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: 4967N

Calculation Name: 3NWJ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3NWJ

Chain ID: A

ChEMBL ID:

UniProt ID: Q8GY88

Base Structure: X-ray

Registration Date: 2023-06-22

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 194
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2135887.465642
FMO2-HF: Nuclear repulsion 2059475.426071
FMO2-HF: Total energy -76412.039571
FMO2-MP2: Total energy -76633.672857


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:82:GLN)


Summations of interaction energy for fragment #1(A:82:GLN)
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.
-13.04-7.151.844-2.933-4.8010.007
Interaction energy analysis for fragmet #1(A:82:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.074 / 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].
3A84ILE00.0300.0093.019-5.230-1.8140.299-1.738-1.9770.009
4A85LEU00.0190.0182.313-3.665-1.9201.516-1.023-2.239-0.002
5A86LYS10.9570.9843.948-1.061-0.6930.002-0.073-0.2960.000
6A87LYS10.9730.9876.403-0.607-0.6070.0000.0000.0000.000
7A88LYS10.9340.9726.8570.0120.0120.0000.0000.0000.000
8A89ALA0-0.0110.0088.067-0.032-0.0320.0000.0000.0000.000
9A90GLU-1-0.986-1.0069.8870.2460.2460.0000.0000.0000.000
10A91GLU-1-0.875-0.94711.689-0.002-0.0020.0000.0000.0000.000
11A92VAL00.0150.02812.149-0.016-0.0160.0000.0000.0000.000
12A93LYS10.8930.94514.223-0.110-0.1100.0000.0000.0000.000
13A94PRO0-0.026-0.01816.224-0.001-0.0010.0000.0000.0000.000
14A95TYR00.0610.05717.385-0.001-0.0010.0000.0000.0000.000
15A96LEU0-0.026-0.01515.955-0.005-0.0050.0000.0000.0000.000
16A97ASN0-0.0200.00319.7730.0070.0070.0000.0000.0000.000
17A98GLY0-0.010-0.01520.6740.0020.0020.0000.0000.0000.000
18A99ARG10.9640.99021.6840.0180.0180.0000.0000.0000.000
19A100SER00.0070.00020.2890.0050.0050.0000.0000.0000.000
20A101MET0-0.021-0.00113.608-0.016-0.0160.0000.0000.0000.000
21A102TYR00.0200.00719.1980.0140.0140.0000.0000.0000.000
22A103LEU0-0.014-0.00514.625-0.016-0.0160.0000.0000.0000.000
23A104VAL00.0190.01219.1930.0190.0190.0000.0000.0000.000
24A105GLY00.0870.02220.900-0.024-0.0240.0000.0000.0000.000
25A106MET00.0320.03722.6640.0220.0220.0000.0000.0000.000
26A107MET0-0.006-0.01123.265-0.006-0.0060.0000.0000.0000.000
27A108GLY00.0770.04422.221-0.007-0.0070.0000.0000.0000.000
28A109SER0-0.010-0.00919.544-0.022-0.0220.0000.0000.0000.000
29A110GLY00.0250.00816.289-0.032-0.0320.0000.0000.0000.000
30A111LYS10.8430.92115.3660.0770.0770.0000.0000.0000.000
31A112THR00.0440.01916.102-0.006-0.0060.0000.0000.0000.000
32A113THR00.004-0.00411.6880.0480.0480.0000.0000.0000.000
33A114VAL00.0290.02011.0680.0130.0130.0000.0000.0000.000
34A115GLY00.0670.03011.409-0.012-0.0120.0000.0000.0000.000
35A116LYS10.9240.96912.560-0.133-0.1330.0000.0000.0000.000
36A117ILE0-0.030-0.0036.3460.0810.0810.0000.0000.0000.000
37A118MET00.012-0.0068.488-0.002-0.0020.0000.0000.0000.000
38A119ALA00.0060.01010.4670.0310.0310.0000.0000.0000.000
39A120ARG10.9740.9817.755-0.811-0.8110.0000.0000.0000.000
40A121SER0-0.087-0.0396.611-0.003-0.0030.0000.0000.0000.000
41A122LEU00.0040.0078.4760.0320.0320.0000.0000.0000.000
42A123GLY0-0.0200.00411.7300.0240.0240.0000.0000.0000.000
43A124TYR0-0.041-0.02113.571-0.006-0.0060.0000.0000.0000.000
44A125THR00.0130.01515.3060.0320.0320.0000.0000.0000.000
45A126PHE00.020-0.00315.306-0.019-0.0190.0000.0000.0000.000
46A127PHE0-0.002-0.01517.3560.0220.0220.0000.0000.0000.000
47A128ASP-1-0.856-0.92020.4000.0040.0040.0000.0000.0000.000
48A129CYS0-0.011-0.00821.8370.0070.0070.0000.0000.0000.000
49A130ASP-1-0.839-0.93325.217-0.005-0.0050.0000.0000.0000.000
50A131THR0-0.005-0.01823.7450.0100.0100.0000.0000.0000.000
51A132LEU0-0.061-0.03025.0400.0070.0070.0000.0000.0000.000
52A133ILE0-0.017-0.00227.4900.0020.0020.0000.0000.0000.000
53A134GLU-1-0.952-0.98128.0980.0400.0400.0000.0000.0000.000
54A135GLN0-0.048-0.02625.7810.0030.0030.0000.0000.0000.000
55A136ALA0-0.055-0.02730.9410.0020.0020.0000.0000.0000.000
56A137MET0-0.060-0.01433.289-0.004-0.0040.0000.0000.0000.000
57A138LYS10.9430.96534.104-0.069-0.0690.0000.0000.0000.000
58A139GLY0-0.0060.00137.866-0.002-0.0020.0000.0000.0000.000
59A140THR00.0000.02038.536-0.002-0.0020.0000.0000.0000.000
60A141SER00.0320.02235.4440.0020.0020.0000.0000.0000.000
61A142VAL00.0530.00831.997-0.003-0.0030.0000.0000.0000.000
62A143ALA00.0150.00135.266-0.004-0.0040.0000.0000.0000.000
63A144GLU-1-0.828-0.91237.0160.0220.0220.0000.0000.0000.000
64A145ILE0-0.037-0.01537.681-0.003-0.0030.0000.0000.0000.000
65A146PHE0-0.043-0.03734.387-0.004-0.0040.0000.0000.0000.000
66A147GLU-1-0.957-0.96439.5250.0050.0050.0000.0000.0000.000
67A148HIS0-0.056-0.03142.544-0.001-0.0010.0000.0000.0000.000
68A149PHE0-0.034-0.03342.140-0.001-0.0010.0000.0000.0000.000
69A150GLY00.0320.04241.407-0.002-0.0020.0000.0000.0000.000
70A151GLU-1-0.901-0.97836.153-0.030-0.0300.0000.0000.0000.000
71A152SER0-0.016-0.00937.651-0.001-0.0010.0000.0000.0000.000
72A153VAL00.0660.03339.4460.0010.0010.0000.0000.0000.000
73A154PHE00.0130.00830.2600.0020.0020.0000.0000.0000.000
74A155ARG10.7770.88331.6320.0280.0280.0000.0000.0000.000
75A156GLU-1-0.923-0.95934.9330.0010.0010.0000.0000.0000.000
76A157LYS11.0001.01534.315-0.017-0.0170.0000.0000.0000.000
77A158GLU-1-0.824-0.91929.104-0.020-0.0200.0000.0000.0000.000
78A159THR0-0.048-0.02331.0960.0000.0000.0000.0000.0000.000
79A160GLU-1-0.969-0.98632.9190.0180.0180.0000.0000.0000.000
80A161ALA00.007-0.00329.0720.0050.0050.0000.0000.0000.000
81A162LEU00.003-0.01326.3600.0040.0040.0000.0000.0000.000
82A163LYS10.9100.96229.231-0.014-0.0140.0000.0000.0000.000
83A164LYS10.9290.97129.743-0.059-0.0590.0000.0000.0000.000
84A165LEU0-0.002-0.01524.2540.0040.0040.0000.0000.0000.000
85A166SER0-0.051-0.01426.7090.0020.0020.0000.0000.0000.000
86A167LEU0-0.030-0.01528.1600.0000.0000.0000.0000.0000.000
87A168MET0-0.046-0.01829.5760.0010.0010.0000.0000.0000.000
88A169TYR0-0.044-0.01324.2150.0060.0060.0000.0000.0000.000
89A170HIS00.0620.03324.097-0.012-0.0120.0000.0000.0000.000
90A171GLN0-0.055-0.02919.1900.0190.0190.0000.0000.0000.000
91A172VAL0-0.0010.01118.9900.0180.0180.0000.0000.0000.000
92A173VAL0-0.037-0.01514.396-0.020-0.0200.0000.0000.0000.000
93A174VAL00.0110.00617.7150.0200.0200.0000.0000.0000.000
94A175SER0-0.0050.02818.532-0.020-0.0200.0000.0000.0000.000
95A176THR0-0.012-0.01220.3390.0180.0180.0000.0000.0000.000
96A177GLY00.1620.08023.312-0.012-0.0120.0000.0000.0000.000
97A178GLY0-0.059-0.04025.859-0.006-0.0060.0000.0000.0000.000
98A179GLY00.012-0.00926.691-0.005-0.0050.0000.0000.0000.000
99A180ALA00.0440.04926.8730.0030.0030.0000.0000.0000.000
100A181VAL0-0.032-0.01726.3340.0050.0050.0000.0000.0000.000
101A182ILE00.0130.01729.289-0.001-0.0010.0000.0000.0000.000
102A183ARG10.9630.98832.9140.0170.0170.0000.0000.0000.000
103A184PRO00.0540.01133.1790.0000.0000.0000.0000.0000.000
104A185ILE0-0.007-0.00134.1290.0010.0010.0000.0000.0000.000
105A186ASN00.030-0.01629.8800.0080.0080.0000.0000.0000.000
106A187TRP00.0040.00825.2760.0020.0020.0000.0000.0000.000
107A188LYS10.9360.98930.2010.0060.0060.0000.0000.0000.000
108A189TYR0-0.036-0.04429.7970.0040.0040.0000.0000.0000.000
109A190MET00.0060.00825.5050.0000.0000.0000.0000.0000.000
110A191HIS00.0140.01825.6060.0000.0000.0000.0000.0000.000
111A192LYS10.8460.94227.7460.0030.0030.0000.0000.0000.000
112A193GLY0-0.018-0.00623.8490.0080.0080.0000.0000.0000.000
113A194ILE0-0.0080.00819.165-0.006-0.0060.0000.0000.0000.000
114A195SER00.0280.01620.468-0.002-0.0020.0000.0000.0000.000
115A196ILE00.017-0.00414.974-0.009-0.0090.0000.0000.0000.000
116A197TRP00.013-0.00818.8190.0060.0060.0000.0000.0000.000
117A198LEU0-0.044-0.01214.801-0.020-0.0200.0000.0000.0000.000
118A199ASP-1-0.856-0.92118.404-0.183-0.1830.0000.0000.0000.000
119A200VAL0-0.021-0.02418.688-0.034-0.0340.0000.0000.0000.000
120A201PRO00.0770.03920.9280.0200.0200.0000.0000.0000.000
121A202LEU00.0730.02623.976-0.004-0.0040.0000.0000.0000.000
122A203GLU-1-0.843-0.91826.350-0.170-0.1700.0000.0000.0000.000
123A204ALA00.004-0.00521.189-0.002-0.0020.0000.0000.0000.000
124A205LEU0-0.057-0.02521.8910.0030.0030.0000.0000.0000.000
125A206ALA00.0110.00524.1270.0120.0120.0000.0000.0000.000
126A207HIS0-0.020-0.00722.0200.0270.0270.0000.0000.0000.000
127A208ARG10.8770.93516.3790.3040.3040.0000.0000.0000.000
128A209ILE0-0.064-0.03222.9240.0180.0180.0000.0000.0000.000
129A210ALA0-0.036-0.01826.0250.0130.0130.0000.0000.0000.000
130A211ALA0-0.0280.00522.9940.0110.0110.0000.0000.0000.000
131A228THR00.0470.01331.947-0.001-0.0010.0000.0000.0000.000
132A229TYR00.0620.02927.9230.0000.0000.0000.0000.0000.000
133A230THR00.0410.00931.500-0.001-0.0010.0000.0000.0000.000
134A231ALA00.0050.01034.3410.0030.0030.0000.0000.0000.000
135A232ALA00.008-0.00529.8100.0040.0040.0000.0000.0000.000
136A233LEU00.0280.00829.8460.0020.0020.0000.0000.0000.000
137A234ASN00.0400.02431.750-0.004-0.0040.0000.0000.0000.000
138A235ARG10.9440.98133.1950.0570.0570.0000.0000.0000.000
139A236LEU0-0.010-0.01527.2040.0030.0030.0000.0000.0000.000
140A237SER00.0430.02931.107-0.003-0.0030.0000.0000.0000.000
141A238THR0-0.021-0.01033.1160.0040.0040.0000.0000.0000.000
142A239ILE0-0.063-0.02930.4640.0030.0030.0000.0000.0000.000
143A240TRP00.019-0.00626.566-0.001-0.0010.0000.0000.0000.000
144A241ASP-1-0.873-0.93131.483-0.086-0.0860.0000.0000.0000.000
145A242ALA0-0.057-0.01534.3430.0050.0050.0000.0000.0000.000
146A243ARG10.8800.93229.6170.0640.0640.0000.0000.0000.000
147A244GLY00.0360.01929.334-0.001-0.0010.0000.0000.0000.000
148A245GLU-1-0.908-0.95429.118-0.079-0.0790.0000.0000.0000.000
149A246ALA0-0.0380.00930.285-0.001-0.0010.0000.0000.0000.000
150A247TYR0-0.042-0.03424.8270.0020.0020.0000.0000.0000.000
151A248THR0-0.056-0.06725.428-0.004-0.0040.0000.0000.0000.000
152A249LYS10.9360.98027.0890.0590.0590.0000.0000.0000.000
153A250ALA0-0.040-0.02522.3570.0070.0070.0000.0000.0000.000
154A251SER0-0.0020.00821.3580.0000.0000.0000.0000.0000.000
155A252ALA00.0310.03018.124-0.004-0.0040.0000.0000.0000.000
156A253ARG10.8710.93119.7380.2080.2080.0000.0000.0000.000
157A254VAL00.0150.01713.620-0.012-0.0120.0000.0000.0000.000
158A255SER00.0060.01416.8070.0020.0020.0000.0000.0000.000
159A256LEU00.034-0.00614.971-0.039-0.0390.0000.0000.0000.000
160A257GLU-1-0.908-0.94416.879-0.311-0.3110.0000.0000.0000.000
161A258ASN00.010-0.01818.070-0.015-0.0150.0000.0000.0000.000
162A259ILE0-0.038-0.01011.716-0.020-0.0200.0000.0000.0000.000
163A260THR0-0.006-0.00614.606-0.051-0.0510.0000.0000.0000.000
164A261LEU0-0.0040.01816.260-0.024-0.0240.0000.0000.0000.000
165A262LYS10.8780.94913.0950.4430.4430.0000.0000.0000.000
166A263LEU0-0.039-0.02910.369-0.012-0.0120.0000.0000.0000.000
167A264GLY00.0000.02214.239-0.072-0.0720.0000.0000.0000.000
168A265TYR0-0.114-0.0879.6160.0340.0340.0000.0000.0000.000
169A266ARG10.9540.98116.5650.4780.4780.0000.0000.0000.000
170A267SER00.0260.00918.6630.0680.0680.0000.0000.0000.000
171A268VAL00.020-0.01216.990-0.054-0.0540.0000.0000.0000.000
172A269SER0-0.093-0.05916.183-0.013-0.0130.0000.0000.0000.000
173A270ASP-1-0.862-0.93014.487-0.554-0.5540.0000.0000.0000.000
174A271LEU0-0.049-0.00211.745-0.134-0.1340.0000.0000.0000.000
175A272THR0-0.018-0.0136.9910.1220.1220.0000.0000.0000.000
176A273PRO0-0.015-0.0329.572-0.003-0.0030.0000.0000.0000.000
177A274ALA00.012-0.0054.055-0.0580.041-0.001-0.021-0.0770.000
178A275GLU-1-0.764-0.8435.970-1.872-1.8720.0000.0000.0000.000
179A276ILE00.0290.0187.4250.2290.2290.0000.0000.0000.000
180A277ALA00.0020.0036.9970.1220.1220.0000.0000.0000.000
181A278ILE0-0.030-0.0163.084-0.1510.1110.028-0.078-0.2120.000
182A279GLU-1-0.760-0.8657.164-0.269-0.2690.0000.0000.0000.000
183A280ALA0-0.045-0.04010.7720.0950.0950.0000.0000.0000.000
184A281PHE0-0.052-0.0437.5350.0680.0680.0000.0000.0000.000
185A282GLU-1-0.870-0.94010.370-0.297-0.2970.0000.0000.0000.000
186A283GLN0-0.065-0.04512.6610.0700.0700.0000.0000.0000.000
187A284VAL0-0.035-0.01814.3830.0300.0300.0000.0000.0000.000
188A285GLN0-0.007-0.02513.7740.0310.0310.0000.0000.0000.000
189A286SER00.0100.02016.1540.0220.0220.0000.0000.0000.000
190A287TYR0-0.042-0.03918.6590.0140.0140.0000.0000.0000.000
191A288LEU0-0.055-0.03617.6790.0120.0120.0000.0000.0000.000
192A289GLU-1-0.940-0.96219.110-0.073-0.0730.0000.0000.0000.000
193A290LYS10.8730.95021.8730.1160.1160.0000.0000.0000.000
194A291GLU-1-0.977-0.97224.477-0.033-0.0330.0000.0000.0000.000