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

tag_button

FMODB ID: QYL9Y

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 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 217
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2216840.021352
FMO2-HF: Nuclear repulsion 2133575.32134
FMO2-HF: Total energy -83264.700012
FMO2-MP2: Total energy -83505.685857


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.
-77.328-75.0960.053-0.86-1.4270.005
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 : -0.930 / q_NPA : -0.976
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].
3H3GLN0-0.013-0.0063.571-5.659-3.9030.000-0.636-1.1210.004
4H4LEU0-0.032-0.0255.987-1.179-1.1790.0000.0000.0000.000
5H5GLN00.0450.0269.779-0.556-0.5560.0000.0000.0000.000
6H6GLN00.000-0.01811.860-0.267-0.2670.0000.0000.0000.000
7H7SER00.0140.02215.5800.2230.2230.0000.0000.0000.000
8H8GLY00.0180.01118.5800.0450.0450.0000.0000.0000.000
9H9ALA0-0.041-0.01620.964-0.167-0.1670.0000.0000.0000.000
10H10GLU-1-0.887-0.94624.00011.31011.3100.0000.0000.0000.000
11H11LEU0-0.031-0.00526.794-0.223-0.2230.0000.0000.0000.000
12H12ALA00.0230.00930.543-0.037-0.0370.0000.0000.0000.000
13H13ARG10.8550.90332.655-8.616-8.6160.0000.0000.0000.000
14H14PRO00.024-0.00635.8910.1230.1230.0000.0000.0000.000
15H15GLY0-0.015-0.00237.286-0.156-0.1560.0000.0000.0000.000
16H16ALA0-0.039-0.00334.513-0.011-0.0110.0000.0000.0000.000
17H17SER0-0.027-0.02431.5660.0900.0900.0000.0000.0000.000
18H18VAL00.0370.02126.388-0.004-0.0040.0000.0000.0000.000
19H19LYS10.9410.96823.601-11.516-11.5160.0000.0000.0000.000
20H20MET00.0050.02821.1080.2730.2730.0000.0000.0000.000
21H21SER0-0.007-0.02217.8620.1860.1860.0000.0000.0000.000
22H22CYS0-0.0220.00314.0910.1870.1870.0000.0000.0000.000
23H23LYS10.9630.99610.586-24.149-24.1490.0000.0000.0000.000
24H24ALA00.0020.0039.3811.2001.2000.0000.0000.0000.000
25H25SER0-0.065-0.0345.7900.7560.7560.0000.0000.0000.000
26H26GLY00.1210.0513.345-0.0030.2690.055-0.200-0.1280.001
27H27TYR0-0.027-0.0103.896-1.392-1.233-0.001-0.022-0.1360.000
28H28THR00.0180.0086.867-0.274-0.2740.0000.0000.0000.000
29H29PHE00.0510.01610.516-1.506-1.5060.0000.0000.0000.000
30H30THR00.025-0.01312.257-0.677-0.6770.0000.0000.0000.000
31H31SER0-0.047-0.01412.587-0.803-0.8030.0000.0000.0000.000
32H32TYR0-0.024-0.00510.073-0.012-0.0120.0000.0000.0000.000
33H33THR0-0.0310.00114.244-0.377-0.3770.0000.0000.0000.000
34H34MET00.0120.00312.0991.0581.0580.0000.0000.0000.000
35H35HIS0-0.012-0.00516.484-1.210-1.2100.0000.0000.0000.000
36H36TRP00.0410.01417.7000.7820.7820.0000.0000.0000.000
37H37VAL0-0.030-0.01619.795-0.564-0.5640.0000.0000.0000.000
38H38LYS10.8810.93921.708-9.627-9.6270.0000.0000.0000.000
39H39GLN00.0350.02122.7400.3020.3020.0000.0000.0000.000
40H40ARG10.8960.96325.346-8.953-8.9530.0000.0000.0000.000
41H41PRO00.0120.00028.4360.1350.1350.0000.0000.0000.000
42H42GLY00.0360.01728.797-0.304-0.3040.0000.0000.0000.000
43H43GLN0-0.027-0.01428.917-0.208-0.2080.0000.0000.0000.000
44H44GLY00.0280.01227.4470.3560.3560.0000.0000.0000.000
45H45LEU0-0.0060.00221.6450.0620.0620.0000.0000.0000.000
46H46GLU-1-0.854-0.92925.2469.3909.3900.0000.0000.0000.000
47H47TRP0-0.0100.00921.4830.0730.0730.0000.0000.0000.000
48H48ILE00.0090.00023.698-0.474-0.4740.0000.0000.0000.000
49H49GLY00.045-0.00523.505-0.517-0.5170.0000.0000.0000.000
50H50TYR0-0.052-0.01520.2920.5580.5580.0000.0000.0000.000
51H51ILE00.0440.01819.007-0.548-0.5480.0000.0000.0000.000
52H52ASN00.0260.03219.2751.2091.2090.0000.0000.0000.000
53H53PRO00.012-0.01216.133-0.665-0.6650.0000.0000.0000.000
54H54SER0-0.068-0.04318.838-0.291-0.2910.0000.0000.0000.000
55H55SER00.002-0.00120.211-0.270-0.2700.0000.0000.0000.000
56H56GLY00.0000.01022.633-0.431-0.4310.0000.0000.0000.000
57H57TYR0-0.0110.00724.196-0.376-0.3760.0000.0000.0000.000
58H58SER00.005-0.00723.8030.4650.4650.0000.0000.0000.000
59H59ASN0-0.0170.00725.245-0.721-0.7210.0000.0000.0000.000
60H60TYR00.0340.01525.9050.4720.4720.0000.0000.0000.000
61H61ASN0-0.0030.00127.886-0.551-0.5510.0000.0000.0000.000
62H62GLN00.0700.02829.4850.1240.1240.0000.0000.0000.000
63H63LYS10.8710.93331.905-9.108-9.1080.0000.0000.0000.000
64H64PHE00.000-0.00928.734-0.041-0.0410.0000.0000.0000.000
65H65LYS10.9180.96830.898-8.693-8.6930.0000.0000.0000.000
66H66ASP-1-0.875-0.92832.5288.2948.2940.0000.0000.0000.000
67H67LYS10.7390.90731.122-8.985-8.9850.0000.0000.0000.000
68H68ALA00.010-0.02326.5730.1660.1660.0000.0000.0000.000
69H69THR0-0.052-0.01527.473-0.241-0.2410.0000.0000.0000.000
70H70LEU0-0.009-0.01422.2130.3200.3200.0000.0000.0000.000
71H71THR00.0050.00722.918-0.043-0.0430.0000.0000.0000.000
72H72ALA0-0.004-0.01518.5460.6240.6240.0000.0000.0000.000
73H73ASP-1-0.809-0.84418.58414.41714.4170.0000.0000.0000.000
74H74LYS10.9920.97417.028-15.443-15.4430.0000.0000.0000.000
75H75SER0-0.108-0.08316.1960.9200.9200.0000.0000.0000.000
76H76SER00.0290.01215.5320.9350.9350.0000.0000.0000.000
77H77SER0-0.048-0.01811.7771.5031.5030.0000.0000.0000.000
78H78THR0-0.012-0.00912.8911.3061.3060.0000.0000.0000.000
79H79ALA0-0.033-0.00215.462-0.933-0.9330.0000.0000.0000.000
80H80TYR0-0.006-0.03117.5840.2030.2030.0000.0000.0000.000
81H81MET00.0170.01820.768-0.292-0.2920.0000.0000.0000.000
82H82GLN0-0.040-0.01623.4010.1740.1740.0000.0000.0000.000
83H83LEU0-0.0020.01026.561-0.108-0.1080.0000.0000.0000.000
84H84SER00.0350.00529.364-0.061-0.0610.0000.0000.0000.000
85H85SER00.0520.01233.069-0.025-0.0250.0000.0000.0000.000
86H86LEU0-0.041-0.00830.581-0.066-0.0660.0000.0000.0000.000
87H87THR00.0410.02034.512-0.318-0.3180.0000.0000.0000.000
88H88SER00.0680.01934.3650.2530.2530.0000.0000.0000.000
89H89GLU-1-0.836-0.91833.9988.4998.4990.0000.0000.0000.000
90H90ASP-1-0.842-0.91830.7149.4399.4390.0000.0000.0000.000
91H91SER0-0.0090.02929.3340.4130.4130.0000.0000.0000.000
92H92ALA0-0.040-0.03026.540-0.184-0.1840.0000.0000.0000.000
93H93VAL00.0090.03620.8810.1290.1290.0000.0000.0000.000
94H94TYR0-0.005-0.05121.698-0.209-0.2090.0000.0000.0000.000
95H95TYR0-0.0010.00416.6670.5800.5800.0000.0000.0000.000
96H97SER00.025-0.00613.5260.5190.5190.0000.0000.0000.000
97H98ARG10.8780.9377.635-26.106-26.1060.0000.0000.0000.000
98H99PRO0-0.053-0.00211.8711.0051.0050.0000.0000.0000.000
99H100VAL0-0.018-0.00910.6360.2920.2920.0000.0000.0000.000
100H101VAL0-0.002-0.01013.637-0.697-0.6970.0000.0000.0000.000
101H102ARG10.9360.97011.911-17.994-17.9940.0000.0000.0000.000
102H103LEU00.0200.01318.519-0.371-0.3710.0000.0000.0000.000
103H104GLY00.0580.02320.386-0.596-0.5960.0000.0000.0000.000
104H105TYR0-0.013-0.00117.5280.6290.6290.0000.0000.0000.000
105H106ASN0-0.047-0.02115.105-0.200-0.2000.0000.0000.0000.000
106H107PHE00.031-0.01014.3730.7500.7500.0000.0000.0000.000
107H108ASP-1-0.779-0.8949.96122.95522.9550.0000.0000.0000.000
108H109TYR00.0070.0185.7732.6922.737-0.001-0.002-0.0420.000
109H110TRP0-0.012-0.02410.235-1.939-1.9390.0000.0000.0000.000
110H111GLY00.0230.01810.8431.3791.3790.0000.0000.0000.000
111H112GLN00.0230.01012.6450.1500.1500.0000.0000.0000.000
112H113GLY0-0.022-0.00514.405-0.876-0.8760.0000.0000.0000.000
113H114SER0-0.049-0.03717.6960.2670.2670.0000.0000.0000.000
114H115THR00.006-0.00720.503-0.436-0.4360.0000.0000.0000.000
115H116LEU0-0.0070.00823.965-0.053-0.0530.0000.0000.0000.000
116H117THR0-0.029-0.01826.992-0.271-0.2710.0000.0000.0000.000
117H118VAL0-0.017-0.00730.463-0.051-0.0510.0000.0000.0000.000
118H119SER00.0440.00733.397-0.251-0.2510.0000.0000.0000.000
119H120SER00.0060.00436.4450.1560.1560.0000.0000.0000.000
120H121ALA00.0480.04837.721-0.128-0.1280.0000.0000.0000.000
121H122LYS10.9700.98537.346-7.129-7.1290.0000.0000.0000.000
122H123THR0-0.005-0.01733.391-0.058-0.0580.0000.0000.0000.000
123H124THR0-0.071-0.02936.005-0.278-0.2780.0000.0000.0000.000
124H125PRO00.0250.01035.7320.1650.1650.0000.0000.0000.000
125H126PRO0-0.0060.01234.414-0.199-0.1990.0000.0000.0000.000
126H127SER0-0.0130.00837.380-0.108-0.1080.0000.0000.0000.000
127H128VAL0-0.001-0.01436.2070.0300.0300.0000.0000.0000.000
128H129TYR0-0.020-0.02339.363-0.129-0.1290.0000.0000.0000.000
129H130PRO00.0120.00341.0890.1650.1650.0000.0000.0000.000
130H131LEU0-0.039-0.00740.504-0.163-0.1630.0000.0000.0000.000
131H132ALA00.0340.01643.1090.1190.1190.0000.0000.0000.000
132H133PRO0-0.0040.00045.375-0.103-0.1030.0000.0000.0000.000
133H134GLY00.0300.01147.966-0.043-0.0430.0000.0000.0000.000
134H135SER0-0.062-0.02651.367-0.113-0.1130.0000.0000.0000.000
135H136ALA00.0500.00251.740-0.095-0.0950.0000.0000.0000.000
136H137ALA00.0200.01647.354-0.015-0.0150.0000.0000.0000.000
137H138GLN00.0460.03448.8770.1720.1720.0000.0000.0000.000
138H139THR0-0.044-0.02650.884-0.015-0.0150.0000.0000.0000.000
139H140ASN0-0.044-0.01146.872-0.103-0.1030.0000.0000.0000.000
140H141SER00.0240.01146.0750.0560.0560.0000.0000.0000.000
141H142MET0-0.058-0.01241.6810.1830.1830.0000.0000.0000.000
142H143VAL00.0340.01642.635-0.144-0.1440.0000.0000.0000.000
143H144THR0-0.029-0.02540.1190.1540.1540.0000.0000.0000.000
144H145LEU0-0.034-0.01339.788-0.175-0.1750.0000.0000.0000.000
145H146GLY00.0770.00738.3600.1620.1620.0000.0000.0000.000
146H147CYS0-0.0980.00334.1280.0740.0740.0000.0000.0000.000
147H148LEU0-0.0040.01037.7320.1170.1170.0000.0000.0000.000
148H149VAL0-0.008-0.00433.983-0.087-0.0870.0000.0000.0000.000
149H150LYS10.9960.97137.208-6.996-6.9960.0000.0000.0000.000
150H151GLY00.0020.00439.533-0.029-0.0290.0000.0000.0000.000
151H152TYR00.0120.00531.682-0.123-0.1230.0000.0000.0000.000
152H153PHE00.0140.02234.3600.0270.0270.0000.0000.0000.000
153H154PRO00.0030.00230.236-0.104-0.1040.0000.0000.0000.000
154H155GLU-1-0.783-0.87728.4299.9699.9690.0000.0000.0000.000
155H156PRO0-0.025-0.02224.6670.1280.1280.0000.0000.0000.000
156H157VAL00.016-0.01027.945-0.051-0.0510.0000.0000.0000.000
157H158THR0-0.060-0.02224.1740.2460.2460.0000.0000.0000.000
158H159VAL00.019-0.01227.324-0.318-0.3180.0000.0000.0000.000
159H160THR0-0.018-0.00726.3340.3250.3250.0000.0000.0000.000
160H161TRP00.008-0.00229.254-0.408-0.4080.0000.0000.0000.000
161H162ASN00.012-0.00531.2850.1240.1240.0000.0000.0000.000
162H163SER0-0.018-0.02628.7680.0700.0700.0000.0000.0000.000
163H164GLY0-0.0060.00226.9060.4230.4230.0000.0000.0000.000
164H165SER0-0.043-0.01527.8710.1140.1140.0000.0000.0000.000
165H166LEU0-0.042-0.00830.205-0.213-0.2130.0000.0000.0000.000
166H167SER00.020-0.00927.183-0.016-0.0160.0000.0000.0000.000
167H168SER00.0220.00429.499-0.007-0.0070.0000.0000.0000.000
168H169GLY00.0230.02231.062-0.052-0.0520.0000.0000.0000.000
169H170VAL0-0.052-0.02230.587-0.262-0.2620.0000.0000.0000.000
170H171HIS00.0250.02931.5540.3380.3380.0000.0000.0000.000
171H172THR0-0.005-0.01029.651-0.337-0.3370.0000.0000.0000.000
172H173PHE0-0.029-0.00930.9060.1840.1840.0000.0000.0000.000
173H174PRO00.012-0.00230.6470.1100.1100.0000.0000.0000.000
174H175ALA00.0200.01631.723-0.290-0.2900.0000.0000.0000.000
175H176VAL0-0.029-0.00733.7210.0170.0170.0000.0000.0000.000
176H177LEU0-0.025-0.01936.243-0.020-0.0200.0000.0000.0000.000
177H178GLN0-0.018-0.02038.232-0.131-0.1310.0000.0000.0000.000
178H179SER0-0.029-0.01841.858-0.042-0.0420.0000.0000.0000.000
179H180ASP-1-0.935-0.96639.8097.3527.3520.0000.0000.0000.000
180H181LEU0-0.033-0.00538.4790.1550.1550.0000.0000.0000.000
181H182TYR0-0.0100.00332.866-0.064-0.0640.0000.0000.0000.000
182H183THR0-0.002-0.00836.710-0.120-0.1200.0000.0000.0000.000
183H184LEU0-0.0050.02531.3080.0090.0090.0000.0000.0000.000
184H185SER00.009-0.00135.629-0.153-0.1530.0000.0000.0000.000
185H186SER00.0100.00232.4240.1760.1760.0000.0000.0000.000
186H187SER00.0240.01035.016-0.147-0.1470.0000.0000.0000.000
187H188VAL00.0350.01734.7360.2690.2690.0000.0000.0000.000
188H189THR0-0.0090.00736.458-0.332-0.3320.0000.0000.0000.000
189H190VAL0-0.0110.00137.2180.2290.2290.0000.0000.0000.000
190H191PRO00.0660.01639.271-0.206-0.2060.0000.0000.0000.000
191H192SER00.0430.01942.5310.0600.0600.0000.0000.0000.000
192H193SER0-0.009-0.00444.682-0.028-0.0280.0000.0000.0000.000
193H194THR0-0.045-0.01939.1710.1080.1080.0000.0000.0000.000
194H195TRP00.0300.02341.9990.0040.0040.0000.0000.0000.000
195H196PRO0-0.036-0.04643.924-0.102-0.1020.0000.0000.0000.000
196H197SER0-0.051-0.01744.6860.0470.0470.0000.0000.0000.000
197H198GLU-1-0.855-0.91640.3927.6277.6270.0000.0000.0000.000
198H199THR0-0.062-0.04438.918-0.114-0.1140.0000.0000.0000.000
199H200VAL00.0290.02337.1950.2180.2180.0000.0000.0000.000
200H201THR00.006-0.01435.883-0.308-0.3080.0000.0000.0000.000
201H203ASN00.0380.00330.262-0.062-0.0620.0000.0000.0000.000
202H204VAL0-0.008-0.00530.7800.2200.2200.0000.0000.0000.000
203H205ALA00.0020.00527.708-0.087-0.0870.0000.0000.0000.000
204H206HIS00.0370.03529.3730.0180.0180.0000.0000.0000.000
205H207PRO00.018-0.00325.381-0.182-0.1820.0000.0000.0000.000
206H208ALA00.0240.02827.956-0.077-0.0770.0000.0000.0000.000
207H209SER0-0.026-0.02629.988-0.213-0.2130.0000.0000.0000.000
208H210SER0-0.035-0.01630.116-0.076-0.0760.0000.0000.0000.000
209H211THR0-0.011-0.01031.148-0.260-0.2600.0000.0000.0000.000
210H212LYS10.9480.95927.497-10.758-10.7580.0000.0000.0000.000
211H213VAL0-0.009-0.00632.740-0.310-0.3100.0000.0000.0000.000
212H214ASP-1-0.817-0.88033.3639.7369.7360.0000.0000.0000.000
213H215LYS10.8860.93735.901-7.820-7.8200.0000.0000.0000.000
214H216LYS10.9680.98238.629-7.373-7.3730.0000.0000.0000.000
215H217ILE0-0.011-0.01539.675-0.172-0.1720.0000.0000.0000.000
216H218VAL0-0.0210.00242.360-0.002-0.0020.0000.0000.0000.000
217H219PRO00.0240.01845.930-0.041-0.0410.0000.0000.0000.000