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: 8235Y

Calculation Name: 3NCV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3NCV

Chain ID: A

ChEMBL ID:

UniProt ID: Q5F8M6

Base Structure: X-ray

Registration Date: 2023-06-20

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 192
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1927884.854822
FMO2-HF: Nuclear repulsion 1853257.403389
FMO2-HF: Total energy -74627.451433
FMO2-MP2: Total energy -74841.221133


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:463:GLU)


Summations of interaction energy for fragment #1(A:463: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.
57.05957.9590.023-0.386-0.5380.003
Interaction energy analysis for fragmet #1(A:463:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.963 / q_NPA : -1.001
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].
3A465PRO00.0060.0273.522-4.402-3.5020.023-0.386-0.5380.003
4A466PRO0-0.0020.0036.551-0.375-0.3750.0000.0000.0000.000
5A467LEU0-0.050-0.0439.075-1.247-1.2470.0000.0000.0000.000
6A468GLY0-0.0110.0038.095-0.976-0.9760.0000.0000.0000.000
7A469PHE0-0.026-0.0205.789-1.509-1.5090.0000.0000.0000.000
8A470ALA0-0.007-0.00710.998-1.002-1.0020.0000.0000.0000.000
9A471ILE0-0.024-0.01513.6610.3650.3650.0000.0000.0000.000
10A472ALA0-0.023-0.01916.194-0.830-0.8300.0000.0000.0000.000
11A473GLN00.0520.03619.6160.3700.3700.0000.0000.0000.000
12A474LEU00.011-0.00522.498-0.387-0.3870.0000.0000.0000.000
13A475LEU00.012-0.01424.862-0.154-0.1540.0000.0000.0000.000
14A476GLY0-0.073-0.03327.650-0.313-0.3130.0000.0000.0000.000
15A477ILE00.0220.01426.6210.0430.0430.0000.0000.0000.000
16A478TYR0-0.0040.00422.4770.1150.1150.0000.0000.0000.000
17A479ILE0-0.0080.00517.432-0.146-0.1460.0000.0000.0000.000
18A480LEU0-0.0120.00018.120-0.099-0.0990.0000.0000.0000.000
19A481ALA00.0450.01412.8750.2420.2420.0000.0000.0000.000
20A482GLN00.0100.0119.809-2.767-2.7670.0000.0000.0000.000
21A483ALA00.0210.0088.3152.1722.1720.0000.0000.0000.000
22A484GLU-1-0.927-0.9765.51236.49336.4930.0000.0000.0000.000
23A485ASP-1-0.917-0.9517.69622.88022.8800.0000.0000.0000.000
24A486SER0-0.084-0.05010.911-2.276-2.2760.0000.0000.0000.000
25A487LEU00.0200.02412.6840.7870.7870.0000.0000.0000.000
26A488LEU0-0.030-0.01012.322-0.625-0.6250.0000.0000.0000.000
27A489LEU00.0140.00716.065-0.176-0.1760.0000.0000.0000.000
28A490ILE00.002-0.01715.919-0.133-0.1330.0000.0000.0000.000
29A491ASP-1-0.907-0.95520.20610.96110.9610.0000.0000.0000.000
30A492MET0-0.009-0.00922.6770.1310.1310.0000.0000.0000.000
31A493HIS00.0490.03923.6750.0240.0240.0000.0000.0000.000
32A494ALA00.0780.05325.891-0.094-0.0940.0000.0000.0000.000
33A495ALA0-0.022-0.02721.0620.0280.0280.0000.0000.0000.000
34A496ALA0-0.004-0.00623.1610.1670.1670.0000.0000.0000.000
35A497GLU-1-0.920-0.94124.60610.00610.0060.0000.0000.0000.000
36A498ARG10.8080.88423.234-11.405-11.4050.0000.0000.0000.000
37A499VAL00.000-0.01520.559-0.043-0.0430.0000.0000.0000.000
38A500ASN0-0.028-0.01523.2960.1760.1760.0000.0000.0000.000
39A501TYR0-0.013-0.00426.519-0.361-0.3610.0000.0000.0000.000
40A502GLU-1-0.847-0.91723.75810.91110.9110.0000.0000.0000.000
41A503LYS10.8670.93821.560-13.699-13.6990.0000.0000.0000.000
42A504MET00.0080.01025.456-0.262-0.2620.0000.0000.0000.000
43A505LYS10.9510.98129.252-9.292-9.2920.0000.0000.0000.000
44A506ARG10.9410.97321.857-12.770-12.7700.0000.0000.0000.000
45A507GLN00.007-0.01128.220-0.108-0.1080.0000.0000.0000.000
46A508ARG10.9180.97229.721-8.443-8.4430.0000.0000.0000.000
47A509GLN0-0.082-0.03430.766-0.020-0.0200.0000.0000.0000.000
48A510GLU-1-1.000-0.99326.62910.78110.7810.0000.0000.0000.000
49A511ASN00.010-0.00130.982-0.145-0.1450.0000.0000.0000.000
50A512GLY0-0.052-0.01633.376-0.250-0.2500.0000.0000.0000.000
51A513ASN0-0.094-0.05035.149-0.149-0.1490.0000.0000.0000.000
52A514LEU0-0.057-0.02831.3290.3410.3410.0000.0000.0000.000
53A515GLN00.0550.03231.183-0.394-0.3940.0000.0000.0000.000
54A516SER00.0030.01532.6090.2870.2870.0000.0000.0000.000
55A517GLN0-0.002-0.00930.4500.1350.1350.0000.0000.0000.000
56A518HIS0-0.008-0.01134.724-0.127-0.1270.0000.0000.0000.000
57A519LEU0-0.053-0.01336.6230.2370.2370.0000.0000.0000.000
58A520LEU0-0.025-0.02035.677-0.182-0.1820.0000.0000.0000.000
59A521ILE0-0.028-0.01639.453-0.221-0.2210.0000.0000.0000.000
60A522PRO0-0.003-0.00241.3240.0880.0880.0000.0000.0000.000
61A523VAL00.0040.01739.755-0.056-0.0560.0000.0000.0000.000
62A524THR0-0.008-0.00343.045-0.009-0.0090.0000.0000.0000.000
63A525PHE0-0.036-0.02244.6420.0990.0990.0000.0000.0000.000
64A526ALA00.0010.01047.354-0.094-0.0940.0000.0000.0000.000
65A527ALA00.0340.00749.2680.1170.1170.0000.0000.0000.000
66A528SER0-0.036-0.02750.573-0.177-0.1770.0000.0000.0000.000
67A529HIS00.029-0.01652.7530.0120.0120.0000.0000.0000.000
68A530GLU-1-0.893-0.95952.1015.8115.8110.0000.0000.0000.000
69A531GLU-1-0.855-0.89947.4176.7126.7120.0000.0000.0000.000
70A532CYS0-0.019-0.00149.8290.0680.0680.0000.0000.0000.000
71A533ALA0-0.005-0.00452.2090.0090.0090.0000.0000.0000.000
72A534ALA00.0710.04148.3120.0060.0060.0000.0000.0000.000
73A535LEU0-0.058-0.04347.1090.0840.0840.0000.0000.0000.000
74A536ALA0-0.100-0.05649.1820.0210.0210.0000.0000.0000.000
75A537ASP-1-0.926-0.94951.3575.8625.8620.0000.0000.0000.000
76A538HIS-1-0.793-0.88746.3406.5586.5580.0000.0000.0000.000
77A539ALA00.0140.01746.0030.2120.2120.0000.0000.0000.000
78A540GLU-1-0.889-0.94645.0916.7676.7670.0000.0000.0000.000
79A541THR0-0.001-0.03542.8260.2340.2340.0000.0000.0000.000
80A542LEU0-0.039-0.01641.7020.2510.2510.0000.0000.0000.000
81A543ALA00.0270.03040.3150.2580.2580.0000.0000.0000.000
82A544GLY00.0310.01539.2160.2270.2270.0000.0000.0000.000
83A545PHE0-0.079-0.06236.2010.3160.3160.0000.0000.0000.000
84A546GLY00.0300.00935.6800.2100.2100.0000.0000.0000.000
85A547LEU0-0.025-0.02736.7620.1300.1300.0000.0000.0000.000
86A548GLU-1-0.893-0.94439.4477.4487.4480.0000.0000.0000.000
87A549LEU00.025-0.00842.4200.0960.0960.0000.0000.0000.000
88A550SER0-0.038-0.02245.144-0.055-0.0550.0000.0000.0000.000
89A551ASP-1-0.797-0.90448.6336.0426.0420.0000.0000.0000.000
90A552MET0-0.062-0.02450.3140.0360.0360.0000.0000.0000.000
91A553GLY00.0100.02253.390-0.105-0.1050.0000.0000.0000.000
92A554GLY0-0.035-0.03755.2840.0550.0550.0000.0000.0000.000
93A555ASN0-0.005-0.00554.308-0.009-0.0090.0000.0000.0000.000
94A556THR0-0.049-0.00150.4320.1080.1080.0000.0000.0000.000
95A557LEU00.0680.04247.684-0.016-0.0160.0000.0000.0000.000
96A558ALA0-0.022-0.02546.1810.0730.0730.0000.0000.0000.000
97A559VAL00.0090.01139.749-0.019-0.0190.0000.0000.0000.000
98A560ARG10.8690.90742.152-7.074-7.0740.0000.0000.0000.000
99A561ALA00.0090.01037.9660.1500.1500.0000.0000.0000.000
100A562ALA00.0510.02835.261-0.175-0.1750.0000.0000.0000.000
101A563PRO00.0100.00332.1390.1760.1760.0000.0000.0000.000
102A564VAL00.0320.02227.7020.2220.2220.0000.0000.0000.000
103A565MET0-0.122-0.02826.8970.1890.1890.0000.0000.0000.000
104A566LEU00.0120.01227.2670.2520.2520.0000.0000.0000.000
105A567GLY00.0080.00328.4150.1550.1550.0000.0000.0000.000
106A568LYN0-0.031-0.01329.069-0.153-0.1530.0000.0000.0000.000
107A569SER0-0.052-0.10731.8630.0730.0730.0000.0000.0000.000
108A570ASP-1-0.837-0.89933.5137.9737.9730.0000.0000.0000.000
109A571VAL00.039-0.00535.7000.0350.0350.0000.0000.0000.000
110A572VAL0-0.0100.01737.641-0.122-0.1220.0000.0000.0000.000
111A573SER0-0.0030.00237.747-0.214-0.2140.0000.0000.0000.000
112A574LEU00.0230.03434.677-0.083-0.0830.0000.0000.0000.000
113A575ALA0-0.013-0.00538.073-0.098-0.0980.0000.0000.0000.000
114A576ARG10.8800.93141.163-7.141-7.1410.0000.0000.0000.000
115A577ASP-1-0.840-0.90438.9947.8437.8430.0000.0000.0000.000
116A578VAL0-0.039-0.03838.552-0.076-0.0760.0000.0000.0000.000
117A579LEU0-0.020-0.01641.238-0.114-0.1140.0000.0000.0000.000
118A580GLY00.0260.01244.581-0.153-0.1530.0000.0000.0000.000
119A581GLU-1-0.910-0.95640.6847.3867.3860.0000.0000.0000.000
120A582LEU0-0.064-0.04843.683-0.030-0.0300.0000.0000.0000.000
121A583ALA00.0400.03246.006-0.137-0.1370.0000.0000.0000.000
122A584GLN0-0.084-0.03546.277-0.122-0.1220.0000.0000.0000.000
123A585VAL0-0.042-0.00246.317-0.016-0.0160.0000.0000.0000.000
124A586GLY00.0770.03349.228-0.058-0.0580.0000.0000.0000.000
125A587SER0-0.061-0.04551.427-0.010-0.0100.0000.0000.0000.000
126A588SER0-0.093-0.05347.3750.0650.0650.0000.0000.0000.000
127A589GLN00.0600.03348.4050.1540.1540.0000.0000.0000.000
128A590THR00.019-0.01245.5130.1230.1230.0000.0000.0000.000
129A591ILE00.0520.05242.3490.2080.2080.0000.0000.0000.000
130A592ALA0-0.059-0.01742.420-0.005-0.0050.0000.0000.0000.000
131A593SER0-0.067-0.03641.3640.1960.1960.0000.0000.0000.000
132A594HIS00.0400.04141.7770.1520.1520.0000.0000.0000.000
133A595GLU-1-0.856-0.94035.9068.6628.6620.0000.0000.0000.000
134A596ASN0-0.022-0.01434.3890.1160.1160.0000.0000.0000.000
135A597ARG10.9120.95335.816-7.043-7.0430.0000.0000.0000.000
136A598ILE00.0850.03937.5400.1260.1260.0000.0000.0000.000
137A599LEU0-0.009-0.02032.2670.1780.1780.0000.0000.0000.000
138A600ALA0-0.051-0.01432.9220.3190.3190.0000.0000.0000.000
139A601THR00.0660.06933.5940.3420.3420.0000.0000.0000.000
140A602MET0-0.037-0.00333.9000.0980.0980.0000.0000.0000.000
141A603SER0-0.129-0.11529.5420.2480.2480.0000.0000.0000.000
142A604CYS0-0.012-0.00429.7960.3960.3960.0000.0000.0000.000
143A605HIS0-0.049-0.01631.9450.1770.1770.0000.0000.0000.000
144A606GLY00.0540.02128.1060.0410.0410.0000.0000.0000.000
145A607SER0-0.012-0.02425.347-0.260-0.2600.0000.0000.0000.000
146A608ILE0-0.025-0.00222.5490.0050.0050.0000.0000.0000.000
147A609ARG10.8770.97726.595-9.912-9.9120.0000.0000.0000.000
148A610ALA00.0730.02229.784-0.243-0.2430.0000.0000.0000.000
149A611GLY0-0.053-0.02231.078-0.116-0.1160.0000.0000.0000.000
150A612ARG10.9080.96829.141-9.587-9.5870.0000.0000.0000.000
151A613ARG10.9280.94927.146-9.985-9.9850.0000.0000.0000.000
152A614LEU00.0110.01922.543-0.102-0.1020.0000.0000.0000.000
153A615THR0-0.003-0.00921.4170.4540.4540.0000.0000.0000.000
154A616LEU00.053-0.00116.6130.1990.1990.0000.0000.0000.000
155A617PRO0-0.005-0.01516.3370.8940.8940.0000.0000.0000.000
156A618GLU-1-0.826-0.89617.42313.50113.5010.0000.0000.0000.000
157A619MET0-0.033-0.00117.9390.2360.2360.0000.0000.0000.000
158A620ASN00.0740.03413.2950.8550.8550.0000.0000.0000.000
159A621ALA0-0.0080.01114.9630.7210.7210.0000.0000.0000.000
160A622LEU00.0450.02117.022-0.142-0.1420.0000.0000.0000.000
161A623LEU0-0.022-0.00713.318-0.238-0.2380.0000.0000.0000.000
162A624ARG10.7950.86410.607-25.375-25.3750.0000.0000.0000.000
163A625ASP-1-0.848-0.93713.77714.96814.9680.0000.0000.0000.000
164A626MET0-0.068-0.01916.285-0.488-0.4880.0000.0000.0000.000
165A627GLU-1-0.768-0.87010.70825.01725.0170.0000.0000.0000.000
166A628ASN0-0.044-0.00313.9040.1410.1410.0000.0000.0000.000
167A629THR0-0.030-0.00715.881-1.177-1.1770.0000.0000.0000.000
168A630PRO0-0.008-0.00718.6940.1750.1750.0000.0000.0000.000
169A631ARG10.8740.91120.474-11.474-11.4740.0000.0000.0000.000
170A632SER00.0160.02017.496-0.482-0.4820.0000.0000.0000.000
171A633ASN00.0060.00519.110-0.492-0.4920.0000.0000.0000.000
172A634GLN00.0450.01820.7070.0370.0370.0000.0000.0000.000
173A635CYS00.0180.04924.531-0.054-0.0540.0000.0000.0000.000
174A636ASN00.0690.01027.3050.1630.1630.0000.0000.0000.000
175A637HIS0-0.042-0.02530.862-0.243-0.2430.0000.0000.0000.000
176A638GLY0-0.0050.01528.246-0.135-0.1350.0000.0000.0000.000
177A639ARG10.9490.97027.882-10.165-10.1650.0000.0000.0000.000
178A640PRO00.0430.01422.9970.1220.1220.0000.0000.0000.000
179A641THR0-0.0090.00620.533-0.395-0.3950.0000.0000.0000.000
180A642TRP0-0.019-0.00715.7800.3800.3800.0000.0000.0000.000
181A643VAL0-0.0040.00319.528-0.356-0.3560.0000.0000.0000.000
182A644LYS10.9440.97012.558-18.372-18.3720.0000.0000.0000.000
183A645LEU00.0190.01916.871-0.662-0.6620.0000.0000.0000.000
184A646THR0-0.013-0.01514.3300.8220.8220.0000.0000.0000.000
185A647LEU00.0650.01613.558-0.988-0.9880.0000.0000.0000.000
186A648LYS10.9370.97216.241-16.881-16.8810.0000.0000.0000.000
187A649GLU-1-0.841-0.91518.63414.06814.0680.0000.0000.0000.000
188A650LEU0-0.037-0.03117.041-0.589-0.5890.0000.0000.0000.000
189A651ASP-1-0.931-0.97320.41512.06912.0690.0000.0000.0000.000
190A652THR0-0.029-0.00722.349-0.649-0.6490.0000.0000.0000.000
191A653LEU0-0.109-0.04023.602-0.505-0.5050.0000.0000.0000.000
192A654PHE0-0.067-0.01823.593-0.572-0.5720.0000.0000.0000.000