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: G68Y1

Calculation Name: 5HD9-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5HD9

Chain ID: A

ChEMBL ID:

UniProt ID: P11014

Base Structure: X-ray

Registration Date: 2023-06-22

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 194
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2377044.172812
FMO2-HF: Nuclear repulsion 2298312.059375
FMO2-HF: Total energy -78732.113437
FMO2-MP2: Total energy -78964.635749


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:4:SER)


Summations of interaction energy for fragment #1(A:4: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.
-35.101-32.32326.337-11.96-17.155-0.037
Interaction energy analysis for fragmet #1(A:4:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.004 / q_NPA : -0.007
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].
3A6PHE00.0230.0152.846-4.536-0.7740.214-2.117-1.8600.012
4A7TYR0-0.094-0.0692.188-4.277-2.6154.255-2.385-3.5320.027
5A8ASN00.0730.0381.831-19.345-24.00015.178-5.899-4.624-0.071
6A9PRO00.0390.0173.1661.0631.5430.032-0.115-0.3980.000
7A10GLN00.0240.0276.0380.3600.3600.0000.0000.0000.000
8A11LYS10.9570.9868.3810.6780.6780.0000.0000.0000.000
9A12MET0-0.0050.0188.6200.1800.1800.0000.0000.0000.000
10A13LEU00.041-0.0058.5130.1250.1250.0000.0000.0000.000
11A14SER0-0.067-0.03911.8290.0740.0740.0000.0000.0000.000
12A15TYR0-0.012-0.00814.1450.0230.0230.0000.0000.0000.000
13A16ASP-1-0.833-0.89615.859-0.104-0.1040.0000.0000.0000.000
14A17ARG10.8060.91917.0680.1210.1210.0000.0000.0000.000
15A18ILE00.0570.04017.7950.0120.0120.0000.0000.0000.000
16A19LEU0-0.018-0.00518.6590.0290.0290.0000.0000.0000.000
17A20ASN0-0.034-0.02914.154-0.063-0.0630.0000.0000.0000.000
18A21PHE00.0260.00915.0210.0510.0510.0000.0000.0000.000
19A22VAL0-0.012-0.0018.904-0.036-0.0360.0000.0000.0000.000
20A23ILE0-0.015-0.01012.3420.0940.0940.0000.0000.0000.000
21A24GLY00.0430.01313.185-0.013-0.0130.0000.0000.0000.000
22A25ALA0-0.010-0.0049.4260.0880.0880.0000.0000.0000.000
23A26ARG10.8910.93510.626-0.546-0.5460.0000.0000.0000.000
24A27GLY00.0370.0148.5830.3800.3800.0000.0000.0000.000
25A28ILE00.0650.0254.3550.1620.233-0.001-0.011-0.0590.000
26A29GLY00.0100.0002.537-0.627-0.3983.404-2.028-1.6050.012
27A30LYS10.8730.9542.886-3.799-5.7080.4082.886-1.386-0.008
28A31SER00.031-0.0315.539-0.247-0.2470.0000.0000.0000.000
29A32TYR0-0.083-0.0542.203-1.772-0.5662.087-1.288-2.005-0.009
30A33ALA00.0530.0222.424-1.4010.0730.749-0.896-1.3260.000
31A34MET0-0.050-0.0213.723-0.964-0.7970.013-0.068-0.1110.000
32A35LYS10.8750.9666.614-1.146-1.1460.0000.0000.0000.000
33A36VAL00.0360.0134.484-0.383-0.273-0.001-0.020-0.0890.000
34A37TYR00.0340.0157.319-0.489-0.4890.0000.0000.0000.000
35A38PRO00.0090.0048.700-0.203-0.2030.0000.0000.0000.000
36A39ILE0-0.0100.01110.322-0.108-0.1080.0000.0000.0000.000
37A40ASN0-0.009-0.0128.374-0.295-0.2950.0000.0000.0000.000
38A41ARG10.8130.87611.654-0.023-0.0230.0000.0000.0000.000
39A42PHE00.0120.00614.303-0.041-0.0410.0000.0000.0000.000
40A43ILE0-0.042-0.02813.890-0.030-0.0300.0000.0000.0000.000
41A44LYS10.8440.93411.6020.1430.1430.0000.0000.0000.000
42A45TYR0-0.009-0.00914.845-0.030-0.0300.0000.0000.0000.000
43A46GLY00.0200.02419.3360.0010.0010.0000.0000.0000.000
44A47GLU-1-0.807-0.83417.093-0.002-0.0020.0000.0000.0000.000
45A48GLN0-0.022-0.01817.9140.0200.0200.0000.0000.0000.000
46A49PHE0-0.017-0.01514.6820.0060.0060.0000.0000.0000.000
47A50ILE0-0.005-0.00517.171-0.007-0.0070.0000.0000.0000.000
48A51TYR0-0.060-0.04812.207-0.016-0.0160.0000.0000.0000.000
49A52VAL00.000-0.01016.197-0.041-0.0410.0000.0000.0000.000
50A53ARG10.7710.84615.254-0.402-0.4020.0000.0000.0000.000
51A54ARG10.7410.85219.372-0.275-0.2750.0000.0000.0000.000
52A55TYR0-0.010-0.01322.627-0.026-0.0260.0000.0000.0000.000
53A56LYS10.9860.98323.294-0.125-0.1250.0000.0000.0000.000
54A57PRO00.0180.00823.9740.0080.0080.0000.0000.0000.000
55A58GLU-1-0.773-0.86519.4010.3070.3070.0000.0000.0000.000
56A59LEU00.0160.00318.3820.0330.0330.0000.0000.0000.000
57A60ALA0-0.041-0.01620.721-0.009-0.0090.0000.0000.0000.000
58A61LYS10.9730.98619.099-0.357-0.3570.0000.0000.0000.000
59A62VAL00.0200.01417.0460.0280.0280.0000.0000.0000.000
60A63SER00.009-0.01217.8600.0110.0110.0000.0000.0000.000
61A64ASN0-0.0020.00716.553-0.033-0.0330.0000.0000.0000.000
62A65TYR0-0.0120.00311.9530.0770.0770.0000.0000.0000.000
63A66PHE00.0640.00712.1030.0840.0840.0000.0000.0000.000
64A67ASN0-0.011-0.00612.402-0.012-0.0120.0000.0000.0000.000
65A68ASP-1-0.910-0.9578.0510.8390.8390.0000.0000.0000.000
66A69VAL0-0.003-0.0156.5490.0370.0370.0000.0000.0000.000
67A70ALA0-0.0050.0008.983-0.089-0.0890.0000.0000.0000.000
68A71GLN00.004-0.0019.647-0.086-0.0860.0000.0000.0000.000
69A72GLU-1-0.849-0.8954.5060.0600.241-0.001-0.019-0.1600.000
70A73PHE0-0.089-0.0488.924-0.049-0.0490.0000.0000.0000.000
71A74PRO00.0540.03412.7800.0210.0210.0000.0000.0000.000
72A75ASP-1-0.930-0.95615.695-0.061-0.0610.0000.0000.0000.000
73A76HIS10.8120.86516.004-0.021-0.0210.0000.0000.0000.000
74A77GLU-1-0.905-0.93317.5850.1170.1170.0000.0000.0000.000
75A78LEU0-0.021-0.01213.2500.0100.0100.0000.0000.0000.000
76A79VAL00.0300.01317.7450.0110.0110.0000.0000.0000.000
77A80VAL0-0.012-0.01017.8600.0000.0000.0000.0000.0000.000
78A81LYS10.9020.95820.566-0.129-0.1290.0000.0000.0000.000
79A82GLY00.0110.00524.180-0.005-0.0050.0000.0000.0000.000
80A83ARG10.7590.84221.996-0.153-0.1530.0000.0000.0000.000
81A84ARG10.8900.95121.823-0.120-0.1200.0000.0000.0000.000
82A85PHE00.0060.00816.5520.0110.0110.0000.0000.0000.000
83A86TYR00.004-0.01919.741-0.020-0.0200.0000.0000.0000.000
84A87ILE00.0440.03415.7660.0200.0200.0000.0000.0000.000
85A88ASP-1-0.753-0.85519.7650.0350.0350.0000.0000.0000.000
86A89GLY00.0120.01022.300-0.011-0.0110.0000.0000.0000.000
87A90LYS10.8320.91221.682-0.040-0.0400.0000.0000.0000.000
88A91LEU0-0.030-0.01422.5460.0130.0130.0000.0000.0000.000
89A92ALA00.0240.01718.242-0.012-0.0120.0000.0000.0000.000
90A93GLY00.0550.01618.4590.0090.0090.0000.0000.0000.000
91A94TRP0-0.033-0.01019.372-0.009-0.0090.0000.0000.0000.000
92A95ALA00.0360.02518.7470.0290.0290.0000.0000.0000.000
93A96ILE00.0200.00619.969-0.022-0.0220.0000.0000.0000.000
94A97PRO0-0.023-0.00221.3740.0160.0160.0000.0000.0000.000
95A98LEU00.0360.00522.903-0.019-0.0190.0000.0000.0000.000
96A99SER0-0.024-0.04624.657-0.017-0.0170.0000.0000.0000.000
97A100VAL0-0.075-0.04327.313-0.010-0.0100.0000.0000.0000.000
98A101TRP00.0640.03825.973-0.002-0.0020.0000.0000.0000.000
99A102GLN00.0160.00327.954-0.002-0.0020.0000.0000.0000.000
100A103SER00.0070.00731.220-0.006-0.0060.0000.0000.0000.000
101A104GLU-1-0.827-0.87326.3730.1360.1360.0000.0000.0000.000
102A105LYS10.8980.95729.000-0.078-0.0780.0000.0000.0000.000
103A106SER0-0.030-0.00230.492-0.006-0.0060.0000.0000.0000.000
104A107ASN0-0.061-0.02128.225-0.005-0.0050.0000.0000.0000.000
105A108ALA00.0340.02129.676-0.002-0.0020.0000.0000.0000.000
106A109TYR0-0.026-0.04723.8520.0130.0130.0000.0000.0000.000
107A110PRO0-0.054-0.02825.993-0.004-0.0040.0000.0000.0000.000
108A111ASN0-0.011-0.01122.518-0.016-0.0160.0000.0000.0000.000
109A112VAL00.0030.01019.6560.0050.0050.0000.0000.0000.000
110A113SER00.0180.00517.2050.0030.0030.0000.0000.0000.000
111A114THR0-0.031-0.02213.091-0.011-0.0110.0000.0000.0000.000
112A115ILE0-0.010-0.00616.2510.0240.0240.0000.0000.0000.000
113A116VAL00.0110.00810.846-0.007-0.0070.0000.0000.0000.000
114A117PHE00.002-0.00513.9080.0000.0000.0000.0000.0000.000
115A118ASP-1-0.744-0.82711.1940.8620.8620.0000.0000.0000.000
116A119GLU-1-0.830-0.89013.9430.4550.4550.0000.0000.0000.000
117A120PHE00.0240.02215.684-0.055-0.0550.0000.0000.0000.000
118A121ILE0-0.0300.00318.323-0.046-0.0460.0000.0000.0000.000
119A122ARG10.8970.94420.158-0.198-0.1980.0000.0000.0000.000
120A123GLU-1-0.725-0.84117.2150.4300.4300.0000.0000.0000.000
121A124LYS10.8610.89518.467-0.362-0.3620.0000.0000.0000.000
122A125ASP-1-0.966-0.96823.6370.1700.1700.0000.0000.0000.000
123A126ASN00.0780.03926.830-0.018-0.0180.0000.0000.0000.000
124A127SER00.0070.00827.2640.0160.0160.0000.0000.0000.000
125A128ASN00.0030.01028.241-0.013-0.0130.0000.0000.0000.000
126A129TYR00.001-0.01123.2670.0210.0210.0000.0000.0000.000
127A130ILE00.0010.00625.644-0.009-0.0090.0000.0000.0000.000
128A131PRO00.0210.00629.074-0.003-0.0030.0000.0000.0000.000
129A132ASN00.0300.00231.3900.0010.0010.0000.0000.0000.000
130A133GLU-1-0.713-0.79623.9060.1890.1890.0000.0000.0000.000
131A134VAL00.0210.01625.2860.0050.0050.0000.0000.0000.000
132A135SER00.0280.01326.725-0.004-0.0040.0000.0000.0000.000
133A136ALA0-0.033-0.00327.365-0.005-0.0050.0000.0000.0000.000
134A137LEU00.011-0.00720.2680.0010.0010.0000.0000.0000.000
135A138LEU00.0380.01924.285-0.001-0.0010.0000.0000.0000.000
136A139ASN00.0490.03826.239-0.002-0.0020.0000.0000.0000.000
137A140LEU0-0.043-0.01121.849-0.002-0.0020.0000.0000.0000.000
138A141MET00.002-0.00221.5970.0030.0030.0000.0000.0000.000
139A142ASP-1-0.886-0.94124.1130.0470.0470.0000.0000.0000.000
140A143THR0-0.129-0.06827.394-0.008-0.0080.0000.0000.0000.000
141A144VAL0-0.053-0.03322.689-0.001-0.0010.0000.0000.0000.000
142A145PHE0-0.011-0.00819.189-0.005-0.0050.0000.0000.0000.000
143A146ARG10.9590.98224.826-0.023-0.0230.0000.0000.0000.000
144A147ASN0-0.004-0.01326.067-0.011-0.0110.0000.0000.0000.000
145A148ARG10.8850.88624.4410.0290.0290.0000.0000.0000.000
146A149GLU-1-0.813-0.87422.930-0.093-0.0930.0000.0000.0000.000
147A150ARG10.8280.89918.6250.1170.1170.0000.0000.0000.000
148A151VAL00.0130.02818.2360.0070.0070.0000.0000.0000.000
149A152ARG10.7440.85613.4640.0690.0690.0000.0000.0000.000
150A153CYS0-0.007-0.00316.8500.0450.0450.0000.0000.0000.000
151A154ILE0-0.021-0.01210.902-0.034-0.0340.0000.0000.0000.000
152A155CYS0-0.0280.00113.9490.0620.0620.0000.0000.0000.000
153A156LEU00.0130.0038.884-0.006-0.0060.0000.0000.0000.000
154A157SER0-0.033-0.02912.749-0.045-0.0450.0000.0000.0000.000
155A158ASN0-0.024-0.01811.954-0.030-0.0300.0000.0000.0000.000
156A159ALA0-0.053-0.02314.408-0.033-0.0330.0000.0000.0000.000
157A160VAL00.0440.01116.5600.0200.0200.0000.0000.0000.000
158A161SER0-0.019-0.00818.545-0.033-0.0330.0000.0000.0000.000
159A162VAL00.0280.00921.379-0.001-0.0010.0000.0000.0000.000
160A163VAL00.0290.02822.864-0.015-0.0150.0000.0000.0000.000
161A164ASN00.001-0.00321.1900.0100.0100.0000.0000.0000.000
162A165PRO00.0470.01024.594-0.013-0.0130.0000.0000.0000.000
163A166TYR00.009-0.02422.148-0.013-0.0130.0000.0000.0000.000
164A167PHE00.0200.00318.367-0.010-0.0100.0000.0000.0000.000
165A168LEU0-0.0090.00524.297-0.013-0.0130.0000.0000.0000.000
166A169PHE0-0.024-0.01227.228-0.009-0.0090.0000.0000.0000.000
167A170PHE0-0.010-0.01823.693-0.006-0.0060.0000.0000.0000.000
168A171ASN0-0.022-0.00327.009-0.006-0.0060.0000.0000.0000.000
169A172LEU0-0.039-0.00521.513-0.008-0.0080.0000.0000.0000.000
170A173VAL00.0230.00124.4520.0150.0150.0000.0000.0000.000
171A174PRO0-0.047-0.01320.276-0.012-0.0120.0000.0000.0000.000
172A175ASP-1-0.772-0.86922.2720.0230.0230.0000.0000.0000.000
173A176VAL00.020-0.00720.038-0.007-0.0070.0000.0000.0000.000
174A177ASN0-0.072-0.03519.7440.0130.0130.0000.0000.0000.000
175A178LYS10.8450.91518.9750.0070.0070.0000.0000.0000.000
176A179ARG10.7860.8847.6570.4660.4660.0000.0000.0000.000
177A180PHE00.009-0.01510.942-0.002-0.0020.0000.0000.0000.000
178A181ASN0-0.019-0.00616.224-0.005-0.0050.0000.0000.0000.000
179A182VAL00.004-0.00418.2380.0030.0030.0000.0000.0000.000
180A183TYR00.0590.03120.5360.0090.0090.0000.0000.0000.000
181A184ASP-1-0.886-0.94022.795-0.053-0.0530.0000.0000.0000.000
182A185ASP-1-0.782-0.86823.338-0.024-0.0240.0000.0000.0000.000
183A186ALA0-0.046-0.01320.2700.0110.0110.0000.0000.0000.000
184A187LEU0-0.018-0.00613.851-0.025-0.0250.0000.0000.0000.000
185A188ILE00.0090.00316.1100.0360.0360.0000.0000.0000.000
186A189GLU-1-0.750-0.8619.461-0.447-0.4470.0000.0000.0000.000
187A190ILE0-0.002-0.00413.3960.0870.0870.0000.0000.0000.000
188A191PRO0-0.028-0.0188.247-0.043-0.0430.0000.0000.0000.000
189A192ASP-1-0.792-0.87410.3450.0560.0560.0000.0000.0000.000
190A193SER0-0.028-0.0346.2430.1890.1890.0000.0000.0000.000
191A194LEU0-0.058-0.0286.9980.4200.4200.0000.0000.0000.000
192A195ASP-1-0.861-0.9009.9210.1650.1650.0000.0000.0000.000
193A196PHE0-0.032-0.0218.906-0.066-0.0660.0000.0000.0000.000
194A197SER0-0.062-0.02513.894-0.114-0.1140.0000.0000.0000.000