FMODB

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

Last updated: 2024-07-23

All entries: 37478

Number of unique PDB entries: 7783

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FMODB ID: 89NNY

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:

Apendix: None


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 193
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2167891.53521
FMO2-HF: Nuclear repulsion 2093668.005906
FMO2-HF: Total energy -74223.529304
FMO2-MP2: Total energy -74443.651443


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.
-6.161-1.3191.53-2.798-3.573-0.004
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 : -0.076 / q_NPA : -0.053
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].
3A3THR0-0.0210.0163.783-0.9311.850-0.036-1.469-1.276-0.002
4A4PRO00.0180.0155.9590.2250.2250.0000.0000.0000.000
5A5ASN00.0230.0168.6400.0770.0770.0000.0000.0000.000
6A6SER0-0.026-0.00312.0390.1350.1350.0000.0000.0000.000
7A7GLU-1-0.741-0.82514.294-0.558-0.5580.0000.0000.0000.000
8A8GLY0-0.0020.01417.8520.0150.0150.0000.0000.0000.000
9A9TRP0-0.031-0.01420.4200.0110.0110.0000.0000.0000.000
10A10HIS00.0270.02018.744-0.053-0.0530.0000.0000.0000.000
11A11ASP-1-0.805-0.90020.867-0.156-0.1560.0000.0000.0000.000
12A12GLY0-0.049-0.02623.6170.0190.0190.0000.0000.0000.000
13A13TYR0-0.026-0.01122.8680.0110.0110.0000.0000.0000.000
14A14TYR0-0.069-0.06222.191-0.010-0.0100.0000.0000.0000.000
15A15TYR0-0.026-0.03214.8520.0480.0480.0000.0000.0000.000
16A16SER0-0.032-0.03217.564-0.037-0.0370.0000.0000.0000.000
17A17TRP0-0.016-0.0248.5460.2040.2040.0000.0000.0000.000
18A18TRP00.000-0.00113.522-0.086-0.0860.0000.0000.0000.000
19A19SER00.0170.0079.527-0.190-0.1900.0000.0000.0000.000
20A20ASP-1-0.813-0.90111.667-1.478-1.4780.0000.0000.0000.000
21A21GLY0-0.039-0.0178.3360.1440.1440.0000.0000.0000.000
22A22GLY0-0.026-0.0087.738-0.357-0.3570.0000.0000.0000.000
23A23ALA0-0.0220.0108.0110.1210.1210.0000.0000.0000.000
24A24GLN0-0.028-0.0022.012-3.791-2.0211.567-1.270-2.066-0.002
25A25ALA00.024-0.0084.1642.1102.401-0.001-0.059-0.2310.000
26A26THR0-0.043-0.0184.862-0.870-0.8700.0000.0000.0000.000
27A27TYR0-0.020-0.0136.9020.5240.5240.0000.0000.0000.000
28A28THR00.002-0.0139.682-0.148-0.1480.0000.0000.0000.000
29A29ASN00.0030.01111.9680.0560.0560.0000.0000.0000.000
30A30LEU0-0.0090.00115.3950.0500.0500.0000.0000.0000.000
31A31GLU-1-0.876-0.94917.819-0.116-0.1160.0000.0000.0000.000
32A32GLY0-0.019-0.00521.4270.0060.0060.0000.0000.0000.000
33A33GLY00.0300.02122.474-0.034-0.0340.0000.0000.0000.000
34A34THR0-0.021-0.00919.304-0.002-0.0020.0000.0000.0000.000
35A35TYR0-0.036-0.01915.625-0.019-0.0190.0000.0000.0000.000
36A36GLU-1-0.841-0.90512.9380.3100.3100.0000.0000.0000.000
37A37ILE0-0.019-0.00210.877-0.158-0.1580.0000.0000.0000.000
38A38SER0-0.023-0.0048.5110.2060.2060.0000.0000.0000.000
39A39TRP00.000-0.0037.478-0.471-0.4710.0000.0000.0000.000
40A40GLY00.004-0.0047.3440.6150.6150.0000.0000.0000.000
41A41ASP-1-0.853-0.9318.362-0.839-0.8390.0000.0000.0000.000
42A42GLY0-0.013-0.0208.676-0.321-0.3210.0000.0000.0000.000
43A43GLY00.000-0.00510.658-0.021-0.0210.0000.0000.0000.000
44A44ASN0-0.060-0.03812.4100.1050.1050.0000.0000.0000.000
45A45LEU0-0.038-0.0209.692-0.265-0.2650.0000.0000.0000.000
46A46VAL00.0400.00913.2170.1760.1760.0000.0000.0000.000
47A47GLY00.0300.01014.993-0.110-0.1100.0000.0000.0000.000
48A48GLY00.0000.00615.9760.0810.0810.0000.0000.0000.000
49A49LYS10.8200.90318.3150.2470.2470.0000.0000.0000.000
50A50GLY00.000-0.00820.9440.0220.0220.0000.0000.0000.000
51A51TRP0-0.009-0.00924.5950.0040.0040.0000.0000.0000.000
52A52ASN0-0.0120.01825.244-0.002-0.0020.0000.0000.0000.000
53A53PRO00.0340.01527.9110.0050.0050.0000.0000.0000.000
54A54GLY0-0.011-0.02630.1420.0100.0100.0000.0000.0000.000
55A55LEU0-0.025-0.01830.8840.0110.0110.0000.0000.0000.000
56A56ASN00.0630.03333.940-0.014-0.0140.0000.0000.0000.000
57A57ALA0-0.038-0.01736.4000.0030.0030.0000.0000.0000.000
58A58ARG10.8720.94630.8660.1870.1870.0000.0000.0000.000
59A59ALA00.0150.01434.465-0.002-0.0020.0000.0000.0000.000
60A60ILE0-0.005-0.00428.256-0.001-0.0010.0000.0000.0000.000
61A61HIS0-0.040-0.02929.651-0.001-0.0010.0000.0000.0000.000
62A62PHE0-0.008-0.00525.107-0.018-0.0180.0000.0000.0000.000
63A63GLU-1-0.858-0.92425.544-0.010-0.0100.0000.0000.0000.000
64A64GLY00.0190.01722.658-0.016-0.0160.0000.0000.0000.000
65A65VAL0-0.079-0.03618.8770.0170.0170.0000.0000.0000.000
66A66TYR00.045-0.00518.381-0.011-0.0110.0000.0000.0000.000
67A67GLN0-0.061-0.03517.3470.0500.0500.0000.0000.0000.000
68A68PRO00.0190.02416.2400.0260.0260.0000.0000.0000.000
69A69ASN0-0.047-0.02615.6340.0210.0210.0000.0000.0000.000
70A70GLY00.0560.01816.337-0.025-0.0250.0000.0000.0000.000
71A71ASN0-0.042-0.02518.1200.0260.0260.0000.0000.0000.000
72A72SER00.0460.02716.968-0.035-0.0350.0000.0000.0000.000
73A73TYR00.0160.00918.5820.0730.0730.0000.0000.0000.000
74A74LEU0-0.0070.01319.745-0.044-0.0440.0000.0000.0000.000
75A75ALA00.027-0.00322.0730.0310.0310.0000.0000.0000.000
76A76VAL0-0.0160.00823.844-0.022-0.0220.0000.0000.0000.000
77A77TYR0-0.042-0.03921.165-0.005-0.0050.0000.0000.0000.000
78A78GLY00.0300.00925.138-0.006-0.0060.0000.0000.0000.000
79A79TRP00.0310.01123.2320.0120.0120.0000.0000.0000.000
80A80THR0-0.038-0.00228.2500.0150.0150.0000.0000.0000.000
81A81ARG10.8230.87227.0680.3240.3240.0000.0000.0000.000
82A82ASN0-0.0850.00033.0610.0090.0090.0000.0000.0000.000
83A83PRO00.035-0.00435.9420.0120.0120.0000.0000.0000.000
84A84LEU00.002-0.02628.516-0.002-0.0020.0000.0000.0000.000
85A85VAL0-0.061-0.01931.2880.0050.0050.0000.0000.0000.000
86A86GLU-1-0.730-0.81123.602-0.460-0.4600.0000.0000.0000.000
87A87TYR0-0.014-0.00628.0650.0210.0210.0000.0000.0000.000
88A88TYR0-0.020-0.03422.679-0.020-0.0200.0000.0000.0000.000
89A89ILE0-0.023-0.01127.7200.0200.0200.0000.0000.0000.000
90A90VAL0-0.009-0.00625.080-0.009-0.0090.0000.0000.0000.000
91A91GLU-1-0.699-0.81126.328-0.112-0.1120.0000.0000.0000.000
92A92ASN0-0.013-0.03724.0290.0260.0260.0000.0000.0000.000
93A93PHE00.0690.02622.714-0.029-0.0290.0000.0000.0000.000
94A94GLY00.0030.02821.0670.0350.0350.0000.0000.0000.000
95A95THR0-0.044-0.03121.7380.0180.0180.0000.0000.0000.000
96A96TYR0-0.015-0.00722.4220.0110.0110.0000.0000.0000.000
97A97ASP-1-0.725-0.81924.508-0.194-0.1940.0000.0000.0000.000
98A98PRO00.0550.03423.4130.0000.0000.0000.0000.0000.000
99A99SER0-0.052-0.03625.384-0.009-0.0090.0000.0000.0000.000
100A100SER0-0.072-0.06228.3310.0200.0200.0000.0000.0000.000
101A101GLY0-0.035-0.01629.625-0.015-0.0150.0000.0000.0000.000
102A102ALA0-0.033-0.01431.574-0.002-0.0020.0000.0000.0000.000
103A103THR0-0.078-0.04433.1950.0150.0150.0000.0000.0000.000
104A104ASP-1-0.868-0.93736.773-0.124-0.1240.0000.0000.0000.000
105A105LEU0-0.059-0.03637.4140.0040.0040.0000.0000.0000.000
106A106GLY00.0010.01939.8670.0050.0050.0000.0000.0000.000
107A107THR0-0.053-0.04038.782-0.005-0.0050.0000.0000.0000.000
108A108VAL0-0.005-0.00538.1500.0030.0030.0000.0000.0000.000
109A109GLU-1-0.926-0.96639.126-0.072-0.0720.0000.0000.0000.000
110A110CYS0-0.063-0.02036.6790.0010.0010.0000.0000.0000.000
111A111ASP-1-0.817-0.91135.515-0.105-0.1050.0000.0000.0000.000
112A112GLY00.0050.00836.5490.0020.0020.0000.0000.0000.000
113A113SER0-0.022-0.04035.5430.0020.0020.0000.0000.0000.000
114A114ILE00.0130.01037.598-0.005-0.0050.0000.0000.0000.000
115A115TYR0-0.041-0.05131.5860.0030.0030.0000.0000.0000.000
116A116ARG10.8420.89531.2560.1400.1400.0000.0000.0000.000
117A117LEU00.0100.00734.119-0.014-0.0140.0000.0000.0000.000
118A118GLY00.0510.02434.4250.0070.0070.0000.0000.0000.000
119A119LYS10.8250.90533.4390.1860.1860.0000.0000.0000.000
120A120THR00.0090.01429.4620.0140.0140.0000.0000.0000.000
121A121THR0-0.038-0.04632.2680.0020.0020.0000.0000.0000.000
122A122ARG10.9070.97423.3310.4240.4240.0000.0000.0000.000
123A123VAL00.0330.00029.4360.0050.0050.0000.0000.0000.000
124A124ASN0-0.066-0.03128.764-0.012-0.0120.0000.0000.0000.000
125A125ALA00.0100.01024.891-0.022-0.0220.0000.0000.0000.000
126A126PRO00.004-0.01320.6260.0200.0200.0000.0000.0000.000
127A127SER0-0.002-0.00222.9920.0110.0110.0000.0000.0000.000
128A128ILE00.0220.00822.755-0.030-0.0300.0000.0000.0000.000
129A129ASP-1-0.816-0.85524.128-0.363-0.3630.0000.0000.0000.000
130A130GLY00.0130.01424.4630.0250.0250.0000.0000.0000.000
131A131THR0-0.052-0.02225.464-0.013-0.0130.0000.0000.0000.000
132A132GLN0-0.026-0.00926.6230.0490.0490.0000.0000.0000.000
133A133THR0-0.016-0.01228.978-0.010-0.0100.0000.0000.0000.000
134A134PHE0-0.020-0.00525.2970.0090.0090.0000.0000.0000.000
135A135ASP-1-0.750-0.83931.111-0.218-0.2180.0000.0000.0000.000
136A136GLN0-0.027-0.03125.5040.0040.0040.0000.0000.0000.000
137A137TYR0-0.053-0.04330.3620.0180.0180.0000.0000.0000.000
138A138TRP00.0430.00424.813-0.010-0.0100.0000.0000.0000.000
139A139SER0-0.002-0.00830.7680.0200.0200.0000.0000.0000.000
140A140VAL0-0.025-0.01328.966-0.010-0.0100.0000.0000.0000.000
141A141ARG10.7960.90430.4890.1060.1060.0000.0000.0000.000
142A142GLN0-0.057-0.02231.386-0.005-0.0050.0000.0000.0000.000
143A143ASP-1-0.888-0.91133.099-0.055-0.0550.0000.0000.0000.000
144A144LYS10.8250.91926.0150.1060.1060.0000.0000.0000.000
145A145ARG10.8270.90328.4960.1140.1140.0000.0000.0000.000
146A146THR0-0.014-0.01724.192-0.019-0.0190.0000.0000.0000.000
147A147SER0-0.010-0.00225.849-0.003-0.0030.0000.0000.0000.000
148A148GLY0-0.0070.00928.5030.0060.0060.0000.0000.0000.000
149A149THR0-0.001-0.00830.729-0.006-0.0060.0000.0000.0000.000
150A150VAL0-0.0160.00130.0050.0050.0050.0000.0000.0000.000
151A151GLN00.0360.01432.966-0.011-0.0110.0000.0000.0000.000
152A152THR00.007-0.01431.9160.0010.0010.0000.0000.0000.000
153A153GLY00.0100.00734.752-0.003-0.0030.0000.0000.0000.000
154A155HIS00.0760.04534.587-0.003-0.0030.0000.0000.0000.000
155A156PHE00.0270.00132.536-0.002-0.0020.0000.0000.0000.000
156A157ASP-1-0.831-0.88937.663-0.106-0.1060.0000.0000.0000.000
157A158ALA0-0.025-0.01438.6690.0040.0040.0000.0000.0000.000
158A159TRP0-0.011-0.02031.591-0.001-0.0010.0000.0000.0000.000
159A160ALA00.0150.01438.9950.0010.0010.0000.0000.0000.000
160A161ARG10.7910.87941.9710.1090.1090.0000.0000.0000.000
161A162ALA0-0.0260.00340.7820.0050.0050.0000.0000.0000.000
162A163GLY0-0.035-0.01442.951-0.001-0.0010.0000.0000.0000.000
163A164LEU0-0.061-0.02136.616-0.005-0.0050.0000.0000.0000.000
164A165ASN00.0140.00438.8910.0070.0070.0000.0000.0000.000
165A166VAL00.0340.02437.105-0.013-0.0130.0000.0000.0000.000
166A167ASN0-0.060-0.04138.3760.0060.0060.0000.0000.0000.000
167A168GLY00.0330.03836.0150.0020.0020.0000.0000.0000.000
168A169ASP-1-0.898-0.94434.566-0.197-0.1970.0000.0000.0000.000
169A170HIS0-0.046-0.03431.741-0.028-0.0280.0000.0000.0000.000
170A171TYR0-0.033-0.02423.3700.0210.0210.0000.0000.0000.000
171A172TYR0-0.014-0.01820.4610.0390.0390.0000.0000.0000.000
172A173GLN0-0.003-0.00626.1860.0140.0140.0000.0000.0000.000
173A174ILE0-0.028-0.01119.9700.0160.0160.0000.0000.0000.000
174A175VAL00.0050.00022.9870.0120.0120.0000.0000.0000.000
175A176ALA0-0.014-0.00119.558-0.019-0.0190.0000.0000.0000.000
176A177THR0-0.002-0.00415.9430.0780.0780.0000.0000.0000.000
177A178GLU-1-0.874-0.94016.124-0.624-0.6240.0000.0000.0000.000
178A179GLY00.0170.03213.8310.1170.1170.0000.0000.0000.000
179A180TYR0-0.001-0.00814.739-0.129-0.1290.0000.0000.0000.000
180A181PHE0-0.050-0.01513.3480.0950.0950.0000.0000.0000.000
181A182SER0-0.014-0.01912.9190.1150.1150.0000.0000.0000.000
182A183SER0-0.032-0.01411.278-0.056-0.0560.0000.0000.0000.000
183A184GLY00.0230.00311.4220.0280.0280.0000.0000.0000.000
184A185TYR0-0.081-0.05311.6910.0080.0080.0000.0000.0000.000
185A186ALA00.001-0.00213.833-0.009-0.0090.0000.0000.0000.000
186A187ARG10.8990.94815.428-0.178-0.1780.0000.0000.0000.000
187A188ILE00.0130.02218.0170.0380.0380.0000.0000.0000.000
188A189THR00.007-0.00220.762-0.017-0.0170.0000.0000.0000.000
189A190VAL0-0.043-0.01922.8900.0100.0100.0000.0000.0000.000
190A191ALA00.004-0.00825.5490.0070.0070.0000.0000.0000.000
191A192ASP-1-0.855-0.91428.894-0.142-0.1420.0000.0000.0000.000
192A193VAL0-0.048-0.02431.9180.0100.0100.0000.0000.0000.000
193A194GLY0-0.024-0.00434.8990.0100.0100.0000.0000.0000.000