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: KGQK3

Calculation Name: 4HYE-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4HYE

Chain ID: A

ChEMBL ID:

UniProt ID: Q8DNC2

Base Structure: X-ray

Registration Date: 2023-09-23

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 200
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2191130.542529
FMO2-HF: Nuclear repulsion 2111822.905785
FMO2-HF: Total energy -79307.636744
FMO2-MP2: Total energy -79536.446881


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:0:HIS)


Summations of interaction energy for fragment #1(A:0: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.
-232.721-224.66114.581-11.067-11.572-0.121
Interaction energy analysis for fragmet #1(A:0:HIS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.827 / q_NPA : 0.904
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].
3A2LYS10.8670.9353.65838.37940.511-0.008-1.097-1.0260.001
4A3VAL0-0.003-0.0126.8552.0642.0640.0000.0000.0000.000
5A4LEU00.0260.0259.4661.5371.5370.0000.0000.0000.000
6A5VAL00.0010.00113.224-0.038-0.0380.0000.0000.0000.000
7A6ALA0-0.020-0.01515.6030.8010.8010.0000.0000.0000.000
8A7GLH0-0.014-0.06319.0970.3480.3480.0000.0000.0000.000
9A8ASP-1-0.822-0.91321.653-11.362-11.3620.0000.0000.0000.000
10A9GLN0-0.0060.01724.9660.2670.2670.0000.0000.0000.000
11A10SER00.027-0.00823.676-0.634-0.6340.0000.0000.0000.000
12A11MET00.0360.03822.827-0.312-0.3120.0000.0000.0000.000
13A12LEU00.0230.00720.987-0.417-0.4170.0000.0000.0000.000
14A13ARG10.8180.89718.90912.83212.8320.0000.0000.0000.000
15A14ASP-1-0.877-0.93718.028-15.618-15.6180.0000.0000.0000.000
16A15ALA00.000-0.00217.836-0.841-0.8410.0000.0000.0000.000
17A16MET0-0.009-0.01215.685-0.530-0.5300.0000.0000.0000.000
18A17CYS0-0.041-0.01313.417-1.528-1.5280.0000.0000.0000.000
19A18GLN00.0070.02312.941-1.412-1.4120.0000.0000.0000.000
20A19LEU0-0.031-0.02613.672-0.868-0.8680.0000.0000.0000.000
21A20LEU00.012-0.0149.752-1.445-1.4450.0000.0000.0000.000
22A21THR0-0.032-0.0258.648-2.873-2.8730.0000.0000.0000.000
23A22LEU0-0.052-0.0238.880-1.113-1.1130.0000.0000.0000.000
24A23GLN0-0.042-0.0127.387-1.232-1.2320.0000.0000.0000.000
25A24PRO00.0100.0005.660-1.772-1.7720.0000.0000.0000.000
26A25ASP-1-0.814-0.9201.841-108.930-107.96311.286-6.233-6.020-0.080
27A26VAL0-0.059-0.0252.219-18.060-15.0672.976-3.104-2.864-0.042
28A27GLU-1-0.892-0.9052.401-37.167-35.7620.329-0.535-1.1990.000
29A28SER00.011-0.0124.1575.7025.8560.000-0.039-0.1150.000
30A29VAL00.0010.0047.676-1.392-1.3920.0000.0000.0000.000
31A30LEU0-0.0020.01710.6901.7941.7940.0000.0000.0000.000
32A31GLN00.0390.00413.8900.6500.6500.0000.0000.0000.000
33A32ALA0-0.0130.00617.1760.6490.6490.0000.0000.0000.000
34A33LYS10.8290.88220.21112.26412.2640.0000.0000.0000.000
35A34ASN00.006-0.01023.3990.4190.4190.0000.0000.0000.000
36A35GLY00.1100.04622.891-0.520-0.5200.0000.0000.0000.000
37A36GLN0-0.016-0.01623.3090.0460.0460.0000.0000.0000.000
38A37GLU-1-0.801-0.88221.679-12.822-12.8220.0000.0000.0000.000
39A38ALA00.0400.00519.073-0.458-0.4580.0000.0000.0000.000
40A39ILE0-0.0120.00819.415-0.499-0.4990.0000.0000.0000.000
41A40GLN0-0.027-0.01021.114-0.009-0.0090.0000.0000.0000.000
42A41LEU0-0.011-0.02117.057-0.105-0.1050.0000.0000.0000.000
43A42LEU0-0.005-0.00415.201-0.618-0.6180.0000.0000.0000.000
44A43GLU-1-0.871-0.92317.553-12.345-12.3450.0000.0000.0000.000
45A44LYS10.7550.87918.76513.57613.5760.0000.0000.0000.000
46A45GLU-1-0.909-0.93812.735-19.058-19.0580.0000.0000.0000.000
47A46SER0-0.040-0.00510.414-0.105-0.1050.0000.0000.0000.000
48A47VAL0-0.004-0.02210.136-1.004-1.0040.0000.0000.0000.000
49A48ASP-1-0.800-0.8835.483-38.223-38.168-0.001-0.002-0.0520.000
50A49ILE0-0.017-0.0246.2461.6271.6270.0000.0000.0000.000
51A50ALA00.0020.00910.066-0.046-0.0460.0000.0000.0000.000
52A51ILE0-0.023-0.02111.4320.5680.5680.0000.0000.0000.000
53A52LEU00.007-0.00614.9760.7510.7510.0000.0000.0000.000
54A53ASP-1-0.749-0.82918.646-12.690-12.6900.0000.0000.0000.000
55A54VAL00.005-0.02021.8040.2490.2490.0000.0000.0000.000
56A55GLU-1-0.988-1.00224.286-9.819-9.8190.0000.0000.0000.000
57A56MET0-0.0220.01021.684-0.392-0.3920.0000.0000.0000.000
58A57PRO00.0250.01526.8830.2760.2760.0000.0000.0000.000
59A58VAL0-0.034-0.02728.076-0.322-0.3220.0000.0000.0000.000
60A59LYS10.8580.93726.14610.57310.5730.0000.0000.0000.000
61A60THR00.026-0.00526.180-0.413-0.4130.0000.0000.0000.000
62A61GLY00.0360.00722.324-0.270-0.2700.0000.0000.0000.000
63A62LEU0-0.016-0.01622.354-0.378-0.3780.0000.0000.0000.000
64A63GLU-1-0.813-0.87624.686-10.423-10.4230.0000.0000.0000.000
65A64VAL0-0.0240.00019.923-0.050-0.0500.0000.0000.0000.000
66A65LEU0-0.022-0.00619.365-0.323-0.3230.0000.0000.0000.000
67A66GLU-1-0.781-0.88021.344-10.956-10.9560.0000.0000.0000.000
68A67TRP00.0030.02419.916-0.081-0.0810.0000.0000.0000.000
69A68ILE00.019-0.00417.0460.0100.0100.0000.0000.0000.000
70A69ARG10.7560.87216.27916.11616.1160.0000.0000.0000.000
71A70SER0-0.058-0.05221.8950.1310.1310.0000.0000.0000.000
72A71GLU-1-0.907-0.92822.111-11.050-11.0500.0000.0000.0000.000
73A72LYS10.7870.89220.96711.54311.5430.0000.0000.0000.000
74A73LEU00.0270.02316.522-0.290-0.2900.0000.0000.0000.000
75A74GLU-1-0.969-0.98213.378-18.364-18.3640.0000.0000.0000.000
76A75THR0-0.046-0.00612.328-0.998-0.9980.0000.0000.0000.000
77A76LYS10.8890.95610.52322.59622.5960.0000.0000.0000.000
78A77VAL0-0.023-0.02412.925-0.270-0.2700.0000.0000.0000.000
79A78VAL0-0.0030.00012.7760.6130.6130.0000.0000.0000.000
80A79VAL00.0160.01015.7550.2220.2220.0000.0000.0000.000
81A80VAL0-0.012-0.00117.7300.0800.0800.0000.0000.0000.000
82A81THR00.0510.02020.4450.6650.6650.0000.0000.0000.000
83A82THR00.0340.01524.202-0.220-0.2200.0000.0000.0000.000
84A83PHE00.0730.01327.0370.0920.0920.0000.0000.0000.000
85A84LYS10.7780.90129.9669.3459.3450.0000.0000.0000.000
86A85ARG10.8720.92928.32410.60110.6010.0000.0000.0000.000
87A86ALA00.0280.01327.992-0.285-0.2850.0000.0000.0000.000
88A87GLY00.010-0.00528.770-0.157-0.1570.0000.0000.0000.000
89A88TYR00.0060.00727.9120.2490.2490.0000.0000.0000.000
90A89PHE00.0160.01523.860-0.236-0.2360.0000.0000.0000.000
91A90GLU-1-0.788-0.89126.701-9.747-9.7470.0000.0000.0000.000
92A91ARG10.7850.85627.77510.32910.3290.0000.0000.0000.000
93A92ALA00.0280.00823.098-0.206-0.2060.0000.0000.0000.000
94A93VAL0-0.026-0.01623.665-0.484-0.4840.0000.0000.0000.000
95A94LYS10.7910.88625.2789.3289.3280.0000.0000.0000.000
96A95ALA00.0170.03624.1120.1200.1200.0000.0000.0000.000
97A96GLY00.013-0.00121.976-0.509-0.5090.0000.0000.0000.000
98A97VAL0-0.041-0.00218.726-0.866-0.8660.0000.0000.0000.000
99A98ASP-1-0.765-0.88615.072-18.424-18.4240.0000.0000.0000.000
100A99ALA0-0.003-0.00815.794-0.115-0.1150.0000.0000.0000.000
101A100TYR0-0.023-0.00217.6270.1360.1360.0000.0000.0000.000
102A101VAL00.0250.00017.1100.3790.3790.0000.0000.0000.000
103A102LEU00.0210.00920.4330.3480.3480.0000.0000.0000.000
104A103LYS10.7780.86920.45112.07412.0740.0000.0000.0000.000
105A104GLU-1-0.999-0.97821.014-13.606-13.6060.0000.0000.0000.000
106A105ARG10.8560.90415.96617.58517.5850.0000.0000.0000.000
107A106SER0-0.011-0.02517.545-0.490-0.4900.0000.0000.0000.000
108A107ILE00.0340.00511.974-0.472-0.4720.0000.0000.0000.000
109A108ALA00.0130.00712.807-1.702-1.7020.0000.0000.0000.000
110A109ASP-1-0.802-0.87512.895-18.061-18.0610.0000.0000.0000.000
111A110LEU0-0.042-0.01212.596-0.509-0.5090.0000.0000.0000.000
112A111MET00.0370.0066.015-0.192-0.1920.0000.0000.0000.000
113A112GLN0-0.0290.0049.053-2.658-2.6580.0000.0000.0000.000
114A113THR00.043-0.00111.3040.0490.0490.0000.0000.0000.000
115A114LEU0-0.048-0.0367.6250.2620.2620.0000.0000.0000.000
116A115HIS0-0.035-0.0123.4591.1501.3930.000-0.051-0.1920.000
117A116THR00.0200.0218.0361.3491.3490.0000.0000.0000.000
118A117VAL0-0.032-0.02110.3620.9730.9730.0000.0000.0000.000
119A118LEU00.002-0.0014.7040.7940.905-0.001-0.006-0.1040.000
120A119GLU-1-0.889-0.9048.780-25.966-25.9660.0000.0000.0000.000
121A120GLY0-0.054-0.03110.7681.9731.9730.0000.0000.0000.000
122A121ARG10.7510.86511.99224.37824.3780.0000.0000.0000.000
123A122LYS10.8700.94115.12614.72214.7220.0000.0000.0000.000
124A123GLU-1-0.784-0.87715.355-18.935-18.9350.0000.0000.0000.000
125A124TYR0-0.019-0.01618.1770.0870.0870.0000.0000.0000.000
126A125SER0-0.008-0.02221.374-0.105-0.1050.0000.0000.0000.000
127A126PRO00.0240.01121.7990.5670.5670.0000.0000.0000.000
128A127GLU-1-0.769-0.87723.679-12.703-12.7030.0000.0000.0000.000
129A128LEU0-0.037-0.02623.5210.5630.5630.0000.0000.0000.000
130A129MET0-0.060-0.02425.1700.5170.5170.0000.0000.0000.000
131A130GLU-1-0.895-0.93828.353-9.555-9.5550.0000.0000.0000.000
132A131MET00.0080.01730.4460.5440.5440.0000.0000.0000.000
133A132VAL0-0.095-0.06329.6950.4050.4050.0000.0000.0000.000
134A133MET0-0.050-0.01932.4850.2600.2600.0000.0000.0000.000
135A134THR0-0.022-0.00734.3870.3250.3250.0000.0000.0000.000
136A135ARG10.8870.95833.5079.4169.4160.0000.0000.0000.000
137A136PRO00.0180.02037.7050.0090.0090.0000.0000.0000.000
138A137ASN00.029-0.01440.047-0.152-0.1520.0000.0000.0000.000
139A138PRO0-0.0100.01739.9960.1800.1800.0000.0000.0000.000
140A139LEU0-0.024-0.01042.1130.1780.1780.0000.0000.0000.000
141A140THR00.023-0.02145.1410.0910.0910.0000.0000.0000.000
142A141GLU-1-0.902-0.95848.294-6.176-6.1760.0000.0000.0000.000
143A142GLN00.017-0.00450.127-0.066-0.0660.0000.0000.0000.000
144A143GLU-1-0.791-0.85046.838-6.710-6.7100.0000.0000.0000.000
145A144ILE00.0390.02044.748-0.079-0.0790.0000.0000.0000.000
146A145ALA0-0.023-0.00546.877-0.049-0.0490.0000.0000.0000.000
147A146VAL00.0250.00248.0530.0070.0070.0000.0000.0000.000
148A147LEU0-0.005-0.01042.206-0.031-0.0310.0000.0000.0000.000
149A148LYS10.9230.97044.8236.7716.7710.0000.0000.0000.000
150A149GLY0-0.012-0.00346.2730.0050.0050.0000.0000.0000.000
151A150ILE0-0.055-0.03343.5840.0020.0020.0000.0000.0000.000
152A151ALA0-0.0040.00142.550-0.060-0.0600.0000.0000.0000.000
153A152ARG10.8590.93143.6716.1526.1520.0000.0000.0000.000
154A153GLY00.0060.00345.8830.1150.1150.0000.0000.0000.000
155A154LEU0-0.066-0.00247.0000.0900.0900.0000.0000.0000.000
156A155SER0-0.008-0.04549.292-0.087-0.0870.0000.0000.0000.000
157A156ASN00.0550.00250.443-0.080-0.0800.0000.0000.0000.000
158A157GLN00.0060.00152.8400.0120.0120.0000.0000.0000.000
159A158GLU-1-0.748-0.82553.393-5.874-5.8740.0000.0000.0000.000
160A159ILE0-0.023-0.01249.4790.0340.0340.0000.0000.0000.000
161A160ALA0-0.054-0.03154.0280.0450.0450.0000.0000.0000.000
162A161ASP-1-0.836-0.91956.883-5.228-5.2280.0000.0000.0000.000
163A162GLN0-0.023-0.00554.696-0.043-0.0430.0000.0000.0000.000
164A163LEU0-0.022-0.01353.046-0.003-0.0030.0000.0000.0000.000
165A164TYR0-0.0380.00257.4860.0810.0810.0000.0000.0000.000
166A165LEU0-0.0090.00756.1850.0360.0360.0000.0000.0000.000
167A166SER00.0320.02759.817-0.026-0.0260.0000.0000.0000.000
168A167ASN00.0690.00556.290-0.187-0.1870.0000.0000.0000.000
169A168GLY00.014-0.00255.882-0.110-0.1100.0000.0000.0000.000
170A169THR00.007-0.00355.853-0.064-0.0640.0000.0000.0000.000
171A170ILE00.0150.03151.947-0.124-0.1240.0000.0000.0000.000
172A171ARG10.8820.93151.4645.7545.7540.0000.0000.0000.000
173A172ASN00.0360.02750.761-0.174-0.1740.0000.0000.0000.000
174A173TYR00.0220.01050.361-0.099-0.0990.0000.0000.0000.000
175A174VAL0-0.011-0.00846.094-0.147-0.1470.0000.0000.0000.000
176A175THR0-0.007-0.00646.094-0.174-0.1740.0000.0000.0000.000
177A176ASN0-0.008-0.01146.012-0.148-0.1480.0000.0000.0000.000
178A177ILE0-0.019-0.00643.097-0.144-0.1440.0000.0000.0000.000
179A178LEU0-0.016-0.02041.690-0.160-0.1600.0000.0000.0000.000
180A179SER0-0.0260.00340.951-0.259-0.2590.0000.0000.0000.000
181A180LYS10.7890.87141.1406.7186.7180.0000.0000.0000.000
182A181LEU0-0.057-0.02238.119-0.140-0.1400.0000.0000.0000.000
183A182ASP-1-0.902-0.93434.799-9.197-9.1970.0000.0000.0000.000
184A183ALA0-0.023-0.01136.365-0.246-0.2460.0000.0000.0000.000
185A184GLY00.0170.01137.3470.1810.1810.0000.0000.0000.000
186A185ASN0-0.016-0.02137.6120.2880.2880.0000.0000.0000.000
187A186ARG10.9270.93840.4826.6106.6100.0000.0000.0000.000
188A187THR00.0280.00838.3900.0680.0680.0000.0000.0000.000
189A188GLU-1-0.776-0.87133.816-9.140-9.1400.0000.0000.0000.000
190A189ALA00.0210.01537.014-0.117-0.1170.0000.0000.0000.000
191A190ALA00.0150.00339.171-0.035-0.0350.0000.0000.0000.000
192A191ASN0-0.011-0.00834.7360.0710.0710.0000.0000.0000.000
193A192ILE00.0550.03533.627-0.102-0.1020.0000.0000.0000.000
194A193ALA00.0320.02235.417-0.064-0.0640.0000.0000.0000.000
195A194LYS10.8260.90234.1568.9128.9120.0000.0000.0000.000
196A195GLU-1-0.835-0.91832.041-9.593-9.5930.0000.0000.0000.000
197A196SER0-0.068-0.02733.645-0.252-0.2520.0000.0000.0000.000
198A197GLY00.0080.02434.9080.0070.0070.0000.0000.0000.000
199A198TRP0-0.023-0.02437.0280.1980.1980.0000.0000.0000.000
200A199LEU0-0.029-0.00840.4190.3840.3840.0000.0000.0000.000