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: 6N7JZ

Calculation Name: 3U8Z-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3U8Z

Chain ID: A

ChEMBL ID:

UniProt ID: P35240

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 260
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3522656.064114
FMO2-HF: Nuclear repulsion 3413870.466116
FMO2-HF: Total energy -108785.597999
FMO2-MP2: Total energy -109100.228738


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:20:LYS)


Summations of interaction energy for fragment #1(A:20:LYS)
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.
38.35542.8250.733-1.696-3.5070.002
Interaction energy analysis for fragmet #1(A:20:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.987 / q_NPA : 0.987
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].
3A22PHE0-0.027-0.0163.8981.4663.570-0.016-1.121-0.9670.001
4A23THR00.0560.0316.740-0.951-0.9510.0000.0000.0000.000
5A24VAL0-0.078-0.04010.2141.2001.2000.0000.0000.0000.000
6A25ARG10.9961.00913.25014.11714.1170.0000.0000.0000.000
7A26ILE0-0.057-0.04415.6950.2410.2410.0000.0000.0000.000
8A27VAL00.0270.01818.4220.0790.0790.0000.0000.0000.000
9A28THR00.0150.00521.6170.1570.1570.0000.0000.0000.000
10A29MET0-0.011-0.01224.1300.1270.1270.0000.0000.0000.000
11A30ASP-1-0.880-0.90125.652-10.853-10.8530.0000.0000.0000.000
12A31ALA00.0200.00223.2670.1500.1500.0000.0000.0000.000
13A32GLU-1-0.967-0.97420.699-13.481-13.4810.0000.0000.0000.000
14A33MET0-0.017-0.01317.668-0.483-0.4830.0000.0000.0000.000
15A34GLU-1-0.884-0.95214.235-17.307-17.3070.0000.0000.0000.000
16A35PHE0-0.013-0.00711.362-0.627-0.6270.0000.0000.0000.000
17A36ASN0-0.010-0.0086.5270.1960.1960.0000.0000.0000.000
18A37CYS0-0.0080.0077.487-1.066-1.0660.0000.0000.0000.000
19A38GLU-1-0.900-0.9523.248-56.517-55.6870.020-0.192-0.658-0.001
20A39MET0-0.023-0.0083.0124.4255.8700.730-0.380-1.7950.002
21A40LYS10.8850.9285.24831.73131.822-0.001-0.003-0.0870.000
22A41TRP00.0570.0417.5832.5612.5610.0000.0000.0000.000
23A42LYS10.9000.9579.79719.37719.3770.0000.0000.0000.000
24A43GLY00.0250.00413.245-0.632-0.6320.0000.0000.0000.000
25A44LYS10.9430.95415.82514.78014.7800.0000.0000.0000.000
26A45ASP-1-0.833-0.90011.143-22.830-22.8300.0000.0000.0000.000
27A46LEU0-0.0020.00411.813-0.534-0.5340.0000.0000.0000.000
28A47PHE0-0.018-0.02313.0620.2950.2950.0000.0000.0000.000
29A48ASP-1-0.838-0.93515.557-16.035-16.0350.0000.0000.0000.000
30A49LEU0-0.040-0.00310.2190.0330.0330.0000.0000.0000.000
31A50VAL0-0.0040.02014.2330.3630.3630.0000.0000.0000.000
32A51CYS0-0.027-0.01416.8950.8290.8290.0000.0000.0000.000
33A52ARG10.9530.97612.20821.85621.8560.0000.0000.0000.000
34A53THR0-0.043-0.03315.733-0.067-0.0670.0000.0000.0000.000
35A54LEU0-0.0100.00318.0290.5310.5310.0000.0000.0000.000
36A55GLY00.0210.02520.8090.6890.6890.0000.0000.0000.000
37A56LEU0-0.061-0.01722.0500.6200.6200.0000.0000.0000.000
38A57ARG10.9430.94222.42311.30711.3070.0000.0000.0000.000
39A58GLU-1-0.785-0.89724.653-10.225-10.2250.0000.0000.0000.000
40A59THR0-0.006-0.01921.7690.3150.3150.0000.0000.0000.000
41A60TRP0-0.0050.00024.894-0.369-0.3690.0000.0000.0000.000
42A61PHE00.0510.03127.1260.1300.1300.0000.0000.0000.000
43A62PHE00.0090.02024.1900.1290.1290.0000.0000.0000.000
44A63GLY0-0.018-0.01522.657-0.151-0.1510.0000.0000.0000.000
45A64LEU0-0.0030.00017.0820.0240.0240.0000.0000.0000.000
46A65GLN0-0.034-0.01321.3460.0230.0230.0000.0000.0000.000
47A66TYR00.0580.02021.800-0.444-0.4440.0000.0000.0000.000
48A67THR00.0580.02323.9490.2110.2110.0000.0000.0000.000
49A68ILE0-0.021-0.00124.571-0.132-0.1320.0000.0000.0000.000
50A69LYS10.8980.92927.4048.9548.9540.0000.0000.0000.000
51A70ASP-1-0.844-0.91330.236-8.541-8.5410.0000.0000.0000.000
52A71THR0-0.157-0.07130.9610.2400.2400.0000.0000.0000.000
53A72VAL00.0960.05228.671-0.281-0.2810.0000.0000.0000.000
54A73ALA0-0.045-0.02225.2390.1880.1880.0000.0000.0000.000
55A74TRP00.0670.03024.224-0.265-0.2650.0000.0000.0000.000
56A75LEU0-0.034-0.00616.3110.1650.1650.0000.0000.0000.000
57A76LYS10.8990.94120.29011.91011.9100.0000.0000.0000.000
58A77MET00.0350.02418.417-0.758-0.7580.0000.0000.0000.000
59A78ASP-1-0.843-0.91717.558-14.973-14.9730.0000.0000.0000.000
60A79LYS10.8850.93117.09513.20713.2070.0000.0000.0000.000
61A80LYS10.9540.97310.37321.50821.5080.0000.0000.0000.000
62A81VAL00.0200.02011.5441.4501.4500.0000.0000.0000.000
63A82LEU0-0.0180.0058.717-0.496-0.4960.0000.0000.0000.000
64A91PRO00.0200.01014.506-0.046-0.0460.0000.0000.0000.000
65A92VAL00.010-0.00412.9450.7570.7570.0000.0000.0000.000
66A93THR00.0150.01015.516-0.475-0.4750.0000.0000.0000.000
67A94PHE0-0.078-0.03615.3420.4070.4070.0000.0000.0000.000
68A95HIS00.0410.02120.089-0.091-0.0910.0000.0000.0000.000
69A96PHE0-0.034-0.02220.557-0.048-0.0480.0000.0000.0000.000
70A97LEU00.0070.00122.7720.3840.3840.0000.0000.0000.000
71A98ALA00.0360.01326.099-0.331-0.3310.0000.0000.0000.000
72A99LYS10.8090.91026.83411.04011.0400.0000.0000.0000.000
73A100PHE0-0.082-0.04428.6590.2830.2830.0000.0000.0000.000
74A101TYR00.1010.04531.872-0.260-0.2600.0000.0000.0000.000
75A102PRO0-0.033-0.00734.0620.0330.0330.0000.0000.0000.000
76A103GLU-1-0.834-0.91136.417-7.486-7.4860.0000.0000.0000.000
77A104ASN00.0190.01739.4700.1210.1210.0000.0000.0000.000
78A105ALA00.000-0.01437.543-0.197-0.1970.0000.0000.0000.000
79A106GLU-1-0.847-0.93337.529-7.585-7.5850.0000.0000.0000.000
80A107GLU-1-1.000-0.99538.865-7.574-7.5740.0000.0000.0000.000
81A108GLU-1-0.830-0.92835.014-8.794-8.7940.0000.0000.0000.000
82A109LEU0-0.073-0.02532.369-0.386-0.3860.0000.0000.0000.000
83A110VAL00.0750.05432.7970.1010.1010.0000.0000.0000.000
84A111GLN0-0.073-0.04925.836-0.129-0.1290.0000.0000.0000.000
85A112GLU-1-0.763-0.87230.978-9.563-9.5630.0000.0000.0000.000
86A113ILE0-0.0100.00525.1310.1370.1370.0000.0000.0000.000
87A114THR0-0.043-0.02928.1000.0550.0550.0000.0000.0000.000
88A115GLN00.1020.05329.6390.1620.1620.0000.0000.0000.000
89A116HIS10.7660.84228.57210.28510.2850.0000.0000.0000.000
90A117LEU0-0.049-0.04125.0700.0470.0470.0000.0000.0000.000
91A118PHE0-0.012-0.01329.5450.0670.0670.0000.0000.0000.000
92A119PHE00.0400.03532.4860.2070.2070.0000.0000.0000.000
93A120LEU0-0.016-0.01129.9060.2400.2400.0000.0000.0000.000
94A121GLN0-0.022-0.00529.680-0.207-0.2070.0000.0000.0000.000
95A122VAL00.0050.00332.7440.1530.1530.0000.0000.0000.000
96A123LYS10.9821.00636.1908.6278.6270.0000.0000.0000.000
97A124LYS10.7980.89232.8688.9328.9320.0000.0000.0000.000
98A125GLN0-0.027-0.02634.1180.2390.2390.0000.0000.0000.000
99A126ILE00.0300.02738.1140.1720.1720.0000.0000.0000.000
100A127LEU0-0.048-0.03138.8940.1410.1410.0000.0000.0000.000
101A128ASP-1-0.860-0.92436.972-8.207-8.2070.0000.0000.0000.000
102A129GLU-1-0.949-0.95940.581-6.623-6.6230.0000.0000.0000.000
103A130LYS10.8180.91235.2148.4558.4550.0000.0000.0000.000
104A131ILE0-0.049-0.01838.9030.0130.0130.0000.0000.0000.000
105A132TYR00.038-0.00242.6360.0580.0580.0000.0000.0000.000
106A133CYS00.0180.01145.719-0.076-0.0760.0000.0000.0000.000
107A134PRO00.0210.02547.7010.0890.0890.0000.0000.0000.000
108A135PRO00.022-0.00550.652-0.082-0.0820.0000.0000.0000.000
109A136GLU-1-0.918-0.95652.050-5.787-5.7870.0000.0000.0000.000
110A137ALA00.0630.02548.206-0.065-0.0650.0000.0000.0000.000
111A138SER00.004-0.00947.304-0.183-0.1830.0000.0000.0000.000
112A139VAL0-0.011-0.00647.476-0.121-0.1210.0000.0000.0000.000
113A140LEU00.0340.02948.929-0.064-0.0640.0000.0000.0000.000
114A141LEU00.0200.02042.863-0.125-0.1250.0000.0000.0000.000
115A142ALA0-0.030-0.01944.016-0.178-0.1780.0000.0000.0000.000
116A143SER0-0.060-0.04644.908-0.081-0.0810.0000.0000.0000.000
117A144TYR00.0750.03642.947-0.043-0.0430.0000.0000.0000.000
118A145ALA0-0.016-0.01540.566-0.199-0.1990.0000.0000.0000.000
119A146VAL0-0.073-0.03540.770-0.158-0.1580.0000.0000.0000.000
120A147GLN0-0.005-0.02242.447-0.170-0.1700.0000.0000.0000.000
121A148ALA00.0300.02737.840-0.071-0.0710.0000.0000.0000.000
122A149LYS10.8200.93937.7727.6017.6010.0000.0000.0000.000
123A150TYR0-0.059-0.04138.453-0.116-0.1160.0000.0000.0000.000
124A151GLY00.0580.03239.5930.0940.0940.0000.0000.0000.000
125A152ASP-1-1.009-0.99040.496-7.345-7.3450.0000.0000.0000.000
126A178GLN0-0.027-0.03344.7530.0460.0460.0000.0000.0000.000
127A179MET0-0.034-0.01443.505-0.157-0.1570.0000.0000.0000.000
128A180THR00.0550.03146.364-0.042-0.0420.0000.0000.0000.000
129A181PRO00.031-0.00348.564-0.130-0.1300.0000.0000.0000.000
130A182GLU-1-0.848-0.92549.655-6.108-6.1080.0000.0000.0000.000
131A183MET00.0020.02446.841-0.058-0.0580.0000.0000.0000.000
132A184TRP0-0.046-0.03340.948-0.303-0.3030.0000.0000.0000.000
133A185GLU-1-0.864-0.94045.595-6.836-6.8360.0000.0000.0000.000
134A186GLU-1-0.955-0.97247.708-6.470-6.4700.0000.0000.0000.000
135A187ARG10.9240.94940.0007.6757.6750.0000.0000.0000.000
136A188ILE0-0.0160.00642.875-0.232-0.2320.0000.0000.0000.000
137A189THR0-0.071-0.05043.553-0.089-0.0890.0000.0000.0000.000
138A190ALA00.0060.00944.187-0.029-0.0290.0000.0000.0000.000
139A191TRP00.0190.02034.675-0.159-0.1590.0000.0000.0000.000
140A192TYR0-0.008-0.02240.170-0.250-0.2500.0000.0000.0000.000
141A193ALA0-0.050-0.02741.261-0.095-0.0950.0000.0000.0000.000
142A194GLU-1-0.901-0.94739.593-7.796-7.7960.0000.0000.0000.000
143A195HIS10.7910.91335.0078.6318.6310.0000.0000.0000.000
144A196ARG11.0091.00237.6337.5067.5060.0000.0000.0000.000
145A197GLY0-0.0230.00334.532-0.067-0.0670.0000.0000.0000.000
146A198ARG10.8860.93131.3009.9259.9250.0000.0000.0000.000
147A199ALA00.0190.01735.389-0.070-0.0700.0000.0000.0000.000
148A200ARG10.8410.90734.0288.8598.8590.0000.0000.0000.000
149A201ASP-1-0.851-0.94036.038-8.217-8.2170.0000.0000.0000.000
150A202GLU-1-0.913-0.97537.720-7.744-7.7440.0000.0000.0000.000
151A203ALA00.0370.03840.4900.0930.0930.0000.0000.0000.000
152A204GLU-1-0.792-0.88734.465-9.249-9.2490.0000.0000.0000.000
153A205MET0-0.0130.00336.766-0.054-0.0540.0000.0000.0000.000
154A206GLU-1-0.841-0.91339.638-6.972-6.9720.0000.0000.0000.000
155A207TYR0-0.019-0.01239.6350.0560.0560.0000.0000.0000.000
156A208LEU0-0.058-0.04435.6430.0500.0500.0000.0000.0000.000
157A209LYS10.8290.92040.1667.2117.2110.0000.0000.0000.000
158A210ILE00.0270.03043.3130.1310.1310.0000.0000.0000.000
159A211ALA0-0.028-0.03040.9130.0620.0620.0000.0000.0000.000
160A212GLN00.012-0.01440.980-0.169-0.1690.0000.0000.0000.000
161A213ASP-1-0.908-0.93742.473-6.705-6.7050.0000.0000.0000.000
162A214LEU0-0.091-0.03843.8370.1700.1700.0000.0000.0000.000
163A215GLU-1-0.888-0.96044.860-6.300-6.3000.0000.0000.0000.000
164A216MET0-0.073-0.01943.223-0.031-0.0310.0000.0000.0000.000
165A217TYR00.0030.02337.811-0.312-0.3120.0000.0000.0000.000
166A218GLY00.003-0.00137.3360.0200.0200.0000.0000.0000.000
167A219VAL0-0.045-0.00238.242-0.110-0.1100.0000.0000.0000.000
168A220ASN0-0.098-0.05435.008-0.256-0.2560.0000.0000.0000.000
169A221TYR00.041-0.00638.1790.0840.0840.0000.0000.0000.000
170A222PHE0-0.050-0.03835.533-0.210-0.2100.0000.0000.0000.000
171A223ALA00.0240.01940.9740.1550.1550.0000.0000.0000.000
172A224ILE0-0.066-0.02642.848-0.129-0.1290.0000.0000.0000.000
173A225ARG10.9650.99545.3506.4856.4850.0000.0000.0000.000
174A226ASN00.0670.04248.182-0.059-0.0590.0000.0000.0000.000
175A227LYS10.9490.95549.8486.1216.1210.0000.0000.0000.000
176A228LYS10.9200.96652.5475.4175.4170.0000.0000.0000.000
177A229GLY00.0230.02651.9920.0690.0690.0000.0000.0000.000
178A230THR0-0.032-0.01952.7970.0110.0110.0000.0000.0000.000
179A231GLU-1-0.930-0.96649.590-6.230-6.2300.0000.0000.0000.000
180A232LEU0-0.020-0.01848.7710.1170.1170.0000.0000.0000.000
181A233LEU0-0.0100.00344.286-0.151-0.1510.0000.0000.0000.000
182A234LEU0-0.041-0.01540.7410.0780.0780.0000.0000.0000.000
183A235GLY00.0500.01942.091-0.125-0.1250.0000.0000.0000.000
184A236VAL0-0.080-0.05537.3030.0590.0590.0000.0000.0000.000
185A237ASP-1-0.680-0.83338.539-7.525-7.5250.0000.0000.0000.000
186A238ALA00.0320.01538.494-0.019-0.0190.0000.0000.0000.000
187A239LEU00.0490.01939.3820.0250.0250.0000.0000.0000.000
188A240GLY0-0.007-0.01642.2170.1460.1460.0000.0000.0000.000
189A241LEU0-0.068-0.02040.668-0.136-0.1360.0000.0000.0000.000
190A242HIS10.8700.91543.7247.1067.1060.0000.0000.0000.000
191A243ILE0-0.024-0.00645.857-0.121-0.1210.0000.0000.0000.000
192A244TYR00.0570.02145.0300.0330.0330.0000.0000.0000.000
193A245ASP-1-0.823-0.93149.672-5.723-5.7230.0000.0000.0000.000
194A246PRO0-0.069-0.04249.143-0.091-0.0910.0000.0000.0000.000
195A247GLU-1-0.908-0.94849.565-6.152-6.1520.0000.0000.0000.000
196A248ASN00.027-0.00151.0810.0110.0110.0000.0000.0000.000
197A249ARG10.9320.96942.2716.9256.9250.0000.0000.0000.000
198A250LEU00.0230.04047.124-0.165-0.1650.0000.0000.0000.000
199A251THR00.0380.01949.526-0.010-0.0100.0000.0000.0000.000
200A252PRO0-0.073-0.02748.8280.0380.0380.0000.0000.0000.000
201A253LYS10.9260.96450.7735.7765.7760.0000.0000.0000.000
202A254ILE0-0.035-0.01851.1750.0940.0940.0000.0000.0000.000
203A255SER00.0260.01548.678-0.186-0.1860.0000.0000.0000.000
204A256PHE0-0.012-0.01046.5820.1190.1190.0000.0000.0000.000
205A257PRO00.0850.04745.772-0.205-0.2050.0000.0000.0000.000
206A258TRP0-0.0090.00039.0390.0470.0470.0000.0000.0000.000
207A259ASN00.0180.00943.628-0.093-0.0930.0000.0000.0000.000
208A260GLU-1-0.932-0.96745.965-6.103-6.1030.0000.0000.0000.000
209A261ILE0-0.045-0.01743.7340.1160.1160.0000.0000.0000.000
210A262ARG10.9410.98045.4956.3616.3610.0000.0000.0000.000
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