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: JL8G9

Calculation Name: 5WQN-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5WQN

Chain ID: A

ChEMBL ID:

UniProt ID: Q9HWU9

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 217
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2407113.233152
FMO2-HF: Nuclear repulsion 2326124.80104
FMO2-HF: Total energy -80988.432112
FMO2-MP2: Total energy -81224.373139


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.
-10.109-2.3225.443-4.02-9.211-0.018
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 : 0.007
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].
3A3ASN0-0.010-0.0083.322-0.6441.6990.056-1.133-1.2660.001
4A4VAL0-0.024-0.0225.2360.5070.606-0.001-0.008-0.0900.000
5A5LEU00.0100.0197.7940.3190.3190.0000.0000.0000.000
6A6ILE0-0.0070.00011.0420.0620.0620.0000.0000.0000.000
7A7VAL00.0210.00113.7430.0680.0680.0000.0000.0000.000
8A8GLY00.0140.01317.0880.0230.0230.0000.0000.0000.000
9A9ALA00.0190.00615.3550.0240.0240.0000.0000.0000.000
10A10SER00.0120.00517.3420.0400.0400.0000.0000.0000.000
11A11ARG10.9790.99320.3850.0950.0950.0000.0000.0000.000
12A12GLY00.0150.01321.200-0.021-0.0210.0000.0000.0000.000
13A13ILE00.0830.03519.0980.0120.0120.0000.0000.0000.000
14A14GLY00.0380.02417.625-0.013-0.0130.0000.0000.0000.000
15A15LEU0-0.036-0.00616.088-0.022-0.0220.0000.0000.0000.000
16A16GLY00.0490.01915.9410.0360.0360.0000.0000.0000.000
17A17LEU0-0.012-0.00114.0570.0280.0280.0000.0000.0000.000
18A18ALA00.0100.00311.638-0.035-0.0350.0000.0000.0000.000
19A19ASP-1-0.790-0.84711.1680.3810.3810.0000.0000.0000.000
20A20ALA00.0530.01911.6760.1020.1020.0000.0000.0000.000
21A21PHE00.002-0.0178.1020.0150.0150.0000.0000.0000.000
22A22LEU0-0.015-0.0017.1620.1010.1010.0000.0000.0000.000
23A23GLN0-0.059-0.0397.9140.4130.4130.0000.0000.0000.000
24A24ARG10.8940.9517.9700.3180.3180.0000.0000.0000.000
25A25GLY00.0080.0144.926-0.121-0.1210.0000.0000.0000.000
26A26ALA0-0.034-0.0132.780-2.510-0.0810.693-1.238-1.884-0.014
27A27GLN0-0.020-0.0092.1670.2092.3413.638-1.417-4.353-0.007
28A28VAL0-0.016-0.0083.564-1.371-1.4050.0360.187-0.1900.000
29A29PHE00.0210.0106.3010.2170.2170.0000.0000.0000.000
30A30ALA00.005-0.00210.117-0.011-0.0110.0000.0000.0000.000
31A31VAL00.0070.01313.3900.0470.0470.0000.0000.0000.000
32A32ALA0-0.007-0.01616.7670.0300.0300.0000.0000.0000.000
33A33ARG10.9790.99720.1870.1430.1430.0000.0000.0000.000
34A34ARG10.9170.94722.9960.1210.1210.0000.0000.0000.000
35A35PRO00.0530.04617.9850.0220.0220.0000.0000.0000.000
36A36GLN00.0490.03020.1530.0190.0190.0000.0000.0000.000
37A37GLY0-0.016-0.00622.1150.0150.0150.0000.0000.0000.000
38A38SER0-0.061-0.04420.8650.0110.0110.0000.0000.0000.000
39A39PRO00.0450.00621.1690.0090.0090.0000.0000.0000.000
40A40GLY00.0090.01920.2030.0240.0240.0000.0000.0000.000
41A41LEU00.017-0.01115.5570.0270.0270.0000.0000.0000.000
42A42GLN0-0.017-0.01116.2460.0420.0420.0000.0000.0000.000
43A43ALA00.0440.02917.1870.0350.0350.0000.0000.0000.000
44A44LEU0-0.056-0.03113.4420.0530.0530.0000.0000.0000.000
45A45ALA00.0040.00212.4950.1040.1040.0000.0000.0000.000
46A46GLU-1-0.963-0.97812.7890.3120.3120.0000.0000.0000.000
47A47ARG10.7890.86612.104-0.411-0.4110.0000.0000.0000.000
48A48ALA0-0.041-0.0228.7660.1440.1440.0000.0000.0000.000
49A49GLY00.0340.0258.4640.2590.2590.0000.0000.0000.000
50A50GLU-1-0.874-0.9396.351-0.020-0.0200.0000.0000.0000.000
51A51ARG10.8400.9313.329-5.347-4.5291.021-0.411-1.4280.002
52A52LEU0-0.032-0.0165.759-0.183-0.1830.0000.0000.0000.000
53A53GLN0-0.048-0.0177.434-0.119-0.1190.0000.0000.0000.000
54A54ALA0-0.017-0.01410.167-0.083-0.0830.0000.0000.0000.000
55A55VAL00.0280.01113.395-0.028-0.0280.0000.0000.0000.000
56A56THR0-0.019-0.02215.8670.0390.0390.0000.0000.0000.000
57A57GLY00.0420.01019.685-0.022-0.0220.0000.0000.0000.000
58A58ASP-1-0.853-0.94521.249-0.175-0.1750.0000.0000.0000.000
59A59LEU00.0520.03821.378-0.006-0.0060.0000.0000.0000.000
60A60ASN00.040-0.00923.602-0.012-0.0120.0000.0000.0000.000
61A61GLN0-0.086-0.04226.2050.0120.0120.0000.0000.0000.000
62A62HIS00.0510.00925.524-0.032-0.0320.0000.0000.0000.000
63A63ASP-1-0.821-0.89524.165-0.273-0.2730.0000.0000.0000.000
64A64CYS0-0.036-0.00419.742-0.022-0.0220.0000.0000.0000.000
65A65ALA00.0350.00619.529-0.041-0.0410.0000.0000.0000.000
66A66GLU-1-0.883-0.91018.883-0.344-0.3440.0000.0000.0000.000
67A67ARG10.7110.81118.6220.2620.2620.0000.0000.0000.000
68A68ILE0-0.013-0.01714.363-0.028-0.0280.0000.0000.0000.000
69A69GLY0-0.010-0.00514.224-0.101-0.1010.0000.0000.0000.000
70A70GLU-1-0.847-0.90414.996-0.391-0.3910.0000.0000.0000.000
71A71MET0-0.0150.00112.125-0.010-0.0100.0000.0000.0000.000
72A72LEU0-0.041-0.0159.026-0.105-0.1050.0000.0000.0000.000
73A73GLY00.0420.04110.077-0.168-0.1680.0000.0000.0000.000
74A74GLU-1-0.899-0.96810.165-1.282-1.2820.0000.0000.0000.000
75A75ARG10.8390.9305.5611.5821.5820.0000.0000.0000.000
76A76ARG10.8500.9058.9771.3841.3840.0000.0000.0000.000
77A77ILE0-0.007-0.0088.817-0.407-0.4070.0000.0000.0000.000
78A78ASP-1-0.770-0.8525.825-4.446-4.4460.0000.0000.0000.000
79A79ARG10.7750.8518.9301.8721.8720.0000.0000.0000.000
80A80LEU00.0120.01410.689-0.063-0.0630.0000.0000.0000.000
81A81ILE0-0.010-0.00213.2560.0940.0940.0000.0000.0000.000
82A82VAL00.0070.00415.6640.0240.0240.0000.0000.0000.000
83A83ASN0-0.051-0.03318.5890.0410.0410.0000.0000.0000.000
84A84ALA00.0280.00720.2580.0210.0210.0000.0000.0000.000
85A85GLY00.0210.00923.820-0.003-0.0030.0000.0000.0000.000
86A86ILE0-0.061-0.02027.3350.0100.0100.0000.0000.0000.000
87A87TYR00.0460.02030.700-0.005-0.0050.0000.0000.0000.000
88A88GLY00.0480.03733.833-0.002-0.0020.0000.0000.0000.000
89A89PRO00.0630.02536.2420.0040.0040.0000.0000.0000.000
90A90GLN0-0.036-0.02639.1710.0000.0000.0000.0000.0000.000
91A91GLN0-0.006-0.01240.6540.0030.0030.0000.0000.0000.000
92A92GLN0-0.088-0.05137.204-0.002-0.0020.0000.0000.0000.000
93A93ASP-1-0.793-0.89341.887-0.065-0.0650.0000.0000.0000.000
94A94VAL0-0.009-0.02543.855-0.003-0.0030.0000.0000.0000.000
95A95ALA0-0.057-0.02145.629-0.001-0.0010.0000.0000.0000.000
96A96GLU-1-0.916-0.94545.488-0.060-0.0600.0000.0000.0000.000
97A97ILE0-0.061-0.01839.321-0.002-0.0020.0000.0000.0000.000
98A98ASP-1-0.753-0.84543.085-0.086-0.0860.0000.0000.0000.000
99A99ALA00.0260.00042.406-0.005-0.0050.0000.0000.0000.000
100A100GLU-1-0.945-0.96840.029-0.097-0.0970.0000.0000.0000.000
101A101GLN0-0.020-0.03738.434-0.008-0.0080.0000.0000.0000.000
102A102THR0-0.025-0.02937.658-0.007-0.0070.0000.0000.0000.000
103A103ALA0-0.011-0.00736.771-0.009-0.0090.0000.0000.0000.000
104A104GLN00.001-0.00533.677-0.010-0.0100.0000.0000.0000.000
105A105LEU00.0060.01832.736-0.011-0.0110.0000.0000.0000.000
106A106PHE00.0300.00132.246-0.012-0.0120.0000.0000.0000.000
107A107LEU0-0.026-0.00231.021-0.016-0.0160.0000.0000.0000.000
108A108THR00.005-0.00727.796-0.019-0.0190.0000.0000.0000.000
109A109ASN0-0.042-0.03327.199-0.020-0.0200.0000.0000.0000.000
110A110ALA00.0450.02127.843-0.011-0.0110.0000.0000.0000.000
111A111ILE00.0110.00827.540-0.021-0.0210.0000.0000.0000.000
112A112ALA0-0.040-0.01426.606-0.018-0.0180.0000.0000.0000.000
113A113PRO0-0.010-0.01723.200-0.030-0.0300.0000.0000.0000.000
114A114LEU00.0470.03422.806-0.039-0.0390.0000.0000.0000.000
115A115ARG10.7990.90324.2520.2340.2340.0000.0000.0000.000
116A116LEU0-0.0060.00418.886-0.015-0.0150.0000.0000.0000.000
117A117ALA00.0180.00519.382-0.046-0.0460.0000.0000.0000.000
118A118ARG10.8420.88720.1160.2700.2700.0000.0000.0000.000
119A119ALA0-0.0260.00822.050-0.018-0.0180.0000.0000.0000.000
120A120LEU0-0.007-0.01315.911-0.025-0.0250.0000.0000.0000.000
121A121SER0-0.014-0.01217.119-0.094-0.0940.0000.0000.0000.000
122A122GLY00.0320.02317.416-0.056-0.0560.0000.0000.0000.000
123A123ARG10.8730.92613.7120.8190.8190.0000.0000.0000.000
124A124VAL0-0.0100.01612.731-0.214-0.2140.0000.0000.0000.000
125A125SER0-0.066-0.0418.4560.2370.2370.0000.0000.0000.000
126A126ARG10.9620.97611.5920.7670.7670.0000.0000.0000.000
127A127GLY00.0330.03112.303-0.062-0.0620.0000.0000.0000.000
128A128GLY0-0.0050.00411.477-0.068-0.0680.0000.0000.0000.000
129A129VAL0-0.037-0.01912.3640.1660.1660.0000.0000.0000.000
130A130VAL00.0010.00914.171-0.107-0.1070.0000.0000.0000.000
131A131ALA0-0.0060.00216.8250.0700.0700.0000.0000.0000.000
132A132PHE0-0.002-0.00418.517-0.017-0.0170.0000.0000.0000.000
133A133MET0-0.0260.01319.5250.0270.0270.0000.0000.0000.000
134A134SER00.023-0.01222.7160.0140.0140.0000.0000.0000.000
135A135SER0-0.003-0.01126.3150.0160.0160.0000.0000.0000.000
136A136GLN00.0610.02428.890-0.005-0.0050.0000.0000.0000.000
137A137MET0-0.039-0.01431.4820.0030.0030.0000.0000.0000.000
138A138ALA0-0.0020.01330.8260.0030.0030.0000.0000.0000.000
139A139SER0-0.060-0.04232.7970.0000.0000.0000.0000.0000.000
140A140LEU00.024-0.00434.4770.0090.0090.0000.0000.0000.000
141A141ALA0-0.037-0.02236.9910.0070.0070.0000.0000.0000.000
142A142LEU0-0.009-0.00233.7980.0060.0060.0000.0000.0000.000
143A143GLY00.0130.01238.0630.0060.0060.0000.0000.0000.000
144A144LEU0-0.017-0.02135.2210.0030.0030.0000.0000.0000.000
145A145SER00.009-0.00736.7650.0010.0010.0000.0000.0000.000
146A146ALA00.0060.00638.2910.0000.0000.0000.0000.0000.000
147A147THR0-0.007-0.00339.9660.0000.0000.0000.0000.0000.000
148A148MET0-0.047-0.01035.650-0.001-0.0010.0000.0000.0000.000
149A149PRO00.0440.03137.774-0.008-0.0080.0000.0000.0000.000
150A150LEU00.0140.01938.555-0.008-0.0080.0000.0000.0000.000
151A151TYR00.0100.00929.013-0.014-0.0140.0000.0000.0000.000
152A152GLY00.0670.04033.730-0.011-0.0110.0000.0000.0000.000
153A153ALA0-0.0020.00134.496-0.010-0.0100.0000.0000.0000.000
154A154SER0-0.053-0.03432.805-0.011-0.0110.0000.0000.0000.000
155A155LYS10.7640.86926.1410.1920.1920.0000.0000.0000.000
156A156ALA00.0320.01430.570-0.012-0.0120.0000.0000.0000.000
157A157ALA0-0.026-0.00532.733-0.008-0.0080.0000.0000.0000.000
158A158LEU0-0.022-0.00625.053-0.009-0.0090.0000.0000.0000.000
159A159ASN00.0320.01528.191-0.025-0.0250.0000.0000.0000.000
160A160SER0-0.0070.00329.232-0.012-0.0120.0000.0000.0000.000
161A161LEU00.0190.01429.352-0.005-0.0050.0000.0000.0000.000
162A162VAL0-0.015-0.01024.223-0.014-0.0140.0000.0000.0000.000
163A163ARG10.8570.90726.9030.2110.2110.0000.0000.0000.000
164A164SER0-0.046-0.02429.1940.0100.0100.0000.0000.0000.000
165A165TRP0-0.023-0.02320.215-0.014-0.0140.0000.0000.0000.000
166A166GLU-1-0.806-0.90825.656-0.282-0.2820.0000.0000.0000.000
167A167GLY0-0.0010.00426.6470.0010.0010.0000.0000.0000.000
168A168GLU-1-0.870-0.90227.369-0.285-0.2850.0000.0000.0000.000
169A169PHE0-0.082-0.03822.354-0.020-0.0200.0000.0000.0000.000
170A170GLU-1-0.965-0.97126.798-0.229-0.2290.0000.0000.0000.000
171A171GLU-1-0.824-0.91721.372-0.347-0.3470.0000.0000.0000.000
172A172LEU0-0.064-0.01020.775-0.020-0.0200.0000.0000.0000.000
173A173PRO0-0.033-0.01217.583-0.023-0.0230.0000.0000.0000.000
174A174PHE00.008-0.01115.269-0.108-0.1080.0000.0000.0000.000
175A175SER0-0.001-0.00616.5310.0840.0840.0000.0000.0000.000
176A176LEU0-0.009-0.00318.298-0.052-0.0520.0000.0000.0000.000
177A177LEU00.0070.00417.7650.0500.0500.0000.0000.0000.000
178A178LEU0-0.026-0.00521.214-0.007-0.0070.0000.0000.0000.000
179A179LEU00.0210.00618.2540.0200.0200.0000.0000.0000.000
180A180HIS00.0430.00722.9870.0030.0030.0000.0000.0000.000
181A181PRO00.0170.00222.7740.0050.0050.0000.0000.0000.000
182A182GLY00.0120.03224.2010.0160.0160.0000.0000.0000.000
183A195LEU00.0410.01826.395-0.002-0.0020.0000.0000.0000.000
184A196SER0-0.104-0.07324.6040.0000.0000.0000.0000.0000.000
185A197VAL00.003-0.02620.454-0.014-0.0140.0000.0000.0000.000
186A198GLU-1-0.906-0.94919.4560.0850.0850.0000.0000.0000.000
187A199GLU-1-0.780-0.84619.302-0.019-0.0190.0000.0000.0000.000
188A200SER0-0.059-0.04120.736-0.027-0.0270.0000.0000.0000.000
189A201ALA00.0230.00016.361-0.032-0.0320.0000.0000.0000.000
190A202ALA00.009-0.00115.836-0.043-0.0430.0000.0000.0000.000
191A203GLY00.0060.01116.590-0.019-0.0190.0000.0000.0000.000
192A204LEU00.010-0.00718.130-0.033-0.0330.0000.0000.0000.000
193A205VAL0-0.023-0.01611.523-0.053-0.0530.0000.0000.0000.000
194A206ALA0-0.058-0.02513.973-0.065-0.0650.0000.0000.0000.000
195A207ALA00.0180.00616.028-0.026-0.0260.0000.0000.0000.000
196A208VAL0-0.019-0.00612.796-0.027-0.0270.0000.0000.0000.000
197A209GLU-1-0.801-0.8799.397-1.252-1.2520.0000.0000.0000.000
198A210ASP-1-0.805-0.87113.010-0.261-0.2610.0000.0000.0000.000
199A211ALA00.0110.00615.8840.0300.0300.0000.0000.0000.000
200A212ALA0-0.0110.00111.582-0.038-0.0380.0000.0000.0000.000
201A213GLY0-0.038-0.02613.6770.0790.0790.0000.0000.0000.000
202A214VAL0-0.064-0.02315.0590.0640.0640.0000.0000.0000.000
203A215ASN0-0.041-0.01917.233-0.025-0.0250.0000.0000.0000.000
204A216ALA00.0810.04019.4600.0410.0410.0000.0000.0000.000
205A217CYS0-0.057-0.01621.396-0.023-0.0230.0000.0000.0000.000
206A218ARG10.7990.88319.9480.3190.3190.0000.0000.0000.000
207A219PHE00.0080.00024.373-0.013-0.0130.0000.0000.0000.000
208A220VAL00.0120.00821.7400.0160.0160.0000.0000.0000.000
209A221ASP-1-0.751-0.87424.735-0.123-0.1230.0000.0000.0000.000
210A222TYR0-0.081-0.05621.791-0.021-0.0210.0000.0000.0000.000
211A223ARG10.8430.91221.8770.0840.0840.0000.0000.0000.000
212A224ASN0-0.036-0.03120.764-0.017-0.0170.0000.0000.0000.000
213A225GLN00.0040.01922.8120.0050.0050.0000.0000.0000.000
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