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: NN4ZQ

Calculation Name: 2FJR-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2FJR

Chain ID: A

ChEMBL ID:

UniProt ID: P08707

Base Structure: X-ray

Registration Date: 2023-09-24

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 OptAll
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 189
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1864967.026094
FMO2-HF: Nuclear repulsion 1792555.533797
FMO2-HF: Total energy -72411.492296
FMO2-MP2: Total energy -72624.427496


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:4:ASP)


Summations of interaction energy for fragment #1(A:4:ASP)
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.
-5.965-9.24716.773-8.147-5.3440.075
Interaction energy analysis for fragmet #1(A:4:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.828 / q_NPA : -0.895
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].
3A6LEU0-0.008-0.0073.929-6.028-3.9800.007-1.074-0.9810.006
4A7GLY0-0.012-0.0015.755-0.810-0.8100.0000.0000.0000.000
5A8TRP00.0190.0104.879-1.260-1.061-0.001-0.006-0.1920.000
6A9SER0-0.001-0.0096.9551.5391.5390.0000.0000.0000.000
7A10ASN0-0.002-0.0288.3300.3230.3230.0000.0000.0000.000
8A11VAL0-0.010-0.0109.554-1.019-1.0190.0000.0000.0000.000
9A12ASP-1-0.820-0.88212.04419.38919.3890.0000.0000.0000.000
10A13VAL0-0.0150.0139.156-0.603-0.6030.0000.0000.0000.000
11A14LEU0-0.050-0.02412.416-1.061-1.0610.0000.0000.0000.000
12A15ASP-1-0.733-0.83014.67815.04815.0480.0000.0000.0000.000
13A16ARG10.8600.93812.514-22.550-22.5500.0000.0000.0000.000
14A17ILE0-0.017-0.00912.943-0.517-0.5170.0000.0000.0000.000
15A18CYS0-0.087-0.04617.225-0.971-0.9710.0000.0000.0000.000
16A19GLU-1-0.911-0.96020.31014.00914.0090.0000.0000.0000.000
17A20ALA0-0.029-0.01619.331-0.614-0.6140.0000.0000.0000.000
18A21TYR0-0.043-0.06018.800-0.085-0.0850.0000.0000.0000.000
19A22GLY00.0130.01723.212-0.612-0.6120.0000.0000.0000.000
20A23PHE0-0.098-0.04721.964-0.480-0.4800.0000.0000.0000.000
21A24SER00.0240.01024.2720.3840.3840.0000.0000.0000.000
22A25GLN0-0.047-0.03325.452-0.032-0.0320.0000.0000.0000.000
23A26LYS10.8450.89918.778-15.326-15.3260.0000.0000.0000.000
24A27ILE00.0050.00022.3830.4010.4010.0000.0000.0000.000
25A28GLN00.0430.02524.9140.1330.1330.0000.0000.0000.000
26A29LEU00.0610.03016.9140.0400.0400.0000.0000.0000.000
27A30ALA0-0.085-0.04020.8420.4700.4700.0000.0000.0000.000
28A31ASN0-0.020-0.02422.1580.2200.2200.0000.0000.0000.000
29A32HIS0-0.027-0.02220.943-0.678-0.6780.0000.0000.0000.000
30A33PHE0-0.042-0.02217.6850.2630.2630.0000.0000.0000.000
31A34ASP-1-0.950-0.96021.27912.38712.3870.0000.0000.0000.000
32A35ILE0-0.052-0.01218.2610.3290.3290.0000.0000.0000.000
33A36ALA00.0350.01522.526-0.404-0.4040.0000.0000.0000.000
34A37SER00.0830.01821.9720.6220.6220.0000.0000.0000.000
35A38SER0-0.0310.00421.6600.4860.4860.0000.0000.0000.000
36A39SER00.0310.00519.1620.3720.3720.0000.0000.0000.000
37A40LEU00.0380.02516.7461.1721.1720.0000.0000.0000.000
38A41SER0-0.009-0.02316.8720.6650.6650.0000.0000.0000.000
39A42ASN0-0.023-0.00615.3190.7470.7470.0000.0000.0000.000
40A43ARG10.7760.87012.808-20.695-20.6950.0000.0000.0000.000
41A44TYR00.021-0.02512.2691.4951.4950.0000.0000.0000.000
42A45THR0-0.049-0.01713.965-0.195-0.1950.0000.0000.0000.000
43A46ARG10.7940.8979.138-28.930-28.9300.0000.0000.0000.000
44A47GLY00.0570.0207.1050.3380.3380.0000.0000.0000.000
45A48ALA0-0.0140.0005.0673.0613.0610.0000.0000.0000.000
46A49ILE00.1130.0624.487-5.763-5.662-0.001-0.007-0.0940.000
47A50SER0-0.0180.0036.963-0.202-0.2020.0000.0000.0000.000
48A51TYR00.010-0.0251.625-35.375-41.00516.768-7.060-4.0770.069
49A52ASP-1-0.806-0.8718.45923.21923.2190.0000.0000.0000.000
50A53PHE00.0480.01411.738-1.626-1.6260.0000.0000.0000.000
51A54ALA00.0410.02410.482-1.360-1.3600.0000.0000.0000.000
52A55ALA0-0.011-0.00512.003-1.328-1.3280.0000.0000.0000.000
53A56HIS0-0.052-0.03113.560-2.028-2.0280.0000.0000.0000.000
54A57CYS00.0630.04915.892-1.180-1.1800.0000.0000.0000.000
55A58ALA00.0050.02915.542-1.102-1.1020.0000.0000.0000.000
56A59LEU0-0.058-0.02516.847-1.074-1.0740.0000.0000.0000.000
57A60GLU-1-0.808-0.87219.63314.32614.3260.0000.0000.0000.000
58A61THR0-0.001-0.02820.106-0.728-0.7280.0000.0000.0000.000
59A62GLY0-0.065-0.04321.061-0.705-0.7050.0000.0000.0000.000
60A63ALA00.0030.01218.417-0.034-0.0340.0000.0000.0000.000
61A64ASN0-0.028-0.02416.7981.8181.8180.0000.0000.0000.000
62A65LEU00.0540.00910.8890.5890.5890.0000.0000.0000.000
63A66GLN0-0.025-0.01611.7283.3163.3160.0000.0000.0000.000
64A67TRP00.0170.04412.9321.5491.5490.0000.0000.0000.000
65A68LEU00.0030.00113.1000.3810.3810.0000.0000.0000.000
66A69LEU0-0.032-0.0317.3090.7130.7130.0000.0000.0000.000
67A70THR0-0.056-0.03510.1990.4380.4380.0000.0000.0000.000
68A71GLY0-0.0140.00312.286-0.857-0.8570.0000.0000.0000.000
69A72GLU-1-0.913-0.94813.71221.44121.4410.0000.0000.0000.000
70A73GLY0-0.054-0.03117.0620.0980.0980.0000.0000.0000.000
71A74GLU-1-0.924-0.96920.27212.35712.3570.0000.0000.0000.000
72A75ALA00.0390.02319.6270.5440.5440.0000.0000.0000.000
73A76PHE00.002-0.00620.7110.3610.3610.0000.0000.0000.000
74A77VAL0-0.018-0.00523.411-0.020-0.0200.0000.0000.0000.000
75A78ASN00.011-0.00726.124-0.457-0.4570.0000.0000.0000.000
76A79ASN0-0.037-0.02427.972-0.329-0.3290.0000.0000.0000.000
77A80ARG10.7740.88422.548-13.074-13.0740.0000.0000.0000.000
78A81GLU-1-0.831-0.90226.19911.06311.0630.0000.0000.0000.000
79A82SER00.0230.03525.948-0.434-0.4340.0000.0000.0000.000
80A83SER0-0.102-0.06226.5970.1790.1790.0000.0000.0000.000
81A84ASP-1-0.828-0.91428.9409.8309.8300.0000.0000.0000.000
82A85ALA00.017-0.00128.8720.2010.2010.0000.0000.0000.000
83A86LYS10.8120.89028.312-10.126-10.1260.0000.0000.0000.000
84A87ARG10.8600.91726.879-12.007-12.0070.0000.0000.0000.000
85A88ILE00.0290.03228.5280.2720.2720.0000.0000.0000.000
86A89GLU-1-0.797-0.89127.68511.34511.3450.0000.0000.0000.000
87A90GLY00.0380.02330.416-0.308-0.3080.0000.0000.0000.000
88A91PHE00.019-0.00731.3530.0970.0970.0000.0000.0000.000
89A92THR0-0.042-0.02036.422-0.234-0.2340.0000.0000.0000.000
90A93LEU0-0.025-0.00340.1070.1090.1090.0000.0000.0000.000
91A94SER0-0.040-0.05242.344-0.227-0.2270.0000.0000.0000.000
92A95GLU-1-0.814-0.88345.0077.2637.2630.0000.0000.0000.000
93A96GLU-1-0.839-0.88245.3906.7236.7230.0000.0000.0000.000
94A97ILE00.0220.02341.3180.1280.1280.0000.0000.0000.000
95A98LEU00.0150.00035.759-0.056-0.0560.0000.0000.0000.000
96A99LYS10.8120.90437.491-7.427-7.4270.0000.0000.0000.000
97A100SER00.0440.01932.487-0.027-0.0270.0000.0000.0000.000
98A101ASP-1-0.808-0.88134.1818.4228.4220.0000.0000.0000.000
99A102LYS10.8280.90132.652-8.223-8.2230.0000.0000.0000.000
100A103GLN00.0030.00426.532-0.262-0.2620.0000.0000.0000.000
101A104LEU0-0.032-0.00631.904-0.156-0.1560.0000.0000.0000.000
102A105SER0-0.016-0.01332.2940.3730.3730.0000.0000.0000.000
103A106VAL0-0.0100.00132.802-0.340-0.3400.0000.0000.0000.000
104A107ASP-1-0.831-0.90733.3539.6419.6410.0000.0000.0000.000
105A108ALA00.0470.03431.592-0.115-0.1150.0000.0000.0000.000
106A109GLN0-0.012-0.02133.486-0.321-0.3210.0000.0000.0000.000
107A110PHE0-0.066-0.02836.699-0.285-0.2850.0000.0000.0000.000
108A111PHE0-0.012-0.01034.114-0.186-0.1860.0000.0000.0000.000
109A112THR0-0.022-0.00336.3290.0520.0520.0000.0000.0000.000
110A113LYS10.9220.94434.783-8.369-8.3690.0000.0000.0000.000
111A114PRO00.0720.04829.217-0.083-0.0830.0000.0000.0000.000
112A115LEU0-0.086-0.03130.363-0.169-0.1690.0000.0000.0000.000
113A116THR00.0230.01725.214-0.088-0.0880.0000.0000.0000.000
114A117ASP-1-0.763-0.85026.21511.78211.7820.0000.0000.0000.000
115A118GLY00.029-0.00327.983-0.425-0.4250.0000.0000.0000.000
116A119MET0-0.097-0.02530.5400.2010.2010.0000.0000.0000.000
117A120ALA00.0150.00533.314-0.243-0.2430.0000.0000.0000.000
118A121ILE0-0.013-0.01135.8350.0040.0040.0000.0000.0000.000
119A122ARG10.8660.92637.452-8.587-8.5870.0000.0000.0000.000
120A123SER00.019-0.02741.5990.0310.0310.0000.0000.0000.000
121A124GLU-1-0.768-0.84044.6146.7236.7230.0000.0000.0000.000
122A125GLY0-0.0050.00847.565-0.106-0.1060.0000.0000.0000.000
123A126LYS10.7970.89845.639-6.701-6.7010.0000.0000.0000.000
124A127ILE0-0.010-0.01539.1970.1130.1130.0000.0000.0000.000
125A128TYR0-0.018-0.02740.968-0.091-0.0910.0000.0000.0000.000
126A129PHE00.0160.00835.6150.2030.2030.0000.0000.0000.000
127A130VAL0-0.034-0.02235.793-0.205-0.2050.0000.0000.0000.000
128A131ASP-1-0.751-0.87633.2099.7719.7710.0000.0000.0000.000
129A132LYS10.8220.87628.328-11.387-11.3870.0000.0000.0000.000
130A133GLN00.0120.00128.141-0.017-0.0170.0000.0000.0000.000
131A134ALA0-0.0510.00331.733-0.107-0.1070.0000.0000.0000.000
132A135SER00.0230.01635.359-0.025-0.0250.0000.0000.0000.000
133A136LEU00.0190.01336.973-0.189-0.1890.0000.0000.0000.000
134A137SER0-0.065-0.04640.038-0.147-0.1470.0000.0000.0000.000
135A138ASP-1-0.809-0.90242.7256.9176.9170.0000.0000.0000.000
136A139GLY00.0270.02844.9020.0970.0970.0000.0000.0000.000
137A140LEU00.0100.01044.3630.0200.0200.0000.0000.0000.000
138A141TRP0-0.055-0.03637.3320.3030.3030.0000.0000.0000.000
139A142LEU0-0.0010.01536.901-0.199-0.1990.0000.0000.0000.000
140A143VAL0-0.016-0.02239.6980.1630.1630.0000.0000.0000.000
141A144ASP-1-0.812-0.89739.0158.1098.1090.0000.0000.0000.000
142A145ILE00.003-0.01541.377-0.045-0.0450.0000.0000.0000.000
143A146LYS10.8540.91143.839-6.851-6.8510.0000.0000.0000.000
144A147GLY00.0290.02541.998-0.096-0.0960.0000.0000.0000.000
145A148ALA0-0.0240.01342.6810.0850.0850.0000.0000.0000.000
146A149ILE0-0.012-0.01738.4580.0760.0760.0000.0000.0000.000
147A150SER0-0.011-0.02642.685-0.116-0.1160.0000.0000.0000.000
148A151ILE0-0.0060.00141.8690.1650.1650.0000.0000.0000.000
149A152ARG10.8030.89044.500-6.891-6.8910.0000.0000.0000.000
150A153GLU-1-0.865-0.93145.7846.8796.8790.0000.0000.0000.000
151A154LEU0-0.021-0.01443.308-0.085-0.0850.0000.0000.0000.000
152A155THR0-0.016-0.01047.336-0.034-0.0340.0000.0000.0000.000
153A156LYS10.8700.93043.136-7.366-7.3660.0000.0000.0000.000
154A157LEU0-0.0050.00448.342-0.146-0.1460.0000.0000.0000.000
155A158PRO0-0.004-0.01949.9520.1230.1230.0000.0000.0000.000
156A159GLY0-0.010-0.00450.818-0.036-0.0360.0000.0000.0000.000
157A160ARG10.9010.95345.100-6.746-6.7460.0000.0000.0000.000
158A161LYS10.9130.95547.296-5.934-5.9340.0000.0000.0000.000
159A162LEU00.004-0.00244.1680.0940.0940.0000.0000.0000.000
160A163HIS0-0.034-0.03448.799-0.135-0.1350.0000.0000.0000.000
161A164VAL0-0.0010.00848.0630.1430.1430.0000.0000.0000.000
162A165ALA00.0440.00950.247-0.163-0.1630.0000.0000.0000.000
163A166GLY00.0360.01150.1380.1490.1490.0000.0000.0000.000
164A167GLY00.0070.01351.7660.0450.0450.0000.0000.0000.000
165A168LYS10.9120.93352.748-5.773-5.7730.0000.0000.0000.000
166A169VAL00.0020.01255.660-0.129-0.1290.0000.0000.0000.000
167A170PRO0-0.0010.01354.1880.1140.1140.0000.0000.0000.000
168A171PHE0-0.036-0.02448.534-0.089-0.0890.0000.0000.0000.000
169A172GLU-1-0.796-0.88152.1525.9195.9190.0000.0000.0000.000
170A173CYS0-0.075-0.03147.415-0.044-0.0440.0000.0000.0000.000
171A174GLY00.0570.03947.683-0.027-0.0270.0000.0000.0000.000
172A175ILE0-0.053-0.03941.9510.0380.0380.0000.0000.0000.000
173A176ASP-1-0.898-0.95042.2267.3357.3350.0000.0000.0000.000
174A177ASP-1-0.852-0.91543.3676.6626.6620.0000.0000.0000.000
175A178ILE0-0.065-0.03943.717-0.069-0.0690.0000.0000.0000.000
176A179LYS10.8790.93835.309-8.750-8.7500.0000.0000.0000.000
177A180THR00.0010.00337.477-0.085-0.0850.0000.0000.0000.000
178A181LEU0-0.052-0.03135.5570.2320.2320.0000.0000.0000.000
179A182GLY00.0590.02634.6800.3430.3430.0000.0000.0000.000
180A183ARG10.8560.93936.444-8.629-8.6290.0000.0000.0000.000
181A184VAL0-0.019-0.01637.9030.1970.1970.0000.0000.0000.000
182A185VAL0-0.057-0.03935.928-0.112-0.1120.0000.0000.0000.000
183A186GLY00.0390.02839.360-0.062-0.0620.0000.0000.0000.000
184A187VAL0-0.051-0.02541.0280.1000.1000.0000.0000.0000.000
185A188TYR0-0.052-0.02442.416-0.068-0.0680.0000.0000.0000.000
186A189SER00.026-0.01344.238-0.004-0.0040.0000.0000.0000.000
187A190GLU-1-0.867-0.90745.8036.9556.9550.0000.0000.0000.000
188A191VAL0-0.030-0.00149.263-0.099-0.0990.0000.0000.0000.000
189A192ASN0-0.024-0.01452.513-0.229-0.2290.0000.0000.0000.000