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: 49GVN

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 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 220
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2245167.159557
FMO2-HF: Nuclear repulsion 2159618.58492
FMO2-HF: Total energy -85548.574637
FMO2-MP2: Total energy -85797.857976


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.
-17.052-16.17912.674-5.73-7.817-0.04
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 : 0.018 / q_NPA : 0.007
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].
3H3GLN0-0.005-0.0071.854-20.953-20.39512.676-5.602-7.632-0.040
4H4LEU00.0210.0144.2181.9522.1020.000-0.052-0.0980.000
5H5VAL0-0.024-0.0087.5550.2800.2800.0000.0000.0000.000
6H6GLN00.0000.01210.0180.0210.0210.0000.0000.0000.000
7H7SER0-0.056-0.03213.6450.1570.1570.0000.0000.0000.000
8H8GLY00.0570.02217.141-0.034-0.0340.0000.0000.0000.000
9H9GLY0-0.0100.00419.9400.0310.0310.0000.0000.0000.000
10H10GLY00.010-0.00121.5860.0210.0210.0000.0000.0000.000
11H11LEU0-0.047-0.02524.6750.0000.0000.0000.0000.0000.000
12H12VAL0-0.0050.00828.1600.0070.0070.0000.0000.0000.000
13H13GLN00.0080.00030.9130.0100.0100.0000.0000.0000.000
14H14PRO0-0.014-0.02533.790-0.015-0.0150.0000.0000.0000.000
15H15GLY0-0.0060.00934.5790.0120.0120.0000.0000.0000.000
16H16GLY0-0.0010.00832.836-0.006-0.0060.0000.0000.0000.000
17H17SER0-0.029-0.02829.845-0.007-0.0070.0000.0000.0000.000
18H18LEU0-0.0020.00124.3290.0090.0090.0000.0000.0000.000
19H19ARG10.9270.95420.6470.7120.7120.0000.0000.0000.000
20H20LEU0-0.0150.02618.870-0.025-0.0250.0000.0000.0000.000
21H21SER00.028-0.00917.3290.0460.0460.0000.0000.0000.000
22H22CYS0-0.079-0.02412.260-0.061-0.0610.0000.0000.0000.000
23H23VAL00.0040.02111.2770.1500.1500.0000.0000.0000.000
24H24ALA00.0130.0148.899-0.358-0.3580.0000.0000.0000.000
25H25SER00.017-0.0024.9801.1331.1330.0000.0000.0000.000
26H26GLY00.0260.0084.284-1.841-1.795-0.001-0.0680.0230.000
27H27PHE0-0.014-0.0125.0420.9111.030-0.001-0.008-0.1100.000
28H28THR00.0450.0268.383-0.014-0.0140.0000.0000.0000.000
29H29PHE00.0300.01212.1090.1820.1820.0000.0000.0000.000
30H30ASN0-0.005-0.00213.5720.0330.0330.0000.0000.0000.000
31H31ASN00.0120.00715.0440.1670.1670.0000.0000.0000.000
32H32TYR0-0.0020.00611.502-0.027-0.0270.0000.0000.0000.000
33H33TRP00.0670.04616.0950.0190.0190.0000.0000.0000.000
34H34MET0-0.058-0.01011.607-0.276-0.2760.0000.0000.0000.000
35H35SER00.061-0.01915.3340.2100.2100.0000.0000.0000.000
36H36TRP0-0.059-0.03315.595-0.191-0.1910.0000.0000.0000.000
37H37VAL00.0030.00216.4830.0950.0950.0000.0000.0000.000
38H38ARG10.7680.85617.9160.3960.3960.0000.0000.0000.000
39H39GLN0-0.0040.00018.046-0.020-0.0200.0000.0000.0000.000
40H40ALA00.0350.02420.7220.0160.0160.0000.0000.0000.000
41H41PRO0-0.003-0.02323.6130.0110.0110.0000.0000.0000.000
42H42GLY00.0000.00723.8940.0120.0120.0000.0000.0000.000
43H43LYS10.9340.97823.9440.2370.2370.0000.0000.0000.000
44H44GLY00.0540.02922.110-0.009-0.0090.0000.0000.0000.000
45H45LEU0-0.016-0.01216.645-0.008-0.0080.0000.0000.0000.000
46H46GLU-1-0.790-0.87420.883-0.376-0.3760.0000.0000.0000.000
47H47TRP0-0.016-0.01319.333-0.014-0.0140.0000.0000.0000.000
48H48VAL0-0.025-0.01620.9350.0560.0560.0000.0000.0000.000
49H49ALA00.034-0.00321.1950.0580.0580.0000.0000.0000.000
50H50ASN0-0.068-0.03519.499-0.031-0.0310.0000.0000.0000.000
51H51ILE0-0.035-0.00519.2270.0760.0760.0000.0000.0000.000
52H52LYS10.9561.00219.6920.5020.5020.0000.0000.0000.000
53H52GLN00.002-0.01219.1510.0470.0470.0000.0000.0000.000
54H53ASP-1-0.802-0.90920.371-0.665-0.6650.0000.0000.0000.000
55H54GLY0-0.036-0.01322.9500.0120.0120.0000.0000.0000.000
56H55ASN0-0.079-0.05023.7690.0390.0390.0000.0000.0000.000
57H56ASP-1-0.840-0.90325.848-0.489-0.4890.0000.0000.0000.000
58H57LYS10.8260.90724.4900.5450.5450.0000.0000.0000.000
59H58TYR0-0.041-0.02124.6180.0630.0630.0000.0000.0000.000
60H59TYR00.0350.00724.622-0.066-0.0660.0000.0000.0000.000
61H60VAL00.0290.03025.8520.0340.0340.0000.0000.0000.000
62H61ASP-1-0.800-0.91327.658-0.337-0.3370.0000.0000.0000.000
63H62SER0-0.0160.00528.4350.0070.0070.0000.0000.0000.000
64H63VAL0-0.008-0.00925.9490.0090.0090.0000.0000.0000.000
65H64LYS10.8460.93229.3890.3530.3530.0000.0000.0000.000
66H65GLY00.0060.01331.1110.0230.0230.0000.0000.0000.000
67H66ARG10.7240.82829.7710.3470.3470.0000.0000.0000.000
68H67PHE00.009-0.00924.989-0.010-0.0100.0000.0000.0000.000
69H68THR0-0.038-0.02626.4460.0220.0220.0000.0000.0000.000
70H69ILE00.0180.03019.481-0.024-0.0240.0000.0000.0000.000
71H70SER0-0.029-0.02521.8400.0480.0480.0000.0000.0000.000
72H71ARG10.8300.90716.7841.1221.1220.0000.0000.0000.000
73H72ASP-1-0.815-0.90118.924-0.758-0.7580.0000.0000.0000.000
74H73ASN00.0490.00317.543-0.230-0.2300.0000.0000.0000.000
75H74ALA0-0.0170.01317.142-0.069-0.0690.0000.0000.0000.000
76H75LYS10.8600.91416.4350.8180.8180.0000.0000.0000.000
77H76ASN0-0.0070.01612.287-0.096-0.0960.0000.0000.0000.000
78H77SER00.005-0.00313.301-0.237-0.2370.0000.0000.0000.000
79H78LEU0-0.006-0.00314.7990.1090.1090.0000.0000.0000.000
80H79PHE0-0.029-0.03217.048-0.024-0.0240.0000.0000.0000.000
81H80LEU00.0130.00619.7980.0190.0190.0000.0000.0000.000
82H81GLN0-0.012-0.00222.091-0.004-0.0040.0000.0000.0000.000
83H82MET0-0.028-0.00623.495-0.007-0.0070.0000.0000.0000.000
84H82ASN00.0570.02027.2060.0170.0170.0000.0000.0000.000
85H82SER00.0130.00631.0180.0060.0060.0000.0000.0000.000
86H82LEU0-0.0090.01427.0730.0020.0020.0000.0000.0000.000
87H83ARG10.8920.93130.9050.2650.2650.0000.0000.0000.000
88H84ALA00.0520.03330.819-0.015-0.0150.0000.0000.0000.000
89H85GLU-1-0.819-0.91230.256-0.247-0.2470.0000.0000.0000.000
90H86ASP-1-0.764-0.83227.110-0.378-0.3780.0000.0000.0000.000
91H87THR0-0.038-0.01625.783-0.039-0.0390.0000.0000.0000.000
92H88ALA0-0.003-0.00922.0530.0180.0180.0000.0000.0000.000
93H89VAL0-0.0220.00616.485-0.008-0.0080.0000.0000.0000.000
94H90TYR00.003-0.01318.211-0.022-0.0220.0000.0000.0000.000
95H91PHE00.014-0.01812.708-0.056-0.0560.0000.0000.0000.000
96H93ALA00.031-0.00211.014-0.295-0.2950.0000.0000.0000.000
97H94ARG10.8050.8728.6842.8892.8890.0000.0000.0000.000
98H95GLU-1-0.786-0.86211.974-0.969-0.9690.0000.0000.0000.000
99H96PHE0-0.029-0.02013.306-0.009-0.0090.0000.0000.0000.000
100H97SER00.014-0.02215.2780.0930.0930.0000.0000.0000.000
101H98SER0-0.039-0.03018.4440.0090.0090.0000.0000.0000.000
102H99TYR0-0.041-0.01519.9080.0630.0630.0000.0000.0000.000
103H100THR0-0.010-0.01222.6440.0320.0320.0000.0000.0000.000
104H100ASP-1-0.885-0.94825.486-0.236-0.2360.0000.0000.0000.000
105H100HIS0-0.032-0.01128.7110.0130.0130.0000.0000.0000.000
106H100LEU0-0.0060.01132.1360.0170.0170.0000.0000.0000.000
107H100GLU-1-0.939-0.97234.163-0.147-0.1470.0000.0000.0000.000
108H100TYR0-0.117-0.06231.628-0.001-0.0010.0000.0000.0000.000
109H100TYR00.0180.01527.6620.0050.0050.0000.0000.0000.000
110H100TYR0-0.032-0.01826.677-0.001-0.0010.0000.0000.0000.000
111H100ASP-1-0.768-0.85222.581-0.606-0.6060.0000.0000.0000.000
112H100TYR0-0.0300.00522.401-0.014-0.0140.0000.0000.0000.000
113H100TYR0-0.036-0.04318.296-0.078-0.0780.0000.0000.0000.000
114H100TYR0-0.010-0.00616.4260.0580.0580.0000.0000.0000.000
115H100MET0-0.017-0.01213.404-0.096-0.0960.0000.0000.0000.000
116H101ASP-1-0.755-0.83610.824-2.088-2.0880.0000.0000.0000.000
117H102VAL0-0.029-0.0045.166-0.496-0.4960.0000.0000.0000.000
118H103TRP00.014-0.0127.1960.5830.5830.0000.0000.0000.000
119H104GLY00.0210.0127.133-0.704-0.7040.0000.0000.0000.000
120H105LYS10.9200.9498.9381.2601.2600.0000.0000.0000.000
121H106GLY00.0490.03210.1780.2210.2210.0000.0000.0000.000
122H107THR0-0.067-0.04813.8730.0460.0460.0000.0000.0000.000
123H108THR0-0.005-0.00117.125-0.015-0.0150.0000.0000.0000.000
124H109VAL0-0.0040.01320.393-0.005-0.0050.0000.0000.0000.000
125H110THR0-0.007-0.00623.5890.0230.0230.0000.0000.0000.000
126H111VAL00.0050.01226.9700.0000.0000.0000.0000.0000.000
127H112SER00.017-0.00230.4240.0140.0140.0000.0000.0000.000
128H113SER00.0450.01333.622-0.006-0.0060.0000.0000.0000.000
129H114ALA0-0.0370.00735.4260.0100.0100.0000.0000.0000.000
130H115SER00.0220.00036.458-0.013-0.0130.0000.0000.0000.000
131H116THR0-0.039-0.02136.3690.0040.0040.0000.0000.0000.000
132H117LYS10.8310.92137.8470.0680.0680.0000.0000.0000.000
133H118GLY00.0750.04238.6960.0000.0000.0000.0000.0000.000
134H119PRO0-0.052-0.02038.681-0.001-0.0010.0000.0000.0000.000
135H120SER00.0080.00140.9360.0010.0010.0000.0000.0000.000
136H121VAL0-0.011-0.01141.9830.0010.0010.0000.0000.0000.000
137H122PHE0-0.004-0.00544.4670.0000.0000.0000.0000.0000.000
138H123PRO0-0.011-0.00245.8160.0030.0030.0000.0000.0000.000
139H124LEU0-0.039-0.01943.672-0.003-0.0030.0000.0000.0000.000
140H125ALA00.0430.02147.8600.0050.0050.0000.0000.0000.000
141H126PRO0-0.0190.00750.531-0.001-0.0010.0000.0000.0000.000
142H134GLY00.0900.04753.3300.0000.0000.0000.0000.0000.000
143H135THR0-0.094-0.04847.760-0.002-0.0020.0000.0000.0000.000
144H136ALA00.0250.02549.560-0.003-0.0030.0000.0000.0000.000
145H137ALA00.002-0.00245.1500.0050.0050.0000.0000.0000.000
146H138LEU00.0100.02145.866-0.005-0.0050.0000.0000.0000.000
147H139GLY00.042-0.00643.6930.0050.0050.0000.0000.0000.000
148H140CYS0-0.0780.00541.7220.0010.0010.0000.0000.0000.000
149H141LEU00.0300.03941.1210.0010.0010.0000.0000.0000.000
150H142VAL0-0.035-0.02337.904-0.002-0.0020.0000.0000.0000.000
151H143LYS10.9860.98338.9920.0410.0410.0000.0000.0000.000
152H144ASP-1-0.813-0.91639.826-0.066-0.0660.0000.0000.0000.000
153H145TYR0-0.045-0.03332.9970.0030.0030.0000.0000.0000.000
154H146PHE00.0330.01832.285-0.007-0.0070.0000.0000.0000.000
155H147PRO00.0350.02030.5350.0040.0040.0000.0000.0000.000
156H148GLU-1-0.769-0.87329.077-0.040-0.0400.0000.0000.0000.000
157H149PRO0-0.052-0.02228.385-0.015-0.0150.0000.0000.0000.000
158H150VAL00.001-0.00530.476-0.001-0.0010.0000.0000.0000.000
159H151THR0-0.042-0.01831.4590.0070.0070.0000.0000.0000.000
160H152VAL0-0.007-0.01633.992-0.007-0.0070.0000.0000.0000.000
161H153SER0-0.0120.00635.9430.0100.0100.0000.0000.0000.000
162H154TRP00.0150.00838.373-0.010-0.0100.0000.0000.0000.000
163H155ASN00.023-0.00441.8080.0030.0030.0000.0000.0000.000
164H156SER0-0.006-0.00842.3510.0020.0020.0000.0000.0000.000
165H157GLY0-0.0020.00939.5600.0030.0030.0000.0000.0000.000
166H158ALA0-0.040-0.01340.4270.0090.0090.0000.0000.0000.000
167H159LEU0-0.021-0.00441.9270.0020.0020.0000.0000.0000.000
168H160THR00.005-0.00437.008-0.002-0.0020.0000.0000.0000.000
169H161SER00.0350.00738.0050.0060.0060.0000.0000.0000.000
170H162GLY00.0350.01439.305-0.007-0.0070.0000.0000.0000.000
171H163VAL0-0.036-0.00337.138-0.009-0.0090.0000.0000.0000.000
172H164HIS00.0110.00732.7800.0150.0150.0000.0000.0000.000
173H165THR0-0.005-0.00333.770-0.012-0.0120.0000.0000.0000.000
174H166PHE0-0.0030.01232.9350.0070.0070.0000.0000.0000.000
175H167PRO00.022-0.00729.126-0.006-0.0060.0000.0000.0000.000
176H168ALA00.0010.01031.109-0.001-0.0010.0000.0000.0000.000
177H169VAL0-0.014-0.00131.774-0.007-0.0070.0000.0000.0000.000
178H170LEU0-0.019-0.01530.841-0.001-0.0010.0000.0000.0000.000
179H171GLN0-0.063-0.03033.8300.0060.0060.0000.0000.0000.000
180H172SER00.028-0.00436.999-0.009-0.0090.0000.0000.0000.000
181H173SER0-0.0130.00638.943-0.007-0.0070.0000.0000.0000.000
182H174GLY00.0080.00835.868-0.004-0.0040.0000.0000.0000.000
183H175LEU0-0.053-0.02135.559-0.006-0.0060.0000.0000.0000.000
184H176TYR00.0160.00529.037-0.003-0.0030.0000.0000.0000.000
185H177SER00.0260.00635.5010.0050.0050.0000.0000.0000.000
186H178LEU00.0100.02933.317-0.001-0.0010.0000.0000.0000.000
187H179SER0-0.010-0.02536.650-0.001-0.0010.0000.0000.0000.000
188H180SER0-0.0110.00537.1870.0060.0060.0000.0000.0000.000
189H181VAL00.009-0.00738.909-0.006-0.0060.0000.0000.0000.000
190H182VAL00.0180.00940.1470.0080.0080.0000.0000.0000.000
191H183THR0-0.0110.00142.517-0.006-0.0060.0000.0000.0000.000
192H184VAL00.0080.00244.6670.0060.0060.0000.0000.0000.000
193H185PRO00.0390.00847.704-0.003-0.0030.0000.0000.0000.000
194H186SER00.0340.01051.113-0.003-0.0030.0000.0000.0000.000
195H187SER0-0.016-0.01153.753-0.003-0.0030.0000.0000.0000.000
196H188SER0-0.030-0.01651.839-0.001-0.0010.0000.0000.0000.000
197H189LEU00.0200.00851.126-0.002-0.0020.0000.0000.0000.000
198H190GLY00.0030.01254.418-0.003-0.0030.0000.0000.0000.000
199H191THR0-0.048-0.02456.272-0.001-0.0010.0000.0000.0000.000
200H192GLN0-0.046-0.02050.2570.0020.0020.0000.0000.0000.000
201H193THR00.0050.00652.199-0.001-0.0010.0000.0000.0000.000
202H194TYR00.0770.02646.8870.0060.0060.0000.0000.0000.000
203H195THR0-0.022-0.03145.742-0.007-0.0070.0000.0000.0000.000
204H197ASN00.020-0.00940.3830.0000.0000.0000.0000.0000.000
205H198VAL00.0030.00038.5340.0030.0030.0000.0000.0000.000
206H199ASN0-0.040-0.03734.765-0.007-0.0070.0000.0000.0000.000
207H200HIS00.0400.02434.4530.0070.0070.0000.0000.0000.000
208H201LYS11.0060.99531.5240.0030.0030.0000.0000.0000.000
209H202PRO0-0.0110.00831.627-0.005-0.0050.0000.0000.0000.000
210H203SER00.001-0.02234.184-0.006-0.0060.0000.0000.0000.000
211H204ASN0-0.073-0.03537.1810.0080.0080.0000.0000.0000.000
212H205THR00.0260.02838.8500.0070.0070.0000.0000.0000.000
213H206LYS10.9180.94238.9150.0010.0010.0000.0000.0000.000
214H207VAL0-0.007-0.00741.888-0.003-0.0030.0000.0000.0000.000
215H208ASP-1-0.835-0.90243.4200.0190.0190.0000.0000.0000.000
216H209LYS10.8900.94345.079-0.003-0.0030.0000.0000.0000.000
217H210ARG10.8820.93046.883-0.015-0.0150.0000.0000.0000.000
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