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: 8NJQY

Calculation Name: 1LGV-B-Xray372

Preferred Name:

Target Type:

Ligand Name: pyroglutamic acid

ligand 3-letter code: PCA

PDB ID: 1LGV

Chain ID: B

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 -2043134.038712
FMO2-HF: Nuclear repulsion 1964563.641828
FMO2-HF: Total energy -78570.396884
FMO2-MP2: Total energy -78800.845473


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(B:1:PCA)


Summations of interaction energy for fragment #1(B: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.
-1.4810.775-0.017-1.313-0.9250.005
Interaction energy analysis for fragmet #1(B:1:PCA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.030 / q_NPA : -0.020
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].
3B3ALA00.0160.0093.8540.0042.002-0.018-1.233-0.7460.005
4B4LEU0-0.007-0.0026.6880.9850.9850.0000.0000.0000.000
5B5THR00.0150.0093.923-1.236-0.9780.001-0.080-0.1790.000
6B6GLN00.012-0.0196.0210.2090.2090.0000.0000.0000.000
7B7PRO00.0170.0218.039-0.076-0.0760.0000.0000.0000.000
8B8ALA00.0790.0519.919-0.179-0.1790.0000.0000.0000.000
9B9SER0-0.010-0.00811.018-0.096-0.0960.0000.0000.0000.000
10B10VAL0-0.028-0.00314.6250.0960.0960.0000.0000.0000.000
11B11SER00.0160.00317.428-0.043-0.0430.0000.0000.0000.000
12B12GLY00.0200.02021.1780.0350.0350.0000.0000.0000.000
13B13SER0-0.025-0.01624.259-0.021-0.0210.0000.0000.0000.000
14B14PRO00.0320.01028.0070.0030.0030.0000.0000.0000.000
15B15GLY0-0.020-0.00430.2560.0070.0070.0000.0000.0000.000
16B16GLN0-0.0140.00227.2060.0080.0080.0000.0000.0000.000
17B17SER00.0230.00525.929-0.019-0.0190.0000.0000.0000.000
18B18ILE0-0.020-0.00119.9190.0240.0240.0000.0000.0000.000
19B19THR00.0160.01018.199-0.043-0.0430.0000.0000.0000.000
20B20VAL00.0030.02714.0140.0470.0470.0000.0000.0000.000
21B21SER0-0.025-0.03713.634-0.029-0.0290.0000.0000.0000.000
22B22CYS0-0.0460.00510.4320.0280.0280.0000.0000.0000.000
23B23THR0-0.027-0.0198.0030.0220.0220.0000.0000.0000.000
24B24GLY00.0840.0318.523-0.037-0.0370.0000.0000.0000.000
25B25VAL00.0230.0119.450-0.287-0.2870.0000.0000.0000.000
26B26SER0-0.054-0.02912.771-0.097-0.0970.0000.0000.0000.000
27B27SER0-0.076-0.0349.067-0.090-0.0900.0000.0000.0000.000
28B28ILE0-0.0020.02110.518-0.152-0.1520.0000.0000.0000.000
29B29VAL00.0560.01812.5230.1270.1270.0000.0000.0000.000
30B30GLY00.0160.00815.643-0.049-0.0490.0000.0000.0000.000
31B31SER00.0150.02015.2610.0160.0160.0000.0000.0000.000
32B32TYR0-0.0100.00017.5370.0300.0300.0000.0000.0000.000
33B33ASN0-0.012-0.01319.5060.0140.0140.0000.0000.0000.000
34B34LEU00.0000.00619.9160.0110.0110.0000.0000.0000.000
35B35VAL0-0.011-0.02015.929-0.053-0.0530.0000.0000.0000.000
36B36SER0-0.020-0.01817.5330.0510.0510.0000.0000.0000.000
37B37TRP0-0.0230.00313.721-0.062-0.0620.0000.0000.0000.000
38B38TYR00.014-0.00117.6170.0230.0230.0000.0000.0000.000
39B39GLN00.0130.01718.235-0.008-0.0080.0000.0000.0000.000
40B40GLN0-0.015-0.02218.435-0.049-0.0490.0000.0000.0000.000
41B41HIS00.0040.01520.891-0.009-0.0090.0000.0000.0000.000
42B42PRO00.041-0.00122.630-0.024-0.0240.0000.0000.0000.000
43B43GLY0-0.002-0.00223.1170.0200.0200.0000.0000.0000.000
44B44LYS10.9200.98524.6120.1590.1590.0000.0000.0000.000
45B45ALA00.0280.02123.145-0.029-0.0290.0000.0000.0000.000
46B46PRO0-0.005-0.01019.4060.0290.0290.0000.0000.0000.000
47B47LYS10.9670.98821.6650.1360.1360.0000.0000.0000.000
48B48LEU0-0.023-0.00521.9180.0000.0000.0000.0000.0000.000
49B49LEU0-0.044-0.02121.3120.0240.0240.0000.0000.0000.000
50B50THR00.004-0.02121.5460.0180.0180.0000.0000.0000.000
51B51TYR00.0450.01921.741-0.034-0.0340.0000.0000.0000.000
52B52GLU-1-0.819-0.91522.698-0.068-0.0680.0000.0000.0000.000
53B53VAL0-0.055-0.00220.0510.0380.0380.0000.0000.0000.000
54B54ASN0-0.018-0.04121.966-0.004-0.0040.0000.0000.0000.000
55B55LYS10.8560.96124.9680.0720.0720.0000.0000.0000.000
56B56ARG10.9230.97025.8890.0110.0110.0000.0000.0000.000
57B57PRO00.0160.01026.4340.0040.0040.0000.0000.0000.000
58B58SER00.024-0.00829.5910.0110.0110.0000.0000.0000.000
59B59GLY0-0.0080.00231.777-0.010-0.0100.0000.0000.0000.000
60B60VAL0-0.083-0.01826.3660.0030.0030.0000.0000.0000.000
61B61SER00.0730.04129.7050.0110.0110.0000.0000.0000.000
62B62ASP-1-0.914-0.97228.9430.0010.0010.0000.0000.0000.000
63B63ARG10.7910.87727.6290.0130.0130.0000.0000.0000.000
64B64PHE0-0.057-0.02023.2910.0140.0140.0000.0000.0000.000
65B65SER00.010-0.00124.1740.0000.0000.0000.0000.0000.000
66B66GLY00.0200.02221.2930.0120.0120.0000.0000.0000.000
67B67SER0-0.008-0.00920.4460.0170.0170.0000.0000.0000.000
68B68LYS10.9400.95816.979-0.091-0.0910.0000.0000.0000.000
69B69SER00.0210.01918.120-0.032-0.0320.0000.0000.0000.000
70B70GLY00.0140.01217.2590.0740.0740.0000.0000.0000.000
71B71ASN00.024-0.0039.732-0.325-0.3250.0000.0000.0000.000
72B72SER00.0520.01912.2090.1570.1570.0000.0000.0000.000
73B73ALA00.0060.01114.149-0.079-0.0790.0000.0000.0000.000
74B74SER00.0140.00615.0110.0760.0760.0000.0000.0000.000
75B75LEU00.0200.03317.397-0.046-0.0460.0000.0000.0000.000
76B76THR0-0.030-0.03419.4780.0340.0340.0000.0000.0000.000
77B77ILE0-0.020-0.01121.132-0.026-0.0260.0000.0000.0000.000
78B78SER00.0170.00524.3460.0170.0170.0000.0000.0000.000
79B79GLY00.0260.00927.797-0.016-0.0160.0000.0000.0000.000
80B80LEU0-0.062-0.01724.012-0.014-0.0140.0000.0000.0000.000
81B81GLN00.0510.01927.9480.0040.0040.0000.0000.0000.000
82B82ALA00.0550.02227.722-0.002-0.0020.0000.0000.0000.000
83B83GLU-1-0.894-0.95527.717-0.046-0.0460.0000.0000.0000.000
84B84ASP-1-0.771-0.85324.484-0.036-0.0360.0000.0000.0000.000
85B85GLU-1-0.815-0.86322.796-0.049-0.0490.0000.0000.0000.000
86B86ALA0-0.055-0.03821.353-0.020-0.0200.0000.0000.0000.000
87B87ASP-1-0.810-0.87316.331-0.285-0.2850.0000.0000.0000.000
88B88TYR0-0.020-0.05116.105-0.001-0.0010.0000.0000.0000.000
89B89TYR0-0.0090.00712.339-0.015-0.0150.0000.0000.0000.000
90B91SER0-0.008-0.01313.012-0.156-0.1560.0000.0000.0000.000
91B92SER00.007-0.01413.8520.1840.1840.0000.0000.0000.000
92B93TYR0-0.0180.01215.539-0.129-0.1290.0000.0000.0000.000
93B94ASP-1-0.750-0.85313.726-0.918-0.9180.0000.0000.0000.000
94B95GLY0-0.025-0.01315.726-0.001-0.0010.0000.0000.0000.000
95B96SER0-0.106-0.07614.0870.0000.0000.0000.0000.0000.000
96B97SER00.023-0.01614.9200.0240.0240.0000.0000.0000.000
97B98THR0-0.071-0.02317.3070.0510.0510.0000.0000.0000.000
98B99SER0-0.007-0.00216.3790.0430.0430.0000.0000.0000.000
99B100VAL0-0.050-0.01615.8030.0080.0080.0000.0000.0000.000
100B101VAL00.0160.01910.934-0.112-0.1120.0000.0000.0000.000
101B102PHE00.002-0.03211.3470.2240.2240.0000.0000.0000.000
102B103GLY00.0180.0058.469-0.335-0.3350.0000.0000.0000.000
103B104GLY0-0.035-0.0277.623-0.064-0.0640.0000.0000.0000.000
104B105GLY0-0.002-0.0028.5190.0770.0770.0000.0000.0000.000
105B106THR0-0.088-0.04610.9010.0490.0490.0000.0000.0000.000
106B107LYS10.8580.89813.3490.2610.2610.0000.0000.0000.000
107B108LEU0-0.064-0.02816.3200.0620.0620.0000.0000.0000.000
108B109THR0-0.045-0.04319.092-0.021-0.0210.0000.0000.0000.000
109B110VAL0-0.040-0.02222.1100.0300.0300.0000.0000.0000.000
110B111LEU0-0.059-0.04724.420-0.009-0.0090.0000.0000.0000.000
111B112GLY00.0570.01827.119-0.001-0.0010.0000.0000.0000.000
112B113GLN0-0.077-0.03229.6320.0010.0010.0000.0000.0000.000
113B114PRO00.0150.00429.3450.0060.0060.0000.0000.0000.000
114B115LYS10.8420.92121.620-0.192-0.1920.0000.0000.0000.000
115B116ALA0-0.034-0.01826.6140.0040.0040.0000.0000.0000.000
116B117ALA00.0550.03025.205-0.007-0.0070.0000.0000.0000.000
117B118PRO0-0.020-0.00122.994-0.011-0.0110.0000.0000.0000.000
118B119SER0-0.011-0.00226.2030.0130.0130.0000.0000.0000.000
119B120VAL0-0.012-0.01624.771-0.012-0.0120.0000.0000.0000.000
120B121THR0-0.030-0.01327.9090.0130.0130.0000.0000.0000.000
121B122LEU0-0.041-0.01927.023-0.010-0.0100.0000.0000.0000.000
122B123PHE0-0.004-0.00329.9880.0070.0070.0000.0000.0000.000
123B124PRO00.0110.01031.309-0.006-0.0060.0000.0000.0000.000
124B125PRO00.0370.02132.050-0.003-0.0030.0000.0000.0000.000
125B126SER00.0010.01134.2780.0070.0070.0000.0000.0000.000
126B127SER00.039-0.00437.652-0.003-0.0030.0000.0000.0000.000
127B128GLU-1-0.933-0.95740.350-0.061-0.0610.0000.0000.0000.000
128B129GLU-1-0.763-0.85732.941-0.089-0.0890.0000.0000.0000.000
129B130LEU00.0010.00035.574-0.002-0.0020.0000.0000.0000.000
130B131GLN0-0.038-0.00738.3410.0010.0010.0000.0000.0000.000
131B132ALA0-0.036-0.01538.746-0.001-0.0010.0000.0000.0000.000
132B133ASN0-0.086-0.05135.959-0.002-0.0020.0000.0000.0000.000
133B134LYS10.8830.91632.1240.0960.0960.0000.0000.0000.000
134B135ALA00.004-0.00432.0230.0100.0100.0000.0000.0000.000
135B136THR0-0.036-0.03128.044-0.013-0.0130.0000.0000.0000.000
136B137LEU0-0.0270.01427.5730.0110.0110.0000.0000.0000.000
137B138VAL00.011-0.00927.563-0.014-0.0140.0000.0000.0000.000
138B139CYS0-0.062-0.01522.7270.0080.0080.0000.0000.0000.000
139B140LEU00.0140.00525.758-0.015-0.0150.0000.0000.0000.000
140B141ILE0-0.010-0.00522.0470.0200.0200.0000.0000.0000.000
141B142SER00.0590.01226.221-0.016-0.0160.0000.0000.0000.000
142B143ASP-1-0.764-0.84828.5210.0150.0150.0000.0000.0000.000
143B144PHE00.0070.02321.6800.0110.0110.0000.0000.0000.000
144B145TYR00.0260.00124.836-0.018-0.0180.0000.0000.0000.000
145B146PRO00.0730.02120.8890.0170.0170.0000.0000.0000.000
146B147GLY00.0180.01022.1380.0090.0090.0000.0000.0000.000
147B148ALA0-0.053-0.02816.670-0.042-0.0420.0000.0000.0000.000
148B149VAL00.0010.00017.8120.0450.0450.0000.0000.0000.000
149B150THR00.0020.00712.514-0.044-0.0440.0000.0000.0000.000
150B151VAL0-0.021-0.00615.7320.0460.0460.0000.0000.0000.000
151B152ALA00.0130.00715.867-0.036-0.0360.0000.0000.0000.000
152B153TRP00.0350.00917.6680.0310.0310.0000.0000.0000.000
153B154LYS10.8130.89619.730-0.130-0.1300.0000.0000.0000.000
154B155ALA00.0550.05522.1970.0000.0000.0000.0000.0000.000
155B156ASP-1-0.766-0.87625.2790.0510.0510.0000.0000.0000.000
156B157SER0-0.051-0.04423.9650.0120.0120.0000.0000.0000.000
157B158SER0-0.009-0.00321.5370.0380.0380.0000.0000.0000.000
158B159PRO0-0.007-0.01017.025-0.022-0.0220.0000.0000.0000.000
159B160VAL0-0.0030.01418.918-0.018-0.0180.0000.0000.0000.000
160B161LYS10.9430.96812.6920.3610.3610.0000.0000.0000.000
161B162ALA0-0.008-0.02217.296-0.022-0.0220.0000.0000.0000.000
162B163GLY00.0860.04119.8650.0280.0280.0000.0000.0000.000
163B164VAL0-0.0410.00218.4570.0230.0230.0000.0000.0000.000
164B165GLU-1-0.888-0.93119.391-0.373-0.3730.0000.0000.0000.000
165B166THR0-0.012-0.01118.6380.0570.0570.0000.0000.0000.000
166B167THR0-0.0190.01619.822-0.029-0.0290.0000.0000.0000.000
167B168LYS10.9580.96518.1120.3970.3970.0000.0000.0000.000
168B169PRO00.0020.00419.6100.0150.0150.0000.0000.0000.000
169B170SER00.0120.01222.579-0.014-0.0140.0000.0000.0000.000
170B171LYS10.8860.94425.9460.0840.0840.0000.0000.0000.000
171B172GLN0-0.016-0.04528.285-0.006-0.0060.0000.0000.0000.000
172B173SER00.0350.00931.5020.0000.0000.0000.0000.0000.000
173B174ASN0-0.026-0.02132.581-0.004-0.0040.0000.0000.0000.000
174B175ASN00.002-0.02031.4730.0010.0010.0000.0000.0000.000
175B176LYS10.8480.96828.559-0.023-0.0230.0000.0000.0000.000
176B177TYR0-0.024-0.00624.612-0.019-0.0190.0000.0000.0000.000
177B178ALA00.000-0.00526.6480.0160.0160.0000.0000.0000.000
178B179ALA0-0.040-0.01022.904-0.022-0.0220.0000.0000.0000.000
179B180SER00.0080.00524.6740.0200.0200.0000.0000.0000.000
180B181SER00.008-0.00620.704-0.018-0.0180.0000.0000.0000.000
181B182TYR00.0180.00023.3120.0280.0280.0000.0000.0000.000
182B183LEU00.0020.01422.184-0.019-0.0190.0000.0000.0000.000
183B184SER0-0.033-0.02524.6890.0110.0110.0000.0000.0000.000
184B185LEU0-0.065-0.02925.898-0.010-0.0100.0000.0000.0000.000
185B186THR00.021-0.02228.1190.0050.0050.0000.0000.0000.000
186B187PRO00.0320.01631.3820.0080.0080.0000.0000.0000.000
187B188GLU-1-0.802-0.88833.344-0.063-0.0630.0000.0000.0000.000
188B189GLN00.0550.04826.1490.0030.0030.0000.0000.0000.000
189B190TRP00.0220.01130.6000.0110.0110.0000.0000.0000.000
190B191LYS10.9050.94531.9750.0370.0370.0000.0000.0000.000
191B192SER0-0.063-0.05031.0950.0060.0060.0000.0000.0000.000
192B193HIS0-0.088-0.01126.684-0.005-0.0050.0000.0000.0000.000
193B194ARG10.9490.96131.445-0.058-0.0580.0000.0000.0000.000
194B195SER0-0.078-0.04829.6560.0050.0050.0000.0000.0000.000
195B196TYR00.016-0.00325.751-0.004-0.0040.0000.0000.0000.000
196B197SER0-0.0010.00924.4420.0110.0110.0000.0000.0000.000
197B199GLN0-0.025-0.04119.1330.0140.0140.0000.0000.0000.000
198B200VAL00.0260.00519.207-0.011-0.0110.0000.0000.0000.000
199B201THR0-0.028-0.02715.7550.0330.0330.0000.0000.0000.000
200B202HIS0-0.026-0.03918.062-0.018-0.0180.0000.0000.0000.000
201B203GLU-1-0.793-0.90118.9420.2090.2090.0000.0000.0000.000
202B204GLY0-0.0010.01117.4420.0160.0160.0000.0000.0000.000
203B205SER0-0.0050.00718.4550.0290.0290.0000.0000.0000.000
204B206THR00.004-0.00118.401-0.033-0.0330.0000.0000.0000.000
205B207VAL0-0.0190.01620.4810.0040.0040.0000.0000.0000.000
206B208GLU-1-0.790-0.89722.9000.1360.1360.0000.0000.0000.000
207B209LYS10.8680.95524.776-0.067-0.0670.0000.0000.0000.000
208B210THR00.0430.00326.605-0.007-0.0070.0000.0000.0000.000
209B211VAL0-0.0150.00028.950-0.002-0.0020.0000.0000.0000.000
210B212ALA00.0380.00231.1830.0020.0020.0000.0000.0000.000
211B213PRO0-0.0070.01133.079-0.003-0.0030.0000.0000.0000.000
212B214THR0-0.045-0.00935.961-0.001-0.0010.0000.0000.0000.000