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: R9KM8

Calculation Name: 4TOY-H-Xray372

Preferred Name:

Target Type:

Ligand Name: pyroglutamic acid

ligand 3-letter code: PCA

PDB ID: 4TOY

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 240
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2617928.370188
FMO2-HF: Nuclear repulsion 2526470.1327
FMO2-HF: Total energy -91458.237488
FMO2-MP2: Total energy -91724.446313


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:PCA)


Summations of interaction energy for fragment #1(H:1:PCA)
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.
1.3994.5230.701-1.744-2.080.001
Interaction energy analysis for fragmet #1(H:1:PCA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.009 / q_NPA : -0.011
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].
3H3GLN0-0.0040.0073.852-1.4560.849-0.018-1.248-1.0380.003
4H4LEU00.0070.0006.9120.2390.2390.0000.0000.0000.000
5H5VAL00.0090.0129.9930.1630.1630.0000.0000.0000.000
6H6GLN00.012-0.01713.1780.0000.0000.0000.0000.0000.000
7H7SER00.0030.01816.1530.0180.0180.0000.0000.0000.000
8H8GLY0-0.024-0.00919.850-0.014-0.0140.0000.0000.0000.000
9H9ALA0-0.0040.00221.6460.0070.0070.0000.0000.0000.000
10H10GLU-1-0.851-0.91223.976-0.350-0.3500.0000.0000.0000.000
11H11LEU0-0.0130.00427.2290.0050.0050.0000.0000.0000.000
12H12LYS10.8020.88829.0260.2920.2920.0000.0000.0000.000
13H13LYS10.8910.94732.6290.1850.1850.0000.0000.0000.000
14H14PRO00.021-0.00135.353-0.008-0.0080.0000.0000.0000.000
15H15GLY0-0.003-0.00136.3560.0070.0070.0000.0000.0000.000
16H16ALA0-0.0280.00133.9060.0000.0000.0000.0000.0000.000
17H17SER00.009-0.00830.9990.0010.0010.0000.0000.0000.000
18H18VAL0-0.040-0.01425.8900.0050.0050.0000.0000.0000.000
19H19LYS10.8770.93024.0640.3470.3470.0000.0000.0000.000
20H20ILE00.0220.04519.393-0.013-0.0130.0000.0000.0000.000
21H21SER00.016-0.00419.278-0.009-0.0090.0000.0000.0000.000
22H22CYS00.0000.00613.133-0.055-0.0550.0000.0000.0000.000
23H23LYS10.9741.00114.4070.6250.6250.0000.0000.0000.000
24H24THR0-0.005-0.0119.966-0.126-0.1260.0000.0000.0000.000
25H25SER00.0150.0028.7010.2800.2800.0000.0000.0000.000
26H26GLY00.0400.0115.113-0.879-0.8790.0000.0000.0000.000
27H27TYR00.0140.0064.389-0.771-0.608-0.001-0.052-0.1100.000
28H28ARG10.8260.9006.3590.3950.3950.0000.0000.0000.000
29H29PHE00.020-0.0019.332-0.044-0.0440.0000.0000.0000.000
30H30ASN00.020-0.01710.7880.0030.0030.0000.0000.0000.000
31H31PHE0-0.038-0.01310.4160.0690.0690.0000.0000.0000.000
32H32TYR0-0.023-0.0155.813-0.341-0.3410.0000.0000.0000.000
33H33HIS00.0430.03711.077-0.074-0.0740.0000.0000.0000.000
34H34ILE0-0.050-0.02911.420-0.214-0.2140.0000.0000.0000.000
35H35ASN00.009-0.02113.1080.2360.2360.0000.0000.0000.000
36H36TRP0-0.001-0.00915.129-0.117-0.1170.0000.0000.0000.000
37H37ILE0-0.0190.00014.9740.0650.0650.0000.0000.0000.000
38H38ARG10.7860.87218.7390.2550.2550.0000.0000.0000.000
39H39GLN00.0440.02320.9880.0380.0380.0000.0000.0000.000
40H40THR0-0.0100.00222.887-0.004-0.0040.0000.0000.0000.000
41H41ALA00.0320.00726.6570.0110.0110.0000.0000.0000.000
42H42GLY0-0.0060.00629.3520.0120.0120.0000.0000.0000.000
43H43ARG10.8010.87028.6680.2290.2290.0000.0000.0000.000
44H44GLY00.0330.04626.1000.0050.0050.0000.0000.0000.000
45H45PRO0-0.038-0.02221.130-0.020-0.0200.0000.0000.0000.000
46H46GLU-1-0.697-0.83522.345-0.230-0.2300.0000.0000.0000.000
47H47TRP0-0.034-0.02217.706-0.018-0.0180.0000.0000.0000.000
48H48MET0-0.048-0.02420.5010.0210.0210.0000.0000.0000.000
49H49GLY00.0610.01620.3140.0440.0440.0000.0000.0000.000
50H50TRP0-0.046-0.00816.974-0.079-0.0790.0000.0000.0000.000
51H51ILE0-0.006-0.00117.4340.0620.0620.0000.0000.0000.000
52H52SER00.0400.02516.387-0.102-0.1020.0000.0000.0000.000
53H52PRO0-0.028-0.01413.7210.0680.0680.0000.0000.0000.000
54H53TYR0-0.0130.00616.2810.0500.0500.0000.0000.0000.000
55H54SER0-0.032-0.01817.9890.0510.0510.0000.0000.0000.000
56H55GLY0-0.0230.00120.4460.0230.0230.0000.0000.0000.000
57H56ASP-1-0.859-0.94620.925-0.228-0.2280.0000.0000.0000.000
58H57LYS10.8490.91020.8740.2430.2430.0000.0000.0000.000
59H58ASN00.0090.02821.6670.0460.0460.0000.0000.0000.000
60H59LEU00.0170.00422.488-0.046-0.0460.0000.0000.0000.000
61H60ALA00.0350.02524.5970.0280.0280.0000.0000.0000.000
62H61PRO00.034-0.00926.243-0.004-0.0040.0000.0000.0000.000
63H62ALA0-0.0210.00128.5030.0050.0050.0000.0000.0000.000
64H63PHE0-0.021-0.02725.274-0.008-0.0080.0000.0000.0000.000
65H64GLN0-0.032-0.00228.159-0.014-0.0140.0000.0000.0000.000
66H65ASP-1-0.865-0.92329.998-0.165-0.1650.0000.0000.0000.000
67H66ARG10.6920.80829.6110.2370.2370.0000.0000.0000.000
68H67VAL00.022-0.00124.124-0.015-0.0150.0000.0000.0000.000
69H68ILE0-0.0160.00226.4340.0120.0120.0000.0000.0000.000
70H69MET0-0.0260.00520.679-0.040-0.0400.0000.0000.0000.000
71H70THR0-0.006-0.01721.6750.0490.0490.0000.0000.0000.000
72H71THR00.001-0.01217.208-0.055-0.0550.0000.0000.0000.000
73H72ASP-1-0.822-0.87518.763-0.445-0.4450.0000.0000.0000.000
74H72THR00.010-0.00718.480-0.024-0.0240.0000.0000.0000.000
75H72GLU-1-0.770-0.83212.683-0.525-0.5250.0000.0000.0000.000
76H72VAL00.0210.01915.9590.0860.0860.0000.0000.0000.000
77H72PRO0-0.016-0.02914.634-0.091-0.0910.0000.0000.0000.000
78H72VAL00.0000.01512.245-0.005-0.0050.0000.0000.0000.000
79H72THR00.0010.00811.0660.0720.0720.0000.0000.0000.000
80H72SER00.0360.01812.593-0.092-0.0920.0000.0000.0000.000
81H72PHE00.0320.0067.7170.0000.0000.0000.0000.0000.000
82H73THR0-0.049-0.0387.136-0.321-0.3210.0000.0000.0000.000
83H74SER0-0.039-0.0399.5260.1240.1240.0000.0000.0000.000
84H75THR00.0130.00010.402-0.287-0.2870.0000.0000.0000.000
85H76GLY00.0280.01812.8050.1620.1620.0000.0000.0000.000
86H77ALA0-0.0210.00114.647-0.096-0.0960.0000.0000.0000.000
87H78ALA00.0380.02315.4650.0790.0790.0000.0000.0000.000
88H79TYR0-0.106-0.08817.120-0.035-0.0350.0000.0000.0000.000
89H80MET0-0.0160.00820.0530.0360.0360.0000.0000.0000.000
90H81GLU-1-0.773-0.86121.914-0.278-0.2780.0000.0000.0000.000
91H82ILE00.0250.00725.6240.0090.0090.0000.0000.0000.000
92H82ARG10.8860.91727.6190.2310.2310.0000.0000.0000.000
93H82ASN00.0090.00731.4420.0000.0000.0000.0000.0000.000
94H82LEU0-0.023-0.00129.0040.0030.0030.0000.0000.0000.000
95H83LYS10.9950.99132.6020.1830.1830.0000.0000.0000.000
96H84PHE00.024-0.00332.624-0.012-0.0120.0000.0000.0000.000
97H85ASP-1-0.893-0.94232.207-0.212-0.2120.0000.0000.0000.000
98H86ASP-1-0.735-0.81628.653-0.256-0.2560.0000.0000.0000.000
99H87THR0-0.0210.00627.578-0.028-0.0280.0000.0000.0000.000
100H88GLY00.0400.00625.5920.0140.0140.0000.0000.0000.000
101H89THR0-0.059-0.01719.334-0.011-0.0110.0000.0000.0000.000
102H90TYR0-0.012-0.02419.9870.0120.0120.0000.0000.0000.000
103H91PHE00.0130.00114.593-0.022-0.0220.0000.0000.0000.000
104H93ALA00.027-0.00110.555-0.127-0.1270.0000.0000.0000.000
105H94LYS10.8500.9683.5336.2226.5580.001-0.131-0.2060.000
106H95GLY00.0420.0309.1550.0050.0050.0000.0000.0000.000
107H96LEU0-0.035-0.0208.585-0.186-0.1860.0000.0000.0000.000
108H97LEU00.027-0.0058.6130.1960.1960.0000.0000.0000.000
109H98ARG10.9260.9688.372-1.441-1.4410.0000.0000.0000.000
110H99ASP-1-0.811-0.89511.5310.0520.0520.0000.0000.0000.000
111H100GLY00.008-0.01214.562-0.053-0.0530.0000.0000.0000.000
112H100SER0-0.037-0.02016.673-0.012-0.0120.0000.0000.0000.000
113H100SER0-0.039-0.03317.109-0.045-0.0450.0000.0000.0000.000
114H100THR00.0050.03013.150-0.044-0.0440.0000.0000.0000.000
115H100TRP00.011-0.00112.388-0.136-0.1360.0000.0000.0000.000
116H100LEU00.0050.01813.618-0.130-0.1300.0000.0000.0000.000
117H100PRO0-0.013-0.00711.720-0.085-0.0850.0000.0000.0000.000
118H101TYR00.0010.0084.8740.1970.1970.0000.0000.0000.000
119H102LEU0-0.049-0.0142.629-0.844-0.5240.719-0.313-0.726-0.002
120H103TRP00.001-0.0266.7270.0710.0710.0000.0000.0000.000
121H104GLY00.0540.0199.074-0.258-0.2580.0000.0000.0000.000
122H105GLN0-0.047-0.01911.4060.0000.0000.0000.0000.0000.000
123H106GLY00.0060.01213.6460.1050.1050.0000.0000.0000.000
124H107THR0-0.061-0.04416.699-0.013-0.0130.0000.0000.0000.000
125H108LEU0-0.0150.00120.1060.0200.0200.0000.0000.0000.000
126H109LEU00.0160.01423.3270.0070.0070.0000.0000.0000.000
127H110THR00.011-0.00526.0540.0160.0160.0000.0000.0000.000
128H111VAL0-0.0060.00029.6870.0020.0020.0000.0000.0000.000
129H112SER00.0300.00332.5610.0140.0140.0000.0000.0000.000
130H113SER00.0580.01035.960-0.004-0.0040.0000.0000.0000.000
131H114ALA00.0010.02937.5870.0060.0060.0000.0000.0000.000
132H115SER00.015-0.01537.603-0.009-0.0090.0000.0000.0000.000
133H116THR0-0.0050.00433.1230.0040.0040.0000.0000.0000.000
134H117LYS10.8150.91835.5930.1770.1770.0000.0000.0000.000
135H118GLY00.0720.03834.230-0.011-0.0110.0000.0000.0000.000
136H119PRO0-0.034-0.00732.3140.0120.0120.0000.0000.0000.000
137H120SER0-0.019-0.00935.4580.0070.0070.0000.0000.0000.000
138H121VAL00.0120.00834.0660.0000.0000.0000.0000.0000.000
139H122PHE00.0020.00137.1150.0070.0070.0000.0000.0000.000
140H123PRO00.0090.01037.944-0.006-0.0060.0000.0000.0000.000
141H124LEU0-0.031-0.01535.8760.0060.0060.0000.0000.0000.000
142H125ALA00.0410.01038.706-0.003-0.0030.0000.0000.0000.000
143H126PRO0-0.0010.00839.6620.0000.0000.0000.0000.0000.000
144H127SER0-0.037-0.00840.2950.0050.0050.0000.0000.0000.000
145H128SER0-0.014-0.03240.556-0.005-0.0050.0000.0000.0000.000
146H129LYS10.8840.93733.1800.1180.1180.0000.0000.0000.000
147H130SER00.021-0.00339.8760.0040.0040.0000.0000.0000.000
148H131THR00.0330.02141.991-0.001-0.0010.0000.0000.0000.000
149H132SER0-0.014-0.00145.0660.0000.0000.0000.0000.0000.000
150H133GLY00.0160.01241.1330.0030.0030.0000.0000.0000.000
151H134GLY00.0280.02040.261-0.003-0.0030.0000.0000.0000.000
152H135THR0-0.068-0.02436.820-0.005-0.0050.0000.0000.0000.000
153H136ALA00.0390.02338.0820.0030.0030.0000.0000.0000.000
154H137ALA0-0.032-0.01635.534-0.006-0.0060.0000.0000.0000.000
155H138LEU00.0230.02934.5830.0070.0070.0000.0000.0000.000
156H139GLY00.038-0.00533.875-0.010-0.0100.0000.0000.0000.000
157H140CYS0-0.0790.00430.385-0.002-0.0020.0000.0000.0000.000
158H141LEU00.0400.04333.658-0.010-0.0100.0000.0000.0000.000
159H142VAL0-0.033-0.02931.1390.0030.0030.0000.0000.0000.000
160H143LYS10.9090.93234.3100.1350.1350.0000.0000.0000.000
161H144ASP-1-0.776-0.87036.887-0.151-0.1510.0000.0000.0000.000
162H145TYR0-0.022-0.03229.6500.0080.0080.0000.0000.0000.000
163H146PHE00.0400.02433.454-0.001-0.0010.0000.0000.0000.000
164H147PRO00.0160.01229.6570.0080.0080.0000.0000.0000.000
165H148GLU-1-0.751-0.85827.145-0.291-0.2910.0000.0000.0000.000
166H149PRO0-0.042-0.02323.225-0.007-0.0070.0000.0000.0000.000
167H150VAL0-0.016-0.01326.1400.0010.0010.0000.0000.0000.000
168H151THR0-0.079-0.03522.070-0.028-0.0280.0000.0000.0000.000
169H152VAL00.022-0.01224.5910.0220.0220.0000.0000.0000.000
170H153SER0-0.0040.01823.646-0.025-0.0250.0000.0000.0000.000
171H154TRP00.0170.00725.4230.0240.0240.0000.0000.0000.000
172H155ASN00.008-0.01526.925-0.012-0.0120.0000.0000.0000.000
173H156SER0-0.017-0.02026.8990.0020.0020.0000.0000.0000.000
174H157GLY0-0.0070.00223.218-0.019-0.0190.0000.0000.0000.000
175H158ALA0-0.029-0.00623.353-0.007-0.0070.0000.0000.0000.000
176H159LEU0-0.036-0.00625.7870.0150.0150.0000.0000.0000.000
177H160THR00.018-0.00521.284-0.006-0.0060.0000.0000.0000.000
178H161SER00.0410.01624.241-0.001-0.0010.0000.0000.0000.000
179H162GLY00.0460.02025.7510.0070.0070.0000.0000.0000.000
180H163VAL0-0.047-0.01525.4810.0100.0100.0000.0000.0000.000
181H164HIS0-0.0170.00026.172-0.012-0.0120.0000.0000.0000.000
182H165THR00.000-0.00725.3080.0170.0170.0000.0000.0000.000
183H166PHE0-0.0060.01226.388-0.012-0.0120.0000.0000.0000.000
184H167PRO00.022-0.00426.267-0.008-0.0080.0000.0000.0000.000
185H168ALA0-0.0030.00628.2210.0170.0170.0000.0000.0000.000
186H169VAL0-0.0030.00730.9190.0020.0020.0000.0000.0000.000
187H170LEU0-0.015-0.01733.884-0.002-0.0020.0000.0000.0000.000
188H171GLN0-0.039-0.02435.4670.0130.0130.0000.0000.0000.000
189H172SER00.0490.00539.140-0.004-0.0040.0000.0000.0000.000
190H173SER0-0.0150.00141.1160.0020.0020.0000.0000.0000.000
191H174GLY00.0030.00938.8140.0000.0000.0000.0000.0000.000
192H175LEU0-0.061-0.02036.826-0.011-0.0110.0000.0000.0000.000
193H176TYR00.0340.00831.1760.0040.0040.0000.0000.0000.000
194H177SER00.001-0.00634.5880.0040.0040.0000.0000.0000.000
195H178LEU00.0120.03128.0850.0000.0000.0000.0000.0000.000
196H179SER0-0.002-0.02031.3710.0170.0170.0000.0000.0000.000
197H180SER0-0.0080.00327.937-0.010-0.0100.0000.0000.0000.000
198H181VAL00.0220.00130.1710.0130.0130.0000.0000.0000.000
199H182VAL00.0200.01329.697-0.012-0.0120.0000.0000.0000.000
200H183THR0-0.022-0.00431.2350.0140.0140.0000.0000.0000.000
201H184VAL00.0040.00232.298-0.005-0.0050.0000.0000.0000.000
202H185PRO00.0710.03034.5090.0050.0050.0000.0000.0000.000
203H186SER00.0470.01937.736-0.005-0.0050.0000.0000.0000.000
204H187SER00.0380.02040.824-0.002-0.0020.0000.0000.0000.000
205H188SER0-0.028-0.02136.916-0.003-0.0030.0000.0000.0000.000
206H189LEU0-0.012-0.01038.603-0.004-0.0040.0000.0000.0000.000
207H190GLY00.0120.00740.639-0.001-0.0010.0000.0000.0000.000
208H191THR0-0.058-0.03340.4070.0020.0020.0000.0000.0000.000
209H192GLN00.0090.02333.758-0.003-0.0030.0000.0000.0000.000
210H193THR0-0.0210.00135.6120.0020.0020.0000.0000.0000.000
211H194TYR0-0.002-0.02132.785-0.010-0.0100.0000.0000.0000.000
212H195ILE00.0260.00432.1510.0060.0060.0000.0000.0000.000
213H197ASN0-0.013-0.03527.3930.0040.0040.0000.0000.0000.000
214H198VAL00.0110.00727.692-0.022-0.0220.0000.0000.0000.000
215H199ASN0-0.030-0.02825.5800.0070.0070.0000.0000.0000.000
216H200HIS00.0350.02727.130-0.010-0.0100.0000.0000.0000.000
217H201LYS11.0321.00321.0250.4830.4830.0000.0000.0000.000
218H202PRO00.0310.02626.7250.0070.0070.0000.0000.0000.000
219H203SER0-0.031-0.02429.3530.0160.0160.0000.0000.0000.000
220H204ASN0-0.058-0.02729.829-0.001-0.0010.0000.0000.0000.000
221H205THR00.0020.00331.1270.0120.0120.0000.0000.0000.000
222H206LYS10.8770.91628.1050.2300.2300.0000.0000.0000.000
223H207VAL0-0.007-0.01031.6220.0150.0150.0000.0000.0000.000
224H208ASP-1-0.822-0.88630.780-0.234-0.2340.0000.0000.0000.000
225H209LYS10.8810.93433.3960.1590.1590.0000.0000.0000.000
226H210ARG10.8940.94235.1880.1130.1130.0000.0000.0000.000
227H211VAL0-0.021-0.01235.6780.0030.0030.0000.0000.0000.000
228H212GLU-1-0.836-0.91738.317-0.108-0.1080.0000.0000.0000.000
229H213PRO0-0.0080.00041.221-0.001-0.0010.0000.0000.0000.000
230H214LYS10.8530.90742.3750.0780.0780.0000.0000.0000.000
231H215SER00.014-0.01444.5290.0000.0000.0000.0000.0000.000
232H216CYS0-0.020-0.01445.7470.0040.0040.0000.0000.0000.000
233H217ASP-1-0.776-0.83944.894-0.078-0.0780.0000.0000.0000.000
234H218LYS11.0210.99247.5630.0620.0620.0000.0000.0000.000
235H219GLY00.0190.02047.8580.0030.0030.0000.0000.0000.000
236H220LEU0-0.050-0.02742.5530.0010.0010.0000.0000.0000.000
237H221GLU-1-0.875-0.95046.586-0.069-0.0690.0000.0000.0000.000
238H222VAL0-0.016-0.00249.3710.0020.0020.0000.0000.0000.000
239H223LEU0-0.059-0.01745.2020.0020.0020.0000.0000.0000.000
240H224PHE0-0.057-0.01443.9280.0000.0000.0000.0000.0000.000