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: GYQV1

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 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 -2043157.53697
FMO2-HF: Nuclear repulsion 1964588.225249
FMO2-HF: Total energy -78569.31172
FMO2-MP2: Total energy -78799.911555


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.
-1.410.755-0.019-1.277-0.8690.005
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 : -0.023 / 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].
3B3ALA00.0170.0113.8540.0192.054-0.018-1.251-0.7670.005
4B4LEU0-0.0070.0006.5601.0251.0250.0000.0000.0000.000
5B5THR00.0240.0144.421-0.947-0.817-0.001-0.026-0.1020.000
6B6GLN00.005-0.0246.3970.2060.2060.0000.0000.0000.000
7B7PRO00.0010.0178.233-0.083-0.0830.0000.0000.0000.000
8B8ALA00.0850.0499.972-0.195-0.1950.0000.0000.0000.000
9B9SER0-0.022-0.01711.081-0.102-0.1020.0000.0000.0000.000
10B10VAL0-0.0150.00814.7040.1040.1040.0000.0000.0000.000
11B11SER00.0080.00017.536-0.052-0.0520.0000.0000.0000.000
12B12GLY00.0350.02421.2830.0370.0370.0000.0000.0000.000
13B13SER0-0.044-0.01924.395-0.023-0.0230.0000.0000.0000.000
14B14PRO00.0470.01428.1430.0050.0050.0000.0000.0000.000
15B15GLY0-0.020-0.00530.4350.0070.0070.0000.0000.0000.000
16B16GLN0-0.0090.00026.8670.0110.0110.0000.0000.0000.000
17B17SER00.0250.01126.024-0.020-0.0200.0000.0000.0000.000
18B18ILE0-0.021-0.00420.0310.0250.0250.0000.0000.0000.000
19B19THR00.0220.01118.282-0.047-0.0470.0000.0000.0000.000
20B20VAL0-0.0010.02214.2240.0510.0510.0000.0000.0000.000
21B21SER0-0.033-0.04813.984-0.032-0.0320.0000.0000.0000.000
22B22CYS0-0.049-0.00910.7910.0490.0490.0000.0000.0000.000
23B23THR0-0.029-0.0167.641-0.026-0.0260.0000.0000.0000.000
24B24GLY00.0760.0238.471-0.023-0.0230.0000.0000.0000.000
25B25VAL00.0230.0139.322-0.297-0.2970.0000.0000.0000.000
26B26SER0-0.053-0.03612.639-0.118-0.1180.0000.0000.0000.000
27B27SER0-0.084-0.0419.001-0.098-0.0980.0000.0000.0000.000
28B28ILE00.0030.02210.510-0.150-0.1500.0000.0000.0000.000
29B29VAL00.0630.02012.4170.1250.1250.0000.0000.0000.000
30B30GLY00.0090.00415.553-0.053-0.0530.0000.0000.0000.000
31B31SER00.0250.02715.1750.0120.0120.0000.0000.0000.000
32B32TYR0-0.0150.00417.4160.0300.0300.0000.0000.0000.000
33B33ASN00.016-0.00519.3780.0120.0120.0000.0000.0000.000
34B34LEU00.0080.00719.7590.0080.0080.0000.0000.0000.000
35B35VAL0-0.014-0.01616.584-0.055-0.0550.0000.0000.0000.000
36B36SER0-0.021-0.02317.7840.0470.0470.0000.0000.0000.000
37B37TRP0-0.0290.00114.225-0.060-0.0600.0000.0000.0000.000
38B38TYR00.008-0.00417.4190.0250.0250.0000.0000.0000.000
39B39GLN00.0060.01018.439-0.013-0.0130.0000.0000.0000.000
40B40GLN0-0.007-0.01018.013-0.050-0.0500.0000.0000.0000.000
41B41HIS00.0160.02420.805-0.013-0.0130.0000.0000.0000.000
42B42PRO00.0290.00222.589-0.027-0.0270.0000.0000.0000.000
43B43GLY0-0.001-0.00823.0750.0220.0220.0000.0000.0000.000
44B44LYS10.9210.97924.5370.1730.1730.0000.0000.0000.000
45B45ALA00.0230.01523.055-0.030-0.0300.0000.0000.0000.000
46B46PRO0-0.003-0.00719.4470.0290.0290.0000.0000.0000.000
47B47LYS10.9820.98921.5500.1460.1460.0000.0000.0000.000
48B48LEU0-0.023-0.01021.9510.0000.0000.0000.0000.0000.000
49B49LEU0-0.050-0.02221.1970.0250.0250.0000.0000.0000.000
50B50THR00.018-0.01321.5520.0160.0160.0000.0000.0000.000
51B51TYR00.0530.02322.066-0.035-0.0350.0000.0000.0000.000
52B52GLU-1-0.897-0.96522.992-0.072-0.0720.0000.0000.0000.000
53B53VAL0-0.0670.00320.4350.0400.0400.0000.0000.0000.000
54B54ASN0-0.006-0.04022.388-0.008-0.0080.0000.0000.0000.000
55B55LYS10.9030.99025.3790.0460.0460.0000.0000.0000.000
56B56ARG10.9140.96926.2980.0040.0040.0000.0000.0000.000
57B57PRO00.0150.01226.7980.0040.0040.0000.0000.0000.000
58B58SER00.028-0.00929.8090.0110.0110.0000.0000.0000.000
59B59GLY0-0.0090.00231.924-0.011-0.0110.0000.0000.0000.000
60B60VAL0-0.070-0.01126.7920.0030.0030.0000.0000.0000.000
61B61SER00.0770.04930.0600.0120.0120.0000.0000.0000.000
62B62ASP-1-0.921-0.98329.2910.0080.0080.0000.0000.0000.000
63B63ARG10.7920.89028.3160.0150.0150.0000.0000.0000.000
64B64PHE0-0.042-0.01123.6710.0140.0140.0000.0000.0000.000
65B65SER00.005-0.00624.5270.0000.0000.0000.0000.0000.000
66B66GLY00.0280.02521.6720.0130.0130.0000.0000.0000.000
67B67SER0-0.016-0.01120.8290.0180.0180.0000.0000.0000.000
68B68LYS10.9570.96617.099-0.155-0.1550.0000.0000.0000.000
69B69SER0-0.0160.00618.043-0.016-0.0160.0000.0000.0000.000
70B70GLY00.0630.03517.1820.0760.0760.0000.0000.0000.000
71B71ASN00.002-0.0099.683-0.380-0.3800.0000.0000.0000.000
72B72SER00.0730.03312.1470.1790.1790.0000.0000.0000.000
73B73ALA00.0010.00614.068-0.087-0.0870.0000.0000.0000.000
74B74SER00.0150.01315.3810.0860.0860.0000.0000.0000.000
75B75LEU00.0220.03517.754-0.049-0.0490.0000.0000.0000.000
76B76THR0-0.031-0.02619.7960.0350.0350.0000.0000.0000.000
77B77ILE0-0.017-0.01321.536-0.027-0.0270.0000.0000.0000.000
78B78SER00.0060.00224.6360.0170.0170.0000.0000.0000.000
79B79GLY00.0260.00128.074-0.016-0.0160.0000.0000.0000.000
80B80LEU0-0.067-0.02224.148-0.015-0.0150.0000.0000.0000.000
81B81GLN00.0240.00228.174-0.004-0.0040.0000.0000.0000.000
82B82ALA00.0540.02527.927-0.002-0.0020.0000.0000.0000.000
83B83GLU-1-0.867-0.94027.898-0.053-0.0530.0000.0000.0000.000
84B84ASP-1-0.791-0.87224.725-0.038-0.0380.0000.0000.0000.000
85B85GLU-1-0.890-0.92523.224-0.066-0.0660.0000.0000.0000.000
86B86ALA0-0.055-0.03421.533-0.020-0.0200.0000.0000.0000.000
87B87ASP-1-0.896-0.93616.208-0.324-0.3240.0000.0000.0000.000
88B88TYR0-0.043-0.06316.3520.0020.0020.0000.0000.0000.000
89B89TYR0-0.0170.00812.138-0.022-0.0220.0000.0000.0000.000
90B91SER0-0.017-0.01013.070-0.169-0.1690.0000.0000.0000.000
91B92SER00.016-0.01913.7240.1920.1920.0000.0000.0000.000
92B93TYR0-0.0140.01815.469-0.136-0.1360.0000.0000.0000.000
93B94ASP-1-0.779-0.89113.002-0.943-0.9430.0000.0000.0000.000
94B95GLY0-0.017-0.01815.617-0.003-0.0030.0000.0000.0000.000
95B96SER0-0.101-0.06513.9240.0010.0010.0000.0000.0000.000
96B97SER00.0380.01514.7870.0270.0270.0000.0000.0000.000
97B98THR0-0.072-0.01817.3070.0480.0480.0000.0000.0000.000
98B99SER0-0.006-0.00616.2750.0330.0330.0000.0000.0000.000
99B100VAL0-0.045-0.01015.5230.0130.0130.0000.0000.0000.000
100B101VAL00.0000.00810.830-0.116-0.1160.0000.0000.0000.000
101B102PHE00.008-0.02611.2120.2380.2380.0000.0000.0000.000
102B103GLY00.0090.0008.509-0.347-0.3470.0000.0000.0000.000
103B104GLY0-0.035-0.0287.621-0.071-0.0710.0000.0000.0000.000
104B105GLY00.0050.0108.3880.0720.0720.0000.0000.0000.000
105B106THR0-0.084-0.04011.0880.0540.0540.0000.0000.0000.000
106B107LYS10.9710.97713.5440.2670.2670.0000.0000.0000.000
107B108LEU0-0.055-0.02316.4530.0650.0650.0000.0000.0000.000
108B109THR0-0.004-0.01019.250-0.022-0.0220.0000.0000.0000.000
109B110VAL0-0.017-0.00322.2230.0330.0330.0000.0000.0000.000
110B111LEU0-0.073-0.05224.366-0.009-0.0090.0000.0000.0000.000
111B112GLY00.0590.02027.2070.0000.0000.0000.0000.0000.000
112B113GLN0-0.064-0.02829.6830.0010.0010.0000.0000.0000.000
113B114PRO00.002-0.00329.3700.0060.0060.0000.0000.0000.000
114B115LYS10.8720.93722.005-0.206-0.2060.0000.0000.0000.000
115B116ALA0-0.028-0.01626.5540.0050.0050.0000.0000.0000.000
116B117ALA00.0480.02725.228-0.008-0.0080.0000.0000.0000.000
117B118PRO0-0.034-0.00923.317-0.011-0.0110.0000.0000.0000.000
118B119SER00.0200.01726.3060.0160.0160.0000.0000.0000.000
119B120VAL0-0.002-0.01325.058-0.015-0.0150.0000.0000.0000.000
120B121THR0-0.038-0.01828.1220.0140.0140.0000.0000.0000.000
121B122LEU0-0.034-0.01727.177-0.012-0.0120.0000.0000.0000.000
122B123PHE0-0.017-0.00930.0910.0090.0090.0000.0000.0000.000
123B124PRO0-0.0010.00231.337-0.008-0.0080.0000.0000.0000.000
124B125PRO00.0450.02331.930-0.002-0.0020.0000.0000.0000.000
125B126SER00.0180.01934.2540.0070.0070.0000.0000.0000.000
126B127SER00.051-0.00137.617-0.003-0.0030.0000.0000.0000.000
127B128GLU-1-0.960-0.96540.263-0.076-0.0760.0000.0000.0000.000
128B129GLU-1-0.802-0.89933.100-0.106-0.1060.0000.0000.0000.000
129B130LEU0-0.008-0.00835.502-0.002-0.0020.0000.0000.0000.000
130B131GLN0-0.036-0.00338.3020.0000.0000.0000.0000.0000.000
131B132ALA0-0.041-0.01838.5510.0000.0000.0000.0000.0000.000
132B133ASN0-0.037-0.02936.237-0.001-0.0010.0000.0000.0000.000
133B134LYS10.9160.94332.2570.1130.1130.0000.0000.0000.000
134B135ALA00.0190.00431.5780.0110.0110.0000.0000.0000.000
135B136THR0-0.043-0.02128.066-0.016-0.0160.0000.0000.0000.000
136B137LEU0-0.0330.00927.5990.0130.0130.0000.0000.0000.000
137B138VAL00.013-0.00527.513-0.017-0.0170.0000.0000.0000.000
138B139CYS0-0.080-0.01622.8010.0060.0060.0000.0000.0000.000
139B140LEU00.0030.00025.896-0.017-0.0170.0000.0000.0000.000
140B141ILE0-0.014-0.01322.5180.0200.0200.0000.0000.0000.000
141B142SER00.018-0.00326.379-0.014-0.0140.0000.0000.0000.000
142B143ASP-1-0.785-0.91928.542-0.002-0.0020.0000.0000.0000.000
143B144PHE0-0.0120.01621.6850.0110.0110.0000.0000.0000.000
144B145TYR00.0340.00024.803-0.019-0.0190.0000.0000.0000.000
145B146PRO00.0680.02120.8890.0180.0180.0000.0000.0000.000
146B147GLY00.0270.01822.0940.0080.0080.0000.0000.0000.000
147B148ALA0-0.063-0.03616.610-0.048-0.0480.0000.0000.0000.000
148B149VAL00.0130.00917.7010.0490.0490.0000.0000.0000.000
149B150THR0-0.024-0.00212.820-0.065-0.0650.0000.0000.0000.000
150B151VAL00.0150.01115.9540.0530.0530.0000.0000.0000.000
151B152ALA00.0110.00316.012-0.045-0.0450.0000.0000.0000.000
152B153TRP00.032-0.00317.7230.0390.0390.0000.0000.0000.000
153B154LYS10.8820.94319.355-0.110-0.1100.0000.0000.0000.000
154B155ALA00.0620.05922.1310.0020.0020.0000.0000.0000.000
155B156ASP-1-0.793-0.89625.1620.0330.0330.0000.0000.0000.000
156B157SER0-0.058-0.05523.8630.0140.0140.0000.0000.0000.000
157B158SER0-0.001-0.00321.3610.0380.0380.0000.0000.0000.000
158B159PRO0-0.020-0.02116.934-0.024-0.0240.0000.0000.0000.000
159B160VAL00.0100.02218.851-0.016-0.0160.0000.0000.0000.000
160B161LYS10.9480.97213.1120.4460.4460.0000.0000.0000.000
161B162ALA0-0.018-0.02817.293-0.023-0.0230.0000.0000.0000.000
162B163GLY00.0790.03919.8240.0310.0310.0000.0000.0000.000
163B164VAL0-0.0420.00118.3780.0270.0270.0000.0000.0000.000
164B165GLU-1-0.890-0.92919.299-0.434-0.4340.0000.0000.0000.000
165B166THR0-0.003-0.01918.7020.0640.0640.0000.0000.0000.000
166B167THR0-0.0130.01619.938-0.034-0.0340.0000.0000.0000.000
167B168LYS10.9530.96318.7260.4300.4300.0000.0000.0000.000
168B169PRO0-0.0010.00119.6440.0190.0190.0000.0000.0000.000
169B170SER00.0060.01222.618-0.012-0.0120.0000.0000.0000.000
170B171LYS10.9340.97525.9770.1060.1060.0000.0000.0000.000
171B172GLN00.013-0.01028.273-0.004-0.0040.0000.0000.0000.000
172B173SER00.0540.01131.4440.0000.0000.0000.0000.0000.000
173B174ASN0-0.0410.01332.395-0.005-0.0050.0000.0000.0000.000
174B175ASN0-0.043-0.05031.5160.0060.0060.0000.0000.0000.000
175B176LYS10.8820.99628.526-0.014-0.0140.0000.0000.0000.000
176B177TYR0-0.027-0.01524.586-0.021-0.0210.0000.0000.0000.000
177B178ALA00.0310.00326.5950.0170.0170.0000.0000.0000.000
178B179ALA0-0.057-0.01723.009-0.025-0.0250.0000.0000.0000.000
179B180SER00.0300.01824.7410.0210.0210.0000.0000.0000.000
180B181SER0-0.0050.01920.977-0.019-0.0190.0000.0000.0000.000
181B182TYR00.0320.00023.2540.0270.0270.0000.0000.0000.000
182B183LEU00.0050.01822.546-0.023-0.0230.0000.0000.0000.000
183B184SER0-0.021-0.01924.6490.0200.0200.0000.0000.0000.000
184B185LEU0-0.079-0.03625.847-0.013-0.0130.0000.0000.0000.000
185B186THR00.0610.02928.0840.0070.0070.0000.0000.0000.000
186B187PRO00.0470.02131.3490.0070.0070.0000.0000.0000.000
187B188GLU-1-0.854-0.93333.223-0.076-0.0760.0000.0000.0000.000
188B189GLN00.0150.02227.0000.0070.0070.0000.0000.0000.000
189B190TRP00.0220.01630.6320.0110.0110.0000.0000.0000.000
190B191LYS10.9060.93931.9920.0500.0500.0000.0000.0000.000
191B192SER0-0.062-0.04631.1120.0060.0060.0000.0000.0000.000
192B193HIS0-0.088-0.01226.585-0.006-0.0060.0000.0000.0000.000
193B194ARG10.9670.97031.347-0.045-0.0450.0000.0000.0000.000
194B195SER0-0.059-0.03529.3950.0000.0000.0000.0000.0000.000
195B196TYR00.0330.01625.937-0.006-0.0060.0000.0000.0000.000
196B197SER0-0.015-0.01224.0420.0100.0100.0000.0000.0000.000
197B199GLN0-0.021-0.04519.2480.0090.0090.0000.0000.0000.000
198B200VAL00.0280.00719.361-0.016-0.0160.0000.0000.0000.000
199B201THR0-0.018-0.00615.9950.0590.0590.0000.0000.0000.000
200B202HIS0-0.042-0.05118.228-0.020-0.0200.0000.0000.0000.000
201B203GLU-1-0.829-0.91618.8850.1900.1900.0000.0000.0000.000
202B204GLY0-0.0150.00217.6270.0200.0200.0000.0000.0000.000
203B205SER0-0.0110.00018.6200.0290.0290.0000.0000.0000.000
204B206THR0-0.021-0.01218.673-0.048-0.0480.0000.0000.0000.000
205B207VAL00.0110.02320.7420.0040.0040.0000.0000.0000.000
206B208GLU-1-0.850-0.92823.0930.1160.1160.0000.0000.0000.000
207B209LYS10.8700.95624.930-0.049-0.0490.0000.0000.0000.000
208B210THR00.0120.00726.684-0.006-0.0060.0000.0000.0000.000
209B211VAL0-0.005-0.00329.003-0.001-0.0010.0000.0000.0000.000
210B212ALA00.0480.00131.1640.0010.0010.0000.0000.0000.000
211B213PRO0-0.0080.00632.989-0.003-0.0030.0000.0000.0000.000
212B214THR0-0.047-0.01035.8950.0050.0050.0000.0000.0000.000