FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 5J7MZ

Calculation Name: 3GQB-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3GQB

Chain ID: A

ChEMBL ID:

UniProt ID: Q56403

Base Structure: X-ray

Registration Date: 2023-09-24

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 OptAll
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 578
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -11855569.915935
FMO2-HF: Nuclear repulsion 11632881.87371
FMO2-HF: Total energy -222688.042224
FMO2-MP2: Total energy -223338.795293


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:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-8.399-2.1415.678-4.217-7.722-0.028
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.036 / q_NPA : -0.020
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].
3A3GLN00.0410.0063.8690.1881.696-0.018-0.614-0.8760.001
4A4GLY00.0510.0226.614-0.027-0.0270.0000.0000.0000.000
5A5VAL0-0.0200.0019.9240.0480.0480.0000.0000.0000.000
6A6ILE00.0030.01213.0100.0000.0000.0000.0000.0000.000
7A7GLN00.0070.00815.497-0.096-0.0960.0000.0000.0000.000
8A8LYS10.8940.93518.137-0.354-0.3540.0000.0000.0000.000
9A9ILE00.0670.04318.7360.0500.0500.0000.0000.0000.000
10A10ALA0-0.025-0.02720.944-0.045-0.0450.0000.0000.0000.000
11A11GLY00.0740.05023.305-0.001-0.0010.0000.0000.0000.000
12A12PRO00.0320.02820.2860.0270.0270.0000.0000.0000.000
13A13ALA00.0020.02518.9140.0590.0590.0000.0000.0000.000
14A14VAL00.004-0.01315.080-0.035-0.0350.0000.0000.0000.000
15A15ILE0-0.0280.00016.1550.0280.0280.0000.0000.0000.000
16A16ALA00.0200.01911.820-0.040-0.0400.0000.0000.0000.000
17A17LYS10.9260.95413.525-0.295-0.2950.0000.0000.0000.000
18A18GLY00.0270.00912.3200.0280.0280.0000.0000.0000.000
19A19MET0-0.0180.0176.902-0.180-0.1800.0000.0000.0000.000
20A20LEU0-0.020-0.0309.2710.1840.1840.0000.0000.0000.000
21A21GLY00.0270.0117.519-0.245-0.2450.0000.0000.0000.000
22A22ALA0-0.038-0.0076.1570.4160.4160.0000.0000.0000.000
23A23ARG10.8410.8976.993-1.608-1.6080.0000.0000.0000.000
24A24MET0-0.004-0.0039.3510.1560.1560.0000.0000.0000.000
25A25TYR0-0.004-0.01211.790-0.042-0.0420.0000.0000.0000.000
26A26ASP-1-0.783-0.8606.3902.6232.6230.0000.0000.0000.000
27A27ILE0-0.012-0.0117.509-0.088-0.0880.0000.0000.0000.000
28A28SER0-0.035-0.0266.9711.1781.1780.0000.0000.0000.000
29A29LYS10.8760.9463.854-4.492-4.2430.003-0.065-0.1880.000
30A30VAL00.004-0.0139.2060.0790.0790.0000.0000.0000.000
31A31GLY00.0600.02612.047-0.104-0.1040.0000.0000.0000.000
32A32GLU-1-0.937-0.98713.0890.5000.5000.0000.0000.0000.000
33A33GLU-1-0.825-0.87815.0130.4480.4480.0000.0000.0000.000
34A34GLY0-0.035-0.00611.5410.0190.0190.0000.0000.0000.000
35A35LEU0-0.027-0.00711.6090.1110.1110.0000.0000.0000.000
36A36VAL00.0300.01510.9460.1680.1680.0000.0000.0000.000
37A37GLY00.0350.01811.789-0.169-0.1690.0000.0000.0000.000
38A38GLU-1-0.823-0.87611.4980.7900.7900.0000.0000.0000.000
39A39ILE0-0.034-0.0128.533-0.102-0.1020.0000.0000.0000.000
40A40ILE0-0.004-0.00412.599-0.083-0.0830.0000.0000.0000.000
41A41ARG10.8970.94115.307-0.463-0.4630.0000.0000.0000.000
42A42LEU00.0060.01010.9990.0990.0990.0000.0000.0000.000
43A43ASP-1-0.926-0.96615.0870.2360.2360.0000.0000.0000.000
44A44GLY00.0420.03917.4740.0100.0100.0000.0000.0000.000
45A45ASP-1-0.934-0.96615.0460.3120.3120.0000.0000.0000.000
46A46THR0-0.087-0.07014.2090.0550.0550.0000.0000.0000.000
47A47ALA00.0400.01811.6900.0180.0180.0000.0000.0000.000
48A48PHE00.0140.00813.663-0.036-0.0360.0000.0000.0000.000
49A49VAL00.005-0.00811.7190.0710.0710.0000.0000.0000.000
50A50GLN00.0490.03914.605-0.121-0.1210.0000.0000.0000.000
51A51VAL00.003-0.01315.1060.0560.0560.0000.0000.0000.000
52A52TYR0-0.083-0.08914.893-0.071-0.0710.0000.0000.0000.000
53A53GLU-1-0.839-0.93015.5040.4890.4890.0000.0000.0000.000
54A54ASP-1-0.803-0.88719.4230.3500.3500.0000.0000.0000.000
55A55THR00.002-0.01518.1270.0110.0110.0000.0000.0000.000
56A56SER0-0.062-0.05620.572-0.010-0.0100.0000.0000.0000.000
57A57GLY00.0120.00323.3590.0030.0030.0000.0000.0000.000
58A58LEU0-0.0160.01316.697-0.002-0.0020.0000.0000.0000.000
59A59LYS10.8240.89419.574-0.388-0.3880.0000.0000.0000.000
60A60VAL0-0.021-0.03018.7180.0420.0420.0000.0000.0000.000
61A61GLY0-0.021-0.01117.599-0.032-0.0320.0000.0000.0000.000
62A62GLU-1-0.775-0.85215.4200.4820.4820.0000.0000.0000.000
63A63PRO00.0250.00110.6600.0170.0170.0000.0000.0000.000
64A64VAL0-0.019-0.0139.1060.0190.0190.0000.0000.0000.000
65A65VAL0-0.024-0.0054.455-0.134-0.058-0.001-0.013-0.0620.000
66A66SER00.0130.0184.2160.4360.7920.001-0.098-0.2600.000
67A67THR0-0.017-0.0342.383-0.4442.1194.102-3.065-3.601-0.018
68A68GLY00.0100.0122.540-5.197-3.6101.512-0.661-2.438-0.012
69A69LEU0-0.018-0.0143.266-2.024-2.1050.0790.299-0.2970.001
70A70PRO00.0390.0306.7610.4610.4610.0000.0000.0000.000
71A71LEU00.0140.00610.116-0.140-0.1400.0000.0000.0000.000
72A72ALA0-0.050-0.02510.261-0.102-0.1020.0000.0000.0000.000
73A73VAL0-0.0100.01012.3430.0530.0530.0000.0000.0000.000
74A74GLU-1-0.796-0.89511.808-0.189-0.1890.0000.0000.0000.000
75A75LEU0-0.006-0.00614.2170.0430.0430.0000.0000.0000.000
76A76GLY00.0800.02517.376-0.042-0.0420.0000.0000.0000.000
77A77PRO0-0.023-0.00519.4600.0220.0220.0000.0000.0000.000
78A78GLY0-0.047-0.04620.416-0.008-0.0080.0000.0000.0000.000
79A79MET0-0.071-0.00119.8650.0160.0160.0000.0000.0000.000
80A80LEU00.0050.00822.5530.0140.0140.0000.0000.0000.000
81A81ASN0-0.041-0.01926.231-0.006-0.0060.0000.0000.0000.000
82A82GLY00.0140.03123.9050.0050.0050.0000.0000.0000.000
83A83ILE00.0260.00424.1130.0020.0020.0000.0000.0000.000
84A84TYR0-0.049-0.02818.6520.0050.0050.0000.0000.0000.000
85A85ASP-1-0.755-0.86518.6150.2700.2700.0000.0000.0000.000
86A86GLY0-0.006-0.02620.345-0.011-0.0110.0000.0000.0000.000
87A87ILE0-0.083-0.04614.9880.0160.0160.0000.0000.0000.000
88A88GLN00.0120.00915.3410.0130.0130.0000.0000.0000.000
89A89ARG10.8960.93714.902-0.383-0.3830.0000.0000.0000.000
90A90PRO00.0070.00517.143-0.003-0.0030.0000.0000.0000.000
91A91LEU00.020-0.00120.1470.0100.0100.0000.0000.0000.000
92A92GLU-1-0.889-0.94722.8720.0990.0990.0000.0000.0000.000
93A93ARG10.8080.88919.716-0.056-0.0560.0000.0000.0000.000
94A94ILE0-0.022-0.01018.7740.0150.0150.0000.0000.0000.000
95A95ARG10.9600.99221.518-0.097-0.0970.0000.0000.0000.000
96A96GLU-1-0.881-0.93623.7630.0770.0770.0000.0000.0000.000
97A97LYS10.8530.93316.725-0.228-0.2280.0000.0000.0000.000
98A98THR0-0.036-0.03221.8110.0140.0140.0000.0000.0000.000
99A99GLY0-0.0130.01224.671-0.002-0.0020.0000.0000.0000.000
100A100ILE0-0.043-0.03627.6000.0010.0010.0000.0000.0000.000
101A101TYR0-0.009-0.00327.593-0.002-0.0020.0000.0000.0000.000
102A102ILE00.0280.02221.6260.0040.0040.0000.0000.0000.000
103A103THR0-0.023-0.00221.0840.0010.0010.0000.0000.0000.000
104A104ARG10.7060.81319.130-0.382-0.3820.0000.0000.0000.000
105A105GLY00.0620.01715.121-0.008-0.0080.0000.0000.0000.000
106A106VAL0-0.056-0.01915.0750.0180.0180.0000.0000.0000.000
107A107VAL0-0.0010.00710.666-0.016-0.0160.0000.0000.0000.000
108A108VAL0-0.048-0.03513.545-0.054-0.0540.0000.0000.0000.000
109A109HIS00.0090.0119.9490.0590.0590.0000.0000.0000.000
110A110ALA00.0080.01813.6670.0120.0120.0000.0000.0000.000
111A111LEU0-0.0320.00815.3520.0000.0000.0000.0000.0000.000
112A112ASP-1-0.817-0.92316.236-0.003-0.0030.0000.0000.0000.000
113A113ARG10.7860.85311.7590.1360.1360.0000.0000.0000.000
114A114GLU-1-0.909-0.94317.052-0.033-0.0330.0000.0000.0000.000
115A115LYS10.8090.92420.3930.0290.0290.0000.0000.0000.000
116A116LYS10.8700.93121.8020.0870.0870.0000.0000.0000.000
117A117TRP00.0470.00521.4680.0190.0190.0000.0000.0000.000
118A118ALA00.0280.01325.665-0.011-0.0110.0000.0000.0000.000
119A119TRP00.0140.00023.9360.0010.0010.0000.0000.0000.000
120A120THR0-0.029-0.02027.0840.0070.0070.0000.0000.0000.000
121A121PRO0-0.0120.00827.807-0.002-0.0020.0000.0000.0000.000
122A122MET0-0.026-0.01528.4100.0100.0100.0000.0000.0000.000
123A123VAL0-0.0290.00125.6590.0040.0040.0000.0000.0000.000
124A124LYS10.8020.87729.0560.1270.1270.0000.0000.0000.000
125A125PRO00.002-0.00928.187-0.006-0.0060.0000.0000.0000.000
126A126GLY00.0020.00728.7190.0130.0130.0000.0000.0000.000
127A127ASP-1-0.782-0.85728.732-0.134-0.1340.0000.0000.0000.000
128A128GLU-1-0.839-0.90127.720-0.194-0.1940.0000.0000.0000.000
129A129VAL0-0.010-0.01623.1030.0100.0100.0000.0000.0000.000
130A130ARG10.9320.93223.5960.1380.1380.0000.0000.0000.000
131A131GLY00.0690.03321.2270.0040.0040.0000.0000.0000.000
132A132GLY0-0.021-0.02021.9210.0200.0200.0000.0000.0000.000
133A133MET0-0.0230.01423.8640.0110.0110.0000.0000.0000.000
134A134VAL00.0180.01024.491-0.013-0.0130.0000.0000.0000.000
135A135LEU00.0190.01220.9160.0000.0000.0000.0000.0000.000
136A136GLY00.032-0.00925.3860.0010.0010.0000.0000.0000.000
137A137THR0-0.026-0.01226.8860.0060.0060.0000.0000.0000.000
138A138VAL00.0250.01624.007-0.005-0.0050.0000.0000.0000.000
139A139PRO0-0.0300.00527.2160.0050.0050.0000.0000.0000.000
140A140GLU-1-0.733-0.88324.530-0.036-0.0360.0000.0000.0000.000
141A141PHE0-0.042-0.02327.5440.0050.0050.0000.0000.0000.000
142A142GLY00.0220.00731.5980.0000.0000.0000.0000.0000.000
143A143PHE0-0.0060.01030.340-0.001-0.0010.0000.0000.0000.000
144A144THR0-0.019-0.01630.256-0.002-0.0020.0000.0000.0000.000
145A145HIS00.0090.01522.906-0.015-0.0150.0000.0000.0000.000
146A146LYS10.8290.90426.6550.0540.0540.0000.0000.0000.000
147A147ILE0-0.014-0.01221.122-0.003-0.0030.0000.0000.0000.000
148A148LEU00.0000.00421.467-0.007-0.0070.0000.0000.0000.000
149A149VAL0-0.0270.00019.829-0.026-0.0260.0000.0000.0000.000
150A150PRO00.0250.01615.4810.0270.0270.0000.0000.0000.000
151A151PRO00.007-0.00417.760-0.003-0.0030.0000.0000.0000.000
152A152ASP-1-0.833-0.90616.304-0.233-0.2330.0000.0000.0000.000
153A153VAL0-0.0070.01315.468-0.022-0.0220.0000.0000.0000.000
154A154ARG10.9050.93018.2730.2630.2630.0000.0000.0000.000
155A155GLY0-0.0110.00520.983-0.029-0.0290.0000.0000.0000.000
156A156ARG10.7710.86723.2330.2010.2010.0000.0000.0000.000
157A157VAL00.0040.00424.016-0.028-0.0280.0000.0000.0000.000
158A158LYS10.8060.91021.4480.3280.3280.0000.0000.0000.000
159A159GLU-1-0.831-0.92321.822-0.272-0.2720.0000.0000.0000.000
160A160VAL0-0.013-0.01223.784-0.015-0.0150.0000.0000.0000.000
161A161LYS10.8310.94821.0260.2230.2230.0000.0000.0000.000
162A162PRO00.0320.02025.5900.0080.0080.0000.0000.0000.000
163A163ALA00.0330.00628.238-0.003-0.0030.0000.0000.0000.000
164A164GLY0-0.0060.00629.0410.0030.0030.0000.0000.0000.000
165A165GLU-1-0.944-0.96326.893-0.066-0.0660.0000.0000.0000.000
166A166TYR0-0.044-0.02621.762-0.005-0.0050.0000.0000.0000.000
167A167THR00.0450.01217.9810.0020.0020.0000.0000.0000.000
168A168VAL00.0290.00215.732-0.020-0.0200.0000.0000.0000.000
169A169GLU-1-0.803-0.87011.839-0.461-0.4610.0000.0000.0000.000
170A170GLU-1-0.827-0.92614.884-0.229-0.2290.0000.0000.0000.000
171A171PRO0-0.0120.00015.5800.0100.0100.0000.0000.0000.000
172A172VAL0-0.016-0.01517.8990.0330.0330.0000.0000.0000.000
173A173VAL0-0.018-0.00720.2170.0260.0260.0000.0000.0000.000
174A174VAL00.0030.01618.188-0.036-0.0360.0000.0000.0000.000
175A175LEU00.0230.01319.1320.0390.0390.0000.0000.0000.000
176A176GLU-1-0.888-0.95721.274-0.232-0.2320.0000.0000.0000.000
177A177ASP-1-0.900-0.93017.665-0.505-0.5050.0000.0000.0000.000
178A178GLY00.0020.01217.764-0.031-0.0310.0000.0000.0000.000
179A179THR0-0.070-0.05414.742-0.055-0.0550.0000.0000.0000.000
180A180GLU-1-0.904-0.96113.439-0.482-0.4820.0000.0000.0000.000
181A181LEU0-0.035-0.02515.184-0.030-0.0300.0000.0000.0000.000
182A182LYS10.8650.93511.9800.5550.5550.0000.0000.0000.000
183A183MET0-0.033-0.01217.2700.0170.0170.0000.0000.0000.000
184A184TYR0-0.044-0.03910.8570.0190.0190.0000.0000.0000.000
185A185HIS00.0350.02113.412-0.035-0.0350.0000.0000.0000.000
186A186THR00.0310.0159.0370.0650.0650.0000.0000.0000.000
187A187TRP0-0.027-0.03912.217-0.054-0.0540.0000.0000.0000.000
188A188PRO00.0210.01012.4320.0510.0510.0000.0000.0000.000
189A189VAL00.0510.01913.745-0.010-0.0100.0000.0000.0000.000
190A190ARG10.7800.88416.466-0.357-0.3570.0000.0000.0000.000
191A191ARG10.7770.89515.7350.1140.1140.0000.0000.0000.000
192A192ALA00.0330.02818.853-0.014-0.0140.0000.0000.0000.000
193A193ARG10.8040.90317.4570.0880.0880.0000.0000.0000.000
194A194PRO0-0.008-0.00720.5740.0070.0070.0000.0000.0000.000
195A195VAL00.0100.00923.597-0.007-0.0070.0000.0000.0000.000
196A196GLN0-0.066-0.02626.9990.0020.0020.0000.0000.0000.000
197A197ARG10.9530.96929.7900.0300.0300.0000.0000.0000.000
198A198LYS10.8780.95129.674-0.013-0.0130.0000.0000.0000.000
199A199LEU0-0.073-0.03933.017-0.002-0.0020.0000.0000.0000.000
200A200ASP-1-0.844-0.91036.439-0.007-0.0070.0000.0000.0000.000
201A201PRO00.008-0.01539.527-0.001-0.0010.0000.0000.0000.000
202A202ASN0-0.023-0.01140.9160.0010.0010.0000.0000.0000.000
203A203THR00.0170.00340.762-0.003-0.0030.0000.0000.0000.000
204A204PRO00.0320.03041.8100.0020.0020.0000.0000.0000.000
205A205PHE00.0020.00036.421-0.002-0.0020.0000.0000.0000.000
206A206LEU0-0.022-0.00940.9780.0020.0020.0000.0000.0000.000
207A207THR0-0.058-0.04841.5870.0020.0020.0000.0000.0000.000
208A208GLY00.0040.00943.1510.0010.0010.0000.0000.0000.000
209A209MET0-0.051-0.02343.9260.0010.0010.0000.0000.0000.000
210A210ARG10.8220.87647.939-0.014-0.0140.0000.0000.0000.000
211A211ILE00.0070.00448.8140.0000.0000.0000.0000.0000.000
212A212LEU0-0.014-0.01043.6630.0010.0010.0000.0000.0000.000
213A213ASP-1-0.719-0.87146.1200.0130.0130.0000.0000.0000.000
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