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: V5ZL1

Calculation Name: 3LRS-H-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3LRS

Chain ID: H

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-06-26

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 221
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2245788.692164
FMO2-HF: Nuclear repulsion 2160739.886373
FMO2-HF: Total energy -85048.805791
FMO2-MP2: Total energy -85294.550723


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(H:1:GLN)


Summations of interaction energy for fragment #1(H:1:GLN)
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.
1.3513.8270.032-1.014-1.4930.004
Interaction energy analysis for fragmet #1(H:1:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.014 / q_NPA : -0.001
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].
3H3GLN00.0130.0123.8070.8192.679-0.016-0.793-1.0510.004
4H4LEU0-0.036-0.0296.221-0.020-0.0200.0000.0000.0000.000
5H5VAL00.0120.0079.6800.2240.2240.0000.0000.0000.000
6H6GLU-1-0.777-0.88212.117-0.039-0.0390.0000.0000.0000.000
7H7SER0-0.041-0.02615.8360.0240.0240.0000.0000.0000.000
8H8GLY00.0300.00418.393-0.013-0.0130.0000.0000.0000.000
9H9GLY0-0.036-0.00821.7770.0080.0080.0000.0000.0000.000
10H10GLY00.0160.01223.765-0.006-0.0060.0000.0000.0000.000
11H11VAL0-0.028-0.02926.5830.0040.0040.0000.0000.0000.000
12H12VAL00.0080.00729.457-0.008-0.0080.0000.0000.0000.000
13H13GLN00.0300.01332.0010.0060.0060.0000.0000.0000.000
14H14PRO00.0510.01935.314-0.004-0.0040.0000.0000.0000.000
15H15GLY0-0.046-0.01437.066-0.002-0.0020.0000.0000.0000.000
16H16GLY0-0.009-0.00135.145-0.004-0.0040.0000.0000.0000.000
17H17SER0-0.036-0.02831.9070.0020.0020.0000.0000.0000.000
18H18LEU00.0160.00426.1610.0020.0020.0000.0000.0000.000
19H19ARG10.9120.96522.1080.1400.1400.0000.0000.0000.000
20H20LEU0-0.0030.02121.025-0.003-0.0030.0000.0000.0000.000
21H21SER00.001-0.02818.306-0.011-0.0110.0000.0000.0000.000
22H22CYS0-0.053-0.01113.986-0.040-0.0400.0000.0000.0000.000
23H23LEU00.0020.02210.450-0.002-0.0020.0000.0000.0000.000
24H24ALA00.0360.0119.552-0.083-0.0830.0000.0000.0000.000
25H25SER0-0.028-0.0225.713-0.138-0.1380.0000.0000.0000.000
26H26GLY00.0490.0213.153-1.087-0.7980.046-0.161-0.1740.000
27H27PHE00.0190.0063.7200.7321.0590.002-0.060-0.2680.000
28H28THR0-0.036-0.0206.7800.1050.1050.0000.0000.0000.000
29H29PHE00.0690.04110.5190.1100.1100.0000.0000.0000.000
30H30HIS00.006-0.01212.2160.0380.0380.0000.0000.0000.000
31H31LYS10.9080.97513.1070.4350.4350.0000.0000.0000.000
32H32TYR00.0240.02110.550-0.017-0.0170.0000.0000.0000.000
33H33GLY00.0410.03214.994-0.016-0.0160.0000.0000.0000.000
34H34MET0-0.057-0.02012.629-0.047-0.0470.0000.0000.0000.000
35H35HIS00.038-0.02316.8160.0200.0200.0000.0000.0000.000
36H36TRP0-0.039-0.02017.764-0.019-0.0190.0000.0000.0000.000
37H37VAL00.000-0.00518.9740.0100.0100.0000.0000.0000.000
38H38ARG10.8090.89320.702-0.049-0.0490.0000.0000.0000.000
39H39GLN0-0.003-0.01521.7860.0280.0280.0000.0000.0000.000
40H40ALA00.0320.02524.4070.0000.0000.0000.0000.0000.000
41H41PRO00.023-0.01126.8730.0170.0170.0000.0000.0000.000
42H42GLY00.0030.00626.858-0.008-0.0080.0000.0000.0000.000
43H43LYS10.9000.96427.663-0.113-0.1130.0000.0000.0000.000
44H44GLY00.0410.02325.8730.0180.0180.0000.0000.0000.000
45H45LEU0-0.0070.00219.586-0.011-0.0110.0000.0000.0000.000
46H46GLU-1-0.793-0.87323.5580.0550.0550.0000.0000.0000.000
47H47TRP0-0.002-0.00221.807-0.002-0.0020.0000.0000.0000.000
48H48VAL0-0.027-0.01123.335-0.005-0.0050.0000.0000.0000.000
49H49ALA00.009-0.01123.174-0.008-0.0080.0000.0000.0000.000
50H50LEU00.0010.03019.916-0.002-0.0020.0000.0000.0000.000
51H51ILE0-0.059-0.02219.8500.0020.0020.0000.0000.0000.000
52H52SER0-0.002-0.01320.035-0.011-0.0110.0000.0000.0000.000
53H52ASP-1-0.839-0.91417.899-0.200-0.2000.0000.0000.0000.000
54H53ASP-1-0.747-0.85618.852-0.178-0.1780.0000.0000.0000.000
55H54GLY0-0.042-0.02821.6280.0040.0040.0000.0000.0000.000
56H55MET0-0.068-0.03222.9440.0160.0160.0000.0000.0000.000
57H56ARG10.8390.91123.2460.1370.1370.0000.0000.0000.000
58H57LYS10.8790.93924.7170.0940.0940.0000.0000.0000.000
59H58TYR00.0230.01525.0140.0050.0050.0000.0000.0000.000
60H59HIS00.034-0.00126.163-0.012-0.0120.0000.0000.0000.000
61H60SER00.0450.03127.9000.0030.0030.0000.0000.0000.000
62H61ASP-1-0.863-0.93729.5140.0020.0020.0000.0000.0000.000
63H62SER0-0.043-0.01131.418-0.002-0.0020.0000.0000.0000.000
64H63MET0-0.036-0.02427.7940.0000.0000.0000.0000.0000.000
65H64TRP0-0.039-0.02732.227-0.005-0.0050.0000.0000.0000.000
66H65GLY00.0280.02033.451-0.002-0.0020.0000.0000.0000.000
67H66ARG10.7170.82432.836-0.011-0.0110.0000.0000.0000.000
68H67VAL0-0.013-0.00527.591-0.003-0.0030.0000.0000.0000.000
69H68THR0-0.017-0.00227.839-0.002-0.0020.0000.0000.0000.000
70H69ILE00.0020.02120.660-0.008-0.0080.0000.0000.0000.000
71H70SER0-0.041-0.04222.8520.0010.0010.0000.0000.0000.000
72H71ARG10.8440.90815.5780.3110.3110.0000.0000.0000.000
73H72ASP-1-0.774-0.85318.761-0.245-0.2450.0000.0000.0000.000
74H73ASN00.015-0.01716.562-0.065-0.0650.0000.0000.0000.000
75H74SER0-0.067-0.04016.189-0.036-0.0360.0000.0000.0000.000
76H75LYS10.8940.93616.2450.2280.2280.0000.0000.0000.000
77H76ASN0-0.0050.01410.6250.0220.0220.0000.0000.0000.000
78H77THR0-0.011-0.01413.030-0.059-0.0590.0000.0000.0000.000
79H78LEU0-0.0050.00815.6730.0390.0390.0000.0000.0000.000
80H79TYR0-0.022-0.02717.6640.0020.0020.0000.0000.0000.000
81H80LEU00.0070.00620.9720.0100.0100.0000.0000.0000.000
82H81GLN0-0.053-0.02423.690-0.006-0.0060.0000.0000.0000.000
83H82PHE00.0390.01625.8500.0070.0070.0000.0000.0000.000
84H82SER00.008-0.00730.206-0.005-0.0050.0000.0000.0000.000
85H82SER00.0130.01333.8860.0050.0050.0000.0000.0000.000
86H82LEU0-0.0010.01730.1710.0040.0040.0000.0000.0000.000
87H83LYS10.9860.99333.884-0.012-0.0120.0000.0000.0000.000
88H84VAL00.0850.04633.8160.0010.0010.0000.0000.0000.000
89H85GLU-1-0.933-0.97133.4610.0400.0400.0000.0000.0000.000
90H86ASP-1-0.796-0.86630.1930.0190.0190.0000.0000.0000.000
91H87THR0-0.063-0.02428.8840.0000.0000.0000.0000.0000.000
92H88ALA0-0.001-0.00525.5970.0090.0090.0000.0000.0000.000
93H89MET0-0.0350.01719.7470.0040.0040.0000.0000.0000.000
94H90PHE00.007-0.01720.8890.0010.0010.0000.0000.0000.000
95H91PHE0-0.001-0.00115.909-0.005-0.0050.0000.0000.0000.000
96H93ALA00.038-0.00313.2350.0420.0420.0000.0000.0000.000
97H94ARG10.7200.8147.4410.3190.3190.0000.0000.0000.000
98H95GLU-1-0.844-0.90313.1620.0850.0850.0000.0000.0000.000
99H96ALA00.0250.02213.092-0.057-0.0570.0000.0000.0000.000
100H97GLY00.0420.00013.7310.0040.0040.0000.0000.0000.000
101H98GLY00.0140.01214.085-0.033-0.0330.0000.0000.0000.000
102H99PRO0-0.0320.00216.0600.0220.0220.0000.0000.0000.000
103H100TYR00.004-0.00812.942-0.016-0.0160.0000.0000.0000.000
104H100TYR0-0.045-0.02318.8280.0090.0090.0000.0000.0000.000
105H100ASN0-0.002-0.00718.601-0.027-0.0270.0000.0000.0000.000
106H100TYR0-0.024-0.03116.1740.0050.0050.0000.0000.0000.000
107H100HIS0-0.0210.00619.1120.0250.0250.0000.0000.0000.000
108H100TYR0-0.004-0.00713.4770.0130.0130.0000.0000.0000.000
109H100MET0-0.015-0.00714.814-0.022-0.0220.0000.0000.0000.000
110H101ASP-1-0.803-0.87810.5760.0990.0990.0000.0000.0000.000
111H102VAL0-0.0180.0047.1270.1870.1870.0000.0000.0000.000
112H103TRP0-0.003-0.0199.541-0.211-0.2110.0000.0000.0000.000
113H104GLY00.0590.04510.1040.0840.0840.0000.0000.0000.000
114H105LYS10.8440.91511.902-0.161-0.1610.0000.0000.0000.000
115H106GLY00.0430.00713.968-0.062-0.0620.0000.0000.0000.000
116H107THR0-0.0160.00117.0020.0100.0100.0000.0000.0000.000
117H108THR0-0.023-0.01719.6650.0090.0090.0000.0000.0000.000
118H109VAL00.0070.01123.137-0.016-0.0160.0000.0000.0000.000
119H110THR0-0.003-0.00826.2660.0120.0120.0000.0000.0000.000
120H111VAL0-0.0130.00129.584-0.008-0.0080.0000.0000.0000.000
121H112SER00.018-0.01532.6180.0030.0030.0000.0000.0000.000
122H113SER00.0190.00435.863-0.003-0.0030.0000.0000.0000.000
123H114ALA0-0.064-0.01338.262-0.002-0.0020.0000.0000.0000.000
124H115SER00.0350.01438.0080.0000.0000.0000.0000.0000.000
125H116THR0-0.040-0.02638.4120.0030.0030.0000.0000.0000.000
126H117LYS10.8150.91540.516-0.038-0.0380.0000.0000.0000.000
127H118GLY00.0890.04041.9470.0040.0040.0000.0000.0000.000
128H119PRO0-0.042-0.02442.479-0.002-0.0020.0000.0000.0000.000
129H120SER0-0.0140.01044.859-0.003-0.0030.0000.0000.0000.000
130H121VAL00.003-0.01346.6380.0030.0030.0000.0000.0000.000
131H122PHE0-0.005-0.00648.584-0.003-0.0030.0000.0000.0000.000
132H123PRO0-0.009-0.00750.0730.0020.0020.0000.0000.0000.000
133H124LEU0-0.018-0.00747.251-0.001-0.0010.0000.0000.0000.000
134H125ALA00.0430.01651.8580.0010.0010.0000.0000.0000.000
135H126PRO00.0140.01754.8020.0010.0010.0000.0000.0000.000
136H127SER00.0330.01455.742-0.001-0.0010.0000.0000.0000.000
137H128SER00.017-0.01557.6060.0010.0010.0000.0000.0000.000
138H129LYN00.009-0.00454.2850.0010.0010.0000.0000.0000.000
139H130SER00.1400.08756.751-0.001-0.0010.0000.0000.0000.000
140H131THR0-0.060-0.03557.4780.0020.0020.0000.0000.0000.000
141H132SER00.0250.01659.3600.0000.0000.0000.0000.0000.000
142H133GLY0-0.053-0.02160.715-0.001-0.0010.0000.0000.0000.000
143H134GLY0-0.022-0.01058.235-0.001-0.0010.0000.0000.0000.000
144H135THR0-0.041-0.00451.977-0.001-0.0010.0000.0000.0000.000
145H136ALA00.0150.02354.8510.0000.0000.0000.0000.0000.000
146H137ALA0-0.022-0.01049.8110.0020.0020.0000.0000.0000.000
147H138LEU00.0120.01651.040-0.002-0.0020.0000.0000.0000.000
148H139GLY00.035-0.01348.5580.0040.0040.0000.0000.0000.000
149H140CYS0-0.092-0.00547.282-0.003-0.0030.0000.0000.0000.000
150H141LEU00.0050.01844.3770.0040.0040.0000.0000.0000.000
151H142VAL00.0090.00042.598-0.004-0.0040.0000.0000.0000.000
152H143LYS10.8930.93042.377-0.042-0.0420.0000.0000.0000.000
153H144ASP-1-0.844-0.89942.4560.0400.0400.0000.0000.0000.000
154H145TYR0-0.005-0.02536.575-0.005-0.0050.0000.0000.0000.000
155H146PHE00.0460.02733.6030.0040.0040.0000.0000.0000.000
156H147PRO00.0210.02233.690-0.005-0.0050.0000.0000.0000.000
157H148GLU-1-0.779-0.86732.3420.0920.0920.0000.0000.0000.000
158H149PRO0-0.036-0.01733.243-0.003-0.0030.0000.0000.0000.000
159H150VAL00.001-0.01835.257-0.007-0.0070.0000.0000.0000.000
160H151THR0-0.076-0.03538.1130.0050.0050.0000.0000.0000.000
161H152VAL00.038-0.00639.819-0.005-0.0050.0000.0000.0000.000
162H153SER0-0.036-0.00242.5570.0040.0040.0000.0000.0000.000
163H154TRP00.0240.00545.153-0.004-0.0040.0000.0000.0000.000
164H155ASN00.009-0.01148.5140.0010.0010.0000.0000.0000.000
165H156SER0-0.012-0.02049.310-0.001-0.0010.0000.0000.0000.000
166H157GLY0-0.014-0.00546.9030.0000.0000.0000.0000.0000.000
167H158ALA0-0.032-0.00247.7510.0020.0020.0000.0000.0000.000
168H159LEU0-0.032-0.00549.347-0.001-0.0010.0000.0000.0000.000
169H160THR0-0.003-0.01144.8880.0010.0010.0000.0000.0000.000
170H161SER00.0090.00445.0110.0050.0050.0000.0000.0000.000
171H162GLY00.0430.02045.939-0.003-0.0030.0000.0000.0000.000
172H163VAL0-0.0090.00543.010-0.003-0.0030.0000.0000.0000.000
173H164HIS00.0050.01341.1790.0090.0090.0000.0000.0000.000
174H165THR00.0250.00838.920-0.007-0.0070.0000.0000.0000.000
175H166PHE0-0.033-0.00537.7160.0070.0070.0000.0000.0000.000
176H167PRO00.023-0.00633.016-0.003-0.0030.0000.0000.0000.000
177H168ALA0-0.0060.00834.440-0.005-0.0050.0000.0000.0000.000
178H169VAL0-0.034-0.00934.0530.0060.0060.0000.0000.0000.000
179H170LEU0-0.012-0.00432.403-0.004-0.0040.0000.0000.0000.000
180H171GLN0-0.055-0.03835.4650.0000.0000.0000.0000.0000.000
181H172SER00.0270.00837.622-0.002-0.0020.0000.0000.0000.000
182H173SER00.014-0.00239.447-0.002-0.0020.0000.0000.0000.000
183H174GLY00.0710.04636.833-0.004-0.0040.0000.0000.0000.000
184H175LEU0-0.097-0.02937.3270.0000.0000.0000.0000.0000.000
185H176TYR00.0250.00531.326-0.001-0.0010.0000.0000.0000.000
186H177SER0-0.011-0.01738.172-0.006-0.0060.0000.0000.0000.000
187H178LEU00.0040.02537.5430.0050.0050.0000.0000.0000.000
188H179SER00.000-0.01540.153-0.007-0.0070.0000.0000.0000.000
189H180SER0-0.007-0.00241.5130.0040.0040.0000.0000.0000.000
190H181VAL00.0200.00943.956-0.005-0.0050.0000.0000.0000.000
191H182VAL00.0220.01045.6300.0040.0040.0000.0000.0000.000
192H183THR0-0.047-0.02248.198-0.001-0.0010.0000.0000.0000.000
193H184VAL00.001-0.00649.9570.0010.0010.0000.0000.0000.000
194H185PRO00.0520.02353.3810.0000.0000.0000.0000.0000.000
195H186SER00.018-0.00856.687-0.001-0.0010.0000.0000.0000.000
196H187SER0-0.012-0.00659.087-0.001-0.0010.0000.0000.0000.000
197H188SER0-0.038-0.01457.843-0.001-0.0010.0000.0000.0000.000
198H189LEU00.0180.00956.9860.0000.0000.0000.0000.0000.000
199H190GLY00.0020.00660.673-0.001-0.0010.0000.0000.0000.000
200H191THR0-0.042-0.01962.205-0.001-0.0010.0000.0000.0000.000
201H192GLN00.0100.02156.541-0.001-0.0010.0000.0000.0000.000
202H193THR0-0.038-0.02657.604-0.001-0.0010.0000.0000.0000.000
203H194TYR00.021-0.00453.2150.0020.0020.0000.0000.0000.000
204H195ILE00.0070.00252.555-0.001-0.0010.0000.0000.0000.000
205H197ASN00.0600.00847.2230.0000.0000.0000.0000.0000.000
206H198VAL0-0.0050.00543.6250.0040.0040.0000.0000.0000.000
207H199ASN0-0.018-0.02242.511-0.005-0.0050.0000.0000.0000.000
208H200HIS00.0390.03338.2600.0020.0020.0000.0000.0000.000
209H201LYS10.9760.97037.146-0.076-0.0760.0000.0000.0000.000
210H202PRO00.0260.02836.396-0.004-0.0040.0000.0000.0000.000
211H203SER0-0.004-0.03538.996-0.004-0.0040.0000.0000.0000.000
212H204ASN0-0.070-0.03741.680-0.001-0.0010.0000.0000.0000.000
213H205THR00.0160.03244.107-0.003-0.0030.0000.0000.0000.000
214H206LYS10.9260.95445.122-0.043-0.0430.0000.0000.0000.000
215H207VAL00.0150.00547.480-0.003-0.0030.0000.0000.0000.000
216H208ASP-1-0.833-0.89948.9800.0480.0480.0000.0000.0000.000
217H209LYS10.9170.95551.449-0.041-0.0410.0000.0000.0000.000
218H210ARG10.8520.91252.998-0.034-0.0340.0000.0000.0000.000
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