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: N159Q

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 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 192
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1928156.146541
FMO2-HF: Nuclear repulsion 1853527.008027
FMO2-HF: Total energy -74629.138513
FMO2-MP2: Total energy -74842.715255


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.
58.70959.7360.006-0.466-0.5660.003
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 : -0.967 / q_NPA : -1.002
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].
3A465PRO00.0000.0223.694-3.773-2.8240.007-0.463-0.4930.003
4A466PRO00.0140.0046.551-0.467-0.4670.0000.0000.0000.000
5A467LEU0-0.045-0.0369.145-1.268-1.2680.0000.0000.0000.000
6A468GLY0-0.0090.0038.273-1.020-1.0200.0000.0000.0000.000
7A469PHE0-0.005-0.0136.224-1.354-1.3540.0000.0000.0000.000
8A470ALA0-0.019-0.00611.160-0.967-0.9670.0000.0000.0000.000
9A471ILE0-0.017-0.00813.8180.3250.3250.0000.0000.0000.000
10A472ALA0-0.018-0.01516.342-0.802-0.8020.0000.0000.0000.000
11A473GLN00.0480.02519.7800.3070.3070.0000.0000.0000.000
12A474LEU00.006-0.00522.662-0.381-0.3810.0000.0000.0000.000
13A475LEU00.022-0.00925.029-0.140-0.1400.0000.0000.0000.000
14A476GLY0-0.062-0.03127.829-0.308-0.3080.0000.0000.0000.000
15A477ILE0-0.0010.00327.1690.0480.0480.0000.0000.0000.000
16A478TYR00.0090.00922.7260.0490.0490.0000.0000.0000.000
17A479ILE00.0010.00917.605-0.141-0.1410.0000.0000.0000.000
18A480LEU0-0.0100.00218.290-0.087-0.0870.0000.0000.0000.000
19A481ALA00.0380.00713.1290.2230.2230.0000.0000.0000.000
20A482GLN0-0.0060.00410.294-2.015-2.0150.0000.0000.0000.000
21A483ALA00.0320.0178.4861.9961.9960.0000.0000.0000.000
22A484GLU-1-0.905-0.9635.18937.08437.162-0.001-0.003-0.0730.000
23A485ASP-1-0.898-0.9497.76221.96521.9650.0000.0000.0000.000
24A486SER0-0.086-0.05810.964-2.187-2.1870.0000.0000.0000.000
25A487LEU00.0030.02112.8360.7360.7360.0000.0000.0000.000
26A488LEU0-0.014-0.00812.689-0.602-0.6020.0000.0000.0000.000
27A489LEU00.0070.00516.239-0.200-0.2000.0000.0000.0000.000
28A490ILE00.014-0.00916.080-0.133-0.1330.0000.0000.0000.000
29A491ASP-1-0.862-0.92320.38610.80610.8060.0000.0000.0000.000
30A492MET00.000-0.00122.8610.1280.1280.0000.0000.0000.000
31A493HIS00.0320.02123.8520.0080.0080.0000.0000.0000.000
32A494ALA00.0720.04625.855-0.089-0.0890.0000.0000.0000.000
33A495ALA0-0.009-0.03321.0720.0270.0270.0000.0000.0000.000
34A496ALA0-0.015-0.01123.1610.1750.1750.0000.0000.0000.000
35A497GLU-1-0.870-0.90324.6069.9179.9170.0000.0000.0000.000
36A498ARG10.8250.90123.334-11.319-11.3190.0000.0000.0000.000
37A499VAL00.000-0.01720.541-0.016-0.0160.0000.0000.0000.000
38A500ASN0-0.038-0.02923.3340.2410.2410.0000.0000.0000.000
39A501TYR00.0160.00726.550-0.309-0.3090.0000.0000.0000.000
40A502GLU-1-0.789-0.85523.78511.03111.0310.0000.0000.0000.000
41A503LYS10.8020.89321.425-13.683-13.6830.0000.0000.0000.000
42A504MET00.0030.00825.478-0.254-0.2540.0000.0000.0000.000
43A505LYS10.8390.90729.093-9.169-9.1690.0000.0000.0000.000
44A506ARG10.9140.96321.216-12.928-12.9280.0000.0000.0000.000
45A507GLN00.0270.01628.240-0.081-0.0810.0000.0000.0000.000
46A508ARG10.8660.92229.733-8.405-8.4050.0000.0000.0000.000
47A509GLN0-0.086-0.03330.960-0.068-0.0680.0000.0000.0000.000
48A510GLU-1-0.971-0.97926.33911.03911.0390.0000.0000.0000.000
49A511ASN0-0.003-0.01230.369-0.187-0.1870.0000.0000.0000.000
50A512GLY0-0.033-0.00633.378-0.249-0.2490.0000.0000.0000.000
51A513ASN0-0.089-0.05135.151-0.187-0.1870.0000.0000.0000.000
52A514LEU0-0.066-0.03831.4690.3320.3320.0000.0000.0000.000
53A515GLN00.0500.02531.197-0.358-0.3580.0000.0000.0000.000
54A516SER00.0000.02032.6040.2820.2820.0000.0000.0000.000
55A517GLN0-0.023-0.02130.1180.1140.1140.0000.0000.0000.000
56A518HIS0-0.044-0.03734.723-0.133-0.1330.0000.0000.0000.000
57A519LEU0-0.041-0.00736.6250.2260.2260.0000.0000.0000.000
58A520LEU0-0.031-0.02136.074-0.177-0.1770.0000.0000.0000.000
59A521ILE0-0.024-0.01539.587-0.221-0.2210.0000.0000.0000.000
60A522PRO00.0020.00341.4260.0960.0960.0000.0000.0000.000
61A523VAL0-0.0010.01139.763-0.062-0.0620.0000.0000.0000.000
62A524THR00.0080.00643.052-0.064-0.0640.0000.0000.0000.000
63A525PHE0-0.067-0.03644.5430.0980.0980.0000.0000.0000.000
64A526ALA00.0090.01347.362-0.090-0.0900.0000.0000.0000.000
65A527ALA00.0220.01049.3270.1210.1210.0000.0000.0000.000
66A528SER0-0.030-0.05350.564-0.176-0.1760.0000.0000.0000.000
67A529HIS00.001-0.02152.757-0.004-0.0040.0000.0000.0000.000
68A530GLU-1-0.881-0.95451.9715.7615.7610.0000.0000.0000.000
69A531GLU-1-0.808-0.86747.4096.6856.6850.0000.0000.0000.000
70A532CYS0-0.016-0.00149.8300.0730.0730.0000.0000.0000.000
71A533ALA0-0.020-0.00852.2100.0110.0110.0000.0000.0000.000
72A534ALA00.0770.03848.3780.0060.0060.0000.0000.0000.000
73A535LEU0-0.063-0.04347.2990.0810.0810.0000.0000.0000.000
74A536ALA0-0.094-0.05149.1810.0240.0240.0000.0000.0000.000
75A537ASP-1-0.922-0.95051.5995.8275.8270.0000.0000.0000.000
76A538HIS-1-0.840-0.90646.4666.5146.5140.0000.0000.0000.000
77A539ALA00.0290.01946.0180.2090.2090.0000.0000.0000.000
78A540GLU-1-0.866-0.92145.0866.8076.8070.0000.0000.0000.000
79A541THR0-0.001-0.03743.0270.2440.2440.0000.0000.0000.000
80A542LEU0-0.056-0.02641.7180.2550.2550.0000.0000.0000.000
81A543ALA00.0220.02540.3110.2570.2570.0000.0000.0000.000
82A544GLY00.0530.02239.2220.2240.2240.0000.0000.0000.000
83A545PHE0-0.084-0.06136.3870.3080.3080.0000.0000.0000.000
84A546GLY00.0300.01235.6780.2040.2040.0000.0000.0000.000
85A547LEU0-0.039-0.03036.7580.1210.1210.0000.0000.0000.000
86A548GLU-1-0.806-0.88739.4457.4507.4500.0000.0000.0000.000
87A549LEU00.0320.00342.4190.0960.0960.0000.0000.0000.000
88A550SER0-0.043-0.03545.145-0.058-0.0580.0000.0000.0000.000
89A551ASP-1-0.803-0.91648.6356.0036.0030.0000.0000.0000.000
90A552MET0-0.074-0.03650.0440.0460.0460.0000.0000.0000.000
91A553GLY00.0550.05253.394-0.099-0.0990.0000.0000.0000.000
92A554GLY0-0.028-0.03455.2890.0550.0550.0000.0000.0000.000
93A555ASN0-0.032-0.01754.297-0.036-0.0360.0000.0000.0000.000
94A556THR0-0.0400.00350.4870.1050.1050.0000.0000.0000.000
95A557LEU00.0370.03947.691-0.021-0.0210.0000.0000.0000.000
96A558ALA0-0.016-0.02446.1750.0730.0730.0000.0000.0000.000
97A559VAL00.0090.01239.714-0.016-0.0160.0000.0000.0000.000
98A560ARG10.8420.89142.155-7.074-7.0740.0000.0000.0000.000
99A561ALA00.0050.00738.0190.1520.1520.0000.0000.0000.000
100A562ALA00.0490.02835.317-0.171-0.1710.0000.0000.0000.000
101A563PRO00.0250.01132.0310.1530.1530.0000.0000.0000.000
102A564VAL00.0320.01727.6650.2140.2140.0000.0000.0000.000
103A565MET0-0.103-0.03026.7730.1400.1400.0000.0000.0000.000
104A566LEU00.0050.01327.2680.2450.2450.0000.0000.0000.000
105A567GLY0-0.001-0.00128.4240.1520.1520.0000.0000.0000.000
106A568LYN0-0.005-0.00229.076-0.127-0.1270.0000.0000.0000.000
107A569SER0-0.032-0.03031.7860.1040.1040.0000.0000.0000.000
108A570ASP-1-0.887-0.94533.5217.8767.8760.0000.0000.0000.000
109A571VAL00.0420.00035.8560.0350.0350.0000.0000.0000.000
110A572VAL0-0.0160.00637.647-0.117-0.1170.0000.0000.0000.000
111A573SER0-0.0080.00537.774-0.194-0.1940.0000.0000.0000.000
112A574LEU00.0180.02534.692-0.078-0.0780.0000.0000.0000.000
113A575ALA0-0.007-0.00438.077-0.093-0.0930.0000.0000.0000.000
114A576ARG10.8650.92841.166-7.091-7.0910.0000.0000.0000.000
115A577ASP-1-0.841-0.90438.8937.8207.8200.0000.0000.0000.000
116A578VAL0-0.048-0.04538.400-0.075-0.0750.0000.0000.0000.000
117A579LEU0-0.002-0.00641.238-0.118-0.1180.0000.0000.0000.000
118A580GLY00.0400.01744.582-0.150-0.1500.0000.0000.0000.000
119A581GLU-1-0.875-0.91640.7897.3437.3430.0000.0000.0000.000
120A582LEU0-0.050-0.03543.363-0.018-0.0180.0000.0000.0000.000
121A583ALA00.0340.02746.036-0.136-0.1360.0000.0000.0000.000
122A584GLN0-0.130-0.05045.116-0.163-0.1630.0000.0000.0000.000
123A585VAL0-0.071-0.01446.133-0.028-0.0280.0000.0000.0000.000
124A586GLY00.1140.04849.261-0.054-0.0540.0000.0000.0000.000
125A587SER0-0.067-0.04651.559-0.001-0.0010.0000.0000.0000.000
126A588SER0-0.078-0.04147.6900.0310.0310.0000.0000.0000.000
127A589GLN00.0320.02548.5000.1590.1590.0000.0000.0000.000
128A590THR0-0.007-0.03746.6370.1150.1150.0000.0000.0000.000
129A591ILE00.0570.05642.4960.2280.2280.0000.0000.0000.000
130A592ALA00.0120.00442.540-0.032-0.0320.0000.0000.0000.000
131A593SER0-0.063-0.04641.3940.1990.1990.0000.0000.0000.000
132A594HIS00.0720.05241.8130.1510.1510.0000.0000.0000.000
133A595GLU-1-0.769-0.85835.7828.6438.6430.0000.0000.0000.000
134A596ASN00.006-0.00334.9350.1760.1760.0000.0000.0000.000
135A597ARG10.8370.90335.855-7.054-7.0540.0000.0000.0000.000
136A598ILE00.0710.03137.6980.1250.1250.0000.0000.0000.000
137A599LEU0-0.010-0.02032.3220.1620.1620.0000.0000.0000.000
138A600ALA0-0.056-0.02132.9570.3130.3130.0000.0000.0000.000
139A601THR00.0460.02233.6350.3150.3150.0000.0000.0000.000
140A602MET0-0.0270.00433.8330.0930.0930.0000.0000.0000.000
141A603SER0-0.091-0.05429.4870.3090.3090.0000.0000.0000.000
142A604CYS0-0.056-0.03129.7990.3980.3980.0000.0000.0000.000
143A605HIS0-0.060-0.02631.9190.1530.1530.0000.0000.0000.000
144A606GLY00.0640.02728.1120.0310.0310.0000.0000.0000.000
145A607SER00.006-0.01725.161-0.241-0.2410.0000.0000.0000.000
146A608ILE0-0.040-0.01822.912-0.008-0.0080.0000.0000.0000.000
147A609ARG10.9230.97226.704-9.801-9.8010.0000.0000.0000.000
148A610ALA00.0900.03929.951-0.266-0.2660.0000.0000.0000.000
149A611GLY0-0.050-0.02531.230-0.133-0.1330.0000.0000.0000.000
150A612ARG10.9080.96729.259-9.514-9.5140.0000.0000.0000.000
151A613ARG10.9160.95227.304-9.918-9.9180.0000.0000.0000.000
152A614LEU00.0090.02122.672-0.086-0.0860.0000.0000.0000.000
153A615THR0-0.011-0.03921.7800.3940.3940.0000.0000.0000.000
154A616LEU00.0560.00316.9340.2140.2140.0000.0000.0000.000
155A617PRO00.016-0.00316.6790.9200.9200.0000.0000.0000.000
156A618GLU-1-0.799-0.85917.76513.39913.3990.0000.0000.0000.000
157A619MET0-0.047-0.00618.1090.2100.2100.0000.0000.0000.000
158A620ASN00.037-0.00112.9621.3611.3610.0000.0000.0000.000
159A621ALA0-0.0050.01414.9730.7230.7230.0000.0000.0000.000
160A622LEU00.0420.01817.032-0.126-0.1260.0000.0000.0000.000
161A623LEU0-0.027-0.00713.502-0.225-0.2250.0000.0000.0000.000
162A624ARG10.7910.84110.554-24.760-24.7600.0000.0000.0000.000
163A625ASP-1-0.787-0.88413.77914.73014.7300.0000.0000.0000.000
164A626MET0-0.073-0.01016.292-0.502-0.5020.0000.0000.0000.000
165A627GLU-1-0.774-0.84710.74624.80524.8050.0000.0000.0000.000
166A628ASN0-0.039-0.00313.9440.1710.1710.0000.0000.0000.000
167A629THR0-0.056-0.03215.906-1.154-1.1540.0000.0000.0000.000
168A630PRO00.0110.00318.7370.1810.1810.0000.0000.0000.000
169A631ARG10.8170.85820.516-11.456-11.4560.0000.0000.0000.000
170A632SER00.0260.01717.656-0.457-0.4570.0000.0000.0000.000
171A633ASN0-0.023-0.00918.863-0.524-0.5240.0000.0000.0000.000
172A634GLN00.0470.03120.771-0.052-0.0520.0000.0000.0000.000
173A635CYS00.0320.03924.596-0.094-0.0940.0000.0000.0000.000
174A636ASN00.0360.00627.3650.0730.0730.0000.0000.0000.000
175A637HIS0-0.032-0.02530.921-0.204-0.2040.0000.0000.0000.000
176A638GLY0-0.0030.01528.329-0.137-0.1370.0000.0000.0000.000
177A639ARG10.8740.92827.953-10.426-10.4260.0000.0000.0000.000
178A640PRO00.0490.01923.0920.1230.1230.0000.0000.0000.000
179A641THR0-0.035-0.00920.942-0.443-0.4430.0000.0000.0000.000
180A642TRP0-0.022-0.00915.5640.3800.3800.0000.0000.0000.000
181A643VAL00.0140.01219.684-0.343-0.3430.0000.0000.0000.000
182A644LYS10.9430.97012.918-17.725-17.7250.0000.0000.0000.000
183A645LEU0-0.0030.00716.953-0.665-0.6650.0000.0000.0000.000
184A646THR0-0.036-0.05914.0520.8320.8320.0000.0000.0000.000
185A647LEU00.0450.01613.255-1.027-1.0270.0000.0000.0000.000
186A648LYS10.9550.97915.897-17.152-17.1520.0000.0000.0000.000
187A649GLU-1-0.805-0.85718.24114.27914.2790.0000.0000.0000.000
188A650LEU0-0.047-0.03317.040-0.598-0.5980.0000.0000.0000.000
189A651ASP-1-0.915-0.96520.46912.06212.0620.0000.0000.0000.000
190A652THR0-0.050-0.03222.398-0.617-0.6170.0000.0000.0000.000
191A653LEU0-0.109-0.03823.400-0.500-0.5000.0000.0000.0000.000
192A654PHE0-0.063-0.01623.357-0.564-0.5640.0000.0000.0000.000