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: 2NJKR

Calculation Name: 2NYI-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2NYI

Chain ID: A

ChEMBL ID:

UniProt ID: J3QW32

Base Structure: X-ray

Registration Date: 2023-09-21

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 175
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1518701.159932
FMO2-HF: Nuclear repulsion 1452637.293088
FMO2-HF: Total energy -66063.866844
FMO2-MP2: Total energy -66257.734287


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:2:GLU)


Summations of interaction energy for fragment #1(A:2: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.
-81.355-87.01833.213-14.536-13.0110.163
Interaction energy analysis for fragmet #1(A:2:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.851 / q_NPA : -0.926
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].
3A4GLN0-0.047-0.0191.770-9.717-15.19617.823-6.199-6.1450.050
4A5SER00.0270.0135.255-4.525-4.489-0.001-0.002-0.0320.000
5A6PHE0-0.029-0.0238.4951.3931.3930.0000.0000.0000.000
6A7VAL00.0110.00911.892-0.844-0.8440.0000.0000.0000.000
7A8VAL0-0.007-0.01015.5080.0690.0690.0000.0000.0000.000
8A9SER0-0.0130.00518.177-0.520-0.5200.0000.0000.0000.000
9A10VAL0-0.012-0.01321.9220.1150.1150.0000.0000.0000.000
10A11ALA00.0300.01424.678-0.201-0.2010.0000.0000.0000.000
11A12GLY00.0130.00328.3820.1030.1030.0000.0000.0000.000
12A13SER00.0340.02731.533-0.094-0.0940.0000.0000.0000.000
13A14ASP-1-0.869-0.95533.5669.4219.4210.0000.0000.0000.000
14A15ARG10.7800.87729.861-10.166-10.1660.0000.0000.0000.000
15A16VAL00.0360.01033.5680.2440.2440.0000.0000.0000.000
16A17GLY0-0.001-0.01130.9160.0020.0020.0000.0000.0000.000
17A18ILE00.0290.05127.4310.2880.2880.0000.0000.0000.000
18A19VAL00.0750.03025.0390.4250.4250.0000.0000.0000.000
19A20HIS0-0.0330.00024.9690.5660.5660.0000.0000.0000.000
20A21ASP-1-0.778-0.87924.99410.84310.8430.0000.0000.0000.000
21A22PHE00.0250.00319.0770.4870.4870.0000.0000.0000.000
22A23SER0-0.010-0.03020.7880.8300.8300.0000.0000.0000.000
23A24TRP0-0.057-0.02520.3260.6380.6380.0000.0000.0000.000
24A25ALA00.0160.00420.3870.3620.3620.0000.0000.0000.000
25A26LEU00.0120.00015.6040.7320.7320.0000.0000.0000.000
26A27LYS10.9610.98415.644-12.329-12.3290.0000.0000.0000.000
27A28ASN0-0.067-0.02416.6370.0960.0960.0000.0000.0000.000
28A29ILE0-0.053-0.01613.5900.0980.0980.0000.0000.0000.000
29A30SER0-0.067-0.03111.5551.2421.2420.0000.0000.0000.000
30A31ALA0-0.0150.00211.0711.7701.7700.0000.0000.0000.000
31A32ASN0-0.029-0.02411.914-2.117-2.1170.0000.0000.0000.000
32A33VAL00.0150.00713.5160.9560.9560.0000.0000.0000.000
33A34GLU-1-0.943-0.96511.73422.67222.6720.0000.0000.0000.000
34A35SER00.002-0.01214.938-1.003-1.0030.0000.0000.0000.000
35A36SER0-0.018-0.01618.1410.2740.2740.0000.0000.0000.000
36A37ARG10.8470.91920.927-12.652-12.6520.0000.0000.0000.000
37A38MET0-0.017-0.01224.2130.2700.2700.0000.0000.0000.000
38A39ALA00.0270.02126.922-0.240-0.2400.0000.0000.0000.000
39A40CYS0-0.034-0.01230.3430.2530.2530.0000.0000.0000.000
40A41LEU00.0530.02033.312-0.184-0.1840.0000.0000.0000.000
41A42GLY0-0.0040.00536.6350.0570.0570.0000.0000.0000.000
42A43GLY0-0.0130.00338.296-0.112-0.1120.0000.0000.0000.000
43A44ASP-1-0.896-0.93133.9009.0459.0450.0000.0000.0000.000
44A45PHE0-0.015-0.03726.5360.0990.0990.0000.0000.0000.000
45A46ALA00.0400.00928.0250.1580.1580.0000.0000.0000.000
46A47MET0-0.052-0.01922.511-0.143-0.1430.0000.0000.0000.000
47A48ILE00.0140.01119.7550.3830.3830.0000.0000.0000.000
48A49VAL0-0.021-0.02117.047-0.221-0.2210.0000.0000.0000.000
49A50LEU0-0.0060.02013.7660.6280.6280.0000.0000.0000.000
50A51VAL00.0220.00312.737-0.475-0.4750.0000.0000.0000.000
51A52SER0-0.002-0.0038.8642.4352.4350.0000.0000.0000.000
52A53LEU00.0480.0078.099-1.947-1.9470.0000.0000.0000.000
53A54ASN0-0.0050.0104.1874.7984.958-0.001-0.056-0.1030.000
54A55ALA00.013-0.0024.938-1.661-1.480-0.001-0.012-0.1680.000
55A56LYS10.8680.9301.905-134.691-135.29015.394-8.268-6.5270.113
56A57ASP-1-0.845-0.9266.72423.64723.6470.0000.0000.0000.000
57A58GLY00.0820.04310.316-0.001-0.0010.0000.0000.0000.000
58A59LYS10.8780.92912.819-22.953-22.9530.0000.0000.0000.000
59A60LEU0-0.0100.01111.784-1.214-1.2140.0000.0000.0000.000
60A61ILE00.0420.01811.793-0.929-0.9290.0000.0000.0000.000
61A62GLN0-0.040-0.03415.458-0.253-0.2530.0000.0000.0000.000
62A63SER0-0.003-0.01317.997-1.063-1.0630.0000.0000.0000.000
63A64ALA0-0.033-0.01317.558-0.808-0.8080.0000.0000.0000.000
64A65LEU0-0.004-0.00818.853-0.736-0.7360.0000.0000.0000.000
65A66GLU-1-0.850-0.91821.36512.82712.8270.0000.0000.0000.000
66A67SER0-0.080-0.03322.997-0.598-0.5980.0000.0000.0000.000
67A68ALA0-0.057-0.02623.311-0.482-0.4820.0000.0000.0000.000
68A69LEU0-0.054-0.01524.558-0.427-0.4270.0000.0000.0000.000
69A70PRO00.0470.02927.0380.0400.0400.0000.0000.0000.000
70A71GLY0-0.031-0.02729.179-0.266-0.2660.0000.0000.0000.000
71A72PHE0-0.034-0.00327.531-0.135-0.1350.0000.0000.0000.000
72A73GLN0-0.0140.00126.8810.3420.3420.0000.0000.0000.000
73A74ILE00.0120.00021.3650.2130.2130.0000.0000.0000.000
74A75SER0-0.0340.00120.7490.1410.1410.0000.0000.0000.000
75A76THR00.0420.00514.7410.4170.4170.0000.0000.0000.000
76A77ARG10.8830.94314.747-19.029-19.0290.0000.0000.0000.000
77A78ARG10.8910.9415.193-42.626-42.588-0.0010.001-0.0360.000
78A79ALA0-0.0080.00410.291-2.062-2.0620.0000.0000.0000.000
79A80SER0-0.020-0.02510.8801.7731.7730.0000.0000.0000.000
80A81SER00.0320.02610.8410.1990.1990.0000.0000.0000.000
81A82VAL00.011-0.00312.075-0.254-0.2540.0000.0000.0000.000
82A83ALA00.0360.00214.126-0.478-0.4780.0000.0000.0000.000
83A84GLU-1-0.807-0.86412.62322.64722.6470.0000.0000.0000.000
84A85ARG10.7540.84414.090-20.495-20.4950.0000.0000.0000.000
85A86HIS0-0.0170.00418.5620.0780.0780.0000.0000.0000.000
86A87VAL00.0240.02220.066-0.480-0.4800.0000.0000.0000.000
87A88SER00.0360.02923.6580.2540.2540.0000.0000.0000.000
88A89PRO00.0350.02825.2910.1010.1010.0000.0000.0000.000
89A90ASP-1-0.884-0.93726.34410.12710.1270.0000.0000.0000.000
90A91THR0-0.086-0.05626.724-0.412-0.4120.0000.0000.0000.000
91A92ARG10.8390.91628.441-10.213-10.2130.0000.0000.0000.000
92A93GLU-1-0.814-0.89926.84311.64011.6400.0000.0000.0000.000
93A94TYR0-0.056-0.05430.490-0.241-0.2410.0000.0000.0000.000
94A95GLU-1-0.831-0.89532.5659.6679.6670.0000.0000.0000.000
95A96LEU0-0.039-0.02335.390-0.195-0.1950.0000.0000.0000.000
96A97TYR0-0.047-0.04636.1590.0870.0870.0000.0000.0000.000
97A98VAL00.0150.00740.686-0.107-0.1070.0000.0000.0000.000
98A99GLU-1-0.812-0.90443.4306.8296.8290.0000.0000.0000.000
99A100GLY00.0610.03646.476-0.102-0.1020.0000.0000.0000.000
100A101PRO0-0.042-0.01949.4910.0410.0410.0000.0000.0000.000
101A102ASP-1-0.861-0.95147.6886.7986.7980.0000.0000.0000.000
102A103SER0-0.052-0.03848.749-0.158-0.1580.0000.0000.0000.000
103A104GLU-1-0.963-0.98648.0966.5316.5310.0000.0000.0000.000
104A105GLY00.004-0.00146.7880.1410.1410.0000.0000.0000.000
105A106ILE00.0170.04044.6050.1160.1160.0000.0000.0000.000
106A107VAL00.0460.01939.7250.1320.1320.0000.0000.0000.000
107A108GLU-1-0.950-0.96340.9847.5777.5770.0000.0000.0000.000
108A109ALA00.0700.04341.8640.1300.1300.0000.0000.0000.000
109A110VAL00.005-0.00539.4970.0890.0890.0000.0000.0000.000
110A111THR0-0.039-0.05336.8450.1980.1980.0000.0000.0000.000
111A112ALA0-0.0070.01337.7020.2170.2170.0000.0000.0000.000
112A113VAL0-0.051-0.02439.4560.0980.0980.0000.0000.0000.000
113A114LEU00.0210.00935.0830.1290.1290.0000.0000.0000.000
114A115ALA00.0120.00534.4610.2260.2260.0000.0000.0000.000
115A116LYS10.8830.94135.266-7.381-7.3810.0000.0000.0000.000
116A117LYS10.7700.87736.759-7.835-7.8350.0000.0000.0000.000
117A118GLY0-0.023-0.00332.7940.1320.1320.0000.0000.0000.000
118A119ALA0-0.032-0.00531.1180.3540.3540.0000.0000.0000.000
119A120ASN0-0.063-0.03026.2810.0440.0440.0000.0000.0000.000
120A121ILE00.0270.01029.527-0.098-0.0980.0000.0000.0000.000
121A122VAL0-0.107-0.04825.2570.4290.4290.0000.0000.0000.000
122A123GLU-1-0.799-0.90127.25411.52411.5240.0000.0000.0000.000
123A124LEU0-0.036-0.02029.880-0.213-0.2130.0000.0000.0000.000
124A125GLU-1-0.960-0.95633.2648.9598.9590.0000.0000.0000.000
125A126THR00.009-0.00735.926-0.114-0.1140.0000.0000.0000.000
126A127GLU-1-0.892-0.93339.5237.3747.3740.0000.0000.0000.000
127A128THR00.001-0.01142.423-0.063-0.0630.0000.0000.0000.000
128A129LEU0-0.040-0.01345.712-0.026-0.0260.0000.0000.0000.000
129A130PRO0-0.026-0.01448.742-0.101-0.1010.0000.0000.0000.000
130A131ALA00.0150.01752.2550.0040.0040.0000.0000.0000.000
131A132PRO0-0.042-0.02955.064-0.033-0.0330.0000.0000.0000.000
132A133PHE0-0.043-0.01157.592-0.098-0.0980.0000.0000.0000.000
133A134ALA00.004-0.01658.3920.0800.0800.0000.0000.0000.000
134A135GLY0-0.008-0.01358.580-0.047-0.0470.0000.0000.0000.000
135A136PHE00.0070.00652.935-0.020-0.0200.0000.0000.0000.000
136A137THR00.0110.01349.584-0.047-0.0470.0000.0000.0000.000
137A138LEU0-0.0470.00548.281-0.029-0.0290.0000.0000.0000.000
138A139PHE00.0520.01942.0320.1190.1190.0000.0000.0000.000
139A140ARG10.8340.90642.812-6.995-6.9950.0000.0000.0000.000
140A141MET0-0.043-0.02837.2160.1110.1110.0000.0000.0000.000
141A142GLY00.0440.03737.589-0.126-0.1260.0000.0000.0000.000
142A143SER0-0.065-0.05433.3510.2150.2150.0000.0000.0000.000
143A144ARG10.8730.95227.651-10.852-10.8520.0000.0000.0000.000
144A145VAL00.010-0.00330.8620.2740.2740.0000.0000.0000.000
145A146ALA00.0150.00128.1380.0290.0290.0000.0000.0000.000
146A147PHE00.0330.00530.0960.0530.0530.0000.0000.0000.000
147A148PRO0-0.007-0.01030.4460.0290.0290.0000.0000.0000.000
148A149PHE00.0970.04632.212-0.293-0.2930.0000.0000.0000.000
149A150PRO0-0.078-0.03634.380-0.288-0.2880.0000.0000.0000.000
150A151LEU0-0.015-0.00334.756-0.244-0.2440.0000.0000.0000.000
151A152TYR0-0.008-0.00137.934-0.203-0.2030.0000.0000.0000.000
152A153GLN00.0380.01239.114-0.149-0.1490.0000.0000.0000.000
153A154GLU-1-0.827-0.89840.4567.7357.7350.0000.0000.0000.000
154A155VAL0-0.028-0.01337.414-0.113-0.1130.0000.0000.0000.000
155A156VAL00.0800.04140.872-0.093-0.0930.0000.0000.0000.000
156A157THR0-0.039-0.01743.465-0.197-0.1970.0000.0000.0000.000
157A158ALA0-0.079-0.03442.863-0.157-0.1570.0000.0000.0000.000
158A159LEU00.018-0.00540.255-0.060-0.0600.0000.0000.0000.000
159A160SER00.0170.01344.607-0.129-0.1290.0000.0000.0000.000
160A161ARG10.9010.94447.979-6.515-6.5150.0000.0000.0000.000
161A162VAL0-0.0040.00744.475-0.101-0.1010.0000.0000.0000.000
162A163GLU-1-0.815-0.90947.3766.6006.6000.0000.0000.0000.000
163A164GLU-1-0.993-0.99549.5265.7635.7630.0000.0000.0000.000
164A165GLU-1-1.069-1.03350.6116.2726.2720.0000.0000.0000.000
165A166PHE0-0.057-0.04748.603-0.051-0.0510.0000.0000.0000.000
166A167GLY0-0.0300.00851.339-0.028-0.0280.0000.0000.0000.000
167A168VAL0-0.116-0.05646.7830.0030.0030.0000.0000.0000.000
168A169ASP-1-0.880-0.93348.3696.2416.2410.0000.0000.0000.000
169A170ILE0-0.078-0.06842.5470.1980.1980.0000.0000.0000.000
170A171ASP-1-0.905-0.92342.3607.0307.0300.0000.0000.0000.000
171A172LEU0-0.057-0.05136.8680.2370.2370.0000.0000.0000.000
172A173GLU-1-0.917-0.95138.3197.5267.5260.0000.0000.0000.000
173A174GLU-1-0.899-0.93334.1209.2839.2830.0000.0000.0000.000
174A175VAL0-0.029-0.01230.097-0.094-0.0940.0000.0000.0000.000
175A176VAL0-0.060-0.02930.6970.1750.1750.0000.0000.0000.000