Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: Q1R3Y

Calculation Name: 2X36-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2X36

Chain ID: A

ChEMBL ID:

UniProt ID: P36776

Base Structure: X-ray

Registration Date: 2023-06-20

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 190
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2017549.171499
FMO2-HF: Nuclear repulsion 1944769.586293
FMO2-HF: Total energy -72779.585207
FMO2-MP2: Total energy -72989.065927


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:756:MET)


Summations of interaction energy for fragment #1(A:756:MET)
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.
-20.896-14.8369.438-5.576-9.92-0.039
Interaction energy analysis for fragmet #1(A:756:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.075 / q_NPA : -0.016
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].
3A758ASP-1-0.915-0.9433.545-4.564-2.255-0.007-1.166-1.1360.002
4A759VAL0-0.021-0.0256.0920.8190.8190.0000.0000.0000.000
5A760THR0-0.027-0.0015.683-0.516-0.5160.0000.0000.0000.000
6A761PRO0-0.0250.0086.6470.3120.3120.0000.0000.0000.000
7A762PRO00.059-0.0079.6420.1260.1260.0000.0000.0000.000
8A763GLY00.0010.0049.739-0.157-0.1570.0000.0000.0000.000
9A764VAL0-0.025-0.0095.0200.1740.1740.0000.0000.0000.000
10A765VAL0-0.002-0.0037.830-0.080-0.0800.0000.0000.0000.000
11A766MET00.0110.0345.6740.3730.3730.0000.0000.0000.000
12A767GLY00.0240.0007.778-0.419-0.4190.0000.0000.0000.000
13A768LEU0-0.081-0.0229.5770.4780.4780.0000.0000.0000.000
14A769ALA00.0170.00311.883-0.182-0.1820.0000.0000.0000.000
15A770TRP0-0.015-0.01413.5070.0040.0040.0000.0000.0000.000
16A771THR0-0.026-0.02312.735-0.084-0.0840.0000.0000.0000.000
17A772ALA00.0030.00116.150-0.083-0.0830.0000.0000.0000.000
18A773MET00.007-0.00615.903-0.063-0.0630.0000.0000.0000.000
19A774GLY00.0190.01216.957-0.058-0.0580.0000.0000.0000.000
20A775GLY00.0420.04614.443-0.055-0.0550.0000.0000.0000.000
21A776SER0-0.092-0.0559.2130.1210.1210.0000.0000.0000.000
22A777THR00.0120.0296.185-0.481-0.4810.0000.0000.0000.000
23A778LEU0-0.028-0.0236.3160.9160.9160.0000.0000.0000.000
24A779PHE00.0710.0152.707-4.022-2.8996.991-2.217-5.896-0.009
25A780VAL0-0.040-0.0144.880-0.898-0.715-0.001-0.040-0.1420.000
26A781GLU-1-0.824-0.9102.506-11.272-8.8812.456-2.152-2.695-0.032
27A782THR0-0.019-0.0186.5290.1730.1730.0000.0000.0000.000
28A783SER00.0140.0079.399-0.227-0.2270.0000.0000.0000.000
29A784LEU0-0.0100.00211.4680.1090.1090.0000.0000.0000.000
30A785ARG10.8520.89713.9260.1790.1790.0000.0000.0000.000
31A786ARG10.8810.94916.1490.2340.2340.0000.0000.0000.000
32A787PRO00.0100.02019.231-0.022-0.0220.0000.0000.0000.000
33A788GLN00.0670.02621.2660.0300.0300.0000.0000.0000.000
34A797ASP-1-0.917-0.97126.736-0.093-0.0930.0000.0000.0000.000
35A798GLY00.0190.00822.831-0.006-0.0060.0000.0000.0000.000
36A799SER0-0.125-0.10120.6170.0230.0230.0000.0000.0000.000
37A800LEU00.003-0.00114.645-0.026-0.0260.0000.0000.0000.000
38A801GLU-1-0.871-0.89314.457-0.182-0.1820.0000.0000.0000.000
39A802VAL00.007-0.00613.080-0.035-0.0350.0000.0000.0000.000
40A803THR0-0.026-0.0179.280-0.039-0.0390.0000.0000.0000.000
41A804GLY00.0660.02110.1890.0340.0340.0000.0000.0000.000
42A805GLN0-0.130-0.05511.041-0.004-0.0040.0000.0000.0000.000
43A806LEU00.0350.04112.8400.0320.0320.0000.0000.0000.000
44A807GLY00.0440.00616.322-0.054-0.0540.0000.0000.0000.000
45A808GLU-1-0.789-0.90919.6250.1580.1580.0000.0000.0000.000
46A809VAL0-0.010-0.00521.882-0.012-0.0120.0000.0000.0000.000
47A810MET00.0380.03514.524-0.016-0.0160.0000.0000.0000.000
48A811LYS10.8520.93817.435-0.203-0.2030.0000.0000.0000.000
49A812GLU-1-0.841-0.91118.7630.0950.0950.0000.0000.0000.000
50A813SER0-0.030-0.02518.184-0.004-0.0040.0000.0000.0000.000
51A814ALA00.015-0.00215.636-0.008-0.0080.0000.0000.0000.000
52A815ARG10.8330.89817.270-0.151-0.1510.0000.0000.0000.000
53A816ILE00.0030.01620.355-0.024-0.0240.0000.0000.0000.000
54A817ALA00.0420.02217.350-0.019-0.0190.0000.0000.0000.000
55A818TYR00.0210.01618.075-0.026-0.0260.0000.0000.0000.000
56A819THR0-0.004-0.01319.486-0.027-0.0270.0000.0000.0000.000
57A820PHE0-0.0170.00521.784-0.013-0.0130.0000.0000.0000.000
58A821ALA00.0330.00319.049-0.013-0.0130.0000.0000.0000.000
59A822ARG10.8560.92621.1140.0580.0580.0000.0000.0000.000
60A823ALA0-0.032-0.02123.336-0.010-0.0100.0000.0000.0000.000
61A824PHE0-0.011-0.00923.018-0.001-0.0010.0000.0000.0000.000
62A825LEU00.0160.00921.342-0.009-0.0090.0000.0000.0000.000
63A826MET0-0.013-0.00824.583-0.008-0.0080.0000.0000.0000.000
64A827GLN0-0.027-0.00427.9830.0020.0020.0000.0000.0000.000
65A828HIS0-0.021-0.00124.2350.0160.0160.0000.0000.0000.000
66A829ALA0-0.014-0.00825.080-0.011-0.0110.0000.0000.0000.000
67A830PRO00.0030.00427.100-0.009-0.0090.0000.0000.0000.000
68A831ALA0-0.056-0.01929.0350.0020.0020.0000.0000.0000.000
69A832ASN0-0.054-0.03721.621-0.008-0.0080.0000.0000.0000.000
70A833ASP-1-0.818-0.90925.573-0.173-0.1730.0000.0000.0000.000
71A834TYR00.0370.02915.9570.0000.0000.0000.0000.0000.000
72A835LEU0-0.008-0.01717.986-0.009-0.0090.0000.0000.0000.000
73A836VAL0-0.042-0.02321.4820.0120.0120.0000.0000.0000.000
74A837THR00.0200.00724.3480.0030.0030.0000.0000.0000.000
75A838SER0-0.037-0.01019.207-0.016-0.0160.0000.0000.0000.000
76A839HIS0-0.0260.03419.2420.0260.0260.0000.0000.0000.000
77A840ILE0-0.031-0.01713.885-0.055-0.0550.0000.0000.0000.000
78A841HIS00.0110.0059.9000.0460.0460.0000.0000.0000.000
79A842LEU0-0.020-0.02910.139-0.070-0.0700.0000.0000.0000.000
80A843HIS00.0330.0274.6370.0220.076-0.001-0.001-0.0510.000
81A844VAL0-0.015-0.0157.5500.1440.1440.0000.0000.0000.000
82A845PRO0-0.0220.0065.333-0.178-0.1780.0000.0000.0000.000
83A846GLU-1-0.837-0.9347.4770.8570.8570.0000.0000.0000.000
84A847GLY0-0.002-0.0219.9530.4450.4450.0000.0000.0000.000
85A848ALA0-0.0080.01312.455-0.115-0.1150.0000.0000.0000.000
86A849THR00.004-0.01415.038-0.106-0.1060.0000.0000.0000.000
87A850PRO00.022-0.01418.370-0.010-0.0100.0000.0000.0000.000
88A851LYS10.9010.94420.274-0.388-0.3880.0000.0000.0000.000
89A852ASP-1-0.758-0.85416.9580.7220.7220.0000.0000.0000.000
90A853GLY0-0.0200.01816.3560.0240.0240.0000.0000.0000.000
91A854PRO00.0820.01716.7360.0230.0230.0000.0000.0000.000
92A855SER0-0.062-0.02517.152-0.017-0.0170.0000.0000.0000.000
93A856ALA00.0090.00313.1530.0140.0140.0000.0000.0000.000
94A857GLY00.0370.02614.820-0.032-0.0320.0000.0000.0000.000
95A858CYS00.0630.03116.032-0.032-0.0320.0000.0000.0000.000
96A859THR00.0120.01110.870-0.117-0.1170.0000.0000.0000.000
97A860ILE00.0320.01012.269-0.059-0.0590.0000.0000.0000.000
98A861VAL0-0.054-0.00713.738-0.096-0.0960.0000.0000.0000.000
99A862THR00.017-0.00614.275-0.076-0.0760.0000.0000.0000.000
100A863ALA00.0130.00810.727-0.090-0.0900.0000.0000.0000.000
101A864LEU00.0200.00412.504-0.132-0.1320.0000.0000.0000.000
102A865LEU0-0.0030.01615.192-0.063-0.0630.0000.0000.0000.000
103A866SER0-0.035-0.02313.093-0.072-0.0720.0000.0000.0000.000
104A867LEU0-0.049-0.02412.212-0.060-0.0600.0000.0000.0000.000
105A868ALA0-0.037-0.02814.350-0.021-0.0210.0000.0000.0000.000
106A869MET0-0.042-0.00918.0770.0190.0190.0000.0000.0000.000
107A870GLY0-0.0120.01716.119-0.003-0.0030.0000.0000.0000.000
108A871ARG10.7910.87317.0610.2780.2780.0000.0000.0000.000
109A872PRO0-0.022-0.00912.2800.0340.0340.0000.0000.0000.000
110A873VAL0-0.0010.01611.4410.0840.0840.0000.0000.0000.000
111A874ARG10.8270.89012.6990.0180.0180.0000.0000.0000.000
112A875GLN0-0.027-0.0379.2950.1770.1770.0000.0000.0000.000
113A876ASN00.001-0.0018.868-0.041-0.0410.0000.0000.0000.000
114A877LEU00.0060.02010.3850.1550.1550.0000.0000.0000.000
115A878ALA00.0180.00610.2930.0960.0960.0000.0000.0000.000
116A879MET00.0160.02812.010-0.087-0.0870.0000.0000.0000.000
117A880THR0-0.020-0.02813.6360.1510.1510.0000.0000.0000.000
118A881GLY00.0640.00816.405-0.064-0.0640.0000.0000.0000.000
119A882GLU-1-0.907-0.93519.2540.2900.2900.0000.0000.0000.000
120A883VAL0-0.062-0.01620.187-0.029-0.0290.0000.0000.0000.000
121A884SER00.0300.02122.638-0.004-0.0040.0000.0000.0000.000
122A885LEU00.043-0.00225.143-0.008-0.0080.0000.0000.0000.000
123A886THR0-0.038-0.01926.970-0.011-0.0110.0000.0000.0000.000
124A887GLY00.0570.03524.800-0.010-0.0100.0000.0000.0000.000
125A888LYS10.8700.92925.588-0.142-0.1420.0000.0000.0000.000
126A889ILE0-0.013-0.00222.0430.0200.0200.0000.0000.0000.000
127A890LEU0-0.048-0.02524.299-0.015-0.0150.0000.0000.0000.000
128A891PRO00.0150.00623.6030.0300.0300.0000.0000.0000.000
129A892VAL0-0.039-0.01319.4980.0140.0140.0000.0000.0000.000
130A893GLY00.0260.01721.976-0.034-0.0340.0000.0000.0000.000
131A894GLY00.029-0.00319.5790.0430.0430.0000.0000.0000.000
132A895ILE00.0500.02418.8060.0640.0640.0000.0000.0000.000
133A896LYS10.9881.01118.901-0.402-0.4020.0000.0000.0000.000
134A897GLU-1-0.841-0.92917.2610.6180.6180.0000.0000.0000.000
135A898LYS10.7950.88914.702-0.582-0.5820.0000.0000.0000.000
136A899THR0-0.003-0.00114.0650.0470.0470.0000.0000.0000.000
137A900ILE0-0.032-0.02114.858-0.010-0.0100.0000.0000.0000.000
138A901ALA0-0.061-0.01610.8980.0270.0270.0000.0000.0000.000
139A902ALA00.1000.03310.1860.1440.1440.0000.0000.0000.000
140A903LYS10.8040.89610.824-0.400-0.4000.0000.0000.0000.000
141A904ARG10.8460.91410.100-1.659-1.6590.0000.0000.0000.000
142A905ALA0-0.050-0.0176.2930.0630.0630.0000.0000.0000.000
143A906GLY00.0290.0237.206-0.324-0.3240.0000.0000.0000.000
144A907VAL0-0.081-0.0348.932-0.160-0.1600.0000.0000.0000.000
145A908THR00.013-0.00610.8400.0250.0250.0000.0000.0000.000
146A909CYS0-0.078-0.02213.709-0.008-0.0080.0000.0000.0000.000
147A910ILE00.0010.00514.4080.0410.0410.0000.0000.0000.000
148A911VAL00.0360.01316.128-0.047-0.0470.0000.0000.0000.000
149A912LEU0-0.032-0.02417.7150.0750.0750.0000.0000.0000.000
150A913PRO00.0760.04720.363-0.041-0.0410.0000.0000.0000.000
151A914ALA0-0.011-0.00423.2840.0080.0080.0000.0000.0000.000
152A915GLU-1-0.873-0.94526.5930.1720.1720.0000.0000.0000.000
153A916ASN0-0.038-0.03823.5350.0150.0150.0000.0000.0000.000
154A917LYS10.9580.98425.107-0.118-0.1180.0000.0000.0000.000
155A918LYS10.7950.87526.860-0.247-0.2470.0000.0000.0000.000
156A919ASP-1-0.832-0.89724.7590.2880.2880.0000.0000.0000.000
157A920PHE00.0050.00619.3090.0130.0130.0000.0000.0000.000
158A921TYR0-0.001-0.02324.127-0.005-0.0050.0000.0000.0000.000
159A922ASP-1-0.902-0.92627.1720.2490.2490.0000.0000.0000.000
160A923LEU0-0.023-0.00421.3220.0280.0280.0000.0000.0000.000
161A924ALA0-0.020-0.01224.446-0.022-0.0220.0000.0000.0000.000
162A925ALA00.0690.01123.8790.0180.0180.0000.0000.0000.000
163A926PHE00.0380.02121.700-0.006-0.0060.0000.0000.0000.000
164A927ILE0-0.060-0.02718.6870.0210.0210.0000.0000.0000.000
165A928THR00.0320.01019.1450.0220.0220.0000.0000.0000.000
166A929GLU-1-0.913-0.95120.9610.1110.1110.0000.0000.0000.000
167A930GLY00.0120.01919.1960.0330.0330.0000.0000.0000.000
168A931LEU0-0.059-0.01114.547-0.009-0.0090.0000.0000.0000.000
169A932GLU-1-0.758-0.82317.846-0.043-0.0430.0000.0000.0000.000
170A933VAL0-0.042-0.02818.4170.0220.0220.0000.0000.0000.000
171A934HIS0-0.052-0.03019.746-0.018-0.0180.0000.0000.0000.000
172A935PHE0-0.032-0.03021.3560.0290.0290.0000.0000.0000.000
173A936VAL00.0150.00121.533-0.019-0.0190.0000.0000.0000.000
174A937GLU-1-0.985-1.00324.6030.1250.1250.0000.0000.0000.000
175A938HIS0-0.002-0.00626.2070.0070.0070.0000.0000.0000.000
176A939TYR00.030-0.01017.803-0.017-0.0170.0000.0000.0000.000
177A940ARG10.7650.83922.5220.0550.0550.0000.0000.0000.000
178A941GLU-1-0.754-0.87224.1060.0700.0700.0000.0000.0000.000
179A942ILE0-0.020-0.02417.857-0.002-0.0020.0000.0000.0000.000
180A943PHE0-0.047-0.02518.961-0.008-0.0080.0000.0000.0000.000
181A944ASP-1-0.759-0.86720.354-0.087-0.0870.0000.0000.0000.000
182A945ILE0-0.058-0.02117.993-0.017-0.0170.0000.0000.0000.000
183A946ALA0-0.036-0.01515.794-0.021-0.0210.0000.0000.0000.000
184A947PHE0-0.009-0.01415.625-0.065-0.0650.0000.0000.0000.000
185A948PRO00.0290.02618.9610.0150.0150.0000.0000.0000.000
186A949ASP-1-0.867-0.93020.903-0.280-0.2800.0000.0000.0000.000
187A950GLU-1-0.884-0.91621.581-0.246-0.2460.0000.0000.0000.000
188A951GLN0-0.030-0.00724.1660.0080.0080.0000.0000.0000.000
189A952ALA00.0100.00727.4500.0080.0080.0000.0000.0000.000
190A953GLU-1-0.946-0.97228.742-0.040-0.0400.0000.0000.0000.000