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: 3948L

Calculation Name: 5CGY-H-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5CGY

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 226
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2280486.318763
FMO2-HF: Nuclear repulsion 2194948.715962
FMO2-HF: Total energy -85537.602801
FMO2-MP2: Total energy -85787.741205


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.
5.8588.1878.673617379884E-19-0.785-1.5460.003
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 : 0.006 / 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].
3H3GLN0-0.020-0.0103.666-1.1760.434-0.011-0.566-1.0340.003
4H4LEU00.004-0.0055.4750.6830.6830.0000.0000.0000.000
5H5VAL0-0.008-0.0088.8250.0960.0960.0000.0000.0000.000
6H6GLN00.015-0.01511.1930.1500.1500.0000.0000.0000.000
7H7SER00.0050.01914.845-0.008-0.0080.0000.0000.0000.000
8H8GLY00.0140.00217.9710.0160.0160.0000.0000.0000.000
9H9SER0-0.014-0.01420.3900.0130.0130.0000.0000.0000.000
10H10GLU-1-0.782-0.87123.244-0.379-0.3790.0000.0000.0000.000
11H11LEU0-0.031-0.00226.2380.0200.0200.0000.0000.0000.000
12H12LYS10.8020.88228.2750.3500.3500.0000.0000.0000.000
13H13LYS11.0021.00532.2010.2210.2210.0000.0000.0000.000
14H14PRO00.0310.01235.109-0.006-0.0060.0000.0000.0000.000
15H15GLY0-0.031-0.01336.5060.0070.0070.0000.0000.0000.000
16H16ALA0-0.030-0.00533.9510.0020.0020.0000.0000.0000.000
17H17SER0-0.005-0.00731.1320.0020.0020.0000.0000.0000.000
18H18VAL0-0.018-0.01025.829-0.005-0.0050.0000.0000.0000.000
19H19LYS10.8970.94923.6150.3810.3810.0000.0000.0000.000
20H20VAL00.0040.01920.569-0.020-0.0200.0000.0000.0000.000
21H21SER00.015-0.00917.818-0.003-0.0030.0000.0000.0000.000
22H22CYS0-0.0480.00013.727-0.057-0.0570.0000.0000.0000.000
23H23LYS10.8650.94210.2721.6441.6440.0000.0000.0000.000
24H24ALA00.0470.0299.500-0.338-0.3380.0000.0000.0000.000
25H25SER0-0.055-0.0376.020-0.391-0.3910.0000.0000.0000.000
26H26GLY00.0630.0273.517-1.373-1.1870.007-0.125-0.0690.000
27H27TYR00.0080.0133.9073.4183.8340.005-0.092-0.3290.000
28H28SER0-0.002-0.0096.642-0.667-0.6670.0000.0000.0000.000
29H29PHE00.0550.01910.4160.0420.0420.0000.0000.0000.000
30H30THR00.0320.00012.0970.0280.0280.0000.0000.0000.000
31H31SER0-0.0330.00112.9790.0420.0420.0000.0000.0000.000
32H32TYR0-0.018-0.01810.9650.1210.1210.0000.0000.0000.000
33H33SER0-0.0120.03013.848-0.117-0.1170.0000.0000.0000.000
34H34ILE0-0.054-0.01413.034-0.046-0.0460.0000.0000.0000.000
35H35ASN00.0130.00315.5660.0750.0750.0000.0000.0000.000
36H36TRP00.019-0.00116.972-0.113-0.1130.0000.0000.0000.000
37H37VAL00.0100.00318.6720.0600.0600.0000.0000.0000.000
38H38ARG10.8190.90720.5190.1600.1600.0000.0000.0000.000
39H39GLN0-0.007-0.00622.4910.0080.0080.0000.0000.0000.000
40H40ALA00.0330.02624.378-0.023-0.0230.0000.0000.0000.000
41H41PRO00.011-0.01627.7020.0070.0070.0000.0000.0000.000
42H42GLY0-0.0260.00328.9020.0130.0130.0000.0000.0000.000
43H43GLN0-0.027-0.00428.8060.0240.0240.0000.0000.0000.000
44H44GLY00.0280.02326.143-0.014-0.0140.0000.0000.0000.000
45H45PRO0-0.024-0.03321.746-0.003-0.0030.0000.0000.0000.000
46H46GLU-1-0.808-0.88524.123-0.165-0.1650.0000.0000.0000.000
47H47TRP00.004-0.00520.067-0.025-0.0250.0000.0000.0000.000
48H48MET0-0.039-0.01522.865-0.002-0.0020.0000.0000.0000.000
49H49GLY00.0300.01122.6960.0150.0150.0000.0000.0000.000
50H50TRP0-0.053-0.00919.404-0.027-0.0270.0000.0000.0000.000
51H51ILE0-0.035-0.02119.0390.0040.0040.0000.0000.0000.000
52H52ASP-1-0.735-0.84518.986-0.024-0.0240.0000.0000.0000.000
53H53THR0-0.061-0.03415.5330.0000.0000.0000.0000.0000.000
54H54ASN0-0.061-0.03218.550-0.041-0.0410.0000.0000.0000.000
55H55THR0-0.056-0.06520.308-0.024-0.0240.0000.0000.0000.000
56H56GLY00.0060.01122.323-0.012-0.0120.0000.0000.0000.000
57H57ASN0-0.038-0.02423.461-0.026-0.0260.0000.0000.0000.000
58H58PRO0-0.018-0.00223.9360.0020.0020.0000.0000.0000.000
59H59THR0-0.0030.00024.3970.0260.0260.0000.0000.0000.000
60H60TYR00.004-0.00224.989-0.024-0.0240.0000.0000.0000.000
61H61ALA00.0250.01026.5660.0200.0200.0000.0000.0000.000
62H62GLN0-0.032-0.03728.239-0.001-0.0010.0000.0000.0000.000
63H63ASP-1-0.871-0.92730.876-0.103-0.1030.0000.0000.0000.000
64H64PHE0-0.049-0.03127.657-0.015-0.0150.0000.0000.0000.000
65H65ALA0-0.0020.00830.098-0.014-0.0140.0000.0000.0000.000
66H66GLY00.0190.00231.6660.0100.0100.0000.0000.0000.000
67H67ARG10.7280.83532.7640.1830.1830.0000.0000.0000.000
68H68PHE00.0010.00127.175-0.018-0.0180.0000.0000.0000.000
69H69VAL00.0050.00727.0560.0150.0150.0000.0000.0000.000
70H70PHE00.0100.00922.265-0.041-0.0410.0000.0000.0000.000
71H71SER0-0.021-0.01722.5450.0220.0220.0000.0000.0000.000
72H72LEU00.0180.00118.061-0.050-0.0500.0000.0000.0000.000
73H73ASP-1-0.825-0.88019.279-0.457-0.4570.0000.0000.0000.000
74H74THR00.013-0.00817.183-0.095-0.0950.0000.0000.0000.000
75H75SER0-0.048-0.02616.553-0.056-0.0560.0000.0000.0000.000
76H76VAL00.0130.00815.360-0.067-0.0670.0000.0000.0000.000
77H77THR0-0.040-0.01711.260-0.196-0.1960.0000.0000.0000.000
78H78THR0-0.013-0.00313.256-0.222-0.2220.0000.0000.0000.000
79H79ALA00.0090.01415.7910.1320.1320.0000.0000.0000.000
80H80TYR0-0.027-0.04217.681-0.082-0.0820.0000.0000.0000.000
81H81LEU00.0220.02420.5600.0490.0490.0000.0000.0000.000
82H82GLN0-0.024-0.01022.844-0.033-0.0330.0000.0000.0000.000
83H83ILE00.0330.03126.0440.0240.0240.0000.0000.0000.000
84H84SER00.0200.00029.097-0.007-0.0070.0000.0000.0000.000
85H85SER0-0.027-0.01832.7390.0090.0090.0000.0000.0000.000
86H86LEU00.0020.01229.6550.0110.0110.0000.0000.0000.000
87H87LYS10.9250.95033.7140.1730.1730.0000.0000.0000.000
88H88ALA00.0680.01933.748-0.011-0.0110.0000.0000.0000.000
89H89GLY00.004-0.00933.381-0.009-0.0090.0000.0000.0000.000
90H90ASP-1-0.755-0.83330.006-0.206-0.2060.0000.0000.0000.000
91H91THR0-0.0110.01528.645-0.027-0.0270.0000.0000.0000.000
92H92ALA0-0.0110.00025.5400.0190.0190.0000.0000.0000.000
93H93VAL0-0.0090.01820.003-0.025-0.0250.0000.0000.0000.000
94H94TYR0-0.010-0.04321.0810.0410.0410.0000.0000.0000.000
95H95TYR00.0350.03016.030-0.073-0.0730.0000.0000.0000.000
96H97ALA00.0400.01012.781-0.093-0.0930.0000.0000.0000.000
97H98THR00.010-0.0069.0380.0790.0790.0000.0000.0000.000
98H99TYR00.011-0.02010.300-0.015-0.0150.0000.0000.0000.000
99H100TYR00.0260.0005.775-0.064-0.0640.0000.0000.0000.000
100H101VAL0-0.006-0.0115.8350.1160.1160.0000.0000.0000.000
101H102ASP-1-0.927-0.9565.1704.5044.621-0.001-0.002-0.1140.000
102H103LEU0-0.075-0.0378.369-0.246-0.2460.0000.0000.0000.000
103H104TRP0-0.057-0.03511.124-0.241-0.2410.0000.0000.0000.000
104H105GLY0-0.033-0.01513.127-0.092-0.0920.0000.0000.0000.000
105H106SER00.0100.00212.7020.1330.1330.0000.0000.0000.000
106H107TYR00.0470.02714.267-0.053-0.0530.0000.0000.0000.000
107H108ARG10.8310.93114.897-0.417-0.4170.0000.0000.0000.000
108H109GLN00.0510.02315.913-0.070-0.0700.0000.0000.0000.000
109H110ASP-1-0.797-0.87818.0240.1610.1610.0000.0000.0000.000
110H111TYR00.0250.00218.443-0.024-0.0240.0000.0000.0000.000
111H112TYR0-0.010-0.00716.917-0.030-0.0300.0000.0000.0000.000
112H113GLY00.0010.02213.7910.0410.0410.0000.0000.0000.000
113H114MET0-0.049-0.05314.404-0.131-0.1310.0000.0000.0000.000
114H115ASP-1-0.789-0.86110.2050.3380.3380.0000.0000.0000.000
115H116VAL0-0.041-0.0206.543-0.064-0.0640.0000.0000.0000.000
116H117TRP0-0.012-0.0169.847-0.037-0.0370.0000.0000.0000.000
117H118GLY00.0000.00110.738-0.201-0.2010.0000.0000.0000.000
118H119HIS0-0.013-0.02310.0580.3020.3020.0000.0000.0000.000
119H120GLY0-0.0020.01114.0830.1130.1130.0000.0000.0000.000
120H121THR0-0.055-0.03417.255-0.048-0.0480.0000.0000.0000.000
121H122LEU0-0.011-0.00119.9490.0540.0540.0000.0000.0000.000
122H123VAL00.0060.00823.391-0.008-0.0080.0000.0000.0000.000
123H124THR0-0.003-0.01126.2460.0290.0290.0000.0000.0000.000
124H125VAL0-0.031-0.01929.639-0.001-0.0010.0000.0000.0000.000
125H126SER00.0230.00732.7510.0170.0170.0000.0000.0000.000
126H127SER0-0.017-0.02335.337-0.004-0.0040.0000.0000.0000.000
127H128ALA0-0.0310.00637.0160.0100.0100.0000.0000.0000.000
128H129SER0-0.024-0.01637.615-0.008-0.0080.0000.0000.0000.000
129H130THR0-0.023-0.02638.8100.0020.0020.0000.0000.0000.000
130H131LYS10.8680.93340.1050.1460.1460.0000.0000.0000.000
131H132GLY00.0540.03442.123-0.005-0.0050.0000.0000.0000.000
132H133PRO0-0.053-0.01443.2550.0030.0030.0000.0000.0000.000
133H134SER0-0.021-0.00945.2310.0040.0040.0000.0000.0000.000
134H135VAL00.0200.01147.416-0.002-0.0020.0000.0000.0000.000
135H136PHE0-0.009-0.00849.2050.0050.0050.0000.0000.0000.000
136H137PRO00.0290.02050.549-0.003-0.0030.0000.0000.0000.000
137H138LEU0-0.0200.00047.2400.0010.0010.0000.0000.0000.000
138H139ALA00.0500.02051.8750.0010.0010.0000.0000.0000.000
139H140PRO00.0190.03154.4570.0000.0000.0000.0000.0000.000
140H141SER00.009-0.00653.6120.0020.0020.0000.0000.0000.000
141H142SER00.021-0.00354.6580.0000.0000.0000.0000.0000.000
142H143LYS10.8990.94857.1700.0380.0380.0000.0000.0000.000
143H144SER00.0520.03560.6890.0010.0010.0000.0000.0000.000
144H145THR0-0.062-0.04462.4980.0020.0020.0000.0000.0000.000
145H146SER00.0690.05861.3630.0010.0010.0000.0000.0000.000
146H147GLY00.0450.01061.166-0.001-0.0010.0000.0000.0000.000
147H148GLY00.0080.01657.611-0.001-0.0010.0000.0000.0000.000
148H149THR00.0110.01053.0790.0000.0000.0000.0000.0000.000
149H150ALA0-0.048-0.03153.8880.0010.0010.0000.0000.0000.000
150H151ALA00.0160.01849.639-0.001-0.0010.0000.0000.0000.000
151H152LEU00.0000.01451.4640.0010.0010.0000.0000.0000.000
152H153GLY00.0440.00548.851-0.003-0.0030.0000.0000.0000.000
153H154CYS0-0.085-0.00347.8540.0020.0020.0000.0000.0000.000
154H155LEU00.0220.02344.907-0.004-0.0040.0000.0000.0000.000
155H156VAL0-0.018-0.01543.1860.0020.0020.0000.0000.0000.000
156H157LYS10.9040.92343.2200.1140.1140.0000.0000.0000.000
157H158ASP-1-0.823-0.89442.359-0.130-0.1300.0000.0000.0000.000
158H159TYR00.008-0.02137.3950.0080.0080.0000.0000.0000.000
159H160PHE00.0430.04633.780-0.008-0.0080.0000.0000.0000.000
160H161PRO00.0120.01033.8840.0090.0090.0000.0000.0000.000
161H162GLU-1-0.751-0.86132.847-0.192-0.1920.0000.0000.0000.000
162H163PRO0-0.033-0.01534.027-0.009-0.0090.0000.0000.0000.000
163H164VAL00.004-0.00635.8900.0060.0060.0000.0000.0000.000
164H165THR0-0.033-0.01238.653-0.003-0.0030.0000.0000.0000.000
165H166VAL00.001-0.02540.7470.0040.0040.0000.0000.0000.000
166H167SER0-0.034-0.01043.425-0.002-0.0020.0000.0000.0000.000
167H168TRP00.0340.01446.0400.0040.0040.0000.0000.0000.000
168H169ASN0-0.011-0.01849.4300.0000.0000.0000.0000.0000.000
169H170SER0-0.001-0.01150.3600.0030.0030.0000.0000.0000.000
170H171GLY0-0.012-0.00447.593-0.002-0.0020.0000.0000.0000.000
171H172ALA0-0.028-0.00348.4430.0010.0010.0000.0000.0000.000
172H173LEU0-0.045-0.00950.1920.0030.0030.0000.0000.0000.000
173H174THR00.0400.00545.766-0.003-0.0030.0000.0000.0000.000
174H175SER00.000-0.00546.375-0.001-0.0010.0000.0000.0000.000
175H176GLY00.0410.01946.9750.0020.0020.0000.0000.0000.000
176H177VAL0-0.044-0.01044.2270.0000.0000.0000.0000.0000.000
177H178HIS00.0070.00738.328-0.004-0.0040.0000.0000.0000.000
178H179THR00.0260.01139.5550.0050.0050.0000.0000.0000.000
179H180PHE0-0.033-0.00938.506-0.004-0.0040.0000.0000.0000.000
180H181PRO00.018-0.00533.552-0.003-0.0030.0000.0000.0000.000
181H182ALA0-0.0050.00135.5050.0080.0080.0000.0000.0000.000
182H183VAL0-0.0130.00334.843-0.007-0.0070.0000.0000.0000.000
183H184LEU00.000-0.00131.474-0.002-0.0020.0000.0000.0000.000
184H185GLN0-0.048-0.03335.2420.0090.0090.0000.0000.0000.000
185H186SER00.0360.00436.370-0.009-0.0090.0000.0000.0000.000
186H187SER00.001-0.00337.457-0.007-0.0070.0000.0000.0000.000
187H188GLY00.0360.01135.455-0.005-0.0050.0000.0000.0000.000
188H189LEU0-0.092-0.03636.236-0.007-0.0070.0000.0000.0000.000
189H190TYR00.0410.00631.419-0.003-0.0030.0000.0000.0000.000
190H191SER0-0.013-0.00138.2280.0110.0110.0000.0000.0000.000
191H192LEU00.0160.04338.500-0.003-0.0030.0000.0000.0000.000
192H193SER00.0250.00040.7750.0090.0090.0000.0000.0000.000
193H194SER0-0.017-0.00642.235-0.001-0.0010.0000.0000.0000.000
194H195VAL00.025-0.00644.4030.0040.0040.0000.0000.0000.000
195H196VAL00.0110.01546.436-0.002-0.0020.0000.0000.0000.000
196H197THR0-0.031-0.01647.7890.0030.0030.0000.0000.0000.000
197H198VAL00.006-0.00650.2410.0000.0000.0000.0000.0000.000
198H199PRO00.0740.03053.8240.0010.0010.0000.0000.0000.000
199H200SER0-0.006-0.02257.025-0.001-0.0010.0000.0000.0000.000
200H201SER00.0180.00958.7360.0000.0000.0000.0000.0000.000
201H202SER0-0.0040.00957.9650.0010.0010.0000.0000.0000.000
202H203LEU0-0.035-0.02555.952-0.002-0.0020.0000.0000.0000.000
203H204GLY00.0130.00459.5850.0020.0020.0000.0000.0000.000
204H205THR0-0.080-0.04161.7370.0010.0010.0000.0000.0000.000
205H206GLN00.0450.03558.4110.0010.0010.0000.0000.0000.000
206H207THR00.0000.00558.053-0.001-0.0010.0000.0000.0000.000
207H208TYR00.0050.00153.482-0.002-0.0020.0000.0000.0000.000
208H209ILE00.0220.00053.1780.0000.0000.0000.0000.0000.000
209H211ASN00.0450.00248.0390.0000.0000.0000.0000.0000.000
210H212VAL00.0100.00844.400-0.005-0.0050.0000.0000.0000.000
211H213ASN0-0.033-0.02041.9430.0050.0050.0000.0000.0000.000
212H214HIS00.0290.02838.6190.0040.0040.0000.0000.0000.000
213H215LYS10.9940.98938.7500.1890.1890.0000.0000.0000.000
214H216PRO00.0150.01337.0650.0030.0030.0000.0000.0000.000
215H217SER0-0.012-0.03239.6720.0030.0030.0000.0000.0000.000
216H218ASN0-0.068-0.02743.1110.0050.0050.0000.0000.0000.000
217H219THR00.0300.02044.6750.0100.0100.0000.0000.0000.000
218H220LYS10.9040.94545.6600.1310.1310.0000.0000.0000.000
219H221VAL00.0080.00248.4070.0040.0040.0000.0000.0000.000
220H222ASP-1-0.832-0.88749.840-0.102-0.1020.0000.0000.0000.000
221H223LYS10.8680.91552.0600.0940.0940.0000.0000.0000.000
222H224ARG10.8640.91253.5980.0670.0670.0000.0000.0000.000
223H225VAL0-0.044-0.02252.3640.0000.0000.0000.0000.0000.000
224H226GLU-1-0.809-0.88555.829-0.063-0.0630.0000.0000.0000.000
225H227PRO0-0.012-0.01058.177-0.002-0.0020.0000.0000.0000.000
226H228LYS10.8690.93959.4130.0560.0560.0000.0000.0000.000