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: 37NML

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 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 212
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1963716.673961
FMO2-HF: Nuclear repulsion 1885145.847984
FMO2-HF: Total energy -78570.825977
FMO2-MP2: Total energy -78801.245117


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.
-1.9610.2780.018-1.086-1.1710.003
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 : -0.023 / q_NPA : -0.029
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].
3A3ALA00.0060.0043.423-1.5000.7390.018-1.086-1.1710.003
4A4LEU0-0.015-0.0135.5340.4740.4740.0000.0000.0000.000
5A5THR0-0.003-0.0148.929-0.004-0.0040.0000.0000.0000.000
6A6GLN00.006-0.02011.201-0.001-0.0010.0000.0000.0000.000
7A7PRO0-0.0140.01413.0670.0330.0330.0000.0000.0000.000
8A8ALA00.1010.04914.106-0.003-0.0030.0000.0000.0000.000
9A9SER0-0.022-0.01215.0680.0630.0630.0000.0000.0000.000
10A10VAL0-0.0180.00218.440-0.032-0.0320.0000.0000.0000.000
11A11SER0-0.031-0.01821.5640.0320.0320.0000.0000.0000.000
12A12GLY00.0590.02924.952-0.017-0.0170.0000.0000.0000.000
13A13SER0-0.036-0.01628.2330.0180.0180.0000.0000.0000.000
14A14PRO00.021-0.00531.419-0.012-0.0120.0000.0000.0000.000
15A15GLY0-0.0200.00232.7280.0020.0020.0000.0000.0000.000
16A16GLN0-0.0100.00130.681-0.007-0.0070.0000.0000.0000.000
17A17SER00.0430.01628.8020.0010.0010.0000.0000.0000.000
18A18ILE0-0.0080.01122.7110.0060.0060.0000.0000.0000.000
19A19THR00.0140.01322.514-0.006-0.0060.0000.0000.0000.000
20A20VAL0-0.0160.00316.8240.0080.0080.0000.0000.0000.000
21A21SER00.0230.01417.2440.0000.0000.0000.0000.0000.000
22A22CYS00.0070.01112.336-0.038-0.0380.0000.0000.0000.000
23A23THR0-0.0180.00014.0580.0000.0000.0000.0000.0000.000
24A24GLY00.0280.01212.465-0.189-0.1890.0000.0000.0000.000
25A25VAL0-0.036-0.01512.860-0.109-0.1090.0000.0000.0000.000
26A26SER0-0.005-0.01514.7440.0270.0270.0000.0000.0000.000
27A27SER00.0230.03615.884-0.067-0.0670.0000.0000.0000.000
28A28ILE0-0.035-0.02215.1860.0690.0690.0000.0000.0000.000
29A29VAL0-0.0190.03117.4640.0770.0770.0000.0000.0000.000
30A30GLY00.0440.02219.493-0.009-0.0090.0000.0000.0000.000
31A31SER0-0.039-0.04021.572-0.006-0.0060.0000.0000.0000.000
32A32TYR00.0030.01118.0250.0650.0650.0000.0000.0000.000
33A33ASN00.027-0.00320.157-0.059-0.0590.0000.0000.0000.000
34A34LEU00.0050.00017.8420.0450.0450.0000.0000.0000.000
35A35VAL00.0130.01315.761-0.072-0.0720.0000.0000.0000.000
36A36SER0-0.013-0.01015.9370.0930.0930.0000.0000.0000.000
37A37TRP0-0.0040.01415.698-0.099-0.0990.0000.0000.0000.000
38A38TYR0-0.029-0.03214.0260.0920.0920.0000.0000.0000.000
39A39GLN00.0070.00716.818-0.008-0.0080.0000.0000.0000.000
40A40GLN0-0.016-0.02313.944-0.020-0.0200.0000.0000.0000.000
41A41HIS00.0090.02017.8690.0230.0230.0000.0000.0000.000
42A42PRO00.027-0.01218.6390.0070.0070.0000.0000.0000.000
43A43GLY00.0120.01318.236-0.015-0.0150.0000.0000.0000.000
44A44LYS10.9270.98019.105-0.022-0.0220.0000.0000.0000.000
45A45ALA00.0240.01317.2940.0120.0120.0000.0000.0000.000
46A46PRO00.0100.00314.0810.0050.0050.0000.0000.0000.000
47A47LYS10.9490.98817.1590.1290.1290.0000.0000.0000.000
48A48LEU0-0.015-0.00518.577-0.015-0.0150.0000.0000.0000.000
49A49LEU0-0.030-0.01919.9650.0360.0360.0000.0000.0000.000
50A50THR00.019-0.01720.5190.0060.0060.0000.0000.0000.000
51A51TYR00.0410.00920.015-0.042-0.0420.0000.0000.0000.000
52A52GLU-1-0.854-0.90720.627-0.319-0.3190.0000.0000.0000.000
53A53VAL0-0.068-0.02420.5880.0300.0300.0000.0000.0000.000
54A54ASN0-0.036-0.02421.8970.0030.0030.0000.0000.0000.000
55A55LYS10.8700.94724.5590.3510.3510.0000.0000.0000.000
56A56ARG10.9160.95424.5660.1610.1610.0000.0000.0000.000
57A57PRO0-0.0180.00423.6410.0130.0130.0000.0000.0000.000
58A58SER00.0650.02626.7430.0080.0080.0000.0000.0000.000
59A59GLY00.0000.00428.811-0.001-0.0010.0000.0000.0000.000
60A60VAL0-0.112-0.04824.8630.0130.0130.0000.0000.0000.000
61A61SER00.0420.03328.012-0.004-0.0040.0000.0000.0000.000
62A62ASP-1-0.887-0.96728.459-0.145-0.1450.0000.0000.0000.000
63A63ARG10.8090.89628.3870.0870.0870.0000.0000.0000.000
64A64PHE0-0.053-0.01923.423-0.009-0.0090.0000.0000.0000.000
65A65SER00.010-0.00325.441-0.004-0.0040.0000.0000.0000.000
66A66GLY00.0220.02522.567-0.009-0.0090.0000.0000.0000.000
67A67SER0-0.008-0.01222.4770.0200.0200.0000.0000.0000.000
68A68LYS10.9150.94619.4470.5670.5670.0000.0000.0000.000
69A69SER0-0.016-0.00121.6910.0420.0420.0000.0000.0000.000
70A70GLY00.0510.03021.989-0.025-0.0250.0000.0000.0000.000
71A71ASN00.0230.00515.922-0.064-0.0640.0000.0000.0000.000
72A72SER00.013-0.00216.952-0.124-0.1240.0000.0000.0000.000
73A73ALA00.0470.02317.1350.0590.0590.0000.0000.0000.000
74A74SER0-0.061-0.04918.481-0.002-0.0020.0000.0000.0000.000
75A75LEU00.0280.03819.3290.0110.0110.0000.0000.0000.000
76A76THR0-0.022-0.02821.1960.0080.0080.0000.0000.0000.000
77A77ILE0-0.031-0.01021.8560.0020.0020.0000.0000.0000.000
78A78SER00.022-0.00525.8960.0120.0120.0000.0000.0000.000
79A79GLY00.0070.00629.6970.0040.0040.0000.0000.0000.000
80A80LEU0-0.062-0.02625.7750.0050.0050.0000.0000.0000.000
81A81GLN00.006-0.02529.0160.0030.0030.0000.0000.0000.000
82A82ALA00.0660.03528.613-0.001-0.0010.0000.0000.0000.000
83A83GLU-1-0.810-0.88827.715-0.015-0.0150.0000.0000.0000.000
84A84ASP-1-0.797-0.86424.936-0.091-0.0910.0000.0000.0000.000
85A85GLU-1-0.833-0.87723.3230.0450.0450.0000.0000.0000.000
86A86ALA0-0.022-0.01819.9910.0120.0120.0000.0000.0000.000
87A87ASP-1-0.816-0.87614.7080.1620.1620.0000.0000.0000.000
88A88TYR0-0.033-0.05116.034-0.038-0.0380.0000.0000.0000.000
89A89TYR0-0.0050.01810.0430.0070.0070.0000.0000.0000.000
90A91SER00.0560.01411.264-0.124-0.1240.0000.0000.0000.000
91A92SER0-0.027-0.01711.6650.2230.2230.0000.0000.0000.000
92A93TYR0-0.049-0.02012.268-0.138-0.1380.0000.0000.0000.000
93A94ASP-1-0.689-0.81511.202-1.553-1.5530.0000.0000.0000.000
94A95GLY0-0.010-0.04013.3440.0910.0910.0000.0000.0000.000
95A96SER0-0.146-0.08311.7410.0670.0670.0000.0000.0000.000
96A97SER00.012-0.0329.6450.0240.0240.0000.0000.0000.000
97A98THR0-0.033-0.00311.6670.0770.0770.0000.0000.0000.000
98A99SER00.0360.0399.7470.1750.1750.0000.0000.0000.000
99A100VAL0-0.023-0.01010.504-0.004-0.0040.0000.0000.0000.000
100A101VAL00.0190.0216.230-0.225-0.2250.0000.0000.0000.000
101A102PHE00.026-0.0116.7790.4650.4650.0000.0000.0000.000
102A103GLY00.0140.0186.806-0.640-0.6400.0000.0000.0000.000
103A104GLY0-0.013-0.0097.311-0.003-0.0030.0000.0000.0000.000
104A105GLY0-0.016-0.0038.2220.3830.3830.0000.0000.0000.000
105A106THR0-0.076-0.04311.6140.0080.0080.0000.0000.0000.000
106A107LYS10.8480.89615.127-0.257-0.2570.0000.0000.0000.000
107A108LEU0-0.033-0.00917.613-0.009-0.0090.0000.0000.0000.000
108A109THR0-0.029-0.02121.1450.0340.0340.0000.0000.0000.000
109A110VAL0-0.007-0.00824.199-0.020-0.0200.0000.0000.0000.000
110A111LEU00.0130.00727.3780.0170.0170.0000.0000.0000.000
111A112GLY00.033-0.00130.059-0.011-0.0110.0000.0000.0000.000
112A113GLN0-0.042-0.02629.624-0.007-0.0070.0000.0000.0000.000
113A114PRO0-0.023-0.00734.3960.0060.0060.0000.0000.0000.000
114A115LYS10.8740.93337.246-0.067-0.0670.0000.0000.0000.000
115A116ALA0-0.036-0.02338.041-0.006-0.0060.0000.0000.0000.000
116A117ALA00.0310.01238.9480.0070.0070.0000.0000.0000.000
117A118PRO0-0.0060.00639.286-0.003-0.0030.0000.0000.0000.000
118A119SER00.0300.02540.863-0.004-0.0040.0000.0000.0000.000
119A120VAL0-0.019-0.01741.9340.0050.0050.0000.0000.0000.000
120A121THR0-0.0110.00543.923-0.007-0.0070.0000.0000.0000.000
121A122LEU0-0.029-0.00544.8250.0050.0050.0000.0000.0000.000
122A123PHE0-0.027-0.01244.314-0.005-0.0050.0000.0000.0000.000
123A124PRO00.0200.00548.1370.0050.0050.0000.0000.0000.000
124A125PRO00.0260.03549.5760.0000.0000.0000.0000.0000.000
125A126SER00.005-0.00150.336-0.004-0.0040.0000.0000.0000.000
126A127SER00.052-0.00452.2110.0020.0020.0000.0000.0000.000
127A128GLU-1-0.894-0.94151.7720.0560.0560.0000.0000.0000.000
128A129GLU-1-0.750-0.83347.9290.0910.0910.0000.0000.0000.000
129A130LEU0-0.005-0.01051.2360.0020.0020.0000.0000.0000.000
130A131GLN0-0.048-0.01454.209-0.001-0.0010.0000.0000.0000.000
131A132ALA0-0.066-0.01751.0830.0000.0000.0000.0000.0000.000
132A133ASN0-0.063-0.03852.1690.0010.0010.0000.0000.0000.000
133A134LYS10.8520.91045.428-0.093-0.0930.0000.0000.0000.000
134A135ALA00.0100.00149.632-0.005-0.0050.0000.0000.0000.000
135A136THR0-0.064-0.06543.6240.0070.0070.0000.0000.0000.000
136A137LEU0-0.0280.01046.153-0.005-0.0050.0000.0000.0000.000
137A138VAL00.0300.00641.2180.0070.0070.0000.0000.0000.000
138A139CYS0-0.073-0.01442.241-0.001-0.0010.0000.0000.0000.000
139A140LEU0-0.005-0.01438.8760.0080.0080.0000.0000.0000.000
140A141ILE00.006-0.00437.942-0.006-0.0060.0000.0000.0000.000
141A142SER00.001-0.03137.5060.0060.0060.0000.0000.0000.000
142A143ASP-1-0.849-0.90837.1240.0500.0500.0000.0000.0000.000
143A144PHE00.0520.03233.846-0.004-0.0040.0000.0000.0000.000
144A145TYR00.0100.00930.0950.0060.0060.0000.0000.0000.000
145A146PRO00.0690.01431.992-0.008-0.0080.0000.0000.0000.000
146A147GLY00.0200.01030.606-0.001-0.0010.0000.0000.0000.000
147A148ALA0-0.024-0.00330.6510.0180.0180.0000.0000.0000.000
148A149VAL0-0.020-0.01332.682-0.012-0.0120.0000.0000.0000.000
149A150THR0-0.029-0.00335.2840.0140.0140.0000.0000.0000.000
150A151VAL00.0250.00637.705-0.010-0.0100.0000.0000.0000.000
151A152ALA00.0010.01240.1270.0070.0070.0000.0000.0000.000
152A153TRP00.027-0.00441.678-0.010-0.0100.0000.0000.0000.000
153A154LYS10.8000.89045.826-0.077-0.0770.0000.0000.0000.000
154A155ALA00.0510.03549.502-0.002-0.0020.0000.0000.0000.000
155A156ASP-1-0.800-0.90252.2750.0700.0700.0000.0000.0000.000
156A157SER0-0.001-0.00353.6590.0000.0000.0000.0000.0000.000
157A158SER0-0.024-0.00552.5260.0010.0010.0000.0000.0000.000
158A159PRO0-0.014-0.02247.1170.0010.0010.0000.0000.0000.000
159A160VAL00.0050.01445.877-0.001-0.0010.0000.0000.0000.000
160A161LYS10.9150.94845.034-0.115-0.1150.0000.0000.0000.000
161A162ALA00.0100.00943.3740.0070.0070.0000.0000.0000.000
162A163GLY00.0760.02942.868-0.006-0.0060.0000.0000.0000.000
163A164VAL0-0.038-0.00939.437-0.004-0.0040.0000.0000.0000.000
164A165GLU-1-0.888-0.92135.3940.2010.2010.0000.0000.0000.000
165A166THR0-0.004-0.00735.045-0.017-0.0170.0000.0000.0000.000
166A167THR0-0.0190.00631.9250.0140.0140.0000.0000.0000.000
167A168LYS10.9430.96325.439-0.283-0.2830.0000.0000.0000.000
168A169PRO00.0150.00329.960-0.004-0.0040.0000.0000.0000.000
169A170SER0-0.018-0.00428.1460.0170.0170.0000.0000.0000.000
170A171LYS10.7940.89526.588-0.058-0.0580.0000.0000.0000.000
171A172GLN00.0290.01329.2350.0070.0070.0000.0000.0000.000
172A173SER00.019-0.00631.624-0.004-0.0040.0000.0000.0000.000
173A174ASN0-0.026-0.01432.752-0.005-0.0050.0000.0000.0000.000
174A175ASN0-0.051-0.05630.0680.0010.0010.0000.0000.0000.000
175A176LYS10.9281.00432.020-0.036-0.0360.0000.0000.0000.000
176A177TYR0-0.005-0.00327.6680.0070.0070.0000.0000.0000.000
177A178ALA0-0.018-0.01232.768-0.008-0.0080.0000.0000.0000.000
178A179ALA0-0.0050.00533.0450.0120.0120.0000.0000.0000.000
179A180SER00.0100.00434.980-0.008-0.0080.0000.0000.0000.000
180A181SER00.0260.00636.6490.0090.0090.0000.0000.0000.000
181A182TYR0-0.011-0.00936.910-0.012-0.0120.0000.0000.0000.000
182A183LEU00.0020.01241.3020.0070.0070.0000.0000.0000.000
183A184SER0-0.027-0.00942.695-0.007-0.0070.0000.0000.0000.000
184A185LEU0-0.030-0.01745.2920.0020.0020.0000.0000.0000.000
185A186THR00.001-0.02348.9840.0000.0000.0000.0000.0000.000
186A187PRO00.0640.01751.865-0.001-0.0010.0000.0000.0000.000
187A188GLU-1-0.826-0.88854.6100.0770.0770.0000.0000.0000.000
188A189GLN0-0.0020.00850.389-0.001-0.0010.0000.0000.0000.000
189A190TRP00.0210.01152.706-0.001-0.0010.0000.0000.0000.000
190A191LYS10.9570.95254.321-0.061-0.0610.0000.0000.0000.000
191A192SER0-0.096-0.02356.633-0.002-0.0020.0000.0000.0000.000
192A193HIS10.8170.90454.874-0.078-0.0780.0000.0000.0000.000
193A194ARG10.9450.97057.762-0.058-0.0580.0000.0000.0000.000
194A195SER0-0.044-0.02355.169-0.002-0.0020.0000.0000.0000.000
195A196TYR00.0340.01549.6990.0010.0010.0000.0000.0000.000
196A197SER0-0.009-0.02349.808-0.004-0.0040.0000.0000.0000.000
197A199GLN0-0.047-0.05344.945-0.002-0.0020.0000.0000.0000.000
198A200VAL00.0370.00640.0300.0080.0080.0000.0000.0000.000
199A201THR00.0060.00540.595-0.009-0.0090.0000.0000.0000.000
200A202HIS0-0.013-0.02235.8410.0050.0050.0000.0000.0000.000
201A203GLU-1-0.849-0.91835.8460.0880.0880.0000.0000.0000.000
202A204GLY00.004-0.00638.982-0.006-0.0060.0000.0000.0000.000
203A205SER0-0.0280.00641.854-0.006-0.0060.0000.0000.0000.000
204A206THR0-0.035-0.03543.2350.0030.0030.0000.0000.0000.000
205A207VAL00.0030.01744.612-0.006-0.0060.0000.0000.0000.000
206A208GLU-1-0.778-0.87145.7910.0810.0810.0000.0000.0000.000
207A209LYS10.8390.92447.733-0.065-0.0650.0000.0000.0000.000
208A210THR00.0540.01649.6620.0050.0050.0000.0000.0000.000
209A211VAL0-0.0010.01350.824-0.003-0.0030.0000.0000.0000.000
210A212ALA00.0530.01253.4840.0020.0020.0000.0000.0000.000
211A213PRO0-0.0040.00156.370-0.002-0.0020.0000.0000.0000.000
212A214THR0-0.0220.00457.728-0.002-0.0020.0000.0000.0000.000