FMODB

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

Last updated: 2024-04-25

All entries: 37426

Number of unique PDB entries: 7782

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FMODB ID: R8N58

Calculation Name: 1X42-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1X42

Chain ID: A

ChEMBL ID:

UniProt ID: O58216

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 229
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3007131.350932
FMO2-HF: Nuclear repulsion 2913932.131446
FMO2-HF: Total energy -93199.219486
FMO2-MP2: Total energy -93471.001112


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.
-14.843-6.2534.763-4.64-8.714-0.033
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 : -0.017 / q_NPA : -0.002
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].
3A3ARG10.7980.8732.434-3.6690.3292.503-2.352-4.149-0.007
4A4ALA0-0.0060.0033.6961.2911.5460.007-0.012-0.2500.000
5A5VAL00.0140.0107.291-0.332-0.3320.0000.0000.0000.000
6A6PHE0-0.044-0.01610.0220.2870.2870.0000.0000.0000.000
7A7PHE00.021-0.00413.179-0.028-0.0280.0000.0000.0000.000
8A8ASP-1-0.762-0.87416.844-0.484-0.4840.0000.0000.0000.000
9A9PHE00.004-0.02920.449-0.003-0.0030.0000.0000.0000.000
10A10VAL00.0270.00923.0470.0040.0040.0000.0000.0000.000
11A11GLY00.0170.02225.750-0.013-0.0130.0000.0000.0000.000
12A12THR0-0.033-0.01319.548-0.029-0.0290.0000.0000.0000.000
13A13LEU0-0.031-0.03118.700-0.006-0.0060.0000.0000.0000.000
14A14LEU0-0.017-0.00522.8140.0320.0320.0000.0000.0000.000
15A15SER0-0.030-0.01226.4910.0000.0000.0000.0000.0000.000
16A16VAL00.0730.02428.7830.0160.0160.0000.0000.0000.000
17A17GLU-1-0.811-0.88730.939-0.270-0.2700.0000.0000.0000.000
18A18GLY00.0640.03132.3170.0170.0170.0000.0000.0000.000
19A19GLU-1-0.812-0.88431.135-0.255-0.2550.0000.0000.0000.000
20A20ALA00.0430.04133.9230.0140.0140.0000.0000.0000.000
21A21LYS10.8570.92235.8080.2100.2100.0000.0000.0000.000
22A22THR0-0.037-0.02835.2250.0120.0120.0000.0000.0000.000
23A23HIS0-0.029-0.04334.4340.0190.0190.0000.0000.0000.000
24A24LEU0-0.026-0.01639.0950.0100.0100.0000.0000.0000.000
25A25LYS10.7800.87141.0020.1460.1460.0000.0000.0000.000
26A26ILE00.0100.02238.1350.0070.0070.0000.0000.0000.000
27A27MET0-0.010-0.00141.1300.0090.0090.0000.0000.0000.000
28A28GLU-1-0.824-0.90245.129-0.126-0.1260.0000.0000.0000.000
29A29GLU-1-0.821-0.87645.315-0.123-0.1230.0000.0000.0000.000
30A30VAL0-0.060-0.03445.2750.0050.0050.0000.0000.0000.000
31A31LEU0-0.074-0.03048.0030.0050.0050.0000.0000.0000.000
32A32GLY00.0200.02050.6790.0050.0050.0000.0000.0000.000
33A33ASP-1-0.939-0.97852.651-0.089-0.0890.0000.0000.0000.000
34A34TYR0-0.077-0.04954.0740.0040.0040.0000.0000.0000.000
35A35PRO0-0.0070.00354.874-0.003-0.0030.0000.0000.0000.000
36A36LEU0-0.034-0.01350.9810.0010.0010.0000.0000.0000.000
37A37ASN00.008-0.00450.166-0.003-0.0030.0000.0000.0000.000
38A38PRO00.1110.05147.095-0.004-0.0040.0000.0000.0000.000
39A39LYS10.9340.96745.2480.1310.1310.0000.0000.0000.000
40A40THR0-0.017-0.00145.910-0.004-0.0040.0000.0000.0000.000
41A41LEU00.0210.00945.603-0.003-0.0030.0000.0000.0000.000
42A42LEU00.005-0.00239.895-0.003-0.0030.0000.0000.0000.000
43A43ASP-1-0.855-0.92542.239-0.165-0.1650.0000.0000.0000.000
44A44GLU-1-0.817-0.89842.906-0.142-0.1420.0000.0000.0000.000
45A45TYR0-0.019-0.05138.5260.0020.0020.0000.0000.0000.000
46A46GLU-1-0.832-0.88637.283-0.221-0.2210.0000.0000.0000.000
47A47LYS10.8440.92838.7660.1470.1470.0000.0000.0000.000
48A48LEU0-0.008-0.01340.047-0.003-0.0030.0000.0000.0000.000
49A49THR0-0.015-0.01837.065-0.007-0.0070.0000.0000.0000.000
50A50ARG10.8350.90434.3000.2290.2290.0000.0000.0000.000
51A51GLU-1-0.898-0.94735.741-0.208-0.2080.0000.0000.0000.000
52A52ALA0-0.0070.00137.710-0.003-0.0030.0000.0000.0000.000
53A53PHE00.015-0.01732.821-0.005-0.0050.0000.0000.0000.000
54A54SER0-0.0150.00433.199-0.019-0.0190.0000.0000.0000.000
55A55ASN0-0.087-0.04133.685-0.001-0.0010.0000.0000.0000.000
56A56TYR00.0170.00833.3540.0080.0080.0000.0000.0000.000
57A57ALA00.0190.02529.229-0.016-0.0160.0000.0000.0000.000
58A58GLY0-0.053-0.02327.4930.0130.0130.0000.0000.0000.000
59A59LYS10.8340.91028.5090.2300.2300.0000.0000.0000.000
60A60PRO0-0.007-0.01930.602-0.014-0.0140.0000.0000.0000.000
61A61TYR0-0.047-0.05130.0960.0050.0050.0000.0000.0000.000
62A62ARG10.7860.86232.0610.1910.1910.0000.0000.0000.000
63A63PRO0-0.0020.00934.154-0.013-0.0130.0000.0000.0000.000
64A64ILE00.017-0.00330.2990.0070.0070.0000.0000.0000.000
65A65ARG10.8680.92934.6060.1650.1650.0000.0000.0000.000
66A66ASP-1-0.912-0.96437.220-0.163-0.1630.0000.0000.0000.000
67A67ILE0-0.041-0.01835.2660.0080.0080.0000.0000.0000.000
68A68GLU-1-0.778-0.86135.589-0.212-0.2120.0000.0000.0000.000
69A69GLU-1-0.781-0.86639.506-0.135-0.1350.0000.0000.0000.000
70A70GLU-1-0.838-0.87142.345-0.150-0.1500.0000.0000.0000.000
71A71VAL0-0.027-0.01040.9950.0080.0080.0000.0000.0000.000
72A72MET00.0040.00243.5540.0090.0090.0000.0000.0000.000
73A73ARG10.7580.85345.2540.1320.1320.0000.0000.0000.000
74A74LYS10.9971.00446.7770.1420.1420.0000.0000.0000.000
75A75LEU0-0.033-0.02244.9370.0050.0050.0000.0000.0000.000
76A76ALA0-0.016-0.00149.0230.0040.0040.0000.0000.0000.000
77A77GLU-1-0.969-0.97651.249-0.101-0.1010.0000.0000.0000.000
78A78LYS10.8030.90150.1700.1250.1250.0000.0000.0000.000
79A79TYR0-0.076-0.07949.6840.0040.0040.0000.0000.0000.000
80A80GLY00.0200.03754.3660.0030.0030.0000.0000.0000.000
81A81PHE00.0020.02948.7730.0030.0030.0000.0000.0000.000
82A82LYS10.9070.92552.7320.0980.0980.0000.0000.0000.000
83A83TYR00.003-0.00844.999-0.003-0.0030.0000.0000.0000.000
84A84PRO00.0050.01846.8330.0050.0050.0000.0000.0000.000
85A85GLU-1-0.761-0.89347.447-0.118-0.1180.0000.0000.0000.000
86A86ASN0-0.0300.00945.483-0.002-0.0020.0000.0000.0000.000
87A87PHE00.0350.01141.363-0.004-0.0040.0000.0000.0000.000
88A88TRP00.0630.01834.691-0.001-0.0010.0000.0000.0000.000
89A89GLU-1-0.909-0.95439.323-0.133-0.1330.0000.0000.0000.000
90A90ILE0-0.053-0.03040.511-0.004-0.0040.0000.0000.0000.000
91A91HIS0-0.0010.00634.917-0.003-0.0030.0000.0000.0000.000
92A92LEU00.0430.04133.599-0.010-0.0100.0000.0000.0000.000
93A93ARG10.8150.87436.1400.1280.1280.0000.0000.0000.000
94A94MET0-0.037-0.02437.843-0.002-0.0020.0000.0000.0000.000
95A95HIS10.8200.87532.4050.2280.2280.0000.0000.0000.000
96A96GLN0-0.051-0.02232.975-0.001-0.0010.0000.0000.0000.000
97A97ARG10.9100.97033.9460.1450.1450.0000.0000.0000.000
98A98TYR0-0.065-0.05235.9850.0070.0070.0000.0000.0000.000
99A99GLY00.0420.05131.776-0.004-0.0040.0000.0000.0000.000
100A100GLU-1-0.878-0.93030.253-0.214-0.2140.0000.0000.0000.000
101A101LEU00.0310.00923.899-0.014-0.0140.0000.0000.0000.000
102A102TYR0-0.026-0.02624.1940.0180.0180.0000.0000.0000.000
103A103PRO0-0.007-0.01924.845-0.011-0.0110.0000.0000.0000.000
104A104GLU-1-0.775-0.85520.600-0.441-0.4410.0000.0000.0000.000
105A105VAL00.0120.01720.213-0.042-0.0420.0000.0000.0000.000
106A106VAL00.0400.01719.126-0.046-0.0460.0000.0000.0000.000
107A107GLU-1-0.919-0.96018.612-0.433-0.4330.0000.0000.0000.000
108A108VAL00.0410.01614.870-0.033-0.0330.0000.0000.0000.000
109A109LEU00.0140.01514.558-0.095-0.0950.0000.0000.0000.000
110A110LYS10.9260.94814.2790.2950.2950.0000.0000.0000.000
111A111SER0-0.094-0.04413.542-0.027-0.0270.0000.0000.0000.000
112A112LEU00.0300.0149.393-0.070-0.0700.0000.0000.0000.000
113A113LYS10.8640.9299.4630.4130.4130.0000.0000.0000.000
114A114GLY0-0.059-0.01610.1090.0670.0670.0000.0000.0000.000
115A115LYS10.7840.8925.9151.5781.5780.0000.0000.0000.000
116A116TYR0-0.047-0.0422.900-1.197-0.5590.133-0.095-0.6750.000
117A117HIS00.0010.0066.5120.4650.4650.0000.0000.0000.000
118A118VAL00.004-0.0078.958-0.260-0.2600.0000.0000.0000.000
119A119GLY00.006-0.00411.7960.1760.1760.0000.0000.0000.000
120A120MET0-0.0430.00614.345-0.026-0.0260.0000.0000.0000.000
121A121ILE0-0.017-0.01615.5400.0250.0250.0000.0000.0000.000
122A122THR0-0.011-0.00619.345-0.009-0.0090.0000.0000.0000.000
123A123ASP-1-0.708-0.82922.980-0.396-0.3960.0000.0000.0000.000
124A124SER0-0.063-0.06126.4640.0020.0020.0000.0000.0000.000
125A125ASP-1-0.678-0.78828.182-0.242-0.2420.0000.0000.0000.000
126A126THR0-0.003-0.04726.052-0.016-0.0160.0000.0000.0000.000
127A127GLU-1-0.945-0.96328.431-0.187-0.1870.0000.0000.0000.000
128A128TYR0-0.002-0.02830.934-0.002-0.0020.0000.0000.0000.000
129A129LEU00.0110.00423.8010.0000.0000.0000.0000.0000.000
130A130MET0-0.024-0.00623.628-0.008-0.0080.0000.0000.0000.000
131A131ALA00.0320.02327.7290.0020.0020.0000.0000.0000.000
132A132HIS0-0.003-0.01928.8520.0030.0030.0000.0000.0000.000
133A133LEU00.023-0.00322.706-0.003-0.0030.0000.0000.0000.000
134A134ASP-1-0.829-0.92126.345-0.243-0.2430.0000.0000.0000.000
135A135ALA0-0.085-0.02328.1510.0080.0080.0000.0000.0000.000
136A136LEU0-0.045-0.02326.3350.0050.0050.0000.0000.0000.000
137A137GLY0-0.0180.00726.646-0.006-0.0060.0000.0000.0000.000
138A138ILE0-0.023-0.02821.508-0.012-0.0120.0000.0000.0000.000
139A139LYS10.8360.94321.2410.2180.2180.0000.0000.0000.000
140A140ASP-1-0.881-0.95721.064-0.290-0.2900.0000.0000.0000.000
141A141LEU0-0.086-0.04717.820-0.001-0.0010.0000.0000.0000.000
142A142PHE0-0.006-0.01515.852-0.080-0.0800.0000.0000.0000.000
143A143ASP-1-0.811-0.88012.281-0.620-0.6200.0000.0000.0000.000
144A144SER0-0.048-0.01414.8500.0190.0190.0000.0000.0000.000
145A145ILE00.0520.01616.564-0.054-0.0540.0000.0000.0000.000
146A146THR0-0.019-0.00218.0820.0520.0520.0000.0000.0000.000
147A147THR00.0100.00020.736-0.026-0.0260.0000.0000.0000.000
148A148SER00.0570.02224.108-0.003-0.0030.0000.0000.0000.000
149A149GLU-1-0.880-0.89626.430-0.233-0.2330.0000.0000.0000.000
150A150GLU-1-0.847-0.90723.158-0.371-0.3710.0000.0000.0000.000
151A151ALA0-0.0060.00223.4100.0120.0120.0000.0000.0000.000
152A152GLY00.0190.01325.2670.0160.0160.0000.0000.0000.000
153A153PHE0-0.061-0.03826.5030.0220.0220.0000.0000.0000.000
154A154PHE00.0180.01926.599-0.028-0.0280.0000.0000.0000.000
155A155LYS10.8090.90521.9250.5490.5490.0000.0000.0000.000
156A156PRO0-0.007-0.02123.2370.0360.0360.0000.0000.0000.000
157A157HIS00.0060.00422.911-0.043-0.0430.0000.0000.0000.000
158A158PRO00.0580.01420.547-0.032-0.0320.0000.0000.0000.000
159A159ARG10.9230.95020.2330.2670.2670.0000.0000.0000.000
160A160ILE0-0.015-0.00221.321-0.012-0.0120.0000.0000.0000.000
161A161PHE00.0320.01616.753-0.028-0.0280.0000.0000.0000.000
162A162GLU-1-0.901-0.94516.677-0.527-0.5270.0000.0000.0000.000
163A163LEU0-0.037-0.01617.187-0.016-0.0160.0000.0000.0000.000
164A164ALA00.0220.01816.0200.0150.0150.0000.0000.0000.000
165A165LEU0-0.007-0.00511.396-0.030-0.0300.0000.0000.0000.000
166A166LYS10.8520.91213.0640.5150.5150.0000.0000.0000.000
167A167LYS10.7630.86915.4120.4970.4970.0000.0000.0000.000
168A168ALA0-0.0080.00310.8370.0590.0590.0000.0000.0000.000
169A169GLY0-0.0130.02210.9530.0200.0200.0000.0000.0000.000
170A170VAL0-0.067-0.0427.5960.0470.0470.0000.0000.0000.000
171A171LYS10.8720.9355.4832.0872.0870.0000.0000.0000.000
172A172GLY00.0820.0298.666-0.428-0.4280.0000.0000.0000.000
173A173GLU-1-0.884-0.9536.204-1.677-1.6770.0000.0000.0000.000
174A174GLU-1-0.862-0.8943.684-3.323-2.8860.000-0.075-0.3630.000
175A175ALA00.006-0.0075.673-0.423-0.4230.0000.0000.0000.000
176A176VAL00.0500.0298.0850.1880.1880.0000.0000.0000.000
177A177TYR0-0.045-0.03610.5170.1630.1630.0000.0000.0000.000
178A178VAL0-0.004-0.00114.1930.0410.0410.0000.0000.0000.000
179A179GLY00.0320.01016.6340.0500.0500.0000.0000.0000.000
180A180ASP-1-0.850-0.92520.258-0.419-0.4190.0000.0000.0000.000
181A181ASN00.0370.03523.2180.0410.0410.0000.0000.0000.000
182A182PRO00.046-0.00122.201-0.032-0.0320.0000.0000.0000.000
183A183VAL00.0120.01122.288-0.029-0.0290.0000.0000.0000.000
184A184LYS10.8730.91823.3720.3570.3570.0000.0000.0000.000
185A185ASP-1-0.746-0.86720.002-0.596-0.5960.0000.0000.0000.000
186A186CYS0-0.074-0.00317.988-0.103-0.1030.0000.0000.0000.000
187A187GLY00.0370.02018.215-0.038-0.0380.0000.0000.0000.000
188A188GLY0-0.019-0.02219.750-0.002-0.0020.0000.0000.0000.000
189A189SER0-0.030-0.03615.177-0.042-0.0420.0000.0000.0000.000
190A190LYS10.8890.95112.5150.9730.9730.0000.0000.0000.000
191A191ASN0-0.042-0.01715.3860.0120.0120.0000.0000.0000.000
192A192LEU0-0.079-0.02814.3860.0590.0590.0000.0000.0000.000
193A193GLY00.0060.00311.668-0.100-0.1000.0000.0000.0000.000
194A194MET0-0.064-0.00710.086-0.157-0.1570.0000.0000.0000.000
195A195THR0-0.018-0.0018.6260.2800.2800.0000.0000.0000.000
196A196SER0-0.039-0.05111.033-0.015-0.0150.0000.0000.0000.000
197A197ILE00.015-0.00511.6160.0240.0240.0000.0000.0000.000
198A198LEU00.003-0.01615.5900.0320.0320.0000.0000.0000.000
199A199LEU0-0.0260.00319.3710.0100.0100.0000.0000.0000.000
200A200ASP-1-0.753-0.89221.394-0.327-0.3270.0000.0000.0000.000
201A201ARG10.8240.88723.3250.4340.4340.0000.0000.0000.000
202A202LYS10.8730.93326.3980.2920.2920.0000.0000.0000.000
203A203GLY0-0.053-0.00327.2780.0180.0180.0000.0000.0000.000
204A204GLU-1-0.962-0.99428.245-0.261-0.2610.0000.0000.0000.000
205A205LYS10.7770.86525.2020.4290.4290.0000.0000.0000.000
206A206ARG10.9150.95526.6440.2630.2630.0000.0000.0000.000
207A207GLU-1-0.970-0.96927.318-0.244-0.2440.0000.0000.0000.000
208A208PHE0-0.024-0.02625.857-0.002-0.0020.0000.0000.0000.000
209A209TRP00.011-0.01822.740-0.025-0.0250.0000.0000.0000.000
210A210ASP-1-0.803-0.87221.381-0.387-0.3870.0000.0000.0000.000
211A211LYS10.7590.86521.3950.3510.3510.0000.0000.0000.000
212A213ASP-1-0.810-0.85413.311-0.985-0.9850.0000.0000.0000.000
213A214PHE00.0270.01310.7860.0190.0190.0000.0000.0000.000
214A215ILE0-0.028-0.00715.936-0.001-0.0010.0000.0000.0000.000
215A216VAL0-0.0210.00416.6650.0000.0000.0000.0000.0000.000
216A217SER0-0.081-0.03819.7870.0370.0370.0000.0000.0000.000
217A218ASP-1-0.783-0.88620.959-0.417-0.4170.0000.0000.0000.000
218A219LEU00.0640.01617.959-0.059-0.0590.0000.0000.0000.000
219A220ARG10.7830.86916.4830.3100.3100.0000.0000.0000.000
220A221GLU-1-0.841-0.92515.941-0.548-0.5480.0000.0000.0000.000
221A222VAL00.0380.01811.978-0.070-0.0700.0000.0000.0000.000
222A223ILE00.000-0.00310.466-0.194-0.1940.0000.0000.0000.000
223A224LYS10.8510.93010.0520.4840.4840.0000.0000.0000.000
224A225ILE00.0660.04510.098-0.012-0.0120.0000.0000.0000.000
225A226VAL0-0.002-0.0055.721-0.136-0.1360.0000.0000.0000.000
226A227ASP-1-0.853-0.9186.270-2.123-2.1230.0000.0000.0000.000
227A228GLU-1-0.971-0.9797.525-0.441-0.4410.0000.0000.0000.000
228A229LEU0-0.064-0.0275.2210.2320.2320.0000.0000.0000.000
229A230ASN0-0.079-0.0102.647-4.353-1.0912.120-2.106-3.277-0.026