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: 22M3R

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 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 -1863782.08329
FMO2-HF: Nuclear repulsion 1791547.385007
FMO2-HF: Total energy -72234.698283
FMO2-MP2: Total energy -72445.768624


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.
-3.009-0.568-0.027-1.315-1.10.007
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 : -0.001 / q_NPA : 0.001
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-1-0.884-0.9503.804-3.027-0.586-0.027-1.315-1.1000.007
4A750VAL0-0.064-0.0226.7680.2120.2120.0000.0000.0000.000
5A751THR0-0.024-0.0039.0960.0070.0070.0000.0000.0000.000
6A752PHE0-0.032-0.02912.3440.0530.0530.0000.0000.0000.000
7A753PHE0-0.0010.00314.608-0.012-0.0120.0000.0000.0000.000
8A754ASP-1-0.886-0.93619.126-0.177-0.1770.0000.0000.0000.000
9A755GLU-1-0.960-0.98222.584-0.081-0.0810.0000.0000.0000.000
10A756LEU0-0.069-0.03324.795-0.002-0.0020.0000.0000.0000.000
11A757LYS10.9550.97526.1090.0870.0870.0000.0000.0000.000
12A758ILE0-0.038-0.02629.642-0.005-0.0050.0000.0000.0000.000
13A759ASP-1-0.890-0.95932.298-0.076-0.0760.0000.0000.0000.000
14A760ASN0-0.061-0.03934.4700.0030.0030.0000.0000.0000.000
15A761LYS10.7870.89437.5320.0620.0620.0000.0000.0000.000
16A762VAL0-0.027-0.01537.637-0.003-0.0030.0000.0000.0000.000
17A763ASP-1-0.857-0.91338.060-0.063-0.0630.0000.0000.0000.000
18A764ILE0-0.0030.00740.0670.0020.0020.0000.0000.0000.000
19A765ILE0-0.004-0.01439.575-0.001-0.0010.0000.0000.0000.000
20A766GLY0-0.032-0.00643.3710.0000.0000.0000.0000.0000.000
21A767ASN00.027-0.02246.566-0.001-0.0010.0000.0000.0000.000
22A768ASN0-0.048-0.01043.160-0.003-0.0030.0000.0000.0000.000
23A769VAL00.0290.03044.161-0.003-0.0030.0000.0000.0000.000
24A770ARG10.8240.89737.9360.0670.0670.0000.0000.0000.000
25A771GLY00.033-0.00241.892-0.001-0.0010.0000.0000.0000.000
26A772GLU-1-0.794-0.86842.546-0.050-0.0500.0000.0000.0000.000
27A773LEU0-0.029-0.00443.1190.0010.0010.0000.0000.0000.000
28A774PRO00.0280.02144.7630.0010.0010.0000.0000.0000.000
29A775ASN00.0290.00048.5240.0020.0020.0000.0000.0000.000
30A776ILE0-0.0180.01750.8050.0020.0020.0000.0000.0000.000
31A777TRP00.0300.00146.6110.0000.0000.0000.0000.0000.000
32A778LEU00.0510.03750.3980.0020.0020.0000.0000.0000.000
33A779GLN0-0.012-0.02449.773-0.001-0.0010.0000.0000.0000.000
34A780TYR0-0.040-0.02147.2440.0000.0000.0000.0000.0000.000
35A781GLY00.0030.03047.110-0.001-0.0010.0000.0000.0000.000
36A782GLN0-0.057-0.06642.082-0.001-0.0010.0000.0000.0000.000
37A783PHE00.0620.01339.634-0.001-0.0010.0000.0000.0000.000
38A784LYS10.8380.92933.3090.0640.0640.0000.0000.0000.000
39A785LEU00.0200.02334.665-0.002-0.0020.0000.0000.0000.000
40A786LYS10.9520.97830.4170.0960.0960.0000.0000.0000.000
41A787ALA00.0080.01628.1330.0020.0020.0000.0000.0000.000
42A788SER0-0.049-0.02626.839-0.007-0.0070.0000.0000.0000.000
43A789GLY00.1210.06823.7220.0110.0110.0000.0000.0000.000
44A790GLY00.0110.00920.8390.0080.0080.0000.0000.0000.000
45A791ASP-1-0.795-0.88917.138-0.152-0.1520.0000.0000.0000.000
46A792GLY0-0.041-0.01718.956-0.010-0.0100.0000.0000.0000.000
47A793THR0-0.112-0.05419.9880.0210.0210.0000.0000.0000.000
48A794TYR0-0.011-0.04322.4480.0100.0100.0000.0000.0000.000
49A795SER0-0.049-0.01225.4730.0080.0080.0000.0000.0000.000
50A796TRP00.0140.00227.8350.0020.0020.0000.0000.0000.000
51A797TYR00.0210.01431.4470.0060.0060.0000.0000.0000.000
52A798SER0-0.014-0.02033.956-0.003-0.0030.0000.0000.0000.000
53A799GLU-1-0.840-0.91037.075-0.002-0.0020.0000.0000.0000.000
54A800ASN00.025-0.00939.3420.0030.0030.0000.0000.0000.000
55A801THR00.0770.03740.988-0.002-0.0020.0000.0000.0000.000
56A802SER0-0.0140.00343.064-0.001-0.0010.0000.0000.0000.000
57A803ILE0-0.067-0.01145.107-0.001-0.0010.0000.0000.0000.000
58A804ALA00.0470.02242.195-0.002-0.0020.0000.0000.0000.000
59A805THR00.0210.01839.6220.0030.0030.0000.0000.0000.000
60A806VAL0-0.0040.00634.765-0.003-0.0030.0000.0000.0000.000
61A807ASP-1-0.751-0.83034.966-0.037-0.0370.0000.0000.0000.000
62A808ALA00.0580.00929.909-0.001-0.0010.0000.0000.0000.000
63A809SER0-0.077-0.06030.072-0.008-0.0080.0000.0000.0000.000
64A810GLY00.0820.03832.115-0.007-0.0070.0000.0000.0000.000
65A811LYS10.8150.90933.6140.0390.0390.0000.0000.0000.000
66A812VAL00.0190.00137.1360.0040.0040.0000.0000.0000.000
67A813THR0-0.045-0.01939.490-0.001-0.0010.0000.0000.0000.000
68A814LEU00.0000.01842.8620.0020.0020.0000.0000.0000.000
69A815ASN0-0.035-0.03444.151-0.001-0.0010.0000.0000.0000.000
70A816GLY00.0050.00247.6330.0010.0010.0000.0000.0000.000
71A817LYS10.8440.93748.9090.0130.0130.0000.0000.0000.000
72A818GLY00.0330.00449.3630.0020.0020.0000.0000.0000.000
73A819SER00.0170.00145.859-0.002-0.0020.0000.0000.0000.000
74A820VAL0-0.023-0.00440.9700.0020.0020.0000.0000.0000.000
75A821VAL00.0000.00537.003-0.004-0.0040.0000.0000.0000.000
76A822ILE00.0020.00234.8940.0020.0020.0000.0000.0000.000
77A823LYS10.8370.90731.8050.0040.0040.0000.0000.0000.000
78A824ALA00.0210.01529.2030.0010.0010.0000.0000.0000.000
79A825THR0-0.006-0.01824.568-0.001-0.0010.0000.0000.0000.000
80A826SER0-0.034-0.04321.5720.0060.0060.0000.0000.0000.000
81A827GLY00.0400.02819.5400.0180.0180.0000.0000.0000.000
82A828ASP-1-0.795-0.86317.472-0.096-0.0960.0000.0000.0000.000
83A829LYS10.8900.93818.699-0.026-0.0260.0000.0000.0000.000
84A830GLN00.0000.02421.0760.0160.0160.0000.0000.0000.000
85A831THR0-0.010-0.02924.1180.0030.0030.0000.0000.0000.000
86A832VAL00.0010.01427.7710.0010.0010.0000.0000.0000.000
87A833SER0-0.014-0.02430.6230.0030.0030.0000.0000.0000.000
88A834TYR00.0190.01334.322-0.002-0.0020.0000.0000.0000.000
89A835THR0-0.062-0.03436.7950.0040.0040.0000.0000.0000.000
90A836ILE00.0020.00640.383-0.002-0.0020.0000.0000.0000.000
91A837LYS10.9490.96943.1580.0270.0270.0000.0000.0000.000
92A838ALA0-0.0070.00146.556-0.001-0.0010.0000.0000.0000.000
93A839PRO00.0370.04449.4520.0000.0000.0000.0000.0000.000
94A840SER00.0110.00151.6750.0010.0010.0000.0000.0000.000
95A841TYR0-0.034-0.03354.8650.0020.0020.0000.0000.0000.000
96A842MET0-0.021-0.00451.586-0.001-0.0010.0000.0000.0000.000
97A843ILE0-0.0180.00354.5200.0010.0010.0000.0000.0000.000
98A844LYS10.8560.91354.6380.0090.0090.0000.0000.0000.000
99A845VAL0-0.027-0.02355.8520.0000.0000.0000.0000.0000.000
100A846ASP-1-0.893-0.93157.400-0.009-0.0090.0000.0000.0000.000
101A847LYS10.8660.92860.0080.0060.0060.0000.0000.0000.000
102A848GLN0-0.004-0.01862.2510.0000.0000.0000.0000.0000.000
103A849ALA0-0.030-0.01065.0570.0010.0010.0000.0000.0000.000
104A850TYR00.0330.03368.4590.0000.0000.0000.0000.0000.000
105A851TYR00.0240.02670.6120.0000.0000.0000.0000.0000.000
106A852ALA00.0350.00271.2310.0000.0000.0000.0000.0000.000
107A853ASP-1-0.809-0.91269.424-0.006-0.0060.0000.0000.0000.000
108A854ALA00.0340.01167.0260.0000.0000.0000.0000.0000.000
109A855MET0-0.030-0.00667.1690.0000.0000.0000.0000.0000.000
110A856SER0-0.038-0.00668.5590.0000.0000.0000.0000.0000.000
111A857ILE00.0050.00363.9310.0000.0000.0000.0000.0000.000
112A858CYS0-0.056-0.00459.9560.0000.0000.0000.0000.0000.000
113A859LYS10.9570.96863.5100.0040.0040.0000.0000.0000.000
114A860ASN0-0.068-0.05766.9790.0000.0000.0000.0000.0000.000
115A861LEU0-0.0060.01162.3250.0000.0000.0000.0000.0000.000
116A862LEU0-0.0110.00563.674-0.001-0.0010.0000.0000.0000.000
117A863PRO00.0320.01962.5170.0000.0000.0000.0000.0000.000
118A864SER0-0.011-0.01664.3200.0000.0000.0000.0000.0000.000
119A865THR00.0320.00765.4310.0000.0000.0000.0000.0000.000
120A866GLN00.0700.02064.4500.0010.0010.0000.0000.0000.000
121A867THR00.0390.03361.7170.0000.0000.0000.0000.0000.000
122A868VAL0-0.0410.00660.452-0.001-0.0010.0000.0000.0000.000
123A869LEU0-0.008-0.00659.1280.0000.0000.0000.0000.0000.000
124A870SER00.014-0.00958.289-0.001-0.0010.0000.0000.0000.000
125A871ASP-1-0.827-0.92157.116-0.026-0.0260.0000.0000.0000.000
126A872ILE0-0.037-0.02053.540-0.001-0.0010.0000.0000.0000.000
127A873TYR0-0.061-0.03553.276-0.001-0.0010.0000.0000.0000.000
128A874ASP-1-0.855-0.92753.341-0.032-0.0320.0000.0000.0000.000
129A875SER0-0.089-0.03850.819-0.002-0.0020.0000.0000.0000.000
130A876TRP0-0.096-0.07045.313-0.002-0.0020.0000.0000.0000.000
131A877GLY00.0460.05249.152-0.002-0.0020.0000.0000.0000.000
132A878ALA0-0.016-0.01351.6820.0020.0020.0000.0000.0000.000
133A879ALA00.0620.01851.195-0.001-0.0010.0000.0000.0000.000
134A880ASN00.006-0.01251.025-0.001-0.0010.0000.0000.0000.000
135A881LYS10.9170.97647.5200.0380.0380.0000.0000.0000.000
136A882TYR0-0.032-0.01945.320-0.002-0.0020.0000.0000.0000.000
137A883SER00.0180.00844.0320.0020.0020.0000.0000.0000.000
138A884HIS10.8760.94146.1740.0170.0170.0000.0000.0000.000
139A885TYR0-0.024-0.04449.0320.0030.0030.0000.0000.0000.000
140A886SER0-0.0070.01047.8360.0000.0000.0000.0000.0000.000
141A887SER0-0.0220.00050.227-0.001-0.0010.0000.0000.0000.000
142A888MET0-0.0220.01752.9930.0000.0000.0000.0000.0000.000
143A889ASN00.0520.01354.968-0.002-0.0020.0000.0000.0000.000
144A890SER0-0.019-0.00657.394-0.001-0.0010.0000.0000.0000.000
145A891ILE00.0280.00555.7230.0010.0010.0000.0000.0000.000
146A892THR00.0070.01660.083-0.001-0.0010.0000.0000.0000.000
147A893ALA00.0310.02561.7040.0010.0010.0000.0000.0000.000
148A894TRP00.021-0.01463.8330.0000.0000.0000.0000.0000.000
149A895ILE00.0010.01365.0580.0000.0000.0000.0000.0000.000
150A896LYS10.9130.96067.7860.0110.0110.0000.0000.0000.000
151A897GLN0-0.021-0.00269.9250.0000.0000.0000.0000.0000.000
152A898THR0-0.008-0.04473.4680.0010.0010.0000.0000.0000.000
153A899SER00.0460.00375.6170.0000.0000.0000.0000.0000.000
154A900SER0-0.036-0.01678.9790.0000.0000.0000.0000.0000.000
155A901GLU-1-0.733-0.85274.323-0.013-0.0130.0000.0000.0000.000
156A902GLN0-0.020-0.00678.0170.0000.0000.0000.0000.0000.000
157A903ARG10.8650.93379.1250.0100.0100.0000.0000.0000.000
158A904SER0-0.013-0.00181.1060.0000.0000.0000.0000.0000.000
159A905GLY00.0060.03079.5120.0000.0000.0000.0000.0000.000
160A906VAL0-0.022-0.02176.7040.0000.0000.0000.0000.0000.000
161A907SER0-0.016-0.02571.4330.0000.0000.0000.0000.0000.000
162A908SER0-0.0090.01170.5450.0000.0000.0000.0000.0000.000
163A909THR0-0.067-0.02966.9300.0000.0000.0000.0000.0000.000
164A910TYR00.0750.02659.134-0.001-0.0010.0000.0000.0000.000
165A911ASN00.0120.01160.3440.0000.0000.0000.0000.0000.000
166A912LEU00.0140.00256.693-0.001-0.0010.0000.0000.0000.000
167A913ILE0-0.071-0.02755.088-0.001-0.0010.0000.0000.0000.000
168A914THR00.024-0.01357.096-0.001-0.0010.0000.0000.0000.000
169A915GLN00.0280.02558.117-0.001-0.0010.0000.0000.0000.000
170A916TYR0-0.023-0.00761.0320.0000.0000.0000.0000.0000.000
171A917PRO00.0000.01564.4960.0010.0010.0000.0000.0000.000
172A918LEU0-0.005-0.00967.1140.0000.0000.0000.0000.0000.000
173A919PRO00.0310.00870.2820.0010.0010.0000.0000.0000.000
174A920GLY00.0230.00273.3670.0000.0000.0000.0000.0000.000
175A921VAL0-0.0070.01671.1530.0000.0000.0000.0000.0000.000
176A922ASN00.0440.02174.4600.0000.0000.0000.0000.0000.000
177A923VAL00.0410.02474.3240.0000.0000.0000.0000.0000.000
178A924ASN0-0.038-0.02173.7260.0000.0000.0000.0000.0000.000
179A925THR0-0.009-0.01671.3360.0000.0000.0000.0000.0000.000
180A926PRO00.005-0.00470.1610.0000.0000.0000.0000.0000.000
181A927ASN0-0.013-0.01766.2080.0000.0000.0000.0000.0000.000
182A928VAL00.0020.01265.829-0.001-0.0010.0000.0000.0000.000
183A929TYR0-0.005-0.02459.1980.0010.0010.0000.0000.0000.000
184A930ALA0-0.010-0.00263.5590.0000.0000.0000.0000.0000.000
185A931VAL00.005-0.00559.2360.0000.0000.0000.0000.0000.000
186A933VAL00.0050.00459.114-0.001-0.0010.0000.0000.0000.000
187A934GLU-1-0.829-0.89856.476-0.009-0.0090.0000.0000.0000.000