Manual

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: 7GR9K

Calculation Name: 5FWH-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5FWH

Chain ID: A

ChEMBL ID:

UniProt ID: A4IKE7

Base Structure: X-ray

Registration Date: 2023-06-20

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 195
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2129747.702839
FMO2-HF: Nuclear repulsion 2052275.981933
FMO2-HF: Total energy -77471.720906
FMO2-MP2: Total energy -77696.785629


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.
-11.131-5.2368.51-5.182-9.223-0.039
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 : -0.002 / q_NPA : -0.019
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].
3A3GLN00.045-0.0072.5340.3691.9753.174-1.090-3.690-0.005
4A4LEU0-0.013-0.0035.802-0.764-0.740-0.001-0.009-0.0140.000
5A5TRP0-0.0130.0018.4550.1150.1150.0000.0000.0000.000
6A6VAL00.011-0.01111.332-0.027-0.0270.0000.0000.0000.000
7A7LEU00.0090.00914.250-0.027-0.0270.0000.0000.0000.000
8A8TYR00.0510.02716.3100.0190.0190.0000.0000.0000.000
9A9GLU-1-0.893-0.94620.1370.0410.0410.0000.0000.0000.000
10A10THR00.0300.03221.598-0.006-0.0060.0000.0000.0000.000
11A11TYR0-0.037-0.01617.188-0.018-0.0180.0000.0000.0000.000
12A12CYS0-0.038-0.01513.0710.0180.0180.0000.0000.0000.000
13A13GLN0-0.031-0.02511.8780.0200.0200.0000.0000.0000.000
14A14LEU0-0.010-0.0015.4900.0030.0030.0000.0000.0000.000
15A15PHE00.0380.0137.5570.0030.0030.0000.0000.0000.000
16A16SER0-0.004-0.0172.888-0.5980.2470.086-0.356-0.575-0.002
17A17LEU0-0.023-0.0175.583-0.450-0.4500.0000.0000.0000.000
18A18THR0-0.013-0.0095.7140.1810.1810.0000.0000.0000.000
19A19ASN0-0.077-0.0696.3450.4190.4190.0000.0000.0000.000
20A20GLU-1-0.896-0.9068.3721.5391.5390.0000.0000.0000.000
21A21GLU-1-0.900-0.93610.3620.7040.7040.0000.0000.0000.000
22A22LYS10.8940.92111.585-0.720-0.7200.0000.0000.0000.000
23A23VAL00.0090.00513.873-0.068-0.0680.0000.0000.0000.000
24A24ILE0-0.0320.00412.281-0.004-0.0040.0000.0000.0000.000
25A25VAL0-0.001-0.01515.554-0.077-0.0770.0000.0000.0000.000
26A26ILE00.0070.01415.4350.0220.0220.0000.0000.0000.000
27A27GLY00.032-0.01217.955-0.033-0.0330.0000.0000.0000.000
28A28ASN0-0.057-0.01920.1630.0140.0140.0000.0000.0000.000
29A29GLN0-0.0110.01322.226-0.027-0.0270.0000.0000.0000.000
30A30LEU0-0.021-0.03320.0630.0160.0160.0000.0000.0000.000
31A31GLU-1-0.973-0.97519.0050.2850.2850.0000.0000.0000.000
32A32HIS0-0.034-0.01318.3100.0330.0330.0000.0000.0000.000
33A33HIS00.0490.03813.350-0.043-0.0430.0000.0000.0000.000
34A34VAL0-0.0090.00412.1340.0170.0170.0000.0000.0000.000
35A35THR0-0.001-0.00614.793-0.024-0.0240.0000.0000.0000.000
36A36VAL00.003-0.00717.899-0.022-0.0220.0000.0000.0000.000
37A37SER00.012-0.02219.891-0.004-0.0040.0000.0000.0000.000
38A38SER0-0.041-0.00923.0170.0000.0000.0000.0000.0000.000
39A39PHE00.0110.01623.146-0.009-0.0090.0000.0000.0000.000
40A40SER0-0.054-0.06525.4250.0140.0140.0000.0000.0000.000
41A41PHE00.0400.00920.9650.0100.0100.0000.0000.0000.000
42A42ARG10.9130.96526.704-0.085-0.0850.0000.0000.0000.000
43A43ASN0-0.073-0.03628.1590.0050.0050.0000.0000.0000.000
44A44GLY00.0000.01327.1840.0050.0050.0000.0000.0000.000
45A45TYR00.0270.00322.141-0.006-0.0060.0000.0000.0000.000
46A46ILE00.000-0.00218.886-0.012-0.0120.0000.0000.0000.000
47A47GLN0-0.019-0.00118.9260.0230.0230.0000.0000.0000.000
48A48ILE00.0160.00413.405-0.051-0.0510.0000.0000.0000.000
49A49GLU-1-0.929-0.96115.0880.4690.4690.0000.0000.0000.000
50A50LYS10.9770.9878.032-1.731-1.7310.0000.0000.0000.000
51A51LYN0-0.0190.00213.053-0.019-0.0190.0000.0000.0000.000
52A52SER0-0.028-0.00612.6510.0480.0480.0000.0000.0000.000
53A53ASP-1-0.918-0.98713.9130.1310.1310.0000.0000.0000.000
54A54GLY0-0.0260.01510.8690.1090.1090.0000.0000.0000.000
55A55SER0-0.014-0.03311.0240.1250.1250.0000.0000.0000.000
56A56THR0-0.061-0.03411.363-0.102-0.1020.0000.0000.0000.000
57A57LEU0-0.018-0.0089.7630.1080.1080.0000.0000.0000.000
58A58ALA00.0570.03813.618-0.076-0.0760.0000.0000.0000.000
59A59VAL00.0170.00416.8740.0550.0550.0000.0000.0000.000
60A60LEU00.004-0.01618.851-0.045-0.0450.0000.0000.0000.000
61A61GLN0-0.0150.01121.9550.0090.0090.0000.0000.0000.000
62A62GLY00.011-0.00624.4430.0010.0010.0000.0000.0000.000
63A63GLY0-0.0130.00324.928-0.007-0.0070.0000.0000.0000.000
64A64ARG10.9050.95225.911-0.124-0.1240.0000.0000.0000.000
65A65GLN0-0.010-0.00821.2950.0210.0210.0000.0000.0000.000
66A66ILE0-0.063-0.03122.279-0.018-0.0180.0000.0000.0000.000
67A67GLY0-0.009-0.01020.837-0.024-0.0240.0000.0000.0000.000
68A68GLU-1-0.895-0.94317.2940.1440.1440.0000.0000.0000.000
69A69LEU0-0.0270.01213.730-0.045-0.0450.0000.0000.0000.000
70A70LYS10.9520.97713.0470.1740.1740.0000.0000.0000.000
71A71PRO00.0470.0009.1810.0050.0050.0000.0000.0000.000
72A72ARG10.8540.93210.3340.7290.7290.0000.0000.0000.000
73A73CYS0-0.076-0.00512.1350.0580.0580.0000.0000.0000.000
74A74SER00.030-0.00114.1550.0190.0190.0000.0000.0000.000
75A75ILE0-0.030-0.01616.723-0.007-0.0070.0000.0000.0000.000
76A76THR0-0.0130.00519.5420.0120.0120.0000.0000.0000.000
77A77ILE0-0.029-0.01721.1370.0020.0020.0000.0000.0000.000
78A78ASP-1-0.880-0.94824.0200.0540.0540.0000.0000.0000.000
79A79VAL0-0.019-0.01723.5710.0130.0130.0000.0000.0000.000
80A80ASP-1-0.844-0.89926.8490.0850.0850.0000.0000.0000.000
81A81GLY0-0.039-0.00129.308-0.009-0.0090.0000.0000.0000.000
82A82GLN0-0.032-0.02725.383-0.015-0.0150.0000.0000.0000.000
83A83GLN0-0.0260.00324.0420.0030.0030.0000.0000.0000.000
84A84MET00.0310.01618.9900.0120.0120.0000.0000.0000.000
85A85THR00.008-0.00217.406-0.015-0.0150.0000.0000.0000.000
86A86ILE0-0.0080.00414.0420.0280.0280.0000.0000.0000.000
87A87ALA00.0320.01313.102-0.053-0.0530.0000.0000.0000.000
88A88TRP0-0.019-0.0126.990-0.063-0.0630.0000.0000.0000.000
89A89SER00.0430.0135.3920.2310.2310.0000.0000.0000.000
90A90GLY00.021-0.0026.934-0.260-0.2600.0000.0000.0000.000
91A91GLU-1-0.961-0.9833.835-0.850-0.6060.000-0.118-0.1260.000
92A92GLU-1-0.946-0.9672.110-8.684-7.6313.745-2.495-2.303-0.031
93A93GLN0-0.058-0.0432.164-0.8200.9561.508-1.094-2.189-0.001
94A94ARG10.9070.9734.1400.7481.008-0.001-0.017-0.2430.000
95A95LYS10.9720.9656.4601.4941.4940.0000.0000.0000.000
96A96TYR0-0.026-0.0208.4800.0710.0710.0000.0000.0000.000
97A97VAL0-0.032-0.03712.197-0.038-0.0380.0000.0000.0000.000
98A98TYR00.0860.04214.3760.0240.0240.0000.0000.0000.000
99A99TYR0-0.023-0.01517.8430.0120.0120.0000.0000.0000.000
100A100VAL00.020-0.01120.0650.0150.0150.0000.0000.0000.000
101A101GLY00.0210.00522.5650.0180.0180.0000.0000.0000.000
102A102GLN0-0.088-0.03525.0900.0220.0220.0000.0000.0000.000
103A103GLN0-0.0160.00623.9500.0110.0110.0000.0000.0000.000
104A104SER0-0.002-0.01626.438-0.001-0.0010.0000.0000.0000.000
105A105GLU-1-0.860-0.93125.932-0.179-0.1790.0000.0000.0000.000
106A106VAL00.0000.01319.981-0.009-0.0090.0000.0000.0000.000
107A107LEU0-0.030-0.00622.9060.0070.0070.0000.0000.0000.000
108A108VAL0-0.0060.00617.813-0.022-0.0220.0000.0000.0000.000
109A109SER00.008-0.02421.0420.0180.0180.0000.0000.0000.000
110A110ASN00.0380.01522.074-0.036-0.0360.0000.0000.0000.000
111A111ASP-1-0.889-0.92123.665-0.177-0.1770.0000.0000.0000.000
112A112PRO00.013-0.01125.607-0.014-0.0140.0000.0000.0000.000
113A113GLN0-0.066-0.04327.154-0.002-0.0020.0000.0000.0000.000
114A114ALA0-0.0240.02823.0110.0040.0040.0000.0000.0000.000
115A115ASP-1-0.799-0.89922.609-0.267-0.2670.0000.0000.0000.000
116A116ILE0-0.058-0.02216.495-0.040-0.0400.0000.0000.0000.000
117A117GLU-1-0.903-0.96119.595-0.278-0.2780.0000.0000.0000.000
118A118THR0-0.053-0.03016.028-0.036-0.0360.0000.0000.0000.000
119A119THR00.008-0.00318.4650.0300.0300.0000.0000.0000.000
120A120ASN0-0.066-0.05614.1420.0700.0700.0000.0000.0000.000
121A121ALA0-0.027-0.01616.7990.0210.0210.0000.0000.0000.000
122A122ARG10.8930.93518.9020.1760.1760.0000.0000.0000.000
123A123PHE0-0.038-0.00716.4850.0170.0170.0000.0000.0000.000
124A124SER0-0.0130.00822.281-0.009-0.0090.0000.0000.0000.000
125A125LEU00.0170.00117.9970.0020.0020.0000.0000.0000.000
126A126ARG10.8920.92522.6300.1650.1650.0000.0000.0000.000
127A127LYS10.8420.94124.8200.2110.2110.0000.0000.0000.000
128A128HIS00.002-0.00926.6060.0140.0140.0000.0000.0000.000
129A129ARG10.8610.92328.6980.1070.1070.0000.0000.0000.000
130A130GLY00.0550.01627.4390.0060.0060.0000.0000.0000.000
131A131GLN0-0.035-0.00224.736-0.007-0.0070.0000.0000.0000.000
132A132TRP00.0150.01021.1840.0110.0110.0000.0000.0000.000
133A133VAL0-0.043-0.02722.9820.0080.0080.0000.0000.0000.000
134A134VAL00.0440.02919.513-0.014-0.0140.0000.0000.0000.000
135A135ILE0-0.050-0.03422.1700.0220.0220.0000.0000.0000.000
136A136PRO00.003-0.00622.095-0.015-0.0150.0000.0000.0000.000
137A137ASP-1-0.869-0.94323.670-0.140-0.1400.0000.0000.0000.000
138A138ASP-1-0.978-0.97325.097-0.098-0.0980.0000.0000.0000.000
139A139ASP-1-0.935-0.97326.624-0.141-0.1410.0000.0000.0000.000
140A140ALA0-0.022-0.01421.0930.0040.0040.0000.0000.0000.000
141A141PRO0-0.034-0.01719.728-0.003-0.0030.0000.0000.0000.000
142A142LEU00.0060.01816.144-0.019-0.0190.0000.0000.0000.000
143A143PHE0-0.041-0.03514.6390.0310.0310.0000.0000.0000.000
144A144LEU00.0250.02015.059-0.046-0.0460.0000.0000.0000.000
145A145ASN0-0.042-0.04113.256-0.009-0.0090.0000.0000.0000.000
146A146GLY00.0270.01513.7480.0370.0370.0000.0000.0000.000
147A147VAL0-0.0080.00114.5210.0330.0330.0000.0000.0000.000
148A148GLN0-0.028-0.01818.257-0.011-0.0110.0000.0000.0000.000
149A149LEU0-0.023-0.00918.7670.0060.0060.0000.0000.0000.000
150A150SER00.002-0.00622.1770.0020.0020.0000.0000.0000.000
151A151ASP-1-0.954-0.96925.496-0.086-0.0860.0000.0000.0000.000
152A152ALA0-0.017-0.01624.961-0.010-0.0100.0000.0000.0000.000
153A153VAL00.0220.02522.2120.0110.0110.0000.0000.0000.000
154A154SER0-0.075-0.04423.105-0.021-0.0210.0000.0000.0000.000
155A155LEU00.0050.01317.8930.0070.0070.0000.0000.0000.000
156A156ARG10.8840.92819.4270.1530.1530.0000.0000.0000.000
157A157ASN00.0350.00516.974-0.038-0.0380.0000.0000.0000.000
158A158GLY0-0.022-0.01113.0780.0230.0230.0000.0000.0000.000
159A159ASP-1-0.827-0.88713.571-0.188-0.1880.0000.0000.0000.000
160A160VAL0-0.063-0.0349.171-0.076-0.0760.0000.0000.0000.000
161A161LEU00.0230.01212.1930.0730.0730.0000.0000.0000.000
162A162LEU0-0.025-0.0148.849-0.090-0.0900.0000.0000.0000.000
163A163CYS00.0670.04112.3330.0430.0430.0000.0000.0000.000
164A164PRO0-0.024-0.01512.432-0.039-0.0390.0000.0000.0000.000
165A165TYR00.019-0.0049.757-0.026-0.0260.0000.0000.0000.000
166A166MET00.0140.0369.475-0.136-0.1360.0000.0000.0000.000
167A167GLN0-0.022-0.0155.0630.1850.1850.0000.0000.0000.000
168A168PHE00.0330.0189.454-0.131-0.1310.0000.0000.0000.000
169A169VAL0-0.020-0.0169.0570.0450.0450.0000.0000.0000.000
170A170PHE00.0300.02612.131-0.033-0.0330.0000.0000.0000.000
171A171ILE0-0.088-0.05011.332-0.012-0.0120.0000.0000.0000.000
172A172GLU-1-0.830-0.88814.825-0.207-0.2070.0000.0000.0000.000
173A173GLU-1-0.871-0.95718.634-0.219-0.2190.0000.0000.0000.000
174A174ASP-1-0.932-0.97621.197-0.272-0.2720.0000.0000.0000.000
175A175LEU0-0.042-0.01216.647-0.017-0.0170.0000.0000.0000.000
176A176LEU00.0280.02014.628-0.016-0.0160.0000.0000.0000.000
177A177ALA0-0.042-0.02210.418-0.039-0.0390.0000.0000.0000.000
178A178VAL00.0470.02211.1400.0350.0350.0000.0000.0000.000
179A179THR0-0.061-0.0404.696-0.358-0.271-0.001-0.003-0.0830.000
180A180SER00.0520.0327.4420.2790.2790.0000.0000.0000.000
181A181SER00.0220.0066.952-0.232-0.2320.0000.0000.0000.000
182A182GLU-1-0.937-0.9507.831-0.562-0.5620.0000.0000.0000.000
183A183GLU-1-0.885-0.91210.903-0.826-0.8260.0000.0000.0000.000
184A184VAL0-0.037-0.00712.0050.0620.0620.0000.0000.0000.000
185A185VAL00.0160.02114.5620.0140.0140.0000.0000.0000.000
186A186SER00.001-0.02618.1340.0110.0110.0000.0000.0000.000
187A187SER0-0.0180.00320.0560.0010.0010.0000.0000.0000.000
188A188LEU0-0.0020.00819.4190.0230.0230.0000.0000.0000.000
189A189THR0-0.010-0.00921.647-0.002-0.0020.0000.0000.0000.000
190A190GLU-1-0.881-0.94916.679-0.568-0.5680.0000.0000.0000.000
191A191THR0-0.020-0.01217.4620.0250.0250.0000.0000.0000.000
192A192MET0-0.111-0.06213.3880.0380.0380.0000.0000.0000.000
193A193PRO0-0.007-0.00115.542-0.022-0.0220.0000.0000.0000.000
194A194PRO00.0630.03912.249-0.044-0.0440.0000.0000.0000.000
195A195LEU0-0.078-0.0217.324-0.173-0.1730.0000.0000.0000.000