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About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: VQL41

Calculation Name: 4JZ5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4JZ5

Chain ID: A

ChEMBL ID:

UniProt ID: B6D7J9

Base Structure: X-ray

Registration Date: 2023-09-23

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 206
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2499556.468337
FMO2-HF: Nuclear repulsion 2418007.240526
FMO2-HF: Total energy -81549.227812
FMO2-MP2: Total energy -81786.545874


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:-3:GLY)


Summations of interaction energy for fragment #1(A:-3: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.
-3.144-0.665-0.019-1.328-1.1320.004
Interaction energy analysis for fragmet #1(A:-3:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.022 / q_NPA : 0.010
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].
3A-1HIS00.0420.0213.766-0.4281.895-0.023-1.280-1.0200.004
4A0MET0-0.0330.0046.7670.6840.6840.0000.0000.0000.000
5A1MET0-0.051-0.0256.243-0.146-0.1460.0000.0000.0000.000
6A2VAL00.0280.0185.500-0.122-0.1220.0000.0000.0000.000
7A3LEU00.0280.0317.9610.1160.1160.0000.0000.0000.000
8A4VAL0-0.016-0.00711.681-0.014-0.0140.0000.0000.0000.000
9A5LEU00.0130.00614.233-0.004-0.0040.0000.0000.0000.000
10A6ASP-1-0.788-0.87617.8930.0890.0890.0000.0000.0000.000
11A7ILE00.0030.00321.133-0.018-0.0180.0000.0000.0000.000
12A8SER00.0370.00824.3230.0140.0140.0000.0000.0000.000
13A9LYS10.8580.94127.997-0.008-0.0080.0000.0000.0000.000
14A10TRP00.008-0.00729.174-0.009-0.0090.0000.0000.0000.000
15A11GLN00.0210.00725.1190.0000.0000.0000.0000.0000.000
16A12PRO00.0040.00728.421-0.002-0.0020.0000.0000.0000.000
17A13THR00.006-0.00229.6380.0030.0030.0000.0000.0000.000
18A14VAL00.0270.01823.618-0.005-0.0050.0000.0000.0000.000
19A15ASN0-0.016-0.00224.5660.0000.0000.0000.0000.0000.000
20A16TYR00.052-0.01222.701-0.021-0.0210.0000.0000.0000.000
21A17SER00.0230.01521.133-0.007-0.0070.0000.0000.0000.000
22A18GLY0-0.046-0.02320.340-0.034-0.0340.0000.0000.0000.000
23A19LEU0-0.018-0.01917.994-0.021-0.0210.0000.0000.0000.000
24A20LYS10.8190.89316.0890.2080.2080.0000.0000.0000.000
25A21GLU-1-0.976-0.96614.376-0.617-0.6170.0000.0000.0000.000
26A22ASP-1-0.851-0.93111.907-0.817-0.8170.0000.0000.0000.000
27A23VAL0-0.107-0.04711.6140.0250.0250.0000.0000.0000.000
28A24GLY00.0040.00111.085-0.024-0.0240.0000.0000.0000.000
29A25PHE0-0.012-0.02912.0010.0720.0720.0000.0000.0000.000
30A26VAL00.0030.00415.078-0.023-0.0230.0000.0000.0000.000
31A27VAL0-0.0020.01118.4750.0180.0180.0000.0000.0000.000
32A28ILE0-0.011-0.00521.013-0.018-0.0180.0000.0000.0000.000
33A29ARG10.8590.92924.592-0.017-0.0170.0000.0000.0000.000
34A30SER00.001-0.01827.705-0.008-0.0080.0000.0000.0000.000
35A31SER00.011-0.00530.180-0.005-0.0050.0000.0000.0000.000
36A32ASN0-0.0240.00632.3800.0040.0040.0000.0000.0000.000
37A33GLY00.0650.02834.990-0.004-0.0040.0000.0000.0000.000
38A34THR00.006-0.02336.8510.0000.0000.0000.0000.0000.000
39A35GLN0-0.0430.00839.224-0.003-0.0030.0000.0000.0000.000
40A36LYS10.8590.91036.237-0.020-0.0200.0000.0000.0000.000
41A37TYR00.0330.00534.2310.0060.0060.0000.0000.0000.000
42A38ASP-1-0.751-0.86331.2480.0070.0070.0000.0000.0000.000
43A39GLU-1-0.762-0.89433.4080.0060.0060.0000.0000.0000.000
44A40ARG10.8550.92130.5190.0270.0270.0000.0000.0000.000
45A41LEU00.0130.02828.991-0.004-0.0040.0000.0000.0000.000
46A42GLU-1-0.799-0.90829.5470.0020.0020.0000.0000.0000.000
47A43GLN0-0.049-0.01629.5010.0000.0000.0000.0000.0000.000
48A44HIS00.0400.02625.863-0.016-0.0160.0000.0000.0000.000
49A45ALA00.0140.01425.871-0.006-0.0060.0000.0000.0000.000
50A46LYS10.9210.96626.4310.0100.0100.0000.0000.0000.000
51A47GLY0-0.030-0.01026.651-0.009-0.0090.0000.0000.0000.000
52A48LEU0-0.024-0.03220.585-0.021-0.0210.0000.0000.0000.000
53A49ASP-1-0.858-0.93022.371-0.033-0.0330.0000.0000.0000.000
54A50LYS10.9220.97624.1190.0930.0930.0000.0000.0000.000
55A51VAL0-0.054-0.02620.688-0.013-0.0130.0000.0000.0000.000
56A52GLY00.0800.05120.010-0.034-0.0340.0000.0000.0000.000
57A53MET0-0.131-0.04715.958-0.006-0.0060.0000.0000.0000.000
58A54PRO00.0070.01014.8540.0240.0240.0000.0000.0000.000
59A55PHE00.032-0.01117.933-0.007-0.0070.0000.0000.0000.000
60A56GLY00.0730.04220.0340.0210.0210.0000.0000.0000.000
61A57LEU0-0.048-0.01921.900-0.023-0.0230.0000.0000.0000.000
62A58TYR00.016-0.01424.0640.0200.0200.0000.0000.0000.000
63A59HIS10.7590.88226.137-0.091-0.0910.0000.0000.0000.000
64A60TYR0-0.054-0.04129.6740.0090.0090.0000.0000.0000.000
65A61ALA0-0.031-0.02931.344-0.006-0.0060.0000.0000.0000.000
66A62LEU0-0.068-0.04233.727-0.003-0.0030.0000.0000.0000.000
67A63PHE00.0030.02033.943-0.002-0.0020.0000.0000.0000.000
68A64GLU-1-0.809-0.91639.0110.0490.0490.0000.0000.0000.000
69A65GLY00.0270.02341.1660.0000.0000.0000.0000.0000.000
70A66GLY00.0130.00542.141-0.003-0.0030.0000.0000.0000.000
71A67GLN00.034-0.00442.2830.0060.0060.0000.0000.0000.000
72A68ASP-1-0.802-0.89741.5610.0570.0570.0000.0000.0000.000
73A69THR0-0.027-0.03936.958-0.001-0.0010.0000.0000.0000.000
74A70ILE00.0100.00837.5110.0040.0040.0000.0000.0000.000
75A71ASN0-0.0010.00638.5040.0010.0010.0000.0000.0000.000
76A72GLU-1-0.718-0.84935.8010.0680.0680.0000.0000.0000.000
77A73ALA0-0.0080.00134.0230.0010.0010.0000.0000.0000.000
78A74ASN00.0370.00934.3000.0050.0050.0000.0000.0000.000
79A75MET0-0.0250.02535.560-0.004-0.0040.0000.0000.0000.000
80A76LEU0-0.0170.00428.117-0.004-0.0040.0000.0000.0000.000
81A77VAL00.0250.00831.465-0.001-0.0010.0000.0000.0000.000
82A78SER0-0.033-0.03133.194-0.004-0.0040.0000.0000.0000.000
83A79ALA0-0.023-0.01331.208-0.006-0.0060.0000.0000.0000.000
84A80TYR00.0390.01726.515-0.008-0.0080.0000.0000.0000.000
85A81LYS10.9780.98630.340-0.069-0.0690.0000.0000.0000.000
86A82LYS10.8750.93833.341-0.025-0.0250.0000.0000.0000.000
87A83CYS0-0.065-0.03228.308-0.008-0.0080.0000.0000.0000.000
88A84ARG10.8720.90228.834-0.066-0.0660.0000.0000.0000.000
89A85GLN0-0.095-0.03130.931-0.002-0.0020.0000.0000.0000.000
90A86LEU0-0.098-0.06431.418-0.007-0.0070.0000.0000.0000.000
91A87GLY00.0120.01530.407-0.008-0.0080.0000.0000.0000.000
92A88ALA0-0.0010.02026.331-0.001-0.0010.0000.0000.0000.000
93A89GLU-1-0.785-0.87524.0560.0720.0720.0000.0000.0000.000
94A90PRO0-0.080-0.02923.1000.0080.0080.0000.0000.0000.000
95A91THR00.016-0.01618.720-0.006-0.0060.0000.0000.0000.000
96A92PHE0-0.045-0.02718.6550.0410.0410.0000.0000.0000.000
97A93LEU0-0.029-0.00221.772-0.031-0.0310.0000.0000.0000.000
98A94PHE00.0220.01318.9130.0220.0220.0000.0000.0000.000
99A95LEU0-0.0110.00925.041-0.021-0.0210.0000.0000.0000.000
100A96ASH0-0.087-0.09026.5480.0100.0100.0000.0000.0000.000
101A97TYR00.043-0.00427.947-0.011-0.0110.0000.0000.0000.000
102A98GLU-1-0.828-0.88229.1670.0860.0860.0000.0000.0000.000
103A99GLU-1-0.816-0.87631.3380.0460.0460.0000.0000.0000.000
104A100VAL0-0.025-0.01835.1470.0050.0050.0000.0000.0000.000
105A101LYS10.8940.93537.955-0.053-0.0530.0000.0000.0000.000
106A102LEU0-0.072-0.01938.546-0.002-0.0020.0000.0000.0000.000
107A103LYS10.8670.92641.921-0.049-0.0490.0000.0000.0000.000
108A104SER0-0.028-0.01144.623-0.001-0.0010.0000.0000.0000.000
109A105GLY00.0500.02942.8670.0020.0020.0000.0000.0000.000
110A106ASN00.009-0.00237.8520.0040.0040.0000.0000.0000.000
111A107VAL00.0620.02133.8230.0020.0020.0000.0000.0000.000
112A108VAL00.0360.03432.8740.0030.0030.0000.0000.0000.000
113A109ASN00.017-0.00134.4350.0090.0090.0000.0000.0000.000
114A110GLU-1-0.792-0.86336.7200.0870.0870.0000.0000.0000.000
115A111CYS0-0.031-0.01731.328-0.001-0.0010.0000.0000.0000.000
116A112GLN0-0.033-0.02130.5600.0090.0090.0000.0000.0000.000
117A113ARG10.8350.90533.418-0.084-0.0840.0000.0000.0000.000
118A114PHE0-0.0010.00330.136-0.001-0.0010.0000.0000.0000.000
119A115ILE00.021-0.00727.509-0.001-0.0010.0000.0000.0000.000
120A116ASP-1-0.846-0.91330.9790.1530.1530.0000.0000.0000.000
121A117HIS0-0.037-0.02533.0440.0010.0010.0000.0000.0000.000
122A118VAL00.002-0.00929.464-0.003-0.0030.0000.0000.0000.000
123A119LYS10.8600.92526.147-0.216-0.2160.0000.0000.0000.000
124A120GLY0-0.0050.00430.3040.0010.0010.0000.0000.0000.000
125A121GLN0-0.067-0.02633.662-0.010-0.0100.0000.0000.0000.000
126A122THR0-0.061-0.04929.597-0.003-0.0030.0000.0000.0000.000
127A123GLY00.0080.02029.300-0.002-0.0020.0000.0000.0000.000
128A124VAL0-0.035-0.00324.0880.0170.0170.0000.0000.0000.000
129A125LYS10.8670.92920.353-0.332-0.3320.0000.0000.0000.000
130A126VAL00.012-0.01023.971-0.016-0.0160.0000.0000.0000.000
131A127GLY00.0060.01422.3580.0180.0180.0000.0000.0000.000
132A128LEU0-0.031-0.01923.190-0.029-0.0290.0000.0000.0000.000
133A129TYR0-0.032-0.03722.1090.0230.0230.0000.0000.0000.000
134A130ALA00.0290.02324.396-0.016-0.0160.0000.0000.0000.000
135A131GLY00.0450.02824.5520.0140.0140.0000.0000.0000.000
136A132ASP-1-0.757-0.85324.1680.1680.1680.0000.0000.0000.000
137A133SER0-0.002-0.01225.7470.0050.0050.0000.0000.0000.000
138A134PHE00.0520.04329.479-0.001-0.0010.0000.0000.0000.000
139A135TRP00.026-0.01223.700-0.002-0.0020.0000.0000.0000.000
140A136LYS10.8690.93427.738-0.146-0.1460.0000.0000.0000.000
141A137THR0-0.040-0.03130.131-0.004-0.0040.0000.0000.0000.000
142A138HIS10.8370.91532.397-0.110-0.1100.0000.0000.0000.000
143A139ASP-1-0.786-0.87632.2590.1370.1370.0000.0000.0000.000
144A140LEU00.0270.00928.2870.0040.0040.0000.0000.0000.000
145A141ASP-1-0.821-0.87126.1160.2430.2430.0000.0000.0000.000
146A142LYS10.8160.89428.261-0.131-0.1310.0000.0000.0000.000
147A143VAL0-0.042-0.01028.713-0.006-0.0060.0000.0000.0000.000
148A144LYS10.8310.92327.775-0.160-0.1600.0000.0000.0000.000
149A145HIS00.0490.00122.868-0.008-0.0080.0000.0000.0000.000
150A146ASP-1-0.766-0.86721.5550.2970.2970.0000.0000.0000.000
151A147LEU0-0.050-0.02616.1570.0460.0460.0000.0000.0000.000
152A148ARG10.7980.89619.460-0.355-0.3550.0000.0000.0000.000
153A149TRP0-0.027-0.01018.6660.0460.0460.0000.0000.0000.000
154A150VAL00.0110.00219.414-0.030-0.0300.0000.0000.0000.000
155A151ALA00.0360.03019.9760.0080.0080.0000.0000.0000.000
156A152ARG10.8320.89121.355-0.125-0.1250.0000.0000.0000.000
157A153TYR00.0590.01621.1580.0040.0040.0000.0000.0000.000
158A154GLY0-0.0280.00523.084-0.012-0.0120.0000.0000.0000.000
159A155VAL0-0.024-0.02623.901-0.003-0.0030.0000.0000.0000.000
160A156ASP-1-0.768-0.83723.724-0.004-0.0040.0000.0000.0000.000
161A157ASN00.0240.00022.113-0.003-0.0030.0000.0000.0000.000
162A158GLY00.0440.02621.312-0.019-0.0190.0000.0000.0000.000
163A159LYS10.9020.94316.2060.2240.2240.0000.0000.0000.000
164A160PRO00.0080.00814.0130.0230.0230.0000.0000.0000.000
165A161SER00.0570.03317.167-0.014-0.0140.0000.0000.0000.000
166A162THR0-0.041-0.03319.1820.0200.0200.0000.0000.0000.000
167A163LYS10.9851.00513.300-0.404-0.4040.0000.0000.0000.000
168A164PRO0-0.034-0.01818.479-0.021-0.0210.0000.0000.0000.000
169A165SER0-0.057-0.05121.2640.0110.0110.0000.0000.0000.000
170A166ILE00.0090.01822.585-0.001-0.0010.0000.0000.0000.000
171A167PRO00.0480.01219.3740.0130.0130.0000.0000.0000.000
172A168TYR0-0.014-0.00713.216-0.052-0.0520.0000.0000.0000.000
173A169ASP-1-0.778-0.89215.0790.5730.5730.0000.0000.0000.000
174A170LEU0-0.038-0.02813.7590.0860.0860.0000.0000.0000.000
175A171TRP0-0.057-0.03214.304-0.027-0.0270.0000.0000.0000.000
176A172GLN00.0520.03216.136-0.011-0.0110.0000.0000.0000.000
177A173TYR00.003-0.01814.008-0.013-0.0130.0000.0000.0000.000
178A174THR0-0.069-0.04418.860-0.025-0.0250.0000.0000.0000.000
179A175SER00.0570.02421.3800.0010.0010.0000.0000.0000.000
180A176LYS10.7790.87823.377-0.002-0.0020.0000.0000.0000.000
181A177GLY00.0220.00720.816-0.016-0.0160.0000.0000.0000.000
182A178ARG10.9510.96420.8200.1870.1870.0000.0000.0000.000
183A179ILE00.0490.01718.002-0.030-0.0300.0000.0000.0000.000
184A180LYS10.9840.98620.9150.2390.2390.0000.0000.0000.000
185A181ALA0-0.023-0.00121.5580.0150.0150.0000.0000.0000.000
186A182ILE00.003-0.00222.2820.0180.0180.0000.0000.0000.000
187A183ALA00.0000.00825.157-0.004-0.0040.0000.0000.0000.000
188A184SER0-0.028-0.01127.610-0.002-0.0020.0000.0000.0000.000
189A185PRO00.0120.01725.627-0.008-0.0080.0000.0000.0000.000
190A186VAL0-0.013-0.00820.8110.0070.0070.0000.0000.0000.000
191A187ASP-1-0.787-0.87721.4750.0210.0210.0000.0000.0000.000
192A188MET0-0.082-0.01815.853-0.013-0.0130.0000.0000.0000.000
193A189ASN00.0220.00315.5730.0550.0550.0000.0000.0000.000
194A190THR0-0.040-0.03110.0790.0110.0110.0000.0000.0000.000
195A191CYS00.003-0.0069.662-0.058-0.0580.0000.0000.0000.000
196A192SER00.0370.0327.3280.0390.0390.0000.0000.0000.000
197A193SER00.0820.0123.360-1.441-1.2850.004-0.048-0.1120.000
198A194ASP-1-0.922-0.9466.4340.9120.9120.0000.0000.0000.000
199A195ILE00.0240.0099.690-0.305-0.3050.0000.0000.0000.000
200A196LEU0-0.013-0.0028.065-0.203-0.2030.0000.0000.0000.000
201A197ASN0-0.038-0.02710.107-0.249-0.2490.0000.0000.0000.000
202A198LYS10.9070.96311.804-0.678-0.6780.0000.0000.0000.000
203A199LEU0-0.042-0.01413.321-0.093-0.0930.0000.0000.0000.000
204A200LYS10.8990.95110.608-0.181-0.1810.0000.0000.0000.000
205A201GLY00.0360.03315.862-0.045-0.0450.0000.0000.0000.000
206A202SER0-0.063-0.01515.272-0.050-0.0500.0000.0000.0000.000