000
14A14GLY 00.0550.02721.8900.0010.0010.0000.0000.0000.000
15A15LYS 10.8660.92022.059-0.037-0.0370.0000.0000.0000.000
16A16ASP -1-0.784-0.87322.0480.0540.0540.0000.0000.0000.000
17A17SER 0-0.025-0.00618.965-0.003-0.0030.0000.0000.0000.000
18A18ASN 0-0.0020.01117.4770.0350.0350.0000.0000.0000.000
19A19TYR 0-0.089-0.09317.4190.0100.0100.0000.0000.0000.000
20A20ALA 00.023-0.00517.434-0.004-0.0040.0000.0000.0000.000
21A21LEU 0-0.010-0.00311.614-0.011-0.0110.0000.0000.0000.000
22A22TYR 00.002-0.00713.0370.0130.0130.0000.0000.0000.000
23A23TRP 0-0.004-0.01414.091-0.002-0.0020.0000.0000.0000.000
24A24ALA 00.0220.02211.258-0.031-0.0310.0000.0000.0000.000
25A25LEU 00.0180.0047.918-0.035-0.0350.0000.0000.0000.000
26A26LYS 10.9410.97610.331-0.056-0.0560.0000.0000.0000.000
27A27SER 0-0.139-0.07212.740-0.039-0.0390.0000.0000.0000.000
28A28GLY 00.0300.0159.289-0.050-0.0500.0000.0000.0000.000
29A29LEU 0-0.0270.0018.493-0.188-0.1880.0000.0000.0000.000
30A30ARG 10.8230.9362.2350.379-0.1712.736-0.772-1.4140.006
31A31VAL 00.0070.0005.832-0.004-0.0040.0000.0000.0000.000
32A32ARG 10.8600.9514.961-0.090-0.0900.0000.0000.0000.000
33A33TYR 00.021-0.0027.5760.0960.0960.0000.0000.0000.000
34A34LEU 00.0110.02711.018-0.055-0.0550.0000.0000.0000.000
35A35VAL 00.027-0.00213.8900.0040.0040.0000.0000.0000.000
36A36SER 0-0.046-0.01316.981-0.015-0.0150.0000.0000.0000.000
37A37MET 00.0050.04120.2000.0040.0040.0000.0000.0000.000
38A38VAL 0-0.012-0.00923.3840.0000.0000.0000.0000.0000.000
39A39SER 00.010-0.00826.706-0.001-0.0010.0000.0000.0000.000
40A40GLU -1-0.924-0.95430.2440.0390.0390.0000.0000.0000.000
41A41ASN 0-0.025-0.00432.179-0.006-0.0060.0000.0000.0000.000
42A42NME 0-0.0040.00235.0950.0000.0000.0000.0000.0000.000
43A50ACE 00.0570.01830.357-0.001-0.0010.0000.0000.0000.000
44A51ASN 0-0.006-0.02027.9030.0010.0010.0000.0000.0000.000
45A52VAL 00.0950.04424.3320.0060.0060.0000.0000.0000.000
46A53GLU -1-0.957-0.91823.5190.1090.1090.0000.0000.0000.000
47A54LEU 00.0310.01924.0260.0110.0110.0000.0000.0000.000
48A55THR 0-0.040-0.08319.8200.0160.0160.0000.0000.0000.000
49A56SER 00.001-0.00618.6830.0260.0260.0000.0000.0000.000
50A57LEU 0-0.0230.00018.6560.0290.0290.0000.0000.0000.000
51A58GLN 00.0570.03017.8180.0250.0250.0000.0000.0000.000
52A59ALA 00.0290.03314.5990.0350.0350.0000.0000.0000.000
53A60ARG 10.9230.96513.956-0.157-0.1570.0000.0000.0000.000
54A61ALA 0-0.006-0.00315.2890.0360.0360.0000.0000.0000.000
55A62LEU 00.0030.01111.9040.0190.0190.0000.0000.0000.000
56A63GLY 0-0.059-0.01510.7530.1180.1180.0000.0000.0000.000
57A64ILE 0-0.037-0.0168.1810.2000.2000.0000.0000.0000.000
58A65PRO 0-0.018-0.0049.001-0.127-0.1270.0000.0000.0000.000
59A66ILE 00.000-0.00611.987-0.025-0.0250.0000.0000.0000.000
60A67ILE 0-0.009-0.00314.317-0.011-0.0110.0000.0000.0000.000
61A68LYS 10.9010.95617.240-0.146-0.1460.0000.0000.0000.000
62A69GLY 00.053-0.00120.919-0.007-0.0070.0000.0000.0000.000
63A70PHE 0-0.040-0.03423.1370.0020.0020.0000.0000.0000.000
64A71THR 00.0310.02626.900-0.005-0.0050.0000.0000.0000.000
65A72LYS 10.8620.90329.598-0.047-0.0470.0000.0000.0000.000
66A73GLY 00.1300.06331.800-0.001-0.0010.0000.0000.0000.000
67A74GLU -1-0.992-0.96433.3320.0220.0220.0000.0000.0000.000
68A75LYS 10.9200.93433.204-0.015-0.0150.0000.0000.0000.000
69A76GLU -1-0.957-0.98033.5830.0050.0050.0000.0000.0000.000
70A77LYS 10.9951.01530.995-0.021-0.0210.0000.0000.0000.000
71A78GLU -1-0.888-0.95228.7910.0280.0280.0000.0000.0000.000
72A79VAL 0-0.036-0.02827.4740.0020.0020.0000.0000.0000.000
73A80GLU -1-0.911-0.95526.830-0.001-0.0010.0000.0000.0000.000
74A81ASP -1-0.842-0.91926.3680.0270.0270.0000.0000.0000.000
75A82LEU 0-0.058-0.03220.9050.0050.0050.0000.0000.0000.000
76A83LYS 10.9230.95221.9850.0220.0220.0000.0000.0000.000
77A84ASN 00.013-0.01522.329-0.007-0.0070.0000.0000.0000.000
78A85VAL 0-0.050-0.00718.4590.0050.0050.0000.0000.0000.000
79A86LEU 0-0.055-0.04317.1570.0050.0050.0000.0000.0000.000
80A87GLU -1-0.918-0.94617.676-0.034-0.0340.0000.0000.0000.000
81A88GLY 0-0.0080.01018.664-0.014-0.0140.0000.0000.0000.000
82A89LEU 0-0.093-0.05113.5200.0160.0160.0000.0000.0000.000
83A90LYS 10.9300.95811.7340.1250.1250.0000.0000.0000.000
84A91VAL 0-0.061-0.02510.473-0.048-0.0480.0000.0000.0000.000
85A92ASP -1-0.813-0.91011.826-0.411-0.4110.0000.0000.0000.000
86A93GLY 00.007-0.01613.5040.0260.0260.0000.0000.0000.000
87A94ILE 0-0.0220.01014.0050.0140.0140.0000.0000.0000.000
88A95VAL 0-0.002-0.00913.430-0.012-0.0120.0000.0000.0000.000
89A96ALA 00.009-0.00616.3990.0250.0250.0000.0000.0000.000
90A97GLY 00.041-0.00919.739-0.002-0.0020.0000.0000.0000.000
91A98ALA 0-0.0380.00121.7240.0010.0010.0000.0000.0000.000
92A99LEU 00.0290.01724.793-0.002-0.0020.0000.0000.0000.000
93A100ALA 00.0740.02627.375-0.004-0.0040.0000.0000.0000.000
94A101SER 00.0090.01030.006-0.004-0.0040.0000.0000.0000.000
95A102ARG 11.0251.00729.9140.0120.0120.0000.0000.0000.000
96A103TYR 00.0400.02031.267-0.002-0.0020.0000.0000.0000.000
97A104GLN 0-0.002-0.01027.866-0.001-0.0010.0000.0000.0000.000
98A105LYS 10.8660.94225.8480.0250.0250.0000.0000.0000.000
99A106GLU -1-0.876-0.93427.085-0.020-0.0200.0000.0000.0000.000
100A107ARG 10.9170.96728.385-0.009-0.0090.0000.0000.0000.000
101A108ILE 00.007-0.00122.408-0.001-0.0010.0000.0000.0000.000
102A109GLU -1-0.898-0.95523.946-0.034-0.0340.0000.0000.0000.000
103A110ASN 0-0.006-0.01025.543-0.011-0.0110.0000.0000.0000.000
104A111VAL 00.0380.03823.028-0.003-0.0030.0000.0000.0000.000
105A112ALA 00.026-0.00220.963-0.005-0.0050.0000.0000.0000.000
106A113ARG 10.8990.95322.4400.0300.0300.0000.0000.0000.000
107A114GLU -1-0.924-0.96225.095-0.031-0.0310.0000.0000.0000.000
108A115LEU 0-0.043-0.01020.5400.0000.0000.0000.0000.0000.000
109A116GLY 0-0.0290.00720.977-0.012-0.0120.0000.0000.0000.000
110A117LEU 0-0.040-0.00816.221-0.017-0.0170.0000.0000.0000.000
111A118LYS 10.9130.95316.8960.2170.2170.0000.0000.0000.000
112A119VAL 00.0170.00517.8780.0060.0060.0000.0000.0000.000
113A120TYR 0-0.0020.00114.447-0.004-0.0040.0000.0000.0000.000
114A121THR 0-0.009-0.01818.9200.0150.0150.0000.0000.0000.000
115A122PRO 00.0090.01118.036-0.003-0.0030.0000.0000.0000.000
116A123ALA 00.032-0.01120.8490.0020.0020.0000.0000.0000.000
117A124TRP 0-0.071-0.04423.8580.0020.0020.0000.0000.0000.000
118A125GLU -1-0.921-0.96226.222-0.018-0.0180.0000.0000.0000.000
119A126LYS 10.8681.00224.679-0.011-0.0110.0000.0000.0000.000
120A127ASP -1-0.839-0.93529.2350.0150.0150.0000.0000.0000.000
121A128PRO 00.0590.02630.8440.0040.0040.0000.0000.0000.000
122A129TYR 0-0.030-0.05131.2740.0040.0040.0000.0000.0000.000
123A130GLN 00.005-0.02630.5700.0040.0040.0000.0000.0000.000
124A131TYR 0-0.069-0.04423.9640.0040.0040.0000.0000.0000.000
125A132MET 0-0.013-0.00627.3370.0080.0080.0000.0000.0000.000
126A133LEU 00.012-0.00228.7840.0060.0060.0000.0000.0000.000
127A134GLU -1-0.837-0.84823.2440.0290.0290.0000.0000.0000.000
128A135ILE 00.0120.00023.4890.0070.0070.0000.0000.0000.000
129A136ILE 0-0.029-0.00524.7850.0090.0090.0000.0000.0000.000
130A137LYS 10.9130.95226.303-0.025-0.0250.0000.0000.0000.000
131A138LEU 0-0.077-0.02720.5090.0040.0040.0000.0000.0000.000
132A139GLY 00.0170.00821.6290.0130.0130.0000.0000.0000.000
133A140PHE 0-0.053-0.02119.0280.0140.0140.0000.0000.0000.000
134A141LYS 10.8260.91923.431-0.101-0.1010.0000.0000.0000.000
135A142VAL 00.014-0.01024.7100.0080.0080.0000.0000.0000.000
136A143VAL 00.0590.03626.908-0.006-0.0060.0000.0000.0000.000
137A144PHE 00.0030.00829.4050.0020.0020.0000.0000.0000.000
138A145VAL 00.012-0.00329.1180.0000.0000.0000.0000.0000.000
139A146ALA 00.0280.01832.145-0.001-0.0010.0000.0000.0000.000
140A147VAL 0-0.055-0.01834.4590.0000.0000.0000.0000.0000.000
141A148SER 0-0.009-0.01737.130-0.001-0.0010.0000.0000.0000.000
142A149ALA 00.0990.05139.309-0.002-0.0020.0000.0000.0000.000
143A150TYR 00.0040.00841.2780.0010.0010.0000.0000.0000.000
144A151GLY 00.0440.01244.089-0.001-0.0010.0000.0000.0000.000
145A152LEU 0-0.072-0.02437.7590.0010.0010.0000.0000.0000.000
146A153ASN 00.0400.06841.8220.0020.0020.0000.0000.0000.000
147A154GLU -1-0.819-0.93841.4090.0390.0390.0000.0000.0000.000
148A155SER 0-0.139-0.10940.9430.0030.0030.0000.0000.0000.000
149A156TRP 00.0240.00736.1030.0030.0030.0000.0000.0000.000
150A157LEU 0-0.0340.00736.0160.0040.0040.0000.0000.0000.000
151A158GLY 00.008-0.01133.618-0.001-0.0010.0000.0000.0000.000
152A159ARG 10.7890.92034.086-0.038-0.0380.0000.0000.0000.000
153A160GLU -1-0.911-0.96729.7560.0800.0800.0000.0000.0000.000
154A161LEU 0-0.039-0.00428.258-0.006-0.0060.0000.0000.0000.000
155A162ASN 00.0640.04030.4880.0000.0000.0000.0000.0000.000
156A163TYR 00.0750.00930.708-0.003-0.0030.0000.0000.0000.000
157A164LYS 10.9610.98934.724-0.040-0.0400.0000.0000.0000.000
158A165ASN 0-0.040-0.05334.663-0.005-0.0050.0000.0000.0000.000
159A166LEU 00.0230.02032.232-0.001-0.0010.0000.0000.0000.000
160A167GLU -1-0.830-0.88635.5050.0210.0210.0000.0000.0000.000
161A168GLU -1-0.934-0.97438.8330.0310.0310.0000.0000.0000.000
162A169LEU 00.0250.01834.505-0.001-0.0010.0000.0000.0000.000
163A170LYS 10.8380.91938.255-0.018-0.0180.0000.0000.0000.000
164A171LYS 10.9210.96439.541-0.020-0.0200.0000.0000.0000.000
165A172LEU 0-0.022-0.02541.435-0.002-0.0020.0000.0000.0000.000
166A173SER 0-0.025-0.01039.268-0.001-0.0010.0000.0000.0000.000
167A174GLU -1-0.858-0.92941.3740.0140.0140.0000.0000.0000.000
168A175LYS 10.8310.90744.188-0.018-0.0180.0000.0000.0000.000
169A176TYR 0-0.024-0.01444.0460.0000.0000.0000.0000.0000.000
170A177GLY 0-0.0090.02043.1220.0000.0000.0000.0000.0000.000
171A178ILE 00.0160.02838.1420.0000.0000.0000.0000.0000.000
172A179HIS 0-0.0570.00535.170-0.001-0.0010.0000.0000.0000.000
173A180ILE 00.006-0.01534.1010.0030.0030.0000.0000.0000.000
174A181ALA 0-0.001-0.02229.9100.0040.0040.0000.0000.0000.000
175A182GLY 00.0000.00630.5990.0040.0040.0000.0000.0000.000
176A183GLU -1-0.841-0.93731.4290.0220.0220.0000.0000.0000.000
177A184GLY 00.012-0.00232.755-0.001-0.0010.0000.0000.0000.000
178A185GLY 00.0050.01133.4850.0000.0000.0000.0000.0000.000
179A186GLU -1-0.881-0.93534.4470.0250.0250.0000.0000.0000.000
180A187PHE 0-0.025-0.01730.8050.0020.0020.0000.0000.0000.000
181A188GLU -1-0.940-0.94229.7400.0580.0580.0000.0000.0000.000
182A189THR 0-0.050-0.04426.8930.0020.0020.0000.0000.0000.000
183A190PHE 00.0420.02123.2330.0050.0050.0000.0000.0000.000
184A191VAL 0-0.036-0.01320.674-0.005-0.0050.0000.0000.0000.000
185A192LEU 00.0210.01322.1840.0150.0150.0000.0000.0000.000
186A193ASP -1-0.777-0.90820.3130.1860.1860.0000.0000.0000.000
187A194MET 00.0140.05614.774-0.015-0.0150.0000.0000.0000.000
188A195PRO 00.028-0.00216.7430.0270.0270.0000.0000.0000.000
189A196PHE 00.021-0.01111.3690.0110.0110.0000.0000.0000.000
190A197PHE 0-0.0720.00113.2920.0680.0680.0000.0000.0000.000
191A198LYS 10.9730.97310.227-0.722-0.7220.0000.0000.0000.000
192A199ALA 0-0.0080.00115.871-0.025-0.0250.0000.0000.0000.000
193A200LYS 10.8950.95319.274-0.131-0.1310.0000.0000.0000.000
194A201ILE 0-0.017-0.00820.6650.0020.0020.0000.0000.0000.000
195A202VAL 00.0120.01224.121-0.010-0.0100.0000.0000.0000.000
196A203ILE 0-0.004-0.01527.7770.0020.0020.0000.0000.0000.000
197A204ASP -1-0.903-0.94030.3650.1000.1000.0000.0000.0000.000
198A205ASP -1-0.898-0.96732.7870.0590.0590.0000.0000.0000.000
199A206ALA 0-0.017-0.00133.4950.0050.0050.0000.0000.0000.000
200A207GLU -1-0.834-0.87535.5400.0480.0480.0000.0000.0000.000
201A208LYS 10.9090.95137.434-0.044-0.0440.0000.0000.0000.000
202A209PHE 00.0250.02238.183-0.001-0.0010.0000.0000.0000.000
203A210TRP 00.0520.02340.4560.0010.0010.0000.0000.0000.000
204A211ASP -1-0.818-0.90642.7380.0310.0310.0000.0000.0000.000
205A212GLY 0-0.002-0.01045.020-0.002-0.0020.0000.0000.0000.000
206A213LEU 0-0.104-0.05145.193-0.002-0.0020.0000.0000.0000.000
207A214SER 0-0.0180.01239.8460.0000.0000.0000.0000.0000.000
208A215GLY 0-0.001-0.01239.3550.0000.0000.0000.0000.0000.000
209A216LYS 10.9290.95235.136-0.045-0.0450.0000.0000.0000.000
210A217PHE 00.001-0.00132.339-0.001-0.0010.0000.0000.0000.000
211A218ILE 00.0050.00932.9090.0040.0040.0000.0000.0000.000
212A219ILE 00.007-0.02428.325-0.001-0.0010.0000.0000.0000.000
213A220LYS 10.8140.90731.456-0.057-0.0570.0000.0000.0000.000
214A221ARG 10.9420.97230.928-0.083-0.0830.0000.0000.0000.000
215A222ALA 00.0180.00327.455-0.003-0.0030.0000.0000.0000.000
216A223HIS 10.8160.91825.994-0.113-0.1130.0000.0000.0000.000
217A224LEU 0-0.020-0.02919.6010.0020.0020.0000.0000.0000.000
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