FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: MV6NZ

Calculation Name: 3NWC-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3NWC

Chain ID: A

ChEMBL ID:

UniProt ID: Q8TZY2

Base Structure: X-ray

Registration Date: 2023-06-21

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 182
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1765218.147939
FMO2-HF: Nuclear repulsion 1695780.219917
FMO2-HF: Total energy -69437.928021
FMO2-MP2: Total energy -69643.259259


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:487:MET)


Summations of interaction energy for fragment #1(A:487:MET)
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.
-23.767-14.77125.918-11.729-23.188-0.016
Interaction energy analysis for fragmet #1(A:487:MET)
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 : 0.018
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].
3A489LEU0-0.004-0.0023.275-0.9301.2900.008-1.057-1.1710.003
4A490GLU-1-0.757-0.8603.308-1.860-1.2770.053-0.273-0.364-0.002
5A491SER0-0.065-0.0425.4430.4080.4080.0000.0000.0000.000
6A492SER00.039-0.0232.1880.258-1.3626.650-1.991-3.0400.004
7A493GLU-1-0.879-0.9281.943-6.056-4.2334.144-1.859-4.108-0.012
8A494ARG10.7560.8443.4941.3251.4720.0230.110-0.2800.000
9A495GLU-1-0.745-0.8414.9120.7850.7850.0000.0000.0000.000
10A496LEU00.0460.0303.019-0.8050.1540.105-0.207-0.8580.000
11A497ILE00.0360.0245.280-0.505-0.451-0.001-0.002-0.0520.000
12A498ALA0-0.059-0.0278.205-0.177-0.1770.0000.0000.0000.000
13A499ALA0-0.013-0.0138.283-0.171-0.1710.0000.0000.0000.000
14A500GLU-1-0.893-0.9518.2122.2412.2410.0000.0000.0000.000
15A501ALA0-0.020-0.01111.066-0.225-0.2250.0000.0000.0000.000
16A502GLN0-0.050-0.02713.144-0.151-0.1510.0000.0000.0000.000
17A503ARG10.7540.83412.331-1.458-1.4580.0000.0000.0000.000
18A504GLU-1-0.889-0.92415.4550.4920.4920.0000.0000.0000.000
19A505VAL0-0.086-0.03517.356-0.083-0.0830.0000.0000.0000.000
20A506ARG10.8290.91716.609-0.624-0.6240.0000.0000.0000.000
21A507GLY00.0740.04120.3980.0140.0140.0000.0000.0000.000
22A508ASN0-0.023-0.02621.694-0.045-0.0450.0000.0000.0000.000
23A509ARG10.9230.95120.789-0.402-0.4020.0000.0000.0000.000
24A510ALA00.007-0.00224.718-0.018-0.0180.0000.0000.0000.000
25A511ALA00.002-0.00224.361-0.022-0.0220.0000.0000.0000.000
26A512GLU-1-0.806-0.90524.3930.3860.3860.0000.0000.0000.000
27A513GLU-1-0.797-0.87927.1520.1860.1860.0000.0000.0000.000
28A514LEU00.0240.01229.229-0.020-0.0200.0000.0000.0000.000
29A515LYS10.7710.90724.185-0.423-0.4230.0000.0000.0000.000
30A516ARG10.8940.94131.042-0.204-0.2040.0000.0000.0000.000
31A517SER0-0.014-0.01734.001-0.016-0.0160.0000.0000.0000.000
32A518GLY0-0.020-0.00735.702-0.012-0.0120.0000.0000.0000.000
33A519ILE0-0.082-0.03734.970-0.009-0.0090.0000.0000.0000.000
34A520GLY00.0200.01734.4640.0110.0110.0000.0000.0000.000
35A521GLY00.0250.00032.995-0.001-0.0010.0000.0000.0000.000
36A522ILE0-0.024-0.02128.3770.0130.0130.0000.0000.0000.000
37A523TYR0-0.040-0.05225.959-0.014-0.0140.0000.0000.0000.000
38A524GLY00.0400.03323.9860.0030.0030.0000.0000.0000.000
39A525THR0-0.058-0.06420.2040.0140.0140.0000.0000.0000.000
40A526LEU0-0.006-0.01517.7050.0000.0000.0000.0000.0000.000
41A527ALA00.0180.01315.4950.0680.0680.0000.0000.0000.000
42A528GLU-1-0.814-0.85515.9340.5610.5610.0000.0000.0000.000
43A529LEU0-0.083-0.04318.415-0.053-0.0530.0000.0000.0000.000
44A530ILE0-0.041-0.00813.339-0.062-0.0620.0000.0000.0000.000
45A531LYS10.8540.92713.311-0.615-0.6150.0000.0000.0000.000
46A532VAL00.0300.0026.946-0.203-0.2030.0000.0000.0000.000
47A533LYS10.7470.85610.398-0.901-0.9010.0000.0000.0000.000
48A534ASP-1-0.868-0.9456.8470.6430.6430.0000.0000.0000.000
49A535GLU-1-0.920-0.9562.061-1.466-1.1881.727-0.714-1.291-0.001
50A536ALA00.0220.0173.0194.6906.5191.593-1.058-2.364-0.011
51A537TYR0-0.024-0.0332.738-3.022-1.7371.448-1.060-1.672-0.015
52A538ALA0-0.0020.0023.354-2.680-1.4500.562-0.565-1.2270.000
53A539LEU00.0300.0142.456-5.784-7.1268.511-2.682-4.4860.022
54A540ALA00.0110.0093.749-2.807-3.0650.0090.493-0.2450.003
55A541ILE0-0.005-0.0105.614-0.944-0.9440.0000.0000.0000.000
56A542GLU-1-0.774-0.8407.3301.1611.1610.0000.0000.0000.000
57A543VAL0-0.024-0.0147.463-0.693-0.6930.0000.0000.0000.000
58A544ALA0-0.031-0.0129.555-0.397-0.3970.0000.0000.0000.000
59A545LEU0-0.026-0.00511.553-0.314-0.3140.0000.0000.0000.000
60A546GLY00.0730.04012.854-0.227-0.2270.0000.0000.0000.000
61A547ASN00.000-0.02814.5000.0450.0450.0000.0000.0000.000
62A548ARG10.8390.92617.347-0.632-0.6320.0000.0000.0000.000
63A549ALA00.0590.04514.716-0.063-0.0630.0000.0000.0000.000
64A550ASP-1-0.811-0.91516.7990.7530.7530.0000.0000.0000.000
65A551ASN0-0.116-0.05820.043-0.106-0.1060.0000.0000.0000.000
66A552VAL00.0280.01422.0350.0250.0250.0000.0000.0000.000
67A553VAL00.0270.01622.828-0.031-0.0310.0000.0000.0000.000
68A554VAL0-0.040-0.03025.639-0.018-0.0180.0000.0000.0000.000
69A555GLU-1-0.763-0.84729.4210.2710.2710.0000.0000.0000.000
70A556ASP-1-0.844-0.93132.0680.2150.2150.0000.0000.0000.000
71A557GLU-1-0.742-0.88033.7230.2200.2200.0000.0000.0000.000
72A558LEU0-0.0100.00335.070-0.005-0.0050.0000.0000.0000.000
73A559VAL0-0.030-0.01132.890-0.004-0.0040.0000.0000.0000.000
74A560ALA00.0200.01732.1390.0040.0040.0000.0000.0000.000
75A561GLU-1-0.843-0.91633.4550.1820.1820.0000.0000.0000.000
76A562LYS10.9010.95036.777-0.193-0.1930.0000.0000.0000.000
77A563ALA00.0500.02532.455-0.006-0.0060.0000.0000.0000.000
78A564ILE0-0.006-0.00732.761-0.002-0.0020.0000.0000.0000.000
79A565LYS10.8150.89335.030-0.183-0.1830.0000.0000.0000.000
80A566TYR0-0.008-0.01434.247-0.014-0.0140.0000.0000.0000.000
81A567LEU0-0.009-0.00730.597-0.006-0.0060.0000.0000.0000.000
82A568LYS10.9140.96334.657-0.198-0.1980.0000.0000.0000.000
83A569GLU-1-0.893-0.95537.5970.1400.1400.0000.0000.0000.000
84A570HIS10.8380.91636.231-0.192-0.1920.0000.0000.0000.000
85A571LYS10.8210.92436.299-0.154-0.1540.0000.0000.0000.000
86A572LEU00.0150.02331.4760.0040.0040.0000.0000.0000.000
87A573GLY00.0250.02530.5210.0220.0220.0000.0000.0000.000
88A574ARG10.9160.94029.170-0.279-0.2790.0000.0000.0000.000
89A575LEU00.0670.03625.3480.0170.0170.0000.0000.0000.000
90A576THR0-0.045-0.01124.641-0.026-0.0260.0000.0000.0000.000
91A577PHE00.0200.00625.7400.0250.0250.0000.0000.0000.000
92A578LEU0-0.006-0.00522.306-0.011-0.0110.0000.0000.0000.000
93A579PRO00.0000.01126.9250.0020.0020.0000.0000.0000.000
94A580LEU00.0480.03426.1760.0000.0000.0000.0000.0000.000
95A581ASN0-0.009-0.01229.5700.0080.0080.0000.0000.0000.000
96A582LYS10.7740.87031.477-0.228-0.2280.0000.0000.0000.000
97A583ILE0-0.079-0.03025.367-0.007-0.0070.0000.0000.0000.000
98A584LYS10.9640.97427.426-0.261-0.2610.0000.0000.0000.000
99A585PRO00.0080.00723.8640.0260.0260.0000.0000.0000.000
100A586LYS10.8310.93020.460-0.506-0.5060.0000.0000.0000.000
101A587HIS00.024-0.00421.5490.0240.0240.0000.0000.0000.000
102A588VAL00.0210.02317.131-0.011-0.0110.0000.0000.0000.000
103A589ASP-1-0.853-0.88720.3790.2440.2440.0000.0000.0000.000
104A590SER0-0.040-0.02919.602-0.024-0.0240.0000.0000.0000.000
105A591SER00.0210.00019.4730.0180.0180.0000.0000.0000.000
106A592VAL0-0.048-0.02115.448-0.025-0.0250.0000.0000.0000.000
107A593GLY00.0580.02113.654-0.035-0.0350.0000.0000.0000.000
108A594LEU0-0.0040.0179.843-0.018-0.0180.0000.0000.0000.000
109A595PRO00.0150.01212.1350.1010.1010.0000.0000.0000.000
110A596ALA00.0610.02411.2170.0560.0560.0000.0000.0000.000
111A597VAL0-0.031-0.02912.1680.1190.1190.0000.0000.0000.000
112A598ASP-1-0.860-0.93013.9970.4980.4980.0000.0000.0000.000
113A599VAL0-0.0250.0018.738-0.067-0.0670.0000.0000.0000.000
114A600ILE0-0.0100.01011.1110.2610.2610.0000.0000.0000.000
115A601GLU-1-0.846-0.90113.4170.4620.4620.0000.0000.0000.000
116A602TYR00.0350.00016.5730.0630.0630.0000.0000.0000.000
117A603ASP-1-0.831-0.90919.2490.3150.3150.0000.0000.0000.000
118A604GLN00.014-0.00523.0130.0360.0360.0000.0000.0000.000
119A605LYS10.8390.91324.974-0.287-0.2870.0000.0000.0000.000
120A606ILE0-0.028-0.02020.802-0.017-0.0170.0000.0000.0000.000
121A607GLU-1-0.781-0.88522.6620.3890.3890.0000.0000.0000.000
122A608ASN0-0.050-0.02622.9220.0280.0280.0000.0000.0000.000
123A609ALA0-0.016-0.01323.1470.0050.0050.0000.0000.0000.000
124A610VAL00.0380.02017.4740.0320.0320.0000.0000.0000.000
125A611LYS10.9130.94218.698-0.386-0.3860.0000.0000.0000.000
126A612PHE0-0.043-0.01120.571-0.015-0.0150.0000.0000.0000.000
127A613ALA0-0.064-0.02617.508-0.014-0.0140.0000.0000.0000.000
128A614LEU00.0450.01512.8290.0240.0240.0000.0000.0000.000
129A615GLY0-0.0160.00015.9800.0020.0020.0000.0000.0000.000
130A616ASP-1-0.925-0.98118.4270.4440.4440.0000.0000.0000.000
131A617THR0-0.026-0.00712.019-0.004-0.0040.0000.0000.0000.000
132A618VAL0-0.040-0.00213.2830.0290.0290.0000.0000.0000.000
133A619ILE00.0000.0066.7520.0480.0480.0000.0000.0000.000
134A620VAL0-0.012-0.0149.405-0.107-0.1070.0000.0000.0000.000
135A621ASN00.0420.0028.0470.0880.0880.0000.0000.0000.000
136A622SER0-0.014-0.0208.350-0.108-0.1080.0000.0000.0000.000
137A623MET00.0440.00710.5860.0760.0760.0000.0000.0000.000
138A624GLU-1-0.839-0.90713.333-0.047-0.0470.0000.0000.0000.000
139A625GLU-1-0.913-0.92712.587-0.109-0.1090.0000.0000.0000.000
140A626ALA00.0360.01913.5280.0370.0370.0000.0000.0000.000
141A627ARG10.8160.88115.6160.0120.0120.0000.0000.0000.000
142A628PRO0-0.018-0.00918.7340.0090.0090.0000.0000.0000.000
143A629HIS00.031-0.01417.4690.0050.0050.0000.0000.0000.000
144A630ILE00.0050.02518.3930.0300.0300.0000.0000.0000.000
145A631GLY00.0110.00920.331-0.021-0.0210.0000.0000.0000.000
146A632LYS10.8430.94021.589-0.161-0.1610.0000.0000.0000.000
147A633VAL0-0.015-0.01416.800-0.001-0.0010.0000.0000.0000.000
148A634ARG10.7670.88614.592-0.763-0.7630.0000.0000.0000.000
149A635MET0-0.041-0.00612.870-0.009-0.0090.0000.0000.0000.000
150A636VAL0-0.0050.0047.7070.0080.0080.0000.0000.0000.000
151A637THR0-0.044-0.0527.912-0.006-0.0060.0000.0000.0000.000
152A638ILE0-0.001-0.0042.4470.0600.4950.519-0.164-0.7900.000
153A639GLU-1-0.841-0.9042.851-3.467-2.1430.568-0.698-1.194-0.007
154A640GLY0-0.0070.0104.6900.3490.398-0.001-0.002-0.0460.000
155A641GLU-1-0.885-0.9186.7050.1620.1620.0000.0000.0000.000
156A642LEU0-0.023-0.01710.1580.0770.0770.0000.0000.0000.000
157A643TYR0-0.003-0.00812.526-0.111-0.1110.0000.0000.0000.000
158A644GLU-1-0.807-0.89815.6040.5900.5900.0000.0000.0000.000
159A645ARG10.8430.88118.064-0.343-0.3430.0000.0000.0000.000
160A646SER0-0.040-0.02620.471-0.028-0.0280.0000.0000.0000.000
161A647GLY00.0340.01321.149-0.030-0.0300.0000.0000.0000.000
162A648ALA0-0.083-0.02320.446-0.018-0.0180.0000.0000.0000.000
163A649ILE00.0160.00416.1540.0320.0320.0000.0000.0000.000
164A650THR0-0.039-0.01313.946-0.027-0.0270.0000.0000.0000.000
165A651GLY00.0630.01912.4710.0360.0360.0000.0000.0000.000
166A652GLY0-0.041-0.01512.179-0.033-0.0330.0000.0000.0000.000
167A653HIS0-0.025-0.00410.7110.0950.0950.0000.0000.0000.000
168A654PHE00.0270.0048.723-0.019-0.0190.0000.0000.0000.000
169A655ARG10.7890.8819.041-0.120-0.1200.0000.0000.0000.000
170A656ALA0-0.010-0.00911.661-0.064-0.0640.0000.0000.0000.000
171A657ARG10.9270.95815.166-0.036-0.0360.0000.0000.0000.000
172A658GLY00.0330.02017.693-0.033-0.0330.0000.0000.0000.000
173A659LEU0-0.021-0.02019.084-0.010-0.0100.0000.0000.0000.000
174A660ALA00.0110.00620.744-0.019-0.0190.0000.0000.0000.000
175A661VAL00.000-0.00619.7590.0090.0090.0000.0000.0000.000
176A662ASP-1-0.842-0.91122.014-0.175-0.1750.0000.0000.0000.000
177A663THR00.0040.00321.629-0.027-0.0270.0000.0000.0000.000
178A664THR0-0.055-0.03623.164-0.024-0.0240.0000.0000.0000.000
179A665LYS10.9480.96521.3770.3400.3400.0000.0000.0000.000
180A666LEU00.0220.01426.8570.0070.0070.0000.0000.0000.000
181A667ARG10.9140.95828.2860.1390.1390.0000.0000.0000.000
182A668LEU00.0140.02527.680-0.001-0.0010.0000.0000.0000.000