Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: NNY3Q

Calculation Name: 4N30-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4N30

Chain ID: A

ChEMBL ID:

UniProt ID: Q7WY37

Base Structure: X-ray

Registration Date: 2023-09-23

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 181
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1901282.635733
FMO2-HF: Nuclear repulsion 1831007.595333
FMO2-HF: Total energy -70275.040399
FMO2-MP2: Total energy -70480.263881


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:40:LYS)


Summations of interaction energy for fragment #1(A:40:LYS)
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.
-111.175-101.9990.705-5.296-4.583-0.042
Interaction energy analysis for fragmet #1(A:40:LYS)
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 : 0.968
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].
3A42LEU00.008-0.0093.406-6.020-3.4200.017-1.424-1.1940.004
4A43PRO0-0.014-0.0015.837-0.871-0.8710.0000.0000.0000.000
5A44ALA00.0180.0186.5533.2543.2540.0000.0000.0000.000
6A45ASN0-0.008-0.0159.4950.4780.4780.0000.0000.0000.000
7A46HIS0-0.016-0.02812.848-0.123-0.1230.0000.0000.0000.000
8A47SER00.0690.04312.4010.2550.2550.0000.0000.0000.000
9A48LEU0-0.032-0.02310.160-0.662-0.6620.0000.0000.0000.000
10A49TYR0-0.084-0.06513.3141.4541.4540.0000.0000.0000.000
11A50GLY00.0600.01714.039-0.907-0.9070.0000.0000.0000.000
12A51ASP-1-0.833-0.90712.780-23.589-23.5890.0000.0000.0000.000
13A52ALA00.024-0.00110.130-2.078-2.0780.0000.0000.0000.000
14A53LYS10.8410.9138.22323.11723.1170.0000.0000.0000.000
15A54ALA0-0.0010.0189.103-0.636-0.6360.0000.0000.0000.000
16A55ARG10.8960.9567.28823.47923.4790.0000.0000.0000.000
17A56TRP0-0.045-0.0276.936-5.498-5.4980.0000.0000.0000.000
18A57THR00.010-0.0076.913-0.915-0.9150.0000.0000.0000.000
19A58ILE0-0.003-0.0078.646-0.319-0.3190.0000.0000.0000.000
20A59ASN0-0.063-0.0268.229-0.057-0.0570.0000.0000.0000.000
21A60GLU-1-0.775-0.88712.173-15.253-15.2530.0000.0000.0000.000
22A61TYR0-0.038-0.01511.748-0.548-0.5480.0000.0000.0000.000
23A62ALA00.046-0.00517.3830.9050.9050.0000.0000.0000.000
24A63ASP-1-0.753-0.86820.625-11.917-11.9170.0000.0000.0000.000
25A64LEU00.0380.00323.2490.1870.1870.0000.0000.0000.000
26A65GLU-1-0.775-0.82325.796-9.636-9.6360.0000.0000.0000.000
27A66CYS0-0.0400.00625.9580.5260.5260.0000.0000.0000.000
28A67PRO00.0470.02728.030-0.227-0.2270.0000.0000.0000.000
29A68PHE00.011-0.02326.6350.0530.0530.0000.0000.0000.000
30A69CYS00.005-0.00323.690-0.420-0.4200.0000.0000.0000.000
31A70LYS10.9430.99324.8359.5969.5960.0000.0000.0000.000
32A71VAL0-0.055-0.02727.3580.0110.0110.0000.0000.0000.000
33A72TYR0-0.038-0.05319.799-0.202-0.2020.0000.0000.0000.000
34A73THR00.028-0.00420.446-0.135-0.1350.0000.0000.0000.000
35A74PRO00.0090.00521.866-0.442-0.4420.0000.0000.0000.000
36A75ARG10.9010.95523.79810.87010.8700.0000.0000.0000.000
37A76LEU00.0070.00716.830-0.183-0.1830.0000.0000.0000.000
38A77LYS10.8630.94019.09413.12513.1250.0000.0000.0000.000
39A78ARG10.9991.00920.16111.91711.9170.0000.0000.0000.000
40A79TRP0-0.010-0.01215.950-0.277-0.2770.0000.0000.0000.000
41A80VAL0-0.0030.00315.235-0.233-0.2330.0000.0000.0000.000
42A81ASP-1-0.831-0.88517.677-14.823-14.8230.0000.0000.0000.000
43A82SER0-0.111-0.05320.2460.2640.2640.0000.0000.0000.000
44A83HIS10.7980.89717.04415.87815.8780.0000.0000.0000.000
45A84PRO00.0800.02015.817-1.048-1.0480.0000.0000.0000.000
46A85ASP-1-0.914-0.93513.033-21.333-21.3330.0000.0000.0000.000
47A86VAL0-0.072-0.03811.339-2.586-2.5860.0000.0000.0000.000
48A87ASN0-0.0130.0128.1280.8210.8210.0000.0000.0000.000
49A88LEU00.0150.01211.809-0.444-0.4440.0000.0000.0000.000
50A89VAL0-0.036-0.0209.233-0.166-0.1660.0000.0000.0000.000
51A90TRP00.0240.01112.4560.4140.4140.0000.0000.0000.000
52A91ARG10.7710.8548.51124.85924.8590.0000.0000.0000.000
53A92HIS0-0.016-0.02514.8481.6131.6130.0000.0000.0000.000
54A93LEU0-0.025-0.03417.096-0.335-0.3350.0000.0000.0000.000
55A94PRO0-0.0020.01519.6160.4480.4480.0000.0000.0000.000
56A95LEU00.000-0.00223.0400.0400.0400.0000.0000.0000.000
57A96GLN00.0520.01225.2730.0770.0770.0000.0000.0000.000
58A97MET0-0.088-0.04527.5780.3300.3300.0000.0000.0000.000
59A98HIS0-0.021-0.03127.4410.5740.5740.0000.0000.0000.000
60A99GLY00.0070.00629.6040.1010.1010.0000.0000.0000.000
61A100GLU-1-0.781-0.89028.478-10.623-10.6230.0000.0000.0000.000
62A101ALA00.0300.03728.881-0.260-0.2600.0000.0000.0000.000
63A102ALA00.0400.01825.633-0.252-0.2520.0000.0000.0000.000
64A103ARG10.8180.89324.11710.01710.0170.0000.0000.0000.000
65A104HIS0-0.003-0.00224.511-0.556-0.5560.0000.0000.0000.000
66A105GLN00.030-0.02026.2600.1110.1110.0000.0000.0000.000
67A106ALA00.000-0.00320.742-0.301-0.3010.0000.0000.0000.000
68A107ARG10.8350.91821.53810.95610.9560.0000.0000.0000.000
69A108LEU00.0070.00523.125-0.215-0.2150.0000.0000.0000.000
70A109VAL00.0100.01420.356-0.061-0.0610.0000.0000.0000.000
71A110GLU-1-0.771-0.86316.733-17.703-17.7030.0000.0000.0000.000
72A111CYS0-0.085-0.03119.971-0.419-0.4190.0000.0000.0000.000
73A112ALA00.0200.00722.9110.2080.2080.0000.0000.0000.000
74A113GLY0-0.026-0.01819.1720.0750.0750.0000.0000.0000.000
75A114ILE0-0.031-0.00919.651-0.142-0.1420.0000.0000.0000.000
76A115GLN0-0.081-0.03921.0190.3040.3040.0000.0000.0000.000
77A116GLY00.022-0.00222.7810.3420.3420.0000.0000.0000.000
78A117GLY0-0.0340.00318.943-0.106-0.1060.0000.0000.0000.000
79A118ALA00.0650.02716.9160.3630.3630.0000.0000.0000.000
80A119LYS10.9510.97218.82212.37612.3760.0000.0000.0000.000
81A120ALA00.0110.02622.2150.4300.4300.0000.0000.0000.000
82A121PHE00.0330.02317.4210.3160.3160.0000.0000.0000.000
83A122TRP00.003-0.02115.8200.8670.8670.0000.0000.0000.000
84A123SER0-0.032-0.02521.8290.4800.4800.0000.0000.0000.000
85A124ALA00.0250.01924.0380.4940.4940.0000.0000.0000.000
86A125ILE00.0020.00519.9120.3780.3780.0000.0000.0000.000
87A126ASP-1-0.887-0.94324.409-12.266-12.2660.0000.0000.0000.000
88A127ALA00.0040.01327.0860.4380.4380.0000.0000.0000.000
89A128ILE00.0200.00125.8920.4060.4060.0000.0000.0000.000
90A129PHE0-0.016-0.00723.8930.3320.3320.0000.0000.0000.000
91A130ALA0-0.090-0.03429.3740.3480.3480.0000.0000.0000.000
92A131GLN0-0.023-0.02632.2740.3560.3560.0000.0000.0000.000
93A132SER0-0.043-0.04431.5330.3950.3950.0000.0000.0000.000
94A133ALA0-0.033-0.01233.5610.0470.0470.0000.0000.0000.000
95A134GLY0-0.038-0.01332.0960.0220.0220.0000.0000.0000.000
96A135ASN0-0.061-0.04331.8380.1420.1420.0000.0000.0000.000
97A136GLY00.012-0.00432.0880.1700.1700.0000.0000.0000.000
98A137GLY0-0.097-0.03533.0040.1500.1500.0000.0000.0000.000
99A138GLY00.001-0.01232.3160.1320.1320.0000.0000.0000.000
100A139LEU0-0.0060.02030.3960.1590.1590.0000.0000.0000.000
101A140PRO00.0520.02034.3460.1460.1460.0000.0000.0000.000
102A141GLY00.0090.00937.349-0.039-0.0390.0000.0000.0000.000
103A142GLY0-0.018-0.00833.720-0.043-0.0430.0000.0000.0000.000
104A143THR0-0.056-0.02532.920-0.257-0.2570.0000.0000.0000.000
105A144LEU0-0.010-0.00828.572-0.030-0.0300.0000.0000.0000.000
106A145ASP-1-0.921-0.95632.747-8.482-8.4820.0000.0000.0000.000
107A146PHE0-0.021-0.03126.570-0.365-0.3650.0000.0000.0000.000
108A147PRO00.0220.01632.200-0.156-0.1560.0000.0000.0000.000
109A148GLU-1-0.927-0.96230.872-9.471-9.4710.0000.0000.0000.000
110A149LEU0-0.097-0.03926.420-0.328-0.3280.0000.0000.0000.000
111A150ASP-1-0.856-0.92830.055-9.017-9.0170.0000.0000.0000.000
112A151GLN00.0320.00030.873-0.292-0.2920.0000.0000.0000.000
113A152ALA00.0690.03832.291-0.088-0.0880.0000.0000.0000.000
114A153ARG10.8540.93725.98110.83210.8320.0000.0000.0000.000
115A154LEU0-0.033-0.02126.049-0.295-0.2950.0000.0000.0000.000
116A155GLU-1-0.858-0.93228.158-9.300-9.3000.0000.0000.0000.000
117A156LYS10.9140.96330.1569.0479.0470.0000.0000.0000.000
118A158ALA00.0400.02025.483-0.275-0.2750.0000.0000.0000.000
119A159LYS10.7550.85326.4969.1449.1440.0000.0000.0000.000
120A160ASP-1-0.819-0.89427.581-9.473-9.4730.0000.0000.0000.000
121A161ASN0-0.024-0.00821.249-0.293-0.2930.0000.0000.0000.000
122A162GLU-1-0.856-0.94221.959-11.598-11.5980.0000.0000.0000.000
123A163LEU0-0.039-0.00717.555-0.437-0.4370.0000.0000.0000.000
124A164ILE00.0720.02917.176-0.591-0.5910.0000.0000.0000.000
125A165ASP-1-0.801-0.87618.205-12.702-12.7020.0000.0000.0000.000
126A166SER0-0.036-0.04516.350-0.069-0.0690.0000.0000.0000.000
127A167ASP-1-0.904-0.93913.401-18.928-18.9280.0000.0000.0000.000
128A168ILE0-0.036-0.02414.338-0.723-0.7230.0000.0000.0000.000
129A169LYS10.8610.92116.66212.33312.3330.0000.0000.0000.000
130A170LEU00.0390.0289.499-0.140-0.1400.0000.0000.0000.000
131A171ASP-1-0.779-0.86411.831-22.335-22.3350.0000.0000.0000.000
132A172ILE00.0100.00613.609-0.034-0.0340.0000.0000.0000.000
133A173ASP-1-0.866-0.91214.795-14.476-14.4760.0000.0000.0000.000
134A174ILE0-0.041-0.0288.890-0.286-0.2860.0000.0000.0000.000
135A175ALA00.0010.01112.898-0.106-0.1060.0000.0000.0000.000
136A176ARG10.9040.93315.56513.82113.8210.0000.0000.0000.000
137A177SER0-0.078-0.03413.5510.1200.1200.0000.0000.0000.000
138A178LYS10.9080.9579.76423.59823.5980.0000.0000.0000.000
139A179GLY00.0150.00415.8510.1850.1850.0000.0000.0000.000
140A180ILE0-0.092-0.04115.2580.3750.3750.0000.0000.0000.000
141A181THR0-0.006-0.01119.5420.3190.3190.0000.0000.0000.000
142A182ALA00.0220.02722.4720.4760.4760.0000.0000.0000.000
143A183THR00.0010.04121.085-0.520-0.5200.0000.0000.0000.000
144A184PRO00.021-0.00920.5230.6730.6730.0000.0000.0000.000
145A185THR0-0.007-0.02417.2340.4510.4510.0000.0000.0000.000
146A186LEU0-0.025-0.00815.365-0.799-0.7990.0000.0000.0000.000
147A187VAL0-0.030-0.02210.1210.3070.3070.0000.0000.0000.000
148A188ILE00.0270.02410.982-1.717-1.7170.0000.0000.0000.000
149A189ARG10.8770.9253.66241.97742.2220.002-0.033-0.2140.000
150A190ASP-1-0.711-0.8446.830-36.383-36.3830.0000.0000.0000.000
151A191ASN0-0.083-0.0562.933-22.001-19.6980.124-1.277-1.148-0.012
152A192GLN00.0060.0122.524-23.931-20.0960.565-2.547-1.853-0.034
153A193THR0-0.043-0.0395.2190.8170.859-0.0010.000-0.0410.000
154A194GLY0-0.020-0.0024.1830.9601.062-0.001-0.015-0.0860.000
155A195ARG10.8640.9645.13224.95825.007-0.0010.000-0.0470.000
156A196SER0-0.002-0.0188.090-3.137-3.1370.0000.0000.0000.000
157A197VAL00.0130.0139.7981.5811.5810.0000.0000.0000.000
158A198LYS10.8810.95113.38715.51015.5100.0000.0000.0000.000
159A199LEU0-0.016-0.01215.5630.8680.8680.0000.0000.0000.000
160A200GLU-1-0.939-0.96518.688-13.599-13.5990.0000.0000.0000.000
161A201GLY00.0430.02121.3990.5340.5340.0000.0000.0000.000
162A202MET0-0.056-0.02321.851-0.551-0.5510.0000.0000.0000.000
163A203ALA0-0.0200.00720.1000.4420.4420.0000.0000.0000.000
164A204ASP-1-0.732-0.82322.037-12.730-12.7300.0000.0000.0000.000
165A205GLU-1-0.902-0.96521.934-13.059-13.0590.0000.0000.0000.000
166A206THR00.001-0.01521.855-0.506-0.5060.0000.0000.0000.000
167A207THR0-0.018-0.01520.427-0.350-0.3500.0000.0000.0000.000
168A208LEU0-0.036-0.00916.827-0.865-0.8650.0000.0000.0000.000
169A209LEU0-0.009-0.00717.451-1.052-1.0520.0000.0000.0000.000
170A210SER0-0.026-0.03418.662-0.477-0.4770.0000.0000.0000.000
171A211ALA0-0.0040.00716.173-0.340-0.3400.0000.0000.0000.000
172A212ILE00.0370.00713.101-1.061-1.0610.0000.0000.0000.000
173A213ASP-1-0.803-0.88914.592-15.994-15.9940.0000.0000.0000.000
174A214TRP0-0.011-0.01113.742-0.510-0.5100.0000.0000.0000.000
175A215LEU0-0.111-0.06110.322-0.418-0.4180.0000.0000.0000.000
176A216ALA0-0.002-0.01011.506-0.908-0.9080.0000.0000.0000.000
177A217LYS10.8700.94213.57415.78915.7890.0000.0000.0000.000
178A218ASP-1-0.938-0.96816.775-15.386-15.3860.0000.0000.0000.000
179A219LEU0-0.122-0.06911.231-0.286-0.2860.0000.0000.0000.000
180A220LEU00.008-0.00413.426-1.632-1.6320.0000.0000.0000.000
181A221GLU-1-0.975-0.96115.629-18.270-18.2700.0000.0000.0000.000