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: 17KLZ

Calculation Name: 1B04-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1B04

Chain ID: A

ChEMBL ID:

UniProt ID: O87703

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 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 312
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -4584946.207017
FMO2-HF: Nuclear repulsion 4462673.354055
FMO2-HF: Total energy -122272.852963
FMO2-MP2: Total energy -122634.312431


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:2:ASP)


Summations of interaction energy for fragment #1(A:2: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.
38.36214.02159.734-20.798-14.5930.128
Interaction energy analysis for fragmet #1(A:2:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.813 / q_NPA : -0.871
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].
3A4GLN0-0.001-0.0183.551-8.214-5.434-0.002-1.274-1.5040.005
4A5GLN0-0.035-0.0282.546-10.931-9.5610.464-0.641-1.1920.002
5A6ALA0-0.0040.0223.679-4.878-3.3980.011-0.799-0.6920.002
6A7GLU-1-0.923-0.9624.97422.01722.181-0.001-0.009-0.1530.000
7A8ARG10.9140.9637.439-26.629-26.6290.0000.0000.0000.000
8A9ARG10.8850.9286.977-31.106-31.1060.0000.0000.0000.000
9A10ALA00.0660.0168.682-2.524-2.5240.0000.0000.0000.000
10A11ALA0-0.048-0.01410.600-2.848-2.8480.0000.0000.0000.000
11A12GLU-1-0.848-0.91411.60423.09023.0900.0000.0000.0000.000
12A13LEU0-0.018-0.00310.037-1.615-1.6150.0000.0000.0000.000
13A14ARG10.9560.98712.628-23.915-23.9150.0000.0000.0000.000
14A15GLU-1-0.957-0.97316.37615.35915.3590.0000.0000.0000.000
15A16LEU0-0.016-0.00915.832-1.243-1.2430.0000.0000.0000.000
16A17LEU0-0.001-0.00315.489-1.062-1.0620.0000.0000.0000.000
17A18ASN0-0.010-0.01519.367-1.003-1.0030.0000.0000.0000.000
18A19ARG10.8910.95321.754-14.800-14.8000.0000.0000.0000.000
19A20TYR00.0320.00319.450-0.796-0.7960.0000.0000.0000.000
20A21GLY00.0070.01823.549-0.395-0.3950.0000.0000.0000.000
21A22TYR00.006-0.00625.013-0.711-0.7110.0000.0000.0000.000
22A23GLU-1-0.917-0.97226.86511.43311.4330.0000.0000.0000.000
23A24TYR0-0.046-0.00523.980-0.488-0.4880.0000.0000.0000.000
24A25TYR00.0170.01025.036-0.465-0.4650.0000.0000.0000.000
25A26VAL0-0.013-0.00729.785-0.341-0.3410.0000.0000.0000.000
26A27LEU0-0.084-0.05131.726-0.358-0.3580.0000.0000.0000.000
27A28ASP-1-0.898-0.92332.4649.1889.1880.0000.0000.0000.000
28A29ARG10.8570.92430.617-10.368-10.3680.0000.0000.0000.000
29A30PRO00.004-0.02730.4490.4310.4310.0000.0000.0000.000
30A31SER00.0450.01328.088-0.155-0.1550.0000.0000.0000.000
31A32VAL0-0.0500.00728.734-0.019-0.0190.0000.0000.0000.000
32A33PRO0-0.016-0.04627.2920.3640.3640.0000.0000.0000.000
33A34ASP-1-0.808-0.87323.98312.76112.7610.0000.0000.0000.000
34A35ALA0-0.021-0.02622.0260.6720.6720.0000.0000.0000.000
35A36GLU-1-0.899-0.94717.66218.29618.2960.0000.0000.0000.000
36A37TYR00.0020.00918.1571.0681.0680.0000.0000.0000.000
37A38ASP-1-0.817-0.92918.31115.85615.8560.0000.0000.0000.000
38A39ARG10.8130.90614.833-16.840-16.8400.0000.0000.0000.000
39A40LEU00.0180.00914.1251.8241.8240.0000.0000.0000.000
40A41MET0-0.004-0.00213.8661.6271.6270.0000.0000.0000.000
41A42GLN0-0.044-0.02614.0371.5701.5700.0000.0000.0000.000
42A43GLU-1-0.882-0.9389.36629.72629.7260.0000.0000.0000.000
43A44LEU0-0.008-0.0089.4053.2873.2870.0000.0000.0000.000
44A45ILE0-0.040-0.01810.3432.1462.1460.0000.0000.0000.000
45A46ALA00.0450.0258.4650.5100.5100.0000.0000.0000.000
46A47ILE0-0.074-0.0305.2544.8694.8690.0000.0000.0000.000
47A48GLU-1-0.801-0.9006.97725.19925.1990.0000.0000.0000.000
48A49GLU-1-0.937-0.9759.46925.86925.8690.0000.0000.0000.000
49A50GLN0-0.088-0.0411.614-10.094-36.34138.865-7.930-4.6880.046
50A51TYR0-0.092-0.0871.708-27.080-30.96820.397-10.145-6.3640.073
51A52PRO00.0460.0447.853-2.124-2.1240.0000.0000.0000.000
52A53GLU-1-0.889-0.9469.40428.80028.8000.0000.0000.0000.000
53A54LEU0-0.006-0.0247.568-0.592-0.5920.0000.0000.0000.000
54A55LYS10.9170.99111.816-19.980-19.9800.0000.0000.0000.000
55A56THR0-0.015-0.00914.032-1.550-1.5500.0000.0000.0000.000
56A57SER00.0400.00616.9910.1540.1540.0000.0000.0000.000
57A58ASP-1-0.805-0.92420.47213.32713.3270.0000.0000.0000.000
58A59SER0-0.073-0.03415.003-0.129-0.1290.0000.0000.0000.000
59A60PRO00.0380.01716.809-0.595-0.5950.0000.0000.0000.000
60A61THR00.024-0.02114.373-1.113-1.1130.0000.0000.0000.000
61A62GLN0-0.095-0.06717.521-1.022-1.0220.0000.0000.0000.000
62A63ARG10.7840.88120.497-13.869-13.8690.0000.0000.0000.000
63A64ILE0-0.0180.00118.083-0.556-0.5560.0000.0000.0000.000
64A65GLY00.0180.01121.543-0.617-0.6170.0000.0000.0000.000
65A66GLY0-0.039-0.02820.9820.5010.5010.0000.0000.0000.000
66A67PRO0-0.024-0.01921.286-0.230-0.2300.0000.0000.0000.000
67A68PRO00.0530.01323.922-0.114-0.1140.0000.0000.0000.000
68A69LEU0-0.0020.02027.1690.2900.2900.0000.0000.0000.000
69A70GLU-1-0.951-0.97729.7469.9209.9200.0000.0000.0000.000
70A71ALA0-0.012-0.01732.679-0.404-0.4040.0000.0000.0000.000
71A72PHE00.0290.01632.5940.3020.3020.0000.0000.0000.000
72A73ARG10.9420.98632.700-9.625-9.6250.0000.0000.0000.000
73A74LYS10.9400.95836.346-7.649-7.6490.0000.0000.0000.000
74A75VAL0-0.042-0.02636.0300.1000.1000.0000.0000.0000.000
75A76ALA00.0240.01438.988-0.147-0.1470.0000.0000.0000.000
76A77HIS0-0.085-0.06635.925-0.242-0.2420.0000.0000.0000.000
77A78ARG11.0471.05536.168-8.591-8.5910.0000.0000.0000.000
78A79VAL00.0450.03141.3050.0090.0090.0000.0000.0000.000
79A80PRO00.0320.02444.3110.0850.0850.0000.0000.0000.000
80A81MET00.0170.01741.8510.0110.0110.0000.0000.0000.000
81A82MET0-0.036-0.00746.435-0.134-0.1340.0000.0000.0000.000
82A83SER00.0390.02649.0280.1500.1500.0000.0000.0000.000
83A84LEU0-0.031-0.03350.849-0.093-0.0930.0000.0000.0000.000
84A85ALA00.0190.01553.644-0.024-0.0240.0000.0000.0000.000
85A86ASN00.0270.00355.2340.1670.1670.0000.0000.0000.000
86A87ALA00.0380.02657.851-0.097-0.0970.0000.0000.0000.000
87A88PHE0-0.016-0.02158.3790.0970.0970.0000.0000.0000.000
88A89GLY00.0170.01761.657-0.014-0.0140.0000.0000.0000.000
89A90GLU-1-0.829-0.90164.0154.9434.9430.0000.0000.0000.000
90A91GLY0-0.047-0.04765.079-0.062-0.0620.0000.0000.0000.000
91A92ASP-1-0.785-0.90263.1525.0955.0950.0000.0000.0000.000
92A93LEU0-0.022-0.01859.4390.0320.0320.0000.0000.0000.000
93A94ARG10.8250.93663.127-4.889-4.8890.0000.0000.0000.000
94A95ASP-1-0.911-0.94766.3184.8084.8080.0000.0000.0000.000
95A96PHE0-0.085-0.04458.069-0.008-0.0080.0000.0000.0000.000
96A97ASP-1-0.724-0.88163.1845.2245.2240.0000.0000.0000.000
97A98ARG10.8820.95664.095-4.783-4.7830.0000.0000.0000.000
98A99ARG10.9260.95962.400-5.270-5.2700.0000.0000.0000.000
99A100VAL00.0230.02960.9090.0160.0160.0000.0000.0000.000
100A101ARG10.9190.95563.731-4.892-4.8920.0000.0000.0000.000
101A102GLN0-0.076-0.03666.555-0.009-0.0090.0000.0000.0000.000
102A103GLU-1-0.937-0.97864.6095.0305.0300.0000.0000.0000.000
103A104VAL0-0.083-0.02561.2830.0370.0370.0000.0000.0000.000
104A105GLY0-0.034-0.00864.2880.0150.0150.0000.0000.0000.000
105A106GLU-1-0.959-0.99464.0234.9954.9950.0000.0000.0000.000
106A107ALA0-0.033-0.01959.3310.0230.0230.0000.0000.0000.000
107A108ALA0-0.0070.01956.655-0.003-0.0030.0000.0000.0000.000
108A109TYR00.009-0.01555.7450.0610.0610.0000.0000.0000.000
109A110VAL0-0.032-0.00248.9890.0290.0290.0000.0000.0000.000
110A111CYS0-0.043-0.00552.163-0.067-0.0670.0000.0000.0000.000
111A112GLU-1-0.854-0.94445.8927.2347.2340.0000.0000.0000.000
112A113LEU00.0270.01146.184-0.130-0.1300.0000.0000.0000.000
113A114ALA0-0.041-0.02246.9580.1570.1570.0000.0000.0000.000
114A115ILE0-0.031-0.00941.982-0.043-0.0430.0000.0000.0000.000
115A116ASP-1-0.849-0.91145.4776.8446.8440.0000.0000.0000.000
116A117GLY0-0.033-0.02142.1030.1390.1390.0000.0000.0000.000
117A118LEU0-0.081-0.03738.004-0.212-0.2120.0000.0000.0000.000
118A119ALA00.0490.03440.1890.1610.1610.0000.0000.0000.000
119A120VAL0-0.024-0.02136.0520.0010.0010.0000.0000.0000.000
120A121SER0-0.016-0.01237.938-0.063-0.0630.0000.0000.0000.000
121A122VAL0-0.0100.00832.7230.2060.2060.0000.0000.0000.000
122A123ARG10.9290.94733.183-9.629-9.6290.0000.0000.0000.000
123A124TYR0-0.019-0.02928.9230.1310.1310.0000.0000.0000.000
124A125GLU-1-0.947-0.98129.6559.8309.8300.0000.0000.0000.000
125A126ASP-1-0.862-0.91127.53411.43211.4320.0000.0000.0000.000
126A127GLY0-0.064-0.05027.3290.4340.4340.0000.0000.0000.000
127A128TYR0-0.042-0.02120.7880.3910.3910.0000.0000.0000.000
128A129PHE0-0.029-0.00626.393-0.587-0.5870.0000.0000.0000.000
129A130VAL00.0080.02026.5890.3240.3240.0000.0000.0000.000
130A131GLN0-0.069-0.06728.603-0.163-0.1630.0000.0000.0000.000
131A132GLY00.005-0.01931.050-0.090-0.0900.0000.0000.0000.000
132A133ALA0-0.005-0.00933.0080.0140.0140.0000.0000.0000.000
133A134THR0-0.0120.01036.380-0.158-0.1580.0000.0000.0000.000
134A135ARG10.9360.95639.235-6.974-6.9740.0000.0000.0000.000
135A136GLY0-0.005-0.02342.760-0.058-0.0580.0000.0000.0000.000
136A137ASP-1-0.875-0.92944.1436.8146.8140.0000.0000.0000.000
137A138GLY0-0.021-0.01446.091-0.167-0.1670.0000.0000.0000.000
138A139THR0-0.104-0.05046.0030.0330.0330.0000.0000.0000.000
139A140THR0-0.033-0.02142.4140.1400.1400.0000.0000.0000.000
140A141GLY00.0520.04040.993-0.139-0.1390.0000.0000.0000.000
141A142GLU-1-0.980-0.99037.2898.2818.2810.0000.0000.0000.000
142A143ASP-1-0.812-0.90332.08610.24410.2440.0000.0000.0000.000
143A144ILE00.001-0.00832.6610.0810.0810.0000.0000.0000.000
144A145THR0-0.0030.01327.9860.2650.2650.0000.0000.0000.000
145A146GLU-1-0.838-0.93324.30213.27813.2780.0000.0000.0000.000
146A147ASN0-0.009-0.02827.0280.5550.5550.0000.0000.0000.000
147A148LEU0-0.0020.01829.4520.0040.0040.0000.0000.0000.000
148A149LYS10.8920.96622.654-13.846-13.8460.0000.0000.0000.000
149A150THR0-0.079-0.03525.1210.3430.3430.0000.0000.0000.000
150A151ILE0-0.0310.00826.711-0.027-0.0270.0000.0000.0000.000
151A152ARG10.9490.96225.121-11.781-11.7810.0000.0000.0000.000
152A153SER0-0.020-0.00827.6480.2370.2370.0000.0000.0000.000
153A154LEU0-0.046-0.00229.493-0.180-0.1800.0000.0000.0000.000
154A155PRO00.0550.03427.2480.5680.5680.0000.0000.0000.000
155A156LEU00.0090.01922.001-0.192-0.1920.0000.0000.0000.000
156A157ARG10.9410.96921.887-13.976-13.9760.0000.0000.0000.000
157A158LEU0-0.076-0.03625.235-0.032-0.0320.0000.0000.0000.000
158A159LYS10.8470.92727.148-10.260-10.2600.0000.0000.0000.000
159A160GLU-1-0.890-0.93828.84110.45710.4570.0000.0000.0000.000
160A161PRO0-0.031-0.01227.4550.0450.0450.0000.0000.0000.000
161A162VAL00.0040.00629.347-0.236-0.2360.0000.0000.0000.000
162A163SER00.0450.02031.6750.4050.4050.0000.0000.0000.000
163A164LEU0-0.052-0.01633.822-0.370-0.3700.0000.0000.0000.000
164A165GLU-1-0.833-0.92635.1708.7428.7420.0000.0000.0000.000
165A166ALA00.0130.02036.676-0.242-0.2420.0000.0000.0000.000
166A167ARG10.7930.86838.192-7.759-7.7590.0000.0000.0000.000
167A168GLY00.0450.02838.407-0.038-0.0380.0000.0000.0000.000
168A169GLU-1-0.886-0.93339.3817.5707.5700.0000.0000.0000.000
169A170ALA00.0080.02636.6810.1570.1570.0000.0000.0000.000
170A171PHE00.000-0.02837.494-0.280-0.2800.0000.0000.0000.000
171A172MET00.0140.02336.3680.2030.2030.0000.0000.0000.000
172A173PRO00.0260.01736.677-0.293-0.2930.0000.0000.0000.000
173A174LYS10.9720.98839.710-6.922-6.9220.0000.0000.0000.000
174A175ALA0-0.0030.01540.323-0.072-0.0720.0000.0000.0000.000
175A176SER0-0.014-0.05035.8560.2900.2900.0000.0000.0000.000
176A177PHE00.0350.02738.1070.0710.0710.0000.0000.0000.000
177A178LEU0-0.022-0.00540.705-0.044-0.0440.0000.0000.0000.000
178A179ARG10.9840.99236.294-8.961-8.9610.0000.0000.0000.000
179A180LEU00.0200.01136.230-0.029-0.0290.0000.0000.0000.000
180A181ASN00.0420.01638.5580.0830.0830.0000.0000.0000.000
181A182GLU-1-0.885-0.93941.3967.6617.6610.0000.0000.0000.000
182A183GLU-1-0.889-0.93935.5469.1119.1110.0000.0000.0000.000
183A184ARG10.8300.93938.552-8.132-8.1320.0000.0000.0000.000
184A185LYS11.0261.02341.037-7.205-7.2050.0000.0000.0000.000
185A186ALA0-0.092-0.05540.487-0.121-0.1210.0000.0000.0000.000
186A187ARG10.8670.94037.383-8.477-8.4770.0000.0000.0000.000
187A188GLY0-0.028-0.01841.719-0.040-0.0400.0000.0000.0000.000
188A189GLU-1-0.976-1.00245.3696.5036.5030.0000.0000.0000.000
189A190GLU-1-0.960-0.93940.3318.0538.0530.0000.0000.0000.000
190A191LEU0-0.027-0.06943.7510.0220.0220.0000.0000.0000.000
191A192PHE0-0.057-0.01738.901-0.071-0.0710.0000.0000.0000.000
192A193ALA0-0.003-0.00444.411-0.059-0.0590.0000.0000.0000.000
193A194ASN00.0400.01445.6750.0070.0070.0000.0000.0000.000
194A195PRO00.0990.04442.2120.1650.1650.0000.0000.0000.000
195A196ARG10.9381.00042.024-7.109-7.1090.0000.0000.0000.000
196A197ASN0-0.061-0.06542.3530.1380.1380.0000.0000.0000.000
197A198ALA00.0490.05139.7880.1510.1510.0000.0000.0000.000
198A199ALA00.0290.02237.6580.2700.2700.0000.0000.0000.000
199A200ALA0-0.008-0.01537.6170.1900.1900.0000.0000.0000.000
200A201GLY0-0.0020.00438.8210.0760.0760.0000.0000.0000.000
201A202SER0-0.055-0.03834.2720.2270.2270.0000.0000.0000.000
202A203LEU00.0050.00632.7080.2590.2590.0000.0000.0000.000
203A204ARG10.9410.98334.702-7.872-7.8720.0000.0000.0000.000
204A205GLN0-0.0320.01031.387-0.078-0.0780.0000.0000.0000.000
205A206LEU00.006-0.00631.9880.1440.1440.0000.0000.0000.000
206A207ASP-1-0.884-0.95627.51512.00412.0040.0000.0000.0000.000
207A208PRO00.0270.03325.212-0.091-0.0910.0000.0000.0000.000
208A209LYS10.9800.98921.026-14.680-14.6800.0000.0000.0000.000
209A210VAL0-0.016-0.00626.390-0.127-0.1270.0000.0000.0000.000
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