FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 16JRZ

Calculation Name: 2C0L-A-Xray372

Preferred Name: Non-specific lipid-transfer protein

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 2C0L

Chain ID: A

ChEMBL ID: CHEMBL5950

UniProt ID: P22307

Base Structure: X-ray

Registration Date: 2023-09-26

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 292
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -4121864.867435
FMO2-HF: Nuclear repulsion 4007485.603715
FMO2-HF: Total energy -114379.26372
FMO2-MP2: Total energy -114711.737693


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:335:HIS)


Summations of interaction energy for fragment #1(A:335:HIS)
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.
-191.028-187.10230.085-16.59-17.42-0.125
Interaction energy analysis for fragmet #1(A:335:HIS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.868 / q_NPA : 0.903
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].
3A337GLN00.0170.0033.1741.3253.7040.002-1.133-1.2480.001
4A338PRO0-0.019-0.0022.845-4.000-2.7480.111-0.302-1.061-0.001
5A339PHE00.0950.0473.9360.2290.3880.003-0.008-0.1540.000
6A340GLU-1-0.801-0.9077.501-25.011-25.0110.0000.0000.0000.000
7A341GLU-1-0.876-0.9221.629-119.322-122.74119.580-9.877-6.284-0.113
8A342GLY00.0490.0185.8260.9940.9940.0000.0000.0000.000
9A343LEU0-0.005-0.0027.7302.5532.5530.0000.0000.0000.000
10A344ARG10.8870.9555.81839.46439.4640.0000.0000.0000.000
11A345ARG10.8590.9433.64250.43550.5800.000-0.014-0.1310.000
12A346LEU00.0140.0039.6071.8931.8930.0000.0000.0000.000
13A347GLN0-0.045-0.01112.5442.4572.4570.0000.0000.0000.000
14A348GLU-1-0.970-0.99010.249-27.959-27.9590.0000.0000.0000.000
15A349GLY00.0270.02414.1030.6640.6640.0000.0000.0000.000
16A350ASP-1-0.854-0.9219.484-28.788-28.7880.0000.0000.0000.000
17A351LEU00.0140.00211.656-1.983-1.9830.0000.0000.0000.000
18A352PRO00.0210.01512.755-1.210-1.2100.0000.0000.0000.000
19A353ASN00.001-0.0437.543-3.433-3.4330.0000.0000.0000.000
20A354ALA00.0180.0128.266-4.076-4.0760.0000.0000.0000.000
21A355VAL0-0.044-0.0179.406-0.926-0.9260.0000.0000.0000.000
22A356LEU00.0180.0118.458-0.586-0.5860.0000.0000.0000.000
23A357LEU0-0.072-0.0152.923-4.229-3.2750.188-0.234-0.908-0.002
24A358PHE0-0.002-0.0076.061-0.721-0.7210.0000.0000.0000.000
25A359GLU-1-0.857-0.9438.909-21.233-21.2330.0000.0000.0000.000
26A360ALA0-0.038-0.0184.0390.3310.448-0.001-0.014-0.1020.000
27A361ALA0-0.060-0.0316.1790.2580.2580.0000.0000.0000.000
28A362VAL00.0070.0057.4721.4791.4790.0000.0000.0000.000
29A363GLN0-0.031-0.0097.935-0.103-0.1030.0000.0000.0000.000
30A364GLN0-0.094-0.0453.9461.4091.492-0.001-0.020-0.0610.000
31A365ASP-1-0.822-0.9238.592-18.155-18.1550.0000.0000.0000.000
32A366PRO00.0040.01211.4270.2190.2190.0000.0000.0000.000
33A367LYS10.9020.95014.11514.70314.7030.0000.0000.0000.000
34A368HIS00.0620.04910.4821.8181.8180.0000.0000.0000.000
35A369MET0-0.0150.00514.179-0.399-0.3990.0000.0000.0000.000
36A370GLU-1-0.835-0.93814.846-17.565-17.5650.0000.0000.0000.000
37A371ALA00.0250.00610.948-0.365-0.3650.0000.0000.0000.000
38A372TRP00.007-0.02012.710-0.261-0.2610.0000.0000.0000.000
39A373GLN00.0290.02715.4231.1861.1860.0000.0000.0000.000
40A374TYR0-0.029-0.00813.4960.5100.5100.0000.0000.0000.000
41A375LEU0-0.0330.02212.387-0.116-0.1160.0000.0000.0000.000
42A376GLY00.008-0.01414.4830.4770.4770.0000.0000.0000.000
43A377THR00.021-0.01317.9260.3040.3040.0000.0000.0000.000
44A378THR00.007-0.01413.9350.3050.3050.0000.0000.0000.000
45A379GLN00.0290.01215.3340.5020.5020.0000.0000.0000.000
46A380ALA00.0260.02217.9110.6080.6080.0000.0000.0000.000
47A381GLU-1-0.861-0.93518.859-15.836-15.8360.0000.0000.0000.000
48A382ASN0-0.009-0.00517.0700.2140.2140.0000.0000.0000.000
49A383GLU-1-0.813-0.88819.396-12.223-12.2230.0000.0000.0000.000
50A384GLN0-0.0030.01618.8660.8490.8490.0000.0000.0000.000
51A385GLU-1-0.681-0.80121.267-12.643-12.6430.0000.0000.0000.000
52A386LEU00.0350.01423.865-0.064-0.0640.0000.0000.0000.000
53A387LEU0-0.003-0.00717.7140.0110.0110.0000.0000.0000.000
54A388ALA00.0080.01219.448-0.457-0.4570.0000.0000.0000.000
55A389ILE00.007-0.00220.525-0.036-0.0360.0000.0000.0000.000
56A390SER0-0.069-0.02920.2320.2260.2260.0000.0000.0000.000
57A391ALA00.0280.01817.0270.1010.1010.0000.0000.0000.000
58A392LEU00.0300.02518.828-0.067-0.0670.0000.0000.0000.000
59A393ARG10.9280.96721.24012.11912.1190.0000.0000.0000.000
60A394ARG10.8560.93317.54314.83414.8340.0000.0000.0000.000
61A395CYS0-0.080-0.03518.7040.2610.2610.0000.0000.0000.000
62A396LEU00.022-0.00520.1320.2250.2250.0000.0000.0000.000
63A397GLU-1-0.920-0.93822.597-12.066-12.0660.0000.0000.0000.000
64A398LEU0-0.152-0.05817.6880.3000.3000.0000.0000.0000.000
65A399LYS10.8050.87722.14112.01812.0180.0000.0000.0000.000
66A400PRO00.0290.02224.281-0.120-0.1200.0000.0000.0000.000
67A401ASP-1-0.809-0.88627.329-11.015-11.0150.0000.0000.0000.000
68A402ASN0-0.035-0.04320.5600.2520.2520.0000.0000.0000.000
69A403GLN00.0650.01624.793-0.110-0.1100.0000.0000.0000.000
70A404THR00.0340.01921.3390.4400.4400.0000.0000.0000.000
71A405ALA00.015-0.00821.568-0.094-0.0940.0000.0000.0000.000
72A406LEU0-0.0250.00223.1740.1760.1760.0000.0000.0000.000
73A407MET00.0160.02226.6930.2890.2890.0000.0000.0000.000
74A408ALA00.004-0.00323.1150.1880.1880.0000.0000.0000.000
75A409LEU00.0030.01024.9890.0720.0720.0000.0000.0000.000
76A410ALA00.0290.01226.2460.2640.2640.0000.0000.0000.000
77A411VAL0-0.020-0.00127.1740.3370.3370.0000.0000.0000.000
78A412SER0-0.003-0.01925.0450.0620.0620.0000.0000.0000.000
79A413PHE0-0.025-0.02927.5270.1170.1170.0000.0000.0000.000
80A414THR0-0.014-0.02830.5300.4240.4240.0000.0000.0000.000
81A415ASN0-0.080-0.05027.6620.5550.5550.0000.0000.0000.000
82A416GLU-1-0.942-0.95929.222-10.560-10.5600.0000.0000.0000.000
83A417SER0-0.048-0.01632.0600.3360.3360.0000.0000.0000.000
84A418LEU0-0.071-0.02231.4460.2680.2680.0000.0000.0000.000
85A419GLN00.0940.04634.802-0.030-0.0300.0000.0000.0000.000
86A420ARG10.8790.94637.1287.6737.6730.0000.0000.0000.000
87A421GLN00.0710.01932.9030.1100.1100.0000.0000.0000.000
88A422ALA00.0210.01932.633-0.212-0.2120.0000.0000.0000.000
89A423CYS0-0.029-0.01633.691-0.027-0.0270.0000.0000.0000.000
90A424GLU-1-0.905-0.96835.040-8.406-8.4060.0000.0000.0000.000
91A425ILE0-0.0110.00129.071-0.035-0.0350.0000.0000.0000.000
92A426LEU00.0180.01532.023-0.136-0.1360.0000.0000.0000.000
93A427ARG10.7870.87133.9467.7977.7970.0000.0000.0000.000
94A428ASP-1-0.802-0.88932.049-8.974-8.9740.0000.0000.0000.000
95A429TRP00.0180.01028.9060.0850.0850.0000.0000.0000.000
96A430LEU0-0.0170.01331.949-0.042-0.0420.0000.0000.0000.000
97A431ARG10.7720.84734.5078.9278.9270.0000.0000.0000.000
98A432TYR0-0.024-0.01430.7730.1480.1480.0000.0000.0000.000
99A433THR00.0300.01931.508-0.393-0.3930.0000.0000.0000.000
100A434PRO0-0.053-0.04132.0370.3100.3100.0000.0000.0000.000
101A435ALA0-0.0140.00435.0930.2280.2280.0000.0000.0000.000
102A436TYR0-0.010-0.05235.2990.3720.3720.0000.0000.0000.000
103A437ALA00.0010.01736.4470.1370.1370.0000.0000.0000.000
104A438HIS0-0.0070.02738.2370.0210.0210.0000.0000.0000.000
105A439LEU0-0.0300.00940.6870.1820.1820.0000.0000.0000.000
106A440VAL0-0.121-0.08538.6600.2650.2650.0000.0000.0000.000
107A454PRO00.0220.00449.2850.0040.0040.0000.0000.0000.000
108A455SER00.0420.00148.989-0.126-0.1260.0000.0000.0000.000
109A456LYS10.9880.98550.2485.8725.8720.0000.0000.0000.000
110A457ARG11.0291.02442.8557.0837.0830.0000.0000.0000.000
111A458ILE0-0.036-0.01144.938-0.137-0.1370.0000.0000.0000.000
112A459LEU00.0320.00945.847-0.096-0.0960.0000.0000.0000.000
113A460GLY00.0420.02847.246-0.018-0.0180.0000.0000.0000.000
114A461SER0-0.039-0.02341.711-0.109-0.1090.0000.0000.0000.000
115A462LEU00.0140.00042.238-0.179-0.1790.0000.0000.0000.000
116A463LEU0-0.0110.01544.539-0.007-0.0070.0000.0000.0000.000
117A464SER00.022-0.00441.750-0.096-0.0960.0000.0000.0000.000
118A465ASP-1-0.842-0.92743.276-6.933-6.9330.0000.0000.0000.000
119A466SER0-0.078-0.04245.8320.1010.1010.0000.0000.0000.000
120A467LEU0-0.043-0.01439.0070.0180.0180.0000.0000.0000.000
121A468PHE00.0330.01240.103-0.059-0.0590.0000.0000.0000.000
122A469LEU0-0.0090.00142.415-0.068-0.0680.0000.0000.0000.000
123A470GLU-1-0.800-0.87443.564-7.242-7.2420.0000.0000.0000.000
124A471VAL00.010-0.00637.763-0.009-0.0090.0000.0000.0000.000
125A472LYS10.8920.95840.8407.0567.0560.0000.0000.0000.000
126A473GLU-1-0.928-0.97442.026-6.603-6.6030.0000.0000.0000.000
127A474LEU0-0.071-0.02641.0730.0470.0470.0000.0000.0000.000
128A475PHE00.0330.00434.462-0.054-0.0540.0000.0000.0000.000
129A476LEU0-0.030-0.01840.3690.0210.0210.0000.0000.0000.000
130A477ALA0-0.085-0.04243.5610.1090.1090.0000.0000.0000.000
131A478ALA00.0220.00339.2430.0600.0600.0000.0000.0000.000
132A479VAL0-0.008-0.00140.032-0.020-0.0200.0000.0000.0000.000
133A480ARG10.9140.95241.9846.8366.8360.0000.0000.0000.000
134A481LEU0-0.052-0.01441.3690.1660.1660.0000.0000.0000.000
135A482ASP-1-0.767-0.84442.517-7.260-7.2600.0000.0000.0000.000
136A483PRO0-0.062-0.01043.217-0.119-0.1190.0000.0000.0000.000
137A484THR0-0.134-0.08544.8960.0180.0180.0000.0000.0000.000
138A485SER0-0.056-0.04739.584-0.152-0.1520.0000.0000.0000.000
139A486ILE0-0.0100.00036.8040.0200.0200.0000.0000.0000.000
140A487ASP-1-0.744-0.84733.927-9.519-9.5190.0000.0000.0000.000
141A488PRO00.001-0.01931.4510.0800.0800.0000.0000.0000.000
142A489ASP-1-0.788-0.87729.131-11.073-11.0730.0000.0000.0000.000
143A490VAL0-0.0010.00031.9130.0310.0310.0000.0000.0000.000
144A491GLN0-0.004-0.00835.2960.1470.1470.0000.0000.0000.000
145A492CYS0-0.034-0.00230.598-0.041-0.0410.0000.0000.0000.000
146A493GLY00.0300.00533.2270.0060.0060.0000.0000.0000.000
147A494LEU0-0.034-0.01234.0850.1700.1700.0000.0000.0000.000
148A495GLY00.0450.01336.0870.2040.2040.0000.0000.0000.000
149A496VAL0-0.024-0.01231.6040.0360.0360.0000.0000.0000.000
150A497LEU00.001-0.00434.8550.1420.1420.0000.0000.0000.000
151A498PHE0-0.016-0.02137.9960.2470.2470.0000.0000.0000.000
152A499ASN0-0.052-0.03536.1780.1300.1300.0000.0000.0000.000
153A500LEU0-0.052-0.01335.7040.1080.1080.0000.0000.0000.000
154A501SER0-0.067-0.06238.9680.0720.0720.0000.0000.0000.000
155A502GLY00.0330.02341.4650.1810.1810.0000.0000.0000.000
156A503GLU-1-0.820-0.85442.847-6.936-6.9360.0000.0000.0000.000
157A504TYR00.0800.01338.761-0.050-0.0500.0000.0000.0000.000
158A505ASP-1-0.850-0.92941.236-7.192-7.1920.0000.0000.0000.000
159A506LYS10.8600.91843.0596.8356.8350.0000.0000.0000.000
160A507ALA00.0050.00837.884-0.102-0.1020.0000.0000.0000.000
161A508VAL00.0090.00638.185-0.249-0.2490.0000.0000.0000.000
162A509ASP-1-0.882-0.92338.759-7.569-7.5690.0000.0000.0000.000
163A510CYS0-0.080-0.02337.824-0.022-0.0220.0000.0000.0000.000
164A511PHE00.020-0.01432.527-0.255-0.2550.0000.0000.0000.000
165A512THR0-0.005-0.01334.671-0.251-0.2510.0000.0000.0000.000
166A513ALA0-0.015-0.00136.901-0.062-0.0620.0000.0000.0000.000
167A514ALA00.0050.00432.737-0.067-0.0670.0000.0000.0000.000
168A515LEU0-0.011-0.01030.651-0.249-0.2490.0000.0000.0000.000
169A516SER0-0.101-0.05533.255-0.053-0.0530.0000.0000.0000.000
170A517VAL0-0.027-0.00432.7100.0210.0210.0000.0000.0000.000
171A518ARG10.7150.82027.46511.00911.0090.0000.0000.0000.000
172A519PRO00.0560.03329.817-0.257-0.2570.0000.0000.0000.000
173A520ASN0-0.013-0.01326.0400.0930.0930.0000.0000.0000.000
174A521ASP-1-0.776-0.87825.258-12.643-12.6430.0000.0000.0000.000
175A522TYR00.003-0.02819.1470.4900.4900.0000.0000.0000.000
176A523LEU00.0240.01521.6130.3200.3200.0000.0000.0000.000
177A524LEU0-0.079-0.04025.5930.3400.3400.0000.0000.0000.000
178A525TRP00.0220.01428.2300.5010.5010.0000.0000.0000.000
179A526ASN00.0760.04926.7410.4950.4950.0000.0000.0000.000
180A527LYS10.8930.96826.87711.64211.6420.0000.0000.0000.000
181A528LEU00.0080.02431.0640.3040.3040.0000.0000.0000.000
182A529GLY00.0520.00532.4120.2960.2960.0000.0000.0000.000
183A530ALA0-0.003-0.00731.5090.2270.2270.0000.0000.0000.000
184A531THR0-0.001-0.00833.5400.2800.2800.0000.0000.0000.000
185A532LEU0-0.0050.01036.5010.2760.2760.0000.0000.0000.000
186A533ALA0-0.007-0.00235.5640.2230.2230.0000.0000.0000.000
187A534ASN0-0.038-0.01535.0000.1740.1740.0000.0000.0000.000
188A535GLY0-0.036-0.01038.7120.2000.2000.0000.0000.0000.000
189A536ASN0-0.077-0.04340.8570.1680.1680.0000.0000.0000.000
190A537GLN0-0.044-0.01340.8060.2340.2340.0000.0000.0000.000
191A538SER00.041-0.00538.580-0.256-0.2560.0000.0000.0000.000
192A539GLU-1-0.927-0.95138.109-8.133-8.1330.0000.0000.0000.000
193A540GLU-1-0.864-0.95038.673-7.821-7.8210.0000.0000.0000.000
194A541ALA0-0.039-0.01635.480-0.240-0.2400.0000.0000.0000.000
195A542VAL00.014-0.00233.984-0.395-0.3950.0000.0000.0000.000
196A543ALA0-0.011-0.00133.310-0.316-0.3160.0000.0000.0000.000
197A544ALA0-0.0090.00832.934-0.213-0.2130.0000.0000.0000.000
198A545TYR00.0160.00029.540-0.435-0.4350.0000.0000.0000.000
199A546ARG10.8460.91528.6059.2659.2650.0000.0000.0000.000
200A547ARG10.8650.94028.8389.7299.7290.0000.0000.0000.000
201A548ALA00.004-0.01226.108-0.387-0.3870.0000.0000.0000.000
202A549LEU0-0.030-0.01923.793-0.585-0.5850.0000.0000.0000.000
203A550GLU-1-0.898-0.92724.215-10.717-10.7170.0000.0000.0000.000
204A551LEU0-0.080-0.03624.371-0.327-0.3270.0000.0000.0000.000
205A552GLN00.0040.00017.890-0.750-0.7500.0000.0000.0000.000
206A553PRO00.0470.03320.1450.1230.1230.0000.0000.0000.000
207A554GLY00.0360.02217.6150.2010.2010.0000.0000.0000.000
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