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

tag_button

FMODB ID: R5ZJ8

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 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 190
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2015222.331648
FMO2-HF: Nuclear repulsion 1942444.762795
FMO2-HF: Total energy -72777.568853
FMO2-MP2: Total energy -72987.051804


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.
-11.428-2.9371.692-3.895-6.284-0.03
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 : -0.052 / q_NPA : -0.032
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-1-0.915-0.9433.321-2.283-0.2820.005-1.024-0.981-0.003
4A759VAL0-0.026-0.0305.7250.3940.3940.0000.0000.0000.000
5A760THR0-0.041-0.0105.543-0.239-0.2390.0000.0000.0000.000
6A761PRO0-0.0110.0126.9980.0340.0340.0000.0000.0000.000
7A762PRO00.046-0.00810.1190.0130.0130.0000.0000.0000.000
8A763GLY0-0.010-0.00210.4650.0570.0570.0000.0000.0000.000
9A764VAL0-0.009-0.0165.018-0.0810.0540.000-0.016-0.1180.000
10A765VAL0-0.006-0.0028.079-0.118-0.1180.0000.0000.0000.000
11A766MET00.0080.0385.930-0.043-0.0430.0000.0000.0000.000
12A767GLY00.0250.0027.9210.0360.0360.0000.0000.0000.000
13A768LEU0-0.087-0.0319.710-0.055-0.0550.0000.0000.0000.000
14A769ALA00.0230.00711.2970.0210.0210.0000.0000.0000.000
15A770TRP00.0060.00012.9380.0220.0220.0000.0000.0000.000
16A771THR0-0.029-0.01512.391-0.001-0.0010.0000.0000.0000.000
17A772ALA0-0.004-0.01815.4350.0160.0160.0000.0000.0000.000
18A773MET00.009-0.00315.8210.0030.0030.0000.0000.0000.000
19A774GLY00.0240.01516.5700.0230.0230.0000.0000.0000.000
20A775GLY00.0220.03814.041-0.023-0.0230.0000.0000.0000.000
21A776SER0-0.077-0.0569.1670.0600.0600.0000.0000.0000.000
22A777THR00.0020.0195.938-0.005-0.0050.0000.0000.0000.000
23A778LEU0-0.028-0.0185.678-0.093-0.0930.0000.0000.0000.000
24A779PHE00.0670.0142.919-3.431-0.0271.369-1.285-3.487-0.009
25A780VAL0-0.039-0.0114.427-0.791-0.657-0.001-0.013-0.1190.000
26A781GLU-1-0.887-0.9442.850-4.897-2.1390.320-1.556-1.522-0.018
27A782THR0-0.0190.0026.756-0.124-0.1240.0000.0000.0000.000
28A783SER00.014-0.00910.2270.0680.0680.0000.0000.0000.000
29A784LEU0-0.037-0.00412.273-0.026-0.0260.0000.0000.0000.000
30A785ARG10.9700.98914.7110.1190.1190.0000.0000.0000.000
31A786ARG10.8720.94716.8090.0690.0690.0000.0000.0000.000
32A787PRO0-0.0030.02220.0590.0000.0000.0000.0000.0000.000
33A788GLN00.0660.02022.276-0.004-0.0040.0000.0000.0000.000
34A797ASP-1-0.971-0.99427.408-0.054-0.0540.0000.0000.0000.000
35A798GLY0-0.014-0.01323.218-0.001-0.0010.0000.0000.0000.000
36A799SER0-0.126-0.11521.306-0.003-0.0030.0000.0000.0000.000
37A800LEU00.0020.00114.8950.0000.0000.0000.0000.0000.000
38A801GLU-1-0.941-0.96214.810-0.154-0.1540.0000.0000.0000.000
39A802VAL00.009-0.00512.927-0.017-0.0170.0000.0000.0000.000
40A803THR0-0.009-0.0059.3700.0530.0530.0000.0000.0000.000
41A804GLY00.0550.0169.825-0.059-0.0590.0000.0000.0000.000
42A805GLN0-0.081-0.02610.6990.0470.0470.0000.0000.0000.000
43A806LEU00.0310.03612.6200.0270.0270.0000.0000.0000.000
44A807GLY00.035-0.00115.9080.0200.0200.0000.0000.0000.000
45A808GLU-1-0.850-0.95919.218-0.117-0.1170.0000.0000.0000.000
46A809VAL0-0.015-0.00420.796-0.001-0.0010.0000.0000.0000.000
47A810MET00.0190.03114.2120.0100.0100.0000.0000.0000.000
48A811LYS10.8990.97817.3940.1430.1430.0000.0000.0000.000
49A812GLU-1-0.861-0.91418.477-0.095-0.0950.0000.0000.0000.000
50A813SER0-0.016-0.02317.7180.0050.0050.0000.0000.0000.000
51A814ALA00.021-0.00215.3530.0010.0010.0000.0000.0000.000
52A815ARG10.8750.92517.0390.1160.1160.0000.0000.0000.000
53A816ILE00.0100.02320.2250.0080.0080.0000.0000.0000.000
54A817ALA00.0410.01817.2140.0060.0060.0000.0000.0000.000
55A818TYR00.0090.00718.3640.0090.0090.0000.0000.0000.000
56A819THR0-0.005-0.01119.4830.0090.0090.0000.0000.0000.000
57A820PHE0-0.0160.02221.6610.0060.0060.0000.0000.0000.000
58A821ALA00.031-0.00619.0800.0040.0040.0000.0000.0000.000
59A822ARG10.9060.96421.1360.0800.0800.0000.0000.0000.000
60A823ALA0-0.026-0.01623.4650.0040.0040.0000.0000.0000.000
61A824PHE0-0.028-0.01023.2080.0040.0040.0000.0000.0000.000
62A825LEU00.0250.00921.5870.0010.0010.0000.0000.0000.000
63A826MET00.005-0.00324.8910.0040.0040.0000.0000.0000.000
64A827GLN0-0.040-0.01028.2540.0040.0040.0000.0000.0000.000
65A828HIS0-0.020-0.00524.2950.0040.0040.0000.0000.0000.000
66A829ALA0-0.0110.00125.6950.0010.0010.0000.0000.0000.000
67A830PRO00.001-0.00327.7120.0000.0000.0000.0000.0000.000
68A831ALA0-0.054-0.01629.7330.0020.0020.0000.0000.0000.000
69A832ASN0-0.050-0.03822.4090.0020.0020.0000.0000.0000.000
70A833ASP-1-0.841-0.92426.217-0.051-0.0510.0000.0000.0000.000
71A834TYR00.0360.03316.800-0.001-0.0010.0000.0000.0000.000
72A835LEU0-0.003-0.01018.468-0.002-0.0020.0000.0000.0000.000
73A836VAL0-0.054-0.02521.832-0.004-0.0040.0000.0000.0000.000
74A837THR00.0290.02324.831-0.001-0.0010.0000.0000.0000.000
75A838SER0-0.014-0.01019.9340.0020.0020.0000.0000.0000.000
76A839HIS0-0.0060.05319.738-0.010-0.0100.0000.0000.0000.000
77A840ILE0-0.034-0.01714.1440.0030.0030.0000.0000.0000.000
78A841HIS00.002-0.02010.7460.0380.0380.0000.0000.0000.000
79A842LEU0-0.022-0.02710.2060.0190.0190.0000.0000.0000.000
80A843HIS00.0250.0364.8510.2910.2910.0000.0000.0000.000
81A844VAL00.003-0.0087.388-0.036-0.0360.0000.0000.0000.000
82A845PRO0-0.0410.0054.763-0.0260.033-0.001-0.001-0.0570.000
83A846GLU-1-0.876-0.9666.857-0.159-0.1590.0000.0000.0000.000
84A847GLY0-0.001-0.0218.686-0.038-0.0380.0000.0000.0000.000
85A848ALA0-0.0060.01311.1900.0520.0520.0000.0000.0000.000
86A849THR00.008-0.00713.9150.0050.0050.0000.0000.0000.000
87A850PRO00.006-0.02117.357-0.007-0.0070.0000.0000.0000.000
88A851LYS10.8840.93319.4420.0850.0850.0000.0000.0000.000
89A852ASP-1-0.728-0.83815.862-0.151-0.1510.0000.0000.0000.000
90A853GLY0-0.0070.01215.636-0.010-0.0100.0000.0000.0000.000
91A854PRO00.0660.00216.118-0.016-0.0160.0000.0000.0000.000
92A855SER0-0.030-0.00516.6650.0000.0000.0000.0000.0000.000
93A856ALA00.0210.00812.662-0.002-0.0020.0000.0000.0000.000
94A857GLY00.0340.03014.379-0.004-0.0040.0000.0000.0000.000
95A858CYS00.0590.03616.607-0.002-0.0020.0000.0000.0000.000
96A859THR00.0480.03710.7760.0060.0060.0000.0000.0000.000
97A860ILE00.0250.00312.0450.0080.0080.0000.0000.0000.000
98A861VAL0-0.057-0.01313.5330.0110.0110.0000.0000.0000.000
99A862THR00.010-0.02814.1790.0110.0110.0000.0000.0000.000
100A863ALA00.0020.00710.7680.0100.0100.0000.0000.0000.000
101A864LEU00.013-0.00212.6060.0180.0180.0000.0000.0000.000
102A865LEU00.0070.02015.3660.0110.0110.0000.0000.0000.000
103A866SER0-0.029-0.04113.4990.0100.0100.0000.0000.0000.000
104A867LEU0-0.053-0.02013.2030.0050.0050.0000.0000.0000.000
105A868ALA0-0.037-0.03415.1300.0030.0030.0000.0000.0000.000
106A869MET0-0.042-0.01218.7030.0050.0050.0000.0000.0000.000
107A870GLY0-0.0080.02316.8350.0010.0010.0000.0000.0000.000
108A871ARG10.9110.96417.3670.1050.1050.0000.0000.0000.000
109A872PRO0-0.0250.00612.3370.0080.0080.0000.0000.0000.000
110A873VAL00.0060.01611.3130.0060.0060.0000.0000.0000.000
111A874ARG10.8860.94912.6520.1280.1280.0000.0000.0000.000
112A875GLN0-0.004-0.0239.8160.0440.0440.0000.0000.0000.000
113A876ASN0-0.017-0.0018.932-0.038-0.0380.0000.0000.0000.000
114A877LEU00.0120.02510.4160.0660.0660.0000.0000.0000.000
115A878ALA00.0250.01410.710-0.060-0.0600.0000.0000.0000.000
116A879MET00.0070.01312.2200.0420.0420.0000.0000.0000.000
117A880THR0-0.004-0.01313.838-0.012-0.0120.0000.0000.0000.000
118A881GLY00.046-0.00116.6010.0120.0120.0000.0000.0000.000
119A882GLU-1-0.918-0.93518.952-0.108-0.1080.0000.0000.0000.000
120A883VAL0-0.058-0.01719.6600.0070.0070.0000.0000.0000.000
121A884SER0-0.0030.00322.2370.0020.0020.0000.0000.0000.000
122A885LEU00.055-0.00424.856-0.002-0.0020.0000.0000.0000.000
123A886THR0-0.034-0.01026.7210.0010.0010.0000.0000.0000.000
124A887GLY00.0640.03124.5390.0020.0020.0000.0000.0000.000
125A888LYS10.9560.97125.3730.0590.0590.0000.0000.0000.000
126A889ILE0-0.0010.04222.102-0.006-0.0060.0000.0000.0000.000
127A890LEU0-0.050-0.01923.9900.0070.0070.0000.0000.0000.000
128A891PRO00.0160.00023.346-0.009-0.0090.0000.0000.0000.000
129A892VAL0-0.035-0.00619.436-0.004-0.0040.0000.0000.0000.000
130A893GLY00.0200.01021.2940.0100.0100.0000.0000.0000.000
131A894GLY00.033-0.00319.363-0.013-0.0130.0000.0000.0000.000
132A895ILE00.0550.02818.556-0.005-0.0050.0000.0000.0000.000
133A896LYS10.9961.01318.8480.0010.0010.0000.0000.0000.000
134A897GLU-1-0.894-0.95716.675-0.040-0.0400.0000.0000.0000.000
135A898LYS10.7910.88614.4940.1390.1390.0000.0000.0000.000
136A899THR00.004-0.00414.052-0.021-0.0210.0000.0000.0000.000
137A900ILE0-0.032-0.00914.8120.0070.0070.0000.0000.0000.000
138A901ALA0-0.054-0.01710.5450.0250.0250.0000.0000.0000.000
139A902ALA00.0960.03710.154-0.007-0.0070.0000.0000.0000.000
140A903LYS10.8070.90710.9950.0070.0070.0000.0000.0000.000
141A904ARG10.8570.9269.545-0.110-0.1100.0000.0000.0000.000
142A905ALA0-0.050-0.0196.4190.1420.1420.0000.0000.0000.000
143A906GLY00.0310.0247.219-0.132-0.1320.0000.0000.0000.000
144A907VAL0-0.069-0.0348.767-0.063-0.0630.0000.0000.0000.000
145A908THR00.004-0.03110.9330.0670.0670.0000.0000.0000.000
146A909CYS0-0.0470.00513.8320.0360.0360.0000.0000.0000.000
147A910ILE0-0.029-0.00614.612-0.029-0.0290.0000.0000.0000.000
148A911VAL00.0470.01816.3990.0170.0170.0000.0000.0000.000
149A912LEU0-0.035-0.02917.926-0.008-0.0080.0000.0000.0000.000
150A913PRO00.0640.04220.5540.0050.0050.0000.0000.0000.000
151A914ALA00.0070.00623.4840.0050.0050.0000.0000.0000.000
152A915GLU-1-0.950-0.99126.803-0.054-0.0540.0000.0000.0000.000
153A916ASN0-0.039-0.05223.664-0.004-0.0040.0000.0000.0000.000
154A917LYS10.9640.98125.2880.0530.0530.0000.0000.0000.000
155A918LYS10.9250.95227.1410.0370.0370.0000.0000.0000.000
156A919ASP-1-0.840-0.88724.678-0.051-0.0510.0000.0000.0000.000
157A920PHE0-0.016-0.00619.8910.0030.0030.0000.0000.0000.000
158A921TYR0-0.004-0.03224.3020.0030.0030.0000.0000.0000.000
159A922ASP-1-0.997-0.99027.408-0.024-0.0240.0000.0000.0000.000
160A923LEU0-0.0190.01921.3760.0040.0040.0000.0000.0000.000
161A924ALA0-0.016-0.01524.3910.0010.0010.0000.0000.0000.000
162A925ALA00.0680.01124.012-0.002-0.0020.0000.0000.0000.000
163A926PHE00.0460.01821.863-0.005-0.0050.0000.0000.0000.000
164A927ILE0-0.040-0.01118.9410.0060.0060.0000.0000.0000.000
165A928THR00.011-0.00419.300-0.006-0.0060.0000.0000.0000.000
166A929GLU-1-0.966-0.96021.106-0.012-0.0120.0000.0000.0000.000
167A930GLY00.0190.00119.1970.0030.0030.0000.0000.0000.000
168A931LEU0-0.053-0.00514.919-0.011-0.0110.0000.0000.0000.000
169A932GLU-1-0.837-0.90617.934-0.104-0.1040.0000.0000.0000.000
170A933VAL0-0.031-0.02018.586-0.016-0.0160.0000.0000.0000.000
171A934HIS0-0.0220.00119.9610.0140.0140.0000.0000.0000.000
172A935PHE0-0.048-0.04221.614-0.007-0.0070.0000.0000.0000.000
173A936VAL00.0380.00021.6670.0030.0030.0000.0000.0000.000
174A937GLU-1-0.954-0.98524.761-0.058-0.0580.0000.0000.0000.000
175A938HIS0-0.003-0.03926.285-0.001-0.0010.0000.0000.0000.000
176A939TYR00.038-0.01017.7690.0000.0000.0000.0000.0000.000
177A940ARG10.7910.88622.5630.0680.0680.0000.0000.0000.000
178A941GLU-1-0.797-0.87624.139-0.076-0.0760.0000.0000.0000.000
179A942ILE0-0.023-0.02818.162-0.005-0.0050.0000.0000.0000.000
180A943PHE0-0.066-0.02519.010-0.012-0.0120.0000.0000.0000.000
181A944ASP-1-0.763-0.89520.351-0.085-0.0850.0000.0000.0000.000
182A945ILE0-0.057-0.01517.830-0.003-0.0030.0000.0000.0000.000
183A946ALA0-0.040-0.02415.687-0.016-0.0160.0000.0000.0000.000
184A947PHE0-0.034-0.03015.691-0.016-0.0160.0000.0000.0000.000
185A948PRO00.0180.01418.9450.0090.0090.0000.0000.0000.000
186A949ASP-1-0.934-0.97021.553-0.090-0.0900.0000.0000.0000.000
187A950GLU-1-0.934-0.96921.628-0.074-0.0740.0000.0000.0000.000
188A951GLN0-0.0100.01024.0790.0010.0010.0000.0000.0000.000
189A952ALA00.0050.00227.388-0.001-0.0010.0000.0000.0000.000
190A953GLU-1-0.950-0.97628.728-0.047-0.0470.0000.0000.0000.000