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: R8918

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 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 178
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2037866.176207
FMO2-HF: Nuclear repulsion 1966364.31196
FMO2-HF: Total energy -71501.864247
FMO2-MP2: Total energy -71715.407116


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.
-8.022-4.430.042-1.553-2.080.003
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 : -0.017 / q_NPA : -0.011
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].
3A2LYS10.9010.9473.258-3.317-0.4620.036-1.235-1.6550.005
4A3VAL0-0.007-0.0035.4020.0990.204-0.001-0.007-0.0970.000
5A4LEU00.0220.0178.739-0.381-0.3810.0000.0000.0000.000
6A5ALA0-0.008-0.00310.5420.2150.2150.0000.0000.0000.000
7A6ILE00.0200.01113.853-0.036-0.0360.0000.0000.0000.000
8A7THR0-0.039-0.06016.5410.0610.0610.0000.0000.0000.000
9A8GLY00.0480.00219.891-0.019-0.0190.0000.0000.0000.000
10A9TYR0-0.082-0.03922.6990.0130.0130.0000.0000.0000.000
11A10LYS10.8850.93926.4750.1850.1850.0000.0000.0000.000
12A11PRO00.0390.00729.0570.0020.0020.0000.0000.0000.000
13A12PHE00.001-0.01031.4960.0030.0030.0000.0000.0000.000
14A13GLU-1-0.811-0.86028.964-0.173-0.1730.0000.0000.0000.000
15A14LEU00.0410.01927.308-0.001-0.0010.0000.0000.0000.000
16A15GLY0-0.0120.01231.9460.0050.0050.0000.0000.0000.000
17A16ILE0-0.0050.01630.1960.0060.0060.0000.0000.0000.000
18A17PHE0-0.013-0.02833.913-0.002-0.0020.0000.0000.0000.000
19A18LYS10.9120.95835.7150.0770.0770.0000.0000.0000.000
20A19GLN00.0460.01729.237-0.009-0.0090.0000.0000.0000.000
21A20ASP-1-0.905-0.94833.092-0.074-0.0740.0000.0000.0000.000
22A21ASP-1-0.832-0.94132.918-0.099-0.0990.0000.0000.0000.000
23A22LYS10.8530.92732.3540.0730.0730.0000.0000.0000.000
24A23ALA00.0860.03630.692-0.003-0.0030.0000.0000.0000.000
25A24LEU00.0170.02127.554-0.011-0.0110.0000.0000.0000.000
26A25TYR00.0080.01927.512-0.011-0.0110.0000.0000.0000.000
27A26TYR00.0370.01026.647-0.004-0.0040.0000.0000.0000.000
28A27ILE0-0.016-0.00124.109-0.014-0.0140.0000.0000.0000.000
29A28LYS10.8660.92522.9980.1110.1110.0000.0000.0000.000
30A29LYS10.9230.97521.7910.1120.1120.0000.0000.0000.000
31A30ALA00.0350.02221.088-0.011-0.0110.0000.0000.0000.000
32A31ILE0-0.026-0.02417.851-0.032-0.0320.0000.0000.0000.000
33A32LYS10.8120.89117.0290.0970.0970.0000.0000.0000.000
34A33ASN00.0180.00516.6480.0010.0010.0000.0000.0000.000
35A34ARG10.8760.94613.3320.4670.4670.0000.0000.0000.000
36A35LEU00.0100.00112.641-0.077-0.0770.0000.0000.0000.000
37A36ILE00.0230.01711.814-0.021-0.0210.0000.0000.0000.000
38A37ALA00.0160.01711.8010.0070.0070.0000.0000.0000.000
39A38PHE0-0.007-0.0198.168-0.041-0.0410.0000.0000.0000.000
40A39LEU0-0.039-0.0157.152-0.097-0.0970.0000.0000.0000.000
41A40ASP-1-0.899-0.9398.296-0.068-0.0680.0000.0000.0000.000
42A41GLU-1-1.034-1.0115.088-1.243-1.2430.0000.0000.0000.000
43A42GLY0-0.050-0.0263.412-2.736-2.1130.008-0.308-0.323-0.002
44A43LEU0-0.060-0.0254.8011.1511.160-0.001-0.003-0.0050.000
45A44GLU-1-0.875-0.9226.9741.5091.5090.0000.0000.0000.000
46A45TRP0-0.012-0.0188.911-0.089-0.0890.0000.0000.0000.000
47A46ILE00.0280.02910.750-0.161-0.1610.0000.0000.0000.000
48A47LEU0-0.017-0.00813.5250.0640.0640.0000.0000.0000.000
49A48ILE0-0.013-0.00115.812-0.037-0.0370.0000.0000.0000.000
50A49SER0-0.062-0.06619.1870.0120.0120.0000.0000.0000.000
51A50GLY00.0570.02922.3410.0240.0240.0000.0000.0000.000
52A51GLN0-0.0160.00624.3550.0240.0240.0000.0000.0000.000
53A52LEU00.0360.00725.938-0.002-0.0020.0000.0000.0000.000
54A53GLY00.002-0.00927.439-0.009-0.0090.0000.0000.0000.000
55A54VAL00.0140.01021.2800.0020.0020.0000.0000.0000.000
56A55GLU-1-0.745-0.82120.846-0.277-0.2770.0000.0000.0000.000
57A56LEU00.0180.01721.903-0.002-0.0020.0000.0000.0000.000
58A57TRP0-0.012-0.02623.8850.0030.0030.0000.0000.0000.000
59A58ALA00.0210.00818.6250.0050.0050.0000.0000.0000.000
60A59ALA00.0050.01219.350-0.002-0.0020.0000.0000.0000.000
61A60GLU-1-0.752-0.87320.649-0.114-0.1140.0000.0000.0000.000
62A61ALA0-0.035-0.01820.0110.0120.0120.0000.0000.0000.000
63A62ALA00.0630.01616.9160.0080.0080.0000.0000.0000.000
64A63TYR0-0.021-0.03618.2660.0140.0140.0000.0000.0000.000
65A64ASP-1-0.871-0.90121.122-0.088-0.0880.0000.0000.0000.000
66A65LEU0-0.050-0.02616.0710.0010.0010.0000.0000.0000.000
67A66GLN0-0.013-0.02017.3520.0060.0060.0000.0000.0000.000
68A67GLU-1-0.914-0.90718.639-0.001-0.0010.0000.0000.0000.000
69A68GLH0-0.109-0.09218.3810.0100.0100.0000.0000.0000.000
70A69TYR0-0.051-0.02112.7030.0130.0130.0000.0000.0000.000
71A70PRO00.0200.01015.476-0.004-0.0040.0000.0000.0000.000
72A71ASP-1-0.921-0.95011.9750.2880.2880.0000.0000.0000.000
73A72LEU0-0.065-0.01312.4090.0270.0270.0000.0000.0000.000
74A73LYS10.8620.94011.295-0.237-0.2370.0000.0000.0000.000
75A74VAL0-0.004-0.01914.360-0.060-0.0600.0000.0000.0000.000
76A75ALA0-0.012-0.00516.3590.0280.0280.0000.0000.0000.000
77A76VAL00.003-0.01317.957-0.039-0.0390.0000.0000.0000.000
78A77ILE0-0.032-0.01017.9750.0210.0210.0000.0000.0000.000
79A78THR00.0210.00121.763-0.021-0.0210.0000.0000.0000.000
80A79PRO0-0.003-0.01024.918-0.002-0.0020.0000.0000.0000.000
81A80PHE0-0.046-0.01925.9980.0050.0050.0000.0000.0000.000
82A81TYR0-0.008-0.01729.312-0.001-0.0010.0000.0000.0000.000
83A82GLU-1-0.792-0.89531.877-0.075-0.0750.0000.0000.0000.000
84A83GLN0-0.069-0.04026.467-0.005-0.0050.0000.0000.0000.000
85A84GLU-1-0.799-0.90731.860-0.099-0.0990.0000.0000.0000.000
86A85LYS10.8340.91333.4720.0860.0860.0000.0000.0000.000
87A86ASN0-0.023-0.02836.8790.0070.0070.0000.0000.0000.000
88A87TRP0-0.065-0.01029.1280.0020.0020.0000.0000.0000.000
89A88LYS10.9050.94236.4770.0910.0910.0000.0000.0000.000
90A89GLU-1-0.820-0.92537.274-0.067-0.0670.0000.0000.0000.000
91A90PRO00.002-0.00737.076-0.002-0.0020.0000.0000.0000.000
92A91ASN0-0.0050.00633.5280.0000.0000.0000.0000.0000.000
93A92LYS10.8930.96932.6170.0660.0660.0000.0000.0000.000
94A93GLU-1-0.868-0.92233.043-0.066-0.0660.0000.0000.0000.000
95A94GLN0-0.111-0.07128.0190.0040.0040.0000.0000.0000.000
96A95TYR0-0.032-0.03827.897-0.010-0.0100.0000.0000.0000.000
97A96GLU-1-0.918-0.96728.398-0.073-0.0730.0000.0000.0000.000
98A97ALA0-0.0140.00529.3570.0030.0030.0000.0000.0000.000
99A98VAL0-0.010-0.00623.2910.0010.0010.0000.0000.0000.000
100A99LEU0-0.010-0.00924.574-0.002-0.0020.0000.0000.0000.000
101A100ALA0-0.055-0.00325.9210.0060.0060.0000.0000.0000.000
102A101GLN0-0.031-0.01323.1680.0170.0170.0000.0000.0000.000
103A102ALA0-0.0350.00421.1480.0030.0030.0000.0000.0000.000
104A103ASP-1-0.800-0.88217.836-0.013-0.0130.0000.0000.0000.000
105A104TYR0-0.056-0.04118.5330.0040.0040.0000.0000.0000.000
106A105GLH00.001-0.02720.464-0.023-0.0230.0000.0000.0000.000
107A106ALA0-0.036-0.00422.6210.0150.0150.0000.0000.0000.000
108A107SER0-0.015-0.01324.410-0.016-0.0160.0000.0000.0000.000
109A108LEU0-0.013-0.01120.8810.0080.0080.0000.0000.0000.000
110A109THR0-0.029-0.01025.0350.0110.0110.0000.0000.0000.000
111A110HIS00.0380.03327.792-0.002-0.0020.0000.0000.0000.000
112A111ARG10.8540.90231.4970.0920.0920.0000.0000.0000.000
113A112PRO00.0580.04032.504-0.008-0.0080.0000.0000.0000.000
114A113TYR0-0.031-0.01032.171-0.003-0.0030.0000.0000.0000.000
115A114GLU-1-0.878-0.91433.541-0.082-0.0820.0000.0000.0000.000
116A115SER00.009-0.00733.2790.0020.0020.0000.0000.0000.000
117A116PRO00.026-0.00131.262-0.007-0.0070.0000.0000.0000.000
118A117LEU0-0.0160.00028.317-0.014-0.0140.0000.0000.0000.000
119A118GLN00.0970.04727.611-0.012-0.0120.0000.0000.0000.000
120A119PHE00.0280.01726.070-0.012-0.0120.0000.0000.0000.000
121A120LYS10.9120.96324.3720.1760.1760.0000.0000.0000.000
122A121GLN00.010-0.00423.173-0.019-0.0190.0000.0000.0000.000
123A122LYS10.9060.97920.5470.2760.2760.0000.0000.0000.000
124A123ASN0-0.001-0.01819.974-0.036-0.0360.0000.0000.0000.000
125A124GLN0-0.027-0.01517.341-0.018-0.0180.0000.0000.0000.000
126A125PHE00.0140.00517.209-0.045-0.0450.0000.0000.0000.000
127A126PHE00.0610.00715.793-0.044-0.0440.0000.0000.0000.000
128A127ILE0-0.0290.02113.544-0.089-0.0890.0000.0000.0000.000
129A128ASP-1-0.839-0.90112.369-0.540-0.5400.0000.0000.0000.000
130A129LYS10.7730.87511.9150.3350.3350.0000.0000.0000.000
131A130SER0-0.0190.00910.1180.0050.0050.0000.0000.0000.000
132A131ASP-1-0.805-0.9024.971-2.778-2.7780.0000.0000.0000.000
133A132GLY00.035-0.0016.526-0.377-0.3770.0000.0000.0000.000
134A133LEU0-0.060-0.0138.9680.2100.2100.0000.0000.0000.000
135A134LEU00.0160.01212.6400.0040.0040.0000.0000.0000.000
136A135LEU0-0.035-0.03314.5500.0660.0660.0000.0000.0000.000
137A136LEU0-0.0150.01218.3160.0110.0110.0000.0000.0000.000
138A137TYR0-0.009-0.03921.2620.0210.0210.0000.0000.0000.000
139A138ASP-1-0.779-0.91022.807-0.201-0.2010.0000.0000.0000.000
140A139PRO0-0.019-0.02423.0380.0080.0080.0000.0000.0000.000
141A140GLU-1-0.910-0.93025.731-0.128-0.1280.0000.0000.0000.000
142A141LYS10.7950.91428.8670.1580.1580.0000.0000.0000.000
143A142GLU-1-0.825-0.88827.014-0.176-0.1760.0000.0000.0000.000
144A143GLY00.0340.02027.985-0.002-0.0020.0000.0000.0000.000
145A144SER0-0.091-0.09927.424-0.014-0.0140.0000.0000.0000.000
146A145PRO00.0000.00922.232-0.005-0.0050.0000.0000.0000.000
147A146LYS10.8770.93622.2730.1750.1750.0000.0000.0000.000
148A147TYR0-0.039-0.02423.028-0.013-0.0130.0000.0000.0000.000
149A148MET00.0060.00116.8610.0120.0120.0000.0000.0000.000
150A149LEU00.0580.04017.691-0.037-0.0370.0000.0000.0000.000
151A150GLY00.0200.01918.504-0.023-0.0230.0000.0000.0000.000
152A151THR0-0.078-0.04318.0280.0130.0130.0000.0000.0000.000
153A152ALA00.0340.01814.534-0.021-0.0210.0000.0000.0000.000
154A153GLU-1-0.820-0.90114.788-0.446-0.4460.0000.0000.0000.000
155A154LYS10.9010.95516.8250.2600.2600.0000.0000.0000.000
156A155ARG10.8020.8958.1911.2171.2170.0000.0000.0000.000
157A156ARG10.8500.92312.2050.3980.3980.0000.0000.0000.000
158A157GLU-1-1.018-1.02713.280-0.238-0.2380.0000.0000.0000.000
159A158GLN0-0.084-0.02514.6750.0650.0650.0000.0000.0000.000
160A159ASP-1-0.791-0.90310.096-0.863-0.8630.0000.0000.0000.000
161A160GLY0-0.0170.0029.292-0.038-0.0380.0000.0000.0000.000
162A161TYR0-0.051-0.0388.182-0.082-0.0820.0000.0000.0000.000
163A162PRO0-0.0020.0126.1780.3010.3010.0000.0000.0000.000
164A163ILE0-0.024-0.0189.337-0.047-0.0470.0000.0000.0000.000
165A164TYR0-0.008-0.0077.6710.0180.0180.0000.0000.0000.000
166A165PHE00.017-0.00314.0400.0260.0260.0000.0000.0000.000
167A166ILE0-0.0130.00017.6990.0010.0010.0000.0000.0000.000
168A167THR0-0.024-0.04520.0950.0230.0230.0000.0000.0000.000
169A168MET0-0.031-0.04223.2500.0080.0080.0000.0000.0000.000
170A169ASP-1-0.832-0.89125.326-0.147-0.1470.0000.0000.0000.000
171A170ASP-1-0.786-0.86420.622-0.272-0.2720.0000.0000.0000.000
172A171LEU0-0.027-0.01423.4720.0080.0080.0000.0000.0000.000
173A172ARG10.7570.86425.7400.1490.1490.0000.0000.0000.000
174A173VAL00.0350.01923.9490.0110.0110.0000.0000.0000.000
175A174THR0-0.054-0.03923.6420.0020.0020.0000.0000.0000.000
176A175VAL0-0.073-0.04225.5020.0100.0100.0000.0000.0000.000
177A176GLU-1-0.935-0.95128.698-0.110-0.1100.0000.0000.0000.000
178A177GLU-1-1.043-1.00623.973-0.142-0.1420.0000.0000.0000.000