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: 4JRMN

Calculation Name: 2ZCX-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2ZCX

Chain ID: A

ChEMBL ID:

UniProt ID: Q9FBX0

Base Structure: X-ray

Registration Date: 2023-09-20

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 205
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2156387.364528
FMO2-HF: Nuclear repulsion 2078712.516677
FMO2-HF: Total energy -77674.84785
FMO2-MP2: Total energy -77904.527872


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:19:GLN)


Summations of interaction energy for fragment #1(A:19:GLN)
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.
-12.381-7.9328.292-3.462-9.280.002
Interaction energy analysis for fragmet #1(A:19:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.080 / q_NPA : 0.034
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].
3A21LYS10.9530.9602.528-5.092-2.8810.367-0.356-2.2220.009
4A22GLN00.0530.0112.202-4.545-3.1404.425-1.955-3.8760.003
5A23GLN00.0590.0242.051-1.479-0.7663.501-1.143-3.072-0.010
6A24ARG10.9000.9554.824-0.530-0.410-0.001-0.008-0.1100.000
7A25GLU-1-0.957-0.9826.5052.0422.0420.0000.0000.0000.000
8A26GLU-1-0.918-0.9607.048-0.755-0.7550.0000.0000.0000.000
9A27ALA00.0310.0248.615-0.125-0.1250.0000.0000.0000.000
10A28ILE0-0.055-0.04110.586-0.003-0.0030.0000.0000.0000.000
11A29LEU0-0.043-0.01211.384-0.034-0.0340.0000.0000.0000.000
12A30ASP-1-0.828-0.90912.252-0.202-0.2020.0000.0000.0000.000
13A31ALA00.0160.01714.683-0.016-0.0160.0000.0000.0000.000
14A32ALA0-0.057-0.03516.319-0.006-0.0060.0000.0000.0000.000
15A33ARG10.8210.87513.504-0.100-0.1000.0000.0000.0000.000
16A34GLU-1-0.923-0.95318.436-0.073-0.0730.0000.0000.0000.000
17A35LEU0-0.013-0.01020.529-0.003-0.0030.0000.0000.0000.000
18A36GLY0-0.007-0.03822.0260.0000.0000.0000.0000.0000.000
19A37THR0-0.100-0.04022.590-0.013-0.0130.0000.0000.0000.000
20A38GLU-1-1.000-0.99524.854-0.002-0.0020.0000.0000.0000.000
21A39ARG10.9340.97926.405-0.068-0.0680.0000.0000.0000.000
22A40GLY00.0420.04527.5010.0060.0060.0000.0000.0000.000
23A41ILE00.0410.01623.3230.0110.0110.0000.0000.0000.000
24A42ARG10.8410.91426.633-0.052-0.0520.0000.0000.0000.000
25A43GLU-1-0.918-0.95528.2700.0870.0870.0000.0000.0000.000
26A44ILE0-0.0350.02022.5030.0050.0050.0000.0000.0000.000
27A45THR0-0.0110.00324.8420.0340.0340.0000.0000.0000.000
28A46LEU00.028-0.01418.781-0.003-0.0030.0000.0000.0000.000
29A47THR0-0.013-0.03320.8170.0280.0280.0000.0000.0000.000
30A48ASP-1-0.820-0.90322.3210.1570.1570.0000.0000.0000.000
31A49ILE00.0330.03217.055-0.011-0.0110.0000.0000.0000.000
32A50ALA0-0.051-0.02517.826-0.001-0.0010.0000.0000.0000.000
33A51ALA0-0.020-0.02718.727-0.007-0.0070.0000.0000.0000.000
34A52THR0-0.023-0.00918.400-0.025-0.0250.0000.0000.0000.000
35A53VAL0-0.036-0.01713.932-0.022-0.0220.0000.0000.0000.000
36A54GLY0-0.0050.02315.636-0.003-0.0030.0000.0000.0000.000
37A55MET0-0.097-0.03112.4520.0310.0310.0000.0000.0000.000
38A56HIS00.0520.01617.2060.0060.0060.0000.0000.0000.000
39A57LYS11.0320.99917.917-0.301-0.3010.0000.0000.0000.000
40A58SER0-0.010-0.00918.9150.0380.0380.0000.0000.0000.000
41A59ALA00.0220.00514.0480.0590.0590.0000.0000.0000.000
42A60LEU00.0300.01814.1100.1130.1130.0000.0000.0000.000
43A61LEU00.002-0.00415.2260.0520.0520.0000.0000.0000.000
44A62ARG10.8640.94912.936-0.917-0.9170.0000.0000.0000.000
45A63TYR0-0.093-0.0417.7120.2170.2170.0000.0000.0000.000
46A64PHE00.0190.00212.0020.0630.0630.0000.0000.0000.000
47A65GLU-1-0.890-0.94215.9180.4820.4820.0000.0000.0000.000
48A66THR00.010-0.00619.454-0.044-0.0440.0000.0000.0000.000
49A67ARG10.9440.96719.858-0.193-0.1930.0000.0000.0000.000
50A68GLU-1-0.816-0.90021.2530.2860.2860.0000.0000.0000.000
51A69GLN00.0420.03617.149-0.001-0.0010.0000.0000.0000.000
52A70ILE0-0.018-0.00216.1160.0410.0410.0000.0000.0000.000
53A71PHE00.0490.00917.630-0.004-0.0040.0000.0000.0000.000
54A72LEU00.0040.03820.055-0.028-0.0280.0000.0000.0000.000
55A73LYS10.9440.97212.137-1.136-1.1360.0000.0000.0000.000
56A74ILE00.0320.01816.414-0.017-0.0170.0000.0000.0000.000
57A75THR0-0.012-0.02717.847-0.063-0.0630.0000.0000.0000.000
58A76ALA0-0.021-0.01917.465-0.036-0.0360.0000.0000.0000.000
59A77GLU-1-0.893-0.93313.0530.3340.3340.0000.0000.0000.000
60A78GLY00.0340.02317.230-0.065-0.0650.0000.0000.0000.000
61A79TRP00.0250.00120.780-0.039-0.0390.0000.0000.0000.000
62A80LYS10.9170.96313.717-0.314-0.3140.0000.0000.0000.000
63A81GLU-1-0.828-0.89018.761-0.143-0.1430.0000.0000.0000.000
64A82TRP00.0450.01420.018-0.020-0.0200.0000.0000.0000.000
65A83SER0-0.016-0.01622.362-0.023-0.0230.0000.0000.0000.000
66A84ALA0-0.009-0.00420.171-0.015-0.0150.0000.0000.0000.000
67A85GLU-1-0.835-0.88922.288-0.184-0.1840.0000.0000.0000.000
68A86LEU0-0.030-0.02424.605-0.007-0.0070.0000.0000.0000.000
69A87CYS0-0.022-0.03125.1250.0010.0010.0000.0000.0000.000
70A88ALA0-0.049-0.01524.465-0.006-0.0060.0000.0000.0000.000
71A89ARG10.8670.90926.4920.1340.1340.0000.0000.0000.000
72A90LEU00.0190.00329.8440.0030.0030.0000.0000.0000.000
73A91ARG10.9120.96324.2600.1380.1380.0000.0000.0000.000
74A92GLU-1-0.957-0.96329.811-0.172-0.1720.0000.0000.0000.000
75A93LEU0-0.062-0.02833.0170.0040.0040.0000.0000.0000.000
76A94PRO0-0.053-0.02135.9660.0010.0010.0000.0000.0000.000
77A95GLY0-0.023-0.03938.8350.0060.0060.0000.0000.0000.000
78A96ALA00.0640.01939.4900.0030.0030.0000.0000.0000.000
79A97ALA0-0.0240.00641.1340.0030.0030.0000.0000.0000.000
80A98PRO00.0480.01540.658-0.002-0.0020.0000.0000.0000.000
81A99ASP-1-0.864-0.94840.652-0.026-0.0260.0000.0000.0000.000
82A100ALA0-0.041-0.01639.340-0.002-0.0020.0000.0000.0000.000
83A101VAL00.0340.02335.321-0.005-0.0050.0000.0000.0000.000
84A102GLY00.016-0.00135.9890.0010.0010.0000.0000.0000.000
85A103GLN0-0.003-0.00436.882-0.002-0.0020.0000.0000.0000.000
86A104VAL00.0170.01631.754-0.004-0.0040.0000.0000.0000.000
87A105PHE0-0.002-0.00232.157-0.001-0.0010.0000.0000.0000.000
88A106ALA0-0.013-0.01532.7890.0040.0040.0000.0000.0000.000
89A107ALA00.0540.03233.6670.0020.0020.0000.0000.0000.000
90A108THR0-0.039-0.02628.3980.0000.0000.0000.0000.0000.000
91A109LEU0-0.0180.00528.9280.0010.0010.0000.0000.0000.000
92A110ALA00.0200.00830.6880.0060.0060.0000.0000.0000.000
93A111ALA0-0.0260.00029.4820.0000.0000.0000.0000.0000.000
94A112ARG10.7500.84124.0360.0780.0780.0000.0000.0000.000
95A113PRO00.0700.03727.7590.0180.0180.0000.0000.0000.000
96A114LEU00.0840.04721.3720.0160.0160.0000.0000.0000.000
97A115PHE0-0.009-0.01223.5670.0220.0220.0000.0000.0000.000
98A116CYS0-0.016-0.00125.1770.0180.0180.0000.0000.0000.000
99A117ASP-1-0.830-0.91427.2570.0660.0660.0000.0000.0000.000
100A118LEU0-0.064-0.03321.8540.0160.0160.0000.0000.0000.000
101A119LEU0-0.058-0.01325.9870.0220.0220.0000.0000.0000.000
102A120ALA0-0.0030.00028.1270.0050.0050.0000.0000.0000.000
103A121GLN0-0.009-0.00326.1770.0200.0200.0000.0000.0000.000
104A122ALA00.0170.00525.9050.0160.0160.0000.0000.0000.000
105A123PRO0-0.049-0.02927.2530.0220.0220.0000.0000.0000.000
106A124LEU00.0630.02330.0910.0060.0060.0000.0000.0000.000
107A125ASN0-0.026-0.00924.7400.0150.0150.0000.0000.0000.000
108A126LEU0-0.052-0.03825.1940.0250.0250.0000.0000.0000.000
109A127GLU-1-0.956-0.97626.4500.1850.1850.0000.0000.0000.000
110A128ARG10.8800.92428.816-0.196-0.1960.0000.0000.0000.000
111A129ASN0-0.0420.00426.2690.0060.0060.0000.0000.0000.000
112A130VAL0-0.0010.00321.7420.0320.0320.0000.0000.0000.000
113A131SER00.0000.01320.965-0.022-0.0220.0000.0000.0000.000
114A132VAL00.0790.01823.4560.0050.0050.0000.0000.0000.000
115A133GLU-1-0.809-0.91020.4980.4390.4390.0000.0000.0000.000
116A134SER0-0.022-0.00219.3220.0550.0550.0000.0000.0000.000
117A135VAL00.0270.01520.301-0.012-0.0120.0000.0000.0000.000
118A136ARG10.8800.93622.112-0.385-0.3850.0000.0000.0000.000
119A137SER0-0.010-0.01217.784-0.002-0.0020.0000.0000.0000.000
120A138PHE00.0010.00319.932-0.026-0.0260.0000.0000.0000.000
121A139LYS10.9220.95420.841-0.252-0.2520.0000.0000.0000.000
122A140ILE00.0260.02521.133-0.030-0.0300.0000.0000.0000.000
123A141ALA00.0240.01018.526-0.026-0.0260.0000.0000.0000.000
124A142THR0-0.024-0.01920.449-0.049-0.0490.0000.0000.0000.000
125A143LEU0-0.024-0.02923.301-0.033-0.0330.0000.0000.0000.000
126A144ASP-1-0.898-0.92621.4190.1710.1710.0000.0000.0000.000
127A145GLU-1-0.889-0.94620.1290.0270.0270.0000.0000.0000.000
128A146VAL0-0.0210.00024.177-0.025-0.0250.0000.0000.0000.000
129A147GLY00.0380.02227.048-0.015-0.0150.0000.0000.0000.000
130A148ARG10.8590.92920.294-0.062-0.0620.0000.0000.0000.000
131A149ILE00.0320.00326.470-0.015-0.0150.0000.0000.0000.000
132A150GLY00.0330.00928.697-0.008-0.0080.0000.0000.0000.000
133A151ALA0-0.061-0.03029.531-0.004-0.0040.0000.0000.0000.000
134A152GLU-1-0.851-0.91629.208-0.079-0.0790.0000.0000.0000.000
135A153LEU00.0060.01032.136-0.004-0.0040.0000.0000.0000.000
136A154ARG10.8450.97132.438-0.027-0.0270.0000.0000.0000.000
137A155ARG10.8390.93232.0320.0700.0700.0000.0000.0000.000
138A156LEU0-0.084-0.02433.993-0.003-0.0030.0000.0000.0000.000
139A157LEU0-0.001-0.01837.669-0.001-0.0010.0000.0000.0000.000
140A158GLY0-0.0110.01839.3230.0030.0030.0000.0000.0000.000
141A159VAL0-0.029-0.00237.6930.0030.0030.0000.0000.0000.000
142A160ASP-1-0.829-0.92838.6170.0280.0280.0000.0000.0000.000
143A161GLU-1-0.908-1.02133.6530.0640.0640.0000.0000.0000.000
144A162THR0-0.024-0.01236.2010.0060.0060.0000.0000.0000.000
145A163GLN00.0840.04538.3240.0010.0010.0000.0000.0000.000
146A164ALA0-0.020-0.00134.308-0.002-0.0020.0000.0000.0000.000
147A165VAL0-0.007-0.00833.0370.0010.0010.0000.0000.0000.000
148A166ASP-1-0.850-0.92034.7290.0540.0540.0000.0000.0000.000
149A167VAL0-0.0260.01135.5540.0000.0000.0000.0000.0000.000
150A168ILE00.0030.00729.939-0.001-0.0010.0000.0000.0000.000
151A169ALA0-0.0060.00132.8740.0030.0030.0000.0000.0000.000
152A170THR0-0.020-0.02533.9280.0030.0030.0000.0000.0000.000
153A171ALA0-0.025-0.01333.338-0.001-0.0010.0000.0000.0000.000
154A172THR0-0.025-0.02229.3500.0020.0020.0000.0000.0000.000
155A173SER0-0.004-0.01131.9220.0060.0060.0000.0000.0000.000
156A174LEU0-0.039-0.01434.2610.0000.0000.0000.0000.0000.000
157A175ALA00.000-0.00632.442-0.004-0.0040.0000.0000.0000.000
158A176GLY00.0390.01931.949-0.002-0.0020.0000.0000.0000.000
159A177ALA00.016-0.00332.7420.0010.0010.0000.0000.0000.000
160A178LEU0-0.034-0.02536.225-0.003-0.0030.0000.0000.0000.000
161A179TRP00.0470.00732.163-0.003-0.0030.0000.0000.0000.000
162A180GLN0-0.088-0.03731.3490.0020.0020.0000.0000.0000.000
163A181MET0-0.080-0.04135.339-0.002-0.0020.0000.0000.0000.000
164A182ALA0-0.0070.00636.555-0.003-0.0030.0000.0000.0000.000
165A183THR0-0.071-0.03433.348-0.003-0.0030.0000.0000.0000.000
166A184PRO00.0060.00736.0800.0070.0070.0000.0000.0000.000
167A185GLY00.0630.03837.2900.0040.0040.0000.0000.0000.000
168A186PRO00.016-0.01036.774-0.004-0.0040.0000.0000.0000.000
169A187HIS00.0650.01639.618-0.006-0.0060.0000.0000.0000.000
170A188ILE00.0130.02241.708-0.002-0.0020.0000.0000.0000.000
171A189GLN0-0.0080.00137.451-0.006-0.0060.0000.0000.0000.000
172A190THR0-0.019-0.01342.658-0.005-0.0050.0000.0000.0000.000
173A191LEU0-0.0020.00645.358-0.002-0.0020.0000.0000.0000.000
174A192TYR0-0.002-0.02642.786-0.001-0.0010.0000.0000.0000.000
175A193ARG10.9360.96441.6310.0060.0060.0000.0000.0000.000
176A194SER0-0.078-0.01348.144-0.002-0.0020.0000.0000.0000.000
177A195ASP-1-0.766-0.88550.9080.0100.0100.0000.0000.0000.000
178A196PRO00.0270.00252.1340.0000.0000.0000.0000.0000.000
179A197ARG10.8220.90454.273-0.014-0.0140.0000.0000.0000.000
180A198LEU0-0.039-0.01149.1590.0020.0020.0000.0000.0000.000
181A199ALA00.0550.03848.8860.0000.0000.0000.0000.0000.000
182A200HIS0-0.020-0.02348.442-0.001-0.0010.0000.0000.0000.000
183A201ALA0-0.051-0.01346.0860.0020.0020.0000.0000.0000.000
184A202VAL0-0.043-0.01443.6850.0020.0020.0000.0000.0000.000
185A203VAL0-0.049-0.02839.716-0.002-0.0020.0000.0000.0000.000
186A204GLU-1-0.880-0.92440.339-0.025-0.0250.0000.0000.0000.000
187A205VAL0-0.002-0.02734.8250.0010.0010.0000.0000.0000.000
188A206GLU-1-0.862-0.93536.744-0.052-0.0520.0000.0000.0000.000
189A207PRO00.0120.00238.1180.0010.0010.0000.0000.0000.000
190A208ARG10.9180.96041.391-0.009-0.0090.0000.0000.0000.000
191A209LEU00.0180.01734.6460.0030.0030.0000.0000.0000.000
192A210ASN00.0450.01639.375-0.001-0.0010.0000.0000.0000.000
193A211ARG10.9100.95440.4020.0110.0110.0000.0000.0000.000
194A212VAL0-0.029-0.00941.2740.0010.0010.0000.0000.0000.000
195A213LEU00.0260.01336.0830.0030.0030.0000.0000.0000.000
196A214GLY00.0540.04240.359-0.001-0.0010.0000.0000.0000.000
197A215ALA0-0.071-0.04742.5920.0000.0000.0000.0000.0000.000
198A216LEU0-0.0170.00739.8160.0010.0010.0000.0000.0000.000
199A217LEU00.0240.00338.0870.0010.0010.0000.0000.0000.000
200A218ARG10.9250.96142.3780.0140.0140.0000.0000.0000.000
201A219GLY00.0290.02645.8980.0000.0000.0000.0000.0000.000
202A220ILE0-0.063-0.02841.3490.0020.0020.0000.0000.0000.000
203A221ALA0-0.001-0.00444.2920.0000.0000.0000.0000.0000.000
204A222ASP-1-1.009-0.98845.782-0.012-0.0120.0000.0000.0000.000
205A223GLY0-0.057-0.03147.7780.0020.0020.0000.0000.0000.000