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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: 2JGYR

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 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 223
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2363525.970122
FMO2-HF: Nuclear repulsion 2277663.603795
FMO2-HF: Total energy -85862.366327
FMO2-MP2: Total energy -86111.073123


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.
0.3213.3210.018-1.311-1.7060.004
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 : -0.008 / q_NPA : -0.006
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].
3H3ASN0-0.088-0.0373.192-0.4852.0790.017-1.184-1.3970.004
4H4LEU00.1090.0505.7240.4940.4940.0000.0000.0000.000
5H5ARG10.8770.9398.1821.4111.4110.0000.0000.0000.000
6H6GLU-1-0.720-0.85111.342-0.717-0.7170.0000.0000.0000.000
7H7SER0-0.101-0.05314.8700.0200.0200.0000.0000.0000.000
8H8GLY00.0690.02316.6310.0140.0140.0000.0000.0000.000
9H9PRO0-0.028-0.00120.272-0.008-0.0080.0000.0000.0000.000
10H10ALA00.0460.02122.951-0.016-0.0160.0000.0000.0000.000
11H11LEU0-0.054-0.02024.266-0.002-0.0020.0000.0000.0000.000
12H12VAL00.0150.01127.9340.0100.0100.0000.0000.0000.000
13H13LYS10.9100.96030.0310.0790.0790.0000.0000.0000.000
14H14PRO00.0380.00633.814-0.003-0.0030.0000.0000.0000.000
15H15THR0-0.052-0.02335.9600.0110.0110.0000.0000.0000.000
16H16GLN0-0.029-0.00432.8410.0010.0010.0000.0000.0000.000
17H17THR00.011-0.01028.974-0.009-0.0090.0000.0000.0000.000
18H18LEU0-0.0230.00824.4840.0060.0060.0000.0000.0000.000
19H19THR00.009-0.00422.6970.0020.0020.0000.0000.0000.000
20H20LEU0-0.045-0.01020.027-0.001-0.0010.0000.0000.0000.000
21H21THR00.0240.01215.7830.0220.0220.0000.0000.0000.000
22H22CYS0-0.101-0.03114.654-0.067-0.0670.0000.0000.0000.000
23H23SER00.0370.02610.8690.1440.1440.0000.0000.0000.000
24H24PHE00.0310.0058.898-0.264-0.2640.0000.0000.0000.000
25H25SER0-0.024-0.0165.4000.4860.4860.0000.0000.0000.000
26H26GLY00.0410.0103.864-1.381-1.1150.002-0.109-0.1590.000
27H27PHE00.0320.0014.417-0.418-0.248-0.001-0.018-0.1500.000
28H28SER00.0450.0207.6330.2170.2170.0000.0000.0000.000
29H29LEU00.0080.0069.6980.1350.1350.0000.0000.0000.000
30H30SER0-0.029-0.01611.352-0.029-0.0290.0000.0000.0000.000
31H31THR0-0.025-0.03011.7710.0070.0070.0000.0000.0000.000
32H32SER0-0.0250.01314.3770.0540.0540.0000.0000.0000.000
33H33GLY0-0.012-0.02917.758-0.028-0.0280.0000.0000.0000.000
34H34MET0-0.0690.00413.622-0.068-0.0680.0000.0000.0000.000
35H35SER00.0170.00718.3420.0420.0420.0000.0000.0000.000
36H35VAL0-0.018-0.01215.978-0.085-0.0850.0000.0000.0000.000
37H35SER00.0270.01118.6090.0900.0900.0000.0000.0000.000
38H36TRP0-0.030-0.02118.047-0.076-0.0760.0000.0000.0000.000
39H37ILE0-0.008-0.00520.3760.0420.0420.0000.0000.0000.000
40H38ARG10.7830.88021.7140.2040.2040.0000.0000.0000.000
41H39GLN00.0150.00123.343-0.026-0.0260.0000.0000.0000.000
42H40PRO00.0420.02425.578-0.003-0.0030.0000.0000.0000.000
43H41PRO00.0230.00227.648-0.010-0.0100.0000.0000.0000.000
44H42GLY0-0.007-0.00128.1890.0170.0170.0000.0000.0000.000
45H43LYS10.9200.97129.1060.1970.1970.0000.0000.0000.000
46H44ALA00.0230.01128.145-0.019-0.0190.0000.0000.0000.000
47H45LEU00.0010.00022.2080.0040.0040.0000.0000.0000.000
48H46GLU-1-0.827-0.89925.917-0.211-0.2110.0000.0000.0000.000
49H47TRP0-0.001-0.00423.744-0.001-0.0010.0000.0000.0000.000
50H48LEU0-0.043-0.02024.5630.0270.0270.0000.0000.0000.000
51H49ALA00.0300.00424.9330.0290.0290.0000.0000.0000.000
52H50LEU0-0.042-0.00222.539-0.038-0.0380.0000.0000.0000.000
53H51ILE0-0.008-0.01221.0860.0370.0370.0000.0000.0000.000
54H52ASP-1-0.745-0.86021.437-0.328-0.3280.0000.0000.0000.000
55H52TRP0-0.033-0.00515.5030.0080.0080.0000.0000.0000.000
56H53ASP-1-0.811-0.91019.226-0.238-0.2380.0000.0000.0000.000
57H54ASP-1-0.924-0.94521.760-0.163-0.1630.0000.0000.0000.000
58H55ASP-1-0.932-0.98524.730-0.122-0.1220.0000.0000.0000.000
59H56THR0-0.086-0.05027.2920.0110.0110.0000.0000.0000.000
60H57TYR0-0.031-0.02926.312-0.019-0.0190.0000.0000.0000.000
61H58TYR0-0.035-0.00926.7080.0210.0210.0000.0000.0000.000
62H59ILE0-0.008-0.01127.772-0.019-0.0190.0000.0000.0000.000
63H60THR00.0130.01129.7510.0140.0140.0000.0000.0000.000
64H61TYR00.0390.01231.4090.0150.0150.0000.0000.0000.000
65H62SER0-0.0010.00333.6860.0170.0170.0000.0000.0000.000
66H62SER00.0380.00035.541-0.001-0.0010.0000.0000.0000.000
67H62SER00.0020.00836.1990.0030.0030.0000.0000.0000.000
68H63LEU00.009-0.00230.5520.0000.0000.0000.0000.0000.000
69H64LYS10.9480.98533.1440.1270.1270.0000.0000.0000.000
70H65THR0-0.027-0.01234.540-0.001-0.0010.0000.0000.0000.000
71H66ARG10.7450.85533.0210.1590.1590.0000.0000.0000.000
72H67LEU00.0000.00827.554-0.005-0.0050.0000.0000.0000.000
73H68THR00.0060.00727.4120.0140.0140.0000.0000.0000.000
74H69ILE0-0.005-0.00221.913-0.016-0.0160.0000.0000.0000.000
75H70SER0-0.0150.00323.3360.0250.0250.0000.0000.0000.000
76H71LYS10.8620.91119.9950.1590.1590.0000.0000.0000.000
77H72ASP-1-0.766-0.84418.7760.0520.0520.0000.0000.0000.000
78H73THR00.038-0.00217.3680.0000.0000.0000.0000.0000.000
79H74SER0-0.094-0.05716.4220.0330.0330.0000.0000.0000.000
80H75LYS10.8810.92214.6400.0210.0210.0000.0000.0000.000
81H76SER0-0.042-0.00511.793-0.057-0.0570.0000.0000.0000.000
82H77GLN0-0.031-0.03412.996-0.083-0.0830.0000.0000.0000.000
83H78VAL00.0180.01515.5670.0430.0430.0000.0000.0000.000
84H79VAL0-0.016-0.01218.231-0.033-0.0330.0000.0000.0000.000
85H80LEU0-0.0090.00920.8490.0110.0110.0000.0000.0000.000
86H81THR0-0.005-0.02223.4020.0170.0170.0000.0000.0000.000
87H82MET0-0.031-0.00426.574-0.007-0.0070.0000.0000.0000.000
88H82THR00.0350.00729.1100.0060.0060.0000.0000.0000.000
89H82ASN00.007-0.00432.521-0.001-0.0010.0000.0000.0000.000
90H82MET0-0.0270.01028.598-0.006-0.0060.0000.0000.0000.000
91H83ASP-1-0.765-0.90133.182-0.114-0.1140.0000.0000.0000.000
92H84PRO00.0170.00133.241-0.012-0.0120.0000.0000.0000.000
93H85VAL0-0.040-0.01733.174-0.012-0.0120.0000.0000.0000.000
94H86ASP-1-0.771-0.84829.950-0.183-0.1830.0000.0000.0000.000
95H87THR0-0.028-0.00128.684-0.017-0.0170.0000.0000.0000.000
96H88ALA0-0.018-0.01425.9670.0000.0000.0000.0000.0000.000
97H89THR0-0.0170.00520.1270.0110.0110.0000.0000.0000.000
98H90TYR0-0.022-0.03421.2910.0030.0030.0000.0000.0000.000
99H91TYR00.005-0.01216.974-0.037-0.0370.0000.0000.0000.000
100H93ALA00.006-0.00415.207-0.099-0.0990.0000.0000.0000.000
101H94ARG10.7960.8719.5361.5131.5130.0000.0000.0000.000
102H95THR0-0.004-0.01415.8180.0040.0040.0000.0000.0000.000
103H96LEU0-0.023-0.01313.1560.0140.0140.0000.0000.0000.000
104H97ARG10.9831.01317.2710.3100.3100.0000.0000.0000.000
105H98VAL0-0.006-0.01118.643-0.023-0.0230.0000.0000.0000.000
106H100SER0-0.048-0.04221.1160.0350.0350.0000.0000.0000.000
107H100GLY00.0180.00924.516-0.011-0.0110.0000.0000.0000.000
108H100ASP-1-0.890-0.93327.171-0.232-0.2320.0000.0000.0000.000
109H100TYR0-0.072-0.03627.1760.0090.0090.0000.0000.0000.000
110H100VAL00.0050.00422.4280.0010.0010.0000.0000.0000.000
111H100ARG10.9400.97322.5240.2670.2670.0000.0000.0000.000
112H100ASP-1-0.891-0.94619.025-0.554-0.5540.0000.0000.0000.000
113H100PHE0-0.0050.00618.360-0.007-0.0070.0000.0000.0000.000
114H101ASP-1-0.705-0.81213.598-1.117-1.1170.0000.0000.0000.000
115H102LEU0-0.058-0.0168.881-0.163-0.1630.0000.0000.0000.000
116H103TRP0-0.009-0.02412.6990.1450.1450.0000.0000.0000.000
117H104GLY00.0120.01811.575-0.196-0.1960.0000.0000.0000.000
118H105ARG10.8180.90011.8960.7600.7600.0000.0000.0000.000
119H106GLY00.0460.02813.6260.0870.0870.0000.0000.0000.000
120H107THR0-0.090-0.05616.606-0.009-0.0090.0000.0000.0000.000
121H108LEU0-0.0020.00718.7920.0180.0180.0000.0000.0000.000
122H109VAL0-0.002-0.00222.3260.0150.0150.0000.0000.0000.000
123H110THR00.001-0.00525.1230.0030.0030.0000.0000.0000.000
124H111VAL00.0030.00828.5840.0090.0090.0000.0000.0000.000
125H112SER00.0250.00131.5810.0070.0070.0000.0000.0000.000
126H113SER00.0320.00934.2050.0010.0010.0000.0000.0000.000
127H114ALA0-0.0040.01035.3570.0090.0090.0000.0000.0000.000
128H115SER00.004-0.01334.258-0.005-0.0050.0000.0000.0000.000
129H116THR0-0.046-0.01729.395-0.003-0.0030.0000.0000.0000.000
130H117LYS10.8700.91731.3240.0820.0820.0000.0000.0000.000
131H118GLY00.0580.03329.626-0.011-0.0110.0000.0000.0000.000
132H119PRO0-0.045-0.01427.8680.0040.0040.0000.0000.0000.000
133H120SER0-0.019-0.00331.1380.0100.0100.0000.0000.0000.000
134H121VAL00.002-0.00729.086-0.008-0.0080.0000.0000.0000.000
135H122PHE0-0.007-0.00432.4100.0110.0110.0000.0000.0000.000
136H123PRO00.000-0.00133.534-0.007-0.0070.0000.0000.0000.000
137H124LEU0-0.038-0.00932.7330.0010.0010.0000.0000.0000.000
138H125ALA00.0110.00734.834-0.003-0.0030.0000.0000.0000.000
139H126PRO00.0160.01935.5100.0000.0000.0000.0000.0000.000
140H136GLY00.0330.00738.209-0.001-0.0010.0000.0000.0000.000
141H137THR0-0.039-0.01633.4660.0020.0020.0000.0000.0000.000
142H138ALA0-0.0040.00334.6960.0040.0040.0000.0000.0000.000
143H139ALA00.0120.01232.964-0.006-0.0060.0000.0000.0000.000
144H140LEU00.0060.01830.1230.0080.0080.0000.0000.0000.000
145H141GLY00.057-0.00530.106-0.012-0.0120.0000.0000.0000.000
146H142CYS0-0.105-0.01925.3320.0070.0070.0000.0000.0000.000
147H143LEU00.0110.02030.428-0.012-0.0120.0000.0000.0000.000
148H144VAL0-0.007-0.01227.3730.0120.0120.0000.0000.0000.000
149H145LYS10.9170.93130.7600.0660.0660.0000.0000.0000.000
150H146ASP-1-0.821-0.88633.401-0.075-0.0750.0000.0000.0000.000
151H147TYR0-0.009-0.02827.1110.0130.0130.0000.0000.0000.000
152H148PHE00.0620.04130.484-0.010-0.0100.0000.0000.0000.000
153H149PRO00.0060.02126.7620.0150.0150.0000.0000.0000.000
154H150GLU-1-0.756-0.86325.223-0.215-0.2150.0000.0000.0000.000
155H151PRO0-0.035-0.02520.718-0.001-0.0010.0000.0000.0000.000
156H152VAL00.015-0.00223.2900.0170.0170.0000.0000.0000.000
157H153THR0-0.060-0.02517.730-0.031-0.0310.0000.0000.0000.000
158H154VAL0-0.015-0.02520.9010.0310.0310.0000.0000.0000.000
159H156SER0-0.043-0.01418.712-0.033-0.0330.0000.0000.0000.000
160H157TRP00.0310.01320.7220.0290.0290.0000.0000.0000.000
161H162ASN0-0.009-0.01821.363-0.007-0.0070.0000.0000.0000.000
162H163SER00.006-0.00918.9750.0090.0090.0000.0000.0000.000
163H164GLY0-0.024-0.00416.6550.0080.0080.0000.0000.0000.000
164H165ALA0-0.026-0.00417.557-0.026-0.0260.0000.0000.0000.000
165H166LEU0-0.034-0.00419.125-0.004-0.0040.0000.0000.0000.000
166H167THR00.021-0.00316.938-0.008-0.0080.0000.0000.0000.000
167H168SER00.0060.00120.396-0.022-0.0220.0000.0000.0000.000
168H169GLY00.0550.02722.7880.0190.0190.0000.0000.0000.000
169H171VAL0-0.050-0.02222.2160.0130.0130.0000.0000.0000.000
170H172HIS00.0110.00923.780-0.031-0.0310.0000.0000.0000.000
171H173THR00.0070.00622.5780.0310.0310.0000.0000.0000.000
172H174PHE0-0.0260.00024.698-0.020-0.0200.0000.0000.0000.000
173H175PRO00.019-0.00526.0030.0000.0000.0000.0000.0000.000
174H176ALA00.0020.00927.2970.0160.0160.0000.0000.0000.000
175H177VAL0-0.023-0.00329.502-0.003-0.0030.0000.0000.0000.000
176H178LEU0-0.014-0.00933.1640.0020.0020.0000.0000.0000.000
177H179GLN0-0.020-0.00234.5360.0000.0000.0000.0000.0000.000
178H180SER00.0430.01337.883-0.002-0.0020.0000.0000.0000.000
179H182SER0-0.019-0.01438.965-0.001-0.0010.0000.0000.0000.000
180H183GLY00.0120.00936.9230.0030.0030.0000.0000.0000.000
181H184LEU0-0.087-0.03234.288-0.006-0.0060.0000.0000.0000.000
182H185TYR00.0430.01130.423-0.001-0.0010.0000.0000.0000.000
183H186SER00.004-0.01031.8350.0120.0120.0000.0000.0000.000
184H187LEU0-0.0040.02225.436-0.007-0.0070.0000.0000.0000.000
185H188SER00.0270.00329.5980.0180.0180.0000.0000.0000.000
186H189SER0-0.029-0.01724.793-0.012-0.0120.0000.0000.0000.000
187H190VAL00.021-0.00127.6040.0180.0180.0000.0000.0000.000
188H191VAL00.0140.01226.178-0.016-0.0160.0000.0000.0000.000
189H192THR0-0.032-0.01428.2120.0140.0140.0000.0000.0000.000
190H193VAL00.003-0.00128.764-0.006-0.0060.0000.0000.0000.000
191H194PRO00.0750.02930.6520.0020.0020.0000.0000.0000.000
192H195SER00.0510.02033.7740.0040.0040.0000.0000.0000.000
193H196SER0-0.005-0.00636.6970.0020.0020.0000.0000.0000.000
194H197SER0-0.025-0.01531.7530.0050.0050.0000.0000.0000.000
195H198LEU0-0.006-0.01833.2160.0030.0030.0000.0000.0000.000
196H199GLY0-0.0110.00435.1840.0030.0030.0000.0000.0000.000
197H200THR0-0.019-0.01332.4840.0040.0040.0000.0000.0000.000
198H203GLN0-0.0080.01326.2300.0150.0150.0000.0000.0000.000
199H205THR00.0020.02028.533-0.002-0.0020.0000.0000.0000.000
200H206TYR00.0210.00727.658-0.005-0.0050.0000.0000.0000.000
201H207ILE00.014-0.00625.8900.0040.0040.0000.0000.0000.000
202H209ASN00.0690.01321.521-0.003-0.0030.0000.0000.0000.000
203H210VAL0-0.0140.00222.715-0.030-0.0300.0000.0000.0000.000
204H211ASN0-0.013-0.01318.3650.0480.0480.0000.0000.0000.000
205H212HIS00.0580.04122.345-0.013-0.0130.0000.0000.0000.000
206H213LYS10.9690.96715.4940.3540.3540.0000.0000.0000.000
207H214PRO00.0100.01422.0190.0170.0170.0000.0000.0000.000
208H215SER0-0.013-0.02424.8630.0160.0160.0000.0000.0000.000
209H216ASN0-0.077-0.03722.7940.0150.0150.0000.0000.0000.000
210H217THR00.0410.03824.7950.0220.0220.0000.0000.0000.000
211H218LYS10.8790.92319.6050.0330.0330.0000.0000.0000.000
212H219VAL00.0090.00324.8120.0130.0130.0000.0000.0000.000
213H220ASP-1-0.831-0.88424.435-0.026-0.0260.0000.0000.0000.000
214H221LYS10.8750.92027.1820.0350.0350.0000.0000.0000.000
215H222ARG10.8570.91329.512-0.009-0.0090.0000.0000.0000.000
216H223VAL0-0.012-0.01530.8830.0000.0000.0000.0000.0000.000
217H226GLU-1-0.862-0.90433.228-0.005-0.0050.0000.0000.0000.000
218H227PRO00.0330.00036.447-0.006-0.0060.0000.0000.0000.000
219H228LYS10.8930.94439.2330.0430.0430.0000.0000.0000.000
220H232SER00.0150.01141.5570.0020.0020.0000.0000.0000.000
221H233CYS0-0.038-0.04044.402-0.002-0.0020.0000.0000.0000.000
222H234ASP-1-0.854-0.90244.292-0.040-0.0400.0000.0000.0000.000
223H235LYS10.9670.99246.8420.0230.0230.0000.0000.0000.000