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: JLKJ9

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 OptAll
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 -1844768.90218
FMO2-HF: Nuclear repulsion 1772238.997563
FMO2-HF: Total energy -72529.904616
FMO2-MP2: Total energy -72739.896269


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.
-85.141-83.463-0.008-0.748-0.9210.003
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 : -0.914 / q_NPA : -0.963
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].
3H3LYS10.8600.9233.855-30.567-29.088-0.007-0.665-0.8070.003
4H4LEU00.0210.0146.291-1.914-1.9140.0000.0000.0000.000
5H5GLN00.0020.01510.0390.3110.3110.0000.0000.0000.000
6H6GLU-1-0.737-0.87412.04318.62418.6240.0000.0000.0000.000
7H7SER0-0.028-0.02715.871-0.063-0.0630.0000.0000.0000.000
8H8GLY00.011-0.00718.507-0.278-0.2780.0000.0000.0000.000
9H9PRO0-0.014-0.01622.3350.0660.0660.0000.0000.0000.000
10H10SER00.0400.02123.980-0.026-0.0260.0000.0000.0000.000
11H11LEU0-0.050-0.00926.048-0.154-0.1540.0000.0000.0000.000
12H12VAL0-0.035-0.01129.071-0.050-0.0500.0000.0000.0000.000
13H13GLN00.0170.01131.909-0.182-0.1820.0000.0000.0000.000
14H14PRO00.0500.00035.3140.1260.1260.0000.0000.0000.000
15H15SER0-0.020-0.00637.486-0.155-0.1550.0000.0000.0000.000
16H16GLN00.0130.03733.937-0.073-0.0730.0000.0000.0000.000
17H17THR0-0.038-0.04930.251-0.059-0.0590.0000.0000.0000.000
18H18LEU00.0460.05725.6890.1040.1040.0000.0000.0000.000
19H19SER0-0.010-0.02926.157-0.072-0.0720.0000.0000.0000.000
20H20LEU0-0.0170.01421.0440.1210.1210.0000.0000.0000.000
21H21THR0-0.007-0.01117.549-0.284-0.2840.0000.0000.0000.000
22H22CYS0-0.064-0.00514.3940.2930.2930.0000.0000.0000.000
23H23THR0-0.0010.00511.695-0.991-0.9910.0000.0000.0000.000
24H24VAL0-0.012-0.0109.7851.0321.0320.0000.0000.0000.000
25H25SER00.0350.0254.805-1.173-1.1730.0000.0000.0000.000
26H26GLY00.0920.0444.1611.6951.7360.000-0.0660.0260.000
27H27PHE0-0.041-0.0304.807-1.031-0.873-0.001-0.017-0.1400.000
28H28SER00.0340.0268.211-0.987-0.9870.0000.0000.0000.000
29H29LEU00.0320.00111.851-0.529-0.5290.0000.0000.0000.000
30H30THR00.0230.00014.911-0.493-0.4930.0000.0000.0000.000
31H31SER0-0.0180.00113.492-0.383-0.3830.0000.0000.0000.000
32H32ASN0-0.024-0.00111.3461.5611.5610.0000.0000.0000.000
33H33SER0-0.030-0.00814.706-1.102-1.1020.0000.0000.0000.000
34H34VAL00.0210.00013.7311.1781.1780.0000.0000.0000.000
35H35HIS00.0210.00916.342-1.533-1.5330.0000.0000.0000.000
36H36TRP0-0.0040.01117.6870.9930.9930.0000.0000.0000.000
37H37VAL0-0.004-0.01119.160-0.700-0.7000.0000.0000.0000.000
38H38ARG10.7600.84720.658-10.410-10.4100.0000.0000.0000.000
39H39GLN00.002-0.00522.5560.3840.3840.0000.0000.0000.000
40H40PRO00.0360.02424.5780.0910.0910.0000.0000.0000.000
41H41PRO0-0.005-0.00127.7200.1810.1810.0000.0000.0000.000
42H42GLY00.0080.00028.344-0.365-0.3650.0000.0000.0000.000
43H43GLN0-0.031-0.00328.630-0.230-0.2300.0000.0000.0000.000
44H44GLY00.0380.02026.6160.3840.3840.0000.0000.0000.000
45H45LEU0-0.016-0.01320.6660.0350.0350.0000.0000.0000.000
46H46GLU-1-0.790-0.87524.42810.21210.2120.0000.0000.0000.000
47H47TRP00.0030.00021.3680.1080.1080.0000.0000.0000.000
48H48MET0-0.012-0.00322.969-0.725-0.7250.0000.0000.0000.000
49H49GLY00.0660.01823.558-0.606-0.6060.0000.0000.0000.000
50H50GLY0-0.0160.00621.1320.6940.6940.0000.0000.0000.000
51H51ILE0-0.050-0.00618.904-0.661-0.6610.0000.0000.0000.000
52H52TRP00.0340.00319.3191.1101.1100.0000.0000.0000.000
53H53GLY00.0530.03618.4570.0100.0100.0000.0000.0000.000
54H54ASP-1-0.797-0.88019.33212.22812.2280.0000.0000.0000.000
55H55GLY0-0.045-0.02721.970-0.417-0.4170.0000.0000.0000.000
56H56ARG10.8910.92823.242-11.906-11.9060.0000.0000.0000.000
57H57THR0-0.003-0.01023.7120.4450.4450.0000.0000.0000.000
58H58ASP-1-0.850-0.90125.2179.9449.9440.0000.0000.0000.000
59H59TYR00.004-0.02525.6250.5330.5330.0000.0000.0000.000
60H60ASN0-0.009-0.01427.831-0.647-0.6470.0000.0000.0000.000
61H61SER00.018-0.01429.402-0.065-0.0650.0000.0000.0000.000
62H62ALA00.0030.02032.721-0.254-0.2540.0000.0000.0000.000
63H63LEU0-0.042-0.02628.233-0.106-0.1060.0000.0000.0000.000
64H64LYS10.8490.92030.816-9.789-9.7890.0000.0000.0000.000
65H65SER00.0030.01532.4240.0000.0000.0000.0000.0000.000
66H66ARG10.8470.91432.433-9.367-9.3670.0000.0000.0000.000
67H67LEU0-0.042-0.01225.6980.1350.1350.0000.0000.0000.000
68H68SER0-0.0270.00228.117-0.090-0.0900.0000.0000.0000.000
69H69ILE00.0170.00821.7070.3110.3110.0000.0000.0000.000
70H70SER0-0.0100.00122.900-0.240-0.2400.0000.0000.0000.000
71H71ARG10.8790.93218.777-13.652-13.6520.0000.0000.0000.000
72H72ASP-1-0.775-0.84418.88612.91412.9140.0000.0000.0000.000
73H73THR0-0.003-0.01916.6910.7090.7090.0000.0000.0000.000
74H74SER0-0.036-0.02815.7480.7120.7120.0000.0000.0000.000
75H75LYS10.8550.91416.207-12.656-12.6560.0000.0000.0000.000
76H76SER0-0.015-0.00110.6690.4590.4590.0000.0000.0000.000
77H77GLN0-0.025-0.02613.2690.1860.1860.0000.0000.0000.000
78H78VAL0-0.010-0.01216.016-0.578-0.5780.0000.0000.0000.000
79H79PHE0-0.006-0.00818.2200.2580.2580.0000.0000.0000.000
80H80LEU00.0280.01321.366-0.069-0.0690.0000.0000.0000.000
81H81LYS10.9260.95623.737-10.239-10.2390.0000.0000.0000.000
82H82MET00.0310.01727.459-0.042-0.0420.0000.0000.0000.000
83H83ASN0-0.0240.00829.993-0.146-0.1460.0000.0000.0000.000
84H84SER0-0.0070.00033.606-0.116-0.1160.0000.0000.0000.000
85H85LEU0-0.040-0.02133.5170.2200.2200.0000.0000.0000.000
86H86GLN00.006-0.02635.559-0.208-0.2080.0000.0000.0000.000
87H87THR00.0190.00434.991-0.051-0.0510.0000.0000.0000.000
88H88ASH00.012-0.00233.6590.2000.2000.0000.0000.0000.000
89H89ASP-1-0.744-0.82230.1739.7719.7710.0000.0000.0000.000
90H90THR0-0.0160.00828.9750.4250.4250.0000.0000.0000.000
91H91ALA0-0.002-0.00325.697-0.121-0.1210.0000.0000.0000.000
92H92ILE00.0030.01820.2740.0860.0860.0000.0000.0000.000
93H93TYR0-0.010-0.03521.397-0.037-0.0370.0000.0000.0000.000
94H94PHE00.0450.01316.1820.4730.4730.0000.0000.0000.000
95H96THR0-0.007-0.01713.4041.0481.0480.0000.0000.0000.000
96H97ARG10.8360.8858.290-28.662-28.6620.0000.0000.0000.000
97H98CYS0-0.0120.03513.5720.4780.4780.0000.0000.0000.000
98H99ARG10.8490.91910.977-24.193-24.1930.0000.0000.0000.000
99H100ARG10.8990.92013.424-19.399-19.3990.0000.0000.0000.000
100H101ASP-1-0.818-0.89514.20919.01319.0130.0000.0000.0000.000
101H102SER0-0.061-0.03815.0560.8230.8230.0000.0000.0000.000
102H103SER00.0140.01017.069-0.266-0.2660.0000.0000.0000.000
103H104TYR0-0.055-0.03317.617-0.365-0.3650.0000.0000.0000.000
104H105VAL00.0580.03615.542-0.282-0.2820.0000.0000.0000.000
105H106VAL00.026-0.01415.1170.8560.8560.0000.0000.0000.000
106H107ASP-1-0.782-0.85010.77626.66826.6680.0000.0000.0000.000
107H108ALA0-0.0020.0108.5192.4372.4370.0000.0000.0000.000
108H109TRP00.012-0.01610.084-2.616-2.6160.0000.0000.0000.000
109H110GLY0-0.0150.00810.3292.2222.2220.0000.0000.0000.000
110H111GLN0-0.039-0.02612.0901.9001.9000.0000.0000.0000.000
111H112GLY00.0100.00214.166-0.771-0.7710.0000.0000.0000.000
112H113ALA0-0.023-0.00817.620-0.238-0.2380.0000.0000.0000.000
113H114SER0-0.0060.00120.119-0.532-0.5320.0000.0000.0000.000
114H115VAL0-0.0020.00023.395-0.103-0.1030.0000.0000.0000.000
115H116THR00.0080.00026.393-0.246-0.2460.0000.0000.0000.000
116H117VAL0-0.040-0.02030.110-0.060-0.0600.0000.0000.0000.000
117H118SER00.029-0.00632.618-0.280-0.2800.0000.0000.0000.000
118H119SER00.0280.00735.7870.1260.1260.0000.0000.0000.000
119H120ALA0-0.0300.00837.312-0.146-0.1460.0000.0000.0000.000
120H121LYS10.9180.94536.288-7.816-7.8160.0000.0000.0000.000
121H122THR00.014-0.01831.5260.0170.0170.0000.0000.0000.000
122H123THR0-0.021-0.01633.972-0.427-0.4270.0000.0000.0000.000
123H124PRO00.0670.04933.0430.2390.2390.0000.0000.0000.000
124H125LYN0-0.019-0.02228.928-0.132-0.1320.0000.0000.0000.000
125H126LEU00.0070.03033.898-0.093-0.0930.0000.0000.0000.000
126H127VAL00.003-0.00832.5690.1210.1210.0000.0000.0000.000
127H128TYR0-0.026-0.02135.644-0.151-0.1510.0000.0000.0000.000
128H129PRO00.0140.01136.4270.2650.2650.0000.0000.0000.000
129H130LEU0-0.016-0.00736.849-0.243-0.2430.0000.0000.0000.000
130H131ALA00.0290.00737.9730.2390.2390.0000.0000.0000.000
131H132PRO00.0290.03240.100-0.227-0.2270.0000.0000.0000.000
132H141VAL00.022-0.00236.312-0.050-0.0500.0000.0000.0000.000
133H142THR0-0.050-0.02434.8610.2820.2820.0000.0000.0000.000
134H143LEU00.0160.00934.200-0.284-0.2840.0000.0000.0000.000
135H144GLY00.0310.00633.5960.3300.3300.0000.0000.0000.000
136H145CYS0-0.066-0.01428.3540.2010.2010.0000.0000.0000.000
137H146LEU00.0330.02734.3480.0940.0940.0000.0000.0000.000
138H147VAL00.006-0.00330.971-0.060-0.0600.0000.0000.0000.000
139H148LYS10.8960.92234.295-7.869-7.8690.0000.0000.0000.000
140H149GLY00.0340.01636.958-0.034-0.0340.0000.0000.0000.000
141H150TYR0-0.005-0.01330.651-0.186-0.1860.0000.0000.0000.000
142H151PHE00.0130.00133.423-0.069-0.0690.0000.0000.0000.000
143H152PRO0-0.0250.00329.366-0.090-0.0900.0000.0000.0000.000
144H153GLU-1-0.779-0.88028.19610.92110.9210.0000.0000.0000.000
145H154PRO0-0.032-0.01023.5290.0170.0170.0000.0000.0000.000
146H155VAL00.014-0.00226.600-0.067-0.0670.0000.0000.0000.000
147H156THR0-0.058-0.03521.0560.6110.6110.0000.0000.0000.000
148H157VAL00.013-0.00224.362-0.431-0.4310.0000.0000.0000.000
149H158THR0-0.018-0.00721.2220.6880.6880.0000.0000.0000.000
150H159TRP0-0.022-0.00824.257-0.282-0.2820.0000.0000.0000.000
151H160ASN0-0.030-0.03124.678-0.157-0.1570.0000.0000.0000.000
152H161SER00.0010.01720.1330.4440.4440.0000.0000.0000.000
153H169HIS00.0160.00528.7340.3800.3800.0000.0000.0000.000
154H170THR00.022-0.01226.462-0.448-0.4480.0000.0000.0000.000
155H171PHE0-0.028-0.00328.8330.2130.2130.0000.0000.0000.000
156H172PRO00.029-0.00330.1880.1400.1400.0000.0000.0000.000
157H173ALA0-0.0020.01530.909-0.296-0.2960.0000.0000.0000.000
158H174VAL0-0.008-0.01032.704-0.085-0.0850.0000.0000.0000.000
159H175LEU0-0.027-0.00836.306-0.040-0.0400.0000.0000.0000.000
160H176GLN00.005-0.01637.817-0.169-0.1690.0000.0000.0000.000
161H177SER00.004-0.00641.1970.0180.0180.0000.0000.0000.000
162H178GLY00.0280.02740.170-0.089-0.0890.0000.0000.0000.000
163H179LEU0-0.042-0.01337.4900.1890.1890.0000.0000.0000.000
164H180TYR00.0260.01933.077-0.121-0.1210.0000.0000.0000.000
165H181THR0-0.058-0.03335.741-0.240-0.2400.0000.0000.0000.000
166H182LEU00.0460.04329.1600.0160.0160.0000.0000.0000.000
167H183THR00.013-0.00433.119-0.198-0.1980.0000.0000.0000.000
168H184SER0-0.0060.00729.5040.2000.2000.0000.0000.0000.000
169H185SER00.0020.00031.400-0.374-0.3740.0000.0000.0000.000
170H186VAL00.0060.01228.8540.3310.3310.0000.0000.0000.000
171H187THR00.0220.00930.936-0.227-0.2270.0000.0000.0000.000
172H196VAL00.0530.02730.5230.0450.0450.0000.0000.0000.000
173H197THR0-0.025-0.01927.853-0.310-0.3100.0000.0000.0000.000
174H199ASN0-0.007-0.00624.933-0.109-0.1090.0000.0000.0000.000
175H200VAL00.013-0.00626.2370.2220.2220.0000.0000.0000.000
176H201ALA00.0330.00224.026-0.064-0.0640.0000.0000.0000.000
177H202HIS0-0.015-0.02126.113-0.020-0.0200.0000.0000.0000.000
178H203PRO00.0580.02522.862-0.306-0.3060.0000.0000.0000.000
179H204ALA00.0360.03125.311-0.168-0.1680.0000.0000.0000.000
180H205SER00.0000.03428.103-0.454-0.4540.0000.0000.0000.000
181H206SER0-0.033-0.01027.162-0.143-0.1430.0000.0000.0000.000
182H207THR0-0.061-0.02128.237-0.186-0.1860.0000.0000.0000.000
183H208LYS10.8940.92324.885-11.287-11.2870.0000.0000.0000.000
184H209VAL0-0.014-0.00627.885-0.359-0.3590.0000.0000.0000.000
185H210ASP-1-0.764-0.84927.34011.61911.6190.0000.0000.0000.000
186H211LYS10.9050.97930.279-8.973-8.9730.0000.0000.0000.000
187H212LYS10.8690.92731.279-9.791-9.7910.0000.0000.0000.000