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: 2JM7R

Calculation Name: 3WZ2-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3WZ2

Chain ID: A

ChEMBL ID:

UniProt ID: Q8U4Q9

Base Structure: X-ray

Registration Date: 2023-06-22

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 226
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2759258.754475
FMO2-HF: Nuclear repulsion 2672011.488314
FMO2-HF: Total energy -87247.266162
FMO2-MP2: Total energy -87501.715353


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:6:PRO)


Summations of interaction energy for fragment #1(A:6:PRO)
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.
-4.8841.0240.293-2.658-3.541-0.004
Interaction energy analysis for fragmet #1(A:6:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.001 / q_NPA : 0.006
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].
3A8ASN00.0020.0123.808-0.9681.607-0.027-1.258-1.2900.003
4A9LEU00.0160.0076.594-0.470-0.4700.0000.0000.0000.000
5A10VAL0-0.048-0.00710.0270.0560.0560.0000.0000.0000.000
6A11LEU00.018-0.00512.790-0.079-0.0790.0000.0000.0000.000
7A12PRO00.0140.02415.4380.0170.0170.0000.0000.0000.000
8A13GLU-1-0.931-0.95617.5160.1530.1530.0000.0000.0000.000
9A14VAL00.0020.00719.306-0.005-0.0050.0000.0000.0000.000
10A15GLU-1-0.948-0.97721.9110.0550.0550.0000.0000.0000.000
11A16ASN0-0.017-0.01624.256-0.005-0.0050.0000.0000.0000.000
12A17ALA00.0080.01921.216-0.006-0.0060.0000.0000.0000.000
13A18ILE00.0160.00323.309-0.011-0.0110.0000.0000.0000.000
14A19PHE00.0120.00215.5600.0040.0040.0000.0000.0000.000
15A20ILE00.0180.00221.086-0.013-0.0130.0000.0000.0000.000
16A21GLU-1-0.764-0.86616.704-0.103-0.1030.0000.0000.0000.000
17A22GLY00.0340.01119.579-0.004-0.0040.0000.0000.0000.000
18A23TYR0-0.048-0.03912.1590.0130.0130.0000.0000.0000.000
19A24PRO0-0.043-0.01416.8830.0010.0010.0000.0000.0000.000
20A25GLY00.0510.01418.928-0.019-0.0190.0000.0000.0000.000
21A26VAL00.0270.00621.5230.0090.0090.0000.0000.0000.000
22A27GLY00.0840.03725.1180.0030.0030.0000.0000.0000.000
23A28LEU0-0.036-0.01922.7940.0060.0060.0000.0000.0000.000
24A29VAL00.0100.02325.1950.0060.0060.0000.0000.0000.000
25A30GLY00.0420.01523.4630.0060.0060.0000.0000.0000.000
26A31HIS0-0.0060.00120.5860.0060.0060.0000.0000.0000.000
27A32ILE00.0250.01923.2420.0100.0100.0000.0000.0000.000
28A33ALA00.0160.01126.5740.0070.0070.0000.0000.0000.000
29A34ALA00.0110.00522.8510.0060.0060.0000.0000.0000.000
30A35ASN0-0.043-0.05022.4460.0170.0170.0000.0000.0000.000
31A36PHE0-0.0100.00425.5540.0060.0060.0000.0000.0000.000
32A37LEU00.0320.00327.2640.0040.0040.0000.0000.0000.000
33A38ALA00.0030.00724.8170.0040.0040.0000.0000.0000.000
34A39LYS10.9320.96626.914-0.010-0.0100.0000.0000.0000.000
35A40GLU-1-0.927-0.96829.6300.0140.0140.0000.0000.0000.000
36A41LEU0-0.091-0.04028.9620.0000.0000.0000.0000.0000.000
37A42ASP-1-0.974-0.98231.0660.0450.0450.0000.0000.0000.000
38A43MET0-0.071-0.02025.7670.0050.0050.0000.0000.0000.000
39A44ASP-1-0.862-0.91625.4510.0750.0750.0000.0000.0000.000
40A45LEU0-0.081-0.05518.888-0.001-0.0010.0000.0000.0000.000
41A46ILE0-0.003-0.00219.6490.0100.0100.0000.0000.0000.000
42A47GLY00.013-0.00716.5650.0290.0290.0000.0000.0000.000
43A48TYR0-0.067-0.03412.209-0.027-0.0270.0000.0000.0000.000
44A49VAL0-0.0160.0038.3140.0670.0670.0000.0000.0000.000
45A50ASP-1-0.924-0.9518.4390.7730.7730.0000.0000.0000.000
46A51SER00.006-0.0293.8550.1370.6240.000-0.285-0.2010.001
47A52LEU00.0030.0024.577-0.219-0.058-0.001-0.009-0.1510.000
48A53PHE0-0.043-0.0232.951-0.733-0.0220.137-0.182-0.6660.000
49A54ILE0-0.023-0.0027.160-0.045-0.0450.0000.0000.0000.000
50A55PRO0-0.015-0.0029.7700.0620.0620.0000.0000.0000.000
51A56PRO00.0090.00712.7120.0180.0180.0000.0000.0000.000
52A57MET0-0.005-0.01614.357-0.019-0.0190.0000.0000.0000.000
53A58SER0-0.046-0.01816.3270.0260.0260.0000.0000.0000.000
54A59LEU0-0.0060.01319.048-0.014-0.0140.0000.0000.0000.000
55A60ILE0-0.013-0.00921.4680.0120.0120.0000.0000.0000.000
56A61LEU00.0090.00323.168-0.009-0.0090.0000.0000.0000.000
57A62GLU-1-0.939-0.97526.3560.0490.0490.0000.0000.0000.000
58A63GLY0-0.027-0.01228.9670.0030.0030.0000.0000.0000.000
59A64ARG10.9600.98324.686-0.063-0.0630.0000.0000.0000.000
60A65PRO00.0010.00020.849-0.008-0.0080.0000.0000.0000.000
61A66THR0-0.026-0.00519.6320.0090.0090.0000.0000.0000.000
62A67PRO00.0530.03314.400-0.014-0.0140.0000.0000.0000.000
63A68PRO00.0570.00813.779-0.011-0.0110.0000.0000.0000.000
64A69LEU0-0.011-0.00210.530-0.035-0.0350.0000.0000.0000.000
65A70ARG10.8020.87614.1520.0140.0140.0000.0000.0000.000
66A71PHE00.0160.00312.733-0.031-0.0310.0000.0000.0000.000
67A72TYR00.0250.01518.3200.0170.0170.0000.0000.0000.000
68A73GLY00.0400.01122.006-0.005-0.0050.0000.0000.0000.000
69A74LYS10.9490.98223.930-0.046-0.0460.0000.0000.0000.000
70A75ASN0-0.030-0.00927.478-0.003-0.0030.0000.0000.0000.000
71A76ASN00.0760.03526.1330.0080.0080.0000.0000.0000.000
72A77ILE0-0.0190.00624.940-0.004-0.0040.0000.0000.0000.000
73A78ILE00.0180.00018.5300.0100.0100.0000.0000.0000.000
74A79ILE0-0.020-0.00621.392-0.014-0.0140.0000.0000.0000.000
75A80ALA0-0.023-0.00116.1720.0150.0150.0000.0000.0000.000
76A81ILE0-0.002-0.00117.703-0.020-0.0200.0000.0000.0000.000
77A82ALA0-0.008-0.01714.8910.0050.0050.0000.0000.0000.000
78A83ASP-1-0.793-0.89716.603-0.007-0.0070.0000.0000.0000.000
79A84ILE0-0.043-0.01312.4900.0000.0000.0000.0000.0000.000
80A85PHE00.0090.00715.458-0.015-0.0150.0000.0000.0000.000
81A86LEU00.0060.0029.506-0.005-0.0050.0000.0000.0000.000
82A87PRO00.0570.0239.4700.0060.0060.0000.0000.0000.000
83A88PRO00.0680.01710.318-0.073-0.0730.0000.0000.0000.000
84A89THR0-0.016-0.0196.5690.0190.0190.0000.0000.0000.000
85A90LEU00.0510.0404.833-0.198-0.1980.0000.0000.0000.000
86A91VAL00.0190.0176.864-0.047-0.0470.0000.0000.0000.000
87A92ASN0-0.023-0.0309.0300.1000.1000.0000.0000.0000.000
88A93GLU-1-0.940-0.9713.268-5.059-3.0850.184-0.924-1.233-0.008
89A94ILE00.0130.0115.7290.1760.1760.0000.0000.0000.000
90A95ALA00.0240.0017.7510.1520.1520.0000.0000.0000.000
91A96LYS10.9260.9796.2860.9160.9160.0000.0000.0000.000
92A97GLU-1-0.937-0.9725.3670.1790.1790.0000.0000.0000.000
93A98ILE00.002-0.0018.3150.1050.1050.0000.0000.0000.000
94A99VAL00.0150.00711.7360.0440.0440.0000.0000.0000.000
95A100ASN0-0.053-0.0328.5360.0010.0010.0000.0000.0000.000
96A101TYR0-0.048-0.05112.2250.0250.0250.0000.0000.0000.000
97A102LEU00.014-0.00513.7990.0030.0030.0000.0000.0000.000
98A103LYS10.9490.97014.6740.0950.0950.0000.0000.0000.000
99A104LYS10.8800.96613.262-0.248-0.2480.0000.0000.0000.000
100A105VAL0-0.038-0.01017.1660.0040.0040.0000.0000.0000.000
101A106ASN0-0.066-0.02819.782-0.014-0.0140.0000.0000.0000.000
102A107ALA0-0.0150.00020.041-0.001-0.0010.0000.0000.0000.000
103A108GLU-1-0.915-0.94922.0140.0010.0010.0000.0000.0000.000
104A109LYS10.8790.93324.0760.0050.0050.0000.0000.0000.000
105A110VAL0-0.0090.00718.5270.0050.0050.0000.0000.0000.000
106A111ILE0-0.001-0.00621.626-0.008-0.0080.0000.0000.0000.000
107A112SER0-0.032-0.02019.3760.0030.0030.0000.0000.0000.000
108A113LEU0-0.038-0.01222.0610.0040.0040.0000.0000.0000.000
109A114ALA00.0330.00523.104-0.007-0.0070.0000.0000.0000.000
110A115GLY00.0210.01424.6470.0090.0090.0000.0000.0000.000
111A116MET0-0.039-0.02726.570-0.007-0.0070.0000.0000.0000.000
112A117GLY0-0.008-0.00628.9180.0050.0050.0000.0000.0000.000
113A118ILE0-0.050-0.02730.543-0.002-0.0020.0000.0000.0000.000
114A119GLY0-0.010-0.00133.9570.0000.0000.0000.0000.0000.000
115A120PHE0-0.064-0.03935.1520.0020.0020.0000.0000.0000.000
116A121PHE0-0.017-0.00337.716-0.001-0.0010.0000.0000.0000.000
117A122LYS10.8340.90738.2570.0360.0360.0000.0000.0000.000
118A123ASP-1-0.891-0.95141.043-0.022-0.0220.0000.0000.0000.000
119A124THR0-0.045-0.02641.0700.0020.0020.0000.0000.0000.000
120A125PHE0-0.033-0.00735.904-0.001-0.0010.0000.0000.0000.000
121A126GLU-1-0.907-0.95437.064-0.025-0.0250.0000.0000.0000.000
122A127VAL0-0.026-0.02531.676-0.003-0.0030.0000.0000.0000.000
123A128TRP0-0.097-0.05931.5180.0010.0010.0000.0000.0000.000
124A129GLY00.0410.01529.7400.0000.0000.0000.0000.0000.000
125A130ILE0-0.079-0.03925.991-0.001-0.0010.0000.0000.0000.000
126A131GLY00.0680.03127.0140.0000.0000.0000.0000.0000.000
127A132GLY0-0.035-0.02924.488-0.005-0.0050.0000.0000.0000.000
128A133SER0-0.048-0.04925.210-0.003-0.0030.0000.0000.0000.000
129A134GLU-1-0.877-0.95928.316-0.040-0.0400.0000.0000.0000.000
130A135GLU-1-0.907-0.95330.743-0.022-0.0220.0000.0000.0000.000
131A136GLU-1-0.779-0.84727.012-0.040-0.0400.0000.0000.0000.000
132A137ASN00.0350.01030.3110.0000.0000.0000.0000.0000.000
133A138LYS10.9310.97132.2920.0330.0330.0000.0000.0000.000
134A139GLU-1-0.785-0.84231.178-0.021-0.0210.0000.0000.0000.000
135A140LEU00.0050.01729.3060.0020.0020.0000.0000.0000.000
136A141GLU-1-0.935-0.97333.783-0.033-0.0330.0000.0000.0000.000
137A142SER0-0.124-0.06636.7080.0030.0030.0000.0000.0000.000
138A143LEU0-0.022-0.00933.8600.0020.0020.0000.0000.0000.000
139A144GLY0-0.048-0.02337.8510.0010.0010.0000.0000.0000.000
140A145VAL0-0.0230.00232.706-0.001-0.0010.0000.0000.0000.000
141A146LYS10.9440.97136.1090.0300.0300.0000.0000.0000.000
142A147ILE00.0190.01232.094-0.002-0.0020.0000.0000.0000.000
143A148LEU0-0.015-0.00228.6310.0010.0010.0000.0000.0000.000
144A149LYS10.9130.95631.6980.0440.0440.0000.0000.0000.000
145A150TYR00.012-0.00531.414-0.002-0.0020.0000.0000.0000.000
146A151GLY00.0280.01629.5790.0040.0040.0000.0000.0000.000
147A152SER0-0.059-0.02824.448-0.007-0.0070.0000.0000.0000.000
148A153ILE00.0670.03521.7120.0050.0050.0000.0000.0000.000
149A154THR0-0.013-0.00219.626-0.012-0.0120.0000.0000.0000.000
150A155GLY00.0290.01116.1840.0090.0090.0000.0000.0000.000
151A156MET00.0190.00811.342-0.014-0.0140.0000.0000.0000.000
152A157SER00.008-0.00815.6530.0020.0020.0000.0000.0000.000
153A158GLY00.0290.02219.0550.0090.0090.0000.0000.0000.000
154A159LYS10.8480.93611.7350.4050.4050.0000.0000.0000.000
155A160LEU00.0570.00714.240-0.004-0.0040.0000.0000.0000.000
156A161LEU00.0160.03516.5860.0110.0110.0000.0000.0000.000
157A162TRP0-0.0040.00217.0890.0190.0190.0000.0000.0000.000
158A163GLU-1-0.928-0.98913.456-0.251-0.2510.0000.0000.0000.000
159A164ALA00.0040.00416.5810.0110.0110.0000.0000.0000.000
160A165SER00.0100.02118.2000.0130.0130.0000.0000.0000.000
161A166ARG10.9180.95416.9590.1700.1700.0000.0000.0000.000
162A167ALA0-0.125-0.05917.0840.0040.0040.0000.0000.0000.000
163A168GLY0-0.010-0.00119.1990.0130.0130.0000.0000.0000.000
164A169LEU0-0.031-0.00318.2560.0090.0090.0000.0000.0000.000
165A170LYS10.8030.89222.4030.0160.0160.0000.0000.0000.000
166A171SER0-0.008-0.00521.1260.0030.0030.0000.0000.0000.000
167A172TYR0-0.026-0.08723.3750.0020.0020.0000.0000.0000.000
168A173VAL0-0.034-0.00222.558-0.005-0.0050.0000.0000.0000.000
169A174LEU00.0130.00825.0910.0040.0040.0000.0000.0000.000
170A175LEU0-0.045-0.02826.161-0.005-0.0050.0000.0000.0000.000
171A176GLY00.0490.02928.8020.0040.0040.0000.0000.0000.000
172A177GLU-1-0.815-0.87730.442-0.044-0.0440.0000.0000.0000.000
173A178THR0-0.026-0.05929.4900.0020.0020.0000.0000.0000.000
174A179PHE00.0420.01732.817-0.002-0.0020.0000.0000.0000.000
175A180GLY00.013-0.01729.821-0.002-0.0020.0000.0000.0000.000
176A181ASP-1-0.955-0.96529.088-0.053-0.0530.0000.0000.0000.000
177A182ARG10.8660.92930.5040.0360.0360.0000.0000.0000.000
178A183PRO0-0.034-0.01028.753-0.003-0.0030.0000.0000.0000.000
179A184ASP-1-0.749-0.84429.704-0.030-0.0300.0000.0000.0000.000
180A185PRO00.0330.00931.252-0.001-0.0010.0000.0000.0000.000
181A186ARG10.9540.98232.3690.0200.0200.0000.0000.0000.000
182A187ALA00.0390.03331.5570.0010.0010.0000.0000.0000.000
183A188ALA0-0.029-0.01929.4960.0000.0000.0000.0000.0000.000
184A189ALA00.007-0.00330.7150.0020.0020.0000.0000.0000.000
185A190ASN00.0640.03133.8890.0030.0030.0000.0000.0000.000
186A191VAL0-0.019-0.00528.0840.0000.0000.0000.0000.0000.000
187A192VAL0-0.016-0.00830.0520.0010.0010.0000.0000.0000.000
188A193GLU-1-0.937-0.96331.886-0.011-0.0110.0000.0000.0000.000
189A194VAL0-0.026-0.02232.3040.0020.0020.0000.0000.0000.000
190A195LEU00.0230.00527.4020.0010.0010.0000.0000.0000.000
191A196ASN00.0040.00331.2280.0050.0050.0000.0000.0000.000
192A197LYS10.9320.96433.9110.0130.0130.0000.0000.0000.000
193A198MET0-0.058-0.01228.3630.0000.0000.0000.0000.0000.000
194A199LEU0-0.034-0.02127.7990.0010.0010.0000.0000.0000.000
195A200GLY0-0.0200.02032.2890.0030.0030.0000.0000.0000.000
196A201LEU0-0.037-0.01530.3440.0030.0030.0000.0000.0000.000
197A202ASN0-0.061-0.04135.037-0.003-0.0030.0000.0000.0000.000
198A203VAL00.0200.00632.7410.0020.0020.0000.0000.0000.000
199A204SER00.0060.01236.031-0.003-0.0030.0000.0000.0000.000
200A205VAL00.0870.02034.6940.0010.0010.0000.0000.0000.000
201A206GLU-1-0.938-0.96736.919-0.006-0.0060.0000.0000.0000.000
202A207PRO0-0.019-0.01936.411-0.001-0.0010.0000.0000.0000.000
203A208LEU00.0000.01831.6510.0000.0000.0000.0000.0000.000
204A209LEU0-0.012-0.01735.469-0.002-0.0020.0000.0000.0000.000
205A210LYS10.9000.95738.232-0.002-0.0020.0000.0000.0000.000
206A211GLU-1-0.909-0.96035.6850.0020.0020.0000.0000.0000.000
207A212ALA0-0.023-0.00535.316-0.001-0.0010.0000.0000.0000.000
208A213GLU-1-0.926-0.96435.322-0.011-0.0110.0000.0000.0000.000
209A214MET00.0380.02434.623-0.001-0.0010.0000.0000.0000.000
210A215ILE0-0.020-0.01730.230-0.001-0.0010.0000.0000.0000.000
211A216GLU-1-0.886-0.93931.266-0.030-0.0300.0000.0000.0000.000
212A217GLU-1-0.965-0.97932.193-0.016-0.0160.0000.0000.0000.000
213A218GLN0-0.078-0.04428.9740.0000.0000.0000.0000.0000.000
214A219LEU0-0.021-0.01725.697-0.001-0.0010.0000.0000.0000.000
215A220ARG10.9931.00627.5080.0190.0190.0000.0000.0000.000
216A221ARG10.9520.97824.6130.0120.0120.0000.0000.0000.000
217A222MET00.0110.00720.513-0.003-0.0030.0000.0000.0000.000
218A223HIS00.0320.02323.436-0.011-0.0110.0000.0000.0000.000
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