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: 664VZ

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 OptAll
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 -1862547.1788
FMO2-HF: Nuclear repulsion 1790312.011644
FMO2-HF: Total energy -72235.167156
FMO2-MP2: Total energy -72446.216794


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.
-2.1170.048-0.017-1.184-0.9640.004
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 : 0.009 / q_NPA : 0.004
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-1-0.884-0.9473.881-2.0830.082-0.017-1.184-0.9640.004
4A750VAL0-0.054-0.0186.7940.0850.0850.0000.0000.0000.000
5A751THR0-0.0290.0009.3150.0290.0290.0000.0000.0000.000
6A752PHE0-0.018-0.02011.7950.0660.0660.0000.0000.0000.000
7A753PHE00.001-0.00514.815-0.017-0.0170.0000.0000.0000.000
8A754ASP-1-0.878-0.92919.377-0.166-0.1660.0000.0000.0000.000
9A755GLU-1-0.935-0.96522.833-0.075-0.0750.0000.0000.0000.000
10A756LEU0-0.070-0.03125.020-0.004-0.0040.0000.0000.0000.000
11A757LYS10.9180.95026.3290.0890.0890.0000.0000.0000.000
12A758ILE0-0.033-0.01229.738-0.006-0.0060.0000.0000.0000.000
13A759ASP-1-0.842-0.92332.234-0.074-0.0740.0000.0000.0000.000
14A760ASN0-0.056-0.05734.6410.0020.0020.0000.0000.0000.000
15A761LYS10.7880.89237.9150.0630.0630.0000.0000.0000.000
16A762VAL0-0.039-0.00237.788-0.004-0.0040.0000.0000.0000.000
17A763ASP-1-0.850-0.91237.919-0.069-0.0690.0000.0000.0000.000
18A764ILE00.0140.00440.1030.0020.0020.0000.0000.0000.000
19A765ILE00.0220.00139.513-0.001-0.0010.0000.0000.0000.000
20A766GLY0-0.012-0.00443.399-0.001-0.0010.0000.0000.0000.000
21A767ASN00.000-0.03046.682-0.001-0.0010.0000.0000.0000.000
22A768ASN0-0.039-0.00943.383-0.003-0.0030.0000.0000.0000.000
23A769VAL00.0360.03843.688-0.004-0.0040.0000.0000.0000.000
24A770ARG10.8080.88238.3460.0690.0690.0000.0000.0000.000
25A771GLY00.009-0.00942.0590.0000.0000.0000.0000.0000.000
26A772GLU-1-0.784-0.86542.505-0.052-0.0520.0000.0000.0000.000
27A773LEU0-0.018-0.00142.9460.0010.0010.0000.0000.0000.000
28A774PRO00.0240.01744.8990.0020.0020.0000.0000.0000.000
29A775ASN00.024-0.00448.6830.0020.0020.0000.0000.0000.000
30A776ILE0-0.0160.01651.0900.0020.0020.0000.0000.0000.000
31A777TRP00.0210.00946.726-0.001-0.0010.0000.0000.0000.000
32A778LEU00.0540.03950.5350.0020.0020.0000.0000.0000.000
33A779GLN00.007-0.01849.925-0.001-0.0010.0000.0000.0000.000
34A780TYR0-0.053-0.02947.2380.0000.0000.0000.0000.0000.000
35A781GLY00.0120.03047.326-0.002-0.0020.0000.0000.0000.000
36A782GLN0-0.052-0.05442.2630.0000.0000.0000.0000.0000.000
37A783PHE00.0280.00639.751-0.001-0.0010.0000.0000.0000.000
38A784LYS10.8360.92433.4930.0700.0700.0000.0000.0000.000
39A785LEU00.0290.02234.7580.0000.0000.0000.0000.0000.000
40A786LYS10.9410.97329.7280.1050.1050.0000.0000.0000.000
41A787ALA00.0110.01128.1810.0010.0010.0000.0000.0000.000
42A788SER0-0.058-0.03626.912-0.007-0.0070.0000.0000.0000.000
43A789GLY00.1030.06424.0070.0120.0120.0000.0000.0000.000
44A790GLY00.0150.01021.0340.0070.0070.0000.0000.0000.000
45A791ASP-1-0.818-0.90517.088-0.163-0.1630.0000.0000.0000.000
46A792GLY0-0.030-0.00218.895-0.022-0.0220.0000.0000.0000.000
47A793THR0-0.126-0.07019.4810.0190.0190.0000.0000.0000.000
48A794TYR0-0.022-0.05522.2230.0100.0100.0000.0000.0000.000
49A795SER0-0.060-0.01625.3570.0080.0080.0000.0000.0000.000
50A796TRP00.020-0.00227.6030.0010.0010.0000.0000.0000.000
51A797TYR00.0190.01131.2410.0050.0050.0000.0000.0000.000
52A798SER0-0.030-0.04034.034-0.004-0.0040.0000.0000.0000.000
53A799GLU-1-0.813-0.89836.656-0.003-0.0030.0000.0000.0000.000
54A800ASN00.023-0.00439.5510.0030.0030.0000.0000.0000.000
55A801THR00.0900.04540.882-0.001-0.0010.0000.0000.0000.000
56A802SER0-0.0230.00043.006-0.001-0.0010.0000.0000.0000.000
57A803ILE0-0.078-0.00945.2850.0000.0000.0000.0000.0000.000
58A804ALA00.0480.01342.303-0.002-0.0020.0000.0000.0000.000
59A805THR00.0030.01739.5650.0030.0030.0000.0000.0000.000
60A806VAL00.0070.00534.561-0.003-0.0030.0000.0000.0000.000
61A807ASP-1-0.759-0.82934.668-0.046-0.0460.0000.0000.0000.000
62A808ALA00.0580.00929.543-0.003-0.0030.0000.0000.0000.000
63A809SER0-0.067-0.05229.741-0.008-0.0080.0000.0000.0000.000
64A810GLY00.0690.03731.820-0.007-0.0070.0000.0000.0000.000
65A811LYS10.8240.90133.3290.0460.0460.0000.0000.0000.000
66A812VAL00.0090.00436.8710.0040.0040.0000.0000.0000.000
67A813THR0-0.038-0.01439.387-0.002-0.0020.0000.0000.0000.000
68A814LEU00.0060.01942.8860.0020.0020.0000.0000.0000.000
69A815ASN0-0.027-0.02944.359-0.001-0.0010.0000.0000.0000.000
70A816GLY00.0180.00947.7690.0010.0010.0000.0000.0000.000
71A817LYS10.8500.92949.1630.0150.0150.0000.0000.0000.000
72A818GLY00.0210.00249.4030.0020.0020.0000.0000.0000.000
73A819SER00.0100.00446.108-0.003-0.0030.0000.0000.0000.000
74A820VAL0-0.030-0.00941.2170.0020.0020.0000.0000.0000.000
75A821VAL0-0.0020.00637.093-0.003-0.0030.0000.0000.0000.000
76A822ILE00.0000.00735.2880.0020.0020.0000.0000.0000.000
77A823LYS10.8110.88232.0880.0070.0070.0000.0000.0000.000
78A824ALA00.0370.02029.0560.0000.0000.0000.0000.0000.000
79A825THR0-0.013-0.00424.4560.0060.0060.0000.0000.0000.000
80A826SER00.002-0.01721.7720.0050.0050.0000.0000.0000.000
81A827GLY00.0110.02319.2340.0190.0190.0000.0000.0000.000
82A828ASP-1-0.781-0.85617.511-0.097-0.0970.0000.0000.0000.000
83A829LYS10.8620.91318.5000.0030.0030.0000.0000.0000.000
84A830GLN0-0.0040.02321.3240.0250.0250.0000.0000.0000.000
85A831THR0-0.005-0.03223.9560.0010.0010.0000.0000.0000.000
86A832VAL0-0.0060.00827.5670.0030.0030.0000.0000.0000.000
87A833SER0-0.005-0.01830.6230.0020.0020.0000.0000.0000.000
88A834TYR00.0370.01634.331-0.002-0.0020.0000.0000.0000.000
89A835THR0-0.053-0.03137.0440.0030.0030.0000.0000.0000.000
90A836ILE00.0420.03940.532-0.002-0.0020.0000.0000.0000.000
91A837LYS10.9190.94643.0700.0280.0280.0000.0000.0000.000
92A838ALA0-0.0010.00046.562-0.001-0.0010.0000.0000.0000.000
93A839PRO00.0240.04449.6590.0000.0000.0000.0000.0000.000
94A840SER00.0230.00651.6900.0010.0010.0000.0000.0000.000
95A841TYR0-0.058-0.04255.0870.0020.0020.0000.0000.0000.000
96A842MET0-0.0050.00251.935-0.002-0.0020.0000.0000.0000.000
97A843ILE0-0.0110.01154.6810.0010.0010.0000.0000.0000.000
98A844LYS10.8570.91754.6220.0110.0110.0000.0000.0000.000
99A845VAL0-0.014-0.02755.9400.0000.0000.0000.0000.0000.000
100A846ASP-1-0.894-0.93757.098-0.012-0.0120.0000.0000.0000.000
101A847LYS10.8060.87959.7550.0090.0090.0000.0000.0000.000
102A848GLN00.0170.00162.1920.0000.0000.0000.0000.0000.000
103A849ALA0-0.009-0.00664.8500.0010.0010.0000.0000.0000.000
104A850TYR00.0290.04468.0570.0000.0000.0000.0000.0000.000
105A851TYR00.0220.02470.5180.0000.0000.0000.0000.0000.000
106A852ALA00.0350.00470.9980.0000.0000.0000.0000.0000.000
107A853ASP-1-0.795-0.88169.232-0.009-0.0090.0000.0000.0000.000
108A854ALA00.0420.02066.8220.0000.0000.0000.0000.0000.000
109A855MET0-0.023-0.00666.9620.0000.0000.0000.0000.0000.000
110A856SER0-0.066-0.03868.7220.0000.0000.0000.0000.0000.000
111A857ILE00.002-0.00463.5130.0000.0000.0000.0000.0000.000
112A858CYS0-0.052-0.00859.9990.0010.0010.0000.0000.0000.000
113A859LYS10.9610.97963.3580.0060.0060.0000.0000.0000.000
114A860ASN0-0.024-0.02667.0680.0000.0000.0000.0000.0000.000
115A861LEU0-0.0380.00162.0910.0000.0000.0000.0000.0000.000
116A862LEU00.0180.00863.715-0.001-0.0010.0000.0000.0000.000
117A863PRO00.0150.00662.6920.0000.0000.0000.0000.0000.000
118A864SER0-0.004-0.00964.6030.0000.0000.0000.0000.0000.000
119A865THR00.0350.01465.8260.0000.0000.0000.0000.0000.000
120A866GLN00.0600.01964.2630.0010.0010.0000.0000.0000.000
121A867THR00.0420.03161.8420.0000.0000.0000.0000.0000.000
122A868VAL0-0.053-0.00860.675-0.001-0.0010.0000.0000.0000.000
123A869LEU0-0.013-0.00959.0220.0000.0000.0000.0000.0000.000
124A870SER0-0.005-0.01158.215-0.001-0.0010.0000.0000.0000.000
125A871ASP-1-0.784-0.88457.259-0.028-0.0280.0000.0000.0000.000
126A872ILE0-0.047-0.01553.385-0.001-0.0010.0000.0000.0000.000
127A873TYR0-0.030-0.01453.260-0.002-0.0020.0000.0000.0000.000
128A874ASP-1-0.867-0.93653.375-0.034-0.0340.0000.0000.0000.000
129A875SER0-0.073-0.04750.828-0.002-0.0020.0000.0000.0000.000
130A876TRP0-0.103-0.06445.121-0.002-0.0020.0000.0000.0000.000
131A877GLY00.0210.03949.083-0.002-0.0020.0000.0000.0000.000
132A878ALA0-0.017-0.00851.4700.0020.0020.0000.0000.0000.000
133A879ALA00.0610.01051.342-0.001-0.0010.0000.0000.0000.000
134A880ASN0-0.006-0.01550.899-0.001-0.0010.0000.0000.0000.000
135A881LYS10.9160.98147.4510.0420.0420.0000.0000.0000.000
136A882TYR0-0.030-0.02845.091-0.003-0.0030.0000.0000.0000.000
137A883SER00.0330.01244.3510.0020.0020.0000.0000.0000.000
138A884HIS10.8660.93546.4840.0220.0220.0000.0000.0000.000
139A885TYR0-0.012-0.02949.3370.0030.0030.0000.0000.0000.000
140A886SER00.001-0.00348.2640.0000.0000.0000.0000.0000.000
141A887SER0-0.0340.00050.591-0.001-0.0010.0000.0000.0000.000
142A888MET0-0.0160.02153.3130.0010.0010.0000.0000.0000.000
143A889ASN00.0420.00555.157-0.003-0.0030.0000.0000.0000.000
144A890SER0-0.010-0.00557.645-0.001-0.0010.0000.0000.0000.000
145A891ILE00.0220.01355.8490.0010.0010.0000.0000.0000.000
146A892THR00.0120.02160.126-0.001-0.0010.0000.0000.0000.000
147A893ALA00.0260.01461.8370.0010.0010.0000.0000.0000.000
148A894TRP00.011-0.02063.9790.0000.0000.0000.0000.0000.000
149A895ILE0-0.0060.01165.1950.0000.0000.0000.0000.0000.000
150A896LYS10.9060.95567.7910.0120.0120.0000.0000.0000.000
151A897GLN0-0.0190.00069.9300.0000.0000.0000.0000.0000.000
152A898THR00.008-0.03673.4940.0010.0010.0000.0000.0000.000
153A899SER00.033-0.00175.6370.0000.0000.0000.0000.0000.000
154A900SER00.0090.01179.1900.0000.0000.0000.0000.0000.000
155A901GLU-1-0.732-0.81874.090-0.015-0.0150.0000.0000.0000.000
156A902GLN0-0.008-0.00578.1160.0000.0000.0000.0000.0000.000
157A903ARG10.8550.91279.2120.0110.0110.0000.0000.0000.000
158A904SER0-0.021-0.01681.0380.0000.0000.0000.0000.0000.000
159A905GLY00.0170.03379.9650.0000.0000.0000.0000.0000.000
160A906VAL0-0.033-0.01576.5590.0000.0000.0000.0000.0000.000
161A907SER0-0.025-0.02971.3020.0000.0000.0000.0000.0000.000
162A908SER0-0.0040.00070.3760.0000.0000.0000.0000.0000.000
163A909THR0-0.073-0.02567.0510.0000.0000.0000.0000.0000.000
164A910TYR00.0730.03059.0250.0000.0000.0000.0000.0000.000
165A911ASN00.0230.01160.3090.0000.0000.0000.0000.0000.000
166A912LEU00.0150.00656.551-0.001-0.0010.0000.0000.0000.000
167A913ILE0-0.075-0.02755.063-0.001-0.0010.0000.0000.0000.000
168A914THR00.027-0.00956.906-0.001-0.0010.0000.0000.0000.000
169A915GLN00.0240.02158.274-0.001-0.0010.0000.0000.0000.000
170A916TYR0-0.0190.00060.9750.0000.0000.0000.0000.0000.000
171A917PRO0-0.0100.00364.5100.0010.0010.0000.0000.0000.000
172A918LEU0-0.005-0.01167.0940.0000.0000.0000.0000.0000.000
173A919PRO00.0260.00070.3090.0010.0010.0000.0000.0000.000
174A920GLY00.0210.00673.2130.0000.0000.0000.0000.0000.000
175A921VAL0-0.0090.01370.9830.0000.0000.0000.0000.0000.000
176A922ASN00.0470.01774.3000.0010.0010.0000.0000.0000.000
177A923VAL00.0160.00874.4510.0000.0000.0000.0000.0000.000
178A924ASN0-0.013-0.00873.9130.0000.0000.0000.0000.0000.000
179A925THR0-0.017-0.01871.7530.0000.0000.0000.0000.0000.000
180A926PRO00.001-0.00270.1270.0000.0000.0000.0000.0000.000
181A927ASN0-0.010-0.01966.3390.0000.0000.0000.0000.0000.000
182A928VAL0-0.0100.01265.675-0.001-0.0010.0000.0000.0000.000
183A929TYR0-0.010-0.03759.4160.0010.0010.0000.0000.0000.000
184A930ALA00.0100.00663.3950.0000.0000.0000.0000.0000.000
185A931VAL0-0.002-0.00759.3520.0000.0000.0000.0000.0000.000
186A933VAL00.002-0.00459.008-0.001-0.0010.0000.0000.0000.000
187A934GLU-1-0.853-0.91057.101-0.011-0.0110.0000.0000.0000.000