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: QVY8Y

Calculation Name: 2NX2-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2NX2

Chain ID: A

ChEMBL ID:

UniProt ID: P50838

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 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 178
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2043529.903586
FMO2-HF: Nuclear repulsion 1972027.542597
FMO2-HF: Total energy -71502.36099
FMO2-MP2: Total energy -71715.830385


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:0:SER)


Summations of interaction energy for fragment #1(A:0:SER)
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.
-7.921-3.8650.268-1.749-2.5730.009
Interaction energy analysis for fragmet #1(A:0:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.005 / q_NPA : -0.003
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].
3A2LYS10.8740.9242.870-5.020-1.4930.271-1.662-2.1360.009
4A3VAL0-0.004-0.0065.1320.0300.160-0.001-0.010-0.1180.000
5A4LEU00.0210.0218.558-0.410-0.4100.0000.0000.0000.000
6A5ALA0-0.0010.00010.3790.2360.2360.0000.0000.0000.000
7A6ILE00.0190.00013.658-0.042-0.0420.0000.0000.0000.000
8A7THR0-0.037-0.05316.4120.0610.0610.0000.0000.0000.000
9A8GLY00.0450.00219.767-0.016-0.0160.0000.0000.0000.000
10A9TYR0-0.064-0.03122.5500.0150.0150.0000.0000.0000.000
11A10LYS10.8710.92526.3240.1870.1870.0000.0000.0000.000
12A11PRO00.0120.00229.0260.0020.0020.0000.0000.0000.000
13A12PHE00.0270.00831.3610.0020.0020.0000.0000.0000.000
14A13GLU-1-0.814-0.86828.812-0.174-0.1740.0000.0000.0000.000
15A14LEU00.0180.00227.396-0.003-0.0030.0000.0000.0000.000
16A15GLY0-0.0040.01332.0480.0050.0050.0000.0000.0000.000
17A16ILE0-0.0010.01830.2300.0070.0070.0000.0000.0000.000
18A17PHE0-0.002-0.02234.123-0.002-0.0020.0000.0000.0000.000
19A18LYS10.8340.89335.1990.0770.0770.0000.0000.0000.000
20A19GLN00.0640.01029.387-0.012-0.0120.0000.0000.0000.000
21A20ASP-1-0.823-0.88833.224-0.071-0.0710.0000.0000.0000.000
22A21ASP-1-0.831-0.93032.747-0.100-0.1000.0000.0000.0000.000
23A22LYS10.8430.92332.4240.0740.0740.0000.0000.0000.000
24A23ALA00.0540.03230.947-0.003-0.0030.0000.0000.0000.000
25A24LEU0-0.006-0.01027.329-0.010-0.0100.0000.0000.0000.000
26A25TYR00.0030.02027.464-0.011-0.0110.0000.0000.0000.000
27A26TYR00.0450.02226.692-0.004-0.0040.0000.0000.0000.000
28A27ILE0-0.0070.00124.158-0.015-0.0150.0000.0000.0000.000
29A28LYS10.8470.91622.9250.1070.1070.0000.0000.0000.000
30A29LYS10.9130.97722.1130.1160.1160.0000.0000.0000.000
31A30ALA00.0200.01921.057-0.011-0.0110.0000.0000.0000.000
32A31ILE0-0.021-0.02117.806-0.031-0.0310.0000.0000.0000.000
33A32LYS10.8290.90217.1760.0940.0940.0000.0000.0000.000
34A33ASN00.004-0.00217.168-0.001-0.0010.0000.0000.0000.000
35A34ARG10.8360.91514.3240.4420.4420.0000.0000.0000.000
36A35LEU00.0020.00112.931-0.078-0.0780.0000.0000.0000.000
37A36ILE00.0230.01112.389-0.021-0.0210.0000.0000.0000.000
38A37ALA00.0240.02411.9500.0030.0030.0000.0000.0000.000
39A38PHE0-0.005-0.0158.413-0.049-0.0490.0000.0000.0000.000
40A39LEU0-0.039-0.0137.627-0.079-0.0790.0000.0000.0000.000
41A40ASP-1-0.865-0.9068.426-0.111-0.1110.0000.0000.0000.000
42A41GLU-1-1.026-1.0095.552-1.120-1.1200.0000.0000.0000.000
43A42GLY0-0.054-0.0243.890-1.717-1.4790.000-0.057-0.1810.000
44A43LEU0-0.082-0.0354.9161.3491.362-0.001-0.003-0.0080.000
45A44GLU-1-0.857-0.9056.7202.0602.0600.0000.0000.0000.000
46A45TRP0-0.027-0.0268.819-0.097-0.0970.0000.0000.0000.000
47A46ILE00.0230.02510.699-0.185-0.1850.0000.0000.0000.000
48A47LEU0-0.014-0.00913.4210.0740.0740.0000.0000.0000.000
49A48ILE0-0.0050.00515.568-0.043-0.0430.0000.0000.0000.000
50A49SER0-0.053-0.06119.0500.0150.0150.0000.0000.0000.000
51A50GLY00.0610.03422.3030.0250.0250.0000.0000.0000.000
52A51GLN0-0.041-0.02024.0590.0170.0170.0000.0000.0000.000
53A52LEU00.0440.01425.784-0.003-0.0030.0000.0000.0000.000
54A53GLY00.003-0.01427.428-0.006-0.0060.0000.0000.0000.000
55A54VAL0-0.0010.00021.2210.0040.0040.0000.0000.0000.000
56A55GLU-1-0.745-0.81420.603-0.275-0.2750.0000.0000.0000.000
57A56LEU00.0070.01421.8020.0010.0010.0000.0000.0000.000
58A57TRP0-0.001-0.02323.8030.0020.0020.0000.0000.0000.000
59A58ALA00.0200.01518.4650.0040.0040.0000.0000.0000.000
60A59ALA00.0210.02119.420-0.001-0.0010.0000.0000.0000.000
61A60GLU-1-0.747-0.86220.706-0.109-0.1090.0000.0000.0000.000
62A61ALA0-0.038-0.02420.1180.0120.0120.0000.0000.0000.000
63A62ALA00.0600.02216.9110.0010.0010.0000.0000.0000.000
64A63TYR0-0.007-0.03018.3840.0150.0150.0000.0000.0000.000
65A64ASP-1-0.871-0.91421.040-0.082-0.0820.0000.0000.0000.000
66A65LEU0-0.050-0.02616.391-0.004-0.0040.0000.0000.0000.000
67A66GLN0-0.026-0.02017.3010.0050.0050.0000.0000.0000.000
68A67GLU-1-0.932-0.91618.6220.0060.0060.0000.0000.0000.000
69A68GLH0-0.105-0.09518.2390.0110.0110.0000.0000.0000.000
70A69TYR0-0.060-0.04812.5040.0160.0160.0000.0000.0000.000
71A70PRO00.0180.01315.368-0.002-0.0020.0000.0000.0000.000
72A71ASP-1-0.929-0.95811.3470.3550.3550.0000.0000.0000.000
73A72LEU0-0.0440.00112.0990.0390.0390.0000.0000.0000.000
74A73LYS10.8550.94010.995-0.343-0.3430.0000.0000.0000.000
75A74VAL0-0.012-0.02414.211-0.063-0.0630.0000.0000.0000.000
76A75ALA0-0.016-0.00415.8930.0270.0270.0000.0000.0000.000
77A76VAL0-0.001-0.01717.587-0.041-0.0410.0000.0000.0000.000
78A77ILE0-0.021-0.00817.5310.0230.0230.0000.0000.0000.000
79A78THR00.008-0.00721.390-0.024-0.0240.0000.0000.0000.000
80A79PRO0-0.001-0.00624.676-0.003-0.0030.0000.0000.0000.000
81A80PHE0-0.041-0.01126.0800.0060.0060.0000.0000.0000.000
82A81TYR00.0130.00529.2900.0000.0000.0000.0000.0000.000
83A82GLU-1-0.781-0.89931.549-0.068-0.0680.0000.0000.0000.000
84A83GLN0-0.069-0.04126.322-0.007-0.0070.0000.0000.0000.000
85A84GLU-1-0.788-0.89731.601-0.091-0.0910.0000.0000.0000.000
86A85LYS10.8150.90633.2590.0740.0740.0000.0000.0000.000
87A86ASN0-0.032-0.02636.7450.0070.0070.0000.0000.0000.000
88A87TRP0-0.059-0.01029.1400.0000.0000.0000.0000.0000.000
89A88LYS10.8840.93336.5500.0870.0870.0000.0000.0000.000
90A89GLU-1-0.732-0.87337.133-0.064-0.0640.0000.0000.0000.000
91A90PRO00.0060.00236.771-0.002-0.0020.0000.0000.0000.000
92A91ASN0-0.0190.00033.3480.0010.0010.0000.0000.0000.000
93A92LYS10.8140.92532.3620.0580.0580.0000.0000.0000.000
94A93GLU-1-0.870-0.93332.692-0.060-0.0600.0000.0000.0000.000
95A94GLN0-0.101-0.06327.9370.0050.0050.0000.0000.0000.000
96A95TYR0-0.027-0.03727.828-0.008-0.0080.0000.0000.0000.000
97A96GLU-1-0.917-0.96928.175-0.063-0.0630.0000.0000.0000.000
98A97ALA0-0.0130.00029.2890.0050.0050.0000.0000.0000.000
99A98VAL0-0.014-0.00223.2680.0010.0010.0000.0000.0000.000
100A99LEU0-0.0010.00124.4280.0000.0000.0000.0000.0000.000
101A100ALA0-0.057-0.01325.7150.0070.0070.0000.0000.0000.000
102A101GLN0-0.042-0.01623.1820.0170.0170.0000.0000.0000.000
103A102ALA0-0.0120.01020.9840.0010.0010.0000.0000.0000.000
104A103ASP-1-0.806-0.89017.4550.0140.0140.0000.0000.0000.000
105A104TYR0-0.043-0.03118.0030.0100.0100.0000.0000.0000.000
106A105GLH0-0.021-0.03019.958-0.028-0.0280.0000.0000.0000.000
107A106ALA0-0.027-0.00622.1560.0150.0150.0000.0000.0000.000
108A107SER0-0.017-0.01023.960-0.016-0.0160.0000.0000.0000.000
109A108LEU0-0.011-0.00620.8710.0070.0070.0000.0000.0000.000
110A109THR0-0.041-0.02724.9420.0100.0100.0000.0000.0000.000
111A110HIS00.0380.03827.089-0.002-0.0020.0000.0000.0000.000
112A111ARG10.8420.89631.1850.0840.0840.0000.0000.0000.000
113A112PRO00.0610.03932.551-0.006-0.0060.0000.0000.0000.000
114A113TYR0-0.026-0.00132.210-0.005-0.0050.0000.0000.0000.000
115A114GLU-1-0.877-0.91533.739-0.074-0.0740.0000.0000.0000.000
116A115SER00.000-0.01333.1190.0010.0010.0000.0000.0000.000
117A116PRO00.0280.00230.991-0.007-0.0070.0000.0000.0000.000
118A117LEU0-0.0110.00928.074-0.015-0.0150.0000.0000.0000.000
119A118GLN00.0860.03527.397-0.013-0.0130.0000.0000.0000.000
120A119PHE00.0340.01325.927-0.012-0.0120.0000.0000.0000.000
121A120LYS10.8980.96024.3870.1790.1790.0000.0000.0000.000
122A121GLN00.010-0.00223.049-0.019-0.0190.0000.0000.0000.000
123A122LYS10.8940.96120.2580.2760.2760.0000.0000.0000.000
124A123ASN0-0.003-0.01219.963-0.037-0.0370.0000.0000.0000.000
125A124GLN0-0.016-0.02017.485-0.026-0.0260.0000.0000.0000.000
126A125PHE00.008-0.00217.149-0.053-0.0530.0000.0000.0000.000
127A126PHE00.0650.01415.685-0.034-0.0340.0000.0000.0000.000
128A127ILE0-0.0220.03213.494-0.096-0.0960.0000.0000.0000.000
129A128ASP-1-0.872-0.92612.428-0.500-0.5000.0000.0000.0000.000
130A129LYS10.7760.88812.1730.4080.4080.0000.0000.0000.000
131A130SER00.0010.0049.8340.0550.0550.0000.0000.0000.000
132A131ASP-1-0.820-0.9104.674-2.875-2.727-0.001-0.017-0.1300.000
133A132GLY00.0320.0036.423-0.386-0.3860.0000.0000.0000.000
134A133LEU0-0.067-0.0198.8620.2300.2300.0000.0000.0000.000
135A134LEU00.0200.01312.4780.0080.0080.0000.0000.0000.000
136A135LEU0-0.036-0.02714.6560.0680.0680.0000.0000.0000.000
137A136LEU0-0.0100.01018.2860.0110.0110.0000.0000.0000.000
138A137TYR0-0.041-0.07621.2490.0180.0180.0000.0000.0000.000
139A138ASP-1-0.791-0.91022.498-0.211-0.2110.0000.0000.0000.000
140A139PRO0-0.005-0.01723.0330.0090.0090.0000.0000.0000.000
141A140GLU-1-0.919-0.93825.660-0.135-0.1350.0000.0000.0000.000
142A141LYS10.7920.91328.3560.1660.1660.0000.0000.0000.000
143A142GLU-1-0.783-0.83326.996-0.192-0.1920.0000.0000.0000.000
144A143GLY00.0340.01427.689-0.005-0.0050.0000.0000.0000.000
145A144SER0-0.050-0.06127.173-0.015-0.0150.0000.0000.0000.000
146A145PRO0-0.0070.00622.193-0.004-0.0040.0000.0000.0000.000
147A146LYS10.8840.93422.3710.1830.1830.0000.0000.0000.000
148A147TYR0-0.022-0.01323.184-0.013-0.0130.0000.0000.0000.000
149A148MET00.0050.01816.7670.0130.0130.0000.0000.0000.000
150A149LEU00.0460.03417.777-0.039-0.0390.0000.0000.0000.000
151A150GLY00.0060.00018.753-0.025-0.0250.0000.0000.0000.000
152A151THR0-0.075-0.04918.4140.0140.0140.0000.0000.0000.000
153A152ALA00.0260.01414.702-0.019-0.0190.0000.0000.0000.000
154A153GLU-1-0.807-0.88314.992-0.474-0.4740.0000.0000.0000.000
155A154LYS10.8060.88116.8790.2630.2630.0000.0000.0000.000
156A155ARG10.7890.8928.0691.2171.2170.0000.0000.0000.000
157A156ARG10.8580.91212.4630.4380.4380.0000.0000.0000.000
158A157GLU-1-0.911-0.95513.639-0.235-0.2350.0000.0000.0000.000
159A158GLN0-0.126-0.06014.9540.0790.0790.0000.0000.0000.000
160A159ASP-1-0.789-0.89210.175-0.888-0.8880.0000.0000.0000.000
161A160GLY0-0.0110.0099.835-0.036-0.0360.0000.0000.0000.000
162A161TYR0-0.055-0.0348.506-0.040-0.0400.0000.0000.0000.000
163A162PRO00.0190.0235.8110.3070.3070.0000.0000.0000.000
164A163ILE0-0.029-0.0199.102-0.032-0.0320.0000.0000.0000.000
165A164TYR00.0040.0037.668-0.002-0.0020.0000.0000.0000.000
166A165PHE00.011-0.00413.9310.0280.0280.0000.0000.0000.000
167A166ILE00.0080.01017.722-0.003-0.0030.0000.0000.0000.000
168A167THR0-0.014-0.03620.3400.0260.0260.0000.0000.0000.000
169A168MET0-0.018-0.03823.3480.0080.0080.0000.0000.0000.000
170A169ASP-1-0.807-0.86325.180-0.151-0.1510.0000.0000.0000.000
171A170ASP-1-0.780-0.85619.903-0.301-0.3010.0000.0000.0000.000
172A171LEU0-0.025-0.00623.1720.0090.0090.0000.0000.0000.000
173A172ARG10.7270.83325.6700.1540.1540.0000.0000.0000.000
174A173VAL00.0300.01623.5900.0110.0110.0000.0000.0000.000
175A174THR0-0.029-0.03323.2880.0050.0050.0000.0000.0000.000
176A175VAL0-0.069-0.04325.3050.0110.0110.0000.0000.0000.000
177A176GLU-1-0.899-0.93328.563-0.115-0.1150.0000.0000.0000.000
178A177GLU-1-1.058-1.02823.569-0.150-0.1500.0000.0000.0000.000