Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: G5QJ1

Calculation Name: 4DEJ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4DEJ

Chain ID: A

ChEMBL ID:

UniProt ID: Q5R0K1

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 OptHSide
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 202
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2447775.508891
FMO2-HF: Nuclear repulsion 2365360.924429
FMO2-HF: Total energy -82414.584462
FMO2-MP2: Total energy -82654.121222


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:7:LYS)


Summations of interaction energy for fragment #1(A:7: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.
-162.432-160.788-0.008-0.626-1.0090.002
Interaction energy analysis for fragmet #1(A:7:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 1.017 / q_NPA : 0.994
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].
3A9SER00.0180.0023.8222.2813.660-0.006-0.617-0.7560.002
4A10VAL0-0.029-0.0106.1683.6303.6300.0000.0000.0000.000
5A11MET00.0040.0176.549-2.065-2.0650.0000.0000.0000.000
6A12THR0-0.007-0.0127.155-1.412-1.4120.0000.0000.0000.000
7A13LEU00.0050.0129.1080.9670.9670.0000.0000.0000.000
8A14TYR0-0.026-0.0399.463-0.839-0.8390.0000.0000.0000.000
9A15SER00.014-0.00214.3071.3351.3350.0000.0000.0000.000
10A16GLY00.0670.02517.760-0.336-0.3360.0000.0000.0000.000
11A17LYS10.8740.91520.11614.16814.1680.0000.0000.0000.000
12A18ASP-1-0.762-0.88923.030-10.549-10.5490.0000.0000.0000.000
13A19ASP-1-0.793-0.85822.727-12.349-12.3490.0000.0000.0000.000
14A20LEU00.0110.01624.962-0.172-0.1720.0000.0000.0000.000
15A21LYS10.8710.88923.45910.86710.8670.0000.0000.0000.000
16A22SER0-0.015-0.03920.554-0.626-0.6260.0000.0000.0000.000
17A23HIS00.0040.03021.028-0.259-0.2590.0000.0000.0000.000
18A24GLN00.0070.00023.490-0.242-0.2420.0000.0000.0000.000
19A25VAL0-0.024-0.01317.168-0.028-0.0280.0000.0000.0000.000
20A26ARG10.7650.83518.98313.34613.3460.0000.0000.0000.000
21A27LEU00.0000.00820.409-0.026-0.0260.0000.0000.0000.000
22A28VAL00.0160.00520.4710.1380.1380.0000.0000.0000.000
23A29LEU0-0.019-0.01815.444-0.025-0.0250.0000.0000.0000.000
24A30ALA00.0170.02319.133-0.196-0.1960.0000.0000.0000.000
25A31GLU-1-0.835-0.87421.908-10.232-10.2320.0000.0000.0000.000
26A32LYS10.6990.83019.78012.11012.1100.0000.0000.0000.000
27A33GLY00.0000.01921.103-0.021-0.0210.0000.0000.0000.000
28A34VAL0-0.062-0.02115.591-0.414-0.4140.0000.0000.0000.000
29A35GLY0-0.0030.00115.4240.1010.1010.0000.0000.0000.000
30A36VAL0-0.038-0.03411.749-1.021-1.0210.0000.0000.0000.000
31A37GLU-1-0.833-0.8907.518-37.906-37.9060.0000.0000.0000.000
32A38ILE0-0.004-0.01111.464-0.343-0.3430.0000.0000.0000.000
33A39THR0-0.0180.00010.970-0.797-0.7970.0000.0000.0000.000
34A40TYR0-0.026-0.03013.3170.6260.6260.0000.0000.0000.000
35A41VAL0-0.006-0.00315.946-0.570-0.5700.0000.0000.0000.000
36A42THR0-0.028-0.01918.3550.5890.5890.0000.0000.0000.000
37A43ASP-1-0.829-0.91821.339-13.094-13.0940.0000.0000.0000.000
38A44GLU-1-0.979-0.97822.793-11.769-11.7690.0000.0000.0000.000
39A45SER0-0.066-0.03718.846-0.351-0.3510.0000.0000.0000.000
40A46THR00.0230.02017.550-0.108-0.1080.0000.0000.0000.000
41A47PRO0-0.001-0.00912.1770.2060.2060.0000.0000.0000.000
42A48GLU-1-0.917-0.95811.276-22.584-22.5840.0000.0000.0000.000
43A49ASP-1-0.849-0.9208.214-30.645-30.6450.0000.0000.0000.000
44A50LEU0-0.041-0.02010.3440.6500.6500.0000.0000.0000.000
45A51LEU0-0.015-0.01313.1221.1161.1160.0000.0000.0000.000
46A52GLN0-0.053-0.01510.820-0.361-0.3610.0000.0000.0000.000
47A53LEU0-0.044-0.0138.3320.5890.5890.0000.0000.0000.000
48A54ASN0-0.010-0.01612.8321.5391.5390.0000.0000.0000.000
49A55PRO0-0.0030.01816.259-0.003-0.0030.0000.0000.0000.000
50A56TYR0-0.050-0.02819.4041.0971.0970.0000.0000.0000.000
51A57PRO0-0.018-0.02421.190-0.385-0.3850.0000.0000.0000.000
52A58GLU-1-0.831-0.89922.537-13.314-13.3140.0000.0000.0000.000
53A59ALA0-0.0020.00617.613-0.070-0.0700.0000.0000.0000.000
54A60LYS10.7920.89817.33312.13312.1330.0000.0000.0000.000
55A61PRO0-0.024-0.00317.6550.6260.6260.0000.0000.0000.000
56A62THR0-0.014-0.02712.4700.5010.5010.0000.0000.0000.000
57A63LEU0-0.0240.00611.466-0.965-0.9650.0000.0000.0000.000
58A64VAL00.0330.0076.2370.4170.4170.0000.0000.0000.000
59A65ASP-1-0.795-0.9017.026-24.410-24.4100.0000.0000.0000.000
60A66ARG10.8080.8924.36129.09429.191-0.001-0.005-0.0900.000
61A67GLU-1-0.875-0.9294.842-31.713-31.545-0.001-0.004-0.1630.000
62A68LEU0-0.080-0.0207.5551.6381.6380.0000.0000.0000.000
63A69VAL00.0220.0139.423-1.096-1.0960.0000.0000.0000.000
64A70LEU0-0.036-0.01511.2661.2941.2940.0000.0000.0000.000
65A71TYR00.0710.02414.564-0.009-0.0090.0000.0000.0000.000
66A72ASN00.008-0.00717.3290.5030.5030.0000.0000.0000.000
67A73ALA00.0840.04419.977-0.308-0.3080.0000.0000.0000.000
68A74GLN0-0.009-0.00921.395-0.010-0.0100.0000.0000.0000.000
69A75ILE00.0000.00018.6090.1110.1110.0000.0000.0000.000
70A76ILE0-0.020-0.00315.982-0.197-0.1970.0000.0000.0000.000
71A77MET0-0.011-0.01118.248-0.139-0.1390.0000.0000.0000.000
72A78GLU-1-0.788-0.86421.051-10.254-10.2540.0000.0000.0000.000
73A79TYR00.0130.01812.0830.2210.2210.0000.0000.0000.000
74A80LEU0-0.024-0.02115.278-0.194-0.1940.0000.0000.0000.000
75A81ASP-1-0.806-0.90518.524-10.940-10.9400.0000.0000.0000.000
76A82GLU-1-0.970-0.97620.905-10.993-10.9930.0000.0000.0000.000
77A83ARG10.8100.90411.27118.11618.1160.0000.0000.0000.000
78A84PHE0-0.032-0.03213.851-0.371-0.3710.0000.0000.0000.000
79A85PRO00.0290.01819.9060.3090.3090.0000.0000.0000.000
80A86HIS0-0.0670.00423.2250.5580.5580.0000.0000.0000.000
81A87PRO00.0640.02423.686-0.388-0.3880.0000.0000.0000.000
82A88PRO00.0210.01025.834-0.318-0.3180.0000.0000.0000.000
83A89LEU00.0340.02224.2910.2280.2280.0000.0000.0000.000
84A90MET0-0.041-0.01426.8260.3070.3070.0000.0000.0000.000
85A91PRO00.0220.01229.3640.0740.0740.0000.0000.0000.000
86A92VAL00.0320.01431.471-0.177-0.1770.0000.0000.0000.000
87A93TYR00.0090.00133.256-0.031-0.0310.0000.0000.0000.000
88A94PRO00.0480.00034.511-0.056-0.0560.0000.0000.0000.000
89A95VAL00.0280.01935.593-0.084-0.0840.0000.0000.0000.000
90A96ALA00.0480.02736.303-0.010-0.0100.0000.0000.0000.000
91A97ARG10.9330.97826.9039.6159.6150.0000.0000.0000.000
92A98GLY00.0060.01132.731-0.191-0.1910.0000.0000.0000.000
93A99THR0-0.011-0.01134.9740.0350.0350.0000.0000.0000.000
94A100SER00.024-0.00532.264-0.015-0.0150.0000.0000.0000.000
95A101ARG10.8690.90826.8899.7449.7440.0000.0000.0000.000
96A102LEU0-0.0190.00631.913-0.095-0.0950.0000.0000.0000.000
97A103MET0-0.015-0.01535.0480.0920.0920.0000.0000.0000.000
98A104MET00.0080.00928.380-0.081-0.0810.0000.0000.0000.000
99A105TYR0-0.0050.01531.3890.0200.0200.0000.0000.0000.000
100A106ARG10.8520.89832.7037.3877.3870.0000.0000.0000.000
101A107ILE00.0170.03532.5490.0680.0680.0000.0000.0000.000
102A108GLU-1-0.826-0.89528.098-10.308-10.3080.0000.0000.0000.000
103A109ARG10.9040.94732.1117.9027.9020.0000.0000.0000.000
104A110ASP-1-0.851-0.90734.867-7.569-7.5690.0000.0000.0000.000
105A111TRP00.007-0.00635.8290.0360.0360.0000.0000.0000.000
106A112TYR00.004-0.03227.956-0.115-0.1150.0000.0000.0000.000
107A113SER0-0.031-0.01633.122-0.104-0.1040.0000.0000.0000.000
108A114LEU0-0.019-0.00834.9530.0270.0270.0000.0000.0000.000
109A115ALA00.0290.00433.6550.0850.0850.0000.0000.0000.000
110A116GLU-1-0.844-0.90031.071-9.881-9.8810.0000.0000.0000.000
111A117LYS10.8550.92734.1317.5847.5840.0000.0000.0000.000
112A118ILE0-0.048-0.02137.4720.1270.1270.0000.0000.0000.000
113A119GLN0-0.006-0.00431.440-0.002-0.0020.0000.0000.0000.000
114A120LYS10.7970.92133.4079.1149.1140.0000.0000.0000.000
115A121ASN0-0.024-0.02237.6340.1020.1020.0000.0000.0000.000
116A122ASP-1-0.837-0.92941.204-7.094-7.0940.0000.0000.0000.000
117A123ALA00.0190.00442.630-0.083-0.0830.0000.0000.0000.000
118A124GLN0-0.014-0.01145.4190.1890.1890.0000.0000.0000.000
119A125ALA00.0120.01040.3810.0270.0270.0000.0000.0000.000
120A126ARG10.8970.94941.1577.4087.4080.0000.0000.0000.000
121A127GLN0-0.066-0.04342.9580.0140.0140.0000.0000.0000.000
122A128GLU-1-0.875-0.94043.198-7.106-7.1060.0000.0000.0000.000
123A129LEU00.0150.01037.528-0.014-0.0140.0000.0000.0000.000
124A130LYS10.8120.91041.6446.6306.6300.0000.0000.0000.000
125A131GLU-1-0.888-0.94844.253-6.264-6.2640.0000.0000.0000.000
126A132GLY0-0.0190.01642.6750.0830.0830.0000.0000.0000.000
127A133ILE00.003-0.01138.8610.0080.0080.0000.0000.0000.000
128A134LEU0-0.034-0.02042.4810.0250.0250.0000.0000.0000.000
129A135SER0-0.043-0.02845.8920.1000.1000.0000.0000.0000.000
130A136LEU0-0.024-0.01841.4480.0720.0720.0000.0000.0000.000
131A137ALA0-0.0020.00244.019-0.069-0.0690.0000.0000.0000.000
132A138PRO0-0.034-0.02345.8190.0080.0080.0000.0000.0000.000
133A139ILE00.0160.02040.3850.0310.0310.0000.0000.0000.000
134A140PHE0-0.038-0.02738.655-0.097-0.0970.0000.0000.0000.000
135A141ALA0-0.067-0.02343.561-0.014-0.0140.0000.0000.0000.000
136A142ASP-1-0.944-0.95544.846-6.371-6.3710.0000.0000.0000.000
137A143THR0-0.039-0.02540.5520.0390.0390.0000.0000.0000.000
138A144PRO0-0.051-0.00939.430-0.038-0.0380.0000.0000.0000.000
139A145TYR00.005-0.00234.944-0.231-0.2310.0000.0000.0000.000
140A146PHE00.0310.00735.7930.2210.2210.0000.0000.0000.000
141A147MET0-0.033-0.01636.740-0.160-0.1600.0000.0000.0000.000
142A148SER0-0.039-0.03035.151-0.010-0.0100.0000.0000.0000.000
143A149GLU-1-0.863-0.94537.844-7.148-7.1480.0000.0000.0000.000
144A150GLU-1-0.976-0.98933.953-8.534-8.5340.0000.0000.0000.000
145A151PHE0-0.041-0.00927.8890.0630.0630.0000.0000.0000.000
146A152SER00.0370.02030.170-0.207-0.2070.0000.0000.0000.000
147A153LEU00.049-0.01824.474-0.099-0.0990.0000.0000.0000.000
148A154VAL0-0.010-0.00528.399-0.118-0.1180.0000.0000.0000.000
149A155ASP-1-0.701-0.83531.473-8.614-8.6140.0000.0000.0000.000
150A156CYS0-0.062-0.01426.231-0.161-0.1610.0000.0000.0000.000
151A157TYR00.0220.00426.785-0.406-0.4060.0000.0000.0000.000
152A158LEU00.0130.02429.8660.0340.0340.0000.0000.0000.000
153A159ALA0-0.0010.00229.7120.1200.1200.0000.0000.0000.000
154A160PRO00.0060.00327.2570.0700.0700.0000.0000.0000.000
155A161LEU0-0.021-0.00129.8030.0620.0620.0000.0000.0000.000
156A162LEU00.012-0.01732.9660.1740.1740.0000.0000.0000.000
157A163TRP0-0.032-0.02131.2290.3010.3010.0000.0000.0000.000
158A164ARG10.7800.87626.99810.88210.8820.0000.0000.0000.000
159A165LEU00.0050.00734.5140.1220.1220.0000.0000.0000.000
160A166PRO00.0330.01137.1690.2010.2010.0000.0000.0000.000
161A167ALA00.0070.00935.5850.1260.1260.0000.0000.0000.000
162A168TYR0-0.019-0.01032.5990.0260.0260.0000.0000.0000.000
163A169GLY00.0050.01738.7980.1670.1670.0000.0000.0000.000
164A170ILE0-0.071-0.03740.2190.2230.2230.0000.0000.0000.000
165A171ASP-1-0.844-0.91642.520-7.080-7.0800.0000.0000.0000.000
166A172LEU0-0.075-0.06044.6750.0700.0700.0000.0000.0000.000
167A173GLU-1-0.852-0.91146.333-6.152-6.1520.0000.0000.0000.000
168A174GLY00.0110.00649.5740.0080.0080.0000.0000.0000.000
169A175GLN0-0.041-0.03051.433-0.078-0.0780.0000.0000.0000.000
170A176GLY00.0690.03549.185-0.045-0.0450.0000.0000.0000.000
171A177ALA00.0590.01446.455-0.141-0.1410.0000.0000.0000.000
172A178LYS10.8800.95546.2836.1796.1790.0000.0000.0000.000
173A179GLU-1-0.851-0.94945.692-6.419-6.4190.0000.0000.0000.000
174A180ILE00.0140.02241.344-0.169-0.1690.0000.0000.0000.000
175A181LYS10.9960.99641.3267.1557.1550.0000.0000.0000.000
176A182GLN0-0.017-0.00941.844-0.041-0.0410.0000.0000.0000.000
177A183TYR0-0.026-0.03135.171-0.123-0.1230.0000.0000.0000.000
178A184MET0-0.026-0.01137.462-0.131-0.1310.0000.0000.0000.000
179A185VAL0-0.048-0.01437.036-0.207-0.2070.0000.0000.0000.000
180A186ARG10.8840.94437.9947.4777.4770.0000.0000.0000.000
181A187LEU0-0.023-0.01032.892-0.216-0.2160.0000.0000.0000.000
182A188PHE0-0.052-0.03932.848-0.265-0.2650.0000.0000.0000.000
183A189GLU-1-0.957-0.97033.366-8.219-8.2190.0000.0000.0000.000
184A190ARG10.8030.89929.3309.7209.7200.0000.0000.0000.000
185A191LYS10.9790.95929.4489.2849.2840.0000.0000.0000.000
186A192THR00.010-0.01325.779-0.145-0.1450.0000.0000.0000.000
187A193PHE00.0170.01225.884-0.421-0.4210.0000.0000.0000.000
188A194GLN0-0.002-0.00727.603-0.237-0.2370.0000.0000.0000.000
189A195ASP-1-0.918-0.95024.108-12.067-12.0670.0000.0000.0000.000
190A196SER0-0.103-0.05022.865-0.539-0.5390.0000.0000.0000.000
191A197LEU0-0.053-0.00123.490-0.336-0.3360.0000.0000.0000.000
192A198THR00.000-0.01522.032-0.188-0.1880.0000.0000.0000.000
193A199GLU-1-0.829-0.93024.059-12.131-12.1310.0000.0000.0000.000
194A200GLU-1-0.813-0.90424.055-12.793-12.7930.0000.0000.0000.000
195A201GLU-1-0.684-0.79725.634-11.838-11.8380.0000.0000.0000.000
196A202LYS10.8220.90925.39012.55312.5530.0000.0000.0000.000
197A203GLU-1-1.016-1.01230.384-9.865-9.8650.0000.0000.0000.000
198A204LEU0-0.0240.00131.3090.3660.3660.0000.0000.0000.000
199A205ALA0-0.030-0.00734.0440.3050.3050.0000.0000.0000.000
200A206ARG10.8620.92531.2959.8929.8920.0000.0000.0000.000
201A207ASN0-0.0200.00134.8100.3850.3850.0000.0000.0000.000
202A208ALA00.0020.02038.2770.1450.1450.0000.0000.0000.000