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: 7GKVK

Calculation Name: 3NCX-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3NCX

Chain ID: A

ChEMBL ID:

UniProt ID: P43261

Base Structure: X-ray

Registration Date: 2023-03-14

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 -1864238.090473
FMO2-HF: Nuclear repulsion 1792004.341126
FMO2-HF: Total energy -72233.749346
FMO2-MP2: Total energy -72444.869565


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:747:ALA)


Summations of interaction energy for fragment #1(A:747:ALA)
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.
-2.382-0.836-0.023-0.745-0.7780.003
Interaction energy analysis for fragmet #1(A:747:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.035 / q_NPA : -0.030
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].
3A749GLU-1-0.890-0.9573.804-2.779-1.233-0.023-0.745-0.7780.003
4A750VAL0-0.061-0.0156.7500.4610.4610.0000.0000.0000.000
5A751THR0-0.024-0.0049.079-0.019-0.0190.0000.0000.0000.000
6A752PHE0-0.034-0.02912.5960.0110.0110.0000.0000.0000.000
7A753PHE00.0080.00214.3840.0050.0050.0000.0000.0000.000
8A754ASP-1-0.899-0.94019.114-0.034-0.0340.0000.0000.0000.000
9A755GLU-1-0.959-0.98122.5720.0110.0110.0000.0000.0000.000
10A756LEU0-0.071-0.02924.8450.0000.0000.0000.0000.0000.000
11A757LYS10.9680.98026.101-0.013-0.0130.0000.0000.0000.000
12A758ILE0-0.032-0.02529.6330.0030.0030.0000.0000.0000.000
13A759ASP-1-0.950-0.99432.2920.0100.0100.0000.0000.0000.000
14A760ASN0-0.048-0.02934.4640.0010.0010.0000.0000.0000.000
15A761LYS10.9250.97937.489-0.006-0.0060.0000.0000.0000.000
16A762VAL00.0160.00437.6330.0030.0030.0000.0000.0000.000
17A763ASP-1-0.901-0.94838.2670.0270.0270.0000.0000.0000.000
18A764ILE00.0050.00940.0670.0040.0040.0000.0000.0000.000
19A765ILE0-0.018-0.02039.7270.0000.0000.0000.0000.0000.000
20A766GLY0-0.035-0.00943.3750.0000.0000.0000.0000.0000.000
21A767ASN00.040-0.01746.5580.0000.0000.0000.0000.0000.000
22A768ASN0-0.050-0.00943.2480.0000.0000.0000.0000.0000.000
23A769VAL00.0410.03944.160-0.002-0.0020.0000.0000.0000.000
24A770ARG10.8710.92937.491-0.021-0.0210.0000.0000.0000.000
25A771GLY00.005-0.02041.889-0.003-0.0030.0000.0000.0000.000
26A772GLU-1-0.930-0.94442.5430.0120.0120.0000.0000.0000.000
27A773LEU0-0.035-0.01443.1840.0000.0000.0000.0000.0000.000
28A774PRO00.0390.02644.761-0.001-0.0010.0000.0000.0000.000
29A775ASN00.0390.00748.5220.0020.0020.0000.0000.0000.000
30A776ILE0-0.0020.02550.8020.0010.0010.0000.0000.0000.000
31A777TRP00.024-0.00146.7660.0020.0020.0000.0000.0000.000
32A778LEU00.0550.03350.390-0.001-0.0010.0000.0000.0000.000
33A779GLN00.002-0.00749.7770.0000.0000.0000.0000.0000.000
34A780TYR0-0.049-0.03047.2750.0000.0000.0000.0000.0000.000
35A781GLY00.0020.02947.1160.0010.0010.0000.0000.0000.000
36A782GLN0-0.065-0.07242.0830.0010.0010.0000.0000.0000.000
37A783PHE00.0570.01239.789-0.002-0.0020.0000.0000.0000.000
38A784LYS10.8720.94834.001-0.051-0.0510.0000.0000.0000.000
39A785LEU00.0250.02334.619-0.004-0.0040.0000.0000.0000.000
40A786LYS10.9390.97730.644-0.036-0.0360.0000.0000.0000.000
41A787ALA00.0180.01928.096-0.004-0.0040.0000.0000.0000.000
42A788SER0-0.045-0.01326.841-0.002-0.0020.0000.0000.0000.000
43A789GLY00.1240.06523.7150.0020.0020.0000.0000.0000.000
44A790GLY0-0.003-0.01120.8320.0120.0120.0000.0000.0000.000
45A791ASP-1-0.783-0.89917.2200.1410.1410.0000.0000.0000.000
46A792GLY0-0.046-0.02018.9530.0170.0170.0000.0000.0000.000
47A793THR0-0.104-0.04520.0420.0060.0060.0000.0000.0000.000
48A794TYR0-0.004-0.02522.453-0.001-0.0010.0000.0000.0000.000
49A795SER0-0.058-0.01125.4760.0050.0050.0000.0000.0000.000
50A796TRP00.0280.00327.841-0.009-0.0090.0000.0000.0000.000
51A797TYR00.0270.01731.4510.0020.0020.0000.0000.0000.000
52A798SER0-0.026-0.02733.960-0.006-0.0060.0000.0000.0000.000
53A799GLU-1-0.892-0.95237.2350.0460.0460.0000.0000.0000.000
54A800ASN00.001-0.02339.344-0.001-0.0010.0000.0000.0000.000
55A801THR00.0640.02841.314-0.001-0.0010.0000.0000.0000.000
56A802SER0-0.050-0.01343.070-0.001-0.0010.0000.0000.0000.000
57A803ILE0-0.0140.01345.093-0.002-0.0020.0000.0000.0000.000
58A804ALA00.0250.00942.196-0.002-0.0020.0000.0000.0000.000
59A805THR00.0190.02539.4400.0020.0020.0000.0000.0000.000
60A806VAL0-0.0050.00934.684-0.003-0.0030.0000.0000.0000.000
61A807ASP-1-0.795-0.86334.8990.0690.0690.0000.0000.0000.000
62A808ALA00.0540.00129.8650.0000.0000.0000.0000.0000.000
63A809SER0-0.096-0.06330.0800.0010.0010.0000.0000.0000.000
64A810GLY00.0630.03432.123-0.004-0.0040.0000.0000.0000.000
65A811LYS10.8640.94133.618-0.058-0.0580.0000.0000.0000.000
66A812VAL00.0210.00337.1410.0030.0030.0000.0000.0000.000
67A813THR0-0.049-0.02339.494-0.003-0.0030.0000.0000.0000.000
68A814LEU0-0.0020.01242.8680.0010.0010.0000.0000.0000.000
69A815ASN0-0.009-0.03043.872-0.001-0.0010.0000.0000.0000.000
70A816GLY00.0110.00447.638-0.001-0.0010.0000.0000.0000.000
71A817LYS10.9040.96648.912-0.020-0.0200.0000.0000.0000.000
72A818GLY00.036-0.00249.3740.0000.0000.0000.0000.0000.000
73A819SER00.004-0.00345.9540.0000.0000.0000.0000.0000.000
74A820VAL0-0.0120.00440.9980.0010.0010.0000.0000.0000.000
75A821VAL00.0220.01537.002-0.002-0.0020.0000.0000.0000.000
76A822ILE00.0000.00334.7930.0030.0030.0000.0000.0000.000
77A823LYS10.8970.95231.755-0.054-0.0540.0000.0000.0000.000
78A824ALA00.0230.01529.2210.0040.0040.0000.0000.0000.000
79A825THR0-0.032-0.04024.540-0.007-0.0070.0000.0000.0000.000
80A826SER0-0.005-0.00721.9420.0060.0060.0000.0000.0000.000
81A827GLY00.0360.02519.5290.0030.0030.0000.0000.0000.000
82A828ASP-1-0.813-0.89317.4540.1030.1030.0000.0000.0000.000
83A829LYS10.8880.93718.696-0.138-0.1380.0000.0000.0000.000
84A830GLN0-0.0130.01121.348-0.021-0.0210.0000.0000.0000.000
85A831THR00.005-0.00624.1120.0080.0080.0000.0000.0000.000
86A832VAL00.0160.02327.767-0.007-0.0070.0000.0000.0000.000
87A833SER0-0.035-0.02830.6170.0050.0050.0000.0000.0000.000
88A834TYR00.0190.01334.317-0.005-0.0050.0000.0000.0000.000
89A835THR0-0.061-0.02836.7910.0010.0010.0000.0000.0000.000
90A836ILE00.0060.00540.419-0.002-0.0020.0000.0000.0000.000
91A837LYS10.9580.96943.156-0.019-0.0190.0000.0000.0000.000
92A838ALA0-0.019-0.00746.5530.0000.0000.0000.0000.0000.000
93A839PRO00.0240.04049.450-0.001-0.0010.0000.0000.0000.000
94A840SER0-0.031-0.02351.6730.0000.0000.0000.0000.0000.000
95A841TYR0-0.049-0.04654.8690.0000.0000.0000.0000.0000.000
96A842MET0-0.016-0.00851.7170.0010.0010.0000.0000.0000.000
97A843ILE0-0.0230.01154.5220.0000.0000.0000.0000.0000.000
98A844LYS10.9000.94654.496-0.024-0.0240.0000.0000.0000.000
99A845VAL0-0.009-0.00955.876-0.001-0.0010.0000.0000.0000.000
100A846ASP-1-0.904-0.93357.4080.0260.0260.0000.0000.0000.000
101A847LYS10.9310.95760.017-0.022-0.0220.0000.0000.0000.000
102A848GLN0-0.010-0.02262.260-0.001-0.0010.0000.0000.0000.000
103A849ALA0-0.0130.00265.0900.0000.0000.0000.0000.0000.000
104A850TYR00.0300.03068.4680.0000.0000.0000.0000.0000.000
105A851TYR00.0090.03270.7540.0000.0000.0000.0000.0000.000
106A852ALA00.028-0.00371.2370.0000.0000.0000.0000.0000.000
107A853ASP-1-0.868-0.94369.6000.0190.0190.0000.0000.0000.000
108A854ALA00.0370.01867.0240.0010.0010.0000.0000.0000.000
109A855MET0-0.0170.00367.1750.0000.0000.0000.0000.0000.000
110A856SER0-0.063-0.02268.5640.0000.0000.0000.0000.0000.000
111A857ILE00.0110.00163.8470.0010.0010.0000.0000.0000.000
112A858CYS0-0.0410.00959.9200.0000.0000.0000.0000.0000.000
113A859LYS10.9570.96763.927-0.021-0.0210.0000.0000.0000.000
114A860ASN0-0.081-0.06666.983-0.001-0.0010.0000.0000.0000.000
115A861LEU0-0.0070.01162.343-0.001-0.0010.0000.0000.0000.000
116A862LEU0-0.0140.00263.6770.0000.0000.0000.0000.0000.000
117A863PRO00.0310.01862.601-0.001-0.0010.0000.0000.0000.000
118A864SER0-0.008-0.01364.3220.0000.0000.0000.0000.0000.000
119A865THR00.0310.00765.432-0.001-0.0010.0000.0000.0000.000
120A866GLN00.0660.02064.3310.0010.0010.0000.0000.0000.000
121A867THR00.0390.02861.5010.0000.0000.0000.0000.0000.000
122A868VAL0-0.0360.01060.4310.0000.0000.0000.0000.0000.000
123A869LEU00.000-0.00459.1290.0010.0010.0000.0000.0000.000
124A870SER00.014-0.01158.2910.0010.0010.0000.0000.0000.000
125A871ASP-1-0.817-0.91157.0580.0120.0120.0000.0000.0000.000
126A872ILE0-0.046-0.02853.3750.0010.0010.0000.0000.0000.000
127A873TYR0-0.063-0.03353.2780.0020.0020.0000.0000.0000.000
128A874ASP-1-0.859-0.92753.3420.0130.0130.0000.0000.0000.000
129A875SER0-0.081-0.03550.7550.0000.0000.0000.0000.0000.000
130A876TRP0-0.106-0.07045.2810.0020.0020.0000.0000.0000.000
131A877GLY00.0330.03749.1540.0010.0010.0000.0000.0000.000
132A878ALA0-0.017-0.01251.6850.0010.0010.0000.0000.0000.000
133A879ALA00.0610.01951.2010.0010.0010.0000.0000.0000.000
134A880ASN00.0320.00151.0410.0010.0010.0000.0000.0000.000
135A881LYS10.9140.97447.585-0.024-0.0240.0000.0000.0000.000
136A882TYR0-0.020-0.00245.2540.0020.0020.0000.0000.0000.000
137A883SER00.0090.00144.192-0.001-0.0010.0000.0000.0000.000
138A884HIS10.8970.95746.322-0.035-0.0350.0000.0000.0000.000
139A885TYR0-0.025-0.03949.108-0.001-0.0010.0000.0000.0000.000
140A886SER0-0.0210.00148.0930.0000.0000.0000.0000.0000.000
141A887SER0-0.034-0.00750.506-0.001-0.0010.0000.0000.0000.000
142A888MET0-0.0120.01253.372-0.001-0.0010.0000.0000.0000.000
143A889ASN00.0520.01255.2480.0010.0010.0000.0000.0000.000
144A890SER0-0.038-0.01757.701-0.001-0.0010.0000.0000.0000.000
145A891ILE00.0340.00655.6230.0010.0010.0000.0000.0000.000
146A892THR00.0060.01760.1350.0000.0000.0000.0000.0000.000
147A893ALA00.0290.02061.7250.0010.0010.0000.0000.0000.000
148A894TRP00.014-0.01563.839-0.001-0.0010.0000.0000.0000.000
149A895ILE0-0.0070.02265.4740.0000.0000.0000.0000.0000.000
150A896LYS10.9240.95767.789-0.013-0.0130.0000.0000.0000.000
151A897GLN0-0.002-0.01769.9280.0000.0000.0000.0000.0000.000
152A898THR0-0.008-0.02073.4710.0000.0000.0000.0000.0000.000
153A899SER00.0330.00275.6190.0000.0000.0000.0000.0000.000
154A900SER0-0.057-0.03879.0080.0000.0000.0000.0000.0000.000
155A901GLU-1-0.787-0.89074.2360.0110.0110.0000.0000.0000.000
156A902GLN0-0.0170.00177.9480.0000.0000.0000.0000.0000.000
157A903ARG10.9090.95579.129-0.009-0.0090.0000.0000.0000.000
158A904SER0-0.021-0.00380.9720.0000.0000.0000.0000.0000.000
159A905GLY00.0150.03379.5170.0000.0000.0000.0000.0000.000
160A906VAL0-0.015-0.01476.7100.0000.0000.0000.0000.0000.000
161A907SER0-0.043-0.02971.4460.0000.0000.0000.0000.0000.000
162A908SER00.0220.02370.5380.0000.0000.0000.0000.0000.000
163A909THR0-0.066-0.03566.9210.0010.0010.0000.0000.0000.000
164A910TYR00.0690.02259.036-0.001-0.0010.0000.0000.0000.000
165A911ASN00.0300.01760.2910.0020.0020.0000.0000.0000.000
166A912LEU00.0150.00256.6700.0000.0000.0000.0000.0000.000
167A913ILE0-0.070-0.02755.2090.0010.0010.0000.0000.0000.000
168A914THR00.011-0.01157.1260.0000.0000.0000.0000.0000.000
169A915GLN00.0300.02358.0710.0000.0000.0000.0000.0000.000
170A916TYR0-0.024-0.01461.036-0.001-0.0010.0000.0000.0000.000
171A917PRO00.0040.01664.5000.0010.0010.0000.0000.0000.000
172A918LEU0-0.008-0.00867.1180.0000.0000.0000.0000.0000.000
173A919PRO00.0350.01070.2870.0000.0000.0000.0000.0000.000
174A920GLY00.017-0.00173.3710.0000.0000.0000.0000.0000.000
175A921VAL0-0.0010.02171.1800.0000.0000.0000.0000.0000.000
176A922ASN00.0560.02474.4660.0000.0000.0000.0000.0000.000
177A923VAL00.0350.01874.3360.0010.0010.0000.0000.0000.000
178A924ASN0-0.035-0.02073.7340.0010.0010.0000.0000.0000.000
179A925THR0-0.005-0.01271.2670.0000.0000.0000.0000.0000.000
180A926PRO00.000-0.00570.4010.0000.0000.0000.0000.0000.000
181A927ASN0-0.015-0.02166.3860.0000.0000.0000.0000.0000.000
182A928VAL00.0040.01365.8750.0000.0000.0000.0000.0000.000
183A929TYR0-0.004-0.00859.8170.0000.0000.0000.0000.0000.000
184A930ALA0-0.011-0.00263.564-0.001-0.0010.0000.0000.0000.000
185A931VAL00.006-0.00559.0380.0010.0010.0000.0000.0000.000
186A933VAL00.003-0.00259.1180.0010.0010.0000.0000.0000.000
187A934GLU-1-0.890-0.94356.2510.0220.0220.0000.0000.0000.000