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: 4914N

Calculation Name: 3QKA-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3QKA

Chain ID: A

ChEMBL ID:

UniProt ID: B2HSK3

Base Structure: X-ray

Registration Date: 2023-09-20

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 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 233
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2614985.254167
FMO2-HF: Nuclear repulsion 2528533.79667
FMO2-HF: Total energy -86451.457497
FMO2-MP2: Total energy -86700.51135


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:ASP)


Summations of interaction energy for fragment #1(A:3:ASP)
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.
-39.752-33.7576.392-5.87-6.5180.063
Interaction energy analysis for fragmet #1(A:3:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.854 / q_NPA : -0.935
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].
3A5VAL0-0.046-0.0381.950-33.315-29.7956.215-5.007-4.7280.063
4A6GLN00.0120.0263.1161.6643.1640.174-0.588-1.0850.000
5A7VAL00.015-0.0084.269-4.516-4.3500.000-0.019-0.1470.000
6A8GLU-1-0.814-0.8687.54324.02024.0200.0000.0000.0000.000
7A9ARG10.8020.86910.505-19.881-19.8810.0000.0000.0000.000
8A10ASN00.0010.00914.100-0.653-0.6530.0000.0000.0000.000
9A11GLY00.0550.02617.609-0.676-0.6760.0000.0000.0000.000
10A12PRO00.0270.02418.7280.8010.8010.0000.0000.0000.000
11A13VAL00.0220.02216.8380.2270.2270.0000.0000.0000.000
12A14THR0-0.012-0.01412.7220.8330.8330.0000.0000.0000.000
13A15THR0-0.039-0.05011.825-0.775-0.7750.0000.0000.0000.000
14A16VAL00.0020.0088.3252.5072.5070.0000.0000.0000.000
15A17ILE00.007-0.0077.201-2.948-2.9480.0000.0000.0000.000
16A18ILE0-0.017-0.0116.6036.0286.0280.0000.0000.0000.000
17A19ASN0-0.022-0.0113.238-9.806-9.1990.004-0.232-0.3800.000
18A20ARG10.7940.8666.184-26.289-26.2890.0000.0000.0000.000
19A21PRO00.0800.0528.201-2.801-2.8010.0000.0000.0000.000
20A22GLN00.0270.0137.883-2.499-2.4990.0000.0000.0000.000
21A23ALA0-0.045-0.02512.173-1.543-1.5430.0000.0000.0000.000
22A24ARG10.9240.95513.891-16.803-16.8030.0000.0000.0000.000
23A25ASN00.011-0.01210.7811.2031.2030.0000.0000.0000.000
24A26ALA00.0360.02512.644-0.228-0.2280.0000.0000.0000.000
25A27VAL0-0.0150.00110.1972.4742.4740.0000.0000.0000.000
26A28ASN00.0550.0439.4380.1940.1940.0000.0000.0000.000
27A29GLY00.0490.03010.6521.5471.5470.0000.0000.0000.000
28A30PRO0-0.001-0.0057.8320.7970.7970.0000.0000.0000.000
29A31THR00.003-0.0106.1804.9654.9650.0000.0000.0000.000
30A32ALA00.0210.0177.2621.0691.0690.0000.0000.0000.000
31A33ALA0-0.005-0.0089.030-1.021-1.0210.0000.0000.0000.000
32A34ALA00.0370.0344.279-1.779-1.577-0.001-0.024-0.1780.000
33A35LEU00.0080.0026.370-1.627-1.6270.0000.0000.0000.000
34A36TYR0-0.022-0.0218.641-2.827-2.8270.0000.0000.0000.000
35A37SER0-0.025-0.0268.205-2.642-2.6420.0000.0000.0000.000
36A38ALA00.0340.0217.370-2.053-2.0530.0000.0000.0000.000
37A39PHE00.023-0.0069.389-2.369-2.3690.0000.0000.0000.000
38A40ALA00.0050.00412.847-1.949-1.9490.0000.0000.0000.000
39A41GLU-1-0.932-0.95910.05728.01128.0110.0000.0000.0000.000
40A42PHE0-0.0100.00113.244-1.059-1.0590.0000.0000.0000.000
41A43ASP-1-0.773-0.87915.00914.44514.4450.0000.0000.0000.000
42A44ARG10.8340.90713.209-22.531-22.5310.0000.0000.0000.000
43A45ASP-1-0.801-0.84316.17417.21717.2170.0000.0000.0000.000
44A46GLU-1-0.885-0.95718.23813.20713.2070.0000.0000.0000.000
45A47SER0-0.114-0.06619.281-0.424-0.4240.0000.0000.0000.000
46A48ALA0-0.043-0.01317.268-0.195-0.1950.0000.0000.0000.000
47A49SER0-0.042-0.03319.339-0.658-0.6580.0000.0000.0000.000
48A50VAL0-0.022-0.01220.317-0.401-0.4010.0000.0000.0000.000
49A51ALA00.0030.00715.3150.6870.6870.0000.0000.0000.000
50A52VAL0-0.010-0.00415.258-1.061-1.0610.0000.0000.0000.000
51A53LEU0-0.0130.00311.5911.7181.7180.0000.0000.0000.000
52A54CYS0-0.044-0.01612.085-1.668-1.6680.0000.0000.0000.000
53A55GLY00.0670.03710.6632.2952.2950.0000.0000.0000.000
54A56ASN00.005-0.0107.097-3.974-3.9740.0000.0000.0000.000
55A57GLY0-0.045-0.02610.944-0.416-0.4160.0000.0000.0000.000
56A58GLY00.0040.01213.328-1.061-1.0610.0000.0000.0000.000
57A59THR0-0.006-0.00815.206-1.496-1.4960.0000.0000.0000.000
58A60PHE0-0.0240.01514.5441.6001.6000.0000.0000.0000.000
59A61CYS0-0.048-0.00813.5371.4191.4190.0000.0000.0000.000
60A62ALA00.0350.01715.460-1.327-1.3270.0000.0000.0000.000
61A63GLY0-0.001-0.01316.148-1.052-1.0520.0000.0000.0000.000
62A64ALA00.0540.01315.3971.3291.3290.0000.0000.0000.000
63A65ASP-1-0.770-0.86913.79020.52720.5270.0000.0000.0000.000
64A66LEU00.0170.00116.044-0.441-0.4410.0000.0000.0000.000
65A67LYS10.8030.89617.401-15.747-15.7470.0000.0000.0000.000
66A68ALA00.0540.04814.562-0.168-0.1680.0000.0000.0000.000
67A69PHE0-0.034-0.01316.596-0.289-0.2890.0000.0000.0000.000
68A70GLY00.0100.01419.910-0.593-0.5930.0000.0000.0000.000
69A71THR0-0.054-0.03016.4010.0580.0580.0000.0000.0000.000
70A72ALA00.0280.00815.720-0.207-0.2070.0000.0000.0000.000
71A73GLU-1-0.898-0.96011.74022.96422.9640.0000.0000.0000.000
72A74ALA0-0.017-0.00613.4361.0641.0640.0000.0000.0000.000
73A75ASN0-0.069-0.07313.9990.5010.5010.0000.0000.0000.000
74A76ALA00.0250.02115.415-1.175-1.1750.0000.0000.0000.000
75A77VAL0-0.002-0.00717.349-0.122-0.1220.0000.0000.0000.000
76A78HIS00.0650.04619.122-1.345-1.3450.0000.0000.0000.000
77A79ARG10.9620.97222.308-10.966-10.9660.0000.0000.0000.000
78A80THR0-0.017-0.00723.385-0.246-0.2460.0000.0000.0000.000
79A81GLY00.0540.02419.6090.3630.3630.0000.0000.0000.000
80A82PRO00.0360.01114.754-0.705-0.7050.0000.0000.0000.000
81A83GLY0-0.0120.01416.660-0.947-0.9470.0000.0000.0000.000
82A84PRO00.0030.00015.6871.3691.3690.0000.0000.0000.000
83A85MET0-0.061-0.01614.0061.2881.2880.0000.0000.0000.000
84A86GLY00.0580.02412.3011.9381.9380.0000.0000.0000.000
85A87PRO0-0.018-0.01511.958-1.336-1.3360.0000.0000.0000.000
86A88SER0-0.046-0.03914.705-1.101-1.1010.0000.0000.0000.000
87A89ARG10.8280.90717.753-16.288-16.2880.0000.0000.0000.000
88A90MET0-0.060-0.00215.601-0.297-0.2970.0000.0000.0000.000
89A91MET0-0.0140.00519.600-0.086-0.0860.0000.0000.0000.000
90A92LEU00.0060.00616.399-0.116-0.1160.0000.0000.0000.000
91A93SER0-0.014-0.02420.704-0.839-0.8390.0000.0000.0000.000
92A94LYS10.7900.91719.188-16.838-16.8380.0000.0000.0000.000
93A95PRO0-0.008-0.01020.6620.4910.4910.0000.0000.0000.000
94A96VAL0-0.008-0.00316.1300.7350.7350.0000.0000.0000.000
95A97ILE0-0.024-0.01218.559-0.850-0.8500.0000.0000.0000.000
96A98ALA00.015-0.00517.6881.0291.0290.0000.0000.0000.000
97A99ALA00.0240.01516.585-1.058-1.0580.0000.0000.0000.000
98A100VAL0-0.061-0.03617.4230.8390.8390.0000.0000.0000.000
99A101SER00.0830.05016.714-0.737-0.7370.0000.0000.0000.000
100A102GLY00.0180.00519.0160.5720.5720.0000.0000.0000.000
101A103TYR0-0.009-0.00719.400-0.716-0.7160.0000.0000.0000.000
102A104ALA00.0360.02318.6801.0971.0970.0000.0000.0000.000
103A105VAL0-0.023-0.00519.711-0.815-0.8150.0000.0000.0000.000
104A106ALA0-0.017-0.01219.9430.7750.7750.0000.0000.0000.000
105A107GLY00.0520.01118.489-0.102-0.1020.0000.0000.0000.000
106A108GLY00.0350.00516.8530.6420.6420.0000.0000.0000.000
107A109LEU00.0060.01417.785-0.008-0.0080.0000.0000.0000.000
108A110GLU-1-0.767-0.89519.88713.80613.8060.0000.0000.0000.000
109A111LEU00.0070.00213.528-0.203-0.2030.0000.0000.0000.000
110A112ALA00.0150.00917.728-0.046-0.0460.0000.0000.0000.000
111A113LEU0-0.053-0.03019.833-0.536-0.5360.0000.0000.0000.000
112A114TRP0-0.069-0.04415.128-0.124-0.1240.0000.0000.0000.000
113A115CYS0-0.0230.01517.9180.3250.3250.0000.0000.0000.000
114A116ASP-1-0.704-0.81320.25913.15913.1590.0000.0000.0000.000
115A117LEU0-0.035-0.01022.527-0.723-0.7230.0000.0000.0000.000
116A118ARG10.7510.85921.966-12.217-12.2170.0000.0000.0000.000
117A119VAL0-0.004-0.00121.815-0.791-0.7910.0000.0000.0000.000
118A120ALA00.0130.00421.8690.6560.6560.0000.0000.0000.000
119A121GLU-1-0.754-0.88120.63814.17414.1740.0000.0000.0000.000
120A122GLN0-0.038-0.02524.265-0.227-0.2270.0000.0000.0000.000
121A123ASP-1-0.827-0.88926.23410.50310.5030.0000.0000.0000.000
122A124ALA0-0.078-0.02422.7630.2140.2140.0000.0000.0000.000
123A125VAL0-0.061-0.04123.668-0.585-0.5850.0000.0000.0000.000
124A126PHE00.0530.02322.9810.8080.8080.0000.0000.0000.000
125A127GLY00.0720.01824.531-0.509-0.5090.0000.0000.0000.000
126A128VAL0-0.0190.00024.5740.6940.6940.0000.0000.0000.000
127A129PHE00.0560.01224.017-0.214-0.2140.0000.0000.0000.000
128A130CYS0-0.0160.00523.597-0.259-0.2590.0000.0000.0000.000
129A131ARG10.8900.95025.512-10.459-10.4590.0000.0000.0000.000
130A132ARG10.9280.95128.677-11.218-11.2180.0000.0000.0000.000
131A133TRP0-0.063-0.03221.120-0.060-0.0600.0000.0000.0000.000
132A134GLY00.0300.03527.5200.0200.0200.0000.0000.0000.000
133A135VAL0-0.037-0.01222.7170.0390.0390.0000.0000.0000.000
134A136PRO0-0.011-0.00625.659-0.134-0.1340.0000.0000.0000.000
135A137LEU0-0.034-0.01423.8910.4860.4860.0000.0000.0000.000
136A138ILE0-0.051-0.03221.417-0.507-0.5070.0000.0000.0000.000
137A139ASP-1-0.767-0.85017.92417.79417.7940.0000.0000.0000.000
138A140GLY00.0450.01920.9410.2270.2270.0000.0000.0000.000
139A141GLY0-0.019-0.01923.898-0.365-0.3650.0000.0000.0000.000
140A142THR0-0.008-0.01925.252-0.275-0.2750.0000.0000.0000.000
141A143VAL0-0.0100.00426.968-0.426-0.4260.0000.0000.0000.000
142A144ARG10.8680.92721.498-14.465-14.4650.0000.0000.0000.000
143A145LEU00.0300.02227.462-0.217-0.2170.0000.0000.0000.000
144A146PRO0-0.025-0.03329.047-0.265-0.2650.0000.0000.0000.000
145A147ARG10.8530.95329.627-10.556-10.5560.0000.0000.0000.000
146A148LEU0-0.0110.01025.897-0.128-0.1280.0000.0000.0000.000
147A149ILE0-0.0030.00730.214-0.102-0.1020.0000.0000.0000.000
148A150GLY00.0350.02832.918-0.335-0.3350.0000.0000.0000.000
149A151HIS00.027-0.01535.1550.2310.2310.0000.0000.0000.000
150A152SER0-0.025-0.00536.2650.0980.0980.0000.0000.0000.000
151A153ARG11.0071.00834.465-8.715-8.7150.0000.0000.0000.000
152A154ALA00.0370.02431.8890.2060.2060.0000.0000.0000.000
153A155MET00.004-0.00232.5070.2560.2560.0000.0000.0000.000
154A156ASP-1-0.810-0.87035.0869.0329.0320.0000.0000.0000.000
155A157MET00.0190.03927.7400.1040.1040.0000.0000.0000.000
156A158ILE0-0.013-0.01129.4620.2470.2470.0000.0000.0000.000
157A159LEU0-0.022-0.00531.4250.1150.1150.0000.0000.0000.000
158A160THR0-0.008-0.02633.8770.1150.1150.0000.0000.0000.000
159A161GLY0-0.033-0.02429.8250.0240.0240.0000.0000.0000.000
160A162ARG10.6740.79229.188-8.921-8.9210.0000.0000.0000.000
161A163ALA0-0.002-0.00428.4500.3490.3490.0000.0000.0000.000
162A164VAL00.005-0.00628.439-0.383-0.3830.0000.0000.0000.000
163A165GLN0-0.006-0.00228.0930.4710.4710.0000.0000.0000.000
164A166ALA00.0440.02326.755-0.140-0.1400.0000.0000.0000.000
165A167ASP-1-0.830-0.91528.5029.4699.4690.0000.0000.0000.000
166A168GLU-1-0.803-0.87232.2709.2139.2130.0000.0000.0000.000
167A169ALA00.003-0.02028.224-0.085-0.0850.0000.0000.0000.000
168A170LEU0-0.0070.01030.3390.0330.0330.0000.0000.0000.000
169A171ALA0-0.0120.00431.788-0.180-0.1800.0000.0000.0000.000
170A172ILE0-0.102-0.06630.945-0.277-0.2770.0000.0000.0000.000
171A173GLY00.0190.01732.081-0.057-0.0570.0000.0000.0000.000
172A174LEU0-0.033-0.00625.7340.2570.2570.0000.0000.0000.000
173A175ALA0-0.012-0.01226.6160.5460.5460.0000.0000.0000.000
174A176ASN00.0180.00326.746-0.013-0.0130.0000.0000.0000.000
175A177ARG10.9210.94826.317-10.923-10.9230.0000.0000.0000.000
176A178VAL00.0110.01626.7520.3750.3750.0000.0000.0000.000
177A179VAL0-0.0080.01323.772-0.320-0.3200.0000.0000.0000.000
178A180PRO00.0350.00126.4640.0800.0800.0000.0000.0000.000
179A181ASN0-0.033-0.04723.5380.4960.4960.0000.0000.0000.000
180A182GLY0-0.023-0.00520.059-0.248-0.2480.0000.0000.0000.000
181A183GLN0-0.011-0.01120.916-0.113-0.1130.0000.0000.0000.000
182A184ALA00.0090.00519.821-0.059-0.0590.0000.0000.0000.000
183A185ARG10.6930.79211.577-21.097-21.0970.0000.0000.0000.000
184A186GLN00.0530.01817.5880.5590.5590.0000.0000.0000.000
185A187ALA00.0660.03519.986-0.212-0.2120.0000.0000.0000.000
186A188ALA0-0.018-0.00718.843-0.405-0.4050.0000.0000.0000.000
187A189GLU-1-0.765-0.84115.27718.77718.7770.0000.0000.0000.000
188A190GLU-1-0.954-0.97619.51912.02512.0250.0000.0000.0000.000
189A191LEU0-0.036-0.01423.222-0.427-0.4270.0000.0000.0000.000
190A192ALA00.028-0.00120.160-0.308-0.3080.0000.0000.0000.000
191A193ALA00.006-0.00322.055-0.155-0.1550.0000.0000.0000.000
192A194GLN0-0.054-0.02823.582-0.593-0.5930.0000.0000.0000.000
193A195LEU0-0.010-0.01424.471-0.374-0.3740.0000.0000.0000.000
194A196ALA0-0.023-0.01523.083-0.190-0.1900.0000.0000.0000.000
195A197ALA0-0.032-0.00425.231-0.186-0.1860.0000.0000.0000.000
196A198LEU0-0.0320.00228.516-0.497-0.4970.0000.0000.0000.000
197A199PRO00.010-0.02229.7940.3070.3070.0000.0000.0000.000
198A200GLN00.0630.04325.7390.3740.3740.0000.0000.0000.000
199A201GLN00.019-0.01428.0300.3430.3430.0000.0000.0000.000
200A202CYS0-0.0130.01230.810-0.113-0.1130.0000.0000.0000.000
201A203LEU00.0390.03426.5540.0810.0810.0000.0000.0000.000
202A204ARG10.9050.93624.394-12.677-12.6770.0000.0000.0000.000
203A205SER0-0.021-0.01128.1200.1110.1110.0000.0000.0000.000
204A206ASP-1-0.883-0.94231.2639.3749.3740.0000.0000.0000.000
205A207ARG10.7510.84722.041-13.627-13.6270.0000.0000.0000.000
206A208LEU0-0.020-0.01425.7900.1100.1100.0000.0000.0000.000
207A209SER0-0.024-0.02729.301-0.047-0.0470.0000.0000.0000.000
208A210ALA00.0210.00430.917-0.074-0.0740.0000.0000.0000.000
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