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About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: R1JY8

Calculation Name: 1D2O-A-Xray309

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1D2O

Chain ID: A

ChEMBL ID:

UniProt ID: Q53654

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 187
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2013794.068636
FMO2-HF: Nuclear repulsion 1939923.266964
FMO2-HF: Total energy -73870.801672
FMO2-MP2: Total energy -74090.134537


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:535:GLU )


Summations of interaction energy for fragment #1(A:535:GLU )
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.
6.9312.4055.441-4.087-6.833-0.012
Interaction energy analysis for fragmet #1(A:535:GLU )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.086 / q_NPA : -0.060
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].
3A537THR 00.0320.0073.26811.56914.9080.269-1.562-2.047-0.003
4A538SER 0-0.004-0.0025.814-1.546-1.5460.0000.0000.0000.000
5A539SER 0-0.0070.0059.5800.0250.0250.0000.0000.0000.000
6A540ILE 00.0160.00512.076-0.193-0.1930.0000.0000.0000.000
7A541GLY 00.0620.01015.426-0.048-0.0480.0000.0000.0000.000
8A542GLU -1-0.970-0.98018.8610.8160.8160.0000.0000.0000.000
9A543LYS 10.8080.92422.560-0.288-0.2880.0000.0000.0000.000
10A544VAL 0-0.014-0.00825.7840.0290.0290.0000.0000.0000.000
11A545TRP 0-0.017-0.02028.711-0.046-0.0460.0000.0000.0000.000
12A546ASP -1-0.922-0.94932.2900.2070.2070.0000.0000.0000.000
13A547ASP -1-0.688-0.84834.6580.1680.1680.0000.0000.0000.000
14A548LYS 10.8840.94337.937-0.155-0.1550.0000.0000.0000.000
15A549ASP -1-0.919-0.96138.2380.2500.2500.0000.0000.0000.000
16A550ASN 00.0160.00838.378-0.017-0.0170.0000.0000.0000.000
17A551GLN 0-0.0090.00840.071-0.003-0.0030.0000.0000.0000.000
18A552ASP -1-0.829-0.89842.9580.0820.0820.0000.0000.0000.000
19A553GLY 0-0.079-0.04142.196-0.010-0.0100.0000.0000.0000.000
20A554LYS 10.8850.94340.750-0.069-0.0690.0000.0000.0000.000
21A555ARG 10.8490.92133.898-0.231-0.2310.0000.0000.0000.000
22A556PRO 0-0.0340.00133.6660.0010.0010.0000.0000.0000.000
23A557GLU -1-0.919-0.97634.4900.2080.2080.0000.0000.0000.000
24A558LYS 10.8780.93729.915-0.029-0.0290.0000.0000.0000.000
25A559VAL 00.0190.03326.754-0.025-0.0250.0000.0000.0000.000
26A560SER 0-0.003-0.01026.0700.0320.0320.0000.0000.0000.000
27A561VAL 0-0.0080.00820.521-0.030-0.0300.0000.0000.0000.000
28A562ASN 0-0.044-0.04621.130-0.025-0.0250.0000.0000.0000.000
29A563LEU 0-0.0170.00113.1600.0140.0140.0000.0000.0000.000
30A564LEU 0-0.018-0.01616.763-0.115-0.1150.0000.0000.0000.000
31A565ALA 00.0080.00012.445-0.059-0.0590.0000.0000.0000.000
32A566ASN 00.0240.00211.8570.1050.1050.0000.0000.0000.000
33A567GLY 00.0470.02015.3100.0620.0620.0000.0000.0000.000
34A568GLU -1-0.934-0.95617.235-1.222-1.2220.0000.0000.0000.000
35A569LYS 10.9540.97417.4180.3430.3430.0000.0000.0000.000
36A570VAL 00.0100.00914.2610.0020.0020.0000.0000.0000.000
37A571LYS 10.8770.93513.2600.6920.6920.0000.0000.0000.000
38A572THR 00.0070.00118.560-0.016-0.0160.0000.0000.0000.000
39A573LEU 0-0.056-0.01918.3730.0410.0410.0000.0000.0000.000
40A574ASP -1-0.872-0.91122.5920.0310.0310.0000.0000.0000.000
41A575VAL 0-0.042-0.01623.2080.0630.0630.0000.0000.0000.000
42A576THR 00.0850.01825.780-0.022-0.0220.0000.0000.0000.000
43A577SER 00.0510.02927.8250.0530.0530.0000.0000.0000.000
44A578GLU -1-0.944-0.95329.2700.3440.3440.0000.0000.0000.000
45A579THR 0-0.061-0.05023.8490.0380.0380.0000.0000.0000.000
46A580ASN 0-0.075-0.07124.8590.0540.0540.0000.0000.0000.000
47A581TRP 0-0.005-0.00926.4650.0210.0210.0000.0000.0000.000
48A582LYS 10.9690.99921.271-0.920-0.9200.0000.0000.0000.000
49A583TYR 0-0.022-0.00817.790-0.078-0.0780.0000.0000.0000.000
50A584GLU -1-0.868-0.96413.4292.2662.2660.0000.0000.0000.000
51A585PHE 0-0.052-0.00113.780-0.139-0.1390.0000.0000.0000.000
52A586LYS 10.9370.94611.797-1.179-1.1790.0000.0000.0000.000
53A587ASP -1-0.926-0.9507.7322.0452.0450.0000.0000.0000.000
54A588LEU 0-0.023-0.0047.843-1.168-1.1680.0000.0000.0000.000
55A589PRO 00.0480.0374.442-0.619-0.5330.000-0.082-0.0050.000
56A590LYS 10.9330.9671.996-0.3711.3242.570-1.389-2.8770.000
57A591TYR 0-0.059-0.0622.0690.4200.7352.602-1.052-1.866-0.009
58A592ASP -1-0.881-0.9355.297-4.615-4.5750.000-0.002-0.0380.000
59A593GLU -1-0.911-0.9468.322-2.529-2.5290.0000.0000.0000.000
60A594GLY 0-0.022-0.0038.0430.7100.7100.0000.0000.0000.000
61A595LYS 10.9220.9577.9891.9171.9170.0000.0000.0000.000
62A596LYS 10.8480.9375.7752.0682.0680.0000.0000.0000.000
63A597ILE 0-0.045-0.0177.3940.9060.9060.0000.0000.0000.000
64A598GLU -1-0.900-0.9549.367-0.972-0.9720.0000.0000.0000.000
65A599TYR 0-0.078-0.0537.8950.2860.2860.0000.0000.0000.000
66A600THR 00.0170.01713.0740.2460.2460.0000.0000.0000.000
67A601VAL 0-0.008-0.01316.780-0.043-0.0430.0000.0000.0000.000
68A602THR 00.005-0.01019.3910.0270.0270.0000.0000.0000.000
69A603GLU -1-0.816-0.91423.0110.1230.1230.0000.0000.0000.000
70A604ASP -1-0.896-0.91825.888-0.204-0.2040.0000.0000.0000.000
71A605HIS 0-0.037-0.04828.6000.0330.0330.0000.0000.0000.000
72A606VAL 0-0.0190.00931.1060.0140.0140.0000.0000.0000.000
73A607LYS 10.9090.93633.774-0.007-0.0070.0000.0000.0000.000
74A608ASP -1-0.872-0.93937.5440.0400.0400.0000.0000.0000.000
75A609TYR 0-0.053-0.04333.9120.0210.0210.0000.0000.0000.000
76A610THR 0-0.003-0.01633.353-0.032-0.0320.0000.0000.0000.000
77A611THR 0-0.036-0.04027.6920.0340.0340.0000.0000.0000.000
78A612ASP -1-0.988-0.98727.6750.0710.0710.0000.0000.0000.000
79A613ILE 0-0.0160.00722.0860.0470.0470.0000.0000.0000.000
80A614ASN 0-0.011-0.01123.193-0.014-0.0140.0000.0000.0000.000
81A615GLY 00.0440.01318.9030.0720.0720.0000.0000.0000.000
82A616THR 0-0.0030.01816.3200.0640.0640.0000.0000.0000.000
83A617THR 0-0.0180.01618.8890.0360.0360.0000.0000.0000.000
84A618ILE 0-0.030-0.00621.996-0.078-0.0780.0000.0000.0000.000
85A619THR 00.003-0.00324.9410.0450.0450.0000.0000.0000.000
86A620ASN 0-0.045-0.03428.560-0.002-0.0020.0000.0000.0000.000
87A621LYS 10.9570.97631.480-0.119-0.1190.0000.0000.0000.000
88A622TYR 0-0.074-0.05434.874-0.023-0.0230.0000.0000.0000.000
89A623THR 0-0.037-0.00837.6000.0030.0030.0000.0000.0000.000
90A624PRO 0-0.0060.01339.943-0.014-0.0140.0000.0000.0000.000
91A625GLY 0-0.051-0.01942.437-0.004-0.0040.0000.0000.0000.000
92A626GLU -1-0.934-0.97139.812-0.020-0.0200.0000.0000.0000.000
93A627THR 0-0.019-0.01335.4190.0010.0010.0000.0000.0000.000
94A628SER 00.0020.00131.6350.0060.0060.0000.0000.0000.000
95A629ALA 0-0.038-0.01631.661-0.007-0.0070.0000.0000.0000.000
96A630THR 0-0.026-0.01325.1290.0180.0180.0000.0000.0000.000
97A631VAL 0-0.028-0.00827.061-0.022-0.0220.0000.0000.0000.000
98A632THR 00.0250.01520.4270.0040.0040.0000.0000.0000.000
99A633LYS 10.7450.90522.7470.7410.7410.0000.0000.0000.000
100A634ASN 0-0.008-0.01320.060-0.161-0.1610.0000.0000.0000.000
101A635TRP 0-0.004-0.01619.6660.1170.1170.0000.0000.0000.000
102A636ASP -1-0.838-0.92019.691-1.275-1.2750.0000.0000.0000.000
103A637ASP -1-0.758-0.87520.206-1.163-1.1630.0000.0000.0000.000
104A638ASN 00.0350.03718.136-0.088-0.0880.0000.0000.0000.000
105A639ASN 00.000-0.01113.533-0.237-0.2370.0000.0000.0000.000
106A640ASN 00.0680.01717.1670.1600.1600.0000.0000.0000.000
107A641GLN 0-0.0360.00819.5560.1140.1140.0000.0000.0000.000
108A642ASP -1-0.873-0.93520.910-0.951-0.9510.0000.0000.0000.000
109A643GLY 00.019-0.01323.0300.0400.0400.0000.0000.0000.000
110A644LYS 10.8650.93323.8610.8130.8130.0000.0000.0000.000
111A645ARG 10.8830.96117.2561.3831.3830.0000.0000.0000.000
112A646PRO 0-0.038-0.00824.6400.0150.0150.0000.0000.0000.000
113A647THR 00.016-0.01324.414-0.047-0.0470.0000.0000.0000.000
114A648GLU -1-0.972-0.98924.737-0.428-0.4280.0000.0000.0000.000
115A649ILE 0-0.041-0.00326.3190.0060.0060.0000.0000.0000.000
116A650LYS 10.9250.96428.9400.2980.2980.0000.0000.0000.000
117A651VAL 00.0450.03629.332-0.007-0.0070.0000.0000.0000.000
118A652GLU -1-0.865-0.95932.240-0.200-0.2000.0000.0000.0000.000
119A653LEU 0-0.0040.01133.877-0.011-0.0110.0000.0000.0000.000
120A654TYR 00.0220.01435.9460.0240.0240.0000.0000.0000.000
121A655GLN 00.0300.00938.515-0.002-0.0020.0000.0000.0000.000
122A656ASP -1-0.884-0.96341.158-0.125-0.1250.0000.0000.0000.000
123A657GLY 00.005-0.00541.6780.0050.0050.0000.0000.0000.000
124A658LYS 10.8460.93142.9860.1260.1260.0000.0000.0000.000
125A659ALA 00.0920.06041.0090.0000.0000.0000.0000.0000.000
126A660THR 0-0.059-0.04438.7910.0170.0170.0000.0000.0000.000
127A661GLY 0-0.0120.00840.5090.0150.0150.0000.0000.0000.000
128A662LYS 10.9030.95736.3530.1120.1120.0000.0000.0000.000
129A663THR 0-0.009-0.01034.193-0.021-0.0210.0000.0000.0000.000
130A664ALA 00.0010.00729.7900.0190.0190.0000.0000.0000.000
131A665ILE 0-0.009-0.01028.603-0.016-0.0160.0000.0000.0000.000
132A666LEU 0-0.0300.00324.7730.0090.0090.0000.0000.0000.000
133A667ASN 00.0860.04023.536-0.026-0.0260.0000.0000.0000.000
134A668GLU -1-0.870-0.94717.407-1.159-1.1590.0000.0000.0000.000
135A669SER 0-0.118-0.05919.8510.0440.0440.0000.0000.0000.000
136A670ASN 00.0270.00022.1150.0140.0140.0000.0000.0000.000
137A671ASN 00.0500.02917.495-0.049-0.0490.0000.0000.0000.000
138A672TRP 0-0.066-0.01918.7900.0010.0010.0000.0000.0000.000
139A673THR 0-0.009-0.02121.0680.0030.0030.0000.0000.0000.000
140A674HIS 0-0.037-0.02523.4960.0530.0530.0000.0000.0000.000
141A675THR 00.0340.02726.863-0.031-0.0310.0000.0000.0000.000
142A676TRP 0-0.045-0.01229.1040.0190.0190.0000.0000.0000.000
143A677THR 00.036-0.00832.9080.0050.0050.0000.0000.0000.000
144A678GLY 00.0220.01535.242-0.010-0.0100.0000.0000.0000.000
145A679LEU 0-0.070-0.02635.262-0.011-0.0110.0000.0000.0000.000
146A680ASP -1-0.842-0.90339.297-0.042-0.0420.0000.0000.0000.000
147A681GLU -1-0.788-0.89639.065-0.036-0.0360.0000.0000.0000.000
148A682LYS 10.8710.91841.7460.0310.0310.0000.0000.0000.000
149A683ALA 00.0790.04845.3340.0020.0020.0000.0000.0000.000
150A684LYS 10.9020.93247.9680.0590.0590.0000.0000.0000.000
151A685GLY 00.0210.01150.198-0.002-0.0020.0000.0000.0000.000
152A686GLN 0-0.035-0.01247.6490.0070.0070.0000.0000.0000.000
153A687GLN 00.0090.00939.426-0.003-0.0030.0000.0000.0000.000
154A688VAL 0-0.0390.00240.901-0.010-0.0100.0000.0000.0000.000
155A689LYS 10.8590.93639.3350.1320.1320.0000.0000.0000.000
156A690TYR 0-0.003-0.03736.011-0.003-0.0030.0000.0000.0000.000
157A691THR 0-0.035-0.00734.523-0.013-0.0130.0000.0000.0000.000
158A692VAL 00.0120.00830.3120.0180.0180.0000.0000.0000.000
159A693GLU -1-0.919-0.94933.676-0.299-0.2990.0000.0000.0000.000
160A694GLU -1-0.821-0.90729.089-0.558-0.5580.0000.0000.0000.000
161A695LEU 0-0.028-0.02032.8280.0110.0110.0000.0000.0000.000
162A696THR 0-0.041-0.01031.0980.0110.0110.0000.0000.0000.000
163A697LYN 00.0500.05432.960-0.023-0.0230.0000.0000.0000.000
164A698VAL 00.0200.00628.252-0.003-0.0030.0000.0000.0000.000
165A699LYS 10.8920.91731.6800.4410.4410.0000.0000.0000.000
166A700GLY 00.0430.02330.719-0.027-0.0270.0000.0000.0000.000
167A701TYR 0-0.055-0.08623.369-0.009-0.0090.0000.0000.0000.000
168A702THR 0-0.084-0.02029.4560.0560.0560.0000.0000.0000.000
169A703THR 00.027-0.01129.244-0.052-0.0520.0000.0000.0000.000
170A704HIS 0-0.020-0.00629.2570.0380.0380.0000.0000.0000.000
171A705VAL 0-0.021-0.01428.825-0.039-0.0390.0000.0000.0000.000
172A706ASP -1-0.914-0.92927.814-0.395-0.3950.0000.0000.0000.000
173A707ASN 00.018-0.03729.6850.0080.0080.0000.0000.0000.000
174A708ASN 0-0.018-0.01930.7450.0570.0570.0000.0000.0000.000
175A709ASP -1-0.759-0.86329.352-0.130-0.1300.0000.0000.0000.000
176A710MET 0-0.049-0.02330.136-0.021-0.0210.0000.0000.0000.000
177A711GLY 00.0370.01829.2890.0020.0020.0000.0000.0000.000
178A712ASN 0-0.009-0.01123.476-0.025-0.0250.0000.0000.0000.000
179A713LEU 0-0.0110.03526.715-0.038-0.0380.0000.0000.0000.000
180A714ILE 00.0220.01222.365-0.034-0.0340.0000.0000.0000.000
181A715THR 0-0.0080.00525.6570.0270.0270.0000.0000.0000.000
182A716THR 0-0.025-0.01423.964-0.067-0.0670.0000.0000.0000.000
183A717ASN 0-0.041-0.03524.5980.0640.0640.0000.0000.0000.000
184A718LYS 10.9520.98124.5490.6890.6890.0000.0000.0000.000
185A719TYR 0-0.046-0.01024.8230.1070.1070.0000.0000.0000.000
186A720THR 0-0.094-0.05826.648-0.029-0.0290.0000.0000.0000.000
187A721PRO -1-0.949-0.95328.390-0.552-0.5520.0000.0000.0000.000