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: MNM9Z

Calculation Name: 3HNR-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3HNR

Chain ID: A

ChEMBL ID:

UniProt ID: Q6HDF0

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 193
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2243144.28239
FMO2-HF: Nuclear repulsion 2166234.015826
FMO2-HF: Total energy -76910.266563
FMO2-MP2: Total energy -77137.812812


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:24:ASP)


Summations of interaction energy for fragment #1(A:24: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.
18.23321.2590.165-1.033-2.1580.006
Interaction energy analysis for fragmet #1(A:24:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.891 / 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].
3A26GLN0-0.039-0.0283.073-14.718-12.6090.098-0.822-1.3850.005
4A27TYR0-0.017-0.0143.065-5.200-4.2830.067-0.211-0.7730.001
5A28LYS10.9730.9964.830-37.101-37.1010.0000.0000.0000.000
6A29GLU-1-0.917-0.9755.48821.62521.6250.0000.0000.0000.000
7A30VAL00.0170.0217.361-1.920-1.9200.0000.0000.0000.000
8A31PHE00.0080.0194.849-1.863-1.8630.0000.0000.0000.000
9A32ALA00.0080.0138.1300.1420.1420.0000.0000.0000.000
10A33HIS0-0.028-0.02310.295-1.358-1.3580.0000.0000.0000.000
11A34TYR00.0190.0499.701-1.488-1.4880.0000.0000.0000.000
12A35GLU-1-0.841-0.94411.82021.07721.0770.0000.0000.0000.000
13A36ASP-1-0.869-0.93014.54716.87516.8750.0000.0000.0000.000
14A37ILE0-0.020-0.02913.005-1.329-1.3290.0000.0000.0000.000
15A38LEU0-0.052-0.02814.351-0.964-0.9640.0000.0000.0000.000
16A39GLU-1-0.919-0.95617.58413.72613.7260.0000.0000.0000.000
17A40ASP-1-0.911-0.96419.84712.47612.4760.0000.0000.0000.000
18A41VAL00.009-0.00919.414-0.686-0.6860.0000.0000.0000.000
19A42VAL0-0.0130.00221.269-0.703-0.7030.0000.0000.0000.000
20A43ASN00.000-0.01023.613-0.642-0.6420.0000.0000.0000.000
21A44LYS10.8370.95723.977-12.844-12.8440.0000.0000.0000.000
22A45SER00.0100.01526.184-0.363-0.3630.0000.0000.0000.000
23A46PHE0-0.031-0.02928.138-0.008-0.0080.0000.0000.0000.000
24A47GLY00.0370.01931.370-0.006-0.0060.0000.0000.0000.000
25A48ASN0-0.074-0.04031.5440.3420.3420.0000.0000.0000.000
26A49VAL00.0490.00525.713-0.056-0.0560.0000.0000.0000.000
27A50LEU0-0.036-0.01127.6210.0030.0030.0000.0000.0000.000
28A51GLU-1-0.789-0.88419.60914.89014.8900.0000.0000.0000.000
29A52PHE0-0.021-0.02522.694-0.149-0.1490.0000.0000.0000.000
30A53GLY0-0.021-0.00518.9380.4280.4280.0000.0000.0000.000
31A54VAL0-0.0180.00517.7860.6650.6650.0000.0000.0000.000
32A55GLY00.0690.03915.4210.8570.8570.0000.0000.0000.000
33A56THR0-0.047-0.04812.499-0.662-0.6620.0000.0000.0000.000
34A57GLY00.0500.00815.634-0.161-0.1610.0000.0000.0000.000
35A58ASN0-0.049-0.04511.539-1.325-1.3250.0000.0000.0000.000
36A59LEU00.0690.03715.976-0.359-0.3590.0000.0000.0000.000
37A60THR00.014-0.03818.299-0.454-0.4540.0000.0000.0000.000
38A61ASN0-0.003-0.00117.374-1.263-1.2630.0000.0000.0000.000
39A62LYS10.9050.95615.979-18.333-18.3330.0000.0000.0000.000
40A63LEU00.0190.01621.078-0.645-0.6450.0000.0000.0000.000
41A64LEU0-0.036-0.02223.666-0.589-0.5890.0000.0000.0000.000
42A65LEU0-0.040-0.00921.121-0.488-0.4880.0000.0000.0000.000
43A66ALA0-0.050-0.01225.131-0.408-0.4080.0000.0000.0000.000
44A67GLY0-0.041-0.02426.966-0.408-0.4080.0000.0000.0000.000
45A68ARG10.8100.91927.087-11.250-11.2500.0000.0000.0000.000
46A69THR00.0090.00829.2390.1520.1520.0000.0000.0000.000
47A70VAL0-0.021-0.00424.7070.0340.0340.0000.0000.0000.000
48A71TYR0-0.012-0.00427.890-0.230-0.2300.0000.0000.0000.000
49A72GLY00.0230.01224.7660.2320.2320.0000.0000.0000.000
50A73ILE0-0.017-0.00123.909-0.454-0.4540.0000.0000.0000.000
51A74GLU-1-0.810-0.92518.79916.37416.3740.0000.0000.0000.000
52A75PRO00.1000.08220.749-0.339-0.3390.0000.0000.0000.000
53A76SER00.0430.03017.501-0.500-0.5000.0000.0000.0000.000
54A77ARG11.0140.98420.483-11.449-11.4490.0000.0000.0000.000
55A78GLU-1-0.956-0.98014.85518.29818.2980.0000.0000.0000.000
56A79MET0-0.0020.00212.6200.5990.5990.0000.0000.0000.000
57A80ARG10.7670.83817.636-12.383-12.3830.0000.0000.0000.000
58A81MET0-0.100-0.03319.970-0.631-0.6310.0000.0000.0000.000
59A82ILE00.0610.02314.279-0.097-0.0970.0000.0000.0000.000
60A83ALA00.0270.02118.1860.0590.0590.0000.0000.0000.000
61A84LYS10.8720.94619.671-12.335-12.3350.0000.0000.0000.000
62A85GLU-1-0.952-0.97419.48713.23613.2360.0000.0000.0000.000
63A86LYS10.8170.91513.719-20.394-20.3940.0000.0000.0000.000
64A87LEU0-0.048-0.00920.025-0.279-0.2790.0000.0000.0000.000
65A88PRO00.0150.01222.733-0.239-0.2390.0000.0000.0000.000
66A89LYS10.9720.97825.460-11.826-11.8260.0000.0000.0000.000
67A90GLU-1-0.970-0.98328.6299.3269.3260.0000.0000.0000.000
68A91PHE0-0.021-0.00923.908-0.106-0.1060.0000.0000.0000.000
69A92SER0-0.027-0.01228.120-0.007-0.0070.0000.0000.0000.000
70A93ILE0-0.003-0.01122.0120.2290.2290.0000.0000.0000.000
71A94THR00.0090.00926.6230.0470.0470.0000.0000.0000.000
72A95GLU-1-0.930-0.95425.28411.72711.7270.0000.0000.0000.000
73A96GLY00.0210.02626.4140.0320.0320.0000.0000.0000.000
74A97ASP-1-0.828-0.93924.77011.60011.6000.0000.0000.0000.000
75A98PHE00.031-0.00120.486-0.363-0.3630.0000.0000.0000.000
76A99LEU0-0.0130.01325.917-0.431-0.4310.0000.0000.0000.000
77A100SER00.001-0.00428.992-0.607-0.6070.0000.0000.0000.000
78A101PHE0-0.026-0.00228.6430.2980.2980.0000.0000.0000.000
79A102GLU-1-0.915-0.95030.6498.8998.8990.0000.0000.0000.000
80A103VAL0-0.015-0.01231.8980.2590.2590.0000.0000.0000.000
81A104PRO0-0.0060.00431.162-0.234-0.2340.0000.0000.0000.000
82A105THR00.009-0.01434.154-0.240-0.2400.0000.0000.0000.000
83A106SER0-0.0340.01436.682-0.197-0.1970.0000.0000.0000.000
84A107ILE0-0.005-0.00131.1540.1650.1650.0000.0000.0000.000
85A108ASP-1-0.839-0.91732.9038.4958.4950.0000.0000.0000.000
86A109THR0-0.087-0.04028.3590.1580.1580.0000.0000.0000.000
87A110ILE00.0180.01426.1870.1110.1110.0000.0000.0000.000
88A111VAL00.018-0.00722.4580.1150.1150.0000.0000.0000.000
89A112SER00.0100.00319.9330.1280.1280.0000.0000.0000.000
90A113THR00.0150.00615.484-0.016-0.0160.0000.0000.0000.000
91A114TYR0-0.036-0.04310.6850.6060.6060.0000.0000.0000.000
92A115ALA00.0360.01614.4550.4590.4590.0000.0000.0000.000
93A116PHE00.0480.01017.170-0.413-0.4130.0000.0000.0000.000
94A117HIS10.8690.92414.163-18.904-18.9040.0000.0000.0000.000
95A118HIS0-0.048-0.01315.1220.5250.5250.0000.0000.0000.000
96A119LEU0-0.0090.00219.531-0.519-0.5190.0000.0000.0000.000
97A120THR00.0250.01323.0190.0240.0240.0000.0000.0000.000
98A121ASP-1-0.781-0.91524.90011.60811.6080.0000.0000.0000.000
99A122ASP-1-0.914-0.95426.8629.3939.3930.0000.0000.0000.000
100A123GLU-1-0.882-0.94425.80711.07811.0780.0000.0000.0000.000
101A124LYS10.7830.89622.233-12.900-12.9000.0000.0000.0000.000
102A125ASN00.0440.01127.148-0.116-0.1160.0000.0000.0000.000
103A126VAL0-0.0180.00630.785-0.286-0.2860.0000.0000.0000.000
104A127ALA0-0.005-0.00727.738-0.210-0.2100.0000.0000.0000.000
105A128ILE00.0060.00027.083-0.190-0.1900.0000.0000.0000.000
106A129ALA00.0150.01330.624-0.235-0.2350.0000.0000.0000.000
107A130LYS10.8140.89432.201-9.574-9.5740.0000.0000.0000.000
108A131TYR0-0.010-0.02326.919-0.020-0.0200.0000.0000.0000.000
109A132SER0-0.032-0.01832.499-0.215-0.2150.0000.0000.0000.000
110A133GLN0-0.051-0.02635.200-0.125-0.1250.0000.0000.0000.000
111A134LEU0-0.055-0.02632.920-0.200-0.2000.0000.0000.0000.000
112A135LEU0-0.0120.02231.451-0.105-0.1050.0000.0000.0000.000
113A136ASN00.0340.01335.933-0.220-0.2200.0000.0000.0000.000
114A137LYS11.0040.99937.554-7.178-7.1780.0000.0000.0000.000
115A138GLY0-0.049-0.02937.153-0.071-0.0710.0000.0000.0000.000
116A139GLY00.0200.02234.5290.1740.1740.0000.0000.0000.000
117A140LYS10.7780.85129.582-10.214-10.2140.0000.0000.0000.000
118A141ILE0-0.0070.00926.1670.0600.0600.0000.0000.0000.000
119A142VAL0-0.0080.00623.056-0.047-0.0470.0000.0000.0000.000
120A143PHE0-0.0260.00721.1380.2670.2670.0000.0000.0000.000
121A144ALA00.0540.03317.111-0.156-0.1560.0000.0000.0000.000
122A145ASP-1-0.790-0.89215.67117.82417.8240.0000.0000.0000.000
123A146THR00.000-0.00313.2210.1330.1330.0000.0000.0000.000
124A147ILE0-0.050-0.01615.645-0.611-0.6110.0000.0000.0000.000
125A148PHE00.003-0.00315.2670.2410.2410.0000.0000.0000.000
126A149ALA00.0180.01920.925-0.525-0.5250.0000.0000.0000.000
127A150ASP-1-0.848-0.94423.78811.05911.0590.0000.0000.0000.000
128A151GLN0-0.055-0.05223.4420.2890.2890.0000.0000.0000.000
129A152ASP-1-0.900-0.93523.59311.92811.9280.0000.0000.0000.000
130A153ALA0-0.025-0.02121.2580.5100.5100.0000.0000.0000.000
131A154TYR0-0.051-0.03517.5420.6690.6690.0000.0000.0000.000
132A155ASP-1-0.774-0.88518.69813.27413.2740.0000.0000.0000.000
133A156LYS10.9070.96319.875-12.178-12.1780.0000.0000.0000.000
134A157THR0-0.049-0.04414.4390.7960.7960.0000.0000.0000.000
135A158VAL00.0170.00514.9221.2171.2170.0000.0000.0000.000
136A159GLU-1-0.913-0.95315.58115.33615.3360.0000.0000.0000.000
137A160ALA00.0030.00615.1930.5810.5810.0000.0000.0000.000
138A161ALA0-0.028-0.02611.3281.0581.0580.0000.0000.0000.000
139A162LYS10.9690.98012.162-14.085-14.0850.0000.0000.0000.000
140A163GLN0-0.130-0.03814.773-0.583-0.5830.0000.0000.0000.000
141A164ARG10.8560.93811.145-22.666-22.6660.0000.0000.0000.000
142A165GLY00.0380.01811.201-0.524-0.5240.0000.0000.0000.000
143A166PHE0-0.046-0.0487.8461.8701.8700.0000.0000.0000.000
144A167HIS00.0960.0469.195-1.283-1.2830.0000.0000.0000.000
145A168GLN0-0.0010.0056.9421.9831.9830.0000.0000.0000.000
146A169LEU00.0200.0187.355-1.263-1.2630.0000.0000.0000.000
147A170ALA00.0300.0108.843-1.546-1.5460.0000.0000.0000.000
148A171ASN00.0180.01511.878-2.128-2.1280.0000.0000.0000.000
149A172ASP-1-0.766-0.84810.23421.68621.6860.0000.0000.0000.000
150A173LEU0-0.004-0.01812.180-1.244-1.2440.0000.0000.0000.000
151A174GLN0-0.065-0.00814.419-0.425-0.4250.0000.0000.0000.000
152A175THR0-0.068-0.00815.343-0.931-0.9310.0000.0000.0000.000
153A176GLU-1-0.916-0.95314.19216.71116.7110.0000.0000.0000.000
154A177TYR00.0070.00617.082-0.618-0.6180.0000.0000.0000.000
155A178TYR0-0.093-0.07312.839-0.409-0.4090.0000.0000.0000.000
156A179THR00.006-0.00119.127-0.583-0.5830.0000.0000.0000.000
157A180ARG10.9470.95321.699-10.658-10.6580.0000.0000.0000.000
158A181ILE00.0380.01222.803-0.238-0.2380.0000.0000.0000.000
159A182PRO00.019-0.00425.465-0.265-0.2650.0000.0000.0000.000
160A183VAL0-0.0230.00527.001-0.343-0.3430.0000.0000.0000.000
161A184MET00.0310.01323.149-0.343-0.3430.0000.0000.0000.000
162A185GLN0-0.047-0.01727.4180.0810.0810.0000.0000.0000.000
163A186THR00.0120.00630.109-0.341-0.3410.0000.0000.0000.000
164A187ILE0-0.0070.00928.254-0.252-0.2520.0000.0000.0000.000
165A188PHE00.014-0.00226.042-0.217-0.2170.0000.0000.0000.000
166A189GLU-1-0.896-0.94631.6128.6068.6060.0000.0000.0000.000
167A190ASN0-0.029-0.01134.847-0.390-0.3900.0000.0000.0000.000
168A191ASN0-0.082-0.03833.259-0.423-0.4230.0000.0000.0000.000
169A192GLY0-0.0050.00935.9410.0230.0230.0000.0000.0000.000
170A193PHE0-0.046-0.02332.565-0.043-0.0430.0000.0000.0000.000
171A194HIS00.0000.01334.224-0.118-0.1180.0000.0000.0000.000
172A195VAL0-0.012-0.02027.7160.0900.0900.0000.0000.0000.000
173A196THR0-0.0030.01127.921-0.246-0.2460.0000.0000.0000.000
174A197PHE0-0.006-0.00824.0590.4010.4010.0000.0000.0000.000
175A198THR00.0130.00322.236-0.332-0.3320.0000.0000.0000.000
176A199ARG10.7820.91417.641-15.022-15.0220.0000.0000.0000.000
177A200LEU00.0310.02516.804-0.239-0.2390.0000.0000.0000.000
178A201ASN00.0450.03311.9920.3910.3910.0000.0000.0000.000
179A202HIS0-0.069-0.03313.983-1.200-1.2000.0000.0000.0000.000
180A203PHE00.0410.00211.663-0.536-0.5360.0000.0000.0000.000
181A204VAL00.0090.02012.770-1.051-1.0510.0000.0000.0000.000
182A205TRP0-0.025-0.01415.569-0.857-0.8570.0000.0000.0000.000
183A206VAL0-0.002-0.00619.2140.2900.2900.0000.0000.0000.000
184A207MET0-0.046-0.01820.865-0.641-0.6410.0000.0000.0000.000
185A208GLU-1-0.831-0.92024.25110.64310.6430.0000.0000.0000.000
186A209ALA00.0220.00827.073-0.339-0.3390.0000.0000.0000.000
187A210THR00.0180.01829.9080.0260.0260.0000.0000.0000.000
188A211LYS10.8320.93833.288-8.233-8.2330.0000.0000.0000.000
189A212GLN0-0.025-0.03135.935-0.285-0.2850.0000.0000.0000.000
190A213LEU0-0.025-0.01139.067-0.201-0.2010.0000.0000.0000.000
191A214GLU-1-0.947-0.98740.5177.1487.1480.0000.0000.0000.000
192A215HIS00.0190.00040.365-0.255-0.2550.0000.0000.0000.000
193A216HIS10.9120.98242.409-6.836-6.8360.0000.0000.0000.000