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: 2JYMR

Calculation Name: 4RNS-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4RNS

Chain ID: A

ChEMBL ID:

UniProt ID: P52679

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 214
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2532766.273853
FMO2-HF: Nuclear repulsion 2448611.236165
FMO2-HF: Total energy -84155.037688
FMO2-MP2: Total energy -84404.829522


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:89:ARG)


Summations of interaction energy for fragment #1(A:89:ARG)
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.
-84.344-85.07122.044-10.056-11.262-0.105
Interaction energy analysis for fragmet #1(A:89:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.871 / q_NPA : 0.900
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].
3A91ASP-1-0.757-0.8363.856-22.535-20.103-0.024-1.214-1.194-0.003
4A92PRO0-0.052-0.0346.363-0.486-0.4860.0000.0000.0000.000
5A93GLY00.0450.0369.8320.7450.7450.0000.0000.0000.000
6A94THR0-0.082-0.0748.6650.3570.3570.0000.0000.0000.000
7A95SER0-0.048-0.0117.311-0.320-0.3200.0000.0000.0000.000
8A96ASN00.0460.0089.283-0.135-0.1350.0000.0000.0000.000
9A97ARG10.7510.8693.70448.43948.610-0.001-0.018-0.1520.000
10A98ASN0-0.0040.00010.1502.3102.3100.0000.0000.0000.000
11A99PHE00.0130.0087.947-1.460-1.4600.0000.0000.0000.000
12A100ARG10.8520.91811.26622.49322.4930.0000.0000.0000.000
13A101ILE00.0120.00813.194-0.735-0.7350.0000.0000.0000.000
14A102ALA00.0200.02215.7110.9700.9700.0000.0000.0000.000
15A103ALA00.016-0.00518.3000.1130.1130.0000.0000.0000.000
16A104SER00.0490.02821.6740.0320.0320.0000.0000.0000.000
17A105ASP-1-0.706-0.85224.767-10.795-10.7950.0000.0000.0000.000
18A106PHE00.018-0.00326.632-0.148-0.1480.0000.0000.0000.000
19A107GLY00.0230.01624.215-0.063-0.0630.0000.0000.0000.000
20A108GLN0-0.030-0.04321.186-0.594-0.5940.0000.0000.0000.000
21A109ALA00.0060.00423.018-0.251-0.2510.0000.0000.0000.000
22A110LEU0-0.060-0.02325.4900.1390.1390.0000.0000.0000.000
23A111MET0-0.0160.00818.938-0.192-0.1920.0000.0000.0000.000
24A112LEU00.013-0.00719.193-0.216-0.2160.0000.0000.0000.000
25A113PRO00.010-0.00221.422-0.256-0.2560.0000.0000.0000.000
26A114ARG10.8390.92122.55011.71511.7150.0000.0000.0000.000
27A115LEU0-0.017-0.00916.537-0.271-0.2710.0000.0000.0000.000
28A116TYR0-0.071-0.05119.392-0.317-0.3170.0000.0000.0000.000
29A117ALA00.0680.03120.970-0.199-0.1990.0000.0000.0000.000
30A118THR00.005-0.00515.9810.1550.1550.0000.0000.0000.000
31A119LEU0-0.0330.00115.251-0.822-0.8220.0000.0000.0000.000
32A120GLU-1-0.832-0.88917.589-13.933-13.9330.0000.0000.0000.000
33A121GLU-1-0.962-0.97619.700-12.559-12.5590.0000.0000.0000.000
34A122THR0-0.148-0.09414.879-0.434-0.4340.0000.0000.0000.000
35A123ALA0-0.039-0.02212.922-1.220-1.2200.0000.0000.0000.000
36A124PRO00.0970.05514.346-0.540-0.5400.0000.0000.0000.000
37A125GLN0-0.055-0.02713.9071.0931.0930.0000.0000.0000.000
38A126VAL0-0.089-0.02210.775-0.946-0.9460.0000.0000.0000.000
39A127ARG10.9370.96713.40619.31519.3150.0000.0000.0000.000
40A128VAL00.028-0.00113.632-1.632-1.6320.0000.0000.0000.000
41A129THR0-0.019-0.00715.2331.4271.4270.0000.0000.0000.000
42A130GLY00.0120.01116.603-0.715-0.7150.0000.0000.0000.000
43A131VAL0-0.022-0.01916.7980.2330.2330.0000.0000.0000.000
44A132ASN00.0340.02319.836-0.288-0.2880.0000.0000.0000.000
45A133LEU00.0140.03722.249-0.507-0.5070.0000.0000.0000.000
46A134ARG10.8800.90721.95513.60013.6000.0000.0000.0000.000
47A135HIS00.0490.03224.626-0.149-0.1490.0000.0000.0000.000
48A136GLY00.0000.03023.6270.2440.2440.0000.0000.0000.000
49A137PRO00.0470.01021.679-0.116-0.1160.0000.0000.0000.000
50A138LEU00.0340.02418.109-0.833-0.8330.0000.0000.0000.000
51A139VAL00.0220.00017.589-1.013-1.0130.0000.0000.0000.000
52A140GLU-1-0.898-0.95516.342-15.576-15.5760.0000.0000.0000.000
53A141GLU-1-0.870-0.90015.378-18.624-18.6240.0000.0000.0000.000
54A142LEU0-0.042-0.02212.979-1.552-1.5520.0000.0000.0000.000
55A143GLU-1-0.870-0.91911.672-24.939-24.9390.0000.0000.0000.000
56A144SER00.012-0.02311.100-2.670-2.6700.0000.0000.0000.000
57A145GLY0-0.044-0.0168.824-1.922-1.9220.0000.0000.0000.000
58A146SER0-0.077-0.0369.617-0.876-0.8760.0000.0000.0000.000
59A147ILE0-0.024-0.01512.3860.9470.9470.0000.0000.0000.000
60A148ASP-1-0.792-0.8787.816-35.034-35.0340.0000.0000.0000.000
61A149ILE0-0.019-0.01010.310-0.434-0.4340.0000.0000.0000.000
62A150ALA00.0300.03013.4400.5870.5870.0000.0000.0000.000
63A151PHE0-0.035-0.03317.164-0.063-0.0630.0000.0000.0000.000
64A152GLY00.0180.00419.8870.4440.4440.0000.0000.0000.000
65A153GLY00.0450.01223.540-0.088-0.0880.0000.0000.0000.000
66A154PHE00.0080.00620.9930.2160.2160.0000.0000.0000.000
67A155PRO00.0040.00624.034-0.393-0.3930.0000.0000.0000.000
68A156THR00.0130.01023.694-0.029-0.0290.0000.0000.0000.000
69A157LEU0-0.059-0.01918.784-0.401-0.4010.0000.0000.0000.000
70A158SER0-0.017-0.01221.7920.1990.1990.0000.0000.0000.000
71A159ALA00.0290.00820.551-0.508-0.5080.0000.0000.0000.000
72A160GLY00.0290.02517.311-0.326-0.3260.0000.0000.0000.000
73A161ILE0-0.056-0.02815.567-1.535-1.5350.0000.0000.0000.000
74A162LYS10.8470.93014.09620.85320.8530.0000.0000.0000.000
75A163THR00.005-0.01216.665-0.120-0.1200.0000.0000.0000.000
76A164GLN00.0320.01618.010-0.649-0.6490.0000.0000.0000.000
77A165THR0-0.019-0.01620.281-0.275-0.2750.0000.0000.0000.000
78A166LEU0-0.067-0.02619.670-0.149-0.1490.0000.0000.0000.000
79A167PHE0-0.042-0.02423.8360.3080.3080.0000.0000.0000.000
80A168ARG10.8630.91627.5019.5889.5880.0000.0000.0000.000
81A169GLU-1-0.789-0.88030.065-9.735-9.7350.0000.0000.0000.000
82A170GLU-1-0.754-0.83731.980-8.862-8.8620.0000.0000.0000.000
83A171TYR0-0.015-0.03733.184-0.133-0.1330.0000.0000.0000.000
84A172VAL0-0.034-0.01337.4660.1960.1960.0000.0000.0000.000
85A173CYS0-0.054-0.01039.949-0.131-0.1310.0000.0000.0000.000
86A174VAL0-0.0030.00040.1960.0100.0100.0000.0000.0000.000
87A175MET00.0040.01643.1810.0060.0060.0000.0000.0000.000
88A176ARG10.8380.88745.9166.4746.4740.0000.0000.0000.000
89A177GLN0-0.055-0.03847.0840.2520.2520.0000.0000.0000.000
90A178SER00.002-0.00149.6100.0790.0790.0000.0000.0000.000
91A179HIS0-0.0060.01749.0460.1650.1650.0000.0000.0000.000
92A180PRO00.009-0.00951.9770.0520.0520.0000.0000.0000.000
93A181ALA00.001-0.01352.5480.0960.0960.0000.0000.0000.000
94A182LEU0-0.0290.00350.060-0.007-0.0070.0000.0000.0000.000
95A183THR0-0.069-0.02853.4190.0250.0250.0000.0000.0000.000
96A184HIS0-0.032-0.00556.0830.1570.1570.0000.0000.0000.000
97A185GLY00.0080.01355.121-0.089-0.0890.0000.0000.0000.000
98A186LEU0-0.030-0.03149.7450.0220.0220.0000.0000.0000.000
99A187ASP-1-0.827-0.90552.296-5.807-5.8070.0000.0000.0000.000
100A188LEU00.0370.00349.226-0.068-0.0680.0000.0000.0000.000
101A189GLU-1-0.773-0.84351.797-5.938-5.9380.0000.0000.0000.000
102A190ALA00.0150.00454.280-0.018-0.0180.0000.0000.0000.000
103A191PHE00.0320.00144.716-0.071-0.0710.0000.0000.0000.000
104A192ARG10.7950.86949.9565.9655.9650.0000.0000.0000.000
105A193GLN0-0.019-0.00651.120-0.046-0.0460.0000.0000.0000.000
106A194CYS0-0.057-0.01350.4590.0450.0450.0000.0000.0000.000
107A195ARG10.8260.91449.0325.9895.9890.0000.0000.0000.000
108A196HIS10.8430.92444.2766.7726.7720.0000.0000.0000.000
109A197ILE0-0.026-0.00439.4330.0380.0380.0000.0000.0000.000
110A198ILE00.0140.01338.315-0.034-0.0340.0000.0000.0000.000
111A199VAL0-0.023-0.01532.675-0.031-0.0310.0000.0000.0000.000
112A200THR0-0.057-0.05733.5770.1900.1900.0000.0000.0000.000
113A201ALA0-0.016-0.03730.112-0.287-0.2870.0000.0000.0000.000
114A202HIS00.017-0.01229.940-0.412-0.4120.0000.0000.0000.000
115A203GLU-1-0.838-0.88130.509-9.715-9.7150.0000.0000.0000.000
116A204PHE0-0.075-0.04525.872-0.444-0.4440.0000.0000.0000.000
117A205ASN0-0.056-0.01625.705-0.713-0.7130.0000.0000.0000.000
118A206HIS00.0230.01025.090-0.169-0.1690.0000.0000.0000.000
119A207VAL00.0440.00127.5090.3640.3640.0000.0000.0000.000
120A208HIS0-0.0080.02129.7630.1830.1830.0000.0000.0000.000
121A209GLU-1-0.857-0.93629.990-9.983-9.9830.0000.0000.0000.000
122A210GLN0-0.018-0.01232.4450.4170.4170.0000.0000.0000.000
123A211VAL0-0.002-0.00735.3530.2920.2920.0000.0000.0000.000
124A212GLU-1-0.795-0.88034.741-8.684-8.6840.0000.0000.0000.000
125A213ALA00.0250.00737.4470.2530.2530.0000.0000.0000.000
126A214ARG10.8220.89539.3907.6437.6430.0000.0000.0000.000
127A215LEU0-0.028-0.01339.7920.2200.2200.0000.0000.0000.000
128A216LEU0-0.026-0.01939.8380.2070.2070.0000.0000.0000.000
129A217GLU-1-0.930-0.94043.465-7.020-7.0200.0000.0000.0000.000
130A218LEU0-0.028-0.00245.2950.1840.1840.0000.0000.0000.000
131A219LEU0-0.035-0.02044.7790.2000.2000.0000.0000.0000.000
132A220PRO00.0170.01948.218-0.003-0.0030.0000.0000.0000.000
133A221PRO00.0560.02648.006-0.090-0.0900.0000.0000.0000.000
134A222GLU-1-0.876-0.93948.586-6.089-6.0890.0000.0000.0000.000
135A223SER0-0.069-0.05649.5410.0930.0930.0000.0000.0000.000
136A224ILE0-0.009-0.00443.457-0.091-0.0910.0000.0000.0000.000
137A225ARG10.9080.97246.2686.3886.3880.0000.0000.0000.000
138A226PHE00.006-0.01041.9910.0100.0100.0000.0000.0000.000
139A227THR00.006-0.01037.881-0.002-0.0020.0000.0000.0000.000
140A228THR0-0.019-0.00335.175-0.077-0.0770.0000.0000.0000.000
141A229GLU-1-0.854-0.92230.573-10.123-10.1230.0000.0000.0000.000
142A230ASN0-0.087-0.03629.540-0.653-0.6530.0000.0000.0000.000
143A231PHE00.0490.00629.4030.3010.3010.0000.0000.0000.000
144A232LEU0-0.015-0.00829.1380.3200.3200.0000.0000.0000.000
145A233VAL00.002-0.00233.1010.2550.2550.0000.0000.0000.000
146A234SER0-0.021-0.03135.4540.2960.2960.0000.0000.0000.000
147A235ALA00.0180.00636.4700.2440.2440.0000.0000.0000.000
148A236VAL00.0430.02037.0430.2010.2010.0000.0000.0000.000
149A237ILE00.0120.00939.2960.2270.2270.0000.0000.0000.000
150A238ALA0-0.0080.01241.2880.2180.2180.0000.0000.0000.000
151A239GLU-1-0.794-0.87440.780-7.617-7.6170.0000.0000.0000.000
152A240GLU-1-0.910-0.95643.206-6.906-6.9060.0000.0000.0000.000
153A241THR0-0.089-0.06345.3550.1990.1990.0000.0000.0000.000
154A242ASP-1-0.779-0.86746.925-6.320-6.3200.0000.0000.0000.000
155A243VAL0-0.093-0.03744.2250.0950.0950.0000.0000.0000.000
156A244ILE0-0.004-0.00844.899-0.085-0.0850.0000.0000.0000.000
157A245LEU00.0020.01137.751-0.033-0.0330.0000.0000.0000.000
158A246THR00.004-0.01339.0700.1490.1490.0000.0000.0000.000
159A247ILE0-0.006-0.00635.266-0.221-0.2210.0000.0000.0000.000
160A248PRO00.0290.01231.4400.1400.1400.0000.0000.0000.000
161A249SER0-0.0020.00034.1540.0900.0900.0000.0000.0000.000
162A250ARG10.7980.87029.94410.34510.3450.0000.0000.0000.000
163A251LEU0-0.0200.00432.083-0.002-0.0020.0000.0000.0000.000
164A252ALA00.0480.01633.7710.1460.1460.0000.0000.0000.000
165A253ARG10.8960.93836.0558.0478.0470.0000.0000.0000.000
166A254TRP0-0.034-0.01132.0680.1740.1740.0000.0000.0000.000
167A255PHE00.0350.00334.4560.0480.0480.0000.0000.0000.000
168A256ALA00.0190.01538.4690.1860.1860.0000.0000.0000.000
169A257ASN0-0.064-0.02337.2870.3380.3380.0000.0000.0000.000
170A258ARG10.8120.88738.6357.9047.9040.0000.0000.0000.000
171A259GLY0-0.0050.00241.8780.1300.1300.0000.0000.0000.000
172A260GLY00.0270.03443.7330.1690.1690.0000.0000.0000.000
173A261LEU0-0.032-0.01840.2030.1200.1200.0000.0000.0000.000
174A262THR00.0080.00144.080-0.056-0.0560.0000.0000.0000.000
175A263ILE0-0.028-0.02340.112-0.091-0.0910.0000.0000.0000.000
176A264PHE0-0.006-0.00743.9140.1580.1580.0000.0000.0000.000
177A265PRO00.0450.00743.958-0.178-0.1780.0000.0000.0000.000
178A266VAL00.0330.02241.0410.0890.0890.0000.0000.0000.000
179A267PRO0-0.027-0.00444.3670.0270.0270.0000.0000.0000.000
180A268ILE0-0.007-0.01943.3260.1280.1280.0000.0000.0000.000
181A269GLU-1-0.883-0.92342.423-7.439-7.4390.0000.0000.0000.000
182A270LEU0-0.016-0.01938.600-0.045-0.0450.0000.0000.0000.000
183A271PRO00.0000.01034.9970.0180.0180.0000.0000.0000.000
184A272SER0-0.013-0.02534.630-0.239-0.2390.0000.0000.0000.000
185A273ILE0-0.011-0.00628.928-0.216-0.2160.0000.0000.0000.000
186A274GLU-1-0.823-0.89226.996-10.994-10.9940.0000.0000.0000.000
187A275VAL0-0.0220.00423.833-0.248-0.2480.0000.0000.0000.000
188A276LYS10.8660.91721.68312.16412.1640.0000.0000.0000.000
189A277GLN0-0.024-0.01915.591-0.742-0.7420.0000.0000.0000.000
190A278TYR00.007-0.00416.9010.4050.4050.0000.0000.0000.000
191A279TRP0-0.009-0.02411.269-0.061-0.0610.0000.0000.0000.000
192A280HIS00.1350.07611.439-0.414-0.4140.0000.0000.0000.000
193A281GLU-1-0.893-0.96111.013-20.822-20.8220.0000.0000.0000.000
194A282ARG10.7860.8908.52926.39826.3980.0000.0000.0000.000
195A283TYR0-0.045-0.0275.169-7.043-7.0430.0000.0000.0000.000
196A284ASP-1-0.813-0.8857.387-24.708-24.7080.0000.0000.0000.000
197A285LYS10.9710.9796.61929.31429.3140.0000.0000.0000.000
198A286ASP-1-0.715-0.8301.777-119.138-123.75318.662-7.643-6.404-0.100
199A287PRO0-0.007-0.0132.2453.5264.6233.408-1.154-3.351-0.002
200A288GLY00.0500.0314.1106.6736.861-0.001-0.027-0.1610.000
201A289ASN0-0.051-0.0285.4088.0818.0810.0000.0000.0000.000
202A290ILE0-0.0120.0036.5214.4174.4170.0000.0000.0000.000
203A291TRP00.0010.0028.0752.6272.6270.0000.0000.0000.000
204A292LEU00.0410.0269.8242.5082.5080.0000.0000.0000.000
205A293ARG10.8610.9228.82829.42829.4280.0000.0000.0000.000
206A294ARG10.8380.91912.76218.72918.7290.0000.0000.0000.000
207A295VAL00.0170.00913.6881.5891.5890.0000.0000.0000.000
208A296ILE00.0690.02214.9721.3731.3730.0000.0000.0000.000
209A297ALA0-0.053-0.01717.2651.0921.0920.0000.0000.0000.000
210A298LYS10.8950.93717.53115.66615.6660.0000.0000.0000.000
211A299ILE0-0.0030.02819.5900.5570.5570.0000.0000.0000.000
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