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: 7629K

Calculation Name: 3H8N-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3H8N

Chain ID: A

ChEMBL ID:

UniProt ID: P43632

Base Structure: X-ray

Registration Date: 2023-09-21

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 -1988857.04797
FMO2-HF: Nuclear repulsion 1912497.801996
FMO2-HF: Total energy -76359.245975
FMO2-MP2: Total energy -76579.31516


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:6:ARG)


Summations of interaction energy for fragment #1(A:6: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.
-83.548-77.1814.867-3.198-8.038-0.003
Interaction energy analysis for fragmet #1(A:6:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.959 / q_NPA : 0.970
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].
3A8PRO0-0.005-0.0073.7650.0161.642-0.022-0.599-1.0050.000
4A9SER0-0.006-0.0066.6061.8371.8370.0000.0000.0000.000
5A10PHE0-0.057-0.0488.709-0.140-0.1400.0000.0000.0000.000
6A11LEU00.0280.02211.8370.8820.8820.0000.0000.0000.000
7A12ALA00.0230.01215.261-0.136-0.1360.0000.0000.0000.000
8A13LEU0-0.055-0.00418.8770.2730.2730.0000.0000.0000.000
9A14PRO00.0500.00421.7320.0560.0560.0000.0000.0000.000
10A15GLY00.0520.01521.594-0.274-0.2740.0000.0000.0000.000
11A16HIS10.8200.90420.17612.27312.2730.0000.0000.0000.000
12A17LEU0-0.043-0.00522.1240.1280.1280.0000.0000.0000.000
13A18VAL00.0150.00525.1750.1510.1510.0000.0000.0000.000
14A19LYS10.9670.98827.9098.8278.8270.0000.0000.0000.000
15A20SER00.0720.02331.016-0.291-0.2910.0000.0000.0000.000
16A21GLU-1-1.003-1.00832.517-8.246-8.2460.0000.0000.0000.000
17A22GLU-1-0.919-0.93830.397-9.560-9.5600.0000.0000.0000.000
18A23THR0-0.051-0.02827.205-0.164-0.1640.0000.0000.0000.000
19A24VAL0-0.0040.01022.3240.0860.0860.0000.0000.0000.000
20A25ILE0-0.008-0.01119.947-0.282-0.2820.0000.0000.0000.000
21A26LEU0-0.003-0.00516.894-0.180-0.1800.0000.0000.0000.000
22A27GLN0-0.013-0.01014.756-0.831-0.8310.0000.0000.0000.000
23A28CYS0-0.043-0.00610.1250.3310.3310.0000.0000.0000.000
24A29TRP00.0180.00010.597-0.116-0.1160.0000.0000.0000.000
25A30SER0-0.056-0.0265.539-2.380-2.3800.0000.0000.0000.000
26A31ASP-1-0.818-0.8876.461-27.671-27.6710.0000.0000.0000.000
27A32VAL0-0.081-0.0382.602-2.460-1.3920.181-0.310-0.939-0.004
28A33MET00.0440.0085.7611.9611.9610.0000.0000.0000.000
29A34PHE0-0.078-0.0362.705-6.909-5.4620.312-0.492-1.2670.000
30A35GLU-1-0.868-0.9166.992-24.742-24.7420.0000.0000.0000.000
31A36HIS10.8390.9008.89726.90726.9070.0000.0000.0000.000
32A37PHE00.0310.0138.738-3.750-3.7500.0000.0000.0000.000
33A38LEU0-0.024-0.01810.7032.4962.4960.0000.0000.0000.000
34A39LEU00.0030.00611.714-1.202-1.2020.0000.0000.0000.000
35A40HIS0-0.023-0.02813.6891.3241.3240.0000.0000.0000.000
36A41ARG10.8620.95315.24013.08613.0860.0000.0000.0000.000
37A42GLU-1-0.879-0.96415.148-16.964-16.9640.0000.0000.0000.000
38A43GLY00.0140.00719.1710.5870.5870.0000.0000.0000.000
39A44LYS10.9310.94222.59210.31810.3180.0000.0000.0000.000
40A45PHE00.0150.01024.996-0.095-0.0950.0000.0000.0000.000
41A46ASN00.0020.03719.6000.2510.2510.0000.0000.0000.000
42A47ASN00.018-0.01419.8770.3960.3960.0000.0000.0000.000
43A48THR00.0100.01315.017-0.747-0.7470.0000.0000.0000.000
44A49LEU0-0.0240.00616.8560.6630.6630.0000.0000.0000.000
45A50HIS00.0600.02313.829-2.164-2.1640.0000.0000.0000.000
46A51LEU0-0.005-0.00214.7121.2321.2320.0000.0000.0000.000
47A52ILE0-0.020-0.01013.752-1.616-1.6160.0000.0000.0000.000
48A53GLY0-0.038-0.01113.6460.5100.5100.0000.0000.0000.000
49A54GLU-1-0.888-0.94312.889-21.831-21.8310.0000.0000.0000.000
50A55HIS00.0440.04010.844-1.328-1.3280.0000.0000.0000.000
51A56HIS0-0.099-0.05413.8141.5541.5540.0000.0000.0000.000
52A57ASP-1-0.880-0.94114.992-19.350-19.3500.0000.0000.0000.000
53A58GLY0-0.0380.00213.9711.0631.0630.0000.0000.0000.000
54A59VAL0-0.010-0.00511.614-1.660-1.6600.0000.0000.0000.000
55A60SER00.007-0.0149.3200.9890.9890.0000.0000.0000.000
56A61LYS10.9470.96111.40616.96816.9680.0000.0000.0000.000
57A62ALA00.0220.02413.4920.5680.5680.0000.0000.0000.000
58A63ASN0-0.021-0.01415.264-0.592-0.5920.0000.0000.0000.000
59A64PHE00.032-0.00313.8590.5700.5700.0000.0000.0000.000
60A65SER0-0.0100.00919.1010.3560.3560.0000.0000.0000.000
61A66ILE0-0.004-0.00420.515-0.141-0.1410.0000.0000.0000.000
62A67GLY00.0500.01923.8530.2540.2540.0000.0000.0000.000
63A68PRO0-0.009-0.03027.549-0.140-0.1400.0000.0000.0000.000
64A69MET0-0.0590.00425.158-0.159-0.1590.0000.0000.0000.000
65A70MET00.0510.01728.7780.4660.4660.0000.0000.0000.000
66A71PRO00.0400.01028.600-0.438-0.4380.0000.0000.0000.000
67A72VAL0-0.0110.00927.684-0.200-0.2000.0000.0000.0000.000
68A73LEU0-0.064-0.02524.520-0.475-0.4750.0000.0000.0000.000
69A74ALA00.0290.03823.808-0.499-0.4990.0000.0000.0000.000
70A75GLY00.0330.00222.6980.0650.0650.0000.0000.0000.000
71A76THR0-0.018-0.01416.536-0.001-0.0010.0000.0000.0000.000
72A77TYR0-0.055-0.05516.020-0.337-0.3370.0000.0000.0000.000
73A78ARG10.8910.9599.78320.64920.6490.0000.0000.0000.000
74A80TYR00.0010.0036.995-1.165-1.1650.0000.0000.0000.000
75A81GLY00.0340.0255.7503.2903.2900.0000.0000.0000.000
76A82SER0-0.012-0.0224.897-5.517-5.5170.0000.0000.0000.000
77A83VAL00.0780.0314.133-0.778-0.665-0.001-0.011-0.1020.000
78A84PRO0-0.0130.0096.4003.7003.7000.0000.0000.0000.000
79A85HIS00.010-0.0019.3580.8880.8880.0000.0000.0000.000
80A86SER0-0.0190.05912.056-0.767-0.7670.0000.0000.0000.000
81A87PRO0-0.005-0.05213.0830.2990.2990.0000.0000.0000.000
82A88TYR0-0.012-0.0278.5710.4880.4880.0000.0000.0000.000
83A89GLN00.013-0.0045.243-3.630-3.6300.0000.0000.0000.000
84A90LEU0-0.058-0.0114.930-5.479-5.408-0.001-0.003-0.0670.000
85A91SER0-0.044-0.0342.050-5.567-4.7532.337-0.975-2.1770.004
86A92ALA0-0.062-0.0262.2936.0757.1332.059-0.767-2.350-0.003
87A93PRO00.0720.0323.978-0.866-0.6960.002-0.041-0.1310.000
88A94SER00.0550.0415.892-1.879-1.8790.0000.0000.0000.000
89A95ASP-1-0.876-0.9398.432-20.957-20.9570.0000.0000.0000.000
90A96PRO0-0.024-0.01410.533-0.137-0.1370.0000.0000.0000.000
91A97LEU00.0140.01414.0180.5780.5780.0000.0000.0000.000
92A98ASP-1-0.836-0.91116.705-13.877-13.8770.0000.0000.0000.000
93A99MET0-0.0220.00118.6340.4800.4800.0000.0000.0000.000
94A100VAL00.0230.00522.6540.2400.2400.0000.0000.0000.000
95A101ILE00.0290.03425.9600.0380.0380.0000.0000.0000.000
96A102ILE0-0.013-0.00928.9830.3270.3270.0000.0000.0000.000
97A103GLY0-0.099-0.07531.5270.0650.0650.0000.0000.0000.000
98A104LEU00.0340.02633.3520.0910.0910.0000.0000.0000.000
99A105TYR00.0250.02135.1310.2340.2340.0000.0000.0000.000
100A106GLU-1-0.894-0.94538.950-6.855-6.8550.0000.0000.0000.000
101A107LYS10.8710.94738.5597.0267.0260.0000.0000.0000.000
102A108PRO0-0.0120.00036.5010.1870.1870.0000.0000.0000.000
103A109SER0-0.041-0.02039.783-0.013-0.0130.0000.0000.0000.000
104A110LEU00.027-0.00735.670-0.113-0.1130.0000.0000.0000.000
105A111SER0-0.034-0.00939.7570.1500.1500.0000.0000.0000.000
106A112ALA00.0410.01540.189-0.127-0.1270.0000.0000.0000.000
107A113GLN00.0110.04241.1040.2680.2680.0000.0000.0000.000
108A114PRO00.029-0.00441.670-0.148-0.1480.0000.0000.0000.000
109A115GLY00.046-0.00443.2780.1380.1380.0000.0000.0000.000
110A116PRO0-0.020-0.00940.747-0.122-0.1220.0000.0000.0000.000
111A117THR0-0.016-0.00140.280-0.147-0.1470.0000.0000.0000.000
112A118VAL0-0.0050.01238.0620.1220.1220.0000.0000.0000.000
113A119GLN00.0590.04240.654-0.005-0.0050.0000.0000.0000.000
114A120ALA00.021-0.01837.596-0.099-0.0990.0000.0000.0000.000
115A121GLY0-0.019-0.01536.6600.1350.1350.0000.0000.0000.000
116A122GLU-1-0.908-0.95137.661-6.731-6.7310.0000.0000.0000.000
117A123ASN0-0.026-0.01736.566-0.359-0.3590.0000.0000.0000.000
118A124VAL00.0050.01237.0580.1660.1660.0000.0000.0000.000
119A125THR0-0.001-0.00436.840-0.243-0.2430.0000.0000.0000.000
120A126LEU0-0.0270.00134.4100.1570.1570.0000.0000.0000.000
121A127SER0-0.004-0.04237.068-0.119-0.1190.0000.0000.0000.000
122A128CYS0-0.070-0.01832.143-0.190-0.1900.0000.0000.0000.000
123A129SER00.0130.00238.4850.1110.1110.0000.0000.0000.000
124A130SER00.0530.01641.132-0.023-0.0230.0000.0000.0000.000
125A131ARG10.9380.97743.1166.1436.1430.0000.0000.0000.000
126A132SER00.0100.01242.0000.0600.0600.0000.0000.0000.000
127A133SER0-0.013-0.02842.0200.0280.0280.0000.0000.0000.000
128A134TYR0-0.058-0.01336.979-0.145-0.1450.0000.0000.0000.000
129A135ASP-1-0.774-0.88835.533-7.872-7.8720.0000.0000.0000.000
130A136MET0-0.123-0.04130.603-0.117-0.1170.0000.0000.0000.000
131A137TYR00.014-0.00233.3480.0780.0780.0000.0000.0000.000
132A138HIS10.8660.90727.7049.5259.5250.0000.0000.0000.000
133A139LEU00.0050.00629.5330.1850.1850.0000.0000.0000.000
134A140SER00.000-0.00727.371-0.236-0.2360.0000.0000.0000.000
135A141ARG10.8810.95026.6969.9529.9520.0000.0000.0000.000
136A142GLU-1-0.865-0.96227.031-9.204-9.2040.0000.0000.0000.000
137A143GLY0-0.020-0.00225.3680.0530.0530.0000.0000.0000.000
138A144GLU-1-0.933-0.95822.463-11.010-11.0100.0000.0000.0000.000
139A145ALA0-0.021-0.01618.8130.0800.0800.0000.0000.0000.000
140A146HIS0-0.007-0.00416.442-0.001-0.0010.0000.0000.0000.000
141A147GLU-1-0.795-0.90521.751-10.940-10.9400.0000.0000.0000.000
142A148ARG10.9060.96725.2209.2229.2220.0000.0000.0000.000
143A149ARG10.9570.97223.78711.03911.0390.0000.0000.0000.000
144A150LEU0-0.0120.00029.091-0.072-0.0720.0000.0000.0000.000
145A151PRO00.0320.00532.290-0.013-0.0130.0000.0000.0000.000
146A152ALA0-0.053-0.01734.7630.1430.1430.0000.0000.0000.000
147A153VAL00.0410.03137.8930.0510.0510.0000.0000.0000.000
148A154ARG10.9520.97740.9786.3546.3540.0000.0000.0000.000
149A155SER0-0.018-0.00944.3160.1320.1320.0000.0000.0000.000
150A156ILE00.0530.01547.3890.0100.0100.0000.0000.0000.000
151A157ASN0-0.001-0.00550.0660.1440.1440.0000.0000.0000.000
152A158GLY0-0.058-0.03249.2030.0510.0510.0000.0000.0000.000
153A159THR0-0.066-0.02344.475-0.037-0.0370.0000.0000.0000.000
154A160PHE00.0260.02041.1440.0180.0180.0000.0000.0000.000
155A161GLN00.021-0.01440.433-0.034-0.0340.0000.0000.0000.000
156A162ALA00.0040.01235.760-0.056-0.0560.0000.0000.0000.000
157A163ASP-1-0.808-0.85537.589-7.119-7.1190.0000.0000.0000.000
158A164PHE0-0.033-0.03530.907-0.185-0.1850.0000.0000.0000.000
159A165PRO00.0020.01833.7460.0750.0750.0000.0000.0000.000
160A166LEU0-0.064-0.05632.080-0.301-0.3010.0000.0000.0000.000
161A167GLY0-0.0030.01332.116-0.212-0.2120.0000.0000.0000.000
162A168PRO0-0.002-0.00632.3510.1400.1400.0000.0000.0000.000
163A169ALA00.0020.00333.334-0.231-0.2310.0000.0000.0000.000
164A170THR00.0390.02630.3510.0690.0690.0000.0000.0000.000
165A171HIS0-0.011-0.01429.5590.0280.0280.0000.0000.0000.000
166A172GLY00.0350.02232.568-0.003-0.0030.0000.0000.0000.000
167A173GLY00.009-0.00331.742-0.329-0.3290.0000.0000.0000.000
168A174THR00.0290.02231.9460.3180.3180.0000.0000.0000.000
169A175TYR00.008-0.01330.670-0.384-0.3840.0000.0000.0000.000
170A176ARG10.8850.94131.8728.9138.9130.0000.0000.0000.000
171A178PHE00.0270.00930.1780.1440.1440.0000.0000.0000.000
172A179GLY00.0610.01833.378-0.060-0.0600.0000.0000.0000.000
173A180SER00.0050.01131.924-0.218-0.2180.0000.0000.0000.000
174A181PHE00.0310.02034.0060.1430.1430.0000.0000.0000.000
175A182ARG10.9120.95132.1808.5428.5420.0000.0000.0000.000
176A183ASP-1-0.954-0.97432.098-8.760-8.7600.0000.0000.0000.000
177A184ALA00.0470.03330.731-0.284-0.2840.0000.0000.0000.000
178A185PRO0-0.045-0.02226.9810.0030.0030.0000.0000.0000.000
179A186TYR0-0.071-0.02721.3940.0910.0910.0000.0000.0000.000
180A187GLU-1-0.902-0.95427.578-9.640-9.6400.0000.0000.0000.000
181A188TRP0-0.061-0.05026.4020.2610.2610.0000.0000.0000.000
182A189SER00.0500.01232.3710.0410.0410.0000.0000.0000.000
183A190ASN0-0.050-0.01434.248-0.374-0.3740.0000.0000.0000.000
184A191SER00.001-0.01533.420-0.043-0.0430.0000.0000.0000.000
185A192SER0-0.0030.00635.1760.1130.1130.0000.0000.0000.000
186A193ASP-1-0.882-0.93437.012-7.237-7.2370.0000.0000.0000.000
187A194PRO0-0.037-0.02835.810-0.055-0.0550.0000.0000.0000.000
188A195LEU00.0200.03336.5290.2020.2020.0000.0000.0000.000
189A196LEU0-0.0070.00236.032-0.232-0.2320.0000.0000.0000.000
190A197VAL0-0.011-0.00835.5170.1830.1830.0000.0000.0000.000
191A198SER0-0.044-0.02336.528-0.168-0.1680.0000.0000.0000.000
192A199VAL00.0120.01135.1840.1220.1220.0000.0000.0000.000
193A200THR0-0.035-0.00438.3490.0060.0060.0000.0000.0000.000