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: K9V13

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 OptHSide
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 -2217059.641981
FMO2-HF: Nuclear repulsion 2133794.395043
FMO2-HF: Total energy -83265.246938
FMO2-MP2: Total energy -83506.154564


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.
-78.382-76.0950.049-0.885-1.450.004
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 : -0.927 / q_NPA : -0.977
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].
3H3GLN0-0.011-0.0053.564-5.720-3.8860.004-0.668-1.1690.004
4H4LEU0-0.036-0.0275.999-1.306-1.3060.0000.0000.0000.000
5H5GLN00.0440.0289.789-0.602-0.6020.0000.0000.0000.000
6H6GLN00.007-0.02711.975-0.256-0.2560.0000.0000.0000.000
7H7SER00.0210.02715.6040.2200.2200.0000.0000.0000.000
8H8GLY00.0160.00918.6960.0570.0570.0000.0000.0000.000
9H9ALA0-0.040-0.01621.031-0.176-0.1760.0000.0000.0000.000
10H10GLU-1-0.892-0.94724.01711.39311.3930.0000.0000.0000.000
11H11LEU0-0.029-0.00826.811-0.214-0.2140.0000.0000.0000.000
12H12ALA00.0200.00730.560-0.038-0.0380.0000.0000.0000.000
13H13ARG10.8670.91532.671-8.495-8.4950.0000.0000.0000.000
14H14PRO00.031-0.00335.9040.1280.1280.0000.0000.0000.000
15H15GLY0-0.018-0.00437.293-0.156-0.1560.0000.0000.0000.000
16H16ALA0-0.040-0.00534.717-0.010-0.0100.0000.0000.0000.000
17H17SER0-0.041-0.02931.8180.0990.0990.0000.0000.0000.000
18H18VAL00.0390.02126.628-0.014-0.0140.0000.0000.0000.000
19H19LYS10.9230.96223.817-11.284-11.2840.0000.0000.0000.000
20H20MET00.0150.03621.1150.2280.2280.0000.0000.0000.000
21H21SER00.008-0.01517.9590.1720.1720.0000.0000.0000.000
22H22CYS0-0.0260.00214.0790.1890.1890.0000.0000.0000.000
23H23LYS10.8950.95511.079-23.175-23.1750.0000.0000.0000.000
24H24ALA00.0050.0099.6061.2211.2210.0000.0000.0000.000
25H25SER0-0.048-0.0336.0700.4120.4120.0000.0000.0000.000
26H26GLY00.1100.0473.3280.2590.4960.047-0.184-0.1000.000
27H27TYR0-0.015-0.0103.885-0.480-0.326-0.001-0.029-0.1240.000
28H28THR00.0140.0076.902-0.376-0.3760.0000.0000.0000.000
29H29PHE00.0490.02210.547-1.387-1.3870.0000.0000.0000.000
30H30THR00.016-0.01612.267-0.687-0.6870.0000.0000.0000.000
31H31SER0-0.046-0.01312.539-0.749-0.7490.0000.0000.0000.000
32H32TYR0-0.019-0.0049.9920.1300.1300.0000.0000.0000.000
33H33THR0-0.0180.00714.219-0.344-0.3440.0000.0000.0000.000
34H34MET0-0.002-0.00512.0830.9870.9870.0000.0000.0000.000
35H35HIS0-0.019-0.01016.484-1.248-1.2480.0000.0000.0000.000
36H36TRP00.0300.01117.7000.7800.7800.0000.0000.0000.000
37H37VAL0-0.035-0.01919.723-0.566-0.5660.0000.0000.0000.000
38H38LYS10.8820.94521.698-9.648-9.6480.0000.0000.0000.000
39H39GLN00.0310.02122.8110.3470.3470.0000.0000.0000.000
40H40ARG10.8270.90225.337-8.830-8.8300.0000.0000.0000.000
41H41PRO00.0230.00028.4270.1410.1410.0000.0000.0000.000
42H42GLY00.0280.01628.791-0.302-0.3020.0000.0000.0000.000
43H43GLN0-0.017-0.00428.899-0.274-0.2740.0000.0000.0000.000
44H44GLY00.0330.02027.4320.3640.3640.0000.0000.0000.000
45H45LEU0-0.0030.00621.4600.0460.0460.0000.0000.0000.000
46H46GLU-1-0.817-0.88925.2129.3009.3000.0000.0000.0000.000
47H47TRP0-0.0120.00121.6830.0740.0740.0000.0000.0000.000
48H48ILE00.0000.00423.468-0.474-0.4740.0000.0000.0000.000
49H49GLY00.0500.00823.504-0.514-0.5140.0000.0000.0000.000
50H50TYR0-0.050-0.01720.2560.5540.5540.0000.0000.0000.000
51H51ILE00.0370.01519.105-0.550-0.5500.0000.0000.0000.000
52H52ASN00.0390.03619.2391.3461.3460.0000.0000.0000.000
53H53PRO00.017-0.00916.022-0.665-0.6650.0000.0000.0000.000
54H54SER0-0.055-0.03118.920-0.345-0.3450.0000.0000.0000.000
55H55SER0-0.021-0.01620.191-0.428-0.4280.0000.0000.0000.000
56H56GLY0-0.0140.00822.608-0.428-0.4280.0000.0000.0000.000
57H57TYR00.0020.01224.203-0.376-0.3760.0000.0000.0000.000
58H58SER00.0250.00323.7790.4460.4460.0000.0000.0000.000
59H59ASN0-0.0220.00325.218-0.709-0.7090.0000.0000.0000.000
60H60TYR00.0160.00125.8780.4240.4240.0000.0000.0000.000
61H61ASN00.0010.00127.961-0.592-0.5920.0000.0000.0000.000
62H62GLN00.0590.01929.4850.0960.0960.0000.0000.0000.000
63H63LYS10.8420.90031.762-9.253-9.2530.0000.0000.0000.000
64H64PHE0-0.003-0.01629.091-0.038-0.0380.0000.0000.0000.000
65H65LYS10.9160.96930.898-8.782-8.7820.0000.0000.0000.000
66H66ASP-1-0.884-0.93132.5428.3408.3400.0000.0000.0000.000
67H67LYS10.7310.88931.227-8.991-8.9910.0000.0000.0000.000
68H68ALA00.009-0.02326.5950.1600.1600.0000.0000.0000.000
69H69THR0-0.035-0.01027.572-0.197-0.1970.0000.0000.0000.000
70H70LEU0-0.012-0.00422.0090.3370.3370.0000.0000.0000.000
71H71THR0-0.015-0.00622.922-0.164-0.1640.0000.0000.0000.000
72H72ALA0-0.005-0.01518.6030.6140.6140.0000.0000.0000.000
73H73ASP-1-0.774-0.82818.80914.47214.4720.0000.0000.0000.000
74H74LYS10.9760.97317.012-15.341-15.3410.0000.0000.0000.000
75H75SER0-0.082-0.04616.1720.9750.9750.0000.0000.0000.000
76H76SER00.034-0.01315.7530.9020.9020.0000.0000.0000.000
77H77SER0-0.046-0.01311.9371.5291.5290.0000.0000.0000.000
78H78THR0-0.016-0.01013.1291.3101.3100.0000.0000.0000.000
79H79ALA0-0.0140.00215.693-0.926-0.9260.0000.0000.0000.000
80H80TYR00.005-0.02717.7760.1520.1520.0000.0000.0000.000
81H81MET00.0130.02020.979-0.305-0.3050.0000.0000.0000.000
82H82GLN0-0.022-0.01523.4010.1880.1880.0000.0000.0000.000
83H83LEU00.0110.01926.402-0.115-0.1150.0000.0000.0000.000
84H84SER00.0230.00029.364-0.185-0.1850.0000.0000.0000.000
85H85SER00.0640.02633.070-0.089-0.0890.0000.0000.0000.000
86H86LEU0-0.066-0.02130.487-0.053-0.0530.0000.0000.0000.000
87H87THR00.0450.01334.532-0.317-0.3170.0000.0000.0000.000
88H88SER00.0990.03434.3690.1950.1950.0000.0000.0000.000
89H89GLU-1-0.821-0.88234.0008.5738.5730.0000.0000.0000.000
90H90ASP-1-0.826-0.90130.6759.3809.3800.0000.0000.0000.000
91H91SER00.0110.03029.3360.4010.4010.0000.0000.0000.000
92H92ALA0-0.042-0.02726.525-0.174-0.1740.0000.0000.0000.000
93H93VAL00.0050.02720.8700.1120.1120.0000.0000.0000.000
94H94TYR00.000-0.04321.698-0.225-0.2250.0000.0000.0000.000
95H95TYR00.0020.00216.7420.5630.5630.0000.0000.0000.000
96H97SER00.025-0.01113.5190.5290.5290.0000.0000.0000.000
97H98ARG10.8760.9267.771-26.070-26.0700.0000.0000.0000.000
98H99PRO0-0.071-0.00911.8431.0261.0260.0000.0000.0000.000
99H100VAL0-0.021-0.00910.5710.3010.3010.0000.0000.0000.000
100H101VAL0-0.018-0.01713.611-0.686-0.6860.0000.0000.0000.000
101H102ARG10.9430.97311.261-18.711-18.7110.0000.0000.0000.000
102H103LEU00.0120.01318.497-0.386-0.3860.0000.0000.0000.000
103H104GLY00.0600.02220.363-0.606-0.6060.0000.0000.0000.000
104H105TYR0-0.017-0.00317.5430.6270.6270.0000.0000.0000.000
105H106ASN0-0.033-0.01715.181-0.176-0.1760.0000.0000.0000.000
106H107PHE00.037-0.00114.3460.7860.7860.0000.0000.0000.000
107H108ASP-1-0.767-0.88110.38322.68022.6800.0000.0000.0000.000
108H109TYR00.0040.0185.2111.1091.171-0.001-0.004-0.0570.000
109H110TRP0-0.019-0.02610.211-2.049-2.0490.0000.0000.0000.000
110H111GLY00.0400.02910.8351.3951.3950.0000.0000.0000.000
111H112GLN0-0.002-0.00212.6450.1870.1870.0000.0000.0000.000
112H113GLY0-0.022-0.00414.408-0.868-0.8680.0000.0000.0000.000
113H114SER0-0.036-0.02917.7000.2790.2790.0000.0000.0000.000
114H115THR0-0.004-0.01420.513-0.203-0.2030.0000.0000.0000.000
115H116LEU0-0.0080.01323.973-0.080-0.0800.0000.0000.0000.000
116H117THR0-0.020-0.01627.001-0.276-0.2760.0000.0000.0000.000
117H118VAL0-0.010-0.00430.472-0.049-0.0490.0000.0000.0000.000
118H119SER00.0450.01133.407-0.247-0.2470.0000.0000.0000.000
119H120SER00.0300.01436.4570.1390.1390.0000.0000.0000.000
120H121ALA00.0110.03137.737-0.140-0.1400.0000.0000.0000.000
121H122LYS10.9650.98037.363-7.131-7.1310.0000.0000.0000.000
122H123THR00.002-0.01433.525-0.072-0.0720.0000.0000.0000.000
123H124THR0-0.075-0.03136.026-0.282-0.2820.0000.0000.0000.000
124H125PRO00.0540.02535.7530.1650.1650.0000.0000.0000.000
125H126PRO0-0.0170.01334.312-0.197-0.1970.0000.0000.0000.000
126H127SER0-0.023-0.00137.398-0.100-0.1000.0000.0000.0000.000
127H128VAL0-0.011-0.02136.1830.0320.0320.0000.0000.0000.000
128H129TYR0-0.019-0.01939.379-0.113-0.1130.0000.0000.0000.000
129H130PRO00.0200.00841.1020.1670.1670.0000.0000.0000.000
130H131LEU0-0.045-0.01640.659-0.162-0.1620.0000.0000.0000.000
131H132ALA00.0290.01543.1170.1220.1220.0000.0000.0000.000
132H133PRO00.004-0.00145.299-0.107-0.1070.0000.0000.0000.000
133H134GLY00.0250.01147.972-0.044-0.0440.0000.0000.0000.000
134H135SER0-0.059-0.02551.364-0.107-0.1070.0000.0000.0000.000
135H136ALA00.0550.00951.742-0.096-0.0960.0000.0000.0000.000
136H137ALA00.0150.01047.344-0.011-0.0110.0000.0000.0000.000
137H138GLN00.0230.01948.8760.1350.1350.0000.0000.0000.000
138H139THR0-0.017-0.01050.885-0.014-0.0140.0000.0000.0000.000
139H140ASN0-0.048-0.01146.731-0.124-0.1240.0000.0000.0000.000
140H141SER00.0440.02046.2110.0610.0610.0000.0000.0000.000
141H142MET0-0.052-0.00841.8060.1730.1730.0000.0000.0000.000
142H143VAL00.0270.01242.959-0.141-0.1410.0000.0000.0000.000
143H144THR0-0.033-0.03239.9740.1510.1510.0000.0000.0000.000
144H145LEU0-0.027-0.00639.793-0.174-0.1740.0000.0000.0000.000
145H146GLY00.0720.00938.3680.1660.1660.0000.0000.0000.000
146H147CYS0-0.0850.00334.1400.0830.0830.0000.0000.0000.000
147H148LEU00.0000.01037.7400.1200.1200.0000.0000.0000.000
148H149VAL0-0.014-0.00533.953-0.091-0.0910.0000.0000.0000.000
149H150LYS10.9490.95137.220-7.074-7.0740.0000.0000.0000.000
150H151GLY00.0070.00639.544-0.028-0.0280.0000.0000.0000.000
151H152TYR00.004-0.00731.812-0.141-0.1410.0000.0000.0000.000
152H153PHE00.0150.02434.3870.0280.0280.0000.0000.0000.000
153H154PRO0-0.0020.00330.214-0.106-0.1060.0000.0000.0000.000
154H155GLU-1-0.783-0.86828.4549.9769.9760.0000.0000.0000.000
155H156PRO0-0.033-0.02424.6580.1310.1310.0000.0000.0000.000
156H157VAL00.028-0.00727.957-0.050-0.0500.0000.0000.0000.000
157H158THR0-0.018-0.00524.1510.2860.2860.0000.0000.0000.000
158H159VAL0-0.020-0.02727.338-0.315-0.3150.0000.0000.0000.000
159H160THR0-0.028-0.01126.2220.3610.3610.0000.0000.0000.000
160H161TRP00.0130.00529.266-0.407-0.4070.0000.0000.0000.000
161H162ASN00.016-0.01431.2970.1340.1340.0000.0000.0000.000
162H163SER0-0.022-0.02129.0750.0390.0390.0000.0000.0000.000
163H164GLY00.0000.00626.9430.4180.4180.0000.0000.0000.000
164H165SER0-0.050-0.02027.8840.1510.1510.0000.0000.0000.000
165H166LEU0-0.044-0.01130.356-0.214-0.2140.0000.0000.0000.000
166H167SER00.020-0.00927.219-0.019-0.0190.0000.0000.0000.000
167H168SER00.0290.00729.502-0.044-0.0440.0000.0000.0000.000
168H169GLY00.0250.02331.060-0.053-0.0530.0000.0000.0000.000
169H170VAL0-0.055-0.02530.605-0.271-0.2710.0000.0000.0000.000
170H171HIS00.0170.02331.5520.2610.2610.0000.0000.0000.000
171H172THR00.0070.00229.658-0.350-0.3500.0000.0000.0000.000
172H173PHE0-0.019-0.00330.9060.1880.1880.0000.0000.0000.000
173H174PRO00.0180.00230.8520.1180.1180.0000.0000.0000.000
174H175ALA00.0130.01231.725-0.291-0.2910.0000.0000.0000.000
175H176VAL0-0.027-0.01033.7240.0170.0170.0000.0000.0000.000
176H177LEU0-0.026-0.01436.213-0.020-0.0200.0000.0000.0000.000
177H178GLN00.009-0.00838.237-0.142-0.1420.0000.0000.0000.000
178H179SER0-0.027-0.02541.8640.0080.0080.0000.0000.0000.000
179H180ASP-1-0.915-0.95639.7987.3957.3950.0000.0000.0000.000
180H181LEU0-0.033-0.00638.4900.1500.1500.0000.0000.0000.000
181H182TYR0-0.0020.00532.630-0.071-0.0710.0000.0000.0000.000
182H183THR0-0.028-0.02236.720-0.154-0.1540.0000.0000.0000.000
183H184LEU00.0090.03531.3250.0150.0150.0000.0000.0000.000
184H185SER00.0370.01335.737-0.176-0.1760.0000.0000.0000.000
185H186SER0-0.019-0.01532.4020.1740.1740.0000.0000.0000.000
186H187SER00.0430.01535.021-0.244-0.2440.0000.0000.0000.000
187H188VAL0-0.008-0.00434.7190.2750.2750.0000.0000.0000.000
188H189THR00.0000.01236.461-0.276-0.2760.0000.0000.0000.000
189H190VAL00.0060.01037.1910.2300.2300.0000.0000.0000.000
190H191PRO00.0680.01939.404-0.201-0.2010.0000.0000.0000.000
191H192SER00.0160.00442.5310.0200.0200.0000.0000.0000.000
192H193SER00.0110.00744.029-0.072-0.0720.0000.0000.0000.000
193H194THR0-0.060-0.02239.1350.0790.0790.0000.0000.0000.000
194H195TRP00.0200.01142.0010.0130.0130.0000.0000.0000.000
195H196PRO0-0.020-0.03343.932-0.098-0.0980.0000.0000.0000.000
196H197SER0-0.043-0.02045.2010.0090.0090.0000.0000.0000.000
197H198GLU-1-0.872-0.92740.5537.6427.6420.0000.0000.0000.000
198H199THR0-0.054-0.03639.016-0.117-0.1170.0000.0000.0000.000
199H200VAL00.0390.03137.0900.2230.2230.0000.0000.0000.000
200H201THR00.009-0.00635.470-0.307-0.3070.0000.0000.0000.000
201H203ASN00.032-0.00130.280-0.029-0.0290.0000.0000.0000.000
202H204VAL0-0.012-0.01030.7960.2290.2290.0000.0000.0000.000
203H205ALA0-0.0110.00027.766-0.095-0.0950.0000.0000.0000.000
204H206HIS00.017-0.00929.392-0.004-0.0040.0000.0000.0000.000
205H207PRO00.019-0.00425.399-0.182-0.1820.0000.0000.0000.000
206H208ALA00.0230.02827.980-0.079-0.0790.0000.0000.0000.000
207H209SER00.001-0.00830.012-0.134-0.1340.0000.0000.0000.000
208H210SER0-0.036-0.01630.124-0.099-0.0990.0000.0000.0000.000
209H211THR0-0.038-0.00731.146-0.295-0.2950.0000.0000.0000.000
210H212LYS10.9940.98927.301-10.786-10.7860.0000.0000.0000.000
211H213VAL0-0.016-0.01132.766-0.309-0.3090.0000.0000.0000.000
212H214ASP-1-0.819-0.88433.3949.7639.7630.0000.0000.0000.000
213H215LYS10.8900.94135.923-7.838-7.8380.0000.0000.0000.000
214H216LYS10.9530.97638.646-7.373-7.3730.0000.0000.0000.000
215H217ILE0-0.021-0.01839.674-0.172-0.1720.0000.0000.0000.000
216H218VAL0-0.0240.00342.374-0.003-0.0030.0000.0000.0000.000
217H219PRO00.0280.02045.945-0.039-0.0390.0000.0000.0000.000