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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: 85K3Y

Calculation Name: 3U9P-H-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3U9P

Chain ID: H

ChEMBL ID:

UniProt ID: P11672

Base Structure: X-ray

Registration Date: 2023-06-26

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 187
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1844676.792691
FMO2-HF: Nuclear repulsion 1772148.412715
FMO2-HF: Total energy -72528.379977
FMO2-MP2: Total energy -72738.422267


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(H:1:GLU)


Summations of interaction energy for fragment #1(H:1:GLU)
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.
-88.102-86.29-0.018-0.905-0.8890.005
Interaction energy analysis for fragmet #1(H:1:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.931 / q_NPA : -0.962
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].
3H3LYS10.8630.9213.843-30.599-28.886-0.016-0.865-0.8320.005
4H4LEU00.0260.0146.465-1.960-1.9600.0000.0000.0000.000
5H5GLN0-0.031-0.01310.2390.3750.3750.0000.0000.0000.000
6H6GLU-1-0.679-0.83212.31417.72617.7260.0000.0000.0000.000
7H7SER0-0.033-0.01716.096-0.087-0.0870.0000.0000.0000.000
8H8GLY00.0210.00318.557-0.369-0.3690.0000.0000.0000.000
9H9PRO0-0.022-0.02122.203-0.025-0.0250.0000.0000.0000.000
10H10SER00.0480.01623.815-0.051-0.0510.0000.0000.0000.000
11H11LEU0-0.033-0.00125.848-0.162-0.1620.0000.0000.0000.000
12H12VAL0-0.037-0.00928.996-0.070-0.0700.0000.0000.0000.000
13H13GLN00.0250.01031.750-0.201-0.2010.0000.0000.0000.000
14H14PRO00.029-0.00335.2840.1030.1030.0000.0000.0000.000
15H15SER0-0.026-0.01036.922-0.208-0.2080.0000.0000.0000.000
16H16GLN0-0.0010.03333.789-0.052-0.0520.0000.0000.0000.000
17H17THR0-0.028-0.04330.2800.0060.0060.0000.0000.0000.000
18H18LEU00.0170.02725.5800.0870.0870.0000.0000.0000.000
19H19SER0-0.010-0.02425.751-0.084-0.0840.0000.0000.0000.000
20H20LEU00.0100.03520.7840.1530.1530.0000.0000.0000.000
21H21THR0-0.038-0.04617.489-0.327-0.3270.0000.0000.0000.000
22H22CYS0-0.075-0.02014.3130.4660.4660.0000.0000.0000.000
23H23THR00.0200.02811.323-0.670-0.6700.0000.0000.0000.000
24H24VAL0-0.019-0.0169.9030.9790.9790.0000.0000.0000.000
25H25SER00.0170.0095.203-0.924-0.9240.0000.0000.0000.000
26H26GLY00.0870.0334.6041.8551.840-0.001-0.0310.0470.000
27H27PHE0-0.043-0.0255.226-0.428-0.314-0.001-0.009-0.1040.000
28H28SER00.0730.0428.496-1.235-1.2350.0000.0000.0000.000
29H29LEU00.0650.03012.141-0.339-0.3390.0000.0000.0000.000
30H30THR00.006-0.00315.078-0.579-0.5790.0000.0000.0000.000
31H31SER0-0.041-0.01513.513-0.326-0.3260.0000.0000.0000.000
32H32ASN0-0.051-0.04111.7421.2831.2830.0000.0000.0000.000
33H33SER0-0.0170.00214.939-0.878-0.8780.0000.0000.0000.000
34H34VAL00.0180.01113.7331.0721.0720.0000.0000.0000.000
35H35HIS00.0040.00216.353-1.454-1.4540.0000.0000.0000.000
36H36TRP00.0050.00017.8480.8640.8640.0000.0000.0000.000
37H37VAL0-0.014-0.00519.393-0.656-0.6560.0000.0000.0000.000
38H38ARG10.8180.91120.657-10.225-10.2250.0000.0000.0000.000
39H39GLN00.016-0.00122.2710.2600.2600.0000.0000.0000.000
40H40PRO00.0380.02024.6920.1110.1110.0000.0000.0000.000
41H41PRO00.0060.02427.5710.1910.1910.0000.0000.0000.000
42H42GLY0-0.011-0.01728.209-0.380-0.3800.0000.0000.0000.000
43H43GLN0-0.024-0.00929.279-0.088-0.0880.0000.0000.0000.000
44H44GLY00.0220.00826.3240.3260.3260.0000.0000.0000.000
45H45LEU0-0.028-0.02020.7240.0580.0580.0000.0000.0000.000
46H46GLU-1-0.830-0.91424.58510.20010.2000.0000.0000.0000.000
47H47TRP0-0.0160.00721.7590.1130.1130.0000.0000.0000.000
48H48MET0-0.0180.01323.064-0.699-0.6990.0000.0000.0000.000
49H49GLY00.033-0.01123.628-0.588-0.5880.0000.0000.0000.000
50H50GLY00.0170.00821.2250.6730.6730.0000.0000.0000.000
51H51ILE0-0.0410.00019.269-0.594-0.5940.0000.0000.0000.000
52H52TRP00.034-0.01219.5061.1501.1500.0000.0000.0000.000
53H53GLY00.0230.02418.353-0.158-0.1580.0000.0000.0000.000
54H54ASP-1-0.794-0.88619.23412.10512.1050.0000.0000.0000.000
55H55GLY0-0.043-0.03222.079-0.432-0.4320.0000.0000.0000.000
56H56ARG10.8970.94823.493-11.716-11.7160.0000.0000.0000.000
57H57THR00.001-0.00924.1120.5190.5190.0000.0000.0000.000
58H58ASP-1-0.894-0.95225.34510.01710.0170.0000.0000.0000.000
59H59TYR00.0280.00325.9560.4340.4340.0000.0000.0000.000
60H60ASN00.0270.00528.003-0.498-0.4980.0000.0000.0000.000
61H61SER00.006-0.01929.661-0.079-0.0790.0000.0000.0000.000
62H62ALA00.0090.01632.672-0.230-0.2300.0000.0000.0000.000
63H63LEU0-0.020-0.02428.612-0.172-0.1720.0000.0000.0000.000
64H64LYS10.8860.96130.762-9.745-9.7450.0000.0000.0000.000
65H65SER0-0.028-0.01632.7280.0820.0820.0000.0000.0000.000
66H66ARG10.9140.96632.480-9.261-9.2610.0000.0000.0000.000
67H67LEU0-0.008-0.00425.9760.1250.1250.0000.0000.0000.000
68H68SER0-0.046-0.01128.344-0.049-0.0490.0000.0000.0000.000
69H69ILE00.0070.01122.0760.3020.3020.0000.0000.0000.000
70H70SER00.0060.01323.462-0.174-0.1740.0000.0000.0000.000
71H71ARG10.8640.91818.626-13.698-13.6980.0000.0000.0000.000
72H72ASP-1-0.811-0.91119.17012.65412.6540.0000.0000.0000.000
73H73THR00.005-0.01517.0480.6770.6770.0000.0000.0000.000
74H74SER0-0.0220.00916.2850.6050.6050.0000.0000.0000.000
75H75LYS10.8760.94216.094-12.155-12.1550.0000.0000.0000.000
76H76SER0-0.0280.00411.4460.5840.5840.0000.0000.0000.000
77H77GLN0-0.029-0.02613.6730.3040.3040.0000.0000.0000.000
78H78VAL00.002-0.00516.053-0.586-0.5860.0000.0000.0000.000
79H79PHE00.0080.00818.4750.2600.2600.0000.0000.0000.000
80H80LEU00.0000.00221.557-0.093-0.0930.0000.0000.0000.000
81H81LYS10.9740.97724.050-10.008-10.0080.0000.0000.0000.000
82H82MET00.0280.01927.340-0.136-0.1360.0000.0000.0000.000
83H83ASN0-0.0410.00129.896-0.025-0.0250.0000.0000.0000.000
84H84SER00.0130.02733.480-0.272-0.2720.0000.0000.0000.000
85H85LEU0-0.065-0.03933.8010.0510.0510.0000.0000.0000.000
86H86GLN00.011-0.03335.202-0.259-0.2590.0000.0000.0000.000
87H87THR00.0450.01834.834-0.074-0.0740.0000.0000.0000.000
88H88ASH0-0.0150.00833.9920.1230.1230.0000.0000.0000.000
89H89ASP-1-0.785-0.88430.2239.6789.6780.0000.0000.0000.000
90H90THR0-0.043-0.00529.0410.3670.3670.0000.0000.0000.000
91H91ALA0-0.010-0.01525.698-0.099-0.0990.0000.0000.0000.000
92H92ILE00.0130.02320.4130.0850.0850.0000.0000.0000.000
93H93TYR0-0.049-0.06621.227-0.129-0.1290.0000.0000.0000.000
94H94PHE00.0330.02915.9830.4020.4020.0000.0000.0000.000
95H96THR0-0.003-0.01113.5431.0031.0030.0000.0000.0000.000
96H97ARG10.9000.9358.267-28.315-28.3150.0000.0000.0000.000
97H98CYS0-0.0190.02613.6180.3940.3940.0000.0000.0000.000
98H99ARG10.8750.93611.559-24.202-24.2020.0000.0000.0000.000
99H100ARG10.8990.92814.306-19.015-19.0150.0000.0000.0000.000
100H101ASP-1-0.839-0.91214.46418.79718.7970.0000.0000.0000.000
101H102SER0-0.039-0.01614.8400.3640.3640.0000.0000.0000.000
102H103SER0-0.007-0.01217.046-0.504-0.5040.0000.0000.0000.000
103H104TYR0-0.061-0.03617.964-0.640-0.6400.0000.0000.0000.000
104H105VAL00.0510.04015.776-0.404-0.4040.0000.0000.0000.000
105H106VAL00.014-0.01015.3270.8100.8100.0000.0000.0000.000
106H107ASP-1-0.804-0.88611.85224.56524.5650.0000.0000.0000.000
107H108ALA0-0.021-0.0148.9132.4522.4520.0000.0000.0000.000
108H109TRP00.0340.00010.416-2.307-2.3070.0000.0000.0000.000
109H110GLY0-0.0320.00110.9331.8061.8060.0000.0000.0000.000
110H111GLN0-0.024-0.01112.1021.4011.4010.0000.0000.0000.000
111H112GLY00.0500.01014.135-0.638-0.6380.0000.0000.0000.000
112H113ALA0-0.066-0.02517.567-0.095-0.0950.0000.0000.0000.000
113H114SER0-0.0150.00119.866-0.507-0.5070.0000.0000.0000.000
114H115VAL00.0320.01023.262-0.055-0.0550.0000.0000.0000.000
115H116THR0-0.009-0.01026.226-0.251-0.2510.0000.0000.0000.000
116H117VAL0-0.017-0.00229.874-0.020-0.0200.0000.0000.0000.000
117H118SER0-0.011-0.02432.662-0.278-0.2780.0000.0000.0000.000
118H119SER00.0460.01935.8370.1030.1030.0000.0000.0000.000
119H120ALA0-0.0180.00137.316-0.064-0.0640.0000.0000.0000.000
120H121LYS10.9240.96936.777-7.849-7.8490.0000.0000.0000.000
121H122THR00.0170.00431.8540.0900.0900.0000.0000.0000.000
122H123THR0-0.004-0.00734.481-0.384-0.3840.0000.0000.0000.000
123H124PRO00.0170.02133.1020.2100.2100.0000.0000.0000.000
124H125LYN00.004-0.02928.729-0.140-0.1400.0000.0000.0000.000
125H126LEU00.0170.02933.648-0.100-0.1000.0000.0000.0000.000
126H127VAL0-0.012-0.00332.260-0.001-0.0010.0000.0000.0000.000
127H128TYR00.025-0.01335.123-0.251-0.2510.0000.0000.0000.000
128H129PRO0-0.018-0.00635.9610.2710.2710.0000.0000.0000.000
129H130LEU0-0.011-0.00936.976-0.252-0.2520.0000.0000.0000.000
130H131ALA00.0440.01537.8750.2250.2250.0000.0000.0000.000
131H132PRO00.0250.02839.983-0.217-0.2170.0000.0000.0000.000
132H141VAL00.003-0.00936.020-0.060-0.0600.0000.0000.0000.000
133H142THR0-0.033-0.01135.6210.3210.3210.0000.0000.0000.000
134H143LEU00.0110.00334.438-0.292-0.2920.0000.0000.0000.000
135H144GLY00.0530.02433.7300.3520.3520.0000.0000.0000.000
136H145CYS0-0.029-0.00528.2090.1160.1160.0000.0000.0000.000
137H146LEU00.0120.00134.0320.0760.0760.0000.0000.0000.000
138H147VAL0-0.005-0.01330.699-0.121-0.1210.0000.0000.0000.000
139H148LYS10.9890.97933.959-7.783-7.7830.0000.0000.0000.000
140H149GLY00.0520.02636.5990.0060.0060.0000.0000.0000.000
141H150TYR00.0390.03530.394-0.116-0.1160.0000.0000.0000.000
142H151PHE00.0180.02733.085-0.062-0.0620.0000.0000.0000.000
143H152PRO0-0.046-0.01829.227-0.075-0.0750.0000.0000.0000.000
144H153GLU-1-0.803-0.91527.59411.00811.0080.0000.0000.0000.000
145H154PRO0-0.027-0.01223.3700.0670.0670.0000.0000.0000.000
146H155VAL00.006-0.02026.234-0.132-0.1320.0000.0000.0000.000
147H156THR0-0.039-0.01320.5970.4460.4460.0000.0000.0000.000
148H157VAL0-0.011-0.02423.947-0.400-0.4000.0000.0000.0000.000
149H158THR0-0.0050.00821.0480.3070.3070.0000.0000.0000.000
150H159TRP00.011-0.00423.984-0.341-0.3410.0000.0000.0000.000
151H160ASN0-0.039-0.01724.456-0.131-0.1310.0000.0000.0000.000
152H161SER00.0010.01520.0100.5060.5060.0000.0000.0000.000
153H169HIS00.0150.00628.2600.3760.3760.0000.0000.0000.000
154H170THR00.018-0.01726.810-0.461-0.4610.0000.0000.0000.000
155H171PHE0-0.035-0.00528.8790.1960.1960.0000.0000.0000.000
156H172PRO00.019-0.00130.1180.1360.1360.0000.0000.0000.000
157H173ALA0-0.0040.00830.993-0.296-0.2960.0000.0000.0000.000
158H174VAL00.004-0.00332.787-0.078-0.0780.0000.0000.0000.000
159H175LEU0-0.034-0.01436.117-0.023-0.0230.0000.0000.0000.000
160H176GLN0-0.027-0.02837.754-0.075-0.0750.0000.0000.0000.000
161H177SER00.0180.00441.085-0.038-0.0380.0000.0000.0000.000
162H178GLY00.0100.01339.566-0.067-0.0670.0000.0000.0000.000
163H179LEU0-0.048-0.01237.1890.2000.2000.0000.0000.0000.000
164H180TYR00.005-0.00832.747-0.116-0.1160.0000.0000.0000.000
165H181THR0-0.034-0.01735.399-0.111-0.1110.0000.0000.0000.000
166H182LEU00.0190.02528.5390.0460.0460.0000.0000.0000.000
167H183THR0-0.011-0.02732.348-0.306-0.3060.0000.0000.0000.000
168H184SER0-0.0020.02029.3000.1690.1690.0000.0000.0000.000
169H185SER0-0.011-0.02031.197-0.342-0.3420.0000.0000.0000.000
170H186VAL0-0.0050.02028.6400.2970.2970.0000.0000.0000.000
171H187THR00.0420.01730.724-0.354-0.3540.0000.0000.0000.000
172H196VAL00.007-0.00230.3520.0990.0990.0000.0000.0000.000
173H197THR0-0.020-0.03828.520-0.218-0.2180.0000.0000.0000.000
174H199ASN0-0.005-0.01324.557-0.191-0.1910.0000.0000.0000.000
175H200VAL0-0.003-0.00325.5830.2920.2920.0000.0000.0000.000
176H201ALA00.0390.01923.718-0.094-0.0940.0000.0000.0000.000
177H202HIS0-0.024-0.00625.737-0.088-0.0880.0000.0000.0000.000
178H203PRO00.0540.02023.199-0.280-0.2800.0000.0000.0000.000
179H204ALA00.0180.02325.521-0.166-0.1660.0000.0000.0000.000
180H205SER00.0120.01728.287-0.346-0.3460.0000.0000.0000.000
181H206SER0-0.064-0.02527.185-0.119-0.1190.0000.0000.0000.000
182H207THR0-0.050-0.01828.260-0.146-0.1460.0000.0000.0000.000
183H208LYS10.9270.92924.727-11.323-11.3230.0000.0000.0000.000
184H209VAL0-0.013-0.02727.458-0.442-0.4420.0000.0000.0000.000
185H210ASP-1-0.776-0.82826.91611.59311.5930.0000.0000.0000.000
186H211LYS10.8560.96429.791-9.062-9.0620.0000.0000.0000.000
187H212LYS10.9140.97531.523-9.577-9.5770.0000.0000.0000.000