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: VK2M1

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 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 292
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -4121146.654926
FMO2-HF: Nuclear repulsion 4006769.006405
FMO2-HF: Total energy -114377.648521
FMO2-MP2: Total energy -114710.149878


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.
-194.918-211.47361.823-23.464-21.807-0.155
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 : 0.840 / q_NPA : 0.895
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].
3A337GLN00.0450.0213.1342.7345.1080.003-1.121-1.2560.001
4A338PRO0-0.0190.0022.786-3.956-2.5700.194-0.368-1.212-0.002
5A339PHE00.1000.0443.801-0.525-0.3630.0050.002-0.1680.000
6A340GLU-1-0.846-0.9307.521-24.958-24.9580.0000.0000.0000.000
7A341GLU-1-0.868-0.9221.509-121.204-142.63244.863-15.286-8.149-0.127
8A342GLY00.0250.0015.6520.8210.8210.0000.0000.0000.000
9A343LEU00.0070.0027.2082.6982.6980.0000.0000.0000.000
10A344ARG10.8980.9566.01638.62138.6210.0000.0000.0000.000
11A345ARG10.8940.9613.32752.65952.9180.003-0.057-0.2050.000
12A346LEU00.0230.0129.2911.9011.9010.0000.0000.0000.000
13A347GLN0-0.045-0.01312.2622.7212.7210.0000.0000.0000.000
14A348GLU-1-0.988-0.99210.360-27.589-27.5890.0000.0000.0000.000
15A349GLY00.0250.02313.9310.6790.6790.0000.0000.0000.000
16A350ASP-1-0.881-0.9279.672-28.146-28.1460.0000.0000.0000.000
17A351LEU00.0150.00111.132-2.208-2.2080.0000.0000.0000.000
18A352PRO00.0070.01012.109-1.328-1.3280.0000.0000.0000.000
19A353ASN00.027-0.0407.070-3.675-3.6750.0000.0000.0000.000
20A354ALA00.0000.0047.580-4.629-4.6290.0000.0000.0000.000
21A355VAL0-0.023-0.0109.078-0.991-0.9910.0000.0000.0000.000
22A356LEU00.0260.0178.287-0.506-0.5060.0000.0000.0000.000
23A357LEU0-0.053-0.0082.358-5.120-3.8510.748-0.508-1.511-0.004
24A358PHE0-0.023-0.0126.053-0.478-0.4780.0000.0000.0000.000
25A359GLU-1-0.918-0.9638.845-22.203-22.2030.0000.0000.0000.000
26A360ALA0-0.016-0.0074.0710.2860.402-0.001-0.013-0.1030.000
27A361ALA0-0.067-0.0386.2000.4760.4760.0000.0000.0000.000
28A362VAL00.0020.0057.4611.6561.6560.0000.0000.0000.000
29A363GLN0-0.016-0.0078.024-0.650-0.6500.0000.0000.0000.000
30A364GLN0-0.098-0.0463.6820.9451.0530.000-0.038-0.0700.000
31A365ASP-1-0.860-0.9418.527-18.437-18.4370.0000.0000.0000.000
32A366PRO00.0100.01511.3670.1990.1990.0000.0000.0000.000
33A367LYS10.9110.94814.07414.83014.8300.0000.0000.0000.000
34A368HIS00.0780.05210.2741.9731.9730.0000.0000.0000.000
35A369MET0-0.0040.00914.145-0.497-0.4970.0000.0000.0000.000
36A370GLU-1-0.859-0.95014.562-18.164-18.1640.0000.0000.0000.000
37A371ALA00.0110.01010.891-0.415-0.4150.0000.0000.0000.000
38A372TRP00.006-0.01212.593-0.329-0.3290.0000.0000.0000.000
39A373GLN00.0540.03115.3220.8550.8550.0000.0000.0000.000
40A374TYR0-0.017-0.00913.4130.5980.5980.0000.0000.0000.000
41A375LEU0-0.0090.04012.234-0.092-0.0920.0000.0000.0000.000
42A376GLY00.008-0.01414.4250.4980.4980.0000.0000.0000.000
43A377THR0-0.030-0.03317.7750.1820.1820.0000.0000.0000.000
44A378THR00.047-0.00813.1970.3400.3400.0000.0000.0000.000
45A379GLN00.0730.02615.7010.3060.3060.0000.0000.0000.000
46A380ALA0-0.0090.00817.7730.6440.6440.0000.0000.0000.000
47A381GLU-1-0.919-0.97518.201-16.193-16.1930.0000.0000.0000.000
48A382ASN0-0.0030.00016.2830.3130.3130.0000.0000.0000.000
49A383GLU-1-0.824-0.90818.720-12.377-12.3770.0000.0000.0000.000
50A384GLN0-0.0080.02518.5180.9880.9880.0000.0000.0000.000
51A385GLU-1-0.680-0.79521.259-12.747-12.7470.0000.0000.0000.000
52A386LEU00.0390.01423.840-0.054-0.0540.0000.0000.0000.000
53A387LEU0-0.003-0.00717.730-0.014-0.0140.0000.0000.0000.000
54A388ALA00.0090.01319.410-0.466-0.4660.0000.0000.0000.000
55A389ILE00.0180.00520.489-0.039-0.0390.0000.0000.0000.000
56A390SER0-0.083-0.03820.1070.2630.2630.0000.0000.0000.000
57A391ALA00.0340.02217.0290.1250.1250.0000.0000.0000.000
58A392LEU00.0170.02018.779-0.046-0.0460.0000.0000.0000.000
59A393ARG10.9340.96721.15912.29912.2990.0000.0000.0000.000
60A394ARG10.8850.95617.83514.91914.9190.0000.0000.0000.000
61A395CYS0-0.077-0.02818.7400.2980.2980.0000.0000.0000.000
62A396LEU00.014-0.01220.0450.2240.2240.0000.0000.0000.000
63A397GLU-1-0.928-0.95922.912-11.904-11.9040.0000.0000.0000.000
64A398LEU0-0.155-0.05517.6750.2980.2980.0000.0000.0000.000
65A399LYS10.8570.91722.11512.32712.3270.0000.0000.0000.000
66A400PRO00.0400.02724.185-0.154-0.1540.0000.0000.0000.000
67A401ASP-1-0.838-0.91427.093-11.037-11.0370.0000.0000.0000.000
68A402ASN0-0.052-0.05120.3100.2690.2690.0000.0000.0000.000
69A403GLN00.0820.02324.673-0.013-0.0130.0000.0000.0000.000
70A404THR00.0280.02221.2490.1580.1580.0000.0000.0000.000
71A405ALA00.010-0.01021.524-0.109-0.1090.0000.0000.0000.000
72A406LEU0-0.0200.00523.0800.1580.1580.0000.0000.0000.000
73A407MET00.0200.02426.6050.2790.2790.0000.0000.0000.000
74A408ALA0-0.002-0.00723.0790.1890.1890.0000.0000.0000.000
75A409LEU0-0.0010.00524.9690.0580.0580.0000.0000.0000.000
76A410ALA00.0330.01226.1790.2620.2620.0000.0000.0000.000
77A411VAL0-0.028-0.01027.0080.3230.3230.0000.0000.0000.000
78A412SER0-0.014-0.04925.0520.0010.0010.0000.0000.0000.000
79A413PHE0-0.028-0.02627.4870.1140.1140.0000.0000.0000.000
80A414THR0-0.019-0.02530.4840.4290.4290.0000.0000.0000.000
81A415ASN0-0.062-0.03027.5550.5830.5830.0000.0000.0000.000
82A416GLU-1-0.939-0.95329.236-10.661-10.6610.0000.0000.0000.000
83A417SER0-0.040-0.01432.0370.3570.3570.0000.0000.0000.000
84A418LEU0-0.078-0.02431.3450.2710.2710.0000.0000.0000.000
85A419GLN00.0900.02334.749-0.034-0.0340.0000.0000.0000.000
86A420ARG10.8770.95837.0667.7587.7580.0000.0000.0000.000
87A421GLN00.0750.01532.8370.1620.1620.0000.0000.0000.000
88A422ALA00.0440.02932.563-0.214-0.2140.0000.0000.0000.000
89A423CYS0-0.032-0.01033.625-0.025-0.0250.0000.0000.0000.000
90A424GLU-1-0.930-0.97534.863-8.537-8.5370.0000.0000.0000.000
91A425ILE00.0090.01328.968-0.046-0.0460.0000.0000.0000.000
92A426LEU00.0180.01331.930-0.138-0.1380.0000.0000.0000.000
93A427ARG10.9030.96133.8607.9157.9150.0000.0000.0000.000
94A428ASP-1-0.919-0.98331.936-9.145-9.1450.0000.0000.0000.000
95A429TRP00.005-0.00428.8720.0930.0930.0000.0000.0000.000
96A430LEU0-0.0200.00531.846-0.033-0.0330.0000.0000.0000.000
97A431ARG10.8800.94334.3778.9018.9010.0000.0000.0000.000
98A432TYR0-0.020-0.01130.5810.0810.0810.0000.0000.0000.000
99A433THR00.0210.02231.384-0.374-0.3740.0000.0000.0000.000
100A434PRO0-0.063-0.04331.9930.3170.3170.0000.0000.0000.000
101A435ALA0-0.0040.00734.9670.2330.2330.0000.0000.0000.000
102A436TYR0-0.030-0.08035.1870.3830.3830.0000.0000.0000.000
103A437ALA0-0.025-0.00136.3530.1340.1340.0000.0000.0000.000
104A438HIS0-0.028-0.01238.1150.0210.0210.0000.0000.0000.000
105A439LEU0-0.0350.00640.4920.1930.1930.0000.0000.0000.000
106A440VAL0-0.069-0.02338.5570.1890.1890.0000.0000.0000.000
107A454PRO00.0190.00249.2240.0120.0120.0000.0000.0000.000
108A455SER00.038-0.00248.880-0.127-0.1270.0000.0000.0000.000
109A456LYS10.9990.99350.1345.9225.9220.0000.0000.0000.000
110A457ARG11.0311.02642.6317.1097.1090.0000.0000.0000.000
111A458ILE0-0.043-0.01045.076-0.144-0.1440.0000.0000.0000.000
112A459LEU00.0350.00945.777-0.095-0.0950.0000.0000.0000.000
113A460GLY00.0390.02847.158-0.019-0.0190.0000.0000.0000.000
114A461SER0-0.027-0.02541.685-0.098-0.0980.0000.0000.0000.000
115A462LEU00.0290.00142.155-0.180-0.1800.0000.0000.0000.000
116A463LEU0-0.044-0.00544.458-0.007-0.0070.0000.0000.0000.000
117A464SER00.0440.02241.980-0.108-0.1080.0000.0000.0000.000
118A465ASP-1-0.862-0.93643.210-6.987-6.9870.0000.0000.0000.000
119A466SER0-0.083-0.04345.7690.1010.1010.0000.0000.0000.000
120A467LEU0-0.028-0.00738.9100.0140.0140.0000.0000.0000.000
121A468PHE00.0310.01339.961-0.062-0.0620.0000.0000.0000.000
122A469LEU0-0.023-0.00942.344-0.064-0.0640.0000.0000.0000.000
123A470GLU-1-0.885-0.95442.937-7.291-7.2910.0000.0000.0000.000
124A471VAL00.009-0.00337.757-0.008-0.0080.0000.0000.0000.000
125A472LYS10.9911.00940.7566.9796.9790.0000.0000.0000.000
126A473GLU-1-0.968-0.99441.950-6.649-6.6490.0000.0000.0000.000
127A474LEU0-0.058-0.02040.5160.0480.0480.0000.0000.0000.000
128A475PHE00.0400.00834.379-0.045-0.0450.0000.0000.0000.000
129A476LEU0-0.041-0.02140.2820.0250.0250.0000.0000.0000.000
130A477ALA0-0.085-0.04343.4790.1120.1120.0000.0000.0000.000
131A478ALA00.0230.00439.1400.0640.0640.0000.0000.0000.000
132A479VAL0-0.008-0.00339.810-0.020-0.0200.0000.0000.0000.000
133A480ARG10.9220.95441.7896.8816.8810.0000.0000.0000.000
134A481LEU0-0.053-0.01341.1510.1720.1720.0000.0000.0000.000
135A482ASP-1-0.782-0.82642.256-7.301-7.3010.0000.0000.0000.000
136A483PRO0-0.048-0.00542.860-0.122-0.1220.0000.0000.0000.000
137A484THR0-0.133-0.10344.4850.0050.0050.0000.0000.0000.000
138A485SER0-0.046-0.04639.194-0.137-0.1370.0000.0000.0000.000
139A486ILE0-0.012-0.00236.0720.0170.0170.0000.0000.0000.000
140A487ASP-1-0.747-0.84033.586-9.604-9.6040.0000.0000.0000.000
141A488PRO0-0.003-0.02131.0310.0790.0790.0000.0000.0000.000
142A489ASP-1-0.858-0.93628.863-11.145-11.1450.0000.0000.0000.000
143A490VAL0-0.003-0.00131.6150.0340.0340.0000.0000.0000.000
144A491GLN0-0.005-0.00734.9720.1560.1560.0000.0000.0000.000
145A492CYS0-0.0170.00530.217-0.046-0.0460.0000.0000.0000.000
146A493GLY00.011-0.00532.8120.0040.0040.0000.0000.0000.000
147A494LEU0-0.029-0.01133.9670.1740.1740.0000.0000.0000.000
148A495GLY00.0480.01535.5800.2000.2000.0000.0000.0000.000
149A496VAL0-0.0230.00131.4150.0270.0270.0000.0000.0000.000
150A497LEU00.0150.00134.6090.1360.1360.0000.0000.0000.000
151A498PHE0-0.004-0.01837.9110.2480.2480.0000.0000.0000.000
152A499ASN0-0.068-0.04935.6840.1260.1260.0000.0000.0000.000
153A500LEU0-0.070-0.02135.4120.0970.0970.0000.0000.0000.000
154A501SER0-0.063-0.04738.8810.0640.0640.0000.0000.0000.000
155A502GLY00.0330.02641.1820.1820.1820.0000.0000.0000.000
156A503GLU-1-0.856-0.90042.477-6.944-6.9440.0000.0000.0000.000
157A504TYR00.0640.00338.114-0.160-0.1600.0000.0000.0000.000
158A505ASP-1-0.868-0.94240.657-7.243-7.2430.0000.0000.0000.000
159A506LYS10.8540.93642.5126.9216.9210.0000.0000.0000.000
160A507ALA0-0.0020.00037.266-0.108-0.1080.0000.0000.0000.000
161A508VAL00.0150.01037.638-0.257-0.2570.0000.0000.0000.000
162A509ASP-1-0.887-0.92238.257-7.636-7.6360.0000.0000.0000.000
163A510CYS0-0.071-0.01837.182-0.027-0.0270.0000.0000.0000.000
164A511PHE00.014-0.01431.892-0.278-0.2780.0000.0000.0000.000
165A512THR0-0.024-0.02634.207-0.247-0.2470.0000.0000.0000.000
166A513ALA0-0.0070.00436.486-0.059-0.0590.0000.0000.0000.000
167A514ALA00.0060.01132.261-0.064-0.0640.0000.0000.0000.000
168A515LEU0-0.031-0.01930.410-0.251-0.2510.0000.0000.0000.000
169A516SER0-0.097-0.06032.907-0.065-0.0650.0000.0000.0000.000
170A517VAL0-0.0160.00432.0260.0160.0160.0000.0000.0000.000
171A518ARG10.8230.91127.05611.25611.2560.0000.0000.0000.000
172A519PRO00.0630.03729.460-0.255-0.2550.0000.0000.0000.000
173A520ASN0-0.016-0.02225.8220.0810.0810.0000.0000.0000.000
174A521ASP-1-0.802-0.89824.883-13.029-13.0290.0000.0000.0000.000
175A522TYR00.0460.00518.4690.5280.5280.0000.0000.0000.000
176A523LEU00.0010.00421.1170.3350.3350.0000.0000.0000.000
177A524LEU0-0.058-0.02825.0820.3410.3410.0000.0000.0000.000
178A525TRP00.0210.01427.6430.5400.5400.0000.0000.0000.000
179A526ASN00.0770.05526.4210.2730.2730.0000.0000.0000.000
180A527LYS10.8880.96525.89211.98511.9850.0000.0000.0000.000
181A528LEU00.0240.03230.4930.2930.2930.0000.0000.0000.000
182A529GLY00.0450.00131.8900.2980.2980.0000.0000.0000.000
183A530ALA00.009-0.00430.9540.2250.2250.0000.0000.0000.000
184A531THR0-0.003-0.01332.9430.2780.2780.0000.0000.0000.000
185A532LEU0-0.0040.00935.9050.2700.2700.0000.0000.0000.000
186A533ALA0-0.014-0.00735.0040.2200.2200.0000.0000.0000.000
187A534ASN0-0.026-0.01034.5820.1990.1990.0000.0000.0000.000
188A535GLY0-0.044-0.01438.0810.2050.2050.0000.0000.0000.000
189A536ASN0-0.091-0.05040.2450.2490.2490.0000.0000.0000.000
190A537GLN0-0.0070.00440.2380.1520.1520.0000.0000.0000.000
191A538SER00.019-0.01538.015-0.228-0.2280.0000.0000.0000.000
192A539GLU-1-0.915-0.94437.562-8.171-8.1710.0000.0000.0000.000
193A540GLU-1-0.877-0.95338.158-7.875-7.8750.0000.0000.0000.000
194A541ALA0-0.039-0.01534.921-0.248-0.2480.0000.0000.0000.000
195A542VAL00.0170.00133.462-0.412-0.4120.0000.0000.0000.000
196A543ALA0-0.005-0.00132.808-0.329-0.3290.0000.0000.0000.000
197A544ALA0-0.0070.00932.373-0.219-0.2190.0000.0000.0000.000
198A545TYR00.014-0.00329.077-0.441-0.4410.0000.0000.0000.000
199A546ARG10.9260.97228.1419.3519.3510.0000.0000.0000.000
200A547ARG10.9731.00928.3969.5929.5920.0000.0000.0000.000
201A548ALA00.006-0.00725.589-0.362-0.3620.0000.0000.0000.000
202A549LEU0-0.040-0.02423.430-0.573-0.5730.0000.0000.0000.000
203A550GLU-1-1.006-0.99423.795-10.914-10.9140.0000.0000.0000.000
204A551LEU0-0.085-0.03924.074-0.318-0.3180.0000.0000.0000.000
205A552GLN00.0170.00617.130-0.690-0.6900.0000.0000.0000.000
206A553PRO00.0360.02819.5920.1450.1450.0000.0000.0000.000
207A554GLY00.0280.00417.1230.1750.1750.0000.0000.0000.000
208A555TYR0-0.060-0.01917.988-0.345-0.3450.0000.0000.0000.000
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