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About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: G5YY1

Calculation Name: 1YNA-A-Xray372

Preferred Name:

Target Type:

Ligand Name: pyroglutamic acid

ligand 3-letter code: PCA

PDB ID: 1YNA

Chain ID: A

ChEMBL ID:

UniProt ID: O43097

Base Structure: X-ray

Registration Date: 2023-09-22

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 193
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2167541.725373
FMO2-HF: Nuclear repulsion 2093318.739115
FMO2-HF: Total energy -74222.986258
FMO2-MP2: Total energy -74443.073415


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(A:1:PCA)


Summations of interaction energy for fragment #1(A: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.
-5.41-1.0890.813-2.191-2.944-0.005
Interaction energy analysis for fragmet #1(A:1:PCA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.077 / q_NPA : -0.054
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].
3A3THR0-0.0180.0263.783-0.9151.892-0.036-1.486-1.286-0.002
4A4PRO00.0200.0155.9280.2150.2150.0000.0000.0000.000
5A5ASN00.0390.0198.7390.0510.0510.0000.0000.0000.000
6A6SER0-0.0350.01112.0860.1340.1340.0000.0000.0000.000
7A7GLU-1-0.776-0.83014.312-0.553-0.5530.0000.0000.0000.000
8A8GLY00.0030.01417.8370.0180.0180.0000.0000.0000.000
9A9TRP0-0.025-0.01220.3950.0090.0090.0000.0000.0000.000
10A10HIS00.0350.01118.349-0.046-0.0460.0000.0000.0000.000
11A11ASP-1-0.780-0.88720.763-0.175-0.1750.0000.0000.0000.000
12A12GLY0-0.059-0.02723.4850.0180.0180.0000.0000.0000.000
13A13TYR0-0.035-0.01122.6550.0120.0120.0000.0000.0000.000
14A14TYR0-0.063-0.07622.013-0.010-0.0100.0000.0000.0000.000
15A15TYR0-0.038-0.05014.8000.0400.0400.0000.0000.0000.000
16A16SER0-0.016-0.00317.520-0.039-0.0390.0000.0000.0000.000
17A17TRP0-0.006-0.0238.5330.2060.2060.0000.0000.0000.000
18A18TRP0-0.002-0.00213.478-0.070-0.0700.0000.0000.0000.000
19A19SER00.0280.0139.486-0.158-0.1580.0000.0000.0000.000
20A20ASP-1-0.831-0.90211.806-1.421-1.4210.0000.0000.0000.000
21A21GLY0-0.039-0.0188.3800.1510.1510.0000.0000.0000.000
22A22GLY0-0.028-0.0117.793-0.328-0.3280.0000.0000.0000.000
23A23ALA0-0.0300.0048.0130.1230.1230.0000.0000.0000.000
24A24GLN0-0.0150.0152.167-2.663-1.4210.850-0.654-1.439-0.003
25A25ALA00.023-0.0154.1922.0922.364-0.001-0.051-0.2190.000
26A26THR0-0.039-0.0145.109-1.158-1.1580.0000.0000.0000.000
27A27TYR0-0.022-0.0146.6030.5760.5760.0000.0000.0000.000
28A28THR00.006-0.0119.487-0.154-0.1540.0000.0000.0000.000
29A29ASN00.0030.01211.7420.0760.0760.0000.0000.0000.000
30A30LEU0-0.019-0.00815.2420.0510.0510.0000.0000.0000.000
31A31GLU-1-0.884-0.95417.591-0.163-0.1630.0000.0000.0000.000
32A32GLY0-0.022-0.00721.2150.0050.0050.0000.0000.0000.000
33A33GLY00.0250.02522.276-0.035-0.0350.0000.0000.0000.000
34A34THR0-0.0010.00918.856-0.004-0.0040.0000.0000.0000.000
35A35TYR0-0.054-0.02415.484-0.032-0.0320.0000.0000.0000.000
36A36GLU-1-0.844-0.88812.9790.1950.1950.0000.0000.0000.000
37A37ILE0-0.018-0.00810.780-0.167-0.1670.0000.0000.0000.000
38A38SER0-0.0220.0028.3260.2290.2290.0000.0000.0000.000
39A39TRP0-0.009-0.0107.468-0.522-0.5220.0000.0000.0000.000
40A40GLY00.003-0.0037.3620.6100.6100.0000.0000.0000.000
41A41ASP-1-0.845-0.9348.362-0.793-0.7930.0000.0000.0000.000
42A42GLY0-0.022-0.0208.676-0.308-0.3080.0000.0000.0000.000
43A43GLY0-0.002-0.00210.659-0.008-0.0080.0000.0000.0000.000
44A44ASN0-0.020-0.02412.4120.0890.0890.0000.0000.0000.000
45A45LEU0-0.052-0.0199.790-0.268-0.2680.0000.0000.0000.000
46A46VAL00.0410.00713.2200.1730.1730.0000.0000.0000.000
47A47GLY00.0260.01014.820-0.108-0.1080.0000.0000.0000.000
48A48GLY0-0.006-0.00215.7970.0800.0800.0000.0000.0000.000
49A49LYS10.8150.90118.2740.2830.2830.0000.0000.0000.000
50A50GLY0-0.001-0.00920.7580.0220.0220.0000.0000.0000.000
51A51TRP0-0.008-0.00224.4230.0030.0030.0000.0000.0000.000
52A52ASN0-0.0240.01825.327-0.001-0.0010.0000.0000.0000.000
53A53PRO00.0440.02127.8220.0050.0050.0000.0000.0000.000
54A54GLY0-0.016-0.03430.0540.0090.0090.0000.0000.0000.000
55A55LEU0-0.029-0.02130.7610.0120.0120.0000.0000.0000.000
56A56ASN00.0730.04333.789-0.015-0.0150.0000.0000.0000.000
57A57ALA0-0.023-0.01436.2530.0020.0020.0000.0000.0000.000
58A58ARG10.8890.96330.6820.1990.1990.0000.0000.0000.000
59A59ALA00.0150.01534.257-0.002-0.0020.0000.0000.0000.000
60A60ILE00.001-0.00627.949-0.001-0.0010.0000.0000.0000.000
61A61HIS0-0.032-0.01129.3010.0000.0000.0000.0000.0000.000
62A62PHE0-0.011-0.00825.231-0.019-0.0190.0000.0000.0000.000
63A63GLU-1-0.868-0.93525.475-0.038-0.0380.0000.0000.0000.000
64A64GLY00.0180.01522.659-0.018-0.0180.0000.0000.0000.000
65A65VAL0-0.084-0.03818.8470.0200.0200.0000.0000.0000.000
66A66TYR00.040-0.00718.442-0.011-0.0110.0000.0000.0000.000
67A67GLN0-0.069-0.03717.3060.0550.0550.0000.0000.0000.000
68A68PRO00.0220.02916.2460.0180.0180.0000.0000.0000.000
69A69ASN0-0.048-0.02715.6380.0310.0310.0000.0000.0000.000
70A70GLY00.0620.01816.337-0.025-0.0250.0000.0000.0000.000
71A71ASN0-0.047-0.03117.9370.0150.0150.0000.0000.0000.000
72A72SER00.0430.03816.983-0.040-0.0400.0000.0000.0000.000
73A73TYR00.0310.01018.5840.0700.0700.0000.0000.0000.000
74A74LEU00.0030.02619.747-0.046-0.0460.0000.0000.0000.000
75A75ALA00.019-0.01122.0750.0330.0330.0000.0000.0000.000
76A76VAL0-0.0170.00923.846-0.024-0.0240.0000.0000.0000.000
77A77TYR0-0.019-0.02920.731-0.011-0.0110.0000.0000.0000.000
78A78GLY00.0190.00324.988-0.007-0.0070.0000.0000.0000.000
79A79TRP00.0200.01723.0450.0140.0140.0000.0000.0000.000
80A80THR0-0.029-0.00428.1720.0130.0130.0000.0000.0000.000
81A81ARG10.8160.84827.6960.3150.3150.0000.0000.0000.000
82A82ASN0-0.0740.01833.0390.0100.0100.0000.0000.0000.000
83A83PRO00.0470.00235.9830.0110.0110.0000.0000.0000.000
84A84LEU00.007-0.02528.721-0.002-0.0020.0000.0000.0000.000
85A85VAL0-0.043-0.00631.3040.0040.0040.0000.0000.0000.000
86A86GLU-1-0.748-0.85723.546-0.466-0.4660.0000.0000.0000.000
87A87TYR0-0.004-0.00428.0640.0210.0210.0000.0000.0000.000
88A88TYR0-0.029-0.02122.900-0.030-0.0300.0000.0000.0000.000
89A89ILE0-0.032-0.01727.7230.0210.0210.0000.0000.0000.000
90A90VAL0-0.002-0.00225.092-0.011-0.0110.0000.0000.0000.000
91A91GLU-1-0.715-0.82526.338-0.129-0.1290.0000.0000.0000.000
92A92ASN0-0.007-0.03124.1080.0260.0260.0000.0000.0000.000
93A93PHE00.0380.00622.711-0.028-0.0280.0000.0000.0000.000
94A94GLY0-0.0060.01821.0680.0320.0320.0000.0000.0000.000
95A95THR0-0.038-0.02921.6360.0190.0190.0000.0000.0000.000
96A96TYR0-0.021-0.01222.0120.0130.0130.0000.0000.0000.000
97A97ASP-1-0.725-0.80524.510-0.207-0.2070.0000.0000.0000.000
98A98PRO00.0500.01923.4570.0010.0010.0000.0000.0000.000
99A99SER0-0.062-0.04825.386-0.007-0.0070.0000.0000.0000.000
100A100SER0-0.043-0.03128.1990.0210.0210.0000.0000.0000.000
101A101GLY0-0.034-0.01629.626-0.014-0.0140.0000.0000.0000.000
102A102ALA0-0.030-0.02131.597-0.001-0.0010.0000.0000.0000.000
103A103THR0-0.100-0.05233.1970.0140.0140.0000.0000.0000.000
104A104ASP-1-0.865-0.93736.775-0.129-0.1290.0000.0000.0000.000
105A105LEU0-0.060-0.03637.4090.0040.0040.0000.0000.0000.000
106A106GLY00.0050.01939.8720.0050.0050.0000.0000.0000.000
107A107THR0-0.048-0.03538.936-0.006-0.0060.0000.0000.0000.000
108A108VAL0-0.004-0.00438.1640.0040.0040.0000.0000.0000.000
109A109GLU-1-0.919-0.96039.128-0.078-0.0780.0000.0000.0000.000
110A110CYS0-0.059-0.01236.6220.0020.0020.0000.0000.0000.000
111A111ASP-1-0.829-0.92035.539-0.114-0.1140.0000.0000.0000.000
112A112GLY00.003-0.00836.5510.0010.0010.0000.0000.0000.000
113A113SER00.0490.02935.5570.0050.0050.0000.0000.0000.000
114A114ILE00.0050.01437.600-0.006-0.0060.0000.0000.0000.000
115A115TYR0-0.065-0.06431.5780.0020.0020.0000.0000.0000.000
116A116ARG10.8260.88230.9450.1550.1550.0000.0000.0000.000
117A117LEU00.0070.00434.121-0.014-0.0140.0000.0000.0000.000
118A118GLY00.0490.02434.4270.0080.0080.0000.0000.0000.000
119A119LYS10.9430.98033.4590.1720.1720.0000.0000.0000.000
120A120THR0-0.0030.01629.4030.0130.0130.0000.0000.0000.000
121A121THR00.001-0.01232.3020.0020.0020.0000.0000.0000.000
122A122ARG10.9140.97023.4530.4210.4210.0000.0000.0000.000
123A123VAL00.0350.00429.4960.0050.0050.0000.0000.0000.000
124A124ASN0-0.063-0.02228.817-0.012-0.0120.0000.0000.0000.000
125A125ALA0-0.006-0.00224.845-0.021-0.0210.0000.0000.0000.000
126A126PRO00.004-0.01020.7790.0190.0190.0000.0000.0000.000
127A127SER0-0.0020.00323.0320.0080.0080.0000.0000.0000.000
128A128ILE00.0350.01522.869-0.028-0.0280.0000.0000.0000.000
129A129ASP-1-0.781-0.81924.150-0.359-0.3590.0000.0000.0000.000
130A130GLY00.0010.01324.4810.0260.0260.0000.0000.0000.000
131A131THR0-0.047-0.02425.377-0.016-0.0160.0000.0000.0000.000
132A132GLN0-0.044-0.03026.6520.0490.0490.0000.0000.0000.000
133A133THR0-0.012-0.01129.021-0.010-0.0100.0000.0000.0000.000
134A134PHE0-0.042-0.01925.3960.0070.0070.0000.0000.0000.000
135A135ASP-1-0.847-0.90231.125-0.224-0.2240.0000.0000.0000.000
136A136GLN0-0.045-0.03625.3610.0050.0050.0000.0000.0000.000
137A137TYR0-0.048-0.04330.3620.0190.0190.0000.0000.0000.000
138A138TRP00.0500.01424.808-0.011-0.0110.0000.0000.0000.000
139A139SER0-0.011-0.02430.7720.0200.0200.0000.0000.0000.000
140A140VAL0-0.019-0.00829.114-0.012-0.0120.0000.0000.0000.000
141A141ARG10.8110.91030.4930.1200.1200.0000.0000.0000.000
142A142GLN0-0.069-0.02731.3880.0000.0000.0000.0000.0000.000
143A143ASP-1-0.907-0.95033.101-0.065-0.0650.0000.0000.0000.000
144A144LYS10.8620.94626.7550.1160.1160.0000.0000.0000.000
145A145ARG10.8270.91028.4920.1300.1300.0000.0000.0000.000
146A146THR0-0.018-0.02124.376-0.018-0.0180.0000.0000.0000.000
147A147SER0-0.012-0.00325.850-0.005-0.0050.0000.0000.0000.000
148A148GLY00.0070.01228.5040.0070.0070.0000.0000.0000.000
149A149THR00.001-0.00430.731-0.007-0.0070.0000.0000.0000.000
150A150VAL0-0.0110.00229.9940.0050.0050.0000.0000.0000.000
151A151GLN00.0350.01532.967-0.012-0.0120.0000.0000.0000.000
152A152THR00.004-0.01431.6790.0010.0010.0000.0000.0000.000
153A153GLY00.0240.01634.596-0.003-0.0030.0000.0000.0000.000
154A155HIS00.0620.04434.380-0.002-0.0020.0000.0000.0000.000
155A156PHE00.019-0.00232.419-0.002-0.0020.0000.0000.0000.000
156A157ASP-1-0.917-0.95137.639-0.119-0.1190.0000.0000.0000.000
157A158ALA0-0.057-0.03638.6870.0050.0050.0000.0000.0000.000
158A159TRP00.009-0.01031.7240.0000.0000.0000.0000.0000.000
159A160ALA00.0190.01538.9970.0010.0010.0000.0000.0000.000
160A161ARG10.8780.94941.9730.1150.1150.0000.0000.0000.000
161A162ALA0-0.0230.00240.8000.0050.0050.0000.0000.0000.000
162A163GLY0-0.037-0.01542.9540.0000.0000.0000.0000.0000.000
163A164LEU0-0.060-0.02236.565-0.004-0.0040.0000.0000.0000.000
164A165ASN00.0070.00538.8730.0050.0050.0000.0000.0000.000
165A166VAL00.0280.01337.230-0.013-0.0130.0000.0000.0000.000
166A167ASN0-0.047-0.03538.2960.0030.0030.0000.0000.0000.000
167A168GLY00.0270.03135.9570.0030.0030.0000.0000.0000.000
168A169ASP-1-0.917-0.95834.708-0.195-0.1950.0000.0000.0000.000
169A170HIS0-0.064-0.04931.608-0.028-0.0280.0000.0000.0000.000
170A171TYR0-0.038-0.04623.3770.0210.0210.0000.0000.0000.000
171A172TYR0-0.011-0.01821.3740.0110.0110.0000.0000.0000.000
172A173GLN0-0.007-0.00126.0750.0130.0130.0000.0000.0000.000
173A174ILE0-0.020-0.00819.7900.0150.0150.0000.0000.0000.000
174A175VAL00.0230.01322.7050.0130.0130.0000.0000.0000.000
175A176ALA0-0.035-0.00419.478-0.021-0.0210.0000.0000.0000.000
176A177THR00.009-0.00615.8030.0910.0910.0000.0000.0000.000
177A178GLU-1-0.890-0.95716.128-0.662-0.6620.0000.0000.0000.000
178A179GLY00.0050.01813.8320.1110.1110.0000.0000.0000.000
179A180TYR00.0010.00214.741-0.115-0.1150.0000.0000.0000.000
180A181PHE0-0.060-0.02413.3720.0930.0930.0000.0000.0000.000
181A182SER0-0.006-0.01912.9180.1070.1070.0000.0000.0000.000
182A183SER0-0.046-0.02011.272-0.066-0.0660.0000.0000.0000.000
183A184GLY00.0310.00711.4230.0410.0410.0000.0000.0000.000
184A185TYR0-0.078-0.06211.691-0.026-0.0260.0000.0000.0000.000
185A186ALA00.005-0.00213.8340.0070.0070.0000.0000.0000.000
186A187ARG10.9060.94815.429-0.125-0.1250.0000.0000.0000.000
187A188ILE00.0100.02018.0180.0440.0440.0000.0000.0000.000
188A189THR00.009-0.00720.483-0.018-0.0180.0000.0000.0000.000
189A190VAL0-0.050-0.02622.7000.0110.0110.0000.0000.0000.000
190A191ALA00.009-0.00725.2980.0070.0070.0000.0000.0000.000
191A192ASP-1-0.872-0.92328.657-0.150-0.1500.0000.0000.0000.000
192A193VAL0-0.046-0.02531.6990.0090.0090.0000.0000.0000.000
193A194GLY0-0.029-0.01234.6600.0100.0100.0000.0000.0000.000