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: K3Y63

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 OptAll
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 -2018335.593985
FMO2-HF: Nuclear repulsion 1945554.855694
FMO2-HF: Total energy -72780.738291
FMO2-MP2: Total energy -72990.362269


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.
-20.535-14.3819.903-5.67-10.388-0.046
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 : -0.064 / q_NPA : -0.017
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-1-0.897-0.9383.867-3.235-1.385-0.013-0.885-0.9520.002
4A759VAL0-0.032-0.0256.2200.7950.7950.0000.0000.0000.000
5A760THR0-0.0140.0065.458-0.438-0.4380.0000.0000.0000.000
6A761PRO0-0.0010.0076.4360.3970.3970.0000.0000.0000.000
7A762PRO00.003-0.0159.4930.1380.1380.0000.0000.0000.000
8A763GLY00.0150.02210.142-0.149-0.1490.0000.0000.0000.000
9A764VAL0-0.041-0.0154.8810.2130.2130.0000.0000.0000.000
10A765VAL00.0080.0007.791-0.095-0.0950.0000.0000.0000.000
11A766MET0-0.0030.0105.2390.3700.3700.0000.0000.0000.000
12A767GLY00.0410.0207.830-0.315-0.3150.0000.0000.0000.000
13A768LEU0-0.051-0.0229.5280.3940.3940.0000.0000.0000.000
14A769ALA00.0180.00712.035-0.177-0.1770.0000.0000.0000.000
15A770TRP0-0.028-0.02313.6890.0530.0530.0000.0000.0000.000
16A771THR0-0.020-0.03012.450-0.049-0.0490.0000.0000.0000.000
17A772ALA00.0170.00215.945-0.084-0.0840.0000.0000.0000.000
18A773MET0-0.017-0.00515.818-0.060-0.0600.0000.0000.0000.000
19A774GLY00.0120.01117.468-0.022-0.0220.0000.0000.0000.000
20A775GLY00.0480.02914.537-0.073-0.0730.0000.0000.0000.000
21A776SER0-0.089-0.0499.0780.1600.1600.0000.0000.0000.000
22A777THR00.0380.0315.879-0.460-0.4600.0000.0000.0000.000
23A778LEU0-0.050-0.0216.3801.0371.0370.0000.0000.0000.000
24A779PHE00.0620.0212.542-5.494-3.8247.277-2.623-6.324-0.015
25A780VAL0-0.009-0.0015.029-0.1960.0370.000-0.048-0.1850.000
26A781GLU-1-0.827-0.9042.492-11.687-9.4442.641-2.104-2.781-0.033
27A782THR0-0.036-0.0366.5990.2060.2060.0000.0000.0000.000
28A783SER00.0030.0049.451-0.222-0.2220.0000.0000.0000.000
29A784LEU00.0080.01011.3790.1330.1330.0000.0000.0000.000
30A785ARG10.8180.88213.5760.1860.1860.0000.0000.0000.000
31A786ARG10.8940.94015.7100.2550.2550.0000.0000.0000.000
32A787PRO00.0100.01419.202-0.020-0.0200.0000.0000.0000.000
33A788GLN00.0200.01021.0930.0350.0350.0000.0000.0000.000
34A797ASP-1-0.804-0.86625.820-0.102-0.1020.0000.0000.0000.000
35A798GLY0-0.008-0.00322.665-0.013-0.0130.0000.0000.0000.000
36A799SER0-0.110-0.08520.3090.0190.0190.0000.0000.0000.000
37A800LEU00.0180.00714.396-0.030-0.0300.0000.0000.0000.000
38A801GLU-1-0.850-0.87414.327-0.186-0.1860.0000.0000.0000.000
39A802VAL0-0.002-0.02012.838-0.020-0.0200.0000.0000.0000.000
40A803THR0-0.033-0.0218.851-0.030-0.0300.0000.0000.0000.000
41A804GLY00.0730.02010.3270.0590.0590.0000.0000.0000.000
42A805GLN0-0.083-0.05711.205-0.032-0.0320.0000.0000.0000.000
43A806LEU0-0.0250.01512.919-0.011-0.0110.0000.0000.0000.000
44A807GLY00.0680.02616.159-0.068-0.0680.0000.0000.0000.000
45A808GLU-1-0.795-0.89219.5210.1650.1650.0000.0000.0000.000
46A809VAL00.0330.01121.615-0.012-0.0120.0000.0000.0000.000
47A810MET00.0090.02614.788-0.011-0.0110.0000.0000.0000.000
48A811LYS10.8360.91217.075-0.205-0.2050.0000.0000.0000.000
49A812GLU-1-0.855-0.91718.5710.0850.0850.0000.0000.0000.000
50A813SER00.0050.00318.128-0.007-0.0070.0000.0000.0000.000
51A814ALA00.0200.00615.602-0.015-0.0150.0000.0000.0000.000
52A815ARG10.8160.89017.299-0.150-0.1500.0000.0000.0000.000
53A816ILE00.0140.01320.639-0.030-0.0300.0000.0000.0000.000
54A817ALA00.0180.01217.497-0.023-0.0230.0000.0000.0000.000
55A818TYR00.0280.00818.234-0.025-0.0250.0000.0000.0000.000
56A819THR0-0.048-0.03119.591-0.029-0.0290.0000.0000.0000.000
57A820PHE0-0.0130.00021.854-0.015-0.0150.0000.0000.0000.000
58A821ALA00.0380.01919.254-0.014-0.0140.0000.0000.0000.000
59A822ARG10.8120.87021.2910.0750.0750.0000.0000.0000.000
60A823ALA0-0.030-0.01523.668-0.009-0.0090.0000.0000.0000.000
61A824PHE00.000-0.00223.017-0.001-0.0010.0000.0000.0000.000
62A825LEU00.0210.00621.308-0.009-0.0090.0000.0000.0000.000
63A826MET0-0.042-0.02024.374-0.008-0.0080.0000.0000.0000.000
64A827GLN0-0.041-0.01227.6070.0080.0080.0000.0000.0000.000
65A828HIS0-0.024-0.01223.9100.0210.0210.0000.0000.0000.000
66A829ALA0-0.005-0.00625.132-0.011-0.0110.0000.0000.0000.000
67A830PRO0-0.009-0.00927.194-0.009-0.0090.0000.0000.0000.000
68A831ALA0-0.058-0.01829.1730.0050.0050.0000.0000.0000.000
69A832ASN0-0.037-0.02921.743-0.013-0.0130.0000.0000.0000.000
70A833ASP-1-0.817-0.89625.444-0.204-0.2040.0000.0000.0000.000
71A834TYR00.0840.05716.1040.0020.0020.0000.0000.0000.000
72A835LEU0-0.009-0.01718.243-0.009-0.0090.0000.0000.0000.000
73A836VAL0-0.063-0.03521.2560.0210.0210.0000.0000.0000.000
74A837THR0-0.007-0.02223.7840.0060.0060.0000.0000.0000.000
75A838SER0-0.0130.00418.934-0.019-0.0190.0000.0000.0000.000
76A839HIS0-0.075-0.01319.3300.0240.0240.0000.0000.0000.000
77A840ILE00.0200.00414.075-0.056-0.0560.0000.0000.0000.000
78A841HIS0-0.020-0.0109.4510.0590.0590.0000.0000.0000.000
79A842LEU00.0210.00710.107-0.073-0.0730.0000.0000.0000.000
80A843HIS00.0090.0194.283-0.0130.064-0.001-0.004-0.0720.000
81A844VAL00.0240.0067.5100.1750.1750.0000.0000.0000.000
82A845PRO0-0.0150.0005.460-0.344-0.263-0.001-0.006-0.0740.000
83A846GLU-1-0.852-0.9257.5940.9040.9040.0000.0000.0000.000
84A847GLY00.0240.00210.0110.4440.4440.0000.0000.0000.000
85A848ALA0-0.0050.00212.550-0.152-0.1520.0000.0000.0000.000
86A849THR00.0510.03014.730-0.105-0.1050.0000.0000.0000.000
87A850PRO00.017-0.00318.451-0.025-0.0250.0000.0000.0000.000
88A851LYS10.8040.88720.544-0.437-0.4370.0000.0000.0000.000
89A852ASP-1-0.714-0.84717.0340.6950.6950.0000.0000.0000.000
90A853GLY00.0020.03216.1680.0190.0190.0000.0000.0000.000
91A854PRO00.0530.00316.4250.0360.0360.0000.0000.0000.000
92A855SER0-0.050-0.01816.932-0.020-0.0200.0000.0000.0000.000
93A856ALA00.0590.03012.9540.0070.0070.0000.0000.0000.000
94A857GLY00.0210.01014.654-0.051-0.0510.0000.0000.0000.000
95A858CYS00.0220.01115.693-0.042-0.0420.0000.0000.0000.000
96A859THR00.0210.02110.510-0.055-0.0550.0000.0000.0000.000
97A860ILE0-0.004-0.00312.503-0.084-0.0840.0000.0000.0000.000
98A861VAL0-0.031-0.00513.760-0.096-0.0960.0000.0000.0000.000
99A862THR00.0190.00414.036-0.072-0.0720.0000.0000.0000.000
100A863ALA0-0.0120.00410.659-0.094-0.0940.0000.0000.0000.000
101A864LEU00.0220.00012.408-0.127-0.1270.0000.0000.0000.000
102A865LEU0-0.0020.00315.048-0.049-0.0490.0000.0000.0000.000
103A866SER0-0.031-0.01812.883-0.079-0.0790.0000.0000.0000.000
104A867LEU0-0.028-0.02012.343-0.066-0.0660.0000.0000.0000.000
105A868ALA0-0.028-0.01414.263-0.010-0.0100.0000.0000.0000.000
106A869MET0-0.0390.00317.6780.0400.0400.0000.0000.0000.000
107A870GLY0-0.0110.00616.076-0.002-0.0020.0000.0000.0000.000
108A871ARG10.7740.85116.2540.3190.3190.0000.0000.0000.000
109A872PRO0-0.0040.00812.4300.0260.0260.0000.0000.0000.000
110A873VAL00.0130.02011.5360.1160.1160.0000.0000.0000.000
111A874ARG10.8100.87112.7390.0400.0400.0000.0000.0000.000
112A875GLN0-0.008-0.0199.6740.1620.1620.0000.0000.0000.000
113A876ASN0-0.046-0.0329.248-0.048-0.0480.0000.0000.0000.000
114A877LEU00.0380.04010.2720.1640.1640.0000.0000.0000.000
115A878ALA0-0.010-0.0119.7810.0270.0270.0000.0000.0000.000
116A879MET0-0.0180.00611.616-0.044-0.0440.0000.0000.0000.000
117A880THR0-0.001-0.01013.4880.1390.1390.0000.0000.0000.000
118A881GLY00.0670.00816.185-0.070-0.0700.0000.0000.0000.000
119A882GLU-1-0.938-0.95218.8960.2830.2830.0000.0000.0000.000
120A883VAL0-0.027-0.01520.401-0.023-0.0230.0000.0000.0000.000
121A884SER00.0150.00922.957-0.001-0.0010.0000.0000.0000.000
122A885LEU00.019-0.00625.264-0.010-0.0100.0000.0000.0000.000
123A886THR0-0.041-0.01826.929-0.010-0.0100.0000.0000.0000.000
124A887GLY00.0550.02825.332-0.012-0.0120.0000.0000.0000.000
125A888LYS10.8300.90525.597-0.139-0.1390.0000.0000.0000.000
126A889ILE0-0.022-0.00321.8580.0170.0170.0000.0000.0000.000
127A890LEU0-0.019-0.01023.815-0.017-0.0170.0000.0000.0000.000
128A891PRO0-0.001-0.00523.3630.0270.0270.0000.0000.0000.000
129A892VAL0-0.057-0.02119.2530.0170.0170.0000.0000.0000.000
130A893GLY00.0270.01621.313-0.026-0.0260.0000.0000.0000.000
131A894GLY00.030-0.00519.1690.0390.0390.0000.0000.0000.000
132A895ILE00.0530.03018.3170.0640.0640.0000.0000.0000.000
133A896LYS10.9961.01818.595-0.411-0.4110.0000.0000.0000.000
134A897GLU-1-0.862-0.93516.9980.6050.6050.0000.0000.0000.000
135A898LYS10.7830.89514.060-0.568-0.5680.0000.0000.0000.000
136A899THR00.0220.00913.5990.0420.0420.0000.0000.0000.000
137A900ILE0-0.051-0.03014.706-0.008-0.0080.0000.0000.0000.000
138A901ALA0-0.072-0.03010.6520.0450.0450.0000.0000.0000.000
139A902ALA00.0650.01710.0680.1320.1320.0000.0000.0000.000
140A903LYS10.8060.88710.487-0.380-0.3800.0000.0000.0000.000
141A904ARG10.8260.90710.228-1.715-1.7150.0000.0000.0000.000
142A905ALA0-0.0160.0005.9910.1850.1850.0000.0000.0000.000
143A906GLY00.0090.0157.238-0.354-0.3540.0000.0000.0000.000
144A907VAL0-0.046-0.0148.801-0.170-0.1700.0000.0000.0000.000
145A908THR0-0.0010.00310.6690.0320.0320.0000.0000.0000.000
146A909CYS0-0.095-0.03413.5150.0110.0110.0000.0000.0000.000
147A910ILE00.0130.00813.8770.0350.0350.0000.0000.0000.000
148A911VAL00.0210.00915.805-0.040-0.0400.0000.0000.0000.000
149A912LEU0-0.005-0.00517.4330.0760.0760.0000.0000.0000.000
150A913PRO00.0260.01820.093-0.042-0.0420.0000.0000.0000.000
151A914ALA00.007-0.00223.1480.0060.0060.0000.0000.0000.000
152A915GLU-1-0.845-0.91726.4280.1620.1620.0000.0000.0000.000
153A916ASN0-0.031-0.02523.4620.0090.0090.0000.0000.0000.000
154A917LYS10.8810.95625.018-0.107-0.1070.0000.0000.0000.000
155A918LYS10.7870.86926.644-0.247-0.2470.0000.0000.0000.000
156A919ASP-1-0.845-0.90424.2840.2810.2810.0000.0000.0000.000
157A920PHE00.0300.00118.8590.0260.0260.0000.0000.0000.000
158A921TYR0-0.049-0.02723.737-0.012-0.0120.0000.0000.0000.000
159A922ASP-1-0.843-0.90227.1120.2410.2410.0000.0000.0000.000
160A923LEU0-0.0380.00020.8910.0250.0250.0000.0000.0000.000
161A924ALA0-0.010-0.00924.517-0.024-0.0240.0000.0000.0000.000
162A925ALA00.0600.02323.7720.0180.0180.0000.0000.0000.000
163A926PHE00.0350.01021.515-0.003-0.0030.0000.0000.0000.000
164A927ILE0-0.064-0.03218.5970.0210.0210.0000.0000.0000.000
165A928THR00.0390.01518.8100.0330.0330.0000.0000.0000.000
166A929GLU-1-0.906-0.94120.5920.1100.1100.0000.0000.0000.000
167A930GLY00.0110.01518.8960.0340.0340.0000.0000.0000.000
168A931LEU0-0.041-0.00914.530-0.001-0.0010.0000.0000.0000.000
169A932GLU-1-0.763-0.82717.819-0.069-0.0690.0000.0000.0000.000
170A933VAL0-0.025-0.01918.3420.0170.0170.0000.0000.0000.000
171A934HIS0-0.028-0.02119.376-0.011-0.0110.0000.0000.0000.000
172A935PHE0-0.018-0.02321.1400.0310.0310.0000.0000.0000.000
173A936VAL00.0130.00921.213-0.020-0.0200.0000.0000.0000.000
174A937GLU-1-0.925-0.97824.4580.1200.1200.0000.0000.0000.000
175A938HIS00.013-0.00926.1170.0110.0110.0000.0000.0000.000
176A939TYR00.001-0.03117.535-0.018-0.0180.0000.0000.0000.000
177A940ARG10.7570.84322.1740.0770.0770.0000.0000.0000.000
178A941GLU-1-0.739-0.86523.6860.0480.0480.0000.0000.0000.000
179A942ILE0-0.011-0.01617.458-0.006-0.0060.0000.0000.0000.000
180A943PHE00.0050.00018.898-0.023-0.0230.0000.0000.0000.000
181A944ASP-1-0.749-0.85720.137-0.118-0.1180.0000.0000.0000.000
182A945ILE0-0.042-0.02117.795-0.019-0.0190.0000.0000.0000.000
183A946ALA0-0.049-0.02215.798-0.031-0.0310.0000.0000.0000.000
184A947PHE0-0.008-0.01415.444-0.073-0.0730.0000.0000.0000.000
185A948PRO00.0130.01418.9800.0130.0130.0000.0000.0000.000
186A949ASP-1-0.863-0.90920.971-0.323-0.3230.0000.0000.0000.000
187A950GLU-1-0.861-0.89821.595-0.282-0.2820.0000.0000.0000.000
188A951GLN0-0.043-0.01924.2610.0090.0090.0000.0000.0000.000
189A952ALA00.0200.01027.2920.0060.0060.0000.0000.0000.000
190A953GLU-1-0.979-0.98528.274-0.054-0.0540.0000.0000.0000.000