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: 49YMN

Calculation Name: 1E6O-H-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1E6O

Chain ID: H

ChEMBL ID:

UniProt ID:

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 217
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2217239.74159
FMO2-HF: Nuclear repulsion 2133974.138437
FMO2-HF: Total energy -83265.603153
FMO2-MP2: Total energy -83506.49581


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.
-83.355-80.3430.471-1.273-2.210.002
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 : -0.908 / q_NPA : -0.964
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].
3H3GLN0-0.0050.0002.750-7.867-5.7550.124-0.832-1.4040.002
4H4LEU0-0.037-0.0246.175-0.711-0.7110.0000.0000.0000.000
5H5GLN00.0660.0459.945-0.693-0.6930.0000.0000.0000.000
6H6GLN0-0.008-0.03311.759-0.388-0.3880.0000.0000.0000.000
7H7SER0-0.0020.00815.4930.1490.1490.0000.0000.0000.000
8H8GLY00.0230.02018.6930.1840.1840.0000.0000.0000.000
9H9ALA0-0.038-0.01920.746-0.094-0.0940.0000.0000.0000.000
10H10GLU-1-0.899-0.95424.00311.61511.6150.0000.0000.0000.000
11H11LEU0-0.041-0.02326.736-0.219-0.2190.0000.0000.0000.000
12H12ALA00.0210.02030.587-0.092-0.0920.0000.0000.0000.000
13H13ARG10.8510.89832.694-8.522-8.5220.0000.0000.0000.000
14H14PRO00.032-0.00636.0980.1240.1240.0000.0000.0000.000
15H15GLY0-0.0100.00537.998-0.129-0.1290.0000.0000.0000.000
16H16ALA0-0.029-0.00134.7730.0170.0170.0000.0000.0000.000
17H17SER0-0.036-0.02131.7550.0820.0820.0000.0000.0000.000
18H18VAL00.0400.01926.567-0.023-0.0230.0000.0000.0000.000
19H19LYS10.8960.94323.746-11.395-11.3950.0000.0000.0000.000
20H20MET00.0450.05621.3170.3060.3060.0000.0000.0000.000
21H21SER0-0.007-0.01818.0730.1350.1350.0000.0000.0000.000
22H22CYS0-0.015-0.00214.1450.1400.1400.0000.0000.0000.000
23H23LYS10.8700.94010.838-24.537-24.5370.0000.0000.0000.000
24H24ALA00.0020.0089.7741.1621.1620.0000.0000.0000.000
25H25SER0-0.030-0.0255.7660.5040.5040.0000.0000.0000.000
26H26GLY00.1040.0432.777-0.876-0.5100.338-0.375-0.3290.002
27H27TYR0-0.012-0.0103.413-1.063-0.6070.010-0.062-0.404-0.002
28H28THR00.0280.0096.268-0.288-0.2880.0000.0000.0000.000
29H29PHE00.0210.01010.054-1.664-1.6640.0000.0000.0000.000
30H30THR00.031-0.01111.711-0.681-0.6810.0000.0000.0000.000
31H31SER0-0.054-0.01612.163-0.788-0.7880.0000.0000.0000.000
32H32TYR0-0.003-0.0019.999-0.040-0.0400.0000.0000.0000.000
33H33THR0-0.032-0.00414.171-0.300-0.3000.0000.0000.0000.000
34H34MET0-0.0010.00612.0510.7170.7170.0000.0000.0000.000
35H35HIS0-0.014-0.01116.340-1.286-1.2860.0000.0000.0000.000
36H36TRP00.011-0.00417.7670.7490.7490.0000.0000.0000.000
37H37VAL0-0.007-0.00319.938-0.549-0.5490.0000.0000.0000.000
38H38LYS10.8540.94122.085-9.580-9.5800.0000.0000.0000.000
39H39GLN00.0290.01723.1690.4070.4070.0000.0000.0000.000
40H40ARG10.8220.90225.632-8.822-8.8220.0000.0000.0000.000
41H41PRO00.0380.01228.6140.1540.1540.0000.0000.0000.000
42H42GLY00.0160.00529.474-0.275-0.2750.0000.0000.0000.000
43H43GLN0-0.0200.00229.447-0.310-0.3100.0000.0000.0000.000
44H44GLY00.0320.01827.6020.3440.3440.0000.0000.0000.000
45H45LEU0-0.0110.00021.7600.0580.0580.0000.0000.0000.000
46H46GLU-1-0.813-0.89425.5999.2959.2950.0000.0000.0000.000
47H47TRP0-0.0030.00221.6530.0630.0630.0000.0000.0000.000
48H48ILE0-0.0030.00323.577-0.494-0.4940.0000.0000.0000.000
49H49GLY00.0500.00223.707-0.526-0.5260.0000.0000.0000.000
50H50TYR0-0.064-0.02119.9750.5040.5040.0000.0000.0000.000
51H51ILE00.0260.00918.922-0.596-0.5960.0000.0000.0000.000
52H52ASN00.0400.03718.9671.4681.4680.0000.0000.0000.000
53H53PRO00.002-0.00415.794-0.578-0.5780.0000.0000.0000.000
54H54SER0-0.045-0.02618.512-0.286-0.2860.0000.0000.0000.000
55H55SER0-0.029-0.02119.601-0.445-0.4450.0000.0000.0000.000
56H56GLY0-0.0180.00522.234-0.497-0.4970.0000.0000.0000.000
57H57TYR00.0240.01723.922-0.271-0.2710.0000.0000.0000.000
58H58SER00.0230.00423.3940.4660.4660.0000.0000.0000.000
59H59ASN0-0.0120.00624.850-0.715-0.7150.0000.0000.0000.000
60H60TYR00.0330.00925.5210.4410.4410.0000.0000.0000.000
61H61ASN0-0.011-0.01127.847-0.630-0.6300.0000.0000.0000.000
62H62GLN00.0500.02529.5900.0840.0840.0000.0000.0000.000
63H63LYS10.8340.89831.993-9.275-9.2750.0000.0000.0000.000
64H64PHE0-0.016-0.02429.004-0.018-0.0180.0000.0000.0000.000
65H65LYS10.9120.96430.678-8.899-8.8990.0000.0000.0000.000
66H66ASP-1-0.844-0.90032.3968.4288.4280.0000.0000.0000.000
67H67LYS10.7260.87331.553-8.956-8.9560.0000.0000.0000.000
68H68ALA00.002-0.01127.0390.1910.1910.0000.0000.0000.000
69H69THR0-0.034-0.01927.513-0.239-0.2390.0000.0000.0000.000
70H70LEU0-0.0250.00822.1360.3280.3280.0000.0000.0000.000
71H71THR0-0.002-0.00822.648-0.213-0.2130.0000.0000.0000.000
72H72ALA0-0.005-0.01818.3470.6360.6360.0000.0000.0000.000
73H73ASP-1-0.739-0.80018.48514.98414.9840.0000.0000.0000.000
74H74LYS10.9740.98516.599-16.002-16.0020.0000.0000.0000.000
75H75SER0-0.088-0.05715.9051.0211.0210.0000.0000.0000.000
76H76SER00.001-0.02715.7121.0521.0520.0000.0000.0000.000
77H77SER0-0.050-0.02411.8561.8751.8750.0000.0000.0000.000
78H78THR00.0170.00812.8101.7891.7890.0000.0000.0000.000
79H79ALA00.0000.00115.460-0.983-0.9830.0000.0000.0000.000
80H80TYR0-0.001-0.02417.5400.2720.2720.0000.0000.0000.000
81H81MET0-0.0060.01420.694-0.303-0.3030.0000.0000.0000.000
82H82GLN00.0080.00423.2960.1380.1380.0000.0000.0000.000
83H83LEU0-0.0050.00126.596-0.050-0.0500.0000.0000.0000.000
84H84SER00.009-0.01829.233-0.167-0.1670.0000.0000.0000.000
85H85SER00.0580.02333.034-0.060-0.0600.0000.0000.0000.000
86H86LEU0-0.052-0.01430.620-0.059-0.0590.0000.0000.0000.000
87H87THR00.024-0.00834.558-0.325-0.3250.0000.0000.0000.000
88H88SER00.0970.03934.5620.1970.1970.0000.0000.0000.000
89H89GLU-1-0.808-0.88034.3008.5778.5770.0000.0000.0000.000
90H90ASP-1-0.832-0.90230.8129.4279.4270.0000.0000.0000.000
91H91SER00.0160.01729.6480.3810.3810.0000.0000.0000.000
92H92ALA0-0.041-0.02526.884-0.191-0.1910.0000.0000.0000.000
93H93VAL00.0150.03021.1690.1460.1460.0000.0000.0000.000
94H94TYR0-0.005-0.03322.081-0.315-0.3150.0000.0000.0000.000
95H95TYR00.010-0.00217.2050.5550.5550.0000.0000.0000.000
96H97SER00.012-0.01413.5360.4730.4730.0000.0000.0000.000
97H98ARG10.8810.9316.977-27.118-27.1180.0000.0000.0000.000
98H99PRO0-0.060-0.00111.7231.0831.0830.0000.0000.0000.000
99H100VAL0-0.014-0.00510.6950.1820.1820.0000.0000.0000.000
100H101VAL0-0.019-0.01313.661-0.717-0.7170.0000.0000.0000.000
101H102ARG10.8820.92711.108-19.003-19.0030.0000.0000.0000.000
102H103LEU00.0270.01818.419-0.418-0.4180.0000.0000.0000.000
103H104GLY00.0450.02220.392-0.631-0.6310.0000.0000.0000.000
104H105TYR00.0010.00417.6710.3620.3620.0000.0000.0000.000
105H106ASN0-0.018-0.01715.686-0.322-0.3220.0000.0000.0000.000
106H107PHE00.0380.01014.2900.9530.9530.0000.0000.0000.000
107H108ASP-1-0.751-0.86510.59422.44022.4400.0000.0000.0000.000
108H109TYR00.0160.0155.3221.4231.501-0.001-0.004-0.0730.000
109H110TRP0-0.024-0.02610.256-1.960-1.9600.0000.0000.0000.000
110H111GLY00.0440.02910.7321.6131.6130.0000.0000.0000.000
111H112GLN0-0.025-0.00712.8350.1780.1780.0000.0000.0000.000
112H113GLY0-0.0100.00014.549-0.879-0.8790.0000.0000.0000.000
113H114SER0-0.029-0.02417.9290.3660.3660.0000.0000.0000.000
114H115THR00.005-0.00720.832-0.193-0.1930.0000.0000.0000.000
115H116LEU00.0040.02124.208-0.091-0.0910.0000.0000.0000.000
116H117THR0-0.012-0.01127.161-0.255-0.2550.0000.0000.0000.000
117H118VAL0-0.021-0.01030.7740.0090.0090.0000.0000.0000.000
118H119SER00.0510.02333.895-0.258-0.2580.0000.0000.0000.000
119H120SER00.0210.00637.1070.1630.1630.0000.0000.0000.000
120H121ALA00.0380.03838.018-0.067-0.0670.0000.0000.0000.000
121H122LYS10.9530.98237.488-7.150-7.1500.0000.0000.0000.000
122H123THR00.0270.00533.525-0.048-0.0480.0000.0000.0000.000
123H124THR0-0.070-0.02836.018-0.294-0.2940.0000.0000.0000.000
124H125PRO00.0500.01935.7060.1710.1710.0000.0000.0000.000
125H126PRO0-0.0260.01034.256-0.198-0.1980.0000.0000.0000.000
126H127SER00.0130.01237.343-0.098-0.0980.0000.0000.0000.000
127H128VAL0-0.007-0.00936.6150.0410.0410.0000.0000.0000.000
128H129TYR0-0.015-0.01339.821-0.114-0.1140.0000.0000.0000.000
129H130PRO00.0290.01641.4680.1500.1500.0000.0000.0000.000
130H131LEU0-0.052-0.02640.976-0.169-0.1690.0000.0000.0000.000
131H132ALA00.0450.02543.6080.1050.1050.0000.0000.0000.000
132H133PRO00.0060.01045.396-0.106-0.1060.0000.0000.0000.000
133H134GLY00.0420.02248.035-0.071-0.0710.0000.0000.0000.000
134H135SER0-0.022-0.02951.576-0.128-0.1280.0000.0000.0000.000
135H136ALA0-0.009-0.00352.151-0.034-0.0340.0000.0000.0000.000
136H137ALA0-0.009-0.01247.675-0.017-0.0170.0000.0000.0000.000
137H138GLN0-0.0060.00549.3600.1170.1170.0000.0000.0000.000
138H139THR00.004-0.00851.393-0.034-0.0340.0000.0000.0000.000
139H140ASN0-0.0310.01146.769-0.136-0.1360.0000.0000.0000.000
140H141SER00.0470.02046.6160.0560.0560.0000.0000.0000.000
141H142MET0-0.0350.01341.9430.1610.1610.0000.0000.0000.000
142H143VAL00.0230.01943.312-0.133-0.1330.0000.0000.0000.000
143H144THR00.010-0.00340.1420.2310.2310.0000.0000.0000.000
144H145LEU0-0.0090.01440.169-0.190-0.1900.0000.0000.0000.000
145H146GLY00.0500.00238.6800.1840.1840.0000.0000.0000.000
146H147CYS0-0.0790.00334.3640.0780.0780.0000.0000.0000.000
147H148LEU00.0160.02337.8660.1330.1330.0000.0000.0000.000
148H149VAL0-0.007-0.00834.111-0.042-0.0420.0000.0000.0000.000
149H150LYS10.9190.94037.351-7.121-7.1210.0000.0000.0000.000
150H151GLY00.0040.00739.673-0.018-0.0180.0000.0000.0000.000
151H152TYR0-0.011-0.01932.234-0.165-0.1650.0000.0000.0000.000
152H153PHE00.0260.00934.8320.0140.0140.0000.0000.0000.000
153H154PRO00.0140.01530.380-0.089-0.0890.0000.0000.0000.000
154H155GLU-1-0.776-0.87628.9999.9799.9790.0000.0000.0000.000
155H156PRO0-0.043-0.01624.7750.1180.1180.0000.0000.0000.000
156H157VAL00.007-0.00728.027-0.017-0.0170.0000.0000.0000.000
157H158THR0-0.034-0.01824.5410.3630.3630.0000.0000.0000.000
158H159VAL0-0.024-0.02527.691-0.273-0.2730.0000.0000.0000.000
159H160THR0-0.018-0.00426.4970.3630.3630.0000.0000.0000.000
160H161TRP00.0100.00229.588-0.435-0.4350.0000.0000.0000.000
161H162ASN00.027-0.00731.2660.1790.1790.0000.0000.0000.000
162H163SER0-0.021-0.01428.8920.0300.0300.0000.0000.0000.000
163H164GLY00.0100.01327.0010.4810.4810.0000.0000.0000.000
164H165SER0-0.056-0.03327.9130.0990.0990.0000.0000.0000.000
165H166LEU0-0.037-0.01030.603-0.289-0.2890.0000.0000.0000.000
166H167SER00.034-0.00227.7210.1050.1050.0000.0000.0000.000
167H168SER00.007-0.00629.822-0.085-0.0850.0000.0000.0000.000
168H169GLY00.0490.03931.052-0.135-0.1350.0000.0000.0000.000
169H170VAL0-0.067-0.02130.817-0.266-0.2660.0000.0000.0000.000
170H171HIS00.0090.01931.8820.2510.2510.0000.0000.0000.000
171H172THR00.0130.00030.312-0.341-0.3410.0000.0000.0000.000
172H173PHE0-0.0220.00731.5000.1810.1810.0000.0000.0000.000
173H174PRO00.017-0.00831.1270.1170.1170.0000.0000.0000.000
174H175ALA00.0020.01731.976-0.282-0.2820.0000.0000.0000.000
175H176VAL0-0.025-0.01333.9070.0020.0020.0000.0000.0000.000
176H177LEU0-0.028-0.00836.567-0.010-0.0100.0000.0000.0000.000
177H178GLN00.0210.00138.576-0.142-0.1420.0000.0000.0000.000
178H179SER0-0.016-0.01742.2260.0030.0030.0000.0000.0000.000
179H180ASP-1-0.904-0.95640.1327.4827.4820.0000.0000.0000.000
180H181LEU0-0.040-0.00438.8080.1700.1700.0000.0000.0000.000
181H182TYR00.0130.00832.966-0.067-0.0670.0000.0000.0000.000
182H183THR0-0.034-0.03237.040-0.215-0.2150.0000.0000.0000.000
183H184LEU00.0210.03431.5630.0300.0300.0000.0000.0000.000
184H185SER00.0190.00235.875-0.118-0.1180.0000.0000.0000.000
185H186SER00.013-0.00332.8200.2140.2140.0000.0000.0000.000
186H187SER0-0.003-0.01135.220-0.314-0.3140.0000.0000.0000.000
187H188VAL00.0140.00434.9040.2840.2840.0000.0000.0000.000
188H189THR0-0.018-0.01136.766-0.210-0.2100.0000.0000.0000.000
189H190VAL0-0.003-0.00337.4800.2450.2450.0000.0000.0000.000
190H191PRO00.0640.01439.538-0.201-0.2010.0000.0000.0000.000
191H192SER0-0.007-0.01442.7130.0150.0150.0000.0000.0000.000
192H193SER00.0220.01744.101-0.085-0.0850.0000.0000.0000.000
193H194THR0-0.058-0.03139.6010.0480.0480.0000.0000.0000.000
194H195TRP00.011-0.00342.5020.0550.0550.0000.0000.0000.000
195H196PRO0-0.020-0.02444.469-0.088-0.0880.0000.0000.0000.000
196H197SER0-0.063-0.03945.6400.0230.0230.0000.0000.0000.000
197H198GLU-1-0.822-0.91040.9827.7107.7100.0000.0000.0000.000
198H199THR0-0.073-0.02839.074-0.117-0.1170.0000.0000.0000.000
199H200VAL00.0250.03037.4400.2380.2380.0000.0000.0000.000
200H201THR00.015-0.00735.650-0.308-0.3080.0000.0000.0000.000
201H203ASN00.019-0.00230.560-0.048-0.0480.0000.0000.0000.000
202H204VAL00.000-0.00331.3510.1940.1940.0000.0000.0000.000
203H205ALA0-0.002-0.00628.261-0.089-0.0890.0000.0000.0000.000
204H206HIS00.0320.02529.880-0.031-0.0310.0000.0000.0000.000
205H207PRO00.0280.00825.316-0.171-0.1710.0000.0000.0000.000
206H208ALA00.0190.01827.596-0.033-0.0330.0000.0000.0000.000
207H209SER0-0.026-0.03629.591-0.256-0.2560.0000.0000.0000.000
208H210SER0-0.034-0.01529.639-0.078-0.0780.0000.0000.0000.000
209H211THR0-0.0120.00430.671-0.132-0.1320.0000.0000.0000.000
210H212LYS10.9610.96627.242-10.713-10.7130.0000.0000.0000.000
211H213VAL0-0.027-0.01732.875-0.325-0.3250.0000.0000.0000.000
212H214ASP-1-0.835-0.90033.2209.7319.7310.0000.0000.0000.000
213H215LYS10.8810.93435.957-7.893-7.8930.0000.0000.0000.000
214H216LYS10.9370.96538.917-7.375-7.3750.0000.0000.0000.000
215H217ILE0-0.032-0.01639.844-0.176-0.1760.0000.0000.0000.000
216H218VAL00.0010.00242.6850.0100.0100.0000.0000.0000.000
217H219PRO00.0070.01646.321-0.056-0.0560.0000.0000.0000.000