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: 72J5K

Calculation Name: 1HU3-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1HU3

Chain ID: A

ChEMBL ID:

UniProt ID: O43432

Base Structure: X-ray

Registration Date: 2023-06-21

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 204
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2450996.933934
FMO2-HF: Nuclear repulsion 2365031.109413
FMO2-HF: Total energy -85965.824522
FMO2-MP2: Total energy -86209.347622


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:1:SER)


Summations of interaction energy for fragment #1(A:1:SER)
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.
-1.8280.9624.564-2.746-4.609-0.023
Interaction energy analysis for fragmet #1(A:1:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.024 / 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].
3A746PRO00.0310.0163.851-0.6850.855-0.016-0.651-0.8730.000
4A747GLU-1-0.749-0.8422.584-0.5420.0800.615-0.383-0.8540.002
5A748ASN0-0.018-0.0192.324-4.754-4.2313.965-1.690-2.799-0.025
6A749ILE00.0430.0324.3530.8360.9410.000-0.022-0.0830.000
7A750LYS10.9550.9667.1951.1601.1600.0000.0000.0000.000
8A751THR0-0.031-0.0135.9360.3330.3330.0000.0000.0000.000
9A752GLN00.0260.0418.3620.3760.3760.0000.0000.0000.000
10A753GLU-1-0.874-0.95110.251-0.538-0.5380.0000.0000.0000.000
11A754LEU0-0.054-0.00911.5500.1170.1170.0000.0000.0000.000
12A755PHE00.011-0.00810.6640.0760.0760.0000.0000.0000.000
13A756ARG10.9160.95413.9130.6030.6030.0000.0000.0000.000
14A757LYS10.8780.94515.5690.3500.3500.0000.0000.0000.000
15A758VAL00.003-0.01016.9860.0420.0420.0000.0000.0000.000
16A759ARG10.8640.91117.3090.3030.3030.0000.0000.0000.000
17A760SER0-0.0060.00420.1270.0350.0350.0000.0000.0000.000
18A761ILE0-0.061-0.03420.7830.0190.0190.0000.0000.0000.000
19A762LEU0-0.026-0.02121.1830.0170.0170.0000.0000.0000.000
20A763ASN0-0.010-0.00622.9880.0190.0190.0000.0000.0000.000
21A764LYS10.8790.97024.9860.1720.1720.0000.0000.0000.000
22A765LEU00.0210.00928.6180.0050.0050.0000.0000.0000.000
23A766THR0-0.018-0.00231.6370.0070.0070.0000.0000.0000.000
24A767PRO0-0.013-0.00531.030-0.004-0.0040.0000.0000.0000.000
25A768GLN00.0420.03527.6210.0030.0030.0000.0000.0000.000
26A769MET0-0.014-0.00731.1340.0030.0030.0000.0000.0000.000
27A770PHE00.064-0.00530.053-0.005-0.0050.0000.0000.0000.000
28A771ASN00.0460.02230.523-0.003-0.0030.0000.0000.0000.000
29A772GLN00.0290.00430.321-0.009-0.0090.0000.0000.0000.000
30A773LEU00.0380.02626.018-0.009-0.0090.0000.0000.0000.000
31A774MET00.0450.02325.956-0.007-0.0070.0000.0000.0000.000
32A775LYS10.9440.98726.0420.0900.0900.0000.0000.0000.000
33A776GLN00.003-0.00123.999-0.009-0.0090.0000.0000.0000.000
34A777VAL00.0310.00221.217-0.018-0.0180.0000.0000.0000.000
35A778SER0-0.065-0.02620.988-0.002-0.0020.0000.0000.0000.000
36A779GLY00.0170.01520.974-0.001-0.0010.0000.0000.0000.000
37A780LEU0-0.072-0.03417.083-0.046-0.0460.0000.0000.0000.000
38A781THR00.0290.01113.3160.0160.0160.0000.0000.0000.000
39A782VAL0-0.024-0.01013.117-0.038-0.0380.0000.0000.0000.000
40A783ASP-1-0.774-0.85810.395-0.005-0.0050.0000.0000.0000.000
41A784THR00.007-0.0057.8680.1530.1530.0000.0000.0000.000
42A785GLU-1-0.767-0.87111.2740.1180.1180.0000.0000.0000.000
43A786GLU-1-0.873-0.9547.7490.0280.0280.0000.0000.0000.000
44A787ARG10.7730.8366.0870.3440.3440.0000.0000.0000.000
45A788LEU00.022-0.00611.556-0.064-0.0640.0000.0000.0000.000
46A789LYS10.8600.92813.0510.0610.0610.0000.0000.0000.000
47A790GLY00.0350.02813.298-0.024-0.0240.0000.0000.0000.000
48A791VAL00.010-0.00214.213-0.020-0.0200.0000.0000.0000.000
49A792ILE0-0.002-0.00216.5730.0010.0010.0000.0000.0000.000
50A793ASP-1-0.844-0.91916.636-0.093-0.0930.0000.0000.0000.000
51A794LEU0-0.036-0.00915.556-0.003-0.0030.0000.0000.0000.000
52A795VAL0-0.011-0.01019.3020.0080.0080.0000.0000.0000.000
53A796PHE0-0.019-0.01822.1570.0110.0110.0000.0000.0000.000
54A797GLU-1-0.866-0.91518.924-0.207-0.2070.0000.0000.0000.000
55A798LYS10.8360.91423.4090.1290.1290.0000.0000.0000.000
56A799ALA0-0.015-0.01325.3300.0080.0080.0000.0000.0000.000
57A800ILE0-0.118-0.06626.4550.0100.0100.0000.0000.0000.000
58A801ASP-1-0.881-0.92127.526-0.108-0.1080.0000.0000.0000.000
59A802GLU-1-0.806-0.89329.299-0.101-0.1010.0000.0000.0000.000
60A803PRO00.0370.02331.5740.0030.0030.0000.0000.0000.000
61A804SER00.0030.00832.9750.0040.0040.0000.0000.0000.000
62A805PHE00.0080.02031.4570.0060.0060.0000.0000.0000.000
63A806SER00.017-0.00930.903-0.001-0.0010.0000.0000.0000.000
64A807VAL00.0240.00631.5710.0020.0020.0000.0000.0000.000
65A808ALA00.0190.02530.6900.0020.0020.0000.0000.0000.000
66A809TYR00.0220.00026.730-0.002-0.0020.0000.0000.0000.000
67A810ALA00.0250.02527.1050.0000.0000.0000.0000.0000.000
68A811ASN0-0.035-0.04028.9380.0070.0070.0000.0000.0000.000
69A812MET0-0.0010.00021.1120.0040.0040.0000.0000.0000.000
70A813CYS0-0.040-0.02124.3680.0000.0000.0000.0000.0000.000
71A814ARG10.9360.96025.4550.0380.0380.0000.0000.0000.000
72A815CYS0-0.038-0.00725.2070.0050.0050.0000.0000.0000.000
73A816LEU00.0250.01019.3470.0020.0020.0000.0000.0000.000
74A817VAL0-0.095-0.02322.1200.0120.0120.0000.0000.0000.000
75A818THR0-0.055-0.02824.2660.0130.0130.0000.0000.0000.000
76A819LEU00.0220.00518.659-0.007-0.0070.0000.0000.0000.000
77A820LYS10.8470.92218.670-0.135-0.1350.0000.0000.0000.000
78A821VAL00.0190.00614.300-0.002-0.0020.0000.0000.0000.000
79A822PRO00.0070.01513.2900.0200.0200.0000.0000.0000.000
80A832ASN00.0190.00618.020-0.020-0.0200.0000.0000.0000.000
81A833PHE00.1050.04420.7810.0040.0040.0000.0000.0000.000
82A834ARG10.9810.97122.339-0.015-0.0150.0000.0000.0000.000
83A835LYS10.8660.95518.347-0.151-0.1510.0000.0000.0000.000
84A836LEU0-0.001-0.00117.282-0.001-0.0010.0000.0000.0000.000
85A837LEU00.0290.02421.125-0.012-0.0120.0000.0000.0000.000
86A838LEU00.0460.03023.864-0.007-0.0070.0000.0000.0000.000
87A839ASN0-0.008-0.00520.820-0.009-0.0090.0000.0000.0000.000
88A840ARG10.8040.89120.3610.0590.0590.0000.0000.0000.000
89A841CYS0-0.045-0.02622.901-0.012-0.0120.0000.0000.0000.000
90A842GLN00.045-0.00626.652-0.004-0.0040.0000.0000.0000.000
91A843LYS10.9821.02919.3690.0600.0600.0000.0000.0000.000
92A844GLU-1-0.816-0.90125.225-0.058-0.0580.0000.0000.0000.000
93A845PHE00.0530.01027.725-0.001-0.0010.0000.0000.0000.000
94A846GLU-1-0.849-0.92327.1330.0190.0190.0000.0000.0000.000
95A847LYS10.8340.93125.6040.0370.0370.0000.0000.0000.000
96A848ASP-1-0.875-0.92628.580-0.020-0.0200.0000.0000.0000.000
97A849LYS10.8130.90131.685-0.011-0.0110.0000.0000.0000.000
98A850ALA0-0.0270.00730.4180.0010.0010.0000.0000.0000.000
99A881ALA00.0650.01538.7630.0010.0010.0000.0000.0000.000
100A882LYS10.9500.98635.9920.0130.0130.0000.0000.0000.000
101A883ASP-1-0.779-0.88838.128-0.019-0.0190.0000.0000.0000.000
102A884LYS10.9700.98535.3050.0490.0490.0000.0000.0000.000
103A885ALA0-0.013-0.00934.637-0.004-0.0040.0000.0000.0000.000
104A886ARG10.8870.93235.2540.0190.0190.0000.0000.0000.000
105A887ARG10.8550.92637.0800.0310.0310.0000.0000.0000.000
106A888ARG10.9330.95225.8660.0640.0640.0000.0000.0000.000
107A889SER0-0.029-0.02832.9760.0000.0000.0000.0000.0000.000
108A890ILE00.0110.00834.5450.0020.0020.0000.0000.0000.000
109A891GLY00.0290.01133.6830.0000.0000.0000.0000.0000.000
110A892ASN00.018-0.00429.276-0.004-0.0040.0000.0000.0000.000
111A893ILE00.0220.01031.6720.0010.0010.0000.0000.0000.000
112A894LYS10.8790.95734.3990.0450.0450.0000.0000.0000.000
113A895PHE00.005-0.01126.1180.0000.0000.0000.0000.0000.000
114A896ILE00.023-0.00129.3110.0030.0030.0000.0000.0000.000
115A897GLY00.0560.01731.7390.0040.0040.0000.0000.0000.000
116A898GLU-1-0.870-0.93732.724-0.033-0.0330.0000.0000.0000.000
117A899LEU0-0.026-0.01927.4790.0020.0020.0000.0000.0000.000
118A900PHE0-0.002-0.01131.5100.0030.0030.0000.0000.0000.000
119A901LYS10.8620.93534.0510.0310.0310.0000.0000.0000.000
120A902LEU0-0.052-0.01431.7000.0000.0000.0000.0000.0000.000
121A903LYS10.9220.96132.8690.0050.0050.0000.0000.0000.000
122A904MET0-0.0490.00028.1000.0050.0050.0000.0000.0000.000
123A905LEU0-0.017-0.00727.9530.0040.0040.0000.0000.0000.000
124A906THR00.0510.01931.309-0.001-0.0010.0000.0000.0000.000
125A907GLU-1-0.842-0.93633.7170.0080.0080.0000.0000.0000.000
126A908ALA0-0.043-0.02334.613-0.002-0.0020.0000.0000.0000.000
127A909ILE00.0340.01830.843-0.001-0.0010.0000.0000.0000.000
128A910MET00.0120.02034.084-0.004-0.0040.0000.0000.0000.000
129A911HIS00.0420.03736.954-0.002-0.0020.0000.0000.0000.000
130A912ASP-1-0.886-0.92834.0860.0060.0060.0000.0000.0000.000
131A913CYS0-0.105-0.05035.097-0.004-0.0040.0000.0000.0000.000
132A914VAL00.0330.01737.303-0.002-0.0020.0000.0000.0000.000
133A915VAL00.0420.02139.843-0.001-0.0010.0000.0000.0000.000
134A916LYS10.7560.86835.7650.0170.0170.0000.0000.0000.000
135A917LEU0-0.062-0.04739.348-0.002-0.0020.0000.0000.0000.000
136A918LEU00.0050.00741.651-0.001-0.0010.0000.0000.0000.000
137A919LYS10.8520.96137.1560.0080.0080.0000.0000.0000.000
138A920ASN0-0.111-0.05940.0350.0000.0000.0000.0000.0000.000
139A921HIS00.0880.04543.675-0.001-0.0010.0000.0000.0000.000
140A922ASP-1-0.760-0.86143.798-0.023-0.0230.0000.0000.0000.000
141A923GLU-1-0.747-0.86246.375-0.021-0.0210.0000.0000.0000.000
142A924GLU-1-0.863-0.93141.566-0.034-0.0340.0000.0000.0000.000
143A925SER0-0.040-0.03142.264-0.001-0.0010.0000.0000.0000.000
144A926LEU00.0410.01843.2590.0010.0010.0000.0000.0000.000
145A927GLU-1-0.731-0.82345.418-0.025-0.0250.0000.0000.0000.000
146A928CYS0-0.045-0.02239.988-0.001-0.0010.0000.0000.0000.000
147A929LEU0-0.002-0.00242.6010.0000.0000.0000.0000.0000.000
148A930CYS00.0210.00844.0140.0020.0020.0000.0000.0000.000
149A931ARG10.8570.92443.5680.0270.0270.0000.0000.0000.000
150A932LEU0-0.031-0.00838.7550.0000.0000.0000.0000.0000.000
151A933LEU00.026-0.00842.3830.0010.0010.0000.0000.0000.000
152A934THR0-0.0030.00345.0410.0020.0020.0000.0000.0000.000
153A935THR0-0.088-0.04441.8880.0000.0000.0000.0000.0000.000
154A936ILE0-0.043-0.03539.0430.0000.0000.0000.0000.0000.000
155A937GLY00.0330.02342.9510.0020.0020.0000.0000.0000.000
156A938LYS11.0080.98245.7400.0080.0080.0000.0000.0000.000
157A939ASP-1-0.970-0.96941.448-0.003-0.0030.0000.0000.0000.000
158A940LEU0-0.040-0.02839.4240.0020.0020.0000.0000.0000.000
159A941ASP-1-0.767-0.84343.1830.0030.0030.0000.0000.0000.000
160A942PHE00.1050.05543.8010.0010.0010.0000.0000.0000.000
161A943GLU-1-0.769-0.90946.5520.0070.0070.0000.0000.0000.000
162A944LYS10.8180.91145.230-0.013-0.0130.0000.0000.0000.000
163A945ALA0-0.050-0.02343.9730.0010.0010.0000.0000.0000.000
164A946LYS10.8510.93645.898-0.005-0.0050.0000.0000.0000.000
165A947PRO00.0760.04248.086-0.001-0.0010.0000.0000.0000.000
166A948ARG10.9160.95741.566-0.012-0.0120.0000.0000.0000.000
167A949MET00.0060.02144.711-0.002-0.0020.0000.0000.0000.000
168A950ASP-1-0.815-0.90347.9310.0020.0020.0000.0000.0000.000
169A951GLN0-0.067-0.02247.9250.0000.0000.0000.0000.0000.000
170A952TYR0-0.016-0.03842.367-0.001-0.0010.0000.0000.0000.000
171A953PHE00.038-0.01148.130-0.001-0.0010.0000.0000.0000.000
172A954ASN00.0230.03151.448-0.001-0.0010.0000.0000.0000.000
173A955GLN0-0.037-0.02947.0300.0000.0000.0000.0000.0000.000
174A956MET0-0.028-0.00948.965-0.002-0.0020.0000.0000.0000.000
175A957GLU-1-0.773-0.85551.947-0.005-0.0050.0000.0000.0000.000
176A958LYS10.8770.92954.3080.0030.0030.0000.0000.0000.000
177A959ILE0-0.046-0.03449.674-0.001-0.0010.0000.0000.0000.000
178A960VAL0-0.001-0.00454.104-0.001-0.0010.0000.0000.0000.000
179A961LYS10.8070.88456.7410.0030.0030.0000.0000.0000.000
180A962GLU-1-0.828-0.88356.880-0.005-0.0050.0000.0000.0000.000
181A963ARG10.9680.98457.1990.0080.0080.0000.0000.0000.000
182A964LYS10.8440.93353.2600.0090.0090.0000.0000.0000.000
183A965THR00.003-0.00451.945-0.001-0.0010.0000.0000.0000.000
184A966SER00.034-0.00753.2650.0010.0010.0000.0000.0000.000
185A967SER00.016-0.01255.8070.0000.0000.0000.0000.0000.000
186A968ARG10.8890.92748.9100.0240.0240.0000.0000.0000.000
187A969ILE00.0230.00149.3150.0000.0000.0000.0000.0000.000
188A970ARG10.8700.94352.9450.0120.0120.0000.0000.0000.000
189A971PHE00.0370.01955.7300.0010.0010.0000.0000.0000.000
190A972MET0-0.034-0.01249.2050.0000.0000.0000.0000.0000.000
191A973LEU0-0.008-0.02149.7420.0000.0000.0000.0000.0000.000
192A974GLN0-0.028-0.03152.7650.0010.0010.0000.0000.0000.000
193A975ASP-1-0.856-0.90053.173-0.013-0.0130.0000.0000.0000.000
194A976VAL0-0.031-0.01648.7870.0010.0010.0000.0000.0000.000
195A977ILE0-0.068-0.04651.9500.0010.0010.0000.0000.0000.000
196A978ASP-1-0.862-0.92054.462-0.007-0.0070.0000.0000.0000.000
197A979LEU00.005-0.00750.6560.0010.0010.0000.0000.0000.000
198A980ARG10.7310.85150.6260.0000.0000.0000.0000.0000.000
199A981LEU0-0.030-0.00953.5270.0010.0010.0000.0000.0000.000
200A982CYS0-0.023-0.00456.4270.0010.0010.0000.0000.0000.000
201A983ASN0-0.070-0.04754.6110.0000.0000.0000.0000.0000.000
202A984TRP0-0.081-0.06248.227-0.001-0.0010.0000.0000.0000.000
203A985VAL0-0.0300.00352.242-0.001-0.0010.0000.0000.0000.000
204A986SER00.0080.00553.941-0.001-0.0010.0000.0000.0000.000