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: LJM49

Calculation Name: 2X36-A-Xray320

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: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 194
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2032532.690493
FMO2-HF: Nuclear repulsion 1959413.31964
FMO2-HF: Total energy -73119.370853
FMO2-MP2: Total energy -73329.948316


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:755:ACE )


Summations of interaction energy for fragment #1(A:755:ACE )
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.
0.6251.7320.004-0.439-0.67-0.001
Interaction energy analysis for fragmet #1(A:755:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.005 / q_NPA : -0.011
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].
3A757TYR 0-0.0010.0053.8630.9471.775-0.004-0.376-0.448-0.001
4A758ASP -1-0.924-0.9474.9220.3060.4110.000-0.006-0.0990.000
5A759VAL 0-0.024-0.0297.2690.0970.0970.0000.0000.0000.000
6A760THR 0-0.041-0.0118.756-0.104-0.1040.0000.0000.0000.000
7A761PRO 0-0.0090.01210.7970.0770.0770.0000.0000.0000.000
8A762PRO 00.044-0.00813.9850.0030.0030.0000.0000.0000.000
9A763GLY 0-0.008-0.00215.749-0.030-0.0300.0000.0000.0000.000
10A764VAL 0-0.013-0.0169.989-0.030-0.0300.0000.0000.0000.000
11A765VAL 0-0.004-0.00311.4770.0390.0390.0000.0000.0000.000
12A766MET 00.0090.0396.419-0.034-0.0340.0000.0000.0000.000
13A767GLY 00.0240.0029.1870.0660.0660.0000.0000.0000.000
14A768LEU 0-0.086-0.0309.6960.0260.0260.0000.0000.0000.000
15A769ALA 00.0240.00711.420-0.029-0.0290.0000.0000.0000.000
16A770TRP 00.004-0.00213.3420.0420.0420.0000.0000.0000.000
17A771THR 0-0.026-0.01312.487-0.025-0.0250.0000.0000.0000.000
18A772ALA 0-0.010-0.02015.4870.0110.0110.0000.0000.0000.000
19A773MET 00.0140.00014.216-0.001-0.0010.0000.0000.0000.000
20A774GLY 00.0240.01514.7980.0250.0250.0000.0000.0000.000
21A775GLY 00.0240.03712.681-0.035-0.0350.0000.0000.0000.000
22A776SER 0-0.080-0.0568.1330.0510.0510.0000.0000.0000.000
23A777THR 00.0000.0185.0620.0930.0930.0000.0000.0000.000
24A778LEU 0-0.024-0.0166.171-0.004-0.0040.0000.0000.0000.000
25A779PHE 00.0670.0153.619-0.335-0.2280.008-0.048-0.0650.000
26A780VAL 0-0.046-0.0138.5060.0120.0120.0000.0000.0000.000
27A781GLU -1-0.881-0.94211.147-0.744-0.7440.0000.0000.0000.000
28A782THR 0-0.0210.00113.7240.0610.0610.0000.0000.0000.000
29A783SER 00.017-0.00917.183-0.024-0.0240.0000.0000.0000.000
30A784LEU 0-0.037-0.00319.7320.0150.0150.0000.0000.0000.000
31A785ARG 10.9720.99122.7620.1300.1300.0000.0000.0000.000
32A786ARG 10.8750.94625.1240.1110.1110.0000.0000.0000.000
33A787PRO 00.0210.02327.891-0.005-0.0050.0000.0000.0000.000
34A788GLN 0-0.016-0.02929.8800.0030.0030.0000.0000.0000.000
35A789NME 00.0410.04430.8930.0040.0040.0000.0000.0000.000
36A796ACE 0-0.080-0.05237.1450.0000.0000.0000.0000.0000.000
37A797ASP -1-0.887-0.95634.848-0.055-0.0550.0000.0000.0000.000
38A798GLY 0-0.0150.00330.628-0.003-0.0030.0000.0000.0000.000
39A799SER 0-0.130-0.11529.0590.0020.0020.0000.0000.0000.000
40A800LEU 00.0050.00322.205-0.007-0.0070.0000.0000.0000.000
41A801GLU -1-0.941-0.96223.457-0.144-0.1440.0000.0000.0000.000
42A802VAL 00.006-0.00520.364-0.015-0.0150.0000.0000.0000.000
43A803THR 0-0.008-0.00517.8360.0140.0140.0000.0000.0000.000
44A804GLY 00.0570.01716.721-0.017-0.0170.0000.0000.0000.000
45A805GLN 0-0.082-0.02717.6500.0210.0210.0000.0000.0000.000
46A806LEU 00.0310.03618.7890.0170.0170.0000.0000.0000.000
47A807GLY 00.036-0.00122.0400.0060.0060.0000.0000.0000.000
48A808GLU -1-0.851-0.95925.196-0.069-0.0690.0000.0000.0000.000
49A809VAL 0-0.015-0.00425.305-0.001-0.0010.0000.0000.0000.000
50A810MET 00.0200.03218.7640.0060.0060.0000.0000.0000.000
51A811LYS 10.8970.97723.2540.0860.0860.0000.0000.0000.000
52A812GLU -1-0.860-0.91324.994-0.056-0.0560.0000.0000.0000.000
53A813SER 0-0.015-0.02222.3320.0010.0010.0000.0000.0000.000
54A814ALA 00.020-0.00321.592-0.001-0.0010.0000.0000.0000.000
55A815ARG 10.8770.92523.0050.0670.0670.0000.0000.0000.000
56A816ILE 00.0120.02525.7650.0030.0030.0000.0000.0000.000
57A817ALA 00.0360.01622.0280.0030.0030.0000.0000.0000.000
58A818TYR 00.0090.00624.0360.0030.0030.0000.0000.0000.000
59A819THR 0-0.002-0.00925.3920.0030.0030.0000.0000.0000.000
60A820PHE 0-0.0160.02125.3040.0050.0050.0000.0000.0000.000
61A821ALA 00.024-0.00923.7470.0030.0030.0000.0000.0000.000
62A822ARG 10.9100.96525.8070.0720.0720.0000.0000.0000.000
63A823ALA 0-0.024-0.01528.8010.0030.0030.0000.0000.0000.000
64A824PHE 0-0.027-0.01026.1450.0050.0050.0000.0000.0000.000
65A825LEU 00.0210.00726.2670.0020.0020.0000.0000.0000.000
66A826MET 00.007-0.00129.0350.0030.0030.0000.0000.0000.000
67A827GLN 0-0.038-0.00932.2210.0050.0050.0000.0000.0000.000
68A828HIS 0-0.023-0.00627.1460.0050.0050.0000.0000.0000.000
69A829ALA 0-0.0080.00129.5300.0010.0010.0000.0000.0000.000
70A830PRO 00.002-0.00131.442-0.004-0.0040.0000.0000.0000.000
71A831ALA 0-0.053-0.01634.0730.0000.0000.0000.0000.0000.000
72A832ASN 0-0.055-0.04027.192-0.005-0.0050.0000.0000.0000.000
73A833ASP -1-0.837-0.92331.349-0.064-0.0640.0000.0000.0000.000
74A834TYR 00.0350.03323.289-0.003-0.0030.0000.0000.0000.000
75A835LEU 0-0.006-0.01124.200-0.006-0.0060.0000.0000.0000.000
76A836VAL 0-0.056-0.02528.087-0.001-0.0010.0000.0000.0000.000
77A837THR 00.0280.02431.473-0.001-0.0010.0000.0000.0000.000
78A838SER 00.004-0.00727.158-0.003-0.0030.0000.0000.0000.000
79A839HIS 0-0.0090.04827.685-0.002-0.0020.0000.0000.0000.000
80A840ILE 0-0.038-0.01821.668-0.011-0.0110.0000.0000.0000.000
81A841HIS 00.002-0.01919.3820.0180.0180.0000.0000.0000.000
82A842LEU 0-0.022-0.02817.203-0.013-0.0130.0000.0000.0000.000
83A843HIS 00.0250.03713.1600.0670.0670.0000.0000.0000.000
84A844VAL 00.008-0.00614.659-0.023-0.0230.0000.0000.0000.000
85A845PRO 0-0.0410.00510.5380.0190.0190.0000.0000.0000.000
86A846GLU -1-0.877-0.96612.872-0.124-0.1240.0000.0000.0000.000
87A847GLY 0-0.001-0.02111.901-0.024-0.0240.0000.0000.0000.000
88A848ALA 0-0.0070.01213.4950.0360.0360.0000.0000.0000.000
89A849THR 00.004-0.00915.901-0.014-0.0140.0000.0000.0000.000
90A850PRO 00.008-0.02019.332-0.003-0.0030.0000.0000.0000.000
91A851LYS 10.8850.93422.2650.0030.0030.0000.0000.0000.000
92A852ASP -1-0.729-0.83917.0060.0280.0280.0000.0000.0000.000
93A853GLY 0-0.0080.01218.738-0.003-0.0030.0000.0000.0000.000
94A854PRO 00.0690.00319.454-0.011-0.0110.0000.0000.0000.000
95A855SER 0-0.035-0.00818.070-0.001-0.0010.0000.0000.0000.000
96A856ALA 00.0270.01116.0790.0050.0050.0000.0000.0000.000
97A857GLY 00.0310.02917.247-0.017-0.0170.0000.0000.0000.000
98A858CYS 00.0610.03518.569-0.012-0.0120.0000.0000.0000.000
99A859THR 00.0500.03813.1450.0000.0000.0000.0000.0000.000
100A860ILE 00.0260.00416.128-0.026-0.0260.0000.0000.0000.000
101A861VAL 0-0.054-0.01217.993-0.010-0.0100.0000.0000.0000.000
102A862THR 00.005-0.03016.5190.0020.0020.0000.0000.0000.000
103A863ALA 00.0090.00915.459-0.004-0.0040.0000.0000.0000.000
104A864LEU 00.009-0.00316.927-0.005-0.0050.0000.0000.0000.000
105A865LEU 00.0040.01820.5950.0000.0000.0000.0000.0000.000
106A866SER 0-0.027-0.04017.490-0.006-0.0060.0000.0000.0000.000
107A867LEU 0-0.054-0.02119.3330.0000.0000.0000.0000.0000.000
108A868ALA 0-0.040-0.03420.4110.0070.0070.0000.0000.0000.000
109A869MET 0-0.039-0.01222.2990.0110.0110.0000.0000.0000.000
110A870GLY 0-0.0100.02321.5110.0060.0060.0000.0000.0000.000
111A871ARG 10.9110.96320.3680.0550.0550.0000.0000.0000.000
112A872PRO 0-0.0210.00715.387-0.008-0.0080.0000.0000.0000.000
113A873VAL 00.0020.01413.6170.0250.0250.0000.0000.0000.000
114A874ARG 10.8850.94914.491-0.081-0.0810.0000.0000.0000.000
115A875GLN 00.000-0.02110.700-0.031-0.0310.0000.0000.0000.000
116A876ASN 0-0.019-0.0029.0110.0790.0790.0000.0000.0000.000
117A877LEU 00.0120.02710.4930.0540.0540.0000.0000.0000.000
118A878ALA 00.0250.0139.978-0.017-0.0170.0000.0000.0000.000
119A879MET 00.0040.01211.9050.0040.0040.0000.0000.0000.000
120A880THR 00.000-0.01213.961-0.003-0.0030.0000.0000.0000.000
121A881GLY 00.044-0.00216.7240.0080.0080.0000.0000.0000.000
122A882GLU -1-0.913-0.93420.372-0.027-0.0270.0000.0000.0000.000
123A883VAL 0-0.057-0.01622.3120.0050.0050.0000.0000.0000.000
124A884SER 0-0.0090.00124.881-0.003-0.0030.0000.0000.0000.000
125A885LEU 00.056-0.00228.262-0.003-0.0030.0000.0000.0000.000
126A886THR 0-0.0100.00030.624-0.001-0.0010.0000.0000.0000.000
127A887GLY 00.0420.02027.2160.0020.0020.0000.0000.0000.000
128A888LYS 10.9520.96927.167-0.002-0.0020.0000.0000.0000.000
129A889ILE 0-0.0010.04322.736-0.004-0.0040.0000.0000.0000.000
130A890LEU 0-0.049-0.01925.2860.0060.0060.0000.0000.0000.000
131A891PRO 00.0150.00124.0770.0010.0010.0000.0000.0000.000
132A892VAL 0-0.036-0.00619.352-0.007-0.0070.0000.0000.0000.000
133A893GLY 00.0230.01121.6280.0050.0050.0000.0000.0000.000
134A894GLY 00.033-0.00318.5510.0000.0000.0000.0000.0000.000
135A895ILE 00.0520.02717.4290.0220.0220.0000.0000.0000.000
136A896LYS 11.0021.01517.436-0.137-0.1370.0000.0000.0000.000
137A897GLU -1-0.895-0.95615.2890.1730.1730.0000.0000.0000.000
138A898LYS 10.7900.88513.2730.0030.0030.0000.0000.0000.000
139A899THR 00.003-0.00512.6110.0430.0430.0000.0000.0000.000
140A900ILE 0-0.026-0.00712.8610.0570.0570.0000.0000.0000.000
141A901ALA 0-0.054-0.0169.1680.0940.0940.0000.0000.0000.000
142A902ALA 00.0920.0348.3200.2160.2160.0000.0000.0000.000
143A903LYS 10.8100.9099.241-0.214-0.2140.0000.0000.0000.000
144A904ARG 10.8550.9267.221-0.677-0.6770.0000.0000.0000.000
145A905ALA 0-0.052-0.0204.5700.2470.3140.000-0.009-0.0580.000
146A906GLY 00.0290.0225.7780.0430.0430.0000.0000.0000.000
147A907VAL 0-0.071-0.0357.594-0.174-0.1740.0000.0000.0000.000
148A908THR 00.007-0.0309.885-0.031-0.0310.0000.0000.0000.000
149A909CYS 0-0.0480.00513.153-0.043-0.0430.0000.0000.0000.000
150A910ILE 0-0.027-0.00613.2590.0000.0000.0000.0000.0000.000
151A911VAL 00.0400.01715.513-0.014-0.0140.0000.0000.0000.000
152A912LEU 0-0.029-0.02817.2010.0000.0000.0000.0000.0000.000
153A913PRO 00.0630.04119.979-0.006-0.0060.0000.0000.0000.000
154A914ALA 00.0090.00723.2240.0090.0090.0000.0000.0000.000
155A915GLU -1-0.948-0.99026.2310.0260.0260.0000.0000.0000.000
156A916ASN 0-0.041-0.05522.800-0.003-0.0030.0000.0000.0000.000
157A917LYS 10.9630.98124.037-0.041-0.0410.0000.0000.0000.000
158A918LYS 10.9260.95325.761-0.054-0.0540.0000.0000.0000.000
159A919ASP -1-0.839-0.88723.4060.0690.0690.0000.0000.0000.000
160A920PHE 0-0.015-0.00618.2620.0090.0090.0000.0000.0000.000
161A921TYR 0-0.004-0.03222.7720.0060.0060.0000.0000.0000.000
162A922ASP -1-0.999-0.99025.7450.0920.0920.0000.0000.0000.000
163A923LEU 0-0.0170.01819.6190.0080.0080.0000.0000.0000.000
164A924ALA 0-0.017-0.01622.374-0.003-0.0030.0000.0000.0000.000
165A925ALA 00.0670.01122.0150.0140.0140.0000.0000.0000.000
166A926PHE 00.0460.01919.6840.0030.0030.0000.0000.0000.000
167A927ILE 0-0.040-0.01217.0060.0320.0320.0000.0000.0000.000
168A928THR 00.012-0.00317.3760.0340.0340.0000.0000.0000.000
169A929GLU -1-0.966-0.96019.4780.1880.1880.0000.0000.0000.000
170A930GLY 00.0190.00217.7550.0360.0360.0000.0000.0000.000
171A931LEU 0-0.056-0.00613.4470.0190.0190.0000.0000.0000.000
172A932GLU -1-0.835-0.90517.0160.0800.0800.0000.0000.0000.000
173A933VAL 0-0.031-0.02017.7520.0060.0060.0000.0000.0000.000
174A934HIS 0-0.0200.00019.476-0.019-0.0190.0000.0000.0000.000
175A935PHE 0-0.051-0.04220.9450.0020.0020.0000.0000.0000.000
176A936VAL 00.041-0.00122.096-0.004-0.0040.0000.0000.0000.000
177A937GLU -1-0.956-0.98524.8450.0220.0220.0000.0000.0000.000
178A938HIS 00.000-0.03927.030-0.007-0.0070.0000.0000.0000.000
179A939TYR 00.029-0.01420.0580.0020.0020.0000.0000.0000.000
180A940ARG 10.8010.89524.1310.0180.0180.0000.0000.0000.000
181A941GLU -1-0.793-0.87625.0870.0190.0190.0000.0000.0000.000
182A942ILE 0-0.022-0.02819.2030.0050.0050.0000.0000.0000.000
183A943PHE 0-0.074-0.02820.361-0.005-0.0050.0000.0000.0000.000
184A944ASP -1-0.747-0.89022.065-0.011-0.0110.0000.0000.0000.000
185A945ILE 0-0.056-0.01518.2000.0050.0050.0000.0000.0000.000
186A946ALA 0-0.039-0.02317.5450.0060.0060.0000.0000.0000.000
187A947PHE 0-0.033-0.03018.343-0.014-0.0140.0000.0000.0000.000
188A948PRO 00.0140.01320.2130.0010.0010.0000.0000.0000.000
189A949ASP -1-0.931-0.96923.198-0.011-0.0110.0000.0000.0000.000
190A950GLU -1-0.932-0.96824.178-0.057-0.0570.0000.0000.0000.000
191A951GLN 0-0.0120.00926.3400.0040.0040.0000.0000.0000.000
192A952ALA 00.001-0.00629.518-0.002-0.0020.0000.0000.0000.000
193A953GLU -1-0.917-0.97730.501-0.012-0.0120.0000.0000.0000.000
194A954NME 0-0.052-0.00329.3630.0010.0010.0000.0000.0000.000