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

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FMODB ID: L7LV9

Calculation Name: 1LGV-A-Xray372

Preferred Name:

Target Type:

Ligand Name: pyroglutamic acid

ligand 3-letter code: PCA

PDB ID: 1LGV

Chain ID: A

ChEMBL ID:

UniProt ID: Q6PJG0

Base Structure: X-ray

Registration Date: 2023-09-26

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 212
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1962934.311766
FMO2-HF: Nuclear repulsion 1884362.916352
FMO2-HF: Total energy -78571.395414
FMO2-MP2: Total energy -78801.757341


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.
-1.0810.7030.01-0.841-0.9520.001
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 : -0.020 / q_NPA : -0.032
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].
3A3ALA00.0110.0113.598-0.8920.8920.010-0.841-0.9520.001
4A4LEU0-0.025-0.0175.6390.4980.4980.0000.0000.0000.000
5A5THR00.0150.0089.4490.1270.1270.0000.0000.0000.000
6A6GLN00.015-0.02111.428-0.001-0.0010.0000.0000.0000.000
7A7PRO0-0.0120.01813.2760.0350.0350.0000.0000.0000.000
8A8ALA00.0830.04513.3190.0180.0180.0000.0000.0000.000
9A9SER0-0.029-0.01014.6620.0840.0840.0000.0000.0000.000
10A10VAL0-0.017-0.00918.413-0.040-0.0400.0000.0000.0000.000
11A11SER0-0.030-0.01721.7410.0330.0330.0000.0000.0000.000
12A12GLY00.0470.02425.323-0.022-0.0220.0000.0000.0000.000
13A13SER0-0.017-0.00828.6910.0200.0200.0000.0000.0000.000
14A14PRO00.003-0.01631.859-0.012-0.0120.0000.0000.0000.000
15A15GLY0-0.0160.00233.4210.0000.0000.0000.0000.0000.000
16A16GLN00.0060.01731.370-0.006-0.0060.0000.0000.0000.000
17A17SER00.0130.00129.3000.0020.0020.0000.0000.0000.000
18A18ILE0-0.0030.01023.1870.0050.0050.0000.0000.0000.000
19A19THR0-0.006-0.01523.026-0.001-0.0010.0000.0000.0000.000
20A20VAL0-0.0120.00917.188-0.002-0.0020.0000.0000.0000.000
21A21SER00.0270.02017.698-0.012-0.0120.0000.0000.0000.000
22A22CYS0-0.032-0.01512.696-0.049-0.0490.0000.0000.0000.000
23A23THR0-0.034-0.01513.7910.0360.0360.0000.0000.0000.000
24A24GLY00.0240.01012.441-0.207-0.2070.0000.0000.0000.000
25A25VAL0-0.032-0.00613.106-0.090-0.0900.0000.0000.0000.000
26A26SER0-0.007-0.01114.9190.0640.0640.0000.0000.0000.000
27A27SER0-0.0020.00815.688-0.058-0.0580.0000.0000.0000.000
28A28ILE0-0.0110.00615.0080.0930.0930.0000.0000.0000.000
29A29VAL00.0020.02517.5280.0750.0750.0000.0000.0000.000
30A30GLY00.0380.02419.135-0.023-0.0230.0000.0000.0000.000
31A31SER0-0.044-0.04621.6890.0060.0060.0000.0000.0000.000
32A32TYR00.0140.02217.9940.0730.0730.0000.0000.0000.000
33A33ASN00.0610.00620.223-0.059-0.0590.0000.0000.0000.000
34A34LEU0-0.0090.01018.0060.0310.0310.0000.0000.0000.000
35A35VAL00.0070.00316.064-0.068-0.0680.0000.0000.0000.000
36A36SER0-0.009-0.01216.0310.0900.0900.0000.0000.0000.000
37A37TRP00.0000.00715.868-0.094-0.0940.0000.0000.0000.000
38A38TYR0-0.009-0.02413.9620.0850.0850.0000.0000.0000.000
39A39GLN00.0460.01817.432-0.002-0.0020.0000.0000.0000.000
40A40GLN0-0.012-0.01314.354-0.007-0.0070.0000.0000.0000.000
41A41HIS00.0120.00818.4600.0320.0320.0000.0000.0000.000
42A42PRO00.018-0.01119.3380.0120.0120.0000.0000.0000.000
43A43GLY00.0090.01219.015-0.024-0.0240.0000.0000.0000.000
44A44LYS10.9320.98019.436-0.076-0.0760.0000.0000.0000.000
45A45ALA00.0470.02517.1580.0270.0270.0000.0000.0000.000
46A46PRO0-0.012-0.01413.9660.0020.0020.0000.0000.0000.000
47A47LYS10.9050.97917.1840.0650.0650.0000.0000.0000.000
48A48LEU0-0.005-0.00218.680-0.017-0.0170.0000.0000.0000.000
49A49LEU0-0.061-0.03020.1410.0370.0370.0000.0000.0000.000
50A50THR0-0.001-0.02220.5920.0130.0130.0000.0000.0000.000
51A51TYR00.0310.01019.959-0.034-0.0340.0000.0000.0000.000
52A52GLU-1-0.840-0.90620.719-0.293-0.2930.0000.0000.0000.000
53A53VAL0-0.059-0.00920.7460.0260.0260.0000.0000.0000.000
54A54ASN0-0.020-0.02821.8690.0030.0030.0000.0000.0000.000
55A55LYS10.8460.94024.7330.3270.3270.0000.0000.0000.000
56A56ARG10.9390.95924.4710.1390.1390.0000.0000.0000.000
57A57PRO0-0.0120.00723.8840.0120.0120.0000.0000.0000.000
58A58SER00.0530.01526.9790.0070.0070.0000.0000.0000.000
59A59GLY0-0.0010.00929.1760.0020.0020.0000.0000.0000.000
60A60VAL0-0.082-0.02824.9180.0120.0120.0000.0000.0000.000
61A61SER0-0.0030.00028.116-0.006-0.0060.0000.0000.0000.000
62A62ASP-1-0.837-0.94028.839-0.114-0.1140.0000.0000.0000.000
63A63ARG10.7610.86528.7470.0570.0570.0000.0000.0000.000
64A64PHE0-0.042-0.00723.774-0.008-0.0080.0000.0000.0000.000
65A65SER0-0.003-0.00925.539-0.005-0.0050.0000.0000.0000.000
66A66GLY00.0290.01922.861-0.009-0.0090.0000.0000.0000.000
67A67SER0-0.026-0.02322.4060.0170.0170.0000.0000.0000.000
68A68LYS10.9120.94119.4800.5420.5420.0000.0000.0000.000
69A69SER0-0.0120.00121.8780.0400.0400.0000.0000.0000.000
70A70GLY00.0550.02822.019-0.028-0.0280.0000.0000.0000.000
71A71ASN00.0280.01315.606-0.053-0.0530.0000.0000.0000.000
72A72SER00.0150.00117.093-0.111-0.1110.0000.0000.0000.000
73A73ALA00.0490.01717.3680.0400.0400.0000.0000.0000.000
74A74SER0-0.041-0.03418.9500.0050.0050.0000.0000.0000.000
75A75LEU00.0000.03019.5120.0150.0150.0000.0000.0000.000
76A76THR00.0060.00321.4630.0140.0140.0000.0000.0000.000
77A77ILE0-0.0070.00722.0040.0010.0010.0000.0000.0000.000
78A78SER00.0400.00126.1710.0120.0120.0000.0000.0000.000
79A79GLY00.0080.01029.9430.0040.0040.0000.0000.0000.000
80A80LEU0-0.044-0.01626.4790.0050.0050.0000.0000.0000.000
81A81GLN0-0.004-0.01729.6460.0000.0000.0000.0000.0000.000
82A82ALA00.0370.01829.1450.0010.0010.0000.0000.0000.000
83A83GLU-1-0.792-0.88228.5070.0160.0160.0000.0000.0000.000
84A84ASP-1-0.766-0.84725.436-0.054-0.0540.0000.0000.0000.000
85A85GLU-1-0.806-0.86923.9290.0850.0850.0000.0000.0000.000
86A86ALA0-0.033-0.01620.7770.0210.0210.0000.0000.0000.000
87A87ASP-1-0.780-0.86615.5030.2650.2650.0000.0000.0000.000
88A88TYR0-0.055-0.04516.456-0.039-0.0390.0000.0000.0000.000
89A89TYR0-0.015-0.00410.7220.0090.0090.0000.0000.0000.000
90A91SER00.0350.01511.389-0.074-0.0740.0000.0000.0000.000
91A92SER0-0.019-0.02111.7480.1990.1990.0000.0000.0000.000
92A93TYR0-0.042-0.01212.193-0.150-0.1500.0000.0000.0000.000
93A94ASP-1-0.689-0.81411.441-1.421-1.4210.0000.0000.0000.000
94A95GLY0-0.052-0.02913.5380.0610.0610.0000.0000.0000.000
95A96SER0-0.102-0.08711.6930.0190.0190.0000.0000.0000.000
96A97SER0-0.018-0.0369.2100.0090.0090.0000.0000.0000.000
97A98THR0-0.028-0.01111.1810.0760.0760.0000.0000.0000.000
98A99SER00.0290.0329.9120.1830.1830.0000.0000.0000.000
99A100VAL0-0.022-0.00810.484-0.035-0.0350.0000.0000.0000.000
100A101VAL00.0060.0156.329-0.231-0.2310.0000.0000.0000.000
101A102PHE00.037-0.0087.1060.3950.3950.0000.0000.0000.000
102A103GLY00.0270.0127.246-0.590-0.5900.0000.0000.0000.000
103A104GLY0-0.029-0.0187.6990.0980.0980.0000.0000.0000.000
104A105GLY0-0.0200.0028.6600.4070.4070.0000.0000.0000.000
105A106THR0-0.054-0.04611.988-0.038-0.0380.0000.0000.0000.000
106A107LYS10.8340.89715.517-0.374-0.3740.0000.0000.0000.000
107A108LEU0-0.032-0.00418.210-0.018-0.0180.0000.0000.0000.000
108A109THR0-0.025-0.01721.6910.0320.0320.0000.0000.0000.000
109A110VAL0-0.028-0.01824.693-0.022-0.0220.0000.0000.0000.000
110A111LEU00.0560.02827.7610.0150.0150.0000.0000.0000.000
111A112GLY00.013-0.01130.407-0.011-0.0110.0000.0000.0000.000
112A113GLN0-0.049-0.03229.971-0.009-0.0090.0000.0000.0000.000
113A114PRO0-0.023-0.00134.8590.0050.0050.0000.0000.0000.000
114A115LYS10.8740.92937.726-0.078-0.0780.0000.0000.0000.000
115A116ALA0-0.046-0.02338.414-0.007-0.0070.0000.0000.0000.000
116A117ALA00.0630.03039.1750.0080.0080.0000.0000.0000.000
117A118PRO0-0.042-0.01239.705-0.003-0.0030.0000.0000.0000.000
118A119SER00.004-0.00341.279-0.006-0.0060.0000.0000.0000.000
119A120VAL0-0.010-0.00742.2530.0070.0070.0000.0000.0000.000
120A121THR0-0.017-0.00444.307-0.008-0.0080.0000.0000.0000.000
121A122LEU0-0.037-0.00845.1190.0060.0060.0000.0000.0000.000
122A123PHE0-0.010-0.00744.723-0.006-0.0060.0000.0000.0000.000
123A124PRO00.0050.00048.6560.0050.0050.0000.0000.0000.000
124A125PRO00.0330.01650.2450.0000.0000.0000.0000.0000.000
125A126SER00.0110.01350.764-0.004-0.0040.0000.0000.0000.000
126A127SER00.0530.00052.7650.0020.0020.0000.0000.0000.000
127A128GLU-1-0.889-0.93251.9840.0620.0620.0000.0000.0000.000
128A129GLU-1-0.769-0.84248.2800.0990.0990.0000.0000.0000.000
129A130LEU0-0.014-0.01451.5240.0020.0020.0000.0000.0000.000
130A131GLN0-0.052-0.03154.625-0.002-0.0020.0000.0000.0000.000
131A132ALA0-0.042-0.00551.174-0.001-0.0010.0000.0000.0000.000
132A133ASN0-0.066-0.03452.2210.0010.0010.0000.0000.0000.000
133A134LYS10.8510.91245.826-0.104-0.1040.0000.0000.0000.000
134A135ALA00.001-0.00449.862-0.005-0.0050.0000.0000.0000.000
135A136THR0-0.057-0.06443.9170.0080.0080.0000.0000.0000.000
136A137LEU0-0.0130.02047.106-0.004-0.0040.0000.0000.0000.000
137A138VAL00.0150.00041.8260.0080.0080.0000.0000.0000.000
138A139CYS0-0.074-0.01542.694-0.002-0.0020.0000.0000.0000.000
139A140LEU00.0170.01839.0710.0090.0090.0000.0000.0000.000
140A141ILE00.000-0.00138.427-0.006-0.0060.0000.0000.0000.000
141A142SER00.015-0.02937.8560.0080.0080.0000.0000.0000.000
142A143ASP-1-0.797-0.87637.7680.0670.0670.0000.0000.0000.000
143A144PHE00.0200.02333.802-0.006-0.0060.0000.0000.0000.000
144A145TYR00.0230.01230.5470.0060.0060.0000.0000.0000.000
145A146PRO00.0800.03031.910-0.009-0.0090.0000.0000.0000.000
146A147GLY00.0190.00230.707-0.002-0.0020.0000.0000.0000.000
147A148ALA0-0.038-0.01830.8210.0180.0180.0000.0000.0000.000
148A149VAL0-0.009-0.00932.475-0.014-0.0140.0000.0000.0000.000
149A150THR0-0.027-0.00434.9110.0150.0150.0000.0000.0000.000
150A151VAL0-0.002-0.01037.516-0.011-0.0110.0000.0000.0000.000
151A152ALA0-0.0030.01039.9790.0070.0070.0000.0000.0000.000
152A153TRP00.0460.00241.928-0.010-0.0100.0000.0000.0000.000
153A154LYS10.7770.88845.894-0.084-0.0840.0000.0000.0000.000
154A155ALA00.0570.03349.591-0.001-0.0010.0000.0000.0000.000
155A156ASP-1-0.785-0.89652.4480.0730.0730.0000.0000.0000.000
156A157SER0-0.012-0.00553.5900.0020.0020.0000.0000.0000.000
157A158SER00.0100.00752.6130.0020.0020.0000.0000.0000.000
158A159PRO0-0.023-0.02247.1360.0020.0020.0000.0000.0000.000
159A160VAL00.0080.00245.6420.0000.0000.0000.0000.0000.000
160A161LYS10.8960.94644.892-0.119-0.1190.0000.0000.0000.000
161A162ALA00.0220.01843.3500.0070.0070.0000.0000.0000.000
162A163GLY00.0540.02143.167-0.006-0.0060.0000.0000.0000.000
163A164VAL0-0.047-0.01539.704-0.003-0.0030.0000.0000.0000.000
164A165GLU-1-0.857-0.91735.4960.2150.2150.0000.0000.0000.000
165A166THR0-0.071-0.04135.021-0.016-0.0160.0000.0000.0000.000
166A167THR0-0.0010.02332.4210.0140.0140.0000.0000.0000.000
167A168LYS10.9660.96825.635-0.314-0.3140.0000.0000.0000.000
168A169PRO00.000-0.00230.414-0.003-0.0030.0000.0000.0000.000
169A170SER0-0.039-0.01628.6480.0210.0210.0000.0000.0000.000
170A171LYS10.7870.90527.590-0.092-0.0920.0000.0000.0000.000
171A172GLN00.0250.01829.6410.0110.0110.0000.0000.0000.000
172A173SER00.021-0.00531.985-0.003-0.0030.0000.0000.0000.000
173A174ASN0-0.011-0.00533.328-0.004-0.0040.0000.0000.0000.000
174A175ASN0-0.027-0.04430.8090.0030.0030.0000.0000.0000.000
175A176LYS10.8830.96332.174-0.053-0.0530.0000.0000.0000.000
176A177TYR00.0060.00928.1220.0110.0110.0000.0000.0000.000
177A178ALA0-0.039-0.02333.203-0.011-0.0110.0000.0000.0000.000
178A179ALA00.0030.00433.4030.0140.0140.0000.0000.0000.000
179A180SER00.007-0.00535.405-0.013-0.0130.0000.0000.0000.000
180A181SER0-0.0010.01237.0990.0090.0090.0000.0000.0000.000
181A182TYR00.006-0.01537.426-0.013-0.0130.0000.0000.0000.000
182A183LEU0-0.0030.00641.6290.0070.0070.0000.0000.0000.000
183A184SER0-0.010-0.00242.813-0.007-0.0070.0000.0000.0000.000
184A185LEU0-0.049-0.03045.4380.0020.0020.0000.0000.0000.000
185A186THR00.008-0.02049.0710.0000.0000.0000.0000.0000.000
186A187PRO00.0260.00752.118-0.001-0.0010.0000.0000.0000.000
187A188GLU-1-0.803-0.88555.0980.0820.0820.0000.0000.0000.000
188A189GLN0-0.0010.00550.3320.0000.0000.0000.0000.0000.000
189A190TRP00.0400.03052.978-0.001-0.0010.0000.0000.0000.000
190A191LYS10.9400.95454.469-0.066-0.0660.0000.0000.0000.000
191A192SER0-0.101-0.03856.314-0.002-0.0020.0000.0000.0000.000
192A193HIS10.8210.90555.103-0.082-0.0820.0000.0000.0000.000
193A194ARG10.9490.97257.979-0.062-0.0620.0000.0000.0000.000
194A195SER0-0.044-0.03255.377-0.002-0.0020.0000.0000.0000.000
195A196TYR00.0360.01549.9350.0010.0010.0000.0000.0000.000
196A197SER0-0.025-0.02549.755-0.004-0.0040.0000.0000.0000.000
197A199GLN0-0.015-0.02945.009-0.002-0.0020.0000.0000.0000.000
198A200VAL00.0400.00540.1950.0080.0080.0000.0000.0000.000
199A201THR00.0130.01840.552-0.009-0.0090.0000.0000.0000.000
200A202HIS0-0.008-0.01835.9090.0050.0050.0000.0000.0000.000
201A203GLU-1-0.850-0.92135.8110.1020.1020.0000.0000.0000.000
202A204GLY00.0020.00838.919-0.006-0.0060.0000.0000.0000.000
203A205SER0-0.025-0.00241.637-0.006-0.0060.0000.0000.0000.000
204A206THR0-0.031-0.03143.1030.0040.0040.0000.0000.0000.000
205A207VAL00.0000.01144.694-0.006-0.0060.0000.0000.0000.000
206A208GLU-1-0.753-0.84846.0240.0890.0890.0000.0000.0000.000
207A209LYS10.8370.91648.092-0.075-0.0750.0000.0000.0000.000
208A210THR00.0360.00049.7190.0040.0040.0000.0000.0000.000
209A211VAL0-0.013-0.00251.234-0.003-0.0030.0000.0000.0000.000
210A212ALA00.0580.01953.8590.0020.0020.0000.0000.0000.000
211A213PRO0-0.0070.00356.700-0.001-0.0010.0000.0000.0000.000
212A214THR0-0.0060.01158.057-0.001-0.0010.0000.0000.0000.000