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: KG4J3

Calculation Name: 1IJQ-A-Xray372

Preferred Name: LDL receptor

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1IJQ

Chain ID: A

ChEMBL ID: CHEMBL3311

UniProt ID: P01130

Base Structure: X-ray

Registration Date: 2023-09-24

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 308
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -4771872.573483
FMO2-HF: Nuclear repulsion 4649144.644964
FMO2-HF: Total energy -122727.92852
FMO2-MP2: Total energy -123083.714696


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:377:ILE)


Summations of interaction energy for fragment #1(A:377:ILE)
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.
-14.482-6.4481.525-3.299-6.262-0.016
Interaction energy analysis for fragmet #1(A:377:ILE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.013 / q_NPA : -0.019
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].
3A379TYR0-0.028-0.0422.778-6.561-1.0091.264-2.368-4.449-0.012
4A380LEU0-0.0070.0024.6950.6500.700-0.001-0.009-0.0410.000
5A381PHE0-0.026-0.0277.456-0.189-0.1890.0000.0000.0000.000
6A382PHE00.029-0.00210.8590.1310.1310.0000.0000.0000.000
7A383THR00.0030.01714.251-0.039-0.0390.0000.0000.0000.000
8A384ASN00.0480.02317.4830.0290.0290.0000.0000.0000.000
9A385ARG10.9851.00119.3620.2370.2370.0000.0000.0000.000
10A386HIS0-0.036-0.03122.2050.0210.0210.0000.0000.0000.000
11A387GLU-1-0.816-0.88517.719-0.522-0.5220.0000.0000.0000.000
12A388VAL00.0130.02013.6110.0220.0220.0000.0000.0000.000
13A389ARG10.8660.92513.1000.5040.5040.0000.0000.0000.000
14A390LYS10.9210.9736.1502.6622.6620.0000.0000.0000.000
15A391MET0-0.0170.0077.5570.1400.1400.0000.0000.0000.000
16A392THR0-0.011-0.0232.970-0.600-0.0900.166-0.128-0.5490.000
17A393LEU0-0.019-0.0234.7580.4240.519-0.001-0.005-0.0880.000
18A394ASP-1-0.826-0.8365.149-1.237-1.145-0.0010.000-0.0920.000
19A395ARG10.8030.9107.8760.5190.5190.0000.0000.0000.000
20A396SER0-0.014-0.0465.879-0.110-0.1100.0000.0000.0000.000
21A397GLU-1-0.884-0.9463.291-7.105-5.8270.092-0.590-0.779-0.005
22A398TYR0-0.032-0.0207.3470.0030.0030.0000.0000.0000.000
23A399THR0-0.036-0.0259.8020.1380.1380.0000.0000.0000.000
24A400SER0-0.013-0.00911.9990.0000.0000.0000.0000.0000.000
25A401LEU0-0.039-0.02310.700-0.025-0.0250.0000.0000.0000.000
26A402ILE0-0.0080.00213.5840.0450.0450.0000.0000.0000.000
27A403PRO00.0600.04317.0520.0380.0380.0000.0000.0000.000
28A404ASN0-0.018-0.01819.7690.0340.0340.0000.0000.0000.000
29A405LEU0-0.0180.00919.7610.0270.0270.0000.0000.0000.000
30A406ARG10.8350.89623.6970.2150.2150.0000.0000.0000.000
31A407ASN0-0.026-0.03425.834-0.003-0.0030.0000.0000.0000.000
32A408VAL0-0.0430.00520.1490.0150.0150.0000.0000.0000.000
33A409VAL00.0330.00922.668-0.010-0.0100.0000.0000.0000.000
34A410ALA0-0.008-0.00320.6810.0090.0090.0000.0000.0000.000
35A411LEU0-0.058-0.03714.086-0.027-0.0270.0000.0000.0000.000
36A412ASP-1-0.752-0.87316.331-0.150-0.1500.0000.0000.0000.000
37A413THR0-0.080-0.04012.375-0.069-0.0690.0000.0000.0000.000
38A414GLU-1-0.798-0.86714.791-0.036-0.0360.0000.0000.0000.000
39A415VAL00.010-0.0048.388-0.049-0.0490.0000.0000.0000.000
40A416ALA0-0.035-0.02110.582-0.060-0.0600.0000.0000.0000.000
41A417SER0-0.028-0.01711.945-0.013-0.0130.0000.0000.0000.000
42A418ASN00.0070.02110.463-0.102-0.1020.0000.0000.0000.000
43A419ARG10.8560.92712.8180.1290.1290.0000.0000.0000.000
44A420ILE0-0.0040.00813.784-0.010-0.0100.0000.0000.0000.000
45A421TYR0-0.022-0.05316.5320.0380.0380.0000.0000.0000.000
46A422TRP00.018-0.00418.880-0.033-0.0330.0000.0000.0000.000
47A423SER00.0290.02121.0520.0220.0220.0000.0000.0000.000
48A424ASP-1-0.768-0.88923.987-0.248-0.2480.0000.0000.0000.000
49A425LEU00.0480.00826.0200.0190.0190.0000.0000.0000.000
50A426SER0-0.104-0.03728.5590.0140.0140.0000.0000.0000.000
51A427GLN00.006-0.01430.2980.0000.0000.0000.0000.0000.000
52A428ARG10.8310.94130.6380.1150.1150.0000.0000.0000.000
53A429MET0-0.023-0.01328.8310.0130.0130.0000.0000.0000.000
54A430ILE00.0240.03724.366-0.011-0.0110.0000.0000.0000.000
55A431CYS0-0.054-0.02623.3630.0160.0160.0000.0000.0000.000
56A432SER00.0090.00520.874-0.006-0.0060.0000.0000.0000.000
57A433THR00.0350.01217.4630.0140.0140.0000.0000.0000.000
58A434GLN0-0.019-0.00715.8400.0280.0280.0000.0000.0000.000
59A435LEU0-0.004-0.00111.5900.0060.0060.0000.0000.0000.000
60A444TYR00.0070.00320.281-0.015-0.0150.0000.0000.0000.000
61A445ASP-1-0.976-0.99123.868-0.184-0.1840.0000.0000.0000.000
62A446THR0-0.064-0.05125.524-0.006-0.0060.0000.0000.0000.000
63A447VAL0-0.0150.00124.4460.0100.0100.0000.0000.0000.000
64A448ILE00.006-0.00527.8240.0180.0180.0000.0000.0000.000
65A449SER00.015-0.00230.204-0.007-0.0070.0000.0000.0000.000
66A450ARG10.9510.99032.8930.0670.0670.0000.0000.0000.000
67A451ASP-1-0.936-0.97034.987-0.063-0.0630.0000.0000.0000.000
68A452ILE00.0310.03329.8370.0030.0030.0000.0000.0000.000
69A453GLN0-0.071-0.03833.811-0.006-0.0060.0000.0000.0000.000
70A454ALA00.0520.00430.761-0.008-0.0080.0000.0000.0000.000
71A455PRO00.0000.00127.2360.0070.0070.0000.0000.0000.000
72A456ASP-1-0.838-0.93626.034-0.140-0.1400.0000.0000.0000.000
73A457GLY00.0210.01523.362-0.010-0.0100.0000.0000.0000.000
74A458LEU0-0.054-0.02621.0510.0130.0130.0000.0000.0000.000
75A459ALA00.0160.00920.554-0.003-0.0030.0000.0000.0000.000
76A460VAL0-0.038-0.02518.4770.0120.0120.0000.0000.0000.000
77A461ASP-1-0.800-0.88919.2400.0740.0740.0000.0000.0000.000
78A462TRP00.020-0.02216.402-0.021-0.0210.0000.0000.0000.000
79A463ILE0-0.077-0.01318.4350.0120.0120.0000.0000.0000.000
80A464HIS0-0.081-0.07420.6110.0030.0030.0000.0000.0000.000
81A465SER0-0.0570.00221.056-0.006-0.0060.0000.0000.0000.000
82A466ASN00.0020.00122.750-0.015-0.0150.0000.0000.0000.000
83A467ILE0-0.0030.00222.457-0.001-0.0010.0000.0000.0000.000
84A468TYR0-0.010-0.03724.1620.0110.0110.0000.0000.0000.000
85A469TRP0-0.004-0.01825.067-0.015-0.0150.0000.0000.0000.000
86A470THR0-0.038-0.02227.1840.0110.0110.0000.0000.0000.000
87A471ASP-1-0.741-0.88629.137-0.097-0.0970.0000.0000.0000.000
88A472SER0-0.021-0.00530.9400.0110.0110.0000.0000.0000.000
89A473VAL0-0.0020.00132.8250.0060.0060.0000.0000.0000.000
90A474LEU0-0.065-0.03535.4400.0070.0070.0000.0000.0000.000
91A475GLY00.0100.02835.5290.0060.0060.0000.0000.0000.000
92A476THR0-0.091-0.05834.4610.0060.0060.0000.0000.0000.000
93A477VAL00.0750.03329.660-0.006-0.0060.0000.0000.0000.000
94A478SER0-0.053-0.02330.6900.0100.0100.0000.0000.0000.000
95A479VAL00.0120.01627.642-0.003-0.0030.0000.0000.0000.000
96A480ALA00.005-0.00528.1710.0010.0010.0000.0000.0000.000
97A481ASP-1-0.726-0.83927.151-0.060-0.0600.0000.0000.0000.000
98A482THR00.014-0.00821.688-0.006-0.0060.0000.0000.0000.000
99A483LYS10.8950.94424.3120.0790.0790.0000.0000.0000.000
100A484GLY00.0120.01627.241-0.004-0.0040.0000.0000.0000.000
101A485VAL0-0.117-0.04429.7740.0040.0040.0000.0000.0000.000
102A486LYS10.8570.92831.8040.0320.0320.0000.0000.0000.000
103A487ARG10.9090.93231.7410.0650.0650.0000.0000.0000.000
104A488LYS10.8440.92733.1780.0170.0170.0000.0000.0000.000
105A489THR0-0.040-0.04133.650-0.005-0.0050.0000.0000.0000.000
106A490LEU0-0.077-0.03531.0020.0050.0050.0000.0000.0000.000
107A491PHE00.0330.01732.7280.0050.0050.0000.0000.0000.000
108A492ARG10.9600.96436.1260.0320.0320.0000.0000.0000.000
109A493GLU-1-0.916-0.94938.246-0.011-0.0110.0000.0000.0000.000
110A494ASN00.0020.00139.138-0.007-0.0070.0000.0000.0000.000
111A495GLY00.0110.00640.2930.0030.0030.0000.0000.0000.000
112A496SER0-0.078-0.02436.069-0.002-0.0020.0000.0000.0000.000
113A497LYS10.9110.95033.2700.0540.0540.0000.0000.0000.000
114A498PRO0-0.043-0.00230.787-0.001-0.0010.0000.0000.0000.000
115A499ARG10.9520.97024.9470.1250.1250.0000.0000.0000.000
116A500ALA00.0360.05022.644-0.011-0.0110.0000.0000.0000.000
117A501ILE00.002-0.01523.1230.0200.0200.0000.0000.0000.000
118A502VAL00.0220.03119.927-0.012-0.0120.0000.0000.0000.000
119A503VAL00.005-0.01420.6700.0080.0080.0000.0000.0000.000
120A504ASP-1-0.752-0.87920.6820.1830.1830.0000.0000.0000.000
121A505PRO0-0.017-0.01819.9080.0000.0000.0000.0000.0000.000
122A506VAL0-0.057-0.00820.1380.0030.0030.0000.0000.0000.000
123A507HIS0-0.086-0.06622.949-0.002-0.0020.0000.0000.0000.000
124A508GLY00.0110.00925.676-0.010-0.0100.0000.0000.0000.000
125A509PHE0-0.047-0.02926.269-0.012-0.0120.0000.0000.0000.000
126A510MET0-0.0070.02425.4860.0000.0000.0000.0000.0000.000
127A511TYR00.018-0.01124.6300.0070.0070.0000.0000.0000.000
128A512TRP00.0190.00625.726-0.008-0.0080.0000.0000.0000.000
129A513THR0-0.013-0.00426.0940.0100.0100.0000.0000.0000.000
130A514ASP-1-0.807-0.91328.562-0.040-0.0400.0000.0000.0000.000
131A515TRP00.0550.02130.3860.0070.0070.0000.0000.0000.000
132A516GLY0-0.010-0.00432.874-0.003-0.0030.0000.0000.0000.000
133A517THR0-0.020-0.00536.4460.0010.0010.0000.0000.0000.000
134A518PRO0-0.017-0.01439.1220.0000.0000.0000.0000.0000.000
135A519ALA00.0390.03233.502-0.001-0.0010.0000.0000.0000.000
136A520LYS10.8620.91733.3870.0190.0190.0000.0000.0000.000
137A521ILE00.0310.02827.486-0.006-0.0060.0000.0000.0000.000
138A522LYS10.8410.93230.5590.0200.0200.0000.0000.0000.000
139A523LYS10.9040.95729.437-0.081-0.0810.0000.0000.0000.000
140A524GLY00.0320.00430.173-0.003-0.0030.0000.0000.0000.000
141A525GLY00.0070.01630.0810.0070.0070.0000.0000.0000.000
142A526LEU00.0000.00225.037-0.009-0.0090.0000.0000.0000.000
143A527ASN00.022-0.00629.331-0.008-0.0080.0000.0000.0000.000
144A528GLY0-0.035-0.02432.547-0.004-0.0040.0000.0000.0000.000
145A529VAL0-0.057-0.00934.368-0.003-0.0030.0000.0000.0000.000
146A530ASP-1-0.900-0.95335.2030.0380.0380.0000.0000.0000.000
147A531ILE0-0.011-0.01634.754-0.001-0.0010.0000.0000.0000.000
148A532TYR0-0.036-0.01234.0630.0020.0020.0000.0000.0000.000
149A533SER00.011-0.00534.691-0.003-0.0030.0000.0000.0000.000
150A534LEU0-0.038-0.00929.3460.0030.0030.0000.0000.0000.000
151A535VAL00.0050.00130.1100.0060.0060.0000.0000.0000.000
152A536THR00.007-0.01333.292-0.005-0.0050.0000.0000.0000.000
153A537GLU-1-0.882-0.92635.9030.0110.0110.0000.0000.0000.000
154A538ASN0-0.066-0.02734.456-0.001-0.0010.0000.0000.0000.000
155A539ILE00.0250.02630.6450.0010.0010.0000.0000.0000.000
156A540GLN0-0.084-0.04632.555-0.004-0.0040.0000.0000.0000.000
157A541TRP0-0.020-0.02830.519-0.005-0.0050.0000.0000.0000.000
158A542PRO0-0.0350.00928.031-0.006-0.0060.0000.0000.0000.000
159A543ASN00.0430.02324.6810.0040.0040.0000.0000.0000.000
160A544GLY00.0140.01521.5260.0050.0050.0000.0000.0000.000
161A545ILE0-0.035-0.03321.4820.0200.0200.0000.0000.0000.000
162A546THR00.0120.00216.5140.0000.0000.0000.0000.0000.000
163A547LEU0-0.012-0.01618.4290.0110.0110.0000.0000.0000.000
164A548ASP-1-0.887-0.92016.7320.4280.4280.0000.0000.0000.000
165A549LEU0-0.024-0.03217.2130.0000.0000.0000.0000.0000.000
166A550LEU00.000-0.00414.756-0.018-0.0180.0000.0000.0000.000
167A551SER00.0070.00318.788-0.015-0.0150.0000.0000.0000.000
168A552GLY0-0.0190.01520.855-0.028-0.0280.0000.0000.0000.000
169A553ARG10.7410.84420.699-0.170-0.1700.0000.0000.0000.000
170A554LEU00.0140.01320.9720.0050.0050.0000.0000.0000.000
171A555TYR00.0290.00619.0240.0090.0090.0000.0000.0000.000
172A556TRP00.012-0.01021.823-0.010-0.0100.0000.0000.0000.000
173A557VAL00.0510.03721.3180.0080.0080.0000.0000.0000.000
174A558ASP-1-0.726-0.87724.257-0.033-0.0330.0000.0000.0000.000
175A559SER0-0.002-0.03126.3450.0010.0010.0000.0000.0000.000
176A560LYS10.8960.96328.4480.0400.0400.0000.0000.0000.000
177A561LEU0-0.062-0.04130.8820.0020.0020.0000.0000.0000.000
178A562HIS10.8630.97128.0600.0640.0640.0000.0000.0000.000
179A563SER00.0460.01426.8070.0030.0030.0000.0000.0000.000
180A564ILE00.0320.02020.279-0.008-0.0080.0000.0000.0000.000
181A565SER0-0.038-0.01524.1880.0140.0140.0000.0000.0000.000
182A566SER00.0180.01222.9970.0070.0070.0000.0000.0000.000
183A567ILE0-0.054-0.01924.893-0.006-0.0060.0000.0000.0000.000
184A568ASP-1-0.759-0.85425.4720.1620.1620.0000.0000.0000.000
185A569VAL00.0390.01124.739-0.018-0.0180.0000.0000.0000.000
186A570ASN0-0.031-0.02127.510-0.008-0.0080.0000.0000.0000.000
187A571GLY00.0220.01530.126-0.007-0.0070.0000.0000.0000.000
188A572GLY0-0.0050.01031.148-0.007-0.0070.0000.0000.0000.000
189A573ASN0-0.011-0.01028.979-0.005-0.0050.0000.0000.0000.000
190A574ARG10.8960.93728.638-0.022-0.0220.0000.0000.0000.000
191A575LYS10.9190.95426.515-0.132-0.1320.0000.0000.0000.000
192A576THR00.0270.01527.451-0.001-0.0010.0000.0000.0000.000
193A577ILE0-0.105-0.03721.6890.0050.0050.0000.0000.0000.000
194A578LEU00.0210.00422.5720.0020.0020.0000.0000.0000.000
195A579GLU-1-0.910-0.95725.662-0.003-0.0030.0000.0000.0000.000
196A580ASP-1-0.854-0.92925.824-0.056-0.0560.0000.0000.0000.000
197A581GLU-1-0.915-0.96927.798-0.059-0.0590.0000.0000.0000.000
198A582LYS10.9110.95027.8880.0670.0670.0000.0000.0000.000
199A583ARG10.9090.95922.6760.0590.0590.0000.0000.0000.000
200A584LEU0-0.0310.01322.295-0.013-0.0130.0000.0000.0000.000
201A585ALA00.0530.03625.3000.0100.0100.0000.0000.0000.000
202A586HIS0-0.066-0.05925.9940.0050.0050.0000.0000.0000.000
203A587PRO00.0380.04322.910-0.019-0.0190.0000.0000.0000.000
204A588PHE0-0.008-0.00621.7520.0130.0130.0000.0000.0000.000
205A589SER00.004-0.00118.0620.0190.0190.0000.0000.0000.000
206A590LEU0-0.021-0.01216.825-0.002-0.0020.0000.0000.0000.000
207A591ALA00.0030.01012.651-0.006-0.0060.0000.0000.0000.000
208A592VAL0-0.012-0.01313.9700.0000.0000.0000.0000.0000.000
209A593PHE00.004-0.0136.104-0.125-0.1250.0000.0000.0000.000
210A594GLU-1-0.914-0.9337.4791.5321.5320.0000.0000.0000.000
211A595ASP-1-0.896-0.95311.6160.2970.2970.0000.0000.0000.000
212A596LYS10.9290.94911.868-0.166-0.1660.0000.0000.0000.000
213A597VAL0-0.017-0.01114.2860.0270.0270.0000.0000.0000.000
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