Manual

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: J34N9

Calculation Name: 1D2O-A-Xray372

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: 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 187
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2014506.112802
FMO2-HF: Nuclear repulsion 1940633.157183
FMO2-HF: Total energy -73872.955619
FMO2-MP2: Total energy -74092.176621


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.
-11.798-10.22420.911-10.634-11.8510.107
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 : -1 / q_Mulliken : -0.849 / q_NPA : -0.915
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].
3A537THR00.011-0.0123.17911.26314.1760.376-1.399-1.8900.003
4A538SER00.010-0.0015.954-4.787-4.7870.0000.0000.0000.000
5A539SER0-0.0170.0049.513-0.153-0.1530.0000.0000.0000.000
6A540ILE00.0090.00712.506-1.313-1.3130.0000.0000.0000.000
7A541GLY00.0610.04315.4500.2200.2200.0000.0000.0000.000
8A542GLU-1-0.918-0.95519.03115.13315.1330.0000.0000.0000.000
9A543LYS10.7720.89922.654-11.607-11.6070.0000.0000.0000.000
10A544VAL0-0.018-0.01825.962-0.222-0.2220.0000.0000.0000.000
11A545TRP0-0.017-0.02128.937-0.072-0.0720.0000.0000.0000.000
12A546ASP-1-0.906-0.94932.5249.2619.2610.0000.0000.0000.000
13A547ASP-1-0.685-0.82335.0348.8788.8780.0000.0000.0000.000
14A548LYS10.8720.92638.244-7.581-7.5810.0000.0000.0000.000
15A549ASP-1-0.927-0.96138.1488.3648.3640.0000.0000.0000.000
16A550ASN00.0220.01438.310-0.205-0.2050.0000.0000.0000.000
17A551GLN00.0080.01740.146-0.202-0.2020.0000.0000.0000.000
18A552ASP-1-0.831-0.88743.1557.1107.1100.0000.0000.0000.000
19A553GLY0-0.044-0.02542.166-0.127-0.1270.0000.0000.0000.000
20A554LYS10.8380.91240.923-7.377-7.3770.0000.0000.0000.000
21A555ARG10.8370.90234.059-9.163-9.1630.0000.0000.0000.000
22A556PRO0-0.0280.00633.630-0.145-0.1450.0000.0000.0000.000
23A557GLU-1-0.902-0.97234.2889.2239.2230.0000.0000.0000.000
24A558LYS10.7550.86929.660-10.518-10.5180.0000.0000.0000.000
25A559VAL00.0050.01926.857-0.298-0.2980.0000.0000.0000.000
26A560SER0-0.017-0.01926.1250.1630.1630.0000.0000.0000.000
27A561VAL00.0080.01520.881-0.090-0.0900.0000.0000.0000.000
28A562ASN0-0.028-0.02821.2580.3130.3130.0000.0000.0000.000
29A563LEU0-0.0130.00413.4310.2870.2870.0000.0000.0000.000
30A564LEU0-0.011-0.01417.325-0.499-0.4990.0000.0000.0000.000
31A565ALA00.0130.00212.7171.3601.3600.0000.0000.0000.000
32A566ASN00.002-0.01612.419-0.253-0.2530.0000.0000.0000.000
33A567GLY00.0550.02216.104-0.774-0.7740.0000.0000.0000.000
34A568GLU-1-0.891-0.92617.34114.27414.2740.0000.0000.0000.000
35A569LYS10.9020.93917.634-11.978-11.9780.0000.0000.0000.000
36A570VAL00.0020.00414.122-0.243-0.2430.0000.0000.0000.000
37A571LYS10.8720.94112.785-22.307-22.3070.0000.0000.0000.000
38A572THR00.013-0.00118.536-0.089-0.0890.0000.0000.0000.000
39A573LEU0-0.041-0.01018.0620.2120.2120.0000.0000.0000.000
40A574ASP-1-0.785-0.85622.43611.31511.3150.0000.0000.0000.000
41A575VAL0-0.047-0.02123.0220.2760.2760.0000.0000.0000.000
42A576THR00.045-0.02125.556-0.373-0.3730.0000.0000.0000.000
43A577SER00.0580.03827.4450.4010.4010.0000.0000.0000.000
44A578GLU-1-0.882-0.90428.40510.78610.7860.0000.0000.0000.000
45A579THR0-0.046-0.03223.3750.0180.0180.0000.0000.0000.000
46A580ASN0-0.094-0.07524.3490.2740.2740.0000.0000.0000.000
47A581TRP0-0.021-0.01226.2210.1390.1390.0000.0000.0000.000
48A582LYS10.9200.97420.796-14.701-14.7010.0000.0000.0000.000
49A583TYR0-0.027-0.02818.173-0.226-0.2260.0000.0000.0000.000
50A584GLU-1-0.866-0.96313.01623.22223.2220.0000.0000.0000.000
51A585PHE0-0.053-0.00913.869-0.434-0.4340.0000.0000.0000.000
52A586LYS10.9220.95111.123-19.478-19.4780.0000.0000.0000.000
53A587ASP-1-0.932-0.9617.48930.89630.8960.0000.0000.0000.000
54A588LEU0-0.024-0.0017.567-3.431-3.4310.0000.0000.0000.000
55A589PRO00.0520.0364.4137.5537.660-0.001-0.091-0.0150.000
56A590LYS10.8790.9451.681-124.351-127.11118.734-8.090-7.8840.095
57A591TYR0-0.050-0.0462.362-3.602-2.2881.802-1.054-2.0620.009
58A592ASP-1-0.910-0.9556.00622.79422.7940.0000.0000.0000.000
59A593GLU-1-0.921-0.9568.23417.59917.5990.0000.0000.0000.000
60A594GLY0-0.024-0.0058.098-1.649-1.6490.0000.0000.0000.000
61A595LYS10.8580.9388.619-19.571-19.5710.0000.0000.0000.000
62A596LYS10.8140.8937.217-26.694-26.6940.0000.0000.0000.000
63A597ILE0-0.029-0.0127.575-3.429-3.4290.0000.0000.0000.000
64A598GLU-1-0.820-0.88610.28124.79424.7940.0000.0000.0000.000
65A599TYR0-0.041-0.0468.156-2.233-2.2330.0000.0000.0000.000
66A600THR00.0120.00813.728-0.311-0.3110.0000.0000.0000.000
67A601VAL0-0.001-0.00317.3860.3720.3720.0000.0000.0000.000
68A602THR00.012-0.01819.864-0.418-0.4180.0000.0000.0000.000
69A603GLU-1-0.767-0.88923.53112.34312.3430.0000.0000.0000.000
70A604ASP-1-0.891-0.91326.30911.62011.6200.0000.0000.0000.000
71A605HIS0-0.034-0.04128.927-0.067-0.0670.0000.0000.0000.000
72A606VAL0-0.0080.00831.440-0.114-0.1140.0000.0000.0000.000
73A607LYS10.7680.84134.187-7.988-7.9880.0000.0000.0000.000
74A608ASP-1-0.830-0.90237.9587.8007.8000.0000.0000.0000.000
75A609TYR0-0.013-0.03234.365-0.103-0.1030.0000.0000.0000.000
76A610THR0-0.015-0.00533.9960.0930.0930.0000.0000.0000.000
77A611THR0-0.031-0.04128.085-0.027-0.0270.0000.0000.0000.000
78A612ASP-1-0.919-0.94728.46311.22211.2220.0000.0000.0000.000
79A613ILE0-0.0070.00722.4710.1950.1950.0000.0000.0000.000
80A614ASN0-0.009-0.01023.5030.4340.4340.0000.0000.0000.000
81A615GLY00.0480.01719.2940.3530.3530.0000.0000.0000.000
82A616THR0-0.012-0.02217.0430.4660.4660.0000.0000.0000.000
83A617THR0-0.0180.01019.336-0.172-0.1720.0000.0000.0000.000
84A618ILE0-0.034-0.00522.430-0.410-0.4100.0000.0000.0000.000
85A619THR00.000-0.00325.395-0.328-0.3280.0000.0000.0000.000
86A620ASN0-0.044-0.01729.042-0.151-0.1510.0000.0000.0000.000
87A621LYS10.9060.95031.708-10.447-10.4470.0000.0000.0000.000
88A622TYR0-0.065-0.04935.305-0.065-0.0650.0000.0000.0000.000
89A623THR0-0.029-0.00338.089-0.033-0.0330.0000.0000.0000.000
90A624PRO00.0130.01040.3460.0080.0080.0000.0000.0000.000
91A625GLY0-0.061-0.02342.933-0.142-0.1420.0000.0000.0000.000
92A626GLU-1-0.935-0.97740.1837.8157.8150.0000.0000.0000.000
93A627THR0-0.026-0.02035.8360.1890.1890.0000.0000.0000.000
94A628SER00.0080.00832.326-0.043-0.0430.0000.0000.0000.000
95A629ALA0-0.035-0.01932.271-0.065-0.0650.0000.0000.0000.000
96A630THR0-0.0070.00525.768-0.049-0.0490.0000.0000.0000.000
97A631VAL0-0.032-0.00127.811-0.113-0.1130.0000.0000.0000.000
98A632THR00.0220.01121.1480.2120.2120.0000.0000.0000.000
99A633LYS10.7420.87423.608-11.930-11.9300.0000.0000.0000.000
100A634ASN0-0.046-0.03620.1640.9850.9850.0000.0000.0000.000
101A635TRP0-0.031-0.02020.454-1.093-1.0930.0000.0000.0000.000
102A636ASP-1-0.835-0.91620.11513.48713.4870.0000.0000.0000.000
103A637ASP-1-0.760-0.89720.70513.10413.1040.0000.0000.0000.000
104A638ASN00.0000.02118.1040.2370.2370.0000.0000.0000.000
105A639ASN00.0300.00613.4030.2750.2750.0000.0000.0000.000
106A640ASN00.0590.01117.641-0.955-0.9550.0000.0000.0000.000
107A641GLN0-0.0130.00819.579-0.871-0.8710.0000.0000.0000.000
108A642ASP-1-0.811-0.86821.29310.30810.3080.0000.0000.0000.000
109A643GLY00.0320.00023.841-0.127-0.1270.0000.0000.0000.000
110A644LYS10.7640.88224.665-10.843-10.8430.0000.0000.0000.000
111A645ARG10.8900.96318.482-15.166-15.1660.0000.0000.0000.000
112A646PRO0-0.051-0.01225.584-0.018-0.0180.0000.0000.0000.000
113A647THR00.026-0.01025.3970.3160.3160.0000.0000.0000.000
114A648GLU-1-0.936-0.96525.69810.97810.9780.0000.0000.0000.000
115A649ILE0-0.065-0.01627.498-0.342-0.3420.0000.0000.0000.000
116A650LYS10.9240.97229.895-8.632-8.6320.0000.0000.0000.000
117A651VAL00.0510.02930.169-0.162-0.1620.0000.0000.0000.000
118A652GLU-1-0.851-0.94733.1317.9527.9520.0000.0000.0000.000
119A653LEU0-0.0020.01134.6730.0590.0590.0000.0000.0000.000
120A654TYR0-0.059-0.03536.746-0.338-0.3380.0000.0000.0000.000
121A655GLN00.010-0.00239.271-0.004-0.0040.0000.0000.0000.000
122A656ASP-1-0.812-0.89841.9037.1157.1150.0000.0000.0000.000
123A657GLY00.004-0.00842.350-0.197-0.1970.0000.0000.0000.000
124A658LYS10.8340.93543.666-7.093-7.0930.0000.0000.0000.000
125A659ALA00.0460.03641.8430.1510.1510.0000.0000.0000.000
126A660THR0-0.046-0.05339.655-0.115-0.1150.0000.0000.0000.000
127A661GLY0-0.0160.00741.326-0.130-0.1300.0000.0000.0000.000
128A662LYS10.8960.95837.141-8.066-8.0660.0000.0000.0000.000
129A663THR0-0.004-0.01435.7530.1220.1220.0000.0000.0000.000
130A664ALA00.0160.01630.6350.0570.0570.0000.0000.0000.000
131A665ILE0-0.008-0.00729.495-0.176-0.1760.0000.0000.0000.000
132A666LEU0-0.0300.00525.7000.2240.2240.0000.0000.0000.000
133A667ASN00.0770.02124.4560.2150.2150.0000.0000.0000.000
134A668GLU-1-0.853-0.92518.44316.71616.7160.0000.0000.0000.000
135A669SER0-0.121-0.06220.6900.4500.4500.0000.0000.0000.000
136A670ASN00.0300.00622.8760.3620.3620.0000.0000.0000.000
137A671ASN0-0.012-0.01617.053-0.804-0.8040.0000.0000.0000.000
138A672TRP0-0.074-0.03319.786-0.404-0.4040.0000.0000.0000.000
139A673THR0-0.007-0.01121.755-0.221-0.2210.0000.0000.0000.000
140A674HIS0-0.021-0.01124.283-0.213-0.2130.0000.0000.0000.000
141A675THR00.0070.00027.6090.1120.1120.0000.0000.0000.000
142A676TRP0-0.059-0.02629.778-0.172-0.1720.0000.0000.0000.000
143A677THR00.038-0.00633.4050.0220.0220.0000.0000.0000.000
144A678GLY00.0260.02135.813-0.129-0.1290.0000.0000.0000.000
145A679LEU0-0.079-0.02935.915-0.225-0.2250.0000.0000.0000.000
146A680ASP-1-0.843-0.91439.9237.4177.4170.0000.0000.0000.000
147A681GLU-1-0.740-0.85239.3578.2688.2680.0000.0000.0000.000
148A682LYS10.8320.89542.309-7.043-7.0430.0000.0000.0000.000
149A683ALA00.0820.04845.909-0.034-0.0340.0000.0000.0000.000
150A684LYS10.9140.94248.589-5.970-5.9700.0000.0000.0000.000
151A685GLY00.0380.01850.739-0.072-0.0720.0000.0000.0000.000
152A686GLN0-0.0080.00548.0990.0320.0320.0000.0000.0000.000
153A687GLN00.0110.01439.715-0.099-0.0990.0000.0000.0000.000
154A688VAL0-0.053-0.00742.048-0.070-0.0700.0000.0000.0000.000
155A689LYS10.8070.87939.901-7.188-7.1880.0000.0000.0000.000
156A690TYR00.011-0.02336.754-0.173-0.1730.0000.0000.0000.000
157A691THR00.0190.01035.1970.0760.0760.0000.0000.0000.000
158A692VAL0-0.024-0.00831.044-0.106-0.1060.0000.0000.0000.000
159A693GLU-1-0.869-0.90834.4578.1008.1000.0000.0000.0000.000
160A694GLU-1-0.781-0.87929.90210.55010.5500.0000.0000.0000.000
161A695LEU0-0.021-0.01733.716-0.230-0.2300.0000.0000.0000.000
162A696THR0-0.038-0.00732.102-0.161-0.1610.0000.0000.0000.000
163A697LYN00.0920.07233.8690.0650.0650.0000.0000.0000.000
164A698VAL00.0230.00829.047-0.010-0.0100.0000.0000.0000.000
165A699LYS10.8670.90932.402-8.266-8.2660.0000.0000.0000.000
166A700GLY00.0270.01431.2080.1870.1870.0000.0000.0000.000
167A701TYR0-0.044-0.06824.119-0.002-0.0020.0000.0000.0000.000
168A702THR0-0.093-0.02729.771-0.339-0.3390.0000.0000.0000.000
169A703THR00.017-0.00929.6010.3720.3720.0000.0000.0000.000
170A704HIS00.0010.00829.426-0.464-0.4640.0000.0000.0000.000
171A705VAL0-0.031-0.01829.1960.3740.3740.0000.0000.0000.000
172A706ASP-1-0.859-0.89828.10910.40910.4090.0000.0000.0000.000
173A707ASN00.013-0.04030.1020.2200.2200.0000.0000.0000.000
174A708ASN0-0.064-0.04730.858-0.514-0.5140.0000.0000.0000.000
175A709ASP-1-0.740-0.85329.76610.26510.2650.0000.0000.0000.000
176A710MET0-0.052-0.02030.6700.1480.1480.0000.0000.0000.000
177A711GLY00.0240.01329.8340.0430.0430.0000.0000.0000.000
178A712ASN0-0.025-0.01124.3100.9940.9940.0000.0000.0000.000
179A713LEU00.0050.04327.250-0.032-0.0320.0000.0000.0000.000
180A714ILE00.0230.01222.7640.3680.3680.0000.0000.0000.000
181A715THR0-0.021-0.00126.340-0.581-0.5810.0000.0000.0000.000
182A716THR00.0090.00224.4120.4750.4750.0000.0000.0000.000
183A717ASN0-0.052-0.03425.127-0.473-0.4730.0000.0000.0000.000
184A718LYS10.9620.99024.951-10.206-10.2060.0000.0000.0000.000
185A719TYR0-0.068-0.05125.096-0.673-0.6730.0000.0000.0000.000
186A720THR0-0.082-0.04826.8900.0930.0930.0000.0000.0000.000
187A721PRO00.0030.01728.489-0.398-0.3980.0000.0000.0000.000