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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: NN22Q

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 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 193
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2169093.855945
FMO2-HF: Nuclear repulsion 2094870.23143
FMO2-HF: Total energy -74223.624514
FMO2-MP2: Total energy -74443.876518


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.
-9.655-6.4955.013-3.468-4.7050.013
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 : -0.049 / q_NPA : -0.044
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].
3A3THR0-0.0210.0083.855-0.2901.465-0.015-0.875-0.8650.001
4A4PRO0-0.0040.0036.0080.3890.3890.0000.0000.0000.000
5A5ASN0-0.0020.0058.8310.0220.0220.0000.0000.0000.000
6A6SER0-0.032-0.01012.0430.1560.1560.0000.0000.0000.000
7A7GLU-1-0.738-0.82014.450-0.612-0.6120.0000.0000.0000.000
8A8GLY0-0.0150.00717.9330.0130.0130.0000.0000.0000.000
9A9TRP0-0.024-0.00720.5050.0190.0190.0000.0000.0000.000
10A10HIS00.0110.01318.874-0.072-0.0720.0000.0000.0000.000
11A11ASP-1-0.806-0.89520.992-0.277-0.2770.0000.0000.0000.000
12A12GLY0-0.034-0.01723.7840.0250.0250.0000.0000.0000.000
13A13TYR0-0.0120.00622.9260.0180.0180.0000.0000.0000.000
14A14TYR0-0.061-0.06222.201-0.015-0.0150.0000.0000.0000.000
15A15TYR0-0.023-0.03215.0700.0550.0550.0000.0000.0000.000
16A16SER0-0.038-0.04517.448-0.039-0.0390.0000.0000.0000.000
17A17TRP0-0.013-0.0188.3950.2220.2220.0000.0000.0000.000
18A18TRP0-0.013-0.00613.500-0.089-0.0890.0000.0000.0000.000
19A19SER00.0240.0069.508-0.197-0.1970.0000.0000.0000.000
20A20ASP-1-0.776-0.88311.358-1.490-1.4900.0000.0000.0000.000
21A21GLY0-0.036-0.0108.0370.1480.1480.0000.0000.0000.000
22A22GLY0-0.041-0.0137.733-0.241-0.2410.0000.0000.0000.000
23A23ALA0-0.0120.0077.9780.0040.0040.0000.0000.0000.000
24A24GLN0-0.0350.0041.911-7.665-6.5405.030-2.559-3.5960.012
25A25ALA00.021-0.0104.5222.0382.264-0.001-0.023-0.2020.000
26A26THR0-0.0150.0044.453-0.942-0.888-0.001-0.011-0.0420.000
27A27TYR0-0.018-0.0186.4190.6830.6830.0000.0000.0000.000
28A28THR0-0.039-0.0429.224-0.260-0.2600.0000.0000.0000.000
29A29ASN00.0110.01611.6210.1040.1040.0000.0000.0000.000
30A30LEU0-0.029-0.01314.7450.0390.0390.0000.0000.0000.000
31A31GLU-1-0.880-0.95017.419-0.242-0.2420.0000.0000.0000.000
32A32GLY0-0.018-0.01021.1390.0160.0160.0000.0000.0000.000
33A33GLY00.0290.02122.260-0.038-0.0380.0000.0000.0000.000
34A34THR0-0.039-0.02118.6670.0020.0020.0000.0000.0000.000
35A35TYR0-0.017-0.01215.393-0.041-0.0410.0000.0000.0000.000
36A36GLU-1-0.800-0.88312.396-0.001-0.0010.0000.0000.0000.000
37A37ILE0-0.0080.00311.033-0.211-0.2110.0000.0000.0000.000
38A38SER0-0.031-0.0128.9740.3170.3170.0000.0000.0000.000
39A39TRP0-0.019-0.0127.743-0.475-0.4750.0000.0000.0000.000
40A40GLY00.013-0.0017.4060.6380.6380.0000.0000.0000.000
41A41ASP-1-0.851-0.9288.453-0.767-0.7670.0000.0000.0000.000
42A42GLY0-0.028-0.0238.120-0.332-0.3320.0000.0000.0000.000
43A43GLY0-0.002-0.00910.216-0.054-0.0540.0000.0000.0000.000
44A44ASN0-0.060-0.03012.0920.1400.1400.0000.0000.0000.000
45A45LEU0-0.032-0.0139.793-0.287-0.2870.0000.0000.0000.000
46A46VAL00.0380.00913.1110.1990.1990.0000.0000.0000.000
47A47GLY00.0280.01115.086-0.137-0.1370.0000.0000.0000.000
48A48GLY0-0.0020.00016.0580.0810.0810.0000.0000.0000.000
49A49LYS10.8090.89418.1350.3830.3830.0000.0000.0000.000
50A50GLY00.0070.00320.9000.0320.0320.0000.0000.0000.000
51A51TRP0-0.011-0.00824.6160.0000.0000.0000.0000.0000.000
52A52ASN00.0230.01225.2500.0050.0050.0000.0000.0000.000
53A53PRO00.0160.01627.8240.0040.0040.0000.0000.0000.000
54A54GLY0-0.020-0.02330.2060.0060.0060.0000.0000.0000.000
55A55LEU0-0.022-0.01530.9030.0140.0140.0000.0000.0000.000
56A56ASN00.0450.02133.813-0.015-0.0150.0000.0000.0000.000
57A57ALA0-0.030-0.01436.1700.0040.0040.0000.0000.0000.000
58A58ARG10.8860.95130.5830.2280.2280.0000.0000.0000.000
59A59ALA00.0140.01734.1000.0000.0000.0000.0000.0000.000
60A60ILE00.0060.01227.9790.0010.0010.0000.0000.0000.000
61A61HIS0-0.035-0.03329.5050.0080.0080.0000.0000.0000.000
62A62PHE00.0110.00624.986-0.024-0.0240.0000.0000.0000.000
63A63GLU-1-0.860-0.92625.320-0.057-0.0570.0000.0000.0000.000
64A64GLY00.0190.01722.494-0.026-0.0260.0000.0000.0000.000
65A65VAL0-0.065-0.03019.3180.0280.0280.0000.0000.0000.000
66A66TYR00.038-0.01218.701-0.024-0.0240.0000.0000.0000.000
67A67GLN0-0.054-0.03017.6690.0500.0500.0000.0000.0000.000
68A68PRO00.0250.03016.6820.0320.0320.0000.0000.0000.000
69A69ASN0-0.050-0.02915.3920.0180.0180.0000.0000.0000.000
70A70GLY00.0590.01716.1270.0020.0020.0000.0000.0000.000
71A71ASN0-0.0010.00018.1240.0270.0270.0000.0000.0000.000
72A72SER00.0210.00917.046-0.020-0.0200.0000.0000.0000.000
73A73TYR00.0060.00818.7140.0640.0640.0000.0000.0000.000
74A74LEU00.0000.01120.023-0.050-0.0500.0000.0000.0000.000
75A75ALA00.0220.00322.4960.0370.0370.0000.0000.0000.000
76A76VAL00.0070.02123.953-0.028-0.0280.0000.0000.0000.000
77A77TYR0-0.046-0.04520.912-0.004-0.0040.0000.0000.0000.000
78A78GLY00.0370.00925.186-0.008-0.0080.0000.0000.0000.000
79A79TRP00.0330.01623.3440.0140.0140.0000.0000.0000.000
80A80THR0-0.042-0.01428.2650.0140.0140.0000.0000.0000.000
81A81ARG10.8320.88426.8460.3650.3650.0000.0000.0000.000
82A82ASN0-0.067-0.03433.1170.0110.0110.0000.0000.0000.000
83A83PRO00.0170.01135.9360.0120.0120.0000.0000.0000.000
84A84LEU0-0.003-0.01328.525-0.004-0.0040.0000.0000.0000.000
85A85VAL0-0.052-0.02231.2620.0070.0070.0000.0000.0000.000
86A86GLU-1-0.739-0.80623.642-0.481-0.4810.0000.0000.0000.000
87A87TYR0-0.039-0.03127.8640.0250.0250.0000.0000.0000.000
88A88TYR0-0.019-0.03222.916-0.022-0.0220.0000.0000.0000.000
89A89ILE0-0.028-0.01328.1040.0240.0240.0000.0000.0000.000
90A90VAL0-0.016-0.01325.397-0.012-0.0120.0000.0000.0000.000
91A91GLU-1-0.714-0.82026.689-0.134-0.1340.0000.0000.0000.000
92A92ASN0-0.021-0.04224.2000.0330.0330.0000.0000.0000.000
93A93PHE00.0620.02322.992-0.032-0.0320.0000.0000.0000.000
94A94GLY00.0190.03721.3750.0360.0360.0000.0000.0000.000
95A95THR0-0.045-0.04021.8100.0070.0070.0000.0000.0000.000
96A96TYR0-0.011-0.00323.0700.0100.0100.0000.0000.0000.000
97A97ASP-1-0.734-0.81124.517-0.190-0.1900.0000.0000.0000.000
98A98PRO00.0450.02323.5710.0010.0010.0000.0000.0000.000
99A99SER0-0.038-0.02825.513-0.007-0.0070.0000.0000.0000.000
100A100SER0-0.086-0.07028.0100.0220.0220.0000.0000.0000.000
101A101GLY0-0.010-0.01029.175-0.012-0.0120.0000.0000.0000.000
102A102ALA0-0.061-0.02631.757-0.002-0.0020.0000.0000.0000.000
103A103THR0-0.076-0.03333.2300.0160.0160.0000.0000.0000.000
104A104ASP-1-0.854-0.93236.703-0.125-0.1250.0000.0000.0000.000
105A105LEU0-0.054-0.02937.5720.0010.0010.0000.0000.0000.000
106A106GLY00.0000.01739.9590.0040.0040.0000.0000.0000.000
107A107THR0-0.050-0.03839.076-0.005-0.0050.0000.0000.0000.000
108A108VAL0-0.005-0.00438.5790.0020.0020.0000.0000.0000.000
109A109GLU-1-0.889-0.94239.533-0.082-0.0820.0000.0000.0000.000
110A110CYS0-0.056-0.01537.1960.0010.0010.0000.0000.0000.000
111A111ASP-1-0.822-0.91035.453-0.131-0.1310.0000.0000.0000.000
112A112GLY0-0.0010.02136.7750.0030.0030.0000.0000.0000.000
113A113SER0-0.053-0.07835.7830.0020.0020.0000.0000.0000.000
114A114ILE00.0040.00937.828-0.006-0.0060.0000.0000.0000.000
115A115TYR0-0.023-0.04631.8360.0040.0040.0000.0000.0000.000
116A116ARG10.8380.89931.2080.1380.1380.0000.0000.0000.000
117A117LEU00.0000.00534.532-0.015-0.0150.0000.0000.0000.000
118A118GLY00.0530.01334.9860.0080.0080.0000.0000.0000.000
119A119LYS10.8180.89633.4390.1900.1900.0000.0000.0000.000
120A120THR00.0140.01429.1800.0150.0150.0000.0000.0000.000
121A121THR0-0.046-0.05232.0660.0050.0050.0000.0000.0000.000
122A122ARG10.8790.96123.0350.4240.4240.0000.0000.0000.000
123A123VAL00.0380.00329.5410.0070.0070.0000.0000.0000.000
124A124ASN0-0.053-0.03328.845-0.010-0.0100.0000.0000.0000.000
125A125ALA00.0190.01824.701-0.017-0.0170.0000.0000.0000.000
126A126PRO0-0.001-0.01420.4030.0150.0150.0000.0000.0000.000
127A127SER0-0.003-0.00222.8250.0200.0200.0000.0000.0000.000
128A128ILE00.0150.00623.038-0.034-0.0340.0000.0000.0000.000
129A129ASP-1-0.828-0.86724.387-0.382-0.3820.0000.0000.0000.000
130A130GLY00.0080.01223.9400.0250.0250.0000.0000.0000.000
131A131THR0-0.056-0.02824.983-0.016-0.0160.0000.0000.0000.000
132A132GLN0-0.022-0.00726.1230.0500.0500.0000.0000.0000.000
133A133THR0-0.013-0.00828.801-0.006-0.0060.0000.0000.0000.000
134A134PHE0-0.044-0.01225.2560.0100.0100.0000.0000.0000.000
135A135ASP-1-0.741-0.83931.331-0.218-0.2180.0000.0000.0000.000
136A136GLN0-0.010-0.00225.4900.0020.0020.0000.0000.0000.000
137A137TYR0-0.025-0.02330.3850.0190.0190.0000.0000.0000.000
138A138TRP00.0470.00425.029-0.014-0.0140.0000.0000.0000.000
139A139SER0-0.0070.00131.2560.0210.0210.0000.0000.0000.000
140A140VAL0-0.026-0.01729.097-0.014-0.0140.0000.0000.0000.000
141A141ARG10.8040.90830.9020.1200.1200.0000.0000.0000.000
142A142GLN0-0.091-0.05031.655-0.003-0.0030.0000.0000.0000.000
143A143ASP-1-0.831-0.87432.957-0.061-0.0610.0000.0000.0000.000
144A144LYS10.8200.91626.2020.0950.0950.0000.0000.0000.000
145A145ARG10.8040.89228.8180.1390.1390.0000.0000.0000.000
146A146THR0-0.008-0.01724.723-0.018-0.0180.0000.0000.0000.000
147A147SER0-0.0110.00326.012-0.005-0.0050.0000.0000.0000.000
148A148GLY0-0.0150.00328.5860.0100.0100.0000.0000.0000.000
149A149THR00.009-0.00330.514-0.011-0.0110.0000.0000.0000.000
150A150VAL0-0.0100.00430.0000.0080.0080.0000.0000.0000.000
151A151GLN00.0300.00632.999-0.015-0.0150.0000.0000.0000.000
152A152THR0-0.002-0.01731.6560.0040.0040.0000.0000.0000.000
153A153GLY00.0190.01134.564-0.001-0.0010.0000.0000.0000.000
154A155HIS00.0630.03334.920-0.001-0.0010.0000.0000.0000.000
155A156PHE00.0220.00132.378-0.001-0.0010.0000.0000.0000.000
156A157ASP-1-0.818-0.88637.466-0.117-0.1170.0000.0000.0000.000
157A158ALA0-0.035-0.01739.0090.0060.0060.0000.0000.0000.000
158A159TRP0-0.028-0.03531.5950.0000.0000.0000.0000.0000.000
159A160ALA00.0010.00339.1210.0010.0010.0000.0000.0000.000
160A161ARG10.7860.87242.1080.1190.1190.0000.0000.0000.000
161A162ALA0-0.0210.00740.6360.0060.0060.0000.0000.0000.000
162A163GLY0-0.032-0.01342.763-0.001-0.0010.0000.0000.0000.000
163A164LEU0-0.050-0.01536.396-0.004-0.0040.0000.0000.0000.000
164A165ASN00.0210.00639.0350.0060.0060.0000.0000.0000.000
165A166VAL00.0080.01736.947-0.015-0.0150.0000.0000.0000.000
166A167ASN0-0.050-0.03338.3530.0050.0050.0000.0000.0000.000
167A168GLY00.0490.04636.3250.0040.0040.0000.0000.0000.000
168A169ASP-1-0.892-0.94134.504-0.225-0.2250.0000.0000.0000.000
169A170HIS0-0.031-0.02031.663-0.032-0.0320.0000.0000.0000.000
170A171TYR0-0.045-0.02323.4100.0220.0220.0000.0000.0000.000
171A172TYR0-0.003-0.01320.9600.0360.0360.0000.0000.0000.000
172A173GLN0-0.006-0.00826.0320.0160.0160.0000.0000.0000.000
173A174ILE0-0.037-0.01419.9800.0100.0100.0000.0000.0000.000
174A175VAL00.0130.01123.0220.0200.0200.0000.0000.0000.000
175A176ALA0-0.003-0.00719.387-0.037-0.0370.0000.0000.0000.000
176A177THR0-0.016-0.00716.7610.0800.0800.0000.0000.0000.000
177A178GLU-1-0.872-0.93816.424-0.618-0.6180.0000.0000.0000.000
178A179GLY00.0160.02614.0300.1240.1240.0000.0000.0000.000
179A180TYR0-0.025-0.01214.285-0.163-0.1630.0000.0000.0000.000
180A181PHE0-0.025-0.01513.2980.0960.0960.0000.0000.0000.000
181A182SER0-0.035-0.01612.8940.1080.1080.0000.0000.0000.000
182A183SER0-0.025-0.01211.487-0.005-0.0050.0000.0000.0000.000
183A184GLY00.0250.00311.802-0.023-0.0230.0000.0000.0000.000
184A185TYR0-0.074-0.04612.0670.0260.0260.0000.0000.0000.000
185A186ALA00.011-0.00214.328-0.006-0.0060.0000.0000.0000.000
186A187ARG10.8970.94715.288-0.075-0.0750.0000.0000.0000.000
187A188ILE0-0.0050.01917.6770.0580.0580.0000.0000.0000.000
188A189THR00.004-0.00220.153-0.032-0.0320.0000.0000.0000.000
189A190VAL0-0.044-0.02022.4730.0200.0200.0000.0000.0000.000
190A191ALA00.003-0.00725.1230.0050.0050.0000.0000.0000.000
191A192ASP-1-0.843-0.92028.590-0.185-0.1850.0000.0000.0000.000
192A193VAL0-0.040-0.01831.7180.0090.0090.0000.0000.0000.000
193A194GLY0-0.047-0.01434.8640.0130.0130.0000.0000.0000.000