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: ZYLGN

Calculation Name: 2CXH-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2CXH

Chain ID: A

ChEMBL ID:

UniProt ID: Q9YC08

Base Structure: X-ray

Registration Date: 2023-03-13

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 180
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1892145.595957
FMO2-HF: Nuclear repulsion 1824236.694794
FMO2-HF: Total energy -67908.901163
FMO2-MP2: Total energy -68110.895941


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:13:GLY)


Summations of interaction energy for fragment #1(A:13:GLY)
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.
-1.7971.6061.608-2.477-2.532-0.007
Interaction energy analysis for fragmet #1(A:13:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.035 / q_NPA : 0.020
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].
3A15ARG10.8390.9233.7100.9613.200-0.008-1.275-0.9550.004
4A16ILE00.0060.0015.817-0.450-0.4500.0000.0000.0000.000
5A17LEU00.0030.0248.9640.3510.3510.0000.0000.0000.000
6A18VAL00.002-0.00510.7740.0120.0120.0000.0000.0000.000
7A19THR00.001-0.02614.4210.1150.1150.0000.0000.0000.000
8A20THR0-0.032-0.02817.202-0.008-0.0080.0000.0000.0000.000
9A21SER00.0590.03020.704-0.011-0.0110.0000.0000.0000.000
10A22ARG10.9150.96522.9500.1610.1610.0000.0000.0000.000
11A23ARG10.9490.97424.9930.0990.0990.0000.0000.0000.000
12A24PRO00.0120.04623.6030.0060.0060.0000.0000.0000.000
13A25SER00.0800.00226.6160.0190.0190.0000.0000.0000.000
14A26PRO0-0.018-0.02327.669-0.014-0.0140.0000.0000.0000.000
15A27ARG10.7950.86227.7380.1540.1540.0000.0000.0000.000
16A28ILE00.0160.02123.299-0.014-0.0140.0000.0000.0000.000
17A29ARG10.9260.95623.1120.1040.1040.0000.0000.0000.000
18A30SER0-0.022-0.00222.966-0.004-0.0040.0000.0000.0000.000
19A31PHE00.0550.01922.3630.0000.0000.0000.0000.0000.000
20A32VAL00.0550.03117.829-0.015-0.0150.0000.0000.0000.000
21A33LYS10.9290.97418.7500.0970.0970.0000.0000.0000.000
22A34ASP-1-0.733-0.83619.867-0.194-0.1940.0000.0000.0000.000
23A35LEU00.0160.02117.4160.0030.0030.0000.0000.0000.000
24A36SER0-0.002-0.02415.257-0.056-0.0560.0000.0000.0000.000
25A37ALA0-0.069-0.01815.659-0.005-0.0050.0000.0000.0000.000
26A38THR0-0.009-0.02717.8600.0440.0440.0000.0000.0000.000
27A39ILE00.0240.00913.0180.0210.0210.0000.0000.0000.000
28A40PRO00.0160.00712.796-0.024-0.0240.0000.0000.0000.000
29A41GLY00.0420.0289.163-0.136-0.1360.0000.0000.0000.000
30A42ALA0-0.024-0.0018.764-0.201-0.2010.0000.0000.0000.000
31A43PHE0-0.021-0.0167.5120.2490.2490.0000.0000.0000.000
32A44ARG10.9440.98812.5160.0990.0990.0000.0000.0000.000
33A45PHE0-0.0010.00113.6180.0350.0350.0000.0000.0000.000
34A46THR0-0.010-0.01015.742-0.025-0.0250.0000.0000.0000.000
35A47ARG10.8050.90518.7810.3140.3140.0000.0000.0000.000
36A48GLY00.0320.00819.8460.0080.0080.0000.0000.0000.000
37A49HIS0-0.030-0.03222.174-0.016-0.0160.0000.0000.0000.000
38A50TYR00.0270.01716.878-0.007-0.0070.0000.0000.0000.000
39A51SER0-0.035-0.05819.114-0.042-0.0420.0000.0000.0000.000
40A52MET0-0.013-0.01315.3930.0180.0180.0000.0000.0000.000
41A53GLU-1-0.784-0.86914.662-0.212-0.2120.0000.0000.0000.000
42A54GLU-1-0.804-0.86714.309-0.113-0.1130.0000.0000.0000.000
43A55LEU0-0.027-0.02613.5270.0230.0230.0000.0000.0000.000
44A56ALA00.0490.03210.223-0.097-0.0970.0000.0000.0000.000
45A57ARG10.8070.8949.2160.0400.0400.0000.0000.0000.000
46A58GLU-1-0.753-0.84410.1670.1600.1600.0000.0000.0000.000
47A59ALA0-0.015-0.0097.7450.1280.1280.0000.0000.0000.000
48A60ILE00.0370.0255.326-0.106-0.1060.0000.0000.0000.000
49A61ILE0-0.030-0.0106.1760.7900.7900.0000.0000.0000.000
50A62ARG10.7510.8577.2490.1660.1660.0000.0000.0000.000
51A63GLY00.0550.0333.052-0.1430.0650.109-0.076-0.2400.001
52A64ALA0-0.068-0.0382.649-3.279-2.8621.507-1.009-0.915-0.012
53A65ASP-1-0.686-0.8213.630-4.212-3.7490.001-0.111-0.3540.000
54A66ARG10.7950.8955.0783.4853.561-0.001-0.006-0.0680.000
55A67ILE00.0100.0118.6430.1570.1570.0000.0000.0000.000
56A68VAL00.0050.00411.6430.0520.0520.0000.0000.0000.000
57A69VAL0-0.032-0.02014.9810.0730.0730.0000.0000.0000.000
58A70VAL0-0.0030.00218.2820.0200.0200.0000.0000.0000.000
59A71GLY0-0.004-0.01621.3350.0220.0220.0000.0000.0000.000
60A72GLU-1-0.769-0.88724.500-0.166-0.1660.0000.0000.0000.000
61A73ARG10.8730.94228.1750.1930.1930.0000.0000.0000.000
62A74ARG10.9610.98031.3130.1350.1350.0000.0000.0000.000
63A75GLY00.0780.05131.7210.0060.0060.0000.0000.0000.000
64A76ASN0-0.062-0.03530.183-0.002-0.0020.0000.0000.0000.000
65A77PRO0-0.002-0.01025.310-0.003-0.0030.0000.0000.0000.000
66A78GLY00.007-0.00626.8940.0100.0100.0000.0000.0000.000
67A79ILE0-0.075-0.03223.5340.0050.0050.0000.0000.0000.000
68A80ILE00.0240.01818.9200.0070.0070.0000.0000.0000.000
69A81ARG10.9330.97919.0430.3490.3490.0000.0000.0000.000
70A82VAL00.0320.01513.360-0.004-0.0040.0000.0000.0000.000
71A83TYR0-0.025-0.02313.0630.1120.1120.0000.0000.0000.000
72A84ALA00.0740.0489.902-0.208-0.2080.0000.0000.0000.000
73A85VAL0-0.080-0.0516.7820.3230.3230.0000.0000.0000.000
74A86GLU-1-0.892-0.9456.477-1.472-1.4720.0000.0000.0000.000
75A87GLY00.0600.0408.5840.2380.2380.0000.0000.0000.000
76A88PRO0-0.047-0.02410.070-0.096-0.0960.0000.0000.0000.000
77A89GLU-1-0.881-0.93611.964-0.221-0.2210.0000.0000.0000.000
78A90ARG10.8580.89413.6220.2600.2600.0000.0000.0000.000
79A91PRO00.0090.03411.765-0.006-0.0060.0000.0000.0000.000
80A92ASP-1-0.772-0.88013.644-0.362-0.3620.0000.0000.0000.000
81A93ASN0-0.099-0.07614.682-0.140-0.1400.0000.0000.0000.000
82A94ILE00.0780.04612.2300.0580.0580.0000.0000.0000.000
83A95VAL00.0090.01016.1710.0550.0550.0000.0000.0000.000
84A96SER0-0.059-0.03818.2870.0120.0120.0000.0000.0000.000
85A97PHE00.0440.01718.5850.0320.0320.0000.0000.0000.000
86A98ILE0-0.014-0.01023.5590.0070.0070.0000.0000.0000.000
87A99VAL00.0420.01924.4580.0010.0010.0000.0000.0000.000
88A100LYS10.9610.99727.1230.2250.2250.0000.0000.0000.000
89A101GLY0-0.020-0.00329.3400.0210.0210.0000.0000.0000.000
90A102VAL0-0.0050.00725.431-0.016-0.0160.0000.0000.0000.000
91A103SER0-0.0240.00728.6040.0180.0180.0000.0000.0000.000
92A104LEU00.011-0.01225.488-0.013-0.0130.0000.0000.0000.000
93A105SER00.0120.00325.5840.0180.0180.0000.0000.0000.000
94A106ARG10.8100.85825.0710.1670.1670.0000.0000.0000.000
95A107GLU-1-0.785-0.84430.247-0.142-0.1420.0000.0000.0000.000
96A108ARG10.8880.94129.5900.1540.1540.0000.0000.0000.000
97A109ARG10.8880.96732.2230.0990.0990.0000.0000.0000.000
98A110TRP00.0530.02227.2090.0120.0120.0000.0000.0000.000
99A111GLY00.0380.01827.5550.0000.0000.0000.0000.0000.000
100A112LEU0-0.019-0.02021.658-0.016-0.0160.0000.0000.0000.000
101A113PRO00.0260.03219.2750.0230.0230.0000.0000.0000.000
102A114SER00.0220.02020.5600.0090.0090.0000.0000.0000.000
103A115LEU0-0.024-0.00415.2610.0140.0140.0000.0000.0000.000
104A116ARG10.7910.87917.0970.0650.0650.0000.0000.0000.000
105A117GLY00.0030.00313.1260.0490.0490.0000.0000.0000.000
106A118GLY0-0.0020.00510.9860.0540.0540.0000.0000.0000.000
107A119GLU-1-0.785-0.88112.045-0.206-0.2060.0000.0000.0000.000
108A120VAL0-0.012-0.01611.358-0.101-0.1010.0000.0000.0000.000
109A121LEU00.002-0.00213.2920.0870.0870.0000.0000.0000.000
110A122VAL0-0.0100.00415.345-0.037-0.0370.0000.0000.0000.000
111A123ALA0-0.003-0.00618.2820.0100.0100.0000.0000.0000.000
112A124ARG10.8790.93620.5150.2220.2220.0000.0000.0000.000
113A125PRO0-0.0100.00424.2020.0100.0100.0000.0000.0000.000
114A126LEU0-0.013-0.02126.9520.0110.0110.0000.0000.0000.000
115A127ASP-1-0.775-0.84430.351-0.192-0.1920.0000.0000.0000.000
116A128SER00.018-0.00330.430-0.012-0.0120.0000.0000.0000.000
117A129GLY00.0290.02431.8800.0040.0040.0000.0000.0000.000
118A130VAL0-0.016-0.01228.679-0.017-0.0170.0000.0000.0000.000
119A131ALA00.001-0.01527.264-0.027-0.0270.0000.0000.0000.000
120A132VAL00.0280.01825.592-0.026-0.0260.0000.0000.0000.000
121A133GLU-1-0.746-0.85524.284-0.296-0.2960.0000.0000.0000.000
122A134PHE0-0.044-0.03522.991-0.042-0.0420.0000.0000.0000.000
123A135ALA0-0.0060.00421.233-0.049-0.0490.0000.0000.0000.000
124A136ASP-1-0.839-0.92419.654-0.450-0.4500.0000.0000.0000.000
125A137ALA0-0.038-0.03118.429-0.075-0.0750.0000.0000.0000.000
126A138PHE0-0.027-0.03417.120-0.081-0.0810.0000.0000.0000.000
127A139VAL0-0.0240.00914.789-0.106-0.1060.0000.0000.0000.000
128A140ILE00.0020.01013.505-0.176-0.1760.0000.0000.0000.000
129A141ALA0-0.028-0.02012.753-0.207-0.2070.0000.0000.0000.000
130A142PHE0-0.058-0.06011.761-0.121-0.1210.0000.0000.0000.000
131A143HIS0-0.020-0.0066.5650.5620.5620.0000.0000.0000.000
132A144ALA0-0.056-0.01011.2950.1220.1220.0000.0000.0000.000
133A145ARG10.9780.97911.7370.5050.5050.0000.0000.0000.000
134A146LEU00.0590.02516.6280.0350.0350.0000.0000.0000.000
135A147LYS10.8400.92519.2370.2390.2390.0000.0000.0000.000
136A148PRO0-0.001-0.00918.878-0.036-0.0360.0000.0000.0000.000
137A149PRO0-0.035-0.01616.4410.0070.0070.0000.0000.0000.000
138A150GLU-1-0.829-0.91619.151-0.160-0.1600.0000.0000.0000.000
139A151ALA0-0.0070.00320.6390.0170.0170.0000.0000.0000.000
140A152ALA0-0.0090.01316.1460.0110.0110.0000.0000.0000.000
141A153GLY00.0520.02017.862-0.018-0.0180.0000.0000.0000.000
142A154TYR0-0.007-0.02116.579-0.047-0.0470.0000.0000.0000.000
143A155VAL0-0.031-0.00217.4110.0410.0410.0000.0000.0000.000
144A156GLU-1-0.828-0.92418.648-0.273-0.2730.0000.0000.0000.000
145A157ALA0-0.020-0.01320.1800.0240.0240.0000.0000.0000.000
146A158VAL00.0080.00921.879-0.006-0.0060.0000.0000.0000.000
147A159ILE0-0.041-0.02322.008-0.004-0.0040.0000.0000.0000.000
148A160GLU-1-0.886-0.94126.551-0.162-0.1620.0000.0000.0000.000
149A161SER0-0.047-0.07230.215-0.012-0.0120.0000.0000.0000.000
150A162LEU0-0.060-0.02331.9980.0110.0110.0000.0000.0000.000
151A163ASP-1-0.759-0.86333.713-0.173-0.1730.0000.0000.0000.000
152A164ALA00.0420.01933.565-0.010-0.0100.0000.0000.0000.000
153A165ARG10.7980.88529.9530.2120.2120.0000.0000.0000.000
154A166THR0-0.071-0.06329.900-0.025-0.0250.0000.0000.0000.000
155A167VAL00.0410.03426.1080.0080.0080.0000.0000.0000.000
156A168ALA00.0160.00429.252-0.001-0.0010.0000.0000.0000.000
157A169VAL00.007-0.00822.708-0.014-0.0140.0000.0000.0000.000
158A170THR0-0.032-0.02325.9380.0180.0180.0000.0000.0000.000
159A171PHE00.0280.02019.007-0.009-0.0090.0000.0000.0000.000
160A172ARG10.9070.94822.9220.1990.1990.0000.0000.0000.000
161A173TYR00.010-0.01719.448-0.026-0.0260.0000.0000.0000.000
162A174GLY00.0270.02123.4830.0140.0140.0000.0000.0000.000
163A175GLY00.0390.03125.7670.0120.0120.0000.0000.0000.000
164A176ALA00.0060.01727.6370.0020.0020.0000.0000.0000.000
165A177PRO0-0.022-0.01226.821-0.015-0.0150.0000.0000.0000.000
166A178VAL0-0.017-0.01522.7030.0130.0130.0000.0000.0000.000
167A179GLY00.0430.01423.024-0.018-0.0180.0000.0000.0000.000
168A180PRO0-0.100-0.04022.1540.0200.0200.0000.0000.0000.000
169A181MET00.0170.02424.561-0.015-0.0150.0000.0000.0000.000
170A182LEU0-0.025-0.02822.0710.0060.0060.0000.0000.0000.000
171A183ARG10.9330.96426.8520.1850.1850.0000.0000.0000.000
172A184LEU0-0.021-0.00922.829-0.001-0.0010.0000.0000.0000.000
173A185GLY00.0290.00527.1660.0170.0170.0000.0000.0000.000
174A186LYS10.8200.89726.5670.2360.2360.0000.0000.0000.000
175A187PRO0-0.055-0.02324.5870.0240.0240.0000.0000.0000.000
176A188ALA00.0130.01527.8610.0050.0050.0000.0000.0000.000
177A189GLU-1-0.828-0.91924.345-0.314-0.3140.0000.0000.0000.000
178A190MET0-0.054-0.00122.359-0.012-0.0120.0000.0000.0000.000
179A191VAL00.0180.00218.675-0.039-0.0390.0000.0000.0000.000
180A192LYS10.8410.93618.1070.4590.4590.0000.0000.0000.000