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: 22R5R

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 OptH
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 -1891856.028112
FMO2-HF: Nuclear repulsion 1823948.054096
FMO2-HF: Total energy -67907.974016
FMO2-MP2: Total energy -68110.039328


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.
-1.773-0.9326.586-3.977-3.448-0.015
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 : 0.004
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].
3A15ARG10.8590.9373.555-0.0862.539-0.016-1.491-1.1170.004
4A16ILE00.0170.0005.667-0.413-0.4130.0000.0000.0000.000
5A17LEU00.0010.0168.7170.3090.3090.0000.0000.0000.000
6A18VAL00.0160.00810.519-0.027-0.0270.0000.0000.0000.000
7A19THR00.005-0.02114.1590.1040.1040.0000.0000.0000.000
8A20THR0-0.035-0.02316.934-0.015-0.0150.0000.0000.0000.000
9A21SER00.0490.03020.412-0.006-0.0060.0000.0000.0000.000
10A22ARG10.9340.95622.9370.1070.1070.0000.0000.0000.000
11A23ARG10.9370.97724.6490.0540.0540.0000.0000.0000.000
12A24PRO00.0030.02523.5570.0020.0020.0000.0000.0000.000
13A25SER00.046-0.02126.3180.0180.0180.0000.0000.0000.000
14A26PRO0-0.001-0.02327.399-0.009-0.0090.0000.0000.0000.000
15A27ARG10.8180.89927.4680.1230.1230.0000.0000.0000.000
16A28ILE00.0220.03023.097-0.012-0.0120.0000.0000.0000.000
17A29ARG10.9650.99222.8070.0560.0560.0000.0000.0000.000
18A30SER0-0.090-0.03822.7120.0010.0010.0000.0000.0000.000
19A31PHE00.0760.02321.8310.0020.0020.0000.0000.0000.000
20A32VAL00.0520.03817.648-0.013-0.0130.0000.0000.0000.000
21A33LYS10.9090.95818.6210.0400.0400.0000.0000.0000.000
22A34ASP-1-0.779-0.88319.776-0.157-0.1570.0000.0000.0000.000
23A35LEU00.0210.00617.4610.0000.0000.0000.0000.0000.000
24A36SER0-0.029-0.03415.105-0.049-0.0490.0000.0000.0000.000
25A37ALA0-0.041-0.00115.344-0.002-0.0020.0000.0000.0000.000
26A38THR0-0.023-0.02017.9140.0310.0310.0000.0000.0000.000
27A39ILE00.0160.00613.0250.0120.0120.0000.0000.0000.000
28A40PRO00.0190.01412.557-0.001-0.0010.0000.0000.0000.000
29A41GLY00.0510.0309.033-0.151-0.1510.0000.0000.0000.000
30A42ALA0-0.0210.0098.717-0.120-0.1200.0000.0000.0000.000
31A43PHE0-0.015-0.0077.5070.2200.2200.0000.0000.0000.000
32A44ARG10.9420.97912.5080.0110.0110.0000.0000.0000.000
33A45PHE00.0330.01313.2610.0450.0450.0000.0000.0000.000
34A46THR0-0.019-0.01815.460-0.036-0.0360.0000.0000.0000.000
35A47ARG10.8250.92718.1880.1990.1990.0000.0000.0000.000
36A48GLY00.0440.01419.5340.0120.0120.0000.0000.0000.000
37A49HIS0-0.029-0.03522.185-0.027-0.0270.0000.0000.0000.000
38A50TYR00.0850.06117.526-0.010-0.0100.0000.0000.0000.000
39A51SER0-0.037-0.01919.589-0.043-0.0430.0000.0000.0000.000
40A52MET0-0.007-0.02016.0190.0240.0240.0000.0000.0000.000
41A53GLU-1-0.811-0.89215.368-0.116-0.1160.0000.0000.0000.000
42A54GLU-1-0.849-0.93714.798-0.002-0.0020.0000.0000.0000.000
43A55LEU0-0.032-0.02513.7480.0390.0390.0000.0000.0000.000
44A56ALA00.0640.03910.871-0.037-0.0370.0000.0000.0000.000
45A57ARG10.9100.9529.771-0.029-0.0290.0000.0000.0000.000
46A58GLU-1-0.886-0.93910.4460.3750.3750.0000.0000.0000.000
47A59ALA0-0.025-0.0157.6980.1530.1530.0000.0000.0000.000
48A60ILE00.0320.0275.7450.1170.1170.0000.0000.0000.000
49A61ILE0-0.0150.0075.8840.9550.9550.0000.0000.0000.000
50A62ARG10.7620.8856.791-0.034-0.0340.0000.0000.0000.000
51A63GLY00.0580.0252.7530.0890.1890.420-0.118-0.4010.002
52A64ALA0-0.087-0.0442.249-1.395-3.5906.183-2.313-1.674-0.021
53A65ASP-1-0.716-0.8373.723-4.538-4.227-0.001-0.055-0.2560.000
54A66ARG10.8480.9325.4792.9062.9060.0000.0000.0000.000
55A67ILE00.0060.0129.1070.1980.1980.0000.0000.0000.000
56A68VAL00.0020.00311.7950.0350.0350.0000.0000.0000.000
57A69VAL0-0.026-0.01414.8110.0810.0810.0000.0000.0000.000
58A70VAL0-0.034-0.02018.0200.0050.0050.0000.0000.0000.000
59A71GLY0-0.009-0.01421.0360.0280.0280.0000.0000.0000.000
60A72GLU-1-0.777-0.87724.274-0.125-0.1250.0000.0000.0000.000
61A73ARG10.9010.94527.7710.1590.1590.0000.0000.0000.000
62A74ARG10.9540.96531.1190.1160.1160.0000.0000.0000.000
63A75GLY00.0850.05731.3810.0060.0060.0000.0000.0000.000
64A76ASN0-0.033-0.01529.9850.0000.0000.0000.0000.0000.000
65A77PRO00.0330.00224.861-0.002-0.0020.0000.0000.0000.000
66A78GLY0-0.046-0.02726.4970.0050.0050.0000.0000.0000.000
67A79ILE0-0.045-0.01923.3960.0020.0020.0000.0000.0000.000
68A80ILE00.0340.02618.6690.0130.0130.0000.0000.0000.000
69A81ARG10.9020.96619.4310.2820.2820.0000.0000.0000.000
70A82VAL00.0230.00813.5950.0100.0100.0000.0000.0000.000
71A83TYR0-0.030-0.02713.3240.1010.1010.0000.0000.0000.000
72A84ALA00.0490.03310.156-0.175-0.1750.0000.0000.0000.000
73A85VAL0-0.071-0.0396.9700.2910.2910.0000.0000.0000.000
74A86GLU-1-0.891-0.9426.927-1.393-1.3930.0000.0000.0000.000
75A87GLY00.0400.0188.8430.1860.1860.0000.0000.0000.000
76A88PRO0-0.065-0.05210.152-0.053-0.0530.0000.0000.0000.000
77A89GLU-1-0.909-0.93512.466-0.298-0.2980.0000.0000.0000.000
78A90ARG10.9210.94613.8260.1750.1750.0000.0000.0000.000
79A91PRO00.0120.02212.331-0.009-0.0090.0000.0000.0000.000
80A92ASP-1-0.802-0.89114.053-0.419-0.4190.0000.0000.0000.000
81A93ASN0-0.113-0.07914.910-0.134-0.1340.0000.0000.0000.000
82A94ILE00.0770.03312.5270.0410.0410.0000.0000.0000.000
83A95VAL00.0460.02316.6360.0420.0420.0000.0000.0000.000
84A96SER0-0.095-0.05118.6050.0200.0200.0000.0000.0000.000
85A97PHE00.0670.03418.4880.0270.0270.0000.0000.0000.000
86A98ILE0-0.034-0.01723.5030.0130.0130.0000.0000.0000.000
87A99VAL00.0250.02224.231-0.003-0.0030.0000.0000.0000.000
88A100LYS10.9380.96326.9450.2010.2010.0000.0000.0000.000
89A101GLY0-0.044-0.03029.3240.0180.0180.0000.0000.0000.000
90A102VAL0-0.0180.00625.348-0.014-0.0140.0000.0000.0000.000
91A103SER00.0060.02128.5570.0160.0160.0000.0000.0000.000
92A104LEU0-0.018-0.02625.478-0.013-0.0130.0000.0000.0000.000
93A105SER00.0110.00125.5000.0160.0160.0000.0000.0000.000
94A106ARG10.9110.93024.5960.1170.1170.0000.0000.0000.000
95A107GLU-1-0.798-0.88830.234-0.109-0.1090.0000.0000.0000.000
96A108ARG10.8770.95330.0700.1300.1300.0000.0000.0000.000
97A109ARG10.9160.97432.3270.0730.0730.0000.0000.0000.000
98A110TRP00.0370.00927.0170.0090.0090.0000.0000.0000.000
99A111GLY00.0190.00427.4970.0020.0020.0000.0000.0000.000
100A112LEU0-0.018-0.01921.683-0.016-0.0160.0000.0000.0000.000
101A113PRO00.0290.02619.4170.0200.0200.0000.0000.0000.000
102A114SER0-0.026-0.01820.6220.0150.0150.0000.0000.0000.000
103A115LEU0-0.039-0.01815.3230.0030.0030.0000.0000.0000.000
104A116ARG10.8590.91316.6930.0350.0350.0000.0000.0000.000
105A117GLY0-0.0180.00712.4890.0650.0650.0000.0000.0000.000
106A118GLY00.007-0.00210.6350.0360.0360.0000.0000.0000.000
107A119GLU-1-0.777-0.87211.656-0.209-0.2090.0000.0000.0000.000
108A120VAL00.0070.00111.804-0.108-0.1080.0000.0000.0000.000
109A121LEU00.001-0.00713.5640.0920.0920.0000.0000.0000.000
110A122VAL00.0220.02115.516-0.060-0.0600.0000.0000.0000.000
111A123ALA0-0.021-0.00318.4660.0300.0300.0000.0000.0000.000
112A124ARG10.9400.96820.5590.2290.2290.0000.0000.0000.000
113A125PRO0-0.0170.00624.2210.0130.0130.0000.0000.0000.000
114A126LEU0-0.003-0.02126.9000.0100.0100.0000.0000.0000.000
115A127ASP-1-0.746-0.81530.340-0.188-0.1880.0000.0000.0000.000
116A128SER00.003-0.01830.567-0.013-0.0130.0000.0000.0000.000
117A129GLY00.0140.01932.3630.0010.0010.0000.0000.0000.000
118A130VAL00.0170.00128.652-0.016-0.0160.0000.0000.0000.000
119A131ALA00.008-0.00927.503-0.026-0.0260.0000.0000.0000.000
120A132VAL00.0220.01425.860-0.028-0.0280.0000.0000.0000.000
121A133GLU-1-0.787-0.88224.767-0.295-0.2950.0000.0000.0000.000
122A134PHE0-0.066-0.05223.332-0.039-0.0390.0000.0000.0000.000
123A135ALA0-0.006-0.00221.515-0.045-0.0450.0000.0000.0000.000
124A136ASP-1-0.856-0.92319.974-0.470-0.4700.0000.0000.0000.000
125A137ALA0-0.040-0.02918.807-0.074-0.0740.0000.0000.0000.000
126A138PHE0-0.041-0.03317.280-0.075-0.0750.0000.0000.0000.000
127A139VAL0-0.0220.01315.328-0.101-0.1010.0000.0000.0000.000
128A140ILE00.0060.01513.779-0.172-0.1720.0000.0000.0000.000
129A141ALA0-0.030-0.03112.928-0.200-0.2000.0000.0000.0000.000
130A142PHE0-0.060-0.06211.953-0.079-0.0790.0000.0000.0000.000
131A143HIS0-0.020-0.0126.9440.4260.4260.0000.0000.0000.000
132A144ALA0-0.056-0.01311.4830.0860.0860.0000.0000.0000.000
133A145ARG10.9840.98112.7010.5450.5450.0000.0000.0000.000
134A146LEU00.0610.02416.6130.0410.0410.0000.0000.0000.000
135A147LYS10.9320.97119.5360.3230.3230.0000.0000.0000.000
136A148PRO0-0.009-0.01319.097-0.043-0.0430.0000.0000.0000.000
137A149PRO0-0.066-0.03516.6690.0070.0070.0000.0000.0000.000
138A150GLU-1-0.854-0.92319.165-0.162-0.1620.0000.0000.0000.000
139A151ALA0-0.034-0.01020.4640.0190.0190.0000.0000.0000.000
140A152ALA0-0.037-0.01216.0900.0110.0110.0000.0000.0000.000
141A153GLY00.0600.03617.669-0.007-0.0070.0000.0000.0000.000
142A154TYR0-0.003-0.03216.782-0.050-0.0500.0000.0000.0000.000
143A155VAL0-0.0320.00817.3520.0410.0410.0000.0000.0000.000
144A156GLU-1-0.889-0.95918.668-0.285-0.2850.0000.0000.0000.000
145A157ALA0-0.015-0.00720.0660.0220.0220.0000.0000.0000.000
146A158VAL0-0.023-0.01521.903-0.008-0.0080.0000.0000.0000.000
147A159ILE0-0.024-0.01922.1230.0050.0050.0000.0000.0000.000
148A160GLU-1-0.875-0.93726.578-0.161-0.1610.0000.0000.0000.000
149A161SER0-0.062-0.08230.272-0.011-0.0110.0000.0000.0000.000
150A162LEU0-0.071-0.03232.0110.0110.0110.0000.0000.0000.000
151A163ASP-1-0.789-0.89433.835-0.162-0.1620.0000.0000.0000.000
152A164ALA00.0290.00633.675-0.011-0.0110.0000.0000.0000.000
153A165ARG10.8660.93330.7500.2000.2000.0000.0000.0000.000
154A166THR0-0.043-0.03630.229-0.017-0.0170.0000.0000.0000.000
155A167VAL00.0460.04526.1110.0060.0060.0000.0000.0000.000
156A168ALA00.0170.00028.965-0.001-0.0010.0000.0000.0000.000
157A169VAL0-0.012-0.00722.608-0.009-0.0090.0000.0000.0000.000
158A170THR0-0.019-0.01826.0490.0190.0190.0000.0000.0000.000
159A171PHE00.0150.01019.035-0.015-0.0150.0000.0000.0000.000
160A172ARG10.9390.96523.0150.1950.1950.0000.0000.0000.000
161A173TYR00.0110.00019.748-0.027-0.0270.0000.0000.0000.000
162A174GLY00.0240.02023.3990.0150.0150.0000.0000.0000.000
163A175GLY00.0100.01325.6210.0110.0110.0000.0000.0000.000
164A176ALA00.010-0.00327.1540.0110.0110.0000.0000.0000.000
165A177PRO0-0.054-0.01126.590-0.015-0.0150.0000.0000.0000.000
166A178VAL00.0100.00022.4700.0140.0140.0000.0000.0000.000
167A179GLY00.0390.01622.926-0.019-0.0190.0000.0000.0000.000
168A180PRO0-0.066-0.01422.0970.0170.0170.0000.0000.0000.000
169A181MET0-0.0010.00524.650-0.014-0.0140.0000.0000.0000.000
170A182LEU0-0.023-0.02621.9420.0110.0110.0000.0000.0000.000
171A183ARG11.0101.03026.6810.1630.1630.0000.0000.0000.000
172A184LEU0-0.036-0.02922.8680.0030.0030.0000.0000.0000.000
173A185GLY00.0350.02027.1410.0120.0120.0000.0000.0000.000
174A186LYS10.8500.91526.9130.2460.2460.0000.0000.0000.000
175A187PRO0-0.079-0.03924.6820.0230.0230.0000.0000.0000.000
176A188ALA0-0.002-0.00127.9360.0040.0040.0000.0000.0000.000
177A189GLU-1-0.846-0.93524.390-0.302-0.3020.0000.0000.0000.000
178A190MET0-0.094-0.03422.562-0.012-0.0120.0000.0000.0000.000
179A191VAL00.0450.00719.166-0.032-0.0320.0000.0000.0000.000
180A192LYS10.8830.99019.1030.4210.4210.0000.0000.0000.000