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: J2Q59

Calculation Name: 2ZB9-A-Xray372

Preferred Name:
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Target Type:
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Ligand Name:
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ligand 3-letter code:
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PDB ID: 2ZB9

Chain ID: A

ChEMBL ID:
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UniProt ID: Q9RK47

Base Structure: X-ray

Registration Date: 2023-09-27

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 188
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1907388.421459
FMO2-HF: Nuclear repulsion 1835803.379755
FMO2-HF: Total energy -71585.041704
FMO2-MP2: Total energy -71798.506058


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:17:GLY)


Summations of interaction energy for fragment #1(A:17: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.
-2.8031.48-0.026-2.326-1.930.003
Interaction energy analysis for fragmet #1(A:17:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.046 / q_NPA : 0.018
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].
3A19ARG10.8990.9543.601-1.7292.331-0.026-2.275-1.7590.003
4A20PRO00.0740.0484.028-0.164-0.0690.000-0.016-0.0780.000
5A21ALA0-0.004-0.0154.261-0.1130.0150.000-0.035-0.0930.000
6A22GLU-1-0.878-0.9405.910-1.506-1.5060.0000.0000.0000.000
7A23GLU-1-0.878-0.9437.969-0.106-0.1060.0000.0000.0000.000
8A24VAL00.0360.0269.0510.1080.1080.0000.0000.0000.000
9A25ARG10.8650.9379.2491.3331.3330.0000.0000.0000.000
10A26ALA00.0130.00611.3740.1310.1310.0000.0000.0000.000
11A27GLU-1-0.899-0.94213.810-0.257-0.2570.0000.0000.0000.000
12A28VAL0-0.033-0.01613.6990.0690.0690.0000.0000.0000.000
13A29LEU0-0.039-0.02714.5490.0520.0520.0000.0000.0000.000
14A30HIS00.0100.01617.2940.0320.0320.0000.0000.0000.000
15A31ALA00.0260.01019.2180.0380.0380.0000.0000.0000.000
16A32VAL0-0.085-0.04118.7200.0320.0320.0000.0000.0000.000
17A33GLY00.0240.00921.4660.0280.0280.0000.0000.0000.000
18A34GLU-1-0.863-0.94323.440-0.196-0.1960.0000.0000.0000.000
19A35LEU0-0.025-0.00724.6080.0220.0220.0000.0000.0000.000
20A36LEU0-0.078-0.03524.3820.0190.0190.0000.0000.0000.000
21A37LEU0-0.003-0.02427.0500.0160.0160.0000.0000.0000.000
22A38THR0-0.073-0.01529.3230.0180.0180.0000.0000.0000.000
23A39GLU-1-0.776-0.86530.105-0.128-0.1280.0000.0000.0000.000
24A40GLY00.0100.02030.5450.0090.0090.0000.0000.0000.000
25A41THR00.025-0.02427.497-0.004-0.0040.0000.0000.0000.000
26A42ALA0-0.022-0.01128.696-0.007-0.0070.0000.0000.0000.000
27A43GLN00.0220.02030.2090.0060.0060.0000.0000.0000.000
28A44LEU0-0.0270.02622.7290.0010.0010.0000.0000.0000.000
29A45THR00.019-0.00824.975-0.001-0.0010.0000.0000.0000.000
30A46PHE00.0480.01117.7790.0060.0060.0000.0000.0000.000
31A47GLU-1-0.838-0.92021.063-0.137-0.1370.0000.0000.0000.000
32A48ARG10.7680.87123.4730.1620.1620.0000.0000.0000.000
33A49VAL00.0650.02818.4270.0060.0060.0000.0000.0000.000
34A50ALA0-0.008-0.00518.666-0.009-0.0090.0000.0000.0000.000
35A51ARG10.8990.95919.6960.1290.1290.0000.0000.0000.000
36A52VAL0-0.045-0.02322.4210.0170.0170.0000.0000.0000.000
37A53SER00.0150.00217.254-0.005-0.0050.0000.0000.0000.000
38A54GLY00.0260.03118.1320.0050.0050.0000.0000.0000.000
39A55VAL0-0.0270.00012.8750.0250.0250.0000.0000.0000.000
40A56SER00.012-0.00814.613-0.021-0.0210.0000.0000.0000.000
41A57LYS10.9520.93915.3570.0840.0840.0000.0000.0000.000
42A58THR0-0.0230.00513.421-0.041-0.0410.0000.0000.0000.000
43A59THR0-0.021-0.0129.784-0.008-0.0080.0000.0000.0000.000
44A60LEU00.0330.02412.175-0.115-0.1150.0000.0000.0000.000
45A61TYR0-0.018-0.02214.688-0.029-0.0290.0000.0000.0000.000
46A62LYS10.8950.9599.6310.2530.2530.0000.0000.0000.000
47A63TRP0-0.029-0.0087.1850.0140.0140.0000.0000.0000.000
48A64TRP0-0.040-0.03512.291-0.010-0.0100.0000.0000.0000.000
49A65PRO00.0310.01816.0040.0570.0570.0000.0000.0000.000
50A66SER00.0510.01418.1990.0440.0440.0000.0000.0000.000
51A67LYS10.9130.95620.7710.1780.1780.0000.0000.0000.000
52A68GLY00.0320.01723.177-0.007-0.0070.0000.0000.0000.000
53A69ALA00.0410.00918.733-0.008-0.0080.0000.0000.0000.000
54A70LEU0-0.0150.00017.944-0.033-0.0330.0000.0000.0000.000
55A71ALA00.003-0.01319.891-0.012-0.0120.0000.0000.0000.000
56A72LEU00.0000.00322.2500.0020.0020.0000.0000.0000.000
57A73ASP-1-0.748-0.86715.784-0.734-0.7340.0000.0000.0000.000
58A74GLY00.0140.00519.429-0.018-0.0180.0000.0000.0000.000
59A75TYR0-0.001-0.00820.5330.0200.0200.0000.0000.0000.000
60A76PHE0-0.006-0.01520.1810.0220.0220.0000.0000.0000.000
61A77HIS10.8560.91816.7020.6230.6230.0000.0000.0000.000
62A78ALA00.0030.02820.8340.0100.0100.0000.0000.0000.000
63A79VAL0-0.049-0.02323.8200.0250.0250.0000.0000.0000.000
64A80GLU-1-0.941-0.97420.020-0.462-0.4620.0000.0000.0000.000
65A81ASP-1-0.891-0.94623.095-0.304-0.3040.0000.0000.0000.000
66A82THR0-0.047-0.02525.5510.0240.0240.0000.0000.0000.000
67A83LEU0-0.072-0.02527.8110.0170.0170.0000.0000.0000.000
68A84ALA00.0430.03826.1560.0000.0000.0000.0000.0000.000
69A85PHE0-0.022-0.02227.8330.0180.0180.0000.0000.0000.000
70A86PRO0-0.0220.01030.029-0.004-0.0040.0000.0000.0000.000
71A87ASP-1-0.860-0.93930.897-0.168-0.1680.0000.0000.0000.000
72A88THR0-0.061-0.05432.8690.0060.0060.0000.0000.0000.000
73A89GLY00.0340.02835.9620.0070.0070.0000.0000.0000.000
74A90ASP-1-0.872-0.91737.875-0.095-0.0950.0000.0000.0000.000
75A91VAL00.0300.00037.613-0.004-0.0040.0000.0000.0000.000
76A92ARG10.8150.89339.1410.0860.0860.0000.0000.0000.000
77A93ALA0-0.005-0.00740.500-0.002-0.0020.0000.0000.0000.000
78A94ASP-1-0.741-0.83535.287-0.141-0.1410.0000.0000.0000.000
79A95LEU00.009-0.00436.016-0.009-0.0090.0000.0000.0000.000
80A96LEU0-0.031-0.00737.719-0.003-0.0030.0000.0000.0000.000
81A97ALA0-0.022-0.00736.612-0.001-0.0010.0000.0000.0000.000
82A98GLN00.0070.00130.8610.0060.0060.0000.0000.0000.000
83A99LEU00.0370.00834.780-0.005-0.0050.0000.0000.0000.000
84A100ARG10.8810.93237.0890.1070.1070.0000.0000.0000.000
85A101ALA00.0270.03033.3030.0020.0020.0000.0000.0000.000
86A102PHE0-0.016-0.02232.087-0.005-0.0050.0000.0000.0000.000
87A103THR00.0370.00634.4750.0000.0000.0000.0000.0000.000
88A104HIS0-0.0190.00735.0460.0070.0070.0000.0000.0000.000
89A105VAL0-0.011-0.01031.0010.0020.0020.0000.0000.0000.000
90A106MET0-0.039-0.02433.432-0.004-0.0040.0000.0000.0000.000
91A107THR0-0.032-0.02435.7570.0070.0070.0000.0000.0000.000
92A108ARG10.8760.94338.0110.1130.1130.0000.0000.0000.000
93A109THR00.0020.02632.311-0.002-0.0020.0000.0000.0000.000
94A110PRO00.0340.00732.5670.0010.0010.0000.0000.0000.000
95A111GLY00.005-0.01330.998-0.004-0.0040.0000.0000.0000.000
96A112GLY00.0730.04631.838-0.007-0.0070.0000.0000.0000.000
97A113ARG10.8590.92532.3140.1520.1520.0000.0000.0000.000
98A114ILE0-0.040-0.02128.562-0.001-0.0010.0000.0000.0000.000
99A115LEU0-0.011-0.00528.149-0.005-0.0050.0000.0000.0000.000
100A116THR00.008-0.00131.1990.0000.0000.0000.0000.0000.000
101A117GLU-1-0.837-0.90433.532-0.139-0.1390.0000.0000.0000.000
102A118LEU0-0.057-0.02227.121-0.001-0.0010.0000.0000.0000.000
103A119ILE0-0.026-0.00331.035-0.002-0.0020.0000.0000.0000.000
104A120GLY00.0310.00832.7730.0050.0050.0000.0000.0000.000
105A121ALA0-0.004-0.00631.8310.0050.0050.0000.0000.0000.000
106A122ALA0-0.032-0.02330.3830.0010.0010.0000.0000.0000.000
107A123GLN0-0.067-0.02931.8950.0050.0050.0000.0000.0000.000
108A124THR0-0.031-0.00934.7370.0080.0080.0000.0000.0000.000
109A125ASP-1-0.881-0.93229.483-0.184-0.1840.0000.0000.0000.000
110A126ALA00.0270.00130.322-0.012-0.0120.0000.0000.0000.000
111A127ASP-1-0.896-0.94625.448-0.226-0.2260.0000.0000.0000.000
112A128LEU0-0.042-0.01425.497-0.030-0.0300.0000.0000.0000.000
113A129ALA00.0120.00126.631-0.018-0.0180.0000.0000.0000.000
114A130THR0-0.074-0.03523.298-0.008-0.0080.0000.0000.0000.000
115A131ALA00.0230.00622.346-0.026-0.0260.0000.0000.0000.000
116A132TYR00.005-0.00122.997-0.028-0.0280.0000.0000.0000.000
117A133ARG10.9360.96125.2380.2260.2260.0000.0000.0000.000
118A134GLN0-0.045-0.03720.103-0.031-0.0310.0000.0000.0000.000
119A135LEU0-0.0200.01017.507-0.037-0.0370.0000.0000.0000.000
120A136TYR00.0540.03220.836-0.003-0.0030.0000.0000.0000.000
121A137SER00.0220.00923.997-0.005-0.0050.0000.0000.0000.000
122A138ALA0-0.0030.00623.6400.0140.0140.0000.0000.0000.000
123A139GLN00.0430.01118.8950.0150.0150.0000.0000.0000.000
124A140ARG10.9160.97023.7390.2940.2940.0000.0000.0000.000
125A141ARG10.8150.88126.7930.2050.2050.0000.0000.0000.000
126A142ALA0-0.033-0.00124.7280.0170.0170.0000.0000.0000.000
127A143LEU00.0500.02123.5450.0120.0120.0000.0000.0000.000
128A144ALA00.0280.01926.9170.0160.0160.0000.0000.0000.000
129A145ALA0-0.045-0.04129.8780.0140.0140.0000.0000.0000.000
130A146GLU-1-0.974-0.97625.358-0.274-0.2740.0000.0000.0000.000
131A147ARG10.8580.91629.5540.1690.1690.0000.0000.0000.000
132A148LEU0-0.007-0.02231.7490.0140.0140.0000.0000.0000.000
133A149ARG10.9370.95728.0050.2210.2210.0000.0000.0000.000
134A150HIS00.0090.02131.7700.0130.0130.0000.0000.0000.000
135A151ALA00.0270.00533.6930.0100.0100.0000.0000.0000.000
136A152ARG10.8170.92835.2690.1420.1420.0000.0000.0000.000
137A153GLU-1-0.982-0.98632.673-0.149-0.1490.0000.0000.0000.000
138A154LEU0-0.055-0.02136.1360.0080.0080.0000.0000.0000.000
139A155GLY0-0.026-0.00639.0170.0060.0060.0000.0000.0000.000
140A156GLN0-0.069-0.05439.9560.0000.0000.0000.0000.0000.000
141A157ILE0-0.012-0.00238.3370.0000.0000.0000.0000.0000.000
142A158ARG10.9100.95842.0150.0900.0900.0000.0000.0000.000
143A159PRO00.0610.00141.115-0.005-0.0050.0000.0000.0000.000
144A160ASP-1-0.880-0.93941.023-0.095-0.0950.0000.0000.0000.000
145A161VAL0-0.0080.00640.1630.0000.0000.0000.0000.0000.000
146A162ASP-1-0.858-0.93136.682-0.150-0.1500.0000.0000.0000.000
147A163VAL00.007-0.02433.5770.0000.0000.0000.0000.0000.000
148A164GLN00.0250.00630.316-0.004-0.0040.0000.0000.0000.000
149A165VAL00.0150.02334.973-0.002-0.0020.0000.0000.0000.000
150A166LEU00.007-0.00137.5900.0010.0010.0000.0000.0000.000
151A167VAL0-0.009-0.00732.6340.0000.0000.0000.0000.0000.000
152A168ASP-1-0.836-0.91135.804-0.163-0.1630.0000.0000.0000.000
153A169GLN0-0.033-0.01937.8160.0040.0040.0000.0000.0000.000
154A170LEU00.0060.02037.6650.0050.0050.0000.0000.0000.000
155A171TRP00.005-0.00934.2230.0020.0020.0000.0000.0000.000
156A172GLY0-0.0150.00336.5550.0000.0000.0000.0000.0000.000
157A173ALA00.0420.02637.6550.0040.0040.0000.0000.0000.000
158A174VAL0-0.003-0.00437.9160.0050.0050.0000.0000.0000.000
159A175TYR0-0.017-0.02131.154-0.003-0.0030.0000.0000.0000.000
160A176HIS00.0140.01337.812-0.001-0.0010.0000.0000.0000.000
161A177ARG10.8990.94940.9730.0990.0990.0000.0000.0000.000
162A178LEU0-0.050-0.02937.1670.0020.0020.0000.0000.0000.000
163A179LEU0-0.067-0.04036.5700.0000.0000.0000.0000.0000.000
164A180ILE0-0.050-0.01240.3640.0030.0030.0000.0000.0000.000
165A181PRO0-0.021-0.00243.6140.0020.0020.0000.0000.0000.000
166A182ASP-1-0.916-0.94845.924-0.081-0.0810.0000.0000.0000.000
167A183GLU-1-0.965-0.98947.890-0.075-0.0750.0000.0000.0000.000
168A184PRO0-0.014-0.00246.886-0.005-0.0050.0000.0000.0000.000
169A185VAL00.0160.00940.954-0.001-0.0010.0000.0000.0000.000
170A186ASP-1-0.865-0.94043.910-0.092-0.0920.0000.0000.0000.000
171A187ASP-1-0.819-0.92244.096-0.103-0.1030.0000.0000.0000.000
172A188ALA00.0010.01845.324-0.001-0.0010.0000.0000.0000.000
173A189PHE0-0.012-0.00642.2120.0000.0000.0000.0000.0000.000
174A190VAL00.0170.00440.923-0.002-0.0020.0000.0000.0000.000
175A191THR0-0.025-0.03443.436-0.002-0.0020.0000.0000.0000.000
176A192ALA00.0020.00745.5490.0010.0010.0000.0000.0000.000
177A193LEU0-0.068-0.01841.4300.0010.0010.0000.0000.0000.000
178A194VAL00.0150.00741.197-0.001-0.0010.0000.0000.0000.000
179A195THR00.011-0.00143.7680.0010.0010.0000.0000.0000.000
180A196ASN0-0.0100.00047.2900.0050.0050.0000.0000.0000.000
181A197LEU0-0.042-0.01141.7290.0020.0020.0000.0000.0000.000
182A198LEU0-0.066-0.03641.9410.0010.0010.0000.0000.0000.000
183A199ASP-1-0.820-0.88445.848-0.081-0.0810.0000.0000.0000.000
184A200GLY0-0.0300.00449.0510.0030.0030.0000.0000.0000.000
185A201VAL00.005-0.01450.6580.0010.0010.0000.0000.0000.000
186A202CYS0-0.067-0.02653.1900.0030.0030.0000.0000.0000.000
187A203PRO00.0180.00456.1840.0000.0000.0000.0000.0000.000
188A204ARG10.9760.99755.5650.0550.0550.0000.0000.0000.000