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: N1ZKQ

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 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 187
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2013751.712172
FMO2-HF: Nuclear repulsion 1939880.696542
FMO2-HF: Total energy -73871.015631
FMO2-MP2: Total energy -74090.358755


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.
41.71951.0933.305-5.181-7.4970.044
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 : -0.886 / q_NPA : -0.962
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].
3A537THR00.0180.0003.26811.43014.6620.269-1.558-1.9420.001
4A538SER0-0.017-0.0115.814-4.517-4.5170.0000.0000.0000.000
5A539SER0-0.0100.0039.5800.0690.0690.0000.0000.0000.000
6A540ILE00.0120.00312.077-1.334-1.3340.0000.0000.0000.000
7A541GLY00.0590.00915.4260.1890.1890.0000.0000.0000.000
8A542GLU-1-0.972-0.98218.86114.65214.6520.0000.0000.0000.000
9A543LYS10.8090.92422.560-11.584-11.5840.0000.0000.0000.000
10A544VAL0-0.011-0.00725.784-0.210-0.2100.0000.0000.0000.000
11A545TRP0-0.017-0.02128.711-0.080-0.0800.0000.0000.0000.000
12A546ASP-1-0.923-0.94932.2909.1349.1340.0000.0000.0000.000
13A547ASP-1-0.689-0.84834.6588.8168.8160.0000.0000.0000.000
14A548LYS10.8830.94337.937-7.515-7.5150.0000.0000.0000.000
15A549ASP-1-0.920-0.96238.2388.2658.2650.0000.0000.0000.000
16A550ASN00.0160.00838.378-0.156-0.1560.0000.0000.0000.000
17A551GLN0-0.0100.00640.071-0.213-0.2130.0000.0000.0000.000
18A552ASP-1-0.827-0.89742.9587.0277.0270.0000.0000.0000.000
19A553GLY0-0.082-0.04242.196-0.102-0.1020.0000.0000.0000.000
20A554LYS10.8850.94340.750-7.320-7.3200.0000.0000.0000.000
21A555ARG10.8490.92133.898-9.067-9.0670.0000.0000.0000.000
22A556PRO0-0.0360.00133.666-0.137-0.1370.0000.0000.0000.000
23A557GLU-1-0.917-0.97734.4909.1309.1300.0000.0000.0000.000
24A558LYS10.8780.93629.915-10.077-10.0770.0000.0000.0000.000
25A559VAL00.0180.03326.754-0.307-0.3070.0000.0000.0000.000
26A560SER0-0.005-0.01126.0690.1650.1650.0000.0000.0000.000
27A561VAL0-0.0050.00920.528-0.095-0.0950.0000.0000.0000.000
28A562ASN0-0.048-0.04921.1990.3570.3570.0000.0000.0000.000
29A563LEU0-0.0100.00413.2230.3010.3010.0000.0000.0000.000
30A564LEU0-0.025-0.02017.052-0.454-0.4540.0000.0000.0000.000
31A565ALA00.0190.00612.8191.2971.2970.0000.0000.0000.000
32A566ASN00.0230.00212.687-0.510-0.5100.0000.0000.0000.000
33A567GLY00.0370.01516.164-0.810-0.8100.0000.0000.0000.000
34A568GLU-1-0.937-0.95817.40614.86114.8610.0000.0000.0000.000
35A569LYS10.9500.97417.684-12.006-12.0060.0000.0000.0000.000
36A570VAL00.0150.01014.257-0.284-0.2840.0000.0000.0000.000
37A571LYS10.8810.93713.260-21.165-21.1650.0000.0000.0000.000
38A572THR00.002-0.00118.560-0.088-0.0880.0000.0000.0000.000
39A573LEU0-0.052-0.01718.3730.2220.2220.0000.0000.0000.000
40A574ASP-1-0.873-0.91222.59211.51111.5110.0000.0000.0000.000
41A575VAL0-0.039-0.01523.2080.2650.2650.0000.0000.0000.000
42A576THR00.0820.01725.780-0.368-0.3680.0000.0000.0000.000
43A577SER00.0500.02927.8250.3910.3910.0000.0000.0000.000
44A578GLU-1-0.944-0.95529.27010.55310.5530.0000.0000.0000.000
45A579THR0-0.058-0.04823.8490.0510.0510.0000.0000.0000.000
46A580ASN0-0.078-0.07124.8590.2650.2650.0000.0000.0000.000
47A581TRP0-0.008-0.01126.4650.1290.1290.0000.0000.0000.000
48A582LYS10.9710.99921.271-14.281-14.2810.0000.0000.0000.000
49A583TYR0-0.024-0.01017.790-0.185-0.1850.0000.0000.0000.000
50A584GLU-1-0.868-0.96313.42923.21323.2130.0000.0000.0000.000
51A585PHE0-0.060-0.00413.780-0.460-0.4600.0000.0000.0000.000
52A586LYS10.9390.94611.797-18.694-18.6940.0000.0000.0000.000
53A587ASP-1-0.923-0.9497.72930.92030.9200.0000.0000.0000.000
54A588LEU0-0.039-0.0127.822-3.017-3.0170.0000.0000.0000.000
55A589PRO00.0460.0404.4347.2487.337-0.001-0.0890.0000.000
56A590LYS10.9460.9762.511-68.233-64.4601.469-2.010-3.2310.025
57A591TYR0-0.060-0.0582.654-8.243-5.9631.568-1.524-2.3240.018
58A592ASP-1-0.897-0.9456.05423.53623.5360.0000.0000.0000.000
59A593GLU-1-0.926-0.9558.31718.23218.2320.0000.0000.0000.000
60A594GLY0-0.024-0.0048.129-1.729-1.7290.0000.0000.0000.000
61A595LYS10.9140.9538.899-17.616-17.6160.0000.0000.0000.000
62A596LYS10.8620.9476.445-32.856-32.8560.0000.0000.0000.000
63A597ILE0-0.052-0.0218.081-2.846-2.8460.0000.0000.0000.000
64A598GLU-1-0.907-0.95710.17823.51023.5100.0000.0000.0000.000
65A599TYR0-0.071-0.0518.241-1.734-1.7340.0000.0000.0000.000
66A600THR00.0090.01313.431-0.679-0.6790.0000.0000.0000.000
67A601VAL0-0.005-0.01217.0140.3930.3930.0000.0000.0000.000
68A602THR00.003-0.01119.451-0.396-0.3960.0000.0000.0000.000
69A603GLU-1-0.814-0.91323.13211.82811.8280.0000.0000.0000.000
70A604ASP-1-0.898-0.91825.90011.40311.4030.0000.0000.0000.000
71A605HIS0-0.037-0.04928.678-0.103-0.1030.0000.0000.0000.000
72A606VAL0-0.0200.01031.116-0.136-0.1360.0000.0000.0000.000
73A607LYS10.9090.93633.784-7.903-7.9030.0000.0000.0000.000
74A608ASP-1-0.872-0.93937.5547.7967.7960.0000.0000.0000.000
75A609TYR0-0.053-0.04333.925-0.074-0.0740.0000.0000.0000.000
76A610THR0-0.006-0.01733.3750.0750.0750.0000.0000.0000.000
77A611THR0-0.035-0.04027.709-0.073-0.0730.0000.0000.0000.000
78A612ASP-1-0.989-0.98727.69811.35511.3550.0000.0000.0000.000
79A613ILE0-0.0160.00622.1070.1890.1890.0000.0000.0000.000
80A614ASN0-0.013-0.01223.2170.4250.4250.0000.0000.0000.000
81A615GLY00.0440.01318.9280.3390.3390.0000.0000.0000.000
82A616THR00.0020.02016.3200.5720.5720.0000.0000.0000.000
83A617THR0-0.0170.01718.889-0.152-0.1520.0000.0000.0000.000
84A618ILE0-0.032-0.00722.007-0.387-0.3870.0000.0000.0000.000
85A619THR0-0.001-0.00524.941-0.329-0.3290.0000.0000.0000.000
86A620ASN0-0.040-0.03328.5600.1510.1510.0000.0000.0000.000
87A621LYS10.9550.97631.480-10.257-10.2570.0000.0000.0000.000
88A622TYR0-0.074-0.05534.874-0.051-0.0510.0000.0000.0000.000
89A623THR0-0.040-0.00937.618-0.025-0.0250.0000.0000.0000.000
90A624PRO0-0.0020.01439.9590.0140.0140.0000.0000.0000.000
91A625GLY0-0.052-0.01942.452-0.153-0.1530.0000.0000.0000.000
92A626GLU-1-0.935-0.97239.8627.7267.7260.0000.0000.0000.000
93A627THR0-0.014-0.01235.4450.2100.2100.0000.0000.0000.000
94A628SER00.0000.00031.746-0.063-0.0630.0000.0000.0000.000
95A629ALA0-0.041-0.01631.967-0.065-0.0650.0000.0000.0000.000
96A630THR0-0.021-0.01125.419-0.016-0.0160.0000.0000.0000.000
97A631VAL0-0.030-0.00927.653-0.102-0.1020.0000.0000.0000.000
98A632THR00.0290.01821.0820.3960.3960.0000.0000.0000.000
99A633LYS10.7450.90323.574-12.274-12.2740.0000.0000.0000.000
100A634ASN0-0.003-0.00920.5120.9660.9660.0000.0000.0000.000
101A635TRP0-0.003-0.01620.456-1.094-1.0940.0000.0000.0000.000
102A636ASP-1-0.829-0.91620.16913.67713.6770.0000.0000.0000.000
103A637ASP-1-0.771-0.88420.75213.10513.1050.0000.0000.0000.000
104A638ASN00.0330.03818.1580.2760.2760.0000.0000.0000.000
105A639ASN00.015-0.00213.9200.8690.8690.0000.0000.0000.000
106A640ASN00.0690.01717.692-0.808-0.8080.0000.0000.0000.000
107A641GLN0-0.0270.01119.803-0.566-0.5660.0000.0000.0000.000
108A642ASP-1-0.886-0.94321.33611.22111.2210.0000.0000.0000.000
109A643GLY00.022-0.01023.897-0.147-0.1470.0000.0000.0000.000
110A644LYS10.8550.92824.716-10.589-10.5890.0000.0000.0000.000
111A645ARG10.8930.96418.253-15.155-15.1550.0000.0000.0000.000
112A646PRO0-0.044-0.01125.642-0.007-0.0070.0000.0000.0000.000
113A647THR00.023-0.01125.3930.3260.3260.0000.0000.0000.000
114A648GLU-1-0.967-0.98625.69810.75810.7580.0000.0000.0000.000
115A649ILE0-0.049-0.00627.269-0.333-0.3330.0000.0000.0000.000
116A650LYS10.9280.96529.895-8.725-8.7250.0000.0000.0000.000
117A651VAL00.0460.03630.217-0.152-0.1520.0000.0000.0000.000
118A652GLU-1-0.868-0.96033.1207.9137.9130.0000.0000.0000.000
119A653LEU00.0010.01334.4300.0580.0580.0000.0000.0000.000
120A654TYR00.0180.01236.608-0.372-0.3720.0000.0000.0000.000
121A655GLN00.0310.01139.1260.2040.2040.0000.0000.0000.000
122A656ASP-1-0.884-0.96341.7347.0577.0570.0000.0000.0000.000
123A657GLY00.004-0.00742.358-0.192-0.1920.0000.0000.0000.000
124A658LYS10.8460.93243.722-6.969-6.9690.0000.0000.0000.000
125A659ALA00.0910.06041.7550.1430.1430.0000.0000.0000.000
126A660THR0-0.055-0.04339.419-0.123-0.1230.0000.0000.0000.000
127A661GLY0-0.0130.00841.201-0.127-0.1270.0000.0000.0000.000
128A662LYS10.9030.95736.879-8.028-8.0280.0000.0000.0000.000
129A663THR0-0.008-0.01134.9750.0810.0810.0000.0000.0000.000
130A664ALA00.0020.00830.4400.0550.0550.0000.0000.0000.000
131A665ILE0-0.010-0.01129.458-0.181-0.1810.0000.0000.0000.000
132A666LEU0-0.0270.00425.6230.2190.2190.0000.0000.0000.000
133A667ASN00.0830.03924.4680.1870.1870.0000.0000.0000.000
134A668GLU-1-0.870-0.94718.31316.87216.8720.0000.0000.0000.000
135A669SER0-0.115-0.05720.5340.3820.3820.0000.0000.0000.000
136A670ASN00.0270.00022.5890.3680.3680.0000.0000.0000.000
137A671ASN00.0550.03317.817-0.136-0.1360.0000.0000.0000.000
138A672TRP0-0.070-0.02219.695-0.458-0.4580.0000.0000.0000.000
139A673THR0-0.005-0.01921.645-0.131-0.1310.0000.0000.0000.000
140A674HIS0-0.039-0.02524.072-0.219-0.2190.0000.0000.0000.000
141A675THR00.0350.02827.1780.0400.0400.0000.0000.0000.000
142A676TRP0-0.048-0.01429.418-0.182-0.1820.0000.0000.0000.000
143A677THR00.038-0.00733.0560.0230.0230.0000.0000.0000.000
144A678GLY00.0240.01535.415-0.126-0.1260.0000.0000.0000.000
145A679LEU0-0.067-0.02535.622-0.208-0.2080.0000.0000.0000.000
146A680ASP-1-0.845-0.90439.5437.3107.3100.0000.0000.0000.000
147A681GLU-1-0.792-0.89739.1018.2408.2400.0000.0000.0000.000
148A682LYS10.8740.91841.934-7.056-7.0560.0000.0000.0000.000
149A683ALA00.0790.04845.557-0.036-0.0360.0000.0000.0000.000
150A684LYS10.9020.93248.277-5.946-5.9460.0000.0000.0000.000
151A685GLY00.0210.01150.376-0.071-0.0710.0000.0000.0000.000
152A686GLN0-0.036-0.01248.018-0.003-0.0030.0000.0000.0000.000
153A687GLN00.0090.01039.642-0.115-0.1150.0000.0000.0000.000
154A688VAL0-0.0400.00141.323-0.078-0.0780.0000.0000.0000.000
155A689LYS10.8620.93739.787-7.147-7.1470.0000.0000.0000.000
156A690TYR0-0.002-0.03736.506-0.146-0.1460.0000.0000.0000.000
157A691THR0-0.032-0.00635.1790.0920.0920.0000.0000.0000.000
158A692VAL00.0050.00631.059-0.103-0.1030.0000.0000.0000.000
159A693GLU-1-0.917-0.94834.4498.1278.1270.0000.0000.0000.000
160A694GLU-1-0.821-0.90730.03910.51810.5180.0000.0000.0000.000
161A695LEU0-0.027-0.01933.746-0.222-0.2220.0000.0000.0000.000
162A696THR0-0.039-0.00832.079-0.165-0.1650.0000.0000.0000.000
163A697LYN00.0520.05533.9300.0770.0770.0000.0000.0000.000
164A698VAL00.0280.01129.106-0.005-0.0050.0000.0000.0000.000
165A699LYS10.8920.91732.457-8.347-8.3470.0000.0000.0000.000
166A700GLY00.0180.00931.2580.1860.1860.0000.0000.0000.000
167A701TYR0-0.051-0.08824.0530.0040.0040.0000.0000.0000.000
168A702THR0-0.095-0.02429.729-0.340-0.3400.0000.0000.0000.000
169A703THR00.033-0.00829.6530.3560.3560.0000.0000.0000.000
170A704HIS0-0.016-0.00429.489-0.410-0.4100.0000.0000.0000.000
171A705VAL0-0.023-0.01429.2490.3940.3940.0000.0000.0000.000
172A706ASP-1-0.908-0.92728.05610.47210.4720.0000.0000.0000.000
173A707ASN00.017-0.03730.1540.2600.2600.0000.0000.0000.000
174A708ASN0-0.016-0.01830.921-0.574-0.5740.0000.0000.0000.000
175A709ASP-1-0.756-0.86029.71210.23610.2360.0000.0000.0000.000
176A710MET0-0.052-0.02530.5630.1450.1450.0000.0000.0000.000
177A711GLY00.0350.01729.4910.0350.0350.0000.0000.0000.000
178A712ASN0-0.009-0.01023.8740.8010.8010.0000.0000.0000.000
179A713LEU0-0.0090.03527.118-0.044-0.0440.0000.0000.0000.000
180A714ILE00.0220.01322.8220.3810.3810.0000.0000.0000.000
181A715THR0-0.0120.00426.401-0.550-0.5500.0000.0000.0000.000
182A716THR0-0.019-0.01024.2440.5010.5010.0000.0000.0000.000
183A717ASN0-0.043-0.03625.164-0.481-0.4810.0000.0000.0000.000
184A718LYS10.9590.98725.005-10.377-10.3770.0000.0000.0000.000
185A719TYR0-0.041-0.00625.077-0.724-0.7240.0000.0000.0000.000
186A720THR0-0.058-0.03826.9380.0900.0900.0000.0000.0000.000
187A721PRO0-0.0270.00528.515-0.418-0.4180.0000.0000.0000.000