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: J2MV9

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 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 212
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1964304.581838
FMO2-HF: Nuclear repulsion 1885734.717088
FMO2-HF: Total energy -78569.86475
FMO2-MP2: Total energy -78800.418245


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.
-4.302-1.110.096-1.686-1.6020
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 : -0.012 / q_NPA : -0.019
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].
3A3ALA00.0010.0003.078-3.620-0.4680.097-1.683-1.5660.000
4A4LEU00.001-0.0075.3320.6410.681-0.001-0.003-0.0360.000
5A5THR0-0.003-0.0158.859-0.028-0.0280.0000.0000.0000.000
6A6GLN00.013-0.01411.142-0.053-0.0530.0000.0000.0000.000
7A7PRO0-0.0290.00812.8510.0580.0580.0000.0000.0000.000
8A8ALA00.1010.04813.421-0.010-0.0100.0000.0000.0000.000
9A9SER0-0.077-0.03914.3810.0510.0510.0000.0000.0000.000
10A10VAL00.0310.02717.738-0.034-0.0340.0000.0000.0000.000
11A11SER0-0.017-0.01921.0040.0300.0300.0000.0000.0000.000
12A12GLY00.0620.03424.312-0.017-0.0170.0000.0000.0000.000
13A13SER0-0.043-0.01227.6810.0190.0190.0000.0000.0000.000
14A14PRO00.019-0.01130.928-0.013-0.0130.0000.0000.0000.000
15A15GLY0-0.0160.00432.3170.0020.0020.0000.0000.0000.000
16A16GLN0-0.010-0.00330.211-0.009-0.0090.0000.0000.0000.000
17A17SER00.0390.01628.6450.0000.0000.0000.0000.0000.000
18A18ILE00.0000.01422.5060.0080.0080.0000.0000.0000.000
19A19THR00.0090.00622.475-0.010-0.0100.0000.0000.0000.000
20A20VAL0-0.0120.00516.7770.0140.0140.0000.0000.0000.000
21A21SER0-0.016-0.00717.883-0.034-0.0340.0000.0000.0000.000
22A22CYS00.0450.02612.264-0.029-0.0290.0000.0000.0000.000
23A23THR0-0.044-0.01413.925-0.009-0.0090.0000.0000.0000.000
24A24GLY00.0400.01512.189-0.197-0.1970.0000.0000.0000.000
25A25VAL0-0.026-0.00712.522-0.118-0.1180.0000.0000.0000.000
26A26SER0-0.013-0.02314.4210.0290.0290.0000.0000.0000.000
27A27SER00.0200.04015.465-0.068-0.0680.0000.0000.0000.000
28A28ILE0-0.035-0.01314.6510.0740.0740.0000.0000.0000.000
29A29VAL0-0.0640.06617.3130.0770.0770.0000.0000.0000.000
30A30GLY00.0580.01919.294-0.012-0.0120.0000.0000.0000.000
31A31SER0-0.003-0.02521.143-0.032-0.0320.0000.0000.0000.000
32A32TYR0-0.026-0.00617.3690.0740.0740.0000.0000.0000.000
33A33ASN00.010-0.00819.770-0.056-0.0560.0000.0000.0000.000
34A34LEU0-0.007-0.01317.2630.0500.0500.0000.0000.0000.000
35A35VAL00.0210.02115.884-0.085-0.0850.0000.0000.0000.000
36A36SER0-0.014-0.01015.6980.1350.1350.0000.0000.0000.000
37A37TRP0-0.0010.01315.530-0.111-0.1110.0000.0000.0000.000
38A38TYR0-0.016-0.01714.0720.0290.0290.0000.0000.0000.000
39A39GLN00.0110.00116.708-0.007-0.0070.0000.0000.0000.000
40A40GLN0-0.028-0.03013.927-0.009-0.0090.0000.0000.0000.000
41A41HIS00.0090.02217.4940.0290.0290.0000.0000.0000.000
42A42PRO00.026-0.01018.5230.0060.0060.0000.0000.0000.000
43A43GLY00.0130.01218.234-0.016-0.0160.0000.0000.0000.000
44A44LYS10.9240.97719.0620.0000.0000.0000.0000.0000.000
45A45ALA00.0280.01817.3090.0110.0110.0000.0000.0000.000
46A46PRO00.0110.00113.7700.0090.0090.0000.0000.0000.000
47A47LYS10.9550.98816.9050.1590.1590.0000.0000.0000.000
48A48LEU0-0.024-0.00418.383-0.016-0.0160.0000.0000.0000.000
49A49LEU0-0.040-0.02019.5960.0430.0430.0000.0000.0000.000
50A50THR00.013-0.02220.4030.0110.0110.0000.0000.0000.000
51A51TYR00.0540.01619.848-0.046-0.0460.0000.0000.0000.000
52A52GLU-1-0.882-0.94220.374-0.358-0.3580.0000.0000.0000.000
53A53VAL0-0.047-0.01020.5080.0350.0350.0000.0000.0000.000
54A54ASN0-0.048-0.03121.6460.0060.0060.0000.0000.0000.000
55A55LYS10.8880.97424.3300.3830.3830.0000.0000.0000.000
56A56ARG10.9360.96924.3820.1810.1810.0000.0000.0000.000
57A57PRO0-0.0270.00423.4570.0160.0160.0000.0000.0000.000
58A58SER00.0600.02326.6070.0090.0090.0000.0000.0000.000
59A59GLY00.0140.00828.726-0.002-0.0020.0000.0000.0000.000
60A60VAL0-0.112-0.04724.7650.0140.0140.0000.0000.0000.000
61A61SER00.0380.02527.962-0.003-0.0030.0000.0000.0000.000
62A62ASP-1-0.895-0.97028.406-0.163-0.1630.0000.0000.0000.000
63A63ARG10.8470.92328.0490.1000.1000.0000.0000.0000.000
64A64PHE0-0.054-0.01523.484-0.008-0.0080.0000.0000.0000.000
65A65SER00.003-0.00925.4490.0010.0010.0000.0000.0000.000
66A66GLY00.0140.02222.406-0.008-0.0080.0000.0000.0000.000
67A67SER00.004-0.00522.2980.0240.0240.0000.0000.0000.000
68A68LYS10.9490.96819.0470.6260.6260.0000.0000.0000.000
69A69SER0-0.025-0.00621.4460.0470.0470.0000.0000.0000.000
70A70GLY00.0510.03021.743-0.024-0.0240.0000.0000.0000.000
71A71ASN00.0250.00215.580-0.076-0.0760.0000.0000.0000.000
72A72SER00.010-0.00416.692-0.128-0.1280.0000.0000.0000.000
73A73ALA00.0540.03116.9760.0600.0600.0000.0000.0000.000
74A74SER0-0.059-0.04218.3360.0010.0010.0000.0000.0000.000
75A75LEU00.0250.03219.4640.0100.0100.0000.0000.0000.000
76A76THR0-0.025-0.02321.1200.0110.0110.0000.0000.0000.000
77A77ILE0-0.032-0.01521.7440.0000.0000.0000.0000.0000.000
78A78SER00.022-0.00525.8460.0150.0150.0000.0000.0000.000
79A79GLY00.0070.00429.6450.0030.0030.0000.0000.0000.000
80A80LEU0-0.066-0.03125.3400.0050.0050.0000.0000.0000.000
81A81GLN0-0.022-0.03828.5800.0070.0070.0000.0000.0000.000
82A82ALA00.0690.03628.051-0.001-0.0010.0000.0000.0000.000
83A83GLU-1-0.842-0.90827.158-0.026-0.0260.0000.0000.0000.000
84A84ASP-1-0.779-0.86524.473-0.102-0.1020.0000.0000.0000.000
85A85GLU-1-0.871-0.90422.7640.0490.0490.0000.0000.0000.000
86A86ALA0-0.039-0.02219.5170.0110.0110.0000.0000.0000.000
87A87ASP-1-0.822-0.88714.1340.1750.1750.0000.0000.0000.000
88A88TYR0-0.036-0.05815.555-0.047-0.0470.0000.0000.0000.000
89A89TYR0-0.0170.0159.2260.0120.0120.0000.0000.0000.000
90A91SER00.017-0.00311.026-0.194-0.1940.0000.0000.0000.000
91A92SER00.014-0.00511.3630.2620.2620.0000.0000.0000.000
92A93TYR0-0.0250.01311.898-0.170-0.1700.0000.0000.0000.000
93A94ASP-1-0.762-0.90510.394-1.783-1.7830.0000.0000.0000.000
94A95GLY00.006-0.07612.9380.0960.0960.0000.0000.0000.000
95A96SER0-0.078-0.04512.3120.0310.0310.0000.0000.0000.000
96A97SER00.0350.0149.8280.0890.0890.0000.0000.0000.000
97A98THR0-0.026-0.00811.7620.0650.0650.0000.0000.0000.000
98A99SER00.0120.0199.5440.1560.1560.0000.0000.0000.000
99A100VAL0-0.010-0.0049.9240.0170.0170.0000.0000.0000.000
100A101VAL00.0070.0185.935-0.316-0.3160.0000.0000.0000.000
101A102PHE00.003-0.0186.5160.5930.5930.0000.0000.0000.000
102A103GLY00.0040.0086.651-0.764-0.7640.0000.0000.0000.000
103A104GLY0-0.012-0.0106.913-0.053-0.0530.0000.0000.0000.000
104A105GLY0-0.012-0.0037.8830.4410.4410.0000.0000.0000.000
105A106THR0-0.067-0.03411.1390.0290.0290.0000.0000.0000.000
106A107LYS10.8700.91914.593-0.295-0.2950.0000.0000.0000.000
107A108LEU0-0.026-0.00916.897-0.006-0.0060.0000.0000.0000.000
108A109THR0-0.034-0.02620.4630.0330.0330.0000.0000.0000.000
109A110VAL00.001-0.00923.511-0.021-0.0210.0000.0000.0000.000
110A111LEU00.0060.01126.8020.0180.0180.0000.0000.0000.000
111A112GLY00.0280.00129.346-0.012-0.0120.0000.0000.0000.000
112A113GLN0-0.050-0.04028.880-0.009-0.0090.0000.0000.0000.000
113A114PRO0-0.038-0.00433.7560.0060.0060.0000.0000.0000.000
114A115LYS10.9550.97836.712-0.072-0.0720.0000.0000.0000.000
115A116ALA0-0.041-0.02737.614-0.007-0.0070.0000.0000.0000.000
116A117ALA00.0330.01238.5680.0080.0080.0000.0000.0000.000
117A118PRO0-0.013-0.00238.951-0.003-0.0030.0000.0000.0000.000
118A119SER00.0500.03340.599-0.004-0.0040.0000.0000.0000.000
119A120VAL0-0.028-0.02141.7720.0060.0060.0000.0000.0000.000
120A121THR0-0.028-0.01743.857-0.007-0.0070.0000.0000.0000.000
121A122LEU0-0.028-0.00744.8220.0060.0060.0000.0000.0000.000
122A123PHE0-0.034-0.01344.452-0.005-0.0050.0000.0000.0000.000
123A124PRO00.007-0.00748.2770.0050.0050.0000.0000.0000.000
124A125PRO00.0410.04049.8190.0000.0000.0000.0000.0000.000
125A126SER00.0100.00450.633-0.003-0.0030.0000.0000.0000.000
126A127SER00.039-0.01152.4580.0020.0020.0000.0000.0000.000
127A128GLU-1-0.912-0.95152.1310.0560.0560.0000.0000.0000.000
128A129GLU-1-0.769-0.85547.8190.0930.0930.0000.0000.0000.000
129A130LEU0-0.001-0.01151.5950.0020.0020.0000.0000.0000.000
130A131GLN0-0.026-0.00554.5710.0010.0010.0000.0000.0000.000
131A132ALA0-0.062-0.01451.420-0.001-0.0010.0000.0000.0000.000
132A133ASN0-0.041-0.02752.5370.0020.0020.0000.0000.0000.000
133A134LYS10.8540.91945.413-0.093-0.0930.0000.0000.0000.000
134A135ALA00.003-0.01349.920-0.005-0.0050.0000.0000.0000.000
135A136THR0-0.042-0.03143.8610.0080.0080.0000.0000.0000.000
136A137LEU0-0.0530.00146.382-0.006-0.0060.0000.0000.0000.000
137A138VAL00.0510.02041.5960.0080.0080.0000.0000.0000.000
138A139CYS0-0.072-0.01042.175-0.001-0.0010.0000.0000.0000.000
139A140LEU00.006-0.01339.0340.0080.0080.0000.0000.0000.000
140A141ILE00.001-0.00437.851-0.006-0.0060.0000.0000.0000.000
141A142SER00.024-0.00137.3620.0070.0070.0000.0000.0000.000
142A143ASP-1-0.874-0.94536.8460.0510.0510.0000.0000.0000.000
143A144PHE00.0290.02833.494-0.003-0.0030.0000.0000.0000.000
144A145TYR00.0140.00329.2580.0050.0050.0000.0000.0000.000
145A146PRO00.0710.01831.600-0.009-0.0090.0000.0000.0000.000
146A147GLY00.0220.01030.311-0.002-0.0020.0000.0000.0000.000
147A148ALA0-0.0140.00030.4200.0190.0190.0000.0000.0000.000
148A149VAL0-0.013-0.01132.441-0.013-0.0130.0000.0000.0000.000
149A150THR0-0.0060.01335.0220.0150.0150.0000.0000.0000.000
150A151VAL00.007-0.00137.572-0.011-0.0110.0000.0000.0000.000
151A152ALA0-0.0100.00339.9090.0070.0070.0000.0000.0000.000
152A153TRP00.0370.00741.610-0.011-0.0110.0000.0000.0000.000
153A154LYS10.7940.88445.599-0.082-0.0820.0000.0000.0000.000
154A155ALA00.0440.03149.245-0.002-0.0020.0000.0000.0000.000
155A156ASP-1-0.810-0.92052.0460.0730.0730.0000.0000.0000.000
156A157SER0-0.037-0.02353.3730.0010.0010.0000.0000.0000.000
157A158SER0-0.007-0.00152.2780.0020.0020.0000.0000.0000.000
158A159PRO0-0.013-0.02046.9240.0020.0020.0000.0000.0000.000
159A160VAL00.0150.01845.561-0.001-0.0010.0000.0000.0000.000
160A161LYS10.9170.95044.788-0.123-0.1230.0000.0000.0000.000
161A162ALA00.0010.00643.1790.0070.0070.0000.0000.0000.000
162A163GLY00.0750.02842.735-0.006-0.0060.0000.0000.0000.000
163A164VAL0-0.034-0.00239.138-0.005-0.0050.0000.0000.0000.000
164A165GLU-1-0.893-0.92735.5570.2070.2070.0000.0000.0000.000
165A166THR0-0.0040.00134.928-0.018-0.0180.0000.0000.0000.000
166A167THR0-0.0130.00532.0050.0120.0120.0000.0000.0000.000
167A168LYS10.9250.95525.670-0.300-0.3000.0000.0000.0000.000
168A169PRO00.0130.00629.370-0.007-0.0070.0000.0000.0000.000
169A170SER0-0.017-0.00828.0410.0190.0190.0000.0000.0000.000
170A171LYS10.8490.93526.010-0.058-0.0580.0000.0000.0000.000
171A172GLN00.0260.01129.0530.0080.0080.0000.0000.0000.000
172A173SER00.007-0.01131.341-0.004-0.0040.0000.0000.0000.000
173A174ASN0-0.0030.00732.494-0.005-0.0050.0000.0000.0000.000
174A175ASN0-0.041-0.04029.7790.0020.0020.0000.0000.0000.000
175A176LYS10.9331.01031.626-0.035-0.0350.0000.0000.0000.000
176A177TYR0-0.009-0.00127.4480.0070.0070.0000.0000.0000.000
177A178ALA0-0.008-0.00732.621-0.008-0.0080.0000.0000.0000.000
178A179ALA0-0.019-0.00632.9750.0140.0140.0000.0000.0000.000
179A180SER00.0100.01434.961-0.012-0.0120.0000.0000.0000.000
180A181SER00.021-0.00736.7500.0100.0100.0000.0000.0000.000
181A182TYR0-0.005-0.00336.952-0.012-0.0120.0000.0000.0000.000
182A183LEU00.0030.01141.3850.0070.0070.0000.0000.0000.000
183A184SER0-0.013-0.00342.898-0.007-0.0070.0000.0000.0000.000
184A185LEU0-0.043-0.02745.4150.0030.0030.0000.0000.0000.000
185A186THR00.0630.03149.048-0.001-0.0010.0000.0000.0000.000
186A187PRO00.0560.01451.964-0.001-0.0010.0000.0000.0000.000
187A188GLU-1-0.869-0.93154.8080.0770.0770.0000.0000.0000.000
188A189GLN0-0.020-0.00350.140-0.001-0.0010.0000.0000.0000.000
189A190TRP00.0240.01052.887-0.001-0.0010.0000.0000.0000.000
190A191LYS10.9470.94754.410-0.063-0.0630.0000.0000.0000.000
191A192SER0-0.092-0.01456.684-0.002-0.0020.0000.0000.0000.000
192A193HIS10.8360.92554.381-0.082-0.0820.0000.0000.0000.000
193A194ARG10.9460.97457.664-0.060-0.0600.0000.0000.0000.000
194A195SER0-0.037-0.01655.321-0.002-0.0020.0000.0000.0000.000
195A196TYR00.0540.02549.4960.0020.0020.0000.0000.0000.000
196A197SER0-0.001-0.00149.762-0.005-0.0050.0000.0000.0000.000
197A199GLN0-0.024-0.04144.784-0.003-0.0030.0000.0000.0000.000
198A200VAL00.0420.00939.8510.0080.0080.0000.0000.0000.000
199A201THR0-0.029-0.02540.083-0.005-0.0050.0000.0000.0000.000
200A202HIS0-0.031-0.03635.3820.0060.0060.0000.0000.0000.000
201A203GLU-1-0.909-0.95935.4550.1020.1020.0000.0000.0000.000
202A204GLY0-0.001-0.01038.637-0.007-0.0070.0000.0000.0000.000
203A205SER0-0.031-0.00141.524-0.006-0.0060.0000.0000.0000.000
204A206THR00.007-0.00442.9560.0060.0060.0000.0000.0000.000
205A207VAL00.0050.03144.332-0.006-0.0060.0000.0000.0000.000
206A208GLU-1-0.808-0.89645.6420.0860.0860.0000.0000.0000.000
207A209LYS10.8780.95847.524-0.067-0.0670.0000.0000.0000.000
208A210THR00.026-0.00549.5870.0030.0030.0000.0000.0000.000
209A211VAL0-0.016-0.00451.004-0.004-0.0040.0000.0000.0000.000
210A212ALA00.0490.00853.5360.0030.0030.0000.0000.0000.000
211A213PRO00.0000.00156.474-0.002-0.0020.0000.0000.0000.000
212A214THR0-0.0210.00457.898-0.001-0.0010.0000.0000.0000.000