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: 667RZ

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 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 180
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1891045.306912
FMO2-HF: Nuclear repulsion 1823136.843579
FMO2-HF: Total energy -67908.463333
FMO2-MP2: Total energy -68110.453152


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.
-1.48-0.6216.586-3.987-3.459-0.015
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 : 0.014 / q_NPA : 0.005
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].
3A15ARG10.8420.9253.553-0.1772.450-0.016-1.494-1.1180.004
4A16ILE00.006-0.0065.667-0.427-0.4270.0000.0000.0000.000
5A17LEU00.0000.0208.7160.3120.3120.0000.0000.0000.000
6A18VAL00.0190.00710.519-0.029-0.0290.0000.0000.0000.000
7A19THR0-0.004-0.03814.1590.1020.1020.0000.0000.0000.000
8A20THR0-0.021-0.01516.933-0.015-0.0150.0000.0000.0000.000
9A21SER00.0550.03320.410-0.006-0.0060.0000.0000.0000.000
10A22ARG10.9150.94922.5730.1020.1020.0000.0000.0000.000
11A23ARG10.9410.97824.6470.0530.0530.0000.0000.0000.000
12A24PRO00.0100.03323.4750.0010.0010.0000.0000.0000.000
13A25SER00.050-0.01926.3170.0190.0190.0000.0000.0000.000
14A26PRO0-0.003-0.02527.399-0.009-0.0090.0000.0000.0000.000
15A27ARG10.7960.86327.4680.1220.1220.0000.0000.0000.000
16A28ILE00.0070.02123.144-0.012-0.0120.0000.0000.0000.000
17A29ARG10.9420.97922.8070.0560.0560.0000.0000.0000.000
18A30SER0-0.038-0.01122.712-0.001-0.0010.0000.0000.0000.000
19A31PHE00.0620.02222.1510.0010.0010.0000.0000.0000.000
20A32VAL00.0610.04017.599-0.013-0.0130.0000.0000.0000.000
21A33LYS10.9220.97518.6210.0430.0430.0000.0000.0000.000
22A34ASP-1-0.747-0.84419.777-0.146-0.1460.0000.0000.0000.000
23A35LEU00.0160.00717.4690.0000.0000.0000.0000.0000.000
24A36SER0-0.024-0.03715.057-0.046-0.0460.0000.0000.0000.000
25A37ALA0-0.051-0.00515.345-0.002-0.0020.0000.0000.0000.000
26A38THR0-0.023-0.02717.9020.0310.0310.0000.0000.0000.000
27A39ILE00.0200.01013.0000.0090.0090.0000.0000.0000.000
28A40PRO00.0260.01712.4410.0010.0010.0000.0000.0000.000
29A41GLY00.0410.0279.032-0.151-0.1510.0000.0000.0000.000
30A42ALA0-0.0240.0078.718-0.121-0.1210.0000.0000.0000.000
31A43PHE0-0.017-0.0107.4000.2160.2160.0000.0000.0000.000
32A44ARG10.9400.98012.5080.0070.0070.0000.0000.0000.000
33A45PHE00.0340.01413.3460.0450.0450.0000.0000.0000.000
34A46THR0-0.015-0.00515.459-0.036-0.0360.0000.0000.0000.000
35A47ARG10.8220.92918.1870.2100.2100.0000.0000.0000.000
36A48GLY00.0440.01519.5330.0120.0120.0000.0000.0000.000
37A49HIS0-0.017-0.03422.178-0.027-0.0270.0000.0000.0000.000
38A50TYR00.0260.01116.649-0.018-0.0180.0000.0000.0000.000
39A51SER0-0.050-0.06319.696-0.043-0.0430.0000.0000.0000.000
40A52MET0-0.022-0.02616.0760.0240.0240.0000.0000.0000.000
41A53GLU-1-0.785-0.87215.371-0.130-0.1300.0000.0000.0000.000
42A54GLU-1-0.797-0.86714.793-0.019-0.0190.0000.0000.0000.000
43A55LEU0-0.043-0.03113.7380.0390.0390.0000.0000.0000.000
44A56ALA00.0650.03710.867-0.037-0.0370.0000.0000.0000.000
45A57ARG10.8490.9129.7670.0040.0040.0000.0000.0000.000
46A58GLU-1-0.798-0.86210.4440.3760.3760.0000.0000.0000.000
47A59ALA0-0.021-0.0097.7310.1540.1540.0000.0000.0000.000
48A60ILE00.0460.0365.7350.1020.1020.0000.0000.0000.000
49A61ILE0-0.0170.0035.8830.9390.9390.0000.0000.0000.000
50A62ARG10.7530.8606.791-0.034-0.0340.0000.0000.0000.000
51A63GLY00.0570.0282.7530.0970.1980.419-0.117-0.4030.002
52A64ALA0-0.085-0.0432.249-1.387-3.5756.184-2.320-1.676-0.021
53A65ASP-1-0.678-0.8183.692-4.447-4.128-0.001-0.056-0.2620.000
54A66ARG10.8120.9195.4823.1113.1110.0000.0000.0000.000
55A67ILE0-0.0010.0099.1050.1970.1970.0000.0000.0000.000
56A68VAL0-0.0030.00111.7930.0360.0360.0000.0000.0000.000
57A69VAL0-0.030-0.01414.8100.0810.0810.0000.0000.0000.000
58A70VAL0-0.026-0.01918.0190.0050.0050.0000.0000.0000.000
59A71GLY0-0.004-0.00821.0350.0280.0280.0000.0000.0000.000
60A72GLU-1-0.753-0.87024.272-0.124-0.1240.0000.0000.0000.000
61A73ARG10.8920.93627.7700.1600.1600.0000.0000.0000.000
62A74ARG10.9520.96831.1180.1130.1130.0000.0000.0000.000
63A75GLY00.0860.05931.3810.0060.0060.0000.0000.0000.000
64A76ASN0-0.059-0.03029.973-0.002-0.0020.0000.0000.0000.000
65A77PRO00.0360.01324.803-0.002-0.0020.0000.0000.0000.000
66A78GLY0-0.037-0.02926.4930.0050.0050.0000.0000.0000.000
67A79ILE0-0.054-0.02323.5130.0010.0010.0000.0000.0000.000
68A80ILE00.0280.02218.6890.0120.0120.0000.0000.0000.000
69A81ARG10.9280.97919.4300.2800.2800.0000.0000.0000.000
70A82VAL00.0180.00313.5790.0090.0090.0000.0000.0000.000
71A83TYR0-0.031-0.03413.4670.1010.1010.0000.0000.0000.000
72A84ALA00.0590.04510.162-0.174-0.1740.0000.0000.0000.000
73A85VAL0-0.067-0.0487.0600.2980.2980.0000.0000.0000.000
74A86GLU-1-0.889-0.9396.930-1.449-1.4490.0000.0000.0000.000
75A87GLY00.0430.0218.8450.1840.1840.0000.0000.0000.000
76A88PRO0-0.058-0.04610.151-0.051-0.0510.0000.0000.0000.000
77A89GLU-1-0.912-0.94112.462-0.258-0.2580.0000.0000.0000.000
78A90ARG10.9410.95613.8250.1870.1870.0000.0000.0000.000
79A91PRO00.0070.01612.253-0.008-0.0080.0000.0000.0000.000
80A92ASP-1-0.808-0.89514.029-0.391-0.3910.0000.0000.0000.000
81A93ASN0-0.126-0.07914.913-0.122-0.1220.0000.0000.0000.000
82A94ILE00.0780.03712.7570.0420.0420.0000.0000.0000.000
83A95VAL00.0370.01616.5240.0430.0430.0000.0000.0000.000
84A96SER0-0.082-0.04118.6090.0160.0160.0000.0000.0000.000
85A97PHE00.0560.02818.4790.0270.0270.0000.0000.0000.000
86A98ILE0-0.021-0.01223.5010.0130.0130.0000.0000.0000.000
87A99VAL00.0300.02024.193-0.002-0.0020.0000.0000.0000.000
88A100LYS10.9480.97526.9440.2050.2050.0000.0000.0000.000
89A101GLY0-0.049-0.03429.3180.0180.0180.0000.0000.0000.000
90A102VAL0-0.0090.00725.358-0.013-0.0130.0000.0000.0000.000
91A103SER0-0.0030.02128.5540.0160.0160.0000.0000.0000.000
92A104LEU0-0.003-0.02225.442-0.014-0.0140.0000.0000.0000.000
93A105SER00.0290.00225.4750.0150.0150.0000.0000.0000.000
94A106ARG10.8040.85924.8960.1190.1190.0000.0000.0000.000
95A107GLU-1-0.772-0.84930.235-0.111-0.1110.0000.0000.0000.000
96A108ARG10.8680.94529.9430.1320.1320.0000.0000.0000.000
97A109ARG10.9070.97232.3380.0740.0740.0000.0000.0000.000
98A110TRP00.0630.02727.2070.0080.0080.0000.0000.0000.000
99A111GLY00.0220.00627.4980.0020.0020.0000.0000.0000.000
100A112LEU0-0.018-0.01821.374-0.016-0.0160.0000.0000.0000.000
101A113PRO00.0340.03019.2950.0190.0190.0000.0000.0000.000
102A114SER0-0.014-0.00820.6210.0150.0150.0000.0000.0000.000
103A115LEU0-0.037-0.00315.2360.0030.0030.0000.0000.0000.000
104A116ARG10.8470.89816.6880.0360.0360.0000.0000.0000.000
105A117GLY0-0.0170.00812.4870.0640.0640.0000.0000.0000.000
106A118GLY00.008-0.00210.6340.0350.0350.0000.0000.0000.000
107A119GLU-1-0.768-0.86611.655-0.204-0.2040.0000.0000.0000.000
108A120VAL0-0.001-0.00911.533-0.107-0.1070.0000.0000.0000.000
109A121LEU0-0.003-0.00213.5620.0920.0920.0000.0000.0000.000
110A122VAL00.0110.01415.516-0.058-0.0580.0000.0000.0000.000
111A123ALA0-0.0120.00018.4660.0310.0310.0000.0000.0000.000
112A124ARG10.8990.94220.5600.2310.2310.0000.0000.0000.000
113A125PRO0-0.0130.01024.2210.0130.0130.0000.0000.0000.000
114A126LEU0-0.003-0.02226.9000.0100.0100.0000.0000.0000.000
115A127ASP-1-0.756-0.83230.341-0.189-0.1890.0000.0000.0000.000
116A128SER00.009-0.01530.567-0.012-0.0120.0000.0000.0000.000
117A129GLY00.0160.01832.3630.0000.0000.0000.0000.0000.000
118A130VAL0-0.008-0.01228.747-0.016-0.0160.0000.0000.0000.000
119A131ALA00.008-0.00727.503-0.026-0.0260.0000.0000.0000.000
120A132VAL00.0230.01325.860-0.027-0.0270.0000.0000.0000.000
121A133GLU-1-0.757-0.85524.767-0.297-0.2970.0000.0000.0000.000
122A134PHE0-0.055-0.04423.328-0.038-0.0380.0000.0000.0000.000
123A135ALA0-0.013-0.00221.515-0.045-0.0450.0000.0000.0000.000
124A136ASP-1-0.844-0.92219.974-0.472-0.4720.0000.0000.0000.000
125A137ALA0-0.037-0.02618.807-0.074-0.0740.0000.0000.0000.000
126A138PHE0-0.037-0.03117.275-0.074-0.0740.0000.0000.0000.000
127A139VAL0-0.0190.01215.361-0.101-0.1010.0000.0000.0000.000
128A140ILE00.0040.01113.779-0.171-0.1710.0000.0000.0000.000
129A141ALA0-0.035-0.02712.935-0.196-0.1960.0000.0000.0000.000
130A142PHE0-0.058-0.06611.956-0.081-0.0810.0000.0000.0000.000
131A143HIS0-0.026-0.0096.7690.4720.4720.0000.0000.0000.000
132A144ALA0-0.057-0.01411.4830.0850.0850.0000.0000.0000.000
133A145ARG10.9900.98412.1980.5720.5720.0000.0000.0000.000
134A146LEU00.0590.02316.6140.0410.0410.0000.0000.0000.000
135A147LYS10.9400.97419.5440.3100.3100.0000.0000.0000.000
136A148PRO0-0.005-0.00919.098-0.042-0.0420.0000.0000.0000.000
137A149PRO0-0.059-0.02716.6470.0020.0020.0000.0000.0000.000
138A150GLU-1-0.892-0.94219.166-0.162-0.1620.0000.0000.0000.000
139A151ALA0-0.021-0.00920.4640.0190.0190.0000.0000.0000.000
140A152ALA0-0.029-0.00716.0750.0110.0110.0000.0000.0000.000
141A153GLY00.0630.03617.678-0.007-0.0070.0000.0000.0000.000
142A154TYR0-0.012-0.03416.782-0.050-0.0500.0000.0000.0000.000
143A155VAL0-0.0340.00417.3460.0410.0410.0000.0000.0000.000
144A156GLU-1-0.854-0.93618.667-0.280-0.2800.0000.0000.0000.000
145A157ALA0-0.011-0.00720.0360.0220.0220.0000.0000.0000.000
146A158VAL0-0.020-0.01121.902-0.009-0.0090.0000.0000.0000.000
147A159ILE0-0.028-0.02322.0860.0050.0050.0000.0000.0000.000
148A160GLU-1-0.887-0.93626.578-0.161-0.1610.0000.0000.0000.000
149A161SER0-0.047-0.06930.272-0.010-0.0100.0000.0000.0000.000
150A162LEU0-0.067-0.03232.0110.0110.0110.0000.0000.0000.000
151A163ASP-1-0.782-0.88333.835-0.162-0.1620.0000.0000.0000.000
152A164ALA00.0380.01433.675-0.011-0.0110.0000.0000.0000.000
153A165ARG10.8420.92230.4540.2020.2020.0000.0000.0000.000
154A166THR0-0.069-0.06430.223-0.017-0.0170.0000.0000.0000.000
155A167VAL00.0410.04526.0860.0060.0060.0000.0000.0000.000
156A168ALA00.0130.00328.965-0.001-0.0010.0000.0000.0000.000
157A169VAL0-0.012-0.01122.599-0.009-0.0090.0000.0000.0000.000
158A170THR0-0.013-0.01526.0490.0190.0190.0000.0000.0000.000
159A171PHE00.0150.01019.185-0.016-0.0160.0000.0000.0000.000
160A172ARG10.9410.96823.0170.1920.1920.0000.0000.0000.000
161A173TYR00.006-0.01619.430-0.027-0.0270.0000.0000.0000.000
162A174GLY00.0250.02023.3980.0150.0150.0000.0000.0000.000
163A175GLY00.0050.01025.6200.0110.0110.0000.0000.0000.000
164A176ALA00.0120.00127.1560.0110.0110.0000.0000.0000.000
165A177PRO0-0.042-0.00926.589-0.015-0.0150.0000.0000.0000.000
166A178VAL0-0.003-0.00622.4970.0140.0140.0000.0000.0000.000
167A179GLY00.0410.01822.919-0.019-0.0190.0000.0000.0000.000
168A180PRO0-0.080-0.03022.1090.0160.0160.0000.0000.0000.000
169A181MET00.0010.00924.650-0.013-0.0130.0000.0000.0000.000
170A182LEU0-0.023-0.02521.8840.0100.0100.0000.0000.0000.000
171A183ARG10.9981.02026.6810.1620.1620.0000.0000.0000.000
172A184LEU0-0.025-0.02022.7710.0030.0030.0000.0000.0000.000
173A185GLY00.0340.01327.1410.0120.0120.0000.0000.0000.000
174A186LYS10.8460.90026.8910.2390.2390.0000.0000.0000.000
175A187PRO0-0.079-0.03624.6330.0230.0230.0000.0000.0000.000
176A188ALA00.0080.00127.9400.0040.0040.0000.0000.0000.000
177A189GLU-1-0.842-0.93224.537-0.298-0.2980.0000.0000.0000.000
178A190MET0-0.064-0.01122.526-0.016-0.0160.0000.0000.0000.000
179A191VAL00.0330.00219.079-0.033-0.0330.0000.0000.0000.000
180A192LYS10.8540.96419.0600.4360.4360.0000.0000.0000.000