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: K9QL3

Calculation Name: 3GHE-H-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3GHE

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 220
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2242692.324881
FMO2-HF: Nuclear repulsion 2157144.006574
FMO2-HF: Total energy -85548.318307
FMO2-MP2: Total energy -85797.550302


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:GLN)


Summations of interaction energy for fragment #1(H:1:GLN)
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.
-17.872-14.49110.011-5.718-7.675-0.033
Interaction energy analysis for fragmet #1(H:1:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.007 / q_NPA : 0.004
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].
3H3GLN00.001-0.0081.947-20.597-17.43210.014-5.620-7.559-0.033
4H4LEU00.0190.0104.3611.6441.765-0.001-0.042-0.0780.000
5H5VAL0-0.030-0.0127.8300.3920.3920.0000.0000.0000.000
6H6GLN00.0410.03310.3190.0700.0700.0000.0000.0000.000
7H7SER0-0.068-0.04013.8380.1120.1120.0000.0000.0000.000
8H8GLY00.0650.02617.102-0.034-0.0340.0000.0000.0000.000
9H9GLY0-0.038-0.00319.9400.0360.0360.0000.0000.0000.000
10H10GLY00.0370.01121.6530.0240.0240.0000.0000.0000.000
11H11LEU0-0.040-0.01324.884-0.004-0.0040.0000.0000.0000.000
12H12VAL0-0.0080.00128.2250.0050.0050.0000.0000.0000.000
13H13GLN00.0160.00930.9700.0090.0090.0000.0000.0000.000
14H14PRO00.003-0.01533.691-0.015-0.0150.0000.0000.0000.000
15H15GLY0-0.028-0.01034.2660.0110.0110.0000.0000.0000.000
16H16GLY0-0.0180.00332.744-0.004-0.0040.0000.0000.0000.000
17H17SER0-0.023-0.03129.740-0.008-0.0080.0000.0000.0000.000
18H18LEU0-0.0020.00424.5320.0080.0080.0000.0000.0000.000
19H19ARG10.9350.96820.7330.6710.6710.0000.0000.0000.000
20H20LEU0-0.0330.00518.823-0.015-0.0150.0000.0000.0000.000
21H21SER00.006-0.01317.0690.0350.0350.0000.0000.0000.000
22H22CYS0-0.070-0.01712.417-0.076-0.0760.0000.0000.0000.000
23H23VAL00.0040.02310.9670.0890.0890.0000.0000.0000.000
24H24ALA00.0180.0179.123-0.398-0.3980.0000.0000.0000.000
25H25SER00.010-0.0085.3851.0611.0610.0000.0000.0000.000
26H26GLY00.0290.0144.118-2.177-2.184-0.001-0.0490.0560.000
27H27PHE0-0.004-0.0124.8600.6480.750-0.001-0.007-0.0940.000
28H28THR00.0280.0188.2100.0450.0450.0000.0000.0000.000
29H29PHE00.0530.02511.8000.1640.1640.0000.0000.0000.000
30H30ASN0-0.020-0.01313.3400.0100.0100.0000.0000.0000.000
31H31ASN00.0150.00214.5820.1820.1820.0000.0000.0000.000
32H32TYR0-0.0150.00011.474-0.051-0.0510.0000.0000.0000.000
33H33TRP00.0850.07216.2470.0060.0060.0000.0000.0000.000
34H34MET0-0.058-0.02411.672-0.223-0.2230.0000.0000.0000.000
35H35SER00.061-0.02515.4200.2100.2100.0000.0000.0000.000
36H36TRP0-0.052-0.02515.869-0.186-0.1860.0000.0000.0000.000
37H37VAL0-0.0020.00216.6430.0990.0990.0000.0000.0000.000
38H38ARG10.7890.88117.8760.3860.3860.0000.0000.0000.000
39H39GLN0-0.003-0.00617.999-0.022-0.0220.0000.0000.0000.000
40H40ALA00.0340.02620.9040.0150.0150.0000.0000.0000.000
41H41PRO00.018-0.01323.5260.0090.0090.0000.0000.0000.000
42H42GLY00.0040.00623.4950.0120.0120.0000.0000.0000.000
43H43LYS10.9270.97523.9680.2310.2310.0000.0000.0000.000
44H44GLY00.0430.02522.176-0.009-0.0090.0000.0000.0000.000
45H45LEU0-0.018-0.01216.733-0.009-0.0090.0000.0000.0000.000
46H46GLU-1-0.821-0.88920.858-0.369-0.3690.0000.0000.0000.000
47H47TRP0-0.028-0.00719.554-0.005-0.0050.0000.0000.0000.000
48H48VAL0-0.018-0.01921.0480.0560.0560.0000.0000.0000.000
49H49ALA00.009-0.01021.2920.0540.0540.0000.0000.0000.000
50H50ASN0-0.032-0.03019.701-0.034-0.0340.0000.0000.0000.000
51H51ILE0-0.056-0.01219.5710.0730.0730.0000.0000.0000.000
52H52LYS10.9911.01020.2390.5080.5080.0000.0000.0000.000
53H52GLN00.019-0.00719.2940.0330.0330.0000.0000.0000.000
54H53ASP-1-0.834-0.92620.905-0.635-0.6350.0000.0000.0000.000
55H54GLY0-0.076-0.03823.0090.0320.0320.0000.0000.0000.000
56H55ASN0-0.037-0.02224.0810.0360.0360.0000.0000.0000.000
57H56ASP-1-0.853-0.91326.334-0.479-0.4790.0000.0000.0000.000
58H57LYS10.8320.92224.7890.5250.5250.0000.0000.0000.000
59H58TYR0-0.036-0.02024.8300.0590.0590.0000.0000.0000.000
60H59TYR00.0220.00124.854-0.060-0.0600.0000.0000.0000.000
61H60VAL00.0590.04326.1480.0290.0290.0000.0000.0000.000
62H61ASP-1-0.799-0.92227.849-0.328-0.3280.0000.0000.0000.000
63H62SER0-0.0100.00629.4170.0030.0030.0000.0000.0000.000
64H63VAL00.005-0.00326.3830.0110.0110.0000.0000.0000.000
65H64LYS10.8460.93929.8400.3460.3460.0000.0000.0000.000
66H65GLY00.0070.00731.4490.0230.0230.0000.0000.0000.000
67H66ARG10.7120.83230.0880.3400.3400.0000.0000.0000.000
68H67PHE00.005-0.01625.071-0.013-0.0130.0000.0000.0000.000
69H68THR0-0.011-0.00226.7900.0140.0140.0000.0000.0000.000
70H69ILE00.0100.02419.740-0.026-0.0260.0000.0000.0000.000
71H70SER0-0.018-0.02022.1090.0450.0450.0000.0000.0000.000
72H71ARG10.8340.91617.0441.0901.0900.0000.0000.0000.000
73H72ASP-1-0.786-0.88519.313-0.742-0.7420.0000.0000.0000.000
74H73ASN00.003-0.02717.559-0.204-0.2040.0000.0000.0000.000
75H74ALA0-0.0030.02217.116-0.069-0.0690.0000.0000.0000.000
76H75LYS10.8690.91716.4480.7570.7570.0000.0000.0000.000
77H76ASN0-0.0100.01112.150-0.068-0.0680.0000.0000.0000.000
78H77SER0-0.003-0.00413.664-0.193-0.1930.0000.0000.0000.000
79H78LEU0-0.025-0.00615.2180.1080.1080.0000.0000.0000.000
80H79PHE0-0.027-0.03717.177-0.012-0.0120.0000.0000.0000.000
81H80LEU00.0330.01020.0160.0120.0120.0000.0000.0000.000
82H81GLN0-0.035-0.01122.204-0.005-0.0050.0000.0000.0000.000
83H82MET0-0.025-0.00723.2310.0070.0070.0000.0000.0000.000
84H82ASN00.0620.02727.2030.0210.0210.0000.0000.0000.000
85H82SER00.0170.00231.0010.0050.0050.0000.0000.0000.000
86H82LEU0-0.0110.01227.1450.0020.0020.0000.0000.0000.000
87H83ARG10.9260.96030.8950.2580.2580.0000.0000.0000.000
88H84ALA00.0680.03830.733-0.014-0.0140.0000.0000.0000.000
89H85GLU-1-0.846-0.92830.304-0.236-0.2360.0000.0000.0000.000
90H86ASP-1-0.786-0.84927.250-0.366-0.3660.0000.0000.0000.000
91H87THR0-0.030-0.00825.859-0.037-0.0370.0000.0000.0000.000
92H88ALA0-0.015-0.01322.1300.0130.0130.0000.0000.0000.000
93H89VAL0-0.0270.00516.561-0.007-0.0070.0000.0000.0000.000
94H90TYR0-0.012-0.03818.235-0.027-0.0270.0000.0000.0000.000
95H91PHE00.029-0.00712.514-0.070-0.0700.0000.0000.0000.000
96H93ALA00.029-0.00511.355-0.276-0.2760.0000.0000.0000.000
97H94ARG10.8050.8828.4732.8492.8490.0000.0000.0000.000
98H95GLU-1-0.814-0.86112.362-0.904-0.9040.0000.0000.0000.000
99H96PHE0-0.036-0.03513.315-0.060-0.0600.0000.0000.0000.000
100H97SER0-0.006-0.01715.3040.0980.0980.0000.0000.0000.000
101H98SER0-0.039-0.02418.1600.0080.0080.0000.0000.0000.000
102H99TYR0-0.021-0.01320.1220.0400.0400.0000.0000.0000.000
103H100THR0-0.010-0.01322.6660.0340.0340.0000.0000.0000.000
104H100ASP-1-0.894-0.95625.578-0.243-0.2430.0000.0000.0000.000
105H100HIS0-0.039-0.00928.4870.0160.0160.0000.0000.0000.000
106H100LEU00.0180.00831.8340.0160.0160.0000.0000.0000.000
107H100GLU-1-0.950-0.96333.826-0.157-0.1570.0000.0000.0000.000
108H100TYR0-0.105-0.05831.982-0.004-0.0040.0000.0000.0000.000
109H100TYR00.0260.01427.5730.0040.0040.0000.0000.0000.000
110H100TYR0-0.045-0.01726.886-0.006-0.0060.0000.0000.0000.000
111H100ASP-1-0.777-0.87022.861-0.594-0.5940.0000.0000.0000.000
112H100TYR0-0.037-0.00822.545-0.004-0.0040.0000.0000.0000.000
113H100TYR0-0.020-0.03418.491-0.084-0.0840.0000.0000.0000.000
114H100TYR0-0.0030.00416.5270.0570.0570.0000.0000.0000.000
115H100MET0-0.015-0.01413.340-0.084-0.0840.0000.0000.0000.000
116H101ASP-1-0.756-0.84210.631-2.102-2.1020.0000.0000.0000.000
117H102VAL0-0.046-0.0135.567-0.463-0.4630.0000.0000.0000.000
118H103TRP00.016-0.0107.6100.5630.5630.0000.0000.0000.000
119H104GLY00.0110.0127.452-0.618-0.6180.0000.0000.0000.000
120H105LYS10.9490.9689.2160.9490.9490.0000.0000.0000.000
121H106GLY00.0000.00110.4370.2050.2050.0000.0000.0000.000
122H107THR0-0.040-0.02913.9730.1000.1000.0000.0000.0000.000
123H108THR00.003-0.00417.114-0.021-0.0210.0000.0000.0000.000
124H109VAL0-0.0110.01220.3990.0060.0060.0000.0000.0000.000
125H110THR0-0.011-0.01023.6500.0230.0230.0000.0000.0000.000
126H111VAL00.0060.01026.9080.0020.0020.0000.0000.0000.000
127H112SER00.014-0.00430.2040.0140.0140.0000.0000.0000.000
128H113SER00.0480.01433.294-0.006-0.0060.0000.0000.0000.000
129H114ALA0-0.0400.00435.4300.0100.0100.0000.0000.0000.000
130H115SER00.0250.00236.366-0.011-0.0110.0000.0000.0000.000
131H116THR0-0.036-0.02535.9210.0040.0040.0000.0000.0000.000
132H117LYS10.8160.90237.4390.0600.0600.0000.0000.0000.000
133H118GLY00.0890.05638.7290.0020.0020.0000.0000.0000.000
134H119PRO0-0.019-0.00938.949-0.003-0.0030.0000.0000.0000.000
135H120SER0-0.039-0.01141.1750.0010.0010.0000.0000.0000.000
136H121VAL00.002-0.01142.1020.0010.0010.0000.0000.0000.000
137H122PHE00.0040.00244.5640.0000.0000.0000.0000.0000.000
138H123PRO0-0.0060.00645.6810.0030.0030.0000.0000.0000.000
139H124LEU0-0.043-0.02443.433-0.003-0.0030.0000.0000.0000.000
140H125ALA00.0320.00747.5970.0050.0050.0000.0000.0000.000
141H126PRO00.0090.02150.272-0.001-0.0010.0000.0000.0000.000
142H134GLY00.0860.04852.9880.0000.0000.0000.0000.0000.000
143H135THR0-0.110-0.06047.658-0.001-0.0010.0000.0000.0000.000
144H136ALA00.0270.01749.188-0.004-0.0040.0000.0000.0000.000
145H137ALA00.0050.01345.1930.0050.0050.0000.0000.0000.000
146H138LEU00.0270.02345.544-0.005-0.0050.0000.0000.0000.000
147H139GLY00.046-0.00543.3950.0060.0060.0000.0000.0000.000
148H140CYS0-0.0810.00141.7800.0010.0010.0000.0000.0000.000
149H141LEU00.0210.02341.1630.0010.0010.0000.0000.0000.000
150H142VAL0-0.030-0.01537.950-0.002-0.0020.0000.0000.0000.000
151H143LYS10.9780.97239.2080.0340.0340.0000.0000.0000.000
152H144ASP-1-0.824-0.91339.746-0.056-0.0560.0000.0000.0000.000
153H145TYR0-0.026-0.01832.8020.0020.0020.0000.0000.0000.000
154H146PHE00.0230.02332.327-0.006-0.0060.0000.0000.0000.000
155H147PRO00.0170.01130.5560.0040.0040.0000.0000.0000.000
156H148GLU-1-0.773-0.87028.680-0.030-0.0300.0000.0000.0000.000
157H149PRO0-0.036-0.02528.170-0.011-0.0110.0000.0000.0000.000
158H150VAL00.020-0.00930.475-0.003-0.0030.0000.0000.0000.000
159H151THR0-0.032-0.00531.3630.0070.0070.0000.0000.0000.000
160H152VAL0-0.014-0.02233.854-0.008-0.0080.0000.0000.0000.000
161H153SER0-0.0060.00635.9290.0110.0110.0000.0000.0000.000
162H154TRP00.0200.02338.325-0.011-0.0110.0000.0000.0000.000
163H155ASN00.0070.00641.7290.0020.0020.0000.0000.0000.000
164H156SER0-0.001-0.01441.8330.0020.0020.0000.0000.0000.000
165H157GLY0-0.015-0.00439.1350.0040.0040.0000.0000.0000.000
166H158ALA0-0.030-0.01039.9500.0080.0080.0000.0000.0000.000
167H159LEU0-0.0230.00641.7660.0030.0030.0000.0000.0000.000
168H160THR00.020-0.00336.690-0.003-0.0030.0000.0000.0000.000
169H161SER00.0010.00037.3740.0080.0080.0000.0000.0000.000
170H162GLY00.0330.01638.820-0.007-0.0070.0000.0000.0000.000
171H163VAL0-0.0190.00036.876-0.011-0.0110.0000.0000.0000.000
172H164HIS00.0150.00632.8980.0120.0120.0000.0000.0000.000
173H165THR00.0040.00833.577-0.013-0.0130.0000.0000.0000.000
174H166PHE0-0.006-0.00132.8820.0070.0070.0000.0000.0000.000
175H167PRO0-0.001-0.00329.121-0.007-0.0070.0000.0000.0000.000
176H168ALA00.0150.00431.139-0.002-0.0020.0000.0000.0000.000
177H169VAL0-0.031-0.00931.880-0.005-0.0050.0000.0000.0000.000
178H170LEU0-0.031-0.01430.885-0.002-0.0020.0000.0000.0000.000
179H171GLN0-0.060-0.04233.8930.0060.0060.0000.0000.0000.000
180H172SER00.0440.00736.736-0.009-0.0090.0000.0000.0000.000
181H173SER0-0.021-0.00238.731-0.008-0.0080.0000.0000.0000.000
182H174GLY00.0110.00735.642-0.005-0.0050.0000.0000.0000.000
183H175LEU0-0.053-0.02435.352-0.004-0.0040.0000.0000.0000.000
184H176TYR00.0130.00629.083-0.005-0.0050.0000.0000.0000.000
185H177SER00.0270.00235.6050.0050.0050.0000.0000.0000.000
186H178LEU00.0180.04233.433-0.001-0.0010.0000.0000.0000.000
187H179SER0-0.001-0.01136.650-0.002-0.0020.0000.0000.0000.000
188H180SER0-0.024-0.01137.2160.0060.0060.0000.0000.0000.000
189H181VAL00.003-0.01138.719-0.005-0.0050.0000.0000.0000.000
190H182VAL00.0380.00539.8920.0080.0080.0000.0000.0000.000
191H183THR0-0.042-0.01442.283-0.006-0.0060.0000.0000.0000.000
192H184VAL00.0010.00144.6370.0060.0060.0000.0000.0000.000
193H185PRO00.0440.01247.474-0.003-0.0030.0000.0000.0000.000
194H186SER00.0610.01250.835-0.003-0.0030.0000.0000.0000.000
195H187SER0-0.026-0.01153.550-0.002-0.0020.0000.0000.0000.000
196H188SER0-0.028-0.01251.844-0.001-0.0010.0000.0000.0000.000
197H189LEU00.0140.00551.151-0.001-0.0010.0000.0000.0000.000
198H190GLY00.0110.01754.345-0.003-0.0030.0000.0000.0000.000
199H191THR0-0.033-0.01856.338-0.001-0.0010.0000.0000.0000.000
200H192GLN0-0.058-0.02849.9460.0020.0020.0000.0000.0000.000
201H193THR0-0.0100.00551.824-0.002-0.0020.0000.0000.0000.000
202H194TYR00.0650.02046.7360.0060.0060.0000.0000.0000.000
203H195THR0-0.005-0.01345.917-0.007-0.0070.0000.0000.0000.000
204H197ASN00.023-0.01640.2740.0000.0000.0000.0000.0000.000
205H198VAL00.0070.00038.2400.0040.0040.0000.0000.0000.000
206H199ASN0-0.054-0.03834.418-0.009-0.0090.0000.0000.0000.000
207H200HIS00.0550.03634.3600.0070.0070.0000.0000.0000.000
208H201LYS10.9940.98231.203-0.018-0.0180.0000.0000.0000.000
209H202PRO0-0.0090.02231.787-0.004-0.0040.0000.0000.0000.000
210H203SER00.002-0.02734.332-0.007-0.0070.0000.0000.0000.000
211H204ASN0-0.085-0.04137.0520.0100.0100.0000.0000.0000.000
212H205THR00.0150.02038.8800.0030.0030.0000.0000.0000.000
213H206LYS10.9270.95738.394-0.014-0.0140.0000.0000.0000.000
214H207VAL00.004-0.00241.602-0.003-0.0030.0000.0000.0000.000
215H208ASP-1-0.833-0.89043.0840.0300.0300.0000.0000.0000.000
216H209LYS10.8880.94145.256-0.011-0.0110.0000.0000.0000.000
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