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: MV5LZ

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 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 214
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2527206.290974
FMO2-HF: Nuclear repulsion 2443052.677542
FMO2-HF: Total energy -84153.613432
FMO2-MP2: Total energy -84403.242463


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.
-41.337-36.796.355-4.458-6.444-0.016
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 : 0.936 / q_NPA : 0.951
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-1-0.791-0.8993.799-25.085-21.532-0.046-1.833-1.674-0.006
4A92PRO0-0.030-0.0096.3850.3680.3680.0000.0000.0000.000
5A93GLY00.0600.03410.0340.6540.6540.0000.0000.0000.000
6A94THR0-0.074-0.0338.1350.3610.3610.0000.0000.0000.000
7A95SER0-0.048-0.0077.532-0.113-0.1130.0000.0000.0000.000
8A96ASN00.0480.0199.508-0.166-0.1660.0000.0000.0000.000
9A97ARG10.7980.9074.93642.16942.1690.0000.0000.0000.000
10A98ASN0-0.001-0.0159.6982.6202.6200.0000.0000.0000.000
11A99PHE0-0.016-0.0098.307-1.748-1.7480.0000.0000.0000.000
12A100ARG10.8940.93612.19421.06921.0690.0000.0000.0000.000
13A101ILE00.0320.00914.110-0.642-0.6420.0000.0000.0000.000
14A102ALA00.0010.01816.7920.8680.8680.0000.0000.0000.000
15A103ALA00.025-0.00319.364-0.013-0.0130.0000.0000.0000.000
16A104SER00.0520.03822.7350.0050.0050.0000.0000.0000.000
17A105ASP-1-0.686-0.85725.745-10.495-10.4950.0000.0000.0000.000
18A106PHE0-0.008-0.01427.602-0.143-0.1430.0000.0000.0000.000
19A107GLY00.0220.00725.320-0.076-0.0760.0000.0000.0000.000
20A108GLN0-0.027-0.02822.325-0.419-0.4190.0000.0000.0000.000
21A109ALA00.0180.00924.236-0.251-0.2510.0000.0000.0000.000
22A110LEU0-0.068-0.02126.5620.1540.1540.0000.0000.0000.000
23A111MET0-0.001-0.00319.704-0.085-0.0850.0000.0000.0000.000
24A112LEU00.0240.00220.175-0.227-0.2270.0000.0000.0000.000
25A113PRO00.0220.01922.494-0.273-0.2730.0000.0000.0000.000
26A114ARG10.8360.93123.48511.40411.4040.0000.0000.0000.000
27A115LEU0-0.015-0.02217.535-0.359-0.3590.0000.0000.0000.000
28A116TYR00.0080.01419.756-0.393-0.3930.0000.0000.0000.000
29A117ALA00.0710.03321.388-0.225-0.2250.0000.0000.0000.000
30A118THR00.0130.00116.1810.0330.0330.0000.0000.0000.000
31A119LEU0-0.0240.00015.540-0.869-0.8690.0000.0000.0000.000
32A120GLU-1-0.921-0.95417.968-14.373-14.3730.0000.0000.0000.000
33A121GLU-1-0.982-0.98719.568-12.810-12.8100.0000.0000.0000.000
34A122THR0-0.133-0.08615.002-0.531-0.5310.0000.0000.0000.000
35A123ALA0-0.053-0.03113.130-1.275-1.2750.0000.0000.0000.000
36A124PRO00.1130.06214.484-0.469-0.4690.0000.0000.0000.000
37A125GLN0-0.048-0.02414.1980.2550.2550.0000.0000.0000.000
38A126VAL0-0.067-0.01111.333-1.186-1.1860.0000.0000.0000.000
39A127ARG10.9290.96913.72519.39019.3900.0000.0000.0000.000
40A128VAL00.0330.01614.361-1.415-1.4150.0000.0000.0000.000
41A129THR0-0.025-0.01516.1261.2141.2140.0000.0000.0000.000
42A130GLY00.0010.00917.598-0.560-0.5600.0000.0000.0000.000
43A131VAL0-0.051-0.03117.4130.3760.3760.0000.0000.0000.000
44A132ASN00.0430.00920.544-0.021-0.0210.0000.0000.0000.000
45A133LEU0-0.0030.00522.605-0.559-0.5590.0000.0000.0000.000
46A134ARG10.9250.95622.23213.18713.1870.0000.0000.0000.000
47A135HIS00.0950.04325.195-0.080-0.0800.0000.0000.0000.000
48A136GLY0-0.0320.00624.1830.1300.1300.0000.0000.0000.000
49A137PRO00.0530.02622.273-0.011-0.0110.0000.0000.0000.000
50A138LEU00.0530.01919.128-0.656-0.6560.0000.0000.0000.000
51A139VAL00.009-0.01318.414-0.911-0.9110.0000.0000.0000.000
52A140GLU-1-0.886-0.95017.075-14.837-14.8370.0000.0000.0000.000
53A141GLU-1-0.861-0.89316.029-17.561-17.5610.0000.0000.0000.000
54A142LEU0-0.078-0.03313.684-1.337-1.3370.0000.0000.0000.000
55A143GLU-1-0.958-0.97412.230-22.534-22.5340.0000.0000.0000.000
56A144SER00.021-0.00711.927-2.329-2.3290.0000.0000.0000.000
57A145GLY0-0.043-0.0179.525-1.678-1.6780.0000.0000.0000.000
58A146SER0-0.098-0.06310.358-1.031-1.0310.0000.0000.0000.000
59A147ILE0-0.026-0.01913.0001.1601.1600.0000.0000.0000.000
60A148ASP-1-0.832-0.8938.965-30.378-30.3780.0000.0000.0000.000
61A149ILE0-0.014-0.01811.532-0.210-0.2100.0000.0000.0000.000
62A150ALA00.0140.02714.7170.5600.5600.0000.0000.0000.000
63A151PHE0-0.039-0.02818.360-0.045-0.0450.0000.0000.0000.000
64A152GLY00.014-0.00421.0960.4630.4630.0000.0000.0000.000
65A153GLY00.0520.01724.685-0.160-0.1600.0000.0000.0000.000
66A154PHE00.0030.00222.2150.2060.2060.0000.0000.0000.000
67A155PRO0-0.0090.01225.144-0.350-0.3500.0000.0000.0000.000
68A156THR00.0410.01325.181-0.040-0.0400.0000.0000.0000.000
69A157LEU0-0.057-0.01320.027-0.353-0.3530.0000.0000.0000.000
70A158SER0-0.015-0.01822.7910.0320.0320.0000.0000.0000.000
71A159ALA00.0370.01721.560-0.443-0.4430.0000.0000.0000.000
72A160GLY00.0400.02718.074-0.276-0.2760.0000.0000.0000.000
73A161ILE0-0.064-0.02716.509-1.353-1.3530.0000.0000.0000.000
74A162LYS10.9400.98714.67518.16918.1690.0000.0000.0000.000
75A163THR0-0.018-0.01617.683-0.005-0.0050.0000.0000.0000.000
76A164GLN00.0420.01119.109-0.542-0.5420.0000.0000.0000.000
77A165THR00.000-0.00721.040-0.235-0.2350.0000.0000.0000.000
78A166LEU0-0.054-0.02021.092-0.070-0.0700.0000.0000.0000.000
79A167PHE0-0.039-0.02425.0440.3040.3040.0000.0000.0000.000
80A168ARG10.9700.99828.7739.3459.3450.0000.0000.0000.000
81A169GLU-1-0.794-0.89131.642-9.293-9.2930.0000.0000.0000.000
82A170GLU-1-0.804-0.87433.382-8.442-8.4420.0000.0000.0000.000
83A171TYR0-0.048-0.06434.215-0.164-0.1640.0000.0000.0000.000
84A172VAL0-0.038-0.01738.5870.1700.1700.0000.0000.0000.000
85A173CYS0-0.040-0.00741.368-0.077-0.0770.0000.0000.0000.000
86A174VAL00.0040.00541.8060.0120.0120.0000.0000.0000.000
87A175MET00.0090.00844.5530.0220.0220.0000.0000.0000.000
88A176ARG10.9060.96147.2406.3156.3150.0000.0000.0000.000
89A177GLN0-0.038-0.02948.3110.1940.1940.0000.0000.0000.000
90A178SER0-0.018-0.01050.8910.0960.0960.0000.0000.0000.000
91A179HIS00.0580.05650.5400.0870.0870.0000.0000.0000.000
92A180PRO00.010-0.00753.4680.0510.0510.0000.0000.0000.000
93A181ALA0-0.001-0.01453.6310.0790.0790.0000.0000.0000.000
94A182LEU0-0.0490.00651.872-0.011-0.0110.0000.0000.0000.000
95A183THR0-0.076-0.03254.4910.0250.0250.0000.0000.0000.000
96A184HIS0-0.026-0.00657.0990.1150.1150.0000.0000.0000.000
97A185GLY00.0330.02455.857-0.079-0.0790.0000.0000.0000.000
98A186LEU0-0.033-0.04951.1850.0090.0090.0000.0000.0000.000
99A187ASP-1-0.864-0.92053.308-5.691-5.6910.0000.0000.0000.000
100A188LEU00.029-0.00450.826-0.041-0.0410.0000.0000.0000.000
101A189GLU-1-0.797-0.90653.201-5.736-5.7360.0000.0000.0000.000
102A190ALA00.0200.02255.8080.0090.0090.0000.0000.0000.000
103A191PHE00.014-0.00246.101-0.076-0.0760.0000.0000.0000.000
104A192ARG10.8220.89251.3205.8715.8710.0000.0000.0000.000
105A193GLN0-0.0150.01252.364-0.029-0.0290.0000.0000.0000.000
106A194CYS0-0.077-0.02151.1470.0360.0360.0000.0000.0000.000
107A195ARG10.9300.96349.5255.9445.9440.0000.0000.0000.000
108A196HIS10.8670.94345.2666.6326.6320.0000.0000.0000.000
109A197ILE0-0.0040.01140.3890.0410.0410.0000.0000.0000.000
110A198ILE00.0100.00439.351-0.040-0.0400.0000.0000.0000.000
111A199VAL0-0.036-0.02434.000-0.033-0.0330.0000.0000.0000.000
112A200THR0-0.015-0.01434.9860.0870.0870.0000.0000.0000.000
113A201ALA0-0.041-0.04531.146-0.268-0.2680.0000.0000.0000.000
114A202HIS00.0270.00731.345-0.243-0.2430.0000.0000.0000.000
115A203GLU-1-0.867-0.92731.411-9.500-9.5000.0000.0000.0000.000
116A204PHE0-0.084-0.04326.999-0.414-0.4140.0000.0000.0000.000
117A205ASN0-0.054-0.01526.854-0.340-0.3400.0000.0000.0000.000
118A206HIS00.0400.01826.218-0.150-0.1500.0000.0000.0000.000
119A207VAL00.034-0.01328.5740.3140.3140.0000.0000.0000.000
120A208HIS00.0010.03930.6840.1850.1850.0000.0000.0000.000
121A209GLU-1-0.848-0.91831.291-9.525-9.5250.0000.0000.0000.000
122A210GLN0-0.026-0.01633.2010.4010.4010.0000.0000.0000.000
123A211VAL0-0.016-0.00736.3010.2820.2820.0000.0000.0000.000
124A212GLU-1-0.813-0.91236.162-8.333-8.3330.0000.0000.0000.000
125A213ALA00.011-0.00538.5070.2340.2340.0000.0000.0000.000
126A214ARG10.8870.94440.4117.4747.4740.0000.0000.0000.000
127A215LEU0-0.035-0.02340.8600.2190.2190.0000.0000.0000.000
128A216LEU0-0.010-0.00841.2190.1910.1910.0000.0000.0000.000
129A217GLU-1-0.980-0.96344.546-6.733-6.7330.0000.0000.0000.000
130A218LEU0-0.035-0.01246.5000.1790.1790.0000.0000.0000.000
131A219LEU0-0.049-0.02245.9550.1900.1900.0000.0000.0000.000
132A220PRO00.0130.01749.182-0.023-0.0230.0000.0000.0000.000
133A221PRO00.0920.05049.209-0.085-0.0850.0000.0000.0000.000
134A222GLU-1-0.915-0.96349.794-5.941-5.9410.0000.0000.0000.000
135A223SER0-0.107-0.07550.4670.0530.0530.0000.0000.0000.000
136A224ILE0-0.028-0.00844.524-0.093-0.0930.0000.0000.0000.000
137A225ARG10.9170.98346.9936.2876.2870.0000.0000.0000.000
138A226PHE0-0.009-0.01342.8060.0030.0030.0000.0000.0000.000
139A227THR00.0500.01338.926-0.019-0.0190.0000.0000.0000.000
140A228THR0-0.049-0.02736.177-0.085-0.0850.0000.0000.0000.000
141A229GLU-1-0.846-0.90931.689-9.530-9.5300.0000.0000.0000.000
142A230ASN0-0.096-0.03230.858-0.539-0.5390.0000.0000.0000.000
143A231PHE00.0530.01130.4710.2680.2680.0000.0000.0000.000
144A232LEU0-0.0030.01830.4080.3090.3090.0000.0000.0000.000
145A233VAL00.0030.00734.2260.2180.2180.0000.0000.0000.000
146A234SER0-0.031-0.06036.4280.2630.2630.0000.0000.0000.000
147A235ALA00.0230.00237.3450.2280.2280.0000.0000.0000.000
148A236VAL00.0140.01137.8570.1860.1860.0000.0000.0000.000
149A237ILE00.0290.00840.2580.2060.2060.0000.0000.0000.000
150A238ALA0-0.031-0.01242.1850.2040.2040.0000.0000.0000.000
151A239GLU-1-0.773-0.86342.295-7.439-7.4390.0000.0000.0000.000
152A240GLU-1-0.946-0.96344.282-6.806-6.8060.0000.0000.0000.000
153A241THR0-0.110-0.06046.4490.1840.1840.0000.0000.0000.000
154A242ASP-1-0.831-0.93448.173-6.153-6.1530.0000.0000.0000.000
155A243VAL0-0.077-0.03345.1980.0730.0730.0000.0000.0000.000
156A244ILE0-0.016-0.01445.677-0.060-0.0600.0000.0000.0000.000
157A245LEU0-0.0050.01038.856-0.055-0.0550.0000.0000.0000.000
158A246THR0-0.015-0.01240.1390.1220.1220.0000.0000.0000.000
159A247ILE0-0.013-0.01036.589-0.198-0.1980.0000.0000.0000.000
160A248PRO00.0320.01632.7030.1490.1490.0000.0000.0000.000
161A249SER00.010-0.00435.4120.0710.0710.0000.0000.0000.000
162A250ARG10.8370.89930.90610.04210.0420.0000.0000.0000.000
163A251LEU0-0.030-0.00133.180-0.017-0.0170.0000.0000.0000.000
164A252ALA00.0510.02034.9270.1350.1350.0000.0000.0000.000
165A253ARG10.9020.94137.1577.8507.8500.0000.0000.0000.000
166A254TRP0-0.042-0.01633.8550.1470.1470.0000.0000.0000.000
167A255PHE00.023-0.00635.4310.0030.0030.0000.0000.0000.000
168A256ALA00.0250.02139.4810.1950.1950.0000.0000.0000.000
169A257ASN0-0.059-0.01638.2560.3450.3450.0000.0000.0000.000
170A258ARG10.8090.87839.6037.8597.8590.0000.0000.0000.000
171A259GLY0-0.052-0.02143.4390.1180.1180.0000.0000.0000.000
172A260GLY00.0380.03244.9160.1550.1550.0000.0000.0000.000
173A261LEU0-0.026-0.01341.7060.1200.1200.0000.0000.0000.000
174A262THR0-0.009-0.00845.6110.0020.0020.0000.0000.0000.000
175A263ILE0-0.015-0.01641.692-0.066-0.0660.0000.0000.0000.000
176A264PHE0-0.020-0.01345.3120.1400.1400.0000.0000.0000.000
177A265PRO00.032-0.00145.316-0.160-0.1600.0000.0000.0000.000
178A266VAL00.0460.01642.5000.0960.0960.0000.0000.0000.000
179A267PRO0-0.0300.00345.8470.0220.0220.0000.0000.0000.000
180A268ILE0-0.017-0.01544.1950.1110.1110.0000.0000.0000.000
181A269GLU-1-0.901-0.94843.893-7.237-7.2370.0000.0000.0000.000
182A270LEU0-0.036-0.02439.829-0.051-0.0510.0000.0000.0000.000
183A271PRO00.0220.01836.7240.0130.0130.0000.0000.0000.000
184A272SER0-0.031-0.03435.806-0.204-0.2040.0000.0000.0000.000
185A273ILE0-0.012-0.01030.381-0.204-0.2040.0000.0000.0000.000
186A274GLU-1-0.945-0.98428.467-10.531-10.5310.0000.0000.0000.000
187A275VAL0-0.0340.00425.247-0.278-0.2780.0000.0000.0000.000
188A276LYS10.9320.96122.62711.86411.8640.0000.0000.0000.000
189A277GLN0-0.018-0.00517.181-0.621-0.6210.0000.0000.0000.000
190A278TYR0-0.006-0.01118.0640.2250.2250.0000.0000.0000.000
191A279TRP0-0.008-0.02212.090-0.178-0.1780.0000.0000.0000.000
192A280HIS00.1550.07712.298-0.231-0.2310.0000.0000.0000.000
193A281GLU-1-0.886-0.94512.042-19.176-19.1760.0000.0000.0000.000
194A282ARG10.8530.9488.28326.47526.4750.0000.0000.0000.000
195A283TYR0-0.049-0.0306.133-5.330-5.3300.0000.0000.0000.000
196A284ASP-1-0.906-0.9638.318-23.611-23.6110.0000.0000.0000.000
197A285LYS10.9720.9676.57328.71428.7140.0000.0000.0000.000
198A286ASP-1-0.820-0.8993.188-71.926-70.0600.033-0.946-0.953-0.008
199A287PRO00.005-0.0101.8734.0613.0546.369-1.654-3.708-0.002
200A288GLY00.0260.0204.5775.0035.138-0.001-0.025-0.1090.000
201A289ASN0-0.001-0.0116.3166.9246.9240.0000.0000.0000.000
202A290ILE0-0.0320.0006.8133.7333.7330.0000.0000.0000.000
203A291TRP0-0.024-0.0138.4142.2282.2280.0000.0000.0000.000
204A292LEU00.0430.02110.0082.2152.2150.0000.0000.0000.000
205A293ARG10.9070.95610.18826.38026.3800.0000.0000.0000.000
206A294ARG10.8970.95612.96918.37718.3770.0000.0000.0000.000
207A295VAL00.013-0.00213.9451.3761.3760.0000.0000.0000.000
208A296ILE00.0420.01816.3441.1661.1660.0000.0000.0000.000
209A297ALA0-0.054-0.02517.8390.9100.9100.0000.0000.0000.000
210A298LYS10.8620.93917.19316.09016.0900.0000.0000.0000.000
211A299ILE0-0.0060.01620.5570.5420.5420.0000.0000.0000.000
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