Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: 1NRQZ

Calculation Name: 3LJB-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3LJB

Chain ID: A

ChEMBL ID:

UniProt ID: P20591

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 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 219
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2661915.157798
FMO2-HF: Nuclear repulsion 2569017.172181
FMO2-HF: Total energy -92897.985617
FMO2-MP2: Total energy -93168.262053


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:366:GLU)


Summations of interaction energy for fragment #1(A:366:GLU)
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.
-12.333-4.7678.714-6.917-9.360.067
Interaction energy analysis for fragmet #1(A:366:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.911 / q_NPA : -0.969
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].
3A368GLU-1-0.856-0.9232.00017.84323.2346.669-5.727-6.3320.065
4A369ASN0-0.021-0.0231.988-17.890-16.2312.039-1.095-2.6020.002
5A370GLU-1-0.921-0.9443.84525.13225.6480.006-0.095-0.4260.000
6A371LYS10.8070.9095.854-45.323-45.3230.0000.0000.0000.000
7A372MET0-0.002-0.0086.825-4.299-4.2990.0000.0000.0000.000
8A373PHE0-0.016-0.0175.940-2.363-2.3630.0000.0000.0000.000
9A374PHE00.0550.0429.737-2.421-2.4210.0000.0000.0000.000
10A375LEU0-0.024-0.01911.383-1.946-1.9460.0000.0000.0000.000
11A376ILE0-0.008-0.01511.125-1.668-1.6680.0000.0000.0000.000
12A377ASP-1-0.881-0.93013.87417.04117.0410.0000.0000.0000.000
13A378LYS10.8120.91315.811-16.042-16.0420.0000.0000.0000.000
14A379VAL0-0.011-0.01117.106-1.036-1.0360.0000.0000.0000.000
15A380ASN0-0.016-0.01217.030-1.203-1.2030.0000.0000.0000.000
16A381ALA0-0.0100.00919.863-0.753-0.7530.0000.0000.0000.000
17A382PHE00.0480.02221.651-0.669-0.6690.0000.0000.0000.000
18A383ASN00.015-0.02122.030-0.803-0.8030.0000.0000.0000.000
19A384GLN00.0280.02423.953-0.479-0.4790.0000.0000.0000.000
20A385ASP-1-0.828-0.90825.79510.56810.5680.0000.0000.0000.000
21A386ILE0-0.076-0.03627.306-0.480-0.4800.0000.0000.0000.000
22A387THR00.016-0.01027.385-0.372-0.3720.0000.0000.0000.000
23A388ALA00.0150.01529.983-0.351-0.3510.0000.0000.0000.000
24A389LEU0-0.039-0.00831.945-0.377-0.3770.0000.0000.0000.000
25A390MET0-0.097-0.02431.487-0.202-0.2020.0000.0000.0000.000
26A391GLN0-0.067-0.03732.562-0.112-0.1120.0000.0000.0000.000
27A392GLY0-0.024-0.00135.890-0.163-0.1630.0000.0000.0000.000
28A393GLU-1-0.920-0.97034.2368.6778.6770.0000.0000.0000.000
29A394GLU-1-0.808-0.88933.3548.4328.4320.0000.0000.0000.000
30A395THR0-0.023-0.00732.353-0.385-0.3850.0000.0000.0000.000
31A396VAL0-0.013-0.01634.9990.1110.1110.0000.0000.0000.000
32A397GLY00.0460.02837.909-0.019-0.0190.0000.0000.0000.000
33A398GLU-1-0.984-0.99939.5217.0107.0100.0000.0000.0000.000
34A399GLU-1-0.972-0.97742.3296.3686.3680.0000.0000.0000.000
35A400ASP-1-0.922-0.94140.7747.4587.4580.0000.0000.0000.000
36A401ILE0-0.086-0.05842.993-0.085-0.0850.0000.0000.0000.000
37A402ARG10.8710.93336.932-7.984-7.9840.0000.0000.0000.000
38A403LEU0-0.002-0.01536.517-0.221-0.2210.0000.0000.0000.000
39A404PHE00.0460.02038.856-0.218-0.2180.0000.0000.0000.000
40A405THR0-0.007-0.00740.988-0.133-0.1330.0000.0000.0000.000
41A406ARG10.9410.97039.791-7.746-7.7460.0000.0000.0000.000
42A407LEU00.0380.02441.094-0.135-0.1350.0000.0000.0000.000
43A408ARG10.9060.96544.669-6.346-6.3460.0000.0000.0000.000
44A409HIS0-0.021-0.02147.081-0.213-0.2130.0000.0000.0000.000
45A410GLU-1-0.791-0.87546.9616.2296.2290.0000.0000.0000.000
46A411PHE00.039-0.00244.528-0.143-0.1430.0000.0000.0000.000
47A412HIS00.0330.03050.246-0.048-0.0480.0000.0000.0000.000
48A413LYS10.8170.88450.375-6.360-6.3600.0000.0000.0000.000
49A414TRP0-0.002-0.00552.221-0.121-0.1210.0000.0000.0000.000
50A415SER00.000-0.00354.262-0.073-0.0730.0000.0000.0000.000
51A416THR0-0.035-0.01456.372-0.132-0.1320.0000.0000.0000.000
52A417ILE0-0.026-0.00355.443-0.114-0.1140.0000.0000.0000.000
53A418ILE00.0280.02255.928-0.105-0.1050.0000.0000.0000.000
54A419GLU-1-0.891-0.93859.8074.9014.9010.0000.0000.0000.000
55A420ASN0-0.013-0.02262.260-0.132-0.1320.0000.0000.0000.000
56A421ASN0-0.006-0.00562.159-0.071-0.0710.0000.0000.0000.000
57A422PHE00.0410.02963.876-0.093-0.0930.0000.0000.0000.000
58A423GLN0-0.065-0.04365.585-0.140-0.1400.0000.0000.0000.000
59A424GLU-1-0.926-0.94966.5664.6894.6890.0000.0000.0000.000
60A425GLY00.0410.01567.885-0.082-0.0820.0000.0000.0000.000
61A426HIS00.0410.01069.344-0.042-0.0420.0000.0000.0000.000
62A427LYS10.9250.97371.652-4.365-4.3650.0000.0000.0000.000
63A428ILE0-0.038-0.02470.361-0.097-0.0970.0000.0000.0000.000
64A429LEU00.0060.00772.769-0.073-0.0730.0000.0000.0000.000
65A430SER00.012-0.01274.935-0.073-0.0730.0000.0000.0000.000
66A431ARG10.9110.95676.827-4.135-4.1350.0000.0000.0000.000
67A432LYS10.8920.96677.200-4.172-4.1720.0000.0000.0000.000
68A433ILE00.0340.01277.800-0.049-0.0490.0000.0000.0000.000
69A434GLN00.0360.02881.057-0.035-0.0350.0000.0000.0000.000
70A435LYS10.9250.96482.435-3.926-3.9260.0000.0000.0000.000
71A436PHE0-0.041-0.03280.371-0.022-0.0220.0000.0000.0000.000
72A437GLU-1-0.968-0.98384.6373.7353.7350.0000.0000.0000.000
73A438ASN0-0.088-0.02387.009-0.084-0.0840.0000.0000.0000.000
74A448PHE00.0470.01280.554-0.006-0.0060.0000.0000.0000.000
75A449VAL00.0190.00681.2820.0410.0410.0000.0000.0000.000
76A450ASN00.004-0.00380.5800.0410.0410.0000.0000.0000.000
77A451TYR00.0020.00473.3030.0380.0380.0000.0000.0000.000
78A452ARG11.0060.99774.835-4.183-4.1830.0000.0000.0000.000
79A453THR00.0030.00974.5430.0600.0600.0000.0000.0000.000
80A454PHE00.001-0.00975.0490.0300.0300.0000.0000.0000.000
81A455GLU-1-0.834-0.91269.9614.6104.6100.0000.0000.0000.000
82A456THR0-0.031-0.02670.2010.0850.0850.0000.0000.0000.000
83A457ILE0-0.026-0.01269.6570.0480.0480.0000.0000.0000.000
84A458VAL00.0250.02166.8060.0490.0490.0000.0000.0000.000
85A459LYS10.8490.93265.628-4.713-4.7130.0000.0000.0000.000
86A460GLN00.008-0.01764.7360.0310.0310.0000.0000.0000.000
87A461GLN0-0.054-0.02664.9740.0910.0910.0000.0000.0000.000
88A462ILE00.0350.02760.4680.0750.0750.0000.0000.0000.000
89A463LYS10.8590.90258.398-5.362-5.3620.0000.0000.0000.000
90A464ALA0-0.030-0.00760.1040.0770.0770.0000.0000.0000.000
91A465LEU0-0.004-0.00257.5530.0560.0560.0000.0000.0000.000
92A466GLU-1-0.802-0.87055.0385.7915.7910.0000.0000.0000.000
93A467GLU-1-0.788-0.88154.2365.9455.9450.0000.0000.0000.000
94A468PRO00.0400.02853.5570.1110.1110.0000.0000.0000.000
95A469ALA0-0.0170.00552.0840.1130.1130.0000.0000.0000.000
96A470VAL0-0.035-0.01849.1690.1590.1590.0000.0000.0000.000
97A471ASP-1-0.905-0.95148.9606.1836.1830.0000.0000.0000.000
98A472MET0-0.052-0.01948.1470.1440.1440.0000.0000.0000.000
99A473LEU0-0.027-0.01043.4250.1640.1640.0000.0000.0000.000
100A474HIS10.8310.89344.516-6.706-6.7060.0000.0000.0000.000
101A475THR00.0000.00944.4280.0930.0930.0000.0000.0000.000
102A476VAL0-0.018-0.02542.1750.1270.1270.0000.0000.0000.000
103A477THR0-0.031-0.03440.1300.1900.1900.0000.0000.0000.000
104A478ASP-1-0.810-0.89139.3827.7287.7280.0000.0000.0000.000
105A479MET0-0.085-0.03239.8250.1810.1810.0000.0000.0000.000
106A480VAL0-0.0070.00535.5910.1610.1610.0000.0000.0000.000
107A481ARG10.8950.95035.117-8.373-8.3730.0000.0000.0000.000
108A482LEU0-0.071-0.01834.7550.2620.2620.0000.0000.0000.000
109A483ALA00.0490.02835.0810.1810.1810.0000.0000.0000.000
110A484PHE00.028-0.00831.1100.2710.2710.0000.0000.0000.000
111A485THR0-0.053-0.04530.3460.4040.4040.0000.0000.0000.000
112A486ASP-1-0.854-0.93230.8999.1399.1390.0000.0000.0000.000
113A487VAL0-0.022-0.00127.1970.2220.2220.0000.0000.0000.000
114A488SER0-0.017-0.03226.5130.5570.5570.0000.0000.0000.000
115A489ILE0-0.037-0.01826.5940.3750.3750.0000.0000.0000.000
116A490LYS10.8720.93027.495-10.563-10.5630.0000.0000.0000.000
117A491ASN0-0.057-0.02023.1560.6850.6850.0000.0000.0000.000
118A492PHE0-0.016-0.02320.3760.7860.7860.0000.0000.0000.000
119A493GLU-1-0.879-0.93223.67510.73310.7330.0000.0000.0000.000
120A494GLU-1-0.918-0.94222.69112.14312.1430.0000.0000.0000.000
121A495PHE0-0.031-0.01417.4960.4450.4450.0000.0000.0000.000
122A496PHE00.0340.00721.590-0.138-0.1380.0000.0000.0000.000
123A497ASN0-0.033-0.02419.577-1.266-1.2660.0000.0000.0000.000
124A498LEU00.0580.05918.016-0.255-0.2550.0000.0000.0000.000
125A499HIS00.0590.05321.414-0.214-0.2140.0000.0000.0000.000
126A500ARG10.8400.91423.889-12.889-12.8890.0000.0000.0000.000
127A501THR0-0.021-0.03021.885-0.313-0.3130.0000.0000.0000.000
128A502ALA00.0370.02424.113-0.280-0.2800.0000.0000.0000.000
129A503LYS10.9290.96525.634-10.061-10.0610.0000.0000.0000.000
130A504SER0-0.071-0.04327.182-0.300-0.3000.0000.0000.0000.000
131A505LYS10.9180.96222.898-13.272-13.2720.0000.0000.0000.000
132A506ILE00.0000.00228.659-0.307-0.3070.0000.0000.0000.000
133A507GLU-1-0.843-0.91731.0178.6098.6090.0000.0000.0000.000
134A508ASP-1-0.918-0.94530.7459.8299.8290.0000.0000.0000.000
135A509ILE0-0.062-0.03928.877-0.253-0.2530.0000.0000.0000.000
136A510ARG10.8000.88433.381-8.065-8.0650.0000.0000.0000.000
137A511ALA00.0130.00336.382-0.258-0.2580.0000.0000.0000.000
138A512GLU-1-0.846-0.89535.4818.1918.1910.0000.0000.0000.000
139A513GLN0-0.009-0.02135.638-0.259-0.2590.0000.0000.0000.000
140A514GLU-1-0.701-0.80838.4817.2767.2760.0000.0000.0000.000
141A515ARG10.8190.88438.806-8.185-8.1850.0000.0000.0000.000
142A516GLU-1-0.826-0.88340.7287.2117.2110.0000.0000.0000.000
143A517GLY00.0350.00442.370-0.163-0.1630.0000.0000.0000.000
144A518GLU-1-0.786-0.90744.0426.3816.3810.0000.0000.0000.000
145A519LYS10.7930.88443.761-7.379-7.3790.0000.0000.0000.000
146A520LEU00.005-0.00245.160-0.166-0.1660.0000.0000.0000.000
147A521ILE00.0080.01147.272-0.159-0.1590.0000.0000.0000.000
148A522ARG10.7330.81250.012-6.230-6.2300.0000.0000.0000.000
149A523LEU0-0.0090.00050.098-0.139-0.1390.0000.0000.0000.000
150A524HIS0-0.025-0.02151.778-0.029-0.0290.0000.0000.0000.000
151A525PHE00.017-0.00353.545-0.121-0.1210.0000.0000.0000.000
152A526GLN0-0.051-0.02355.215-0.040-0.0400.0000.0000.0000.000
153A527MET0-0.045-0.01752.685-0.093-0.0930.0000.0000.0000.000
154A528GLU-1-0.714-0.84357.3835.3485.3480.0000.0000.0000.000
155A529GLN0-0.123-0.03659.805-0.193-0.1930.0000.0000.0000.000
156A530ILE0-0.019-0.01060.804-0.089-0.0890.0000.0000.0000.000
157A531VAL0-0.029-0.00163.4720.0300.0300.0000.0000.0000.000
158A532TYR0-0.030-0.01062.5220.0280.0280.0000.0000.0000.000
159A573SER0-0.035-0.02682.925-0.029-0.0290.0000.0000.0000.000
160A574MET0-0.014-0.01580.2310.0340.0340.0000.0000.0000.000
161A575GLU-1-0.824-0.93979.2284.1234.1230.0000.0000.0000.000
162A576GLU-1-0.842-0.91078.2833.9873.9870.0000.0000.0000.000
163A577ILE0-0.044-0.02276.6960.0590.0590.0000.0000.0000.000
164A578PHE0-0.019-0.00674.7260.0740.0740.0000.0000.0000.000
165A579GLN00.012-0.00574.0050.1240.1240.0000.0000.0000.000
166A580HIS00.0100.02471.4130.0440.0440.0000.0000.0000.000
167A581LEU0-0.012-0.01370.8880.0800.0800.0000.0000.0000.000
168A582MET00.0040.01169.1720.0840.0840.0000.0000.0000.000
169A583ALA0-0.0070.01268.4880.0720.0720.0000.0000.0000.000
170A584TYR00.003-0.03463.5520.0400.0400.0000.0000.0000.000
171A585HIS00.0270.01364.3650.0380.0380.0000.0000.0000.000
172A586GLN00.0050.02063.7840.1310.1310.0000.0000.0000.000
173A587GLU-1-0.854-0.91461.4465.1975.1970.0000.0000.0000.000
174A588ALA00.0340.01160.2030.1020.1020.0000.0000.0000.000
175A589SER0-0.042-0.03459.0680.0960.0960.0000.0000.0000.000
176A590LYS10.8800.94158.275-5.054-5.0540.0000.0000.0000.000
177A591ARG10.8200.89555.742-5.232-5.2320.0000.0000.0000.000
178A592ILE00.0100.02354.3270.1450.1450.0000.0000.0000.000
179A593SER00.013-0.01253.6800.0930.0930.0000.0000.0000.000
180A594SER0-0.067-0.01851.6750.1060.1060.0000.0000.0000.000
181A595HIS0-0.022-0.04249.1070.2410.2410.0000.0000.0000.000
182A596ILE00.0280.01948.9000.1390.1390.0000.0000.0000.000
183A597PRO00.0190.00947.3790.1510.1510.0000.0000.0000.000
184A598LEU0-0.0200.00744.3030.1810.1810.0000.0000.0000.000
185A599ILE00.0050.00744.1080.2110.2110.0000.0000.0000.000
186A600ILE00.0350.00743.2310.2100.2100.0000.0000.0000.000
187A601GLN00.0060.00940.8980.1730.1730.0000.0000.0000.000
188A602PHE0-0.025-0.00238.6810.2570.2570.0000.0000.0000.000
189A603PHE00.0280.02038.3860.2370.2370.0000.0000.0000.000
190A604MET0-0.050-0.01437.6120.2430.2430.0000.0000.0000.000
191A605LEU00.0120.01435.4680.0640.0640.0000.0000.0000.000
192A606GLN0-0.023-0.01934.9670.4320.4320.0000.0000.0000.000
193A607THR00.010-0.00333.7870.3360.3360.0000.0000.0000.000
194A608TYR0-0.070-0.05332.6540.3160.3160.0000.0000.0000.000
195A609GLY00.0610.01231.2430.3280.3280.0000.0000.0000.000
196A610GLN00.0130.00829.3560.4360.4360.0000.0000.0000.000
197A611GLN0-0.019-0.01528.2690.5770.5770.0000.0000.0000.000
198A612LEU00.0110.01927.0120.4570.4570.0000.0000.0000.000
199A613GLN0-0.009-0.01224.9380.3960.3960.0000.0000.0000.000
200A614LYS10.8870.92723.409-10.064-10.0640.0000.0000.0000.000
201A615ALA0-0.010-0.00223.2080.5360.5360.0000.0000.0000.000
202A616MET00.0090.01221.0820.4210.4210.0000.0000.0000.000
203A617LEU00.0270.01718.7350.7920.7920.0000.0000.0000.000
204A618GLN0-0.015-0.00518.2200.7020.7020.0000.0000.0000.000
205A619LEU0-0.044-0.02417.7780.4020.4020.0000.0000.0000.000
206A620LEU00.0190.01513.1660.9690.9690.0000.0000.0000.000
207A621GLN0-0.064-0.00513.7441.0491.0490.0000.0000.0000.000
208A622ASP-1-0.848-0.91114.64721.73121.7310.0000.0000.0000.000
209A623LYS10.8960.9276.284-41.338-41.3380.0000.0000.0000.000
210A624ASP-1-0.889-0.93310.29331.35531.3550.0000.0000.0000.000
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