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: 7249K

Calculation Name: 3QHZ-H-Xray372

Preferred Name:

Target Type:

Ligand Name: pyroglutamic acid

ligand 3-letter code: PCA

PDB ID: 3QHZ

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 OptH
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 223
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2361667.12794
FMO2-HF: Nuclear repulsion 2275805.29606
FMO2-HF: Total energy -85861.831879
FMO2-MP2: Total energy -86110.519092


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.
-0.1363.1060.027-1.428-1.840.003
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 : 0.005 / q_NPA : -0.002
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].
3H3ASN0-0.080-0.0273.238-1.2291.5390.024-1.285-1.5070.003
4H4LEU00.1110.0545.6260.5050.5050.0000.0000.0000.000
5H5ARG10.8770.9368.7731.2301.2300.0000.0000.0000.000
6H6GLU-1-0.726-0.85711.299-0.649-0.6490.0000.0000.0000.000
7H7SER0-0.116-0.05314.8560.0260.0260.0000.0000.0000.000
8H8GLY00.0620.01816.6390.0130.0130.0000.0000.0000.000
9H9PRO0-0.035-0.00220.288-0.007-0.0070.0000.0000.0000.000
10H10ALA00.0510.02122.832-0.015-0.0150.0000.0000.0000.000
11H11LEU0-0.048-0.01924.143-0.003-0.0030.0000.0000.0000.000
12H12VAL00.0150.01627.8310.0100.0100.0000.0000.0000.000
13H13LYS10.9510.98029.9900.0640.0640.0000.0000.0000.000
14H14PRO00.0370.00433.776-0.002-0.0020.0000.0000.0000.000
15H15THR0-0.043-0.01735.9380.0100.0100.0000.0000.0000.000
16H16GLN0-0.037-0.01132.8160.0020.0020.0000.0000.0000.000
17H17THR00.018-0.00829.021-0.009-0.0090.0000.0000.0000.000
18H18LEU0-0.0240.00824.3080.0070.0070.0000.0000.0000.000
19H19THR00.004-0.00922.7710.0000.0000.0000.0000.0000.000
20H20LEU0-0.043-0.00720.0530.0020.0020.0000.0000.0000.000
21H21THR00.0170.01215.9550.0200.0200.0000.0000.0000.000
22H22CYS0-0.098-0.03314.497-0.058-0.0580.0000.0000.0000.000
23H23SER00.0260.01611.1750.1360.1360.0000.0000.0000.000
24H24PHE00.0270.0019.097-0.250-0.2500.0000.0000.0000.000
25H25SER0-0.024-0.0235.7680.5730.5730.0000.0000.0000.000
26H26GLY00.0380.0053.621-1.525-1.2350.004-0.122-0.1720.000
27H27PHE00.024-0.0014.1580.0130.197-0.001-0.021-0.1610.000
28H28SER00.0360.0157.4880.2550.2550.0000.0000.0000.000
29H29LEU00.0250.0129.6100.1300.1300.0000.0000.0000.000
30H30SER0-0.040-0.01911.231-0.006-0.0060.0000.0000.0000.000
31H31THR0-0.028-0.02611.5460.0080.0080.0000.0000.0000.000
32H32SER0-0.0180.02014.1870.0490.0490.0000.0000.0000.000
33H33GLY0-0.016-0.02517.595-0.023-0.0230.0000.0000.0000.000
34H34MET0-0.0560.00113.433-0.064-0.0640.0000.0000.0000.000
35H35SER00.0070.01018.1800.0470.0470.0000.0000.0000.000
36H35VAL0-0.003-0.00916.049-0.081-0.0810.0000.0000.0000.000
37H35SER00.0320.01218.5190.0830.0830.0000.0000.0000.000
38H36TRP0-0.023-0.01518.019-0.071-0.0710.0000.0000.0000.000
39H37ILE0-0.003-0.00320.0110.0380.0380.0000.0000.0000.000
40H38ARG10.8040.90521.6070.1840.1840.0000.0000.0000.000
41H39GLN00.000-0.00923.321-0.020-0.0200.0000.0000.0000.000
42H40PRO00.0370.02425.468-0.004-0.0040.0000.0000.0000.000
43H41PRO00.0230.00127.559-0.009-0.0090.0000.0000.0000.000
44H42GLY0-0.0070.00028.0840.0160.0160.0000.0000.0000.000
45H43LYS10.9250.97128.9950.1810.1810.0000.0000.0000.000
46H44ALA00.0240.01028.017-0.017-0.0170.0000.0000.0000.000
47H45LEU0-0.003-0.00222.3060.0030.0030.0000.0000.0000.000
48H46GLU-1-0.852-0.92625.804-0.191-0.1910.0000.0000.0000.000
49H47TRP0-0.007-0.00723.6380.0000.0000.0000.0000.0000.000
50H48LEU0-0.042-0.02024.4260.0250.0250.0000.0000.0000.000
51H49ALA00.0310.00224.8200.0270.0270.0000.0000.0000.000
52H50LEU0-0.0310.00922.504-0.034-0.0340.0000.0000.0000.000
53H51ILE0-0.020-0.01820.9830.0360.0360.0000.0000.0000.000
54H52ASP-1-0.755-0.86921.437-0.302-0.3020.0000.0000.0000.000
55H52TRP0-0.062-0.03515.1600.0070.0070.0000.0000.0000.000
56H53ASP-1-0.824-0.92819.204-0.210-0.2100.0000.0000.0000.000
57H54ASP-1-0.915-0.93421.504-0.141-0.1410.0000.0000.0000.000
58H55ASP-1-0.960-1.00524.441-0.110-0.1100.0000.0000.0000.000
59H56THR0-0.088-0.04626.9490.0100.0100.0000.0000.0000.000
60H57TYR0-0.033-0.02926.131-0.017-0.0170.0000.0000.0000.000
61H58TYR0-0.0210.00026.9540.0180.0180.0000.0000.0000.000
62H59ILE0-0.002-0.00927.668-0.017-0.0170.0000.0000.0000.000
63H60THR00.0070.00829.6460.0130.0130.0000.0000.0000.000
64H61TYR00.0420.01331.2930.0140.0140.0000.0000.0000.000
65H62SER00.0010.00033.6770.0160.0160.0000.0000.0000.000
66H62SER00.028-0.00335.426-0.001-0.0010.0000.0000.0000.000
67H62SER00.0060.00836.0400.0020.0020.0000.0000.0000.000
68H63LEU00.014-0.00230.4420.0000.0000.0000.0000.0000.000
69H64LYS10.9520.98733.0640.1120.1120.0000.0000.0000.000
70H65THR0-0.037-0.01734.4590.0000.0000.0000.0000.0000.000
71H66ARG10.7600.87532.9200.1430.1430.0000.0000.0000.000
72H67LEU0-0.0070.00727.437-0.004-0.0040.0000.0000.0000.000
73H68THR00.0130.01327.6110.0120.0120.0000.0000.0000.000
74H69ILE0-0.003-0.00221.839-0.015-0.0150.0000.0000.0000.000
75H70SER0-0.0220.00123.6280.0220.0220.0000.0000.0000.000
76H71LYS10.9110.95319.7420.1400.1400.0000.0000.0000.000
77H72ASP-1-0.807-0.88018.9360.0590.0590.0000.0000.0000.000
78H73THR00.031-0.00617.0120.0060.0060.0000.0000.0000.000
79H74SER0-0.088-0.04816.0760.0310.0310.0000.0000.0000.000
80H75LYS10.9430.96314.440-0.029-0.0290.0000.0000.0000.000
81H76SER0-0.040-0.00211.836-0.054-0.0540.0000.0000.0000.000
82H77GLN0-0.043-0.03713.387-0.087-0.0870.0000.0000.0000.000
83H78VAL00.0280.01815.9290.0330.0330.0000.0000.0000.000
84H79VAL0-0.019-0.01318.476-0.029-0.0290.0000.0000.0000.000
85H80LEU0-0.0180.00421.0990.0070.0070.0000.0000.0000.000
86H81THR00.010-0.01323.5140.0090.0090.0000.0000.0000.000
87H82MET0-0.034-0.00526.753-0.006-0.0060.0000.0000.0000.000
88H82THR00.0380.00629.1600.0050.0050.0000.0000.0000.000
89H82ASN00.002-0.00532.644-0.003-0.0030.0000.0000.0000.000
90H82MET0-0.0340.00328.522-0.006-0.0060.0000.0000.0000.000
91H83ASP-1-0.766-0.90033.145-0.101-0.1010.0000.0000.0000.000
92H84PRO00.010-0.00433.192-0.011-0.0110.0000.0000.0000.000
93H85VAL0-0.041-0.02033.117-0.011-0.0110.0000.0000.0000.000
94H86ASP-1-0.768-0.86129.867-0.165-0.1650.0000.0000.0000.000
95H87THR0-0.027-0.00428.510-0.015-0.0150.0000.0000.0000.000
96H88ALA0-0.024-0.01625.882-0.001-0.0010.0000.0000.0000.000
97H89THR0-0.0150.00720.0560.0120.0120.0000.0000.0000.000
98H90TYR0-0.024-0.02521.2160.0030.0030.0000.0000.0000.000
99H91TYR00.009-0.00316.583-0.033-0.0330.0000.0000.0000.000
100H93ALA00.005-0.00615.069-0.096-0.0960.0000.0000.0000.000
101H94ARG10.8050.8819.5901.3621.3620.0000.0000.0000.000
102H95THR0-0.0130.00015.7130.0060.0060.0000.0000.0000.000
103H96LEU0-0.024-0.01613.1290.0100.0100.0000.0000.0000.000
104H97ARG10.9911.01617.2340.2770.2770.0000.0000.0000.000
105H98VAL00.003-0.00118.700-0.017-0.0170.0000.0000.0000.000
106H100SER0-0.029-0.03321.0750.0310.0310.0000.0000.0000.000
107H100GLY00.0220.01024.459-0.011-0.0110.0000.0000.0000.000
108H100ASP-1-0.911-0.94427.053-0.188-0.1880.0000.0000.0000.000
109H100TYR0-0.101-0.05027.2010.0070.0070.0000.0000.0000.000
110H100VAL0-0.0010.00022.6340.0000.0000.0000.0000.0000.000
111H100ARG10.9530.97922.5130.2380.2380.0000.0000.0000.000
112H100ASP-1-0.901-0.95219.189-0.481-0.4810.0000.0000.0000.000
113H100PHE00.008-0.00218.152-0.008-0.0080.0000.0000.0000.000
114H101ASP-1-0.724-0.83513.607-0.980-0.9800.0000.0000.0000.000
115H102LEU0-0.055-0.0158.648-0.148-0.1480.0000.0000.0000.000
116H103TRP00.006-0.01012.5260.1260.1260.0000.0000.0000.000
117H104GLY00.0120.01411.464-0.192-0.1920.0000.0000.0000.000
118H105ARG10.8690.92011.7490.7410.7410.0000.0000.0000.000
119H106GLY00.0450.02913.5350.0800.0800.0000.0000.0000.000
120H107THR0-0.082-0.04716.554-0.005-0.0050.0000.0000.0000.000
121H108LEU0-0.0060.00218.7510.0170.0170.0000.0000.0000.000
122H109VAL0-0.004-0.00122.2870.0160.0160.0000.0000.0000.000
123H110THR00.001-0.00825.0920.0020.0020.0000.0000.0000.000
124H111VAL00.0040.01028.5580.0090.0090.0000.0000.0000.000
125H112SER00.0210.00031.5560.0060.0060.0000.0000.0000.000
126H113SER00.003-0.00634.1060.0010.0010.0000.0000.0000.000
127H114ALA0-0.023-0.00135.2590.0080.0080.0000.0000.0000.000
128H115SER00.010-0.00934.111-0.004-0.0040.0000.0000.0000.000
129H116THR0-0.040-0.01229.139-0.004-0.0040.0000.0000.0000.000
130H117LYS10.9040.94431.0890.0740.0740.0000.0000.0000.000
131H118GLY00.0560.03029.340-0.010-0.0100.0000.0000.0000.000
132H119PRO0-0.043-0.01227.5410.0030.0030.0000.0000.0000.000
133H120SER0-0.028-0.01030.7930.0120.0120.0000.0000.0000.000
134H121VAL00.008-0.00328.720-0.008-0.0080.0000.0000.0000.000
135H122PHE0-0.022-0.01332.0440.0100.0100.0000.0000.0000.000
136H123PRO0-0.0030.00233.356-0.007-0.0070.0000.0000.0000.000
137H124LEU0-0.040-0.01032.6580.0010.0010.0000.0000.0000.000
138H125ALA00.0170.00834.873-0.003-0.0030.0000.0000.0000.000
139H126PRO00.0140.01835.2950.0000.0000.0000.0000.0000.000
140H136GLY00.0360.00638.142-0.001-0.0010.0000.0000.0000.000
141H137THR0-0.047-0.01533.5450.0020.0020.0000.0000.0000.000
142H138ALA00.0080.00734.6520.0040.0040.0000.0000.0000.000
143H139ALA00.0130.01332.979-0.006-0.0060.0000.0000.0000.000
144H140LEU00.0060.01929.9750.0080.0080.0000.0000.0000.000
145H141GLY00.053-0.00830.139-0.012-0.0120.0000.0000.0000.000
146H142CYS0-0.104-0.01825.1890.0060.0060.0000.0000.0000.000
147H143LEU00.0180.02330.455-0.011-0.0110.0000.0000.0000.000
148H144VAL0-0.017-0.01827.3240.0110.0110.0000.0000.0000.000
149H145LYS10.9780.97630.6520.0570.0570.0000.0000.0000.000
150H146ASP-1-0.877-0.93733.159-0.069-0.0690.0000.0000.0000.000
151H147TYR0-0.023-0.03227.1650.0110.0110.0000.0000.0000.000
152H148PHE00.0500.03330.382-0.009-0.0090.0000.0000.0000.000
153H149PRO0-0.0030.01526.6040.0140.0140.0000.0000.0000.000
154H150GLU-1-0.766-0.88125.195-0.199-0.1990.0000.0000.0000.000
155H151PRO0-0.030-0.02320.7610.0010.0010.0000.0000.0000.000
156H152VAL00.0210.00023.1440.0170.0170.0000.0000.0000.000
157H153THR0-0.067-0.02717.750-0.029-0.0290.0000.0000.0000.000
158H154VAL0-0.010-0.02320.8770.0300.0300.0000.0000.0000.000
159H156SER0-0.043-0.01718.553-0.032-0.0320.0000.0000.0000.000
160H157TRP00.0280.01020.5980.0300.0300.0000.0000.0000.000
161H162ASN00.000-0.00721.265-0.005-0.0050.0000.0000.0000.000
162H163SER00.002-0.01018.9120.0070.0070.0000.0000.0000.000
163H164GLY0-0.031-0.00816.5720.0050.0050.0000.0000.0000.000
164H165ALA0-0.021-0.00317.409-0.027-0.0270.0000.0000.0000.000
165H166LEU0-0.034-0.00318.985-0.004-0.0040.0000.0000.0000.000
166H167THR00.015-0.00616.947-0.006-0.0060.0000.0000.0000.000
167H168SER00.0000.00020.363-0.018-0.0180.0000.0000.0000.000
168H169GLY00.0620.02822.7280.0180.0180.0000.0000.0000.000
169H171VAL0-0.040-0.01722.2590.0130.0130.0000.0000.0000.000
170H172HIS00.0020.00423.762-0.028-0.0280.0000.0000.0000.000
171H173THR0-0.001-0.00422.5810.0300.0300.0000.0000.0000.000
172H174PHE0-0.0120.00324.667-0.019-0.0190.0000.0000.0000.000
173H175PRO00.005-0.01125.7400.0010.0010.0000.0000.0000.000
174H176ALA00.0100.01327.2570.0150.0150.0000.0000.0000.000
175H177VAL0-0.026-0.00129.476-0.003-0.0030.0000.0000.0000.000
176H178LEU0-0.005-0.00733.1360.0020.0020.0000.0000.0000.000
177H179GLN0-0.018-0.00834.5080.0000.0000.0000.0000.0000.000
178H180SER00.0300.00737.865-0.002-0.0020.0000.0000.0000.000
179H182SER0-0.015-0.01138.833-0.001-0.0010.0000.0000.0000.000
180H183GLY00.0160.01036.9070.0030.0030.0000.0000.0000.000
181H184LEU0-0.082-0.02734.280-0.005-0.0050.0000.0000.0000.000
182H185TYR00.0420.01230.453-0.001-0.0010.0000.0000.0000.000
183H186SER00.0040.00431.8490.0120.0120.0000.0000.0000.000
184H187LEU0-0.0010.02125.554-0.006-0.0060.0000.0000.0000.000
185H188SER00.018-0.00129.5660.0170.0170.0000.0000.0000.000
186H189SER0-0.027-0.00624.865-0.011-0.0110.0000.0000.0000.000
187H190VAL00.0230.00027.6160.0170.0170.0000.0000.0000.000
188H191VAL00.0200.01426.419-0.016-0.0160.0000.0000.0000.000
189H192THR0-0.037-0.01828.2280.0140.0140.0000.0000.0000.000
190H193VAL00.002-0.00228.796-0.006-0.0060.0000.0000.0000.000
191H194PRO00.0680.02430.4960.0030.0030.0000.0000.0000.000
192H195SER00.0540.02033.7410.0030.0030.0000.0000.0000.000
193H196SER0-0.010-0.00836.5990.0020.0020.0000.0000.0000.000
194H197SER0-0.017-0.01231.5580.0040.0040.0000.0000.0000.000
195H198LEU0-0.003-0.01533.0430.0020.0020.0000.0000.0000.000
196H199GLY0-0.0090.00535.0200.0030.0030.0000.0000.0000.000
197H200THR0-0.058-0.02632.8940.0040.0040.0000.0000.0000.000
198H203GLN00.0320.02926.0290.0140.0140.0000.0000.0000.000
199H205THR0-0.036-0.00628.8170.0000.0000.0000.0000.0000.000
200H206TYR00.011-0.00327.580-0.007-0.0070.0000.0000.0000.000
201H207ILE00.018-0.00225.9610.0040.0040.0000.0000.0000.000
202H209ASN00.0590.01721.272-0.001-0.0010.0000.0000.0000.000
203H210VAL0-0.0060.00522.363-0.029-0.0290.0000.0000.0000.000
204H211ASN0-0.016-0.01918.1250.0430.0430.0000.0000.0000.000
205H212HIS00.0560.04221.984-0.014-0.0140.0000.0000.0000.000
206H213LYS10.9530.96014.8650.3030.3030.0000.0000.0000.000
207H214PRO00.0100.01221.7890.0180.0180.0000.0000.0000.000
208H215SER0-0.012-0.01524.6740.0150.0150.0000.0000.0000.000
209H216ASN0-0.075-0.03522.9560.0170.0170.0000.0000.0000.000
210H217THR00.0380.02924.5990.0210.0210.0000.0000.0000.000
211H218LYS10.9020.93719.3220.0010.0010.0000.0000.0000.000
212H219VAL00.0020.00324.4850.0120.0120.0000.0000.0000.000
213H220ASP-1-0.822-0.88824.290-0.027-0.0270.0000.0000.0000.000
214H221LYS10.9180.94826.9520.0360.0360.0000.0000.0000.000
215H222ARG10.9610.98729.396-0.005-0.0050.0000.0000.0000.000
216H223VAL0-0.040-0.03230.7050.0010.0010.0000.0000.0000.000
217H226GLU-1-0.945-0.96733.171-0.008-0.0080.0000.0000.0000.000
218H227PRO00.0400.00736.383-0.006-0.0060.0000.0000.0000.000
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