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

tag_button

FMODB ID: 6N5MZ

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 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 223
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2362913.798357
FMO2-HF: Nuclear repulsion 2277051.206727
FMO2-HF: Total energy -85862.59163
FMO2-MP2: Total energy -86111.423233


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.
0.5843.2420.009-1.193-1.4720.003
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 : 0.007 / q_NPA : -0.001
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].
3H3ASN0-0.094-0.0483.555-0.3061.9030.006-1.062-1.1520.003
4H4LEU00.0940.0495.7040.5400.5400.0000.0000.0000.000
5H5ARG10.8900.9428.2651.3671.3670.0000.0000.0000.000
6H6GLU-1-0.694-0.84011.546-0.698-0.6980.0000.0000.0000.000
7H7SER0-0.074-0.03614.7490.0280.0280.0000.0000.0000.000
8H8GLY00.0650.02516.8300.0030.0030.0000.0000.0000.000
9H9PRO0-0.0190.00820.600-0.001-0.0010.0000.0000.0000.000
10H10ALA00.0540.01622.820-0.013-0.0130.0000.0000.0000.000
11H11LEU0-0.059-0.02624.372-0.002-0.0020.0000.0000.0000.000
12H12VAL00.0100.01328.1420.0090.0090.0000.0000.0000.000
13H13LYS10.8550.92930.4210.0650.0650.0000.0000.0000.000
14H14PRO00.0430.00634.269-0.002-0.0020.0000.0000.0000.000
15H15THR0-0.056-0.02136.3430.0110.0110.0000.0000.0000.000
16H16GLN0-0.0070.00533.300-0.001-0.0010.0000.0000.0000.000
17H17THR00.010-0.00629.497-0.009-0.0090.0000.0000.0000.000
18H18LEU0-0.0220.00924.8090.0070.0070.0000.0000.0000.000
19H19THR00.002-0.01823.1090.0040.0040.0000.0000.0000.000
20H20LEU0-0.052-0.01820.4060.0020.0020.0000.0000.0000.000
21H21THR00.0170.01116.1350.0100.0100.0000.0000.0000.000
22H22CYS0-0.095-0.02014.978-0.045-0.0450.0000.0000.0000.000
23H23SER00.0230.01211.2800.1600.1600.0000.0000.0000.000
24H24PHE00.0350.0069.103-0.237-0.2370.0000.0000.0000.000
25H25SER00.0060.0136.1550.6070.6070.0000.0000.0000.000
26H26GLY00.0310.0043.755-1.431-1.1690.004-0.112-0.1530.000
27H27PHE00.0360.0044.332-0.258-0.071-0.001-0.019-0.1670.000
28H28SER00.0510.0327.7430.2370.2370.0000.0000.0000.000
29H29LEU00.0180.0109.9080.1020.1020.0000.0000.0000.000
30H30SER0-0.038-0.01811.325-0.019-0.0190.0000.0000.0000.000
31H31THR0-0.042-0.04511.671-0.001-0.0010.0000.0000.0000.000
32H32SER0-0.059-0.02014.2540.0470.0470.0000.0000.0000.000
33H33GLY00.016-0.00917.715-0.016-0.0160.0000.0000.0000.000
34H34MET0-0.0370.01013.806-0.057-0.0570.0000.0000.0000.000
35H35SER00.0060.00718.6320.0420.0420.0000.0000.0000.000
36H35VAL0-0.019-0.01116.074-0.088-0.0880.0000.0000.0000.000
37H35SER00.0210.00918.6370.0950.0950.0000.0000.0000.000
38H36TRP0-0.024-0.02118.481-0.073-0.0730.0000.0000.0000.000
39H37ILE00.0020.00420.3920.0410.0410.0000.0000.0000.000
40H38ARG10.7500.85722.0580.2090.2090.0000.0000.0000.000
41H39GLN00.0260.01523.448-0.029-0.0290.0000.0000.0000.000
42H40PRO00.0400.02225.7340.0000.0000.0000.0000.0000.000
43H41PRO0-0.004-0.01028.143-0.010-0.0100.0000.0000.0000.000
44H42GLY00.0030.00828.5490.0150.0150.0000.0000.0000.000
45H43LYS10.9220.97229.1480.1960.1960.0000.0000.0000.000
46H44ALA00.0420.01928.122-0.020-0.0200.0000.0000.0000.000
47H45LEU00.0020.00322.3720.0040.0040.0000.0000.0000.000
48H46GLU-1-0.826-0.90226.199-0.210-0.2100.0000.0000.0000.000
49H47TRP00.002-0.00523.920-0.003-0.0030.0000.0000.0000.000
50H48LEU0-0.040-0.01924.6830.0280.0280.0000.0000.0000.000
51H49ALA00.0350.00424.9950.0290.0290.0000.0000.0000.000
52H50LEU0-0.040-0.00122.648-0.037-0.0370.0000.0000.0000.000
53H51ILE0-0.007-0.00721.2480.0400.0400.0000.0000.0000.000
54H52ASP-1-0.741-0.84821.462-0.352-0.3520.0000.0000.0000.000
55H52TRP0-0.030-0.01615.3340.0090.0090.0000.0000.0000.000
56H53ASP-1-0.807-0.89819.115-0.282-0.2820.0000.0000.0000.000
57H54ASP-1-0.848-0.91321.634-0.200-0.2000.0000.0000.0000.000
58H55ASP-1-0.878-0.95024.441-0.158-0.1580.0000.0000.0000.000
59H56THR0-0.077-0.04826.9100.0150.0150.0000.0000.0000.000
60H57TYR0-0.027-0.02426.219-0.022-0.0220.0000.0000.0000.000
61H58TYR0-0.058-0.03326.3090.0260.0260.0000.0000.0000.000
62H59ILE0-0.008-0.01127.790-0.018-0.0180.0000.0000.0000.000
63H60THR00.0090.01329.8120.0130.0130.0000.0000.0000.000
64H61TYR00.0590.01931.3920.0160.0160.0000.0000.0000.000
65H62SER00.0180.01033.9000.0190.0190.0000.0000.0000.000
66H62SER00.019-0.00435.724-0.001-0.0010.0000.0000.0000.000
67H62SER00.0140.01735.8110.0040.0040.0000.0000.0000.000
68H63LEU00.0000.00230.612-0.001-0.0010.0000.0000.0000.000
69H64LYS10.9180.95833.3610.1380.1380.0000.0000.0000.000
70H65THR0-0.013-0.00134.7090.0010.0010.0000.0000.0000.000
71H66ARG10.7250.82933.4510.1550.1550.0000.0000.0000.000
72H67LEU0-0.0110.00327.721-0.002-0.0020.0000.0000.0000.000
73H68THR0-0.004-0.00328.0180.0160.0160.0000.0000.0000.000
74H69ILE0-0.018-0.00422.051-0.014-0.0140.0000.0000.0000.000
75H70SER0-0.0130.00723.5580.0270.0270.0000.0000.0000.000
76H71LYS10.8410.90420.2140.1720.1720.0000.0000.0000.000
77H72ASP-1-0.747-0.82218.8680.0340.0340.0000.0000.0000.000
78H73THR00.0510.00617.093-0.008-0.0080.0000.0000.0000.000
79H74SER0-0.090-0.06416.4240.0380.0380.0000.0000.0000.000
80H75LYS10.8350.89314.8920.0170.0170.0000.0000.0000.000
81H76SER0-0.0370.00211.749-0.045-0.0450.0000.0000.0000.000
82H77GLN0-0.030-0.03013.146-0.076-0.0760.0000.0000.0000.000
83H78VAL00.0280.01115.7440.0310.0310.0000.0000.0000.000
84H79VAL0-0.017-0.00318.520-0.034-0.0340.0000.0000.0000.000
85H80LEU00.0100.01821.0360.0130.0130.0000.0000.0000.000
86H81THR0-0.005-0.02523.6160.0250.0250.0000.0000.0000.000
87H82MET0-0.043-0.00626.798-0.012-0.0120.0000.0000.0000.000
88H82THR00.0530.02029.5810.0060.0060.0000.0000.0000.000
89H82ASN00.004-0.00432.9860.0000.0000.0000.0000.0000.000
90H82MET0-0.0240.01229.164-0.008-0.0080.0000.0000.0000.000
91H83ASP-1-0.789-0.90933.573-0.107-0.1070.0000.0000.0000.000
92H84PRO00.006-0.00433.805-0.011-0.0110.0000.0000.0000.000
93H85VAL0-0.034-0.01533.728-0.011-0.0110.0000.0000.0000.000
94H86ASP-1-0.751-0.83330.392-0.178-0.1780.0000.0000.0000.000
95H87THR0-0.036-0.00629.152-0.015-0.0150.0000.0000.0000.000
96H88ALA0-0.013-0.01026.342-0.001-0.0010.0000.0000.0000.000
97H89THR0-0.0170.00420.5090.0130.0130.0000.0000.0000.000
98H90TYR00.005-0.01421.728-0.003-0.0030.0000.0000.0000.000
99H91TYR00.003-0.02617.203-0.032-0.0320.0000.0000.0000.000
100H93ALA00.0100.00315.275-0.110-0.1100.0000.0000.0000.000
101H94ARG10.7760.8509.3081.6361.6360.0000.0000.0000.000
102H95THR0-0.004-0.01215.8030.0070.0070.0000.0000.0000.000
103H96LEU0-0.013-0.01013.1270.0320.0320.0000.0000.0000.000
104H97ARG10.8580.95717.2400.3580.3580.0000.0000.0000.000
105H98VAL0-0.002-0.01518.737-0.033-0.0330.0000.0000.0000.000
106H100SER0-0.046-0.03921.1180.0360.0360.0000.0000.0000.000
107H100GLY00.0140.00624.576-0.009-0.0090.0000.0000.0000.000
108H100ASP-1-0.863-0.91027.218-0.251-0.2510.0000.0000.0000.000
109H100TYR0-0.067-0.04527.317-0.002-0.0020.0000.0000.0000.000
110H100VAL00.0120.01222.702-0.002-0.0020.0000.0000.0000.000
111H100ARG10.9230.96322.4680.2950.2950.0000.0000.0000.000
112H100ASP-1-0.887-0.94418.824-0.604-0.6040.0000.0000.0000.000
113H100PHE0-0.020-0.00918.2970.0130.0130.0000.0000.0000.000
114H101ASP-1-0.700-0.80913.274-1.250-1.2500.0000.0000.0000.000
115H102LEU0-0.053-0.0058.759-0.156-0.1560.0000.0000.0000.000
116H103TRP0-0.006-0.02212.4150.1790.1790.0000.0000.0000.000
117H104GLY00.0030.01711.474-0.228-0.2280.0000.0000.0000.000
118H105ARG10.7280.82711.7950.6910.6910.0000.0000.0000.000
119H106GLY00.0420.02113.9070.0880.0880.0000.0000.0000.000
120H107THR0-0.066-0.03316.826-0.010-0.0100.0000.0000.0000.000
121H108LEU00.0040.01719.3900.0130.0130.0000.0000.0000.000
122H109VAL0-0.013-0.00522.8870.0140.0140.0000.0000.0000.000
123H110THR0-0.010-0.00925.6070.0010.0010.0000.0000.0000.000
124H111VAL00.0130.00929.0760.0100.0100.0000.0000.0000.000
125H112SER00.0280.00032.0310.0070.0070.0000.0000.0000.000
126H113SER00.0510.01934.6100.0010.0010.0000.0000.0000.000
127H114ALA00.0060.02835.3760.0090.0090.0000.0000.0000.000
128H115SER00.024-0.01133.975-0.004-0.0040.0000.0000.0000.000
129H116THR0-0.052-0.02429.3250.0000.0000.0000.0000.0000.000
130H117LYS10.8500.91531.4960.0640.0640.0000.0000.0000.000
131H118GLY00.0580.03529.507-0.011-0.0110.0000.0000.0000.000
132H119PRO0-0.033-0.01227.7760.0020.0020.0000.0000.0000.000
133H120SER0-0.018-0.00431.0350.0110.0110.0000.0000.0000.000
134H121VAL00.000-0.00329.305-0.009-0.0090.0000.0000.0000.000
135H122PHE00.0090.00132.6120.0100.0100.0000.0000.0000.000
136H123PRO0-0.013-0.00433.655-0.007-0.0070.0000.0000.0000.000
137H124LEU0-0.033-0.01532.8830.0020.0020.0000.0000.0000.000
138H125ALA00.0170.00734.982-0.003-0.0030.0000.0000.0000.000
139H126PRO0-0.0130.00835.413-0.001-0.0010.0000.0000.0000.000
140H136GLY00.0370.00838.586-0.001-0.0010.0000.0000.0000.000
141H137THR0-0.037-0.01533.8780.0030.0030.0000.0000.0000.000
142H138ALA00.0050.00934.8380.0050.0050.0000.0000.0000.000
143H139ALA00.0120.00932.965-0.006-0.0060.0000.0000.0000.000
144H140LEU00.0020.01929.8980.0080.0080.0000.0000.0000.000
145H141GLY00.0550.00030.299-0.012-0.0120.0000.0000.0000.000
146H142CYS0-0.0840.00125.1950.0100.0100.0000.0000.0000.000
147H143LEU00.0320.04030.250-0.013-0.0130.0000.0000.0000.000
148H144VAL0-0.030-0.02527.8000.0120.0120.0000.0000.0000.000
149H145LYS10.8960.91931.0690.0530.0530.0000.0000.0000.000
150H146ASP-1-0.779-0.87433.206-0.060-0.0600.0000.0000.0000.000
151H147TYR0-0.001-0.01127.4800.0130.0130.0000.0000.0000.000
152H148PHE00.0560.02930.966-0.009-0.0090.0000.0000.0000.000
153H149PRO00.0280.03427.1470.0150.0150.0000.0000.0000.000
154H150GLU-1-0.741-0.85725.600-0.191-0.1910.0000.0000.0000.000
155H151PRO0-0.041-0.02121.0120.0000.0000.0000.0000.0000.000
156H152VAL0-0.011-0.01323.4030.0180.0180.0000.0000.0000.000
157H153THR0-0.091-0.04418.268-0.033-0.0330.0000.0000.0000.000
158H154VAL00.014-0.01221.1320.0320.0320.0000.0000.0000.000
159H156SER0-0.030-0.00318.790-0.032-0.0320.0000.0000.0000.000
160H157TRP00.0250.01020.8150.0280.0280.0000.0000.0000.000
161H162ASN00.000-0.01920.980-0.010-0.0100.0000.0000.0000.000
162H163SER0-0.010-0.01519.3810.0100.0100.0000.0000.0000.000
163H164GLY0-0.0030.00616.4830.0210.0210.0000.0000.0000.000
164H165ALA0-0.037-0.01017.253-0.027-0.0270.0000.0000.0000.000
165H166LEU0-0.042-0.01119.143-0.003-0.0030.0000.0000.0000.000
166H167THR00.022-0.00217.084-0.009-0.0090.0000.0000.0000.000
167H168SER00.0310.01120.567-0.022-0.0220.0000.0000.0000.000
168H169GLY00.0570.02823.0570.0180.0180.0000.0000.0000.000
169H171VAL0-0.059-0.01922.4540.0120.0120.0000.0000.0000.000
170H172HIS00.0130.01123.995-0.032-0.0320.0000.0000.0000.000
171H173THR0-0.010-0.00622.8800.0310.0310.0000.0000.0000.000
172H174PHE0-0.0160.00725.093-0.021-0.0210.0000.0000.0000.000
173H175PRO00.025-0.00726.0420.0020.0020.0000.0000.0000.000
174H176ALA0-0.0030.00827.4520.0160.0160.0000.0000.0000.000
175H177VAL0-0.0150.00129.741-0.005-0.0050.0000.0000.0000.000
176H178LEU0-0.023-0.01233.4250.0050.0050.0000.0000.0000.000
177H179GLN0-0.0130.00034.6450.0000.0000.0000.0000.0000.000
178H180SER00.0320.00637.986-0.002-0.0020.0000.0000.0000.000
179H182SER0-0.009-0.00639.2160.0000.0000.0000.0000.0000.000
180H183GLY00.0070.00737.2980.0030.0030.0000.0000.0000.000
181H184LEU0-0.076-0.02534.622-0.005-0.0050.0000.0000.0000.000
182H185TYR00.0360.01030.764-0.004-0.0040.0000.0000.0000.000
183H186SER0-0.002-0.01932.2580.0130.0130.0000.0000.0000.000
184H187LEU00.0060.02425.657-0.007-0.0070.0000.0000.0000.000
185H188SER0-0.004-0.02329.3290.0200.0200.0000.0000.0000.000
186H189SER0-0.0150.00224.907-0.013-0.0130.0000.0000.0000.000
187H190VAL00.023-0.00227.4140.0190.0190.0000.0000.0000.000
188H191VAL00.0050.00826.112-0.016-0.0160.0000.0000.0000.000
189H192THR0-0.016-0.00828.2580.0130.0130.0000.0000.0000.000
190H193VAL00.0080.00328.762-0.006-0.0060.0000.0000.0000.000
191H194PRO00.0710.02630.8780.0000.0000.0000.0000.0000.000
192H195SER00.014-0.00333.9800.0060.0060.0000.0000.0000.000
193H196SER00.0020.00136.4620.0020.0020.0000.0000.0000.000
194H197SER0-0.011-0.01031.6140.0050.0050.0000.0000.0000.000
195H198LEU0-0.009-0.01233.3740.0050.0050.0000.0000.0000.000
196H199GLY0-0.0050.01035.2680.0030.0030.0000.0000.0000.000
197H200THR0-0.042-0.02832.5150.0030.0030.0000.0000.0000.000
198H203GLN00.0090.01926.1590.0160.0160.0000.0000.0000.000
199H205THR0-0.0080.01628.513-0.004-0.0040.0000.0000.0000.000
200H206TYR00.0300.01027.739-0.002-0.0020.0000.0000.0000.000
201H207ILE00.017-0.00125.6480.0030.0030.0000.0000.0000.000
202H209ASN00.0570.00721.515-0.001-0.0010.0000.0000.0000.000
203H210VAL0-0.0150.00322.529-0.029-0.0290.0000.0000.0000.000
204H211ASN00.001-0.01519.0240.0520.0520.0000.0000.0000.000
205H212HIS00.0200.02222.336-0.019-0.0190.0000.0000.0000.000
206H213LYS10.9880.98215.5630.3000.3000.0000.0000.0000.000
207H214PRO00.0040.01122.0940.0170.0170.0000.0000.0000.000
208H215SER00.0140.00725.1310.0150.0150.0000.0000.0000.000
209H216ASN0-0.043-0.02722.4860.0170.0170.0000.0000.0000.000
210H217THR00.0210.01124.2590.0190.0190.0000.0000.0000.000
211H218LYS10.8600.92120.116-0.017-0.0170.0000.0000.0000.000
212H219VAL00.004-0.00325.1430.0100.0100.0000.0000.0000.000
213H220ASP-1-0.849-0.89324.1900.0210.0210.0000.0000.0000.000
214H221LYS10.8730.92026.9740.0110.0110.0000.0000.0000.000
215H222ARG10.8640.91529.486-0.032-0.0320.0000.0000.0000.000
216H223VAL0-0.013-0.01330.581-0.001-0.0010.0000.0000.0000.000
217H226GLU-1-0.849-0.90732.9450.0160.0160.0000.0000.0000.000
218H227PRO00.040-0.00236.323-0.007-0.0070.0000.0000.0000.000
219H228LYS10.8560.93439.0930.0320.0320.0000.0000.0000.000
220H232SER00.0220.01341.5810.0020.0020.0000.0000.0000.000
221H233CYS0-0.047-0.04344.195-0.002-0.0020.0000.0000.0000.000
222H234ASP-1-0.833-0.88843.918-0.030-0.0300.0000.0000.0000.000
223H235LYS10.9700.99046.6570.0140.0140.0000.0000.0000.000