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: QVVNY

Calculation Name: 4HA7-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4HA7

Chain ID: A

ChEMBL ID:

UniProt ID: P33312

Base Structure: X-ray

Registration Date: 2023-09-21

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 OptAll
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 226
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2766828.67617
FMO2-HF: Nuclear repulsion 2678683.593722
FMO2-HF: Total energy -88145.082448
FMO2-MP2: Total energy -88403.043237


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:8:GLU)


Summations of interaction energy for fragment #1(A:8: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.
-92.425-84.5424.673-5.179-7.3780.027
Interaction energy analysis for fragmet #1(A:8:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.933 / q_NPA : -0.971
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].
3A10LEU00.006-0.0022.012-15.114-9.9864.464-4.386-5.2060.022
4A11PRO00.037-0.0012.812-8.567-6.9530.205-0.578-1.2410.004
5A12GLN0-0.042-0.0225.944-4.543-4.5430.0000.0000.0000.000
6A13PHE0-0.009-0.0126.461-2.406-2.4060.0000.0000.0000.000
7A14LEU00.032-0.0036.329-2.879-2.8790.0000.0000.0000.000
8A15GLN00.0270.0309.592-2.365-2.3650.0000.0000.0000.000
9A16ASN0-0.023-0.01811.643-2.358-2.3580.0000.0000.0000.000
10A17TYR0-0.056-0.03512.388-2.096-2.0960.0000.0000.0000.000
11A18LEU00.0250.03410.480-0.686-0.6860.0000.0000.0000.000
12A19PRO00.029-0.00214.673-0.830-0.8300.0000.0000.0000.000
13A20ASN0-0.045-0.02117.365-1.412-1.4120.0000.0000.0000.000
14A21ALA00.0220.03216.323-0.240-0.2400.0000.0000.0000.000
15A22GLY0-0.041-0.02518.401-0.532-0.5320.0000.0000.0000.000
16A23GLN0-0.103-0.05920.269-0.981-0.9810.0000.0000.0000.000
17A24THR00.003-0.02423.4800.2190.2190.0000.0000.0000.000
18A25GLU-1-0.911-0.91326.9039.9289.9280.0000.0000.0000.000
19A26ASN0-0.006-0.00628.1920.4230.4230.0000.0000.0000.000
20A27THR0-0.011-0.00627.805-0.245-0.2450.0000.0000.0000.000
21A28ILE00.0580.02730.6670.1270.1270.0000.0000.0000.000
22A29VAL00.0060.01027.4860.0230.0230.0000.0000.0000.000
23A30PRO0-0.0320.00524.7860.1330.1330.0000.0000.0000.000
24A31PHE00.0320.01218.435-0.021-0.0210.0000.0000.0000.000
25A32VAL0-0.009-0.00221.5760.4940.4940.0000.0000.0000.000
26A33THR0-0.024-0.03616.4270.2710.2710.0000.0000.0000.000
27A34LEU0-0.006-0.00118.707-0.005-0.0050.0000.0000.0000.000
28A35THR0-0.066-0.04614.1181.1401.1400.0000.0000.0000.000
29A36TYR00.034-0.00315.703-0.853-0.8530.0000.0000.0000.000
30A37ALA00.0010.00314.0771.3471.3470.0000.0000.0000.000
31A38GLN0-0.033-0.01015.841-1.414-1.4140.0000.0000.0000.000
32A39SER0-0.034-0.03917.1881.1421.1420.0000.0000.0000.000
33A40LEU00.0420.01518.444-0.077-0.0770.0000.0000.0000.000
34A41ASP-1-0.784-0.85821.03412.98412.9840.0000.0000.0000.000
35A42ALA00.0100.01222.208-0.547-0.5470.0000.0000.0000.000
36A43ARG10.7780.88823.018-12.299-12.2990.0000.0000.0000.000
37A44VAL00.0160.00220.1180.8550.8550.0000.0000.0000.000
38A45SER0-0.102-0.04922.118-0.120-0.1200.0000.0000.0000.000
39A46ARG10.9760.98621.676-14.269-14.2690.0000.0000.0000.000
40A47GLY00.0280.03525.134-0.504-0.5040.0000.0000.0000.000
41A57PRO00.023-0.0088.289-1.319-1.3190.0000.0000.0000.000
42A58GLU-1-0.816-0.9074.34542.08142.355-0.001-0.034-0.2400.000
43A59THR00.037-0.0045.5402.5462.577-0.0010.000-0.0290.000
44A60LYS10.9340.9798.219-25.751-25.7510.0000.0000.0000.000
45A61THR00.019-0.0025.224-6.044-6.0440.0000.0000.0000.000
46A62MET00.0290.0305.966-0.718-0.7180.0000.0000.0000.000
47A63THR0-0.016-0.0086.869-4.094-4.0940.0000.0000.0000.000
48A64HIS0-0.008-0.0049.981-2.407-2.4070.0000.0000.0000.000
49A65TYR00.0550.0305.836-1.490-1.4900.0000.0000.0000.000
50A66LEU00.0320.0229.063-2.525-2.5250.0000.0000.0000.000
51A67ARG10.7960.86811.606-22.038-22.0380.0000.0000.0000.000
52A68HIS0-0.0260.00012.452-2.968-2.9680.0000.0000.0000.000
53A69HIS0-0.048-0.02711.001-0.891-0.8910.0000.0000.0000.000
54A70HIS0-0.025-0.01214.741-1.401-1.4010.0000.0000.0000.000
55A71ASP-1-0.747-0.81918.27113.94313.9430.0000.0000.0000.000
56A72GLY00.0070.00421.290-0.468-0.4680.0000.0000.0000.000
57A73ILE0-0.060-0.02617.1990.6550.6550.0000.0000.0000.000
58A74LEU0-0.0010.00820.795-0.610-0.6100.0000.0000.0000.000
59A75VAL00.006-0.01621.7870.5880.5880.0000.0000.0000.000
60A76GLY00.0410.03024.316-0.557-0.5570.0000.0000.0000.000
61A77SER0-0.021-0.02527.4600.2010.2010.0000.0000.0000.000
62A78GLY0-0.004-0.00530.134-0.088-0.0880.0000.0000.0000.000
63A79THR0-0.010-0.02524.2980.2740.2740.0000.0000.0000.000
64A80VAL0-0.020-0.00525.2380.2630.2630.0000.0000.0000.000
65A81LEU0-0.063-0.03726.982-0.450-0.4500.0000.0000.0000.000
66A82ALA0-0.0160.00427.415-0.209-0.2090.0000.0000.0000.000
67A83ASP-1-0.921-0.94822.74214.66514.6650.0000.0000.0000.000
68A84ASN0-0.006-0.00524.953-0.240-0.2400.0000.0000.0000.000
69A85PRO00.0190.00821.0470.3330.3330.0000.0000.0000.000
70A86GLY00.014-0.02121.257-0.392-0.3920.0000.0000.0000.000
71A87LEU0-0.036-0.02419.216-0.273-0.2730.0000.0000.0000.000
72A88ASN00.0040.00318.8940.7300.7300.0000.0000.0000.000
73A89CYS0-0.036-0.00913.0780.6220.6220.0000.0000.0000.000
74A90LYS10.8320.9228.671-34.763-34.7630.0000.0000.0000.000
75A91TRP00.0660.01811.0901.0211.0210.0000.0000.0000.000
76A92GLY0-0.001-0.0027.4911.3921.3920.0000.0000.0000.000
77A93PRO0-0.016-0.0014.209-0.738-0.546-0.001-0.024-0.1670.000
78A94ASP-1-0.849-0.9376.15129.44029.4400.0000.0000.0000.000
79A95PRO0-0.057-0.0109.017-2.659-2.6590.0000.0000.0000.000
80A96ALA0-0.028-0.03612.1750.8210.8210.0000.0000.0000.000
81A97ALA00.0430.02015.229-0.850-0.8500.0000.0000.0000.000
82A98ASN0-0.021-0.00818.545-0.978-0.9780.0000.0000.0000.000
83A99SER00.0200.01718.0320.4550.4550.0000.0000.0000.000
84A100PRO00.0620.05917.183-0.784-0.7840.0000.0000.0000.000
85A101ARG10.7700.83920.027-11.101-11.1010.0000.0000.0000.000
86A102PRO0-0.009-0.01223.0780.1860.1860.0000.0000.0000.000
87A103ILE00.0120.01724.177-0.580-0.5800.0000.0000.0000.000
88A104ILE00.009-0.00125.7930.3640.3640.0000.0000.0000.000
89A105ILE00.0060.00627.921-0.443-0.4430.0000.0000.0000.000
90A106ASP-1-0.763-0.87330.4039.3399.3390.0000.0000.0000.000
91A107THR00.0310.02033.546-0.219-0.2190.0000.0000.0000.000
92A108LYS10.8770.93936.329-8.519-8.5190.0000.0000.0000.000
93A109GLN00.0110.01837.178-0.226-0.2260.0000.0000.0000.000
94A110LYS10.9170.95935.530-9.169-9.1690.0000.0000.0000.000
95A111TRP0-0.043-0.02928.5570.0130.0130.0000.0000.0000.000
96A112ARG10.8190.89733.559-8.943-8.9430.0000.0000.0000.000
97A113PHE00.0280.01428.7100.3990.3990.0000.0000.0000.000
98A114ASP-1-0.865-0.91332.1549.1139.1130.0000.0000.0000.000
99A115GLY00.0180.01133.691-0.051-0.0510.0000.0000.0000.000
100A116SER0-0.084-0.05028.8210.4300.4300.0000.0000.0000.000
101A117LYS10.9510.95622.039-14.451-14.4510.0000.0000.0000.000
102A118MET00.0090.01124.1160.1410.1410.0000.0000.0000.000
103A119GLN0-0.008-0.00426.1970.1660.1660.0000.0000.0000.000
104A120GLU-1-0.814-0.90026.74012.14312.1430.0000.0000.0000.000
105A121LEU0-0.037-0.01521.9540.1200.1200.0000.0000.0000.000
106A122PHE0-0.0090.00425.6580.0620.0620.0000.0000.0000.000
107A123ILE00.0320.02427.548-0.118-0.1180.0000.0000.0000.000
108A124LYS10.7460.86525.338-12.764-12.7640.0000.0000.0000.000
109A125ARG10.8960.95126.544-10.220-10.2200.0000.0000.0000.000
110A126GLN00.0200.01222.0640.4610.4610.0000.0000.0000.000
111A127GLY0-0.007-0.01021.4600.9480.9480.0000.0000.0000.000
112A128LYS10.8270.91121.987-14.459-14.4590.0000.0000.0000.000
113A129PRO00.0250.03125.7080.2460.2460.0000.0000.0000.000
114A130PRO00.0240.00427.4990.1920.1920.0000.0000.0000.000
115A131ILE00.0240.02827.949-0.342-0.3420.0000.0000.0000.000
116A132VAL0-0.025-0.02129.5350.3300.3300.0000.0000.0000.000
117A133VAL00.0090.00529.885-0.300-0.3000.0000.0000.0000.000
118A134VAL0-0.038-0.02032.7260.0050.0050.0000.0000.0000.000
119A135THR00.016-0.00336.2440.1210.1210.0000.0000.0000.000
120A136SER0-0.027-0.01938.912-0.166-0.1660.0000.0000.0000.000
121A137GLU-1-0.772-0.88840.6997.6727.6720.0000.0000.0000.000
122A138PRO0-0.0180.00338.726-0.033-0.0330.0000.0000.0000.000
123A139ILE0-0.0020.00741.084-0.146-0.1460.0000.0000.0000.000
124A140ILE0-0.033-0.01440.102-0.157-0.1570.0000.0000.0000.000
125A141LYS10.8270.90439.213-7.355-7.3550.0000.0000.0000.000
126A142GLU-1-0.769-0.87635.7609.0259.0250.0000.0000.0000.000
127A143GLN00.023-0.00837.1120.1500.1500.0000.0000.0000.000
128A144HIS0-0.005-0.02233.2310.3320.3320.0000.0000.0000.000
129A145VAL0-0.0510.00132.5270.3600.3600.0000.0000.0000.000
130A146ASP-1-0.787-0.85632.1309.3299.3290.0000.0000.0000.000
131A147TYR0-0.001-0.01833.3760.1690.1690.0000.0000.0000.000
132A148ALA00.0460.03832.733-0.176-0.1760.0000.0000.0000.000
133A149ILE0-0.010-0.01034.7260.0860.0860.0000.0000.0000.000
134A150CYS0-0.0310.01034.693-0.059-0.0590.0000.0000.0000.000
135A151PRO00.0370.00736.833-0.116-0.1160.0000.0000.0000.000
136A152ILE0-0.003-0.00237.6740.2870.2870.0000.0000.0000.000
137A153ASN00.002-0.01237.702-0.297-0.2970.0000.0000.0000.000
138A154ASP-1-0.884-0.95639.6967.3487.3480.0000.0000.0000.000
139A155THR0-0.046-0.01240.799-0.142-0.1420.0000.0000.0000.000
140A156THR00.001-0.00236.480-0.045-0.0450.0000.0000.0000.000
141A157LYS10.8750.94238.521-8.176-8.1760.0000.0000.0000.000
142A158LEU0-0.035-0.01434.4880.0390.0390.0000.0000.0000.000
143A159VAL00.0340.01632.534-0.167-0.1670.0000.0000.0000.000
144A160ASP-1-0.821-0.89734.3969.2159.2150.0000.0000.0000.000
145A161TRP00.002-0.02528.2850.2340.2340.0000.0000.0000.000
146A162LYS10.8460.93630.540-9.643-9.6430.0000.0000.0000.000
147A163LYS10.8670.90132.091-8.663-8.6630.0000.0000.0000.000
148A164LEU00.0210.01029.822-0.007-0.0070.0000.0000.0000.000
149A165PHE0-0.013-0.02324.9470.2150.2150.0000.0000.0000.000
150A166GLU-1-0.847-0.91729.3309.4599.4590.0000.0000.0000.000
151A167ILE00.0270.01931.9260.0060.0060.0000.0000.0000.000
152A168LEU0-0.021-0.01926.4880.0360.0360.0000.0000.0000.000
153A169LYS10.7900.90727.218-11.004-11.0040.0000.0000.0000.000
154A170GLU-1-0.902-0.96930.0418.7498.7490.0000.0000.0000.000
155A171GLU-1-0.943-0.96533.5028.5428.5420.0000.0000.0000.000
156A172PHE0-0.033-0.02930.2130.0400.0400.0000.0000.0000.000
157A173ASN0-0.054-0.01528.7150.3160.3160.0000.0000.0000.000
158A174ILE0-0.025-0.01324.0290.4970.4970.0000.0000.0000.000
159A175ARG10.8610.88321.715-13.626-13.6260.0000.0000.0000.000
160A176SER0-0.0020.00019.540-0.125-0.1250.0000.0000.0000.000
161A177VAL0-0.044-0.02520.9990.0110.0110.0000.0000.0000.000
162A178MET00.0040.04013.6640.2000.2000.0000.0000.0000.000
163A179VAL0-0.019-0.02118.630-0.746-0.7460.0000.0000.0000.000
164A180GLU-1-0.716-0.83715.86319.98219.9820.0000.0000.0000.000
165A181GLY0-0.036-0.01019.278-0.150-0.1500.0000.0000.0000.000
166A182GLY00.0610.00722.560-0.747-0.7470.0000.0000.0000.000
167A183ALA00.0380.03224.801-0.075-0.0750.0000.0000.0000.000
168A184ASN0-0.005-0.00825.954-0.193-0.1930.0000.0000.0000.000
169A185VAL00.0160.02125.179-0.332-0.3320.0000.0000.0000.000
170A186ILE00.0170.00720.991-0.111-0.1110.0000.0000.0000.000
171A187ASN00.013-0.01124.4690.2800.2800.0000.0000.0000.000
172A188GLN0-0.0030.01327.535-0.564-0.5640.0000.0000.0000.000
173A189LEU00.012-0.00524.299-0.186-0.1860.0000.0000.0000.000
174A190LEU00.0140.00322.4800.0850.0850.0000.0000.0000.000
175A191LEU0-0.025-0.00826.101-0.104-0.1040.0000.0000.0000.000
176A192ARG10.8040.87528.016-10.311-10.3110.0000.0000.0000.000
177A193SER00.0790.02726.8780.2940.2940.0000.0000.0000.000
178A194ASP-1-0.830-0.86027.96710.17110.1710.0000.0000.0000.000
179A195ILE0-0.068-0.03725.868-0.201-0.2010.0000.0000.0000.000
180A196VAL0-0.005-0.00121.5380.3600.3600.0000.0000.0000.000
181A197ASN00.0000.02021.231-0.130-0.1300.0000.0000.0000.000
182A198SER0-0.035-0.04216.586-0.046-0.0460.0000.0000.0000.000
183A199LEU0-0.024-0.00518.083-0.347-0.3470.0000.0000.0000.000
184A200ILE00.0110.00311.5360.4250.4250.0000.0000.0000.000
185A201ILE0-0.0010.01514.5350.0020.0020.0000.0000.0000.000
186A202THR00.0190.00911.3702.1822.1820.0000.0000.0000.000
187A203ILE0-0.019-0.01913.272-1.895-1.8950.0000.0000.0000.000
188A204GLY00.0590.04313.7851.4741.4740.0000.0000.0000.000
189A205SER0-0.052-0.05414.571-1.817-1.8170.0000.0000.0000.000
190A206THR0-0.035-0.02616.780-0.961-0.9610.0000.0000.0000.000
191A207PHE00.018-0.00119.6220.0260.0260.0000.0000.0000.000
192A208LEU0-0.051-0.03420.6880.0350.0350.0000.0000.0000.000
193A209GLY00.0190.02024.422-0.408-0.4080.0000.0000.0000.000
194A210SER00.015-0.01828.0690.1340.1340.0000.0000.0000.000
195A211SER00.0000.00230.187-0.035-0.0350.0000.0000.0000.000
196A212GLY0-0.0090.01327.250-0.102-0.1020.0000.0000.0000.000
197A213THR0-0.027-0.03726.361-0.002-0.0020.0000.0000.0000.000
198A214GLU-1-0.822-0.89925.62511.69411.6940.0000.0000.0000.000
199A215VAL0-0.046-0.02221.464-0.273-0.2730.0000.0000.0000.000
200A216SER00.0520.02824.6490.3650.3650.0000.0000.0000.000
201A217PRO0-0.0340.00226.403-0.253-0.2530.0000.0000.0000.000
202A218PRO0-0.019-0.01829.094-0.190-0.1900.0000.0000.0000.000
203A219GLN0-0.016-0.00631.772-0.348-0.3480.0000.0000.0000.000
204A220THR00.0110.00030.7940.2560.2560.0000.0000.0000.000
205A221VAL00.0100.01125.951-0.186-0.1860.0000.0000.0000.000
206A222ASN0-0.0080.00726.6940.4660.4660.0000.0000.0000.000
207A223LEU00.0240.00620.1720.1190.1190.0000.0000.0000.000
208A224LYS10.8530.90822.611-13.268-13.2680.0000.0000.0000.000
209A225ASP-1-0.805-0.88919.67914.24614.2460.0000.0000.0000.000
210A226MET0-0.0140.01517.6380.6890.6890.0000.0000.0000.000
211A227SER0-0.0140.00013.2050.2320.2320.0000.0000.0000.000
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