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: 9Y5M2

Calculation Name: 3NCX-A-Xray313

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: 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 188
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -1867121.559796
FMO2-HF: Nuclear repulsion 1794736.551869
FMO2-HF: Total energy -72385.007927
FMO2-MP2: Total energy -72596.540952


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:746:ACE )


Summations of interaction energy for fragment #1(A:746:ACE )
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.
0.0331.043-0.006-0.439-0.565-0.001
Interaction energy analysis for fragmet #1(A:746:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.008 / q_NPA : -0.019
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].
3A748THR 0-0.0210.0053.8120.8101.820-0.006-0.439-0.565-0.001
4A749GLU -1-0.884-0.9536.407-0.701-0.7010.0000.0000.0000.000
5A750VAL 0-0.060-0.01510.0910.0290.0290.0000.0000.0000.000
6A751THR 0-0.025-0.00412.5270.0490.0490.0000.0000.0000.000
7A752PHE 0-0.034-0.02915.772-0.011-0.0110.0000.0000.0000.000
8A753PHE 00.0060.00116.9240.0120.0120.0000.0000.0000.000
9A754ASP -1-0.898-0.94022.156-0.100-0.1000.0000.0000.0000.000
10A755GLU -1-0.957-0.98125.528-0.081-0.0810.0000.0000.0000.000
11A756LEU 0-0.071-0.02827.3380.0070.0070.0000.0000.0000.000
12A757LYS 10.9680.98028.7160.0530.0530.0000.0000.0000.000
13A758ILE 0-0.034-0.02532.1840.0020.0020.0000.0000.0000.000
14A759ASP -1-0.952-0.99534.519-0.037-0.0370.0000.0000.0000.000
15A760ASN 0-0.048-0.02836.6870.0030.0030.0000.0000.0000.000
16A761LYS 10.9250.98039.6860.0290.0290.0000.0000.0000.000
17A762VAL 00.0150.00339.525-0.001-0.0010.0000.0000.0000.000
18A763ASP -1-0.899-0.94839.645-0.013-0.0130.0000.0000.0000.000
19A764ILE 00.0080.01141.4660.0010.0010.0000.0000.0000.000
20A765ILE 0-0.023-0.02140.4960.0010.0010.0000.0000.0000.000
21A766GLY 0-0.031-0.00744.2450.0010.0010.0000.0000.0000.000
22A767ASN 00.042-0.01647.6030.0000.0000.0000.0000.0000.000
23A768ASN 0-0.056-0.01244.1040.0000.0000.0000.0000.0000.000
24A769VAL 00.0420.04045.402-0.001-0.0010.0000.0000.0000.000
25A770ARG 10.8680.92838.6940.0160.0160.0000.0000.0000.000
26A771GLY 00.004-0.02143.581-0.001-0.0010.0000.0000.0000.000
27A772GLU -1-0.931-0.94544.399-0.025-0.0250.0000.0000.0000.000
28A773LEU 0-0.040-0.01644.9600.0010.0010.0000.0000.0000.000
29A774PRO 00.0380.02546.5560.0000.0000.0000.0000.0000.000
30A775ASN 00.0360.00650.2530.0000.0000.0000.0000.0000.000
31A776ILE 00.0030.03052.6490.0000.0000.0000.0000.0000.000
32A777TRP 00.019-0.00348.3270.0000.0000.0000.0000.0000.000
33A778LEU 00.0540.03351.3180.0010.0010.0000.0000.0000.000
34A779GLN 00.011-0.00250.7770.0000.0000.0000.0000.0000.000
35A780TYR 0-0.055-0.03447.9750.0010.0010.0000.0000.0000.000
36A781GLY 00.0040.03047.7700.0010.0010.0000.0000.0000.000
37A782GLN 0-0.068-0.07442.8320.0000.0000.0000.0000.0000.000
38A783PHE 00.0600.01441.2410.0000.0000.0000.0000.0000.000
39A784LYS 10.8650.94534.6430.0130.0130.0000.0000.0000.000
40A785LEU 00.0260.02436.223-0.001-0.0010.0000.0000.0000.000
41A786LYS 10.9430.97732.1550.0280.0280.0000.0000.0000.000
42A787ALA 00.0140.01829.996-0.001-0.0010.0000.0000.0000.000
43A788SER 0-0.040-0.01228.9510.0010.0010.0000.0000.0000.000
44A789GLY 00.1200.06326.317-0.001-0.0010.0000.0000.0000.000
45A790GLY 0-0.004-0.01123.3900.0070.0070.0000.0000.0000.000
46A791ASP -1-0.785-0.90019.009-0.107-0.1070.0000.0000.0000.000
47A792GLY 0-0.048-0.02020.8590.0090.0090.0000.0000.0000.000
48A793THR 0-0.104-0.04520.8050.0150.0150.0000.0000.0000.000
49A794TYR 0-0.003-0.02423.592-0.003-0.0030.0000.0000.0000.000
50A795SER 0-0.059-0.01226.7180.0070.0070.0000.0000.0000.000
51A796TRP 00.0320.00528.840-0.005-0.0050.0000.0000.0000.000
52A797TYR 00.0210.01432.5730.0020.0020.0000.0000.0000.000
53A798SER 0-0.020-0.02535.107-0.002-0.0020.0000.0000.0000.000
54A799GLU -1-0.899-0.95438.857-0.032-0.0320.0000.0000.0000.000
55A800ASN 00.004-0.02240.7330.0020.0020.0000.0000.0000.000
56A801THR 00.0580.02541.9570.0000.0000.0000.0000.0000.000
57A802SER 0-0.050-0.01343.9560.0010.0010.0000.0000.0000.000
58A803ILE 0-0.0090.01846.4120.0010.0010.0000.0000.0000.000
59A804ALA 00.0330.01343.4480.0010.0010.0000.0000.0000.000
60A805THR 00.0130.02240.006-0.001-0.0010.0000.0000.0000.000
61A806VAL 0-0.0060.00935.6190.0000.0000.0000.0000.0000.000
62A807ASP -1-0.795-0.86435.455-0.011-0.0110.0000.0000.0000.000
63A808ALA 00.051-0.00130.138-0.003-0.0030.0000.0000.0000.000
64A809SER 0-0.099-0.06530.671-0.001-0.0010.0000.0000.0000.000
65A810GLY 00.0620.03332.717-0.002-0.0020.0000.0000.0000.000
66A811LYS 10.8630.93934.6270.0050.0050.0000.0000.0000.000
67A812VAL 00.0230.00437.9750.0010.0010.0000.0000.0000.000
68A813THR 0-0.050-0.02440.4860.0020.0020.0000.0000.0000.000
69A814LEU 0-0.0010.01443.687-0.001-0.0010.0000.0000.0000.000
70A815ASN 0-0.019-0.03444.5390.0020.0020.0000.0000.0000.000
71A816GLY 00.0110.00448.4950.0010.0010.0000.0000.0000.000
72A817LYS 10.9030.97250.1730.0120.0120.0000.0000.0000.000
73A818GLY 00.035-0.00450.9010.0000.0000.0000.0000.0000.000
74A819SER 0-0.003-0.00647.9020.0000.0000.0000.0000.0000.000
75A820VAL 0-0.0130.00242.5040.0000.0000.0000.0000.0000.000
76A821VAL 00.0170.01338.863-0.001-0.0010.0000.0000.0000.000
77A822ILE 00.0020.00336.3570.0010.0010.0000.0000.0000.000
78A823LYS 10.8970.95233.5450.0390.0390.0000.0000.0000.000
79A824ALA 00.0210.01430.9040.0030.0030.0000.0000.0000.000
80A825THR 0-0.033-0.04026.049-0.002-0.0020.0000.0000.0000.000
81A826SER 0-0.005-0.00723.9710.0080.0080.0000.0000.0000.000
82A827GLY 00.0350.02520.9350.0010.0010.0000.0000.0000.000
83A828ASP -1-0.813-0.89319.774-0.126-0.1260.0000.0000.0000.000
84A829LYS 10.8850.93620.8510.0930.0930.0000.0000.0000.000
85A830GLN 0-0.0150.01023.7230.0090.0090.0000.0000.0000.000
86A831THR 00.008-0.00526.5040.0100.0100.0000.0000.0000.000
87A832VAL 00.0160.02229.9850.0000.0000.0000.0000.0000.000
88A833SER 0-0.037-0.02832.9580.0050.0050.0000.0000.0000.000
89A834TYR 00.0190.01336.538-0.001-0.0010.0000.0000.0000.000
90A835THR 0-0.063-0.02938.9110.0020.0020.0000.0000.0000.000
91A836ILE 00.0070.00542.2330.0000.0000.0000.0000.0000.000
92A837LYS 10.9510.96545.0250.0260.0260.0000.0000.0000.000
93A838ALA 0-0.015-0.00548.5540.0010.0010.0000.0000.0000.000
94A839PRO 00.0210.03751.2090.0000.0000.0000.0000.0000.000
95A840SER 0-0.045-0.03353.4090.0000.0000.0000.0000.0000.000
96A841TYR 0-0.042-0.03756.4800.0000.0000.0000.0000.0000.000
97A842MET 0-0.041-0.01852.842-0.001-0.0010.0000.0000.0000.000
98A843ILE 0-0.0250.01055.6980.0000.0000.0000.0000.0000.000
99A844LYS 10.8940.94155.4050.0080.0080.0000.0000.0000.000
100A845VAL 0-0.015-0.01356.5250.0000.0000.0000.0000.0000.000
101A846ASP -1-0.901-0.93257.834-0.004-0.0040.0000.0000.0000.000
102A847LYS 10.9230.95260.4300.0020.0020.0000.0000.0000.000
103A848GLN 0-0.011-0.02162.4600.0000.0000.0000.0000.0000.000
104A849ALA 0-0.0160.00065.2810.0000.0000.0000.0000.0000.000
105A850TYR 00.0260.02868.7370.0000.0000.0000.0000.0000.000
106A851TYR 00.0150.03471.2760.0000.0000.0000.0000.0000.000
107A852ALA 00.017-0.00771.8970.0000.0000.0000.0000.0000.000
108A853ASP -1-0.867-0.94269.889-0.002-0.0020.0000.0000.0000.000
109A854ALA 00.0410.01967.6620.0000.0000.0000.0000.0000.000
110A855MET 0-0.0270.00067.8840.0000.0000.0000.0000.0000.000
111A856SER 0-0.060-0.02169.4010.0000.0000.0000.0000.0000.000
112A857ILE 00.010-0.00164.4420.0000.0000.0000.0000.0000.000
113A932CYS 0-0.0480.00460.7920.0000.0000.0000.0000.0000.000
114A859LYS 10.9580.96864.8470.0060.0060.0000.0000.0000.000
115A860ASN 0-0.090-0.07167.9170.0000.0000.0000.0000.0000.000
116A861LEU 00.0040.01763.5910.0000.0000.0000.0000.0000.000
117A862LEU 0-0.0210.00064.7990.0000.0000.0000.0000.0000.000
118A863PRO 00.0360.02263.7580.0000.0000.0000.0000.0000.000
119A864SER 0-0.009-0.01365.5090.0000.0000.0000.0000.0000.000
120A865THR 00.0260.00466.7820.0000.0000.0000.0000.0000.000
121A866GLN 00.0640.01865.5360.0000.0000.0000.0000.0000.000
122A867THR 00.0330.02563.0800.0000.0000.0000.0000.0000.000
123A868VAL 0-0.0270.01661.8060.0000.0000.0000.0000.0000.000
124A869LEU 00.002-0.00260.4390.0000.0000.0000.0000.0000.000
125A870SER 00.009-0.01559.4390.0000.0000.0000.0000.0000.000
126A871ASP -1-0.819-0.91258.610-0.010-0.0100.0000.0000.0000.000
127A872ILE 0-0.037-0.02254.537-0.001-0.0010.0000.0000.0000.000
128A873TYR 0-0.064-0.03354.4830.0000.0000.0000.0000.0000.000
129A874ASP -1-0.866-0.93054.501-0.009-0.0090.0000.0000.0000.000
130A875SER 0-0.078-0.03352.270-0.001-0.0010.0000.0000.0000.000
131A876TRP 0-0.108-0.07046.457-0.001-0.0010.0000.0000.0000.000
132A877GLY 00.0330.03650.1640.0000.0000.0000.0000.0000.000
133A878ALA 0-0.021-0.01452.6430.0000.0000.0000.0000.0000.000
134A879ALA 00.0670.02251.8230.0000.0000.0000.0000.0000.000
135A880ASN 00.025-0.00151.509-0.001-0.0010.0000.0000.0000.000
136A881LYS 10.9150.97448.0990.0040.0040.0000.0000.0000.000
137A882TYR 0-0.018-0.00146.120-0.001-0.0010.0000.0000.0000.000
138A883SER 00.0080.00144.3210.0010.0010.0000.0000.0000.000
139A884HIS 10.8950.95746.4610.0040.0040.0000.0000.0000.000
140A885TYR 0-0.022-0.03749.2910.0010.0010.0000.0000.0000.000
141A886SER 0-0.0230.00048.0810.0000.0000.0000.0000.0000.000
142A887SER 0-0.036-0.00850.4800.0000.0000.0000.0000.0000.000
143A888MET 0-0.0120.01253.1300.0000.0000.0000.0000.0000.000
144A889ASN 00.0500.01055.2720.0000.0000.0000.0000.0000.000
145A890SER 0-0.042-0.01857.712-0.001-0.0010.0000.0000.0000.000
146A891ILE 00.0320.00555.9550.0000.0000.0000.0000.0000.000
147A892THR 00.0140.01960.510-0.001-0.0010.0000.0000.0000.000
148A893ALA 00.0280.02162.4200.0000.0000.0000.0000.0000.000
149A894TRP 00.013-0.01764.5030.0000.0000.0000.0000.0000.000
150A895ILE 0-0.0040.02466.4380.0000.0000.0000.0000.0000.000
151A896LYS 10.9290.96068.7740.0060.0060.0000.0000.0000.000
152A897GLN 0-0.004-0.01971.0160.0000.0000.0000.0000.0000.000
153A898THR 0-0.006-0.02074.5220.0000.0000.0000.0000.0000.000
154A899SER 00.0300.00176.8350.0000.0000.0000.0000.0000.000
155A900SER 0-0.059-0.03980.2070.0000.0000.0000.0000.0000.000
156A901GLU -1-0.787-0.89075.293-0.004-0.0040.0000.0000.0000.000
157A902GLN 0-0.0190.00178.9950.0000.0000.0000.0000.0000.000
158A903ARG 10.9090.95580.0980.0040.0040.0000.0000.0000.000
159A904SER 0-0.022-0.00481.8400.0000.0000.0000.0000.0000.000
160A905GLY 00.0120.03280.2410.0000.0000.0000.0000.0000.000
161A906VAL 0-0.016-0.01477.3880.0000.0000.0000.0000.0000.000
162A907SER 0-0.043-0.02972.3190.0000.0000.0000.0000.0000.000
163A908SER 00.0200.02171.4760.0000.0000.0000.0000.0000.000
164A909THR 0-0.062-0.03267.5820.0000.0000.0000.0000.0000.000
165A910TYR 00.0680.02160.0560.0000.0000.0000.0000.0000.000
166A911ASN 00.0360.01960.7810.0000.0000.0000.0000.0000.000
167A912LEU 00.0140.00357.4130.0000.0000.0000.0000.0000.000
168A913ILE 0-0.069-0.02655.6520.0000.0000.0000.0000.0000.000
169A914THR 00.009-0.01357.6780.0000.0000.0000.0000.0000.000
170A915GLN 00.0270.02258.9470.0000.0000.0000.0000.0000.000
171A916TYR 0-0.024-0.01461.8500.0000.0000.0000.0000.0000.000
172A917PRO 00.0070.01865.1990.0000.0000.0000.0000.0000.000
173A918LEU 0-0.012-0.01067.9570.0000.0000.0000.0000.0000.000
174A919PRO 00.0380.01071.0190.0000.0000.0000.0000.0000.000
175A920GLY 00.012-0.00374.1980.0000.0000.0000.0000.0000.000
176A921VAL 00.0000.02171.7540.0000.0000.0000.0000.0000.000
177A922ASN 00.0550.02375.0450.0000.0000.0000.0000.0000.000
178A923VAL 00.0400.02074.8960.0000.0000.0000.0000.0000.000
179A924ASN 0-0.038-0.02074.1700.0000.0000.0000.0000.0000.000
180A925THR 0-0.007-0.01371.5170.0000.0000.0000.0000.0000.000
181A926PRO 0-0.002-0.00670.3630.0000.0000.0000.0000.0000.000
182A927ASN 0-0.017-0.02266.4400.0000.0000.0000.0000.0000.000
183A928VAL 00.0030.01366.1860.0000.0000.0000.0000.0000.000
184A929TYR 0-0.004-0.00959.8290.0000.0000.0000.0000.0000.000
185A930ALA 0-0.011-0.00263.9900.0000.0000.0000.0000.0000.000
186A931VAL 00.002-0.00759.8670.0000.0000.0000.0000.0000.000
187A933VAL 0-0.008-0.01260.1160.0000.0000.0000.0000.0000.000
188A934GLU -2-1.707-1.85857.914-0.019-0.0190.0000.0000.0000.000