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

tag_button

FMODB ID: 1756Z

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 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 194
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2376063.429737
FMO2-HF: Nuclear repulsion 2297331.640053
FMO2-HF: Total energy -78731.789684
FMO2-MP2: Total energy -78964.332431


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.
-39.708-31.46218.201-11.676-14.771-0.025
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 : -0.010 / q_NPA : -0.009
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].
3A6PHE00.0400.0152.987-4.164-0.5510.141-1.971-1.7830.011
4A7TYR0-0.092-0.0642.162-6.282-4.4384.121-2.470-3.4950.030
5A8ASN00.0790.0351.904-19.049-21.16910.884-4.762-4.001-0.065
6A9PRO00.0310.0173.3881.0191.4150.012-0.088-0.3210.000
7A10GLN00.0370.0246.3180.3450.3450.0000.0000.0000.000
8A11LYS10.9640.9898.5190.6640.6640.0000.0000.0000.000
9A12MET0-0.0060.0158.8340.1530.1530.0000.0000.0000.000
10A13LEU00.034-0.0058.6610.1100.1100.0000.0000.0000.000
11A14SER0-0.079-0.03912.0450.0590.0590.0000.0000.0000.000
12A15TYR0-0.018-0.01414.3310.0240.0240.0000.0000.0000.000
13A16ASP-1-0.831-0.88715.828-0.071-0.0710.0000.0000.0000.000
14A17ARG10.8270.92917.1440.0830.0830.0000.0000.0000.000
15A18ILE00.0530.03517.8830.0190.0190.0000.0000.0000.000
16A19LEU0-0.0110.00818.9200.0350.0350.0000.0000.0000.000
17A20ASN0-0.035-0.03014.093-0.066-0.0660.0000.0000.0000.000
18A21PHE00.0260.01415.1900.0600.0600.0000.0000.0000.000
19A22VAL0-0.0030.0088.761-0.028-0.0280.0000.0000.0000.000
20A23ILE0-0.016-0.01712.2060.1110.1110.0000.0000.0000.000
21A24GLY00.0370.01712.893-0.007-0.0070.0000.0000.0000.000
22A25ALA0-0.024-0.0159.0920.1290.1290.0000.0000.0000.000
23A26ARG10.9961.00510.013-0.774-0.7740.0000.0000.0000.000
24A27GLY00.0260.0038.3350.5360.5360.0000.0000.0000.000
25A28ILE00.0770.0304.1150.1750.273-0.001-0.020-0.0770.000
26A29GLY00.0020.0062.747-1.441-0.2871.296-1.236-1.2140.009
27A30LYS10.8820.9642.988-5.597-5.2970.2270.599-1.125-0.004
28A31SER00.0370.0025.642-0.348-0.3480.0000.0000.0000.000
29A32TYR0-0.068-0.0532.345-1.552-0.2691.012-0.920-1.375-0.006
30A33ALA00.0370.0072.455-1.621-0.2240.496-0.753-1.1410.000
31A34MET0-0.054-0.0243.653-1.008-0.8710.014-0.044-0.1080.000
32A35LYS10.8660.9636.592-1.288-1.2880.0000.0000.0000.000
33A36VAL00.0420.0124.889-0.303-0.3030.0000.0000.0000.000
34A37TYR00.0190.0047.402-0.466-0.4660.0000.0000.0000.000
35A38PRO00.0210.0058.837-0.222-0.2220.0000.0000.0000.000
36A39ILE0-0.0050.01410.486-0.111-0.1110.0000.0000.0000.000
37A40ASN00.002-0.0048.705-0.278-0.2780.0000.0000.0000.000
38A41ARG10.8120.87911.994-0.020-0.0200.0000.0000.0000.000
39A42PHE00.0010.01314.436-0.039-0.0390.0000.0000.0000.000
40A43ILE0-0.035-0.01613.933-0.032-0.0320.0000.0000.0000.000
41A44LYS10.8470.93311.6880.2400.2400.0000.0000.0000.000
42A45TYR0-0.011-0.01915.260-0.032-0.0320.0000.0000.0000.000
43A46GLY00.0180.02619.1160.0040.0040.0000.0000.0000.000
44A47GLU-1-0.819-0.84817.1760.0090.0090.0000.0000.0000.000
45A48GLN0-0.005-0.02018.0910.0200.0200.0000.0000.0000.000
46A49PHE0-0.014-0.01414.7370.0120.0120.0000.0000.0000.000
47A50ILE00.000-0.00217.281-0.007-0.0070.0000.0000.0000.000
48A51TYR0-0.062-0.04312.121-0.016-0.0160.0000.0000.0000.000
49A52VAL00.002-0.01016.332-0.041-0.0410.0000.0000.0000.000
50A53ARG10.7830.86215.065-0.516-0.5160.0000.0000.0000.000
51A54ARG10.7550.85419.302-0.345-0.3450.0000.0000.0000.000
52A55TYR0-0.017-0.02522.470-0.036-0.0360.0000.0000.0000.000
53A56LYS10.9980.98922.966-0.154-0.1540.0000.0000.0000.000
54A57PRO00.0180.01023.8100.0100.0100.0000.0000.0000.000
55A58GLU-1-0.790-0.88419.3650.3870.3870.0000.0000.0000.000
56A59LEU0-0.014-0.01118.2830.0390.0390.0000.0000.0000.000
57A60ALA0-0.022-0.00820.668-0.018-0.0180.0000.0000.0000.000
58A61LYS10.9690.98019.101-0.415-0.4150.0000.0000.0000.000
59A62VAL00.0280.01917.4750.0300.0300.0000.0000.0000.000
60A63SER00.0300.00818.1560.0090.0090.0000.0000.0000.000
61A64ASN0-0.026-0.01816.628-0.042-0.0420.0000.0000.0000.000
62A65TYR0-0.0080.00712.1320.0880.0880.0000.0000.0000.000
63A66PHE00.050-0.00412.4370.0910.0910.0000.0000.0000.000
64A67ASN0-0.001-0.00212.758-0.035-0.0350.0000.0000.0000.000
65A68ASP-1-0.922-0.9588.0720.9550.9550.0000.0000.0000.000
66A69VAL00.007-0.0126.895-0.009-0.0090.0000.0000.0000.000
67A70ALA00.0050.0109.245-0.109-0.1090.0000.0000.0000.000
68A71GLN00.001-0.00710.026-0.089-0.0890.0000.0000.0000.000
69A72GLU-1-0.853-0.8974.664-0.346-0.202-0.001-0.011-0.1310.000
70A73PHE0-0.108-0.0549.319-0.074-0.0740.0000.0000.0000.000
71A74PRO00.0430.03312.8900.0380.0380.0000.0000.0000.000
72A75ASP-1-0.922-0.95015.616-0.108-0.1080.0000.0000.0000.000
73A76HIS10.7960.86015.9000.0230.0230.0000.0000.0000.000
74A77GLU-1-0.902-0.93017.5810.0990.0990.0000.0000.0000.000
75A78LEU0-0.007-0.00513.4230.0150.0150.0000.0000.0000.000
76A79VAL00.013-0.00117.9280.0060.0060.0000.0000.0000.000
77A80VAL00.0030.00318.1500.0110.0110.0000.0000.0000.000
78A81LYS10.9420.97920.890-0.130-0.1300.0000.0000.0000.000
79A82GLY00.0020.00624.488-0.003-0.0030.0000.0000.0000.000
80A83ARG10.7660.84222.128-0.183-0.1830.0000.0000.0000.000
81A84ARG10.9100.96521.849-0.133-0.1330.0000.0000.0000.000
82A85PHE00.0110.00816.7030.0090.0090.0000.0000.0000.000
83A86TYR0-0.014-0.03119.710-0.021-0.0210.0000.0000.0000.000
84A87ILE00.0480.03415.7380.0190.0190.0000.0000.0000.000
85A88ASP-1-0.800-0.89019.7490.0110.0110.0000.0000.0000.000
86A89GLY0-0.007-0.00522.148-0.012-0.0120.0000.0000.0000.000
87A90LYS10.8850.95722.484-0.028-0.0280.0000.0000.0000.000
88A91LEU0-0.031-0.01422.4020.0140.0140.0000.0000.0000.000
89A92ALA00.0220.01718.306-0.012-0.0120.0000.0000.0000.000
90A93GLY00.0580.01518.2620.0100.0100.0000.0000.0000.000
91A94TRP0-0.038-0.00719.328-0.012-0.0120.0000.0000.0000.000
92A95ALA00.0230.02018.8210.0310.0310.0000.0000.0000.000
93A96ILE00.010-0.00219.931-0.031-0.0310.0000.0000.0000.000
94A97PRO0-0.011-0.00721.4450.0210.0210.0000.0000.0000.000
95A98LEU00.0190.00722.839-0.021-0.0210.0000.0000.0000.000
96A99SER0-0.013-0.03724.578-0.020-0.0200.0000.0000.0000.000
97A100VAL0-0.096-0.05327.198-0.015-0.0150.0000.0000.0000.000
98A101TRP00.0840.04626.118-0.001-0.0010.0000.0000.0000.000
99A102GLN00.0310.00927.999-0.003-0.0030.0000.0000.0000.000
100A103SER0-0.004-0.00931.268-0.007-0.0070.0000.0000.0000.000
101A104GLU-1-0.835-0.88426.4270.1630.1630.0000.0000.0000.000
102A105LYS10.8990.95529.068-0.104-0.1040.0000.0000.0000.000
103A106SER0-0.0360.00630.738-0.006-0.0060.0000.0000.0000.000
104A107ASN0-0.045-0.01228.696-0.008-0.0080.0000.0000.0000.000
105A108ALA00.0260.01529.649-0.002-0.0020.0000.0000.0000.000
106A109TYR0-0.035-0.05124.0170.0150.0150.0000.0000.0000.000
107A110PRO0-0.056-0.02425.856-0.004-0.0040.0000.0000.0000.000
108A111ASN0-0.006-0.00722.637-0.015-0.0150.0000.0000.0000.000
109A112VAL00.0060.02019.6410.0060.0060.0000.0000.0000.000
110A113SER00.010-0.00117.6350.0010.0010.0000.0000.0000.000
111A114THR0-0.032-0.02012.996-0.005-0.0050.0000.0000.0000.000
112A115ILE0-0.0040.00216.4530.0190.0190.0000.0000.0000.000
113A116VAL00.0040.01010.9200.0040.0040.0000.0000.0000.000
114A117PHE00.003-0.00314.051-0.014-0.0140.0000.0000.0000.000
115A118ASP-1-0.777-0.88311.4911.0591.0590.0000.0000.0000.000
116A119GLU-1-0.842-0.89214.1410.5740.5740.0000.0000.0000.000
117A120PHE00.0130.00815.809-0.069-0.0690.0000.0000.0000.000
118A121ILE0-0.0240.00618.261-0.061-0.0610.0000.0000.0000.000
119A122ARG10.9240.95520.319-0.257-0.2570.0000.0000.0000.000
120A123GLU-1-0.781-0.85817.2260.5470.5470.0000.0000.0000.000
121A124LYS10.8450.87518.923-0.437-0.4370.0000.0000.0000.000
122A125ASP-1-0.974-0.98123.8790.2130.2130.0000.0000.0000.000
123A126ASN00.0810.03226.822-0.023-0.0230.0000.0000.0000.000
124A127SER00.0250.03227.4240.0190.0190.0000.0000.0000.000
125A128ASN0-0.045-0.02828.077-0.019-0.0190.0000.0000.0000.000
126A129TYR0-0.010-0.01023.3420.0230.0230.0000.0000.0000.000
127A130ILE0-0.0030.00425.886-0.012-0.0120.0000.0000.0000.000
128A131PRO00.0400.01529.204-0.001-0.0010.0000.0000.0000.000
129A132ASN00.018-0.00431.5540.0010.0010.0000.0000.0000.000
130A133GLU-1-0.686-0.77524.1300.2450.2450.0000.0000.0000.000
131A134VAL00.0170.00925.5740.0060.0060.0000.0000.0000.000
132A135SER00.0340.01426.936-0.002-0.0020.0000.0000.0000.000
133A136ALA0-0.0180.00527.403-0.006-0.0060.0000.0000.0000.000
134A137LEU00.004-0.00420.5250.0010.0010.0000.0000.0000.000
135A138LEU00.0530.02424.624-0.002-0.0020.0000.0000.0000.000
136A139ASN00.0380.03326.530-0.005-0.0050.0000.0000.0000.000
137A140LEU0-0.032-0.00322.139-0.005-0.0050.0000.0000.0000.000
138A141MET0-0.009-0.01621.8290.0040.0040.0000.0000.0000.000
139A142ASP-1-0.884-0.93724.3030.0690.0690.0000.0000.0000.000
140A143THR0-0.146-0.07727.527-0.010-0.0100.0000.0000.0000.000
141A144VAL0-0.044-0.03022.517-0.005-0.0050.0000.0000.0000.000
142A145PHE0-0.031-0.00719.155-0.003-0.0030.0000.0000.0000.000
143A146ARG10.9790.99724.968-0.033-0.0330.0000.0000.0000.000
144A147ASN00.004-0.02226.132-0.009-0.0090.0000.0000.0000.000
145A148ARG10.8800.89124.4390.0030.0030.0000.0000.0000.000
146A149GLU-1-0.835-0.88822.998-0.086-0.0860.0000.0000.0000.000
147A150ARG10.8270.89219.1310.1110.1110.0000.0000.0000.000
148A151VAL00.0090.02119.1030.0160.0160.0000.0000.0000.000
149A152ARG10.7850.88513.5380.0080.0080.0000.0000.0000.000
150A153CYS0-0.010-0.01216.8760.0460.0460.0000.0000.0000.000
151A154ILE0-0.025-0.02410.950-0.024-0.0240.0000.0000.0000.000
152A155CYS0-0.026-0.00913.9260.0590.0590.0000.0000.0000.000
153A156LEU0-0.0040.0048.9560.0170.0170.0000.0000.0000.000
154A157SER00.006-0.00312.877-0.074-0.0740.0000.0000.0000.000
155A158ASN0-0.010-0.01511.621-0.017-0.0170.0000.0000.0000.000
156A159ALA0-0.052-0.00314.028-0.051-0.0510.0000.0000.0000.000
157A160VAL00.0540.00216.3720.0310.0310.0000.0000.0000.000
158A161SER0-0.0070.01218.595-0.043-0.0430.0000.0000.0000.000
159A162VAL00.0290.01121.0530.0050.0050.0000.0000.0000.000
160A163VAL00.0240.01622.747-0.018-0.0180.0000.0000.0000.000
161A164ASN0-0.006-0.00521.2230.0000.0000.0000.0000.0000.000
162A165PRO00.0530.00524.790-0.013-0.0130.0000.0000.0000.000
163A166TYR00.008-0.02422.163-0.016-0.0160.0000.0000.0000.000
164A167PHE00.0140.00218.329-0.010-0.0100.0000.0000.0000.000
165A168LEU00.0060.01324.279-0.017-0.0170.0000.0000.0000.000
166A169PHE0-0.053-0.01827.230-0.012-0.0120.0000.0000.0000.000
167A170PHE0-0.013-0.02524.022-0.008-0.0080.0000.0000.0000.000
168A171ASN0-0.0340.00127.185-0.007-0.0070.0000.0000.0000.000
169A172LEU0-0.035-0.01221.676-0.008-0.0080.0000.0000.0000.000
170A173VAL00.015-0.00625.0280.0170.0170.0000.0000.0000.000
171A174PRO0-0.043-0.01120.580-0.012-0.0120.0000.0000.0000.000
172A175ASP-1-0.764-0.86722.3000.0540.0540.0000.0000.0000.000
173A176VAL00.015-0.00720.065-0.001-0.0010.0000.0000.0000.000
174A177ASN0-0.056-0.02819.6040.0210.0210.0000.0000.0000.000
175A178LYS10.8270.91319.015-0.031-0.0310.0000.0000.0000.000
176A179ARG10.7970.8997.7710.3220.3220.0000.0000.0000.000
177A180PHE00.015-0.01511.0930.0220.0220.0000.0000.0000.000
178A181ASN0-0.0200.00016.440-0.025-0.0250.0000.0000.0000.000
179A182VAL00.004-0.00918.5810.0110.0110.0000.0000.0000.000
180A183TYR00.0560.02820.7020.0090.0090.0000.0000.0000.000
181A184ASP-1-0.874-0.93122.633-0.024-0.0240.0000.0000.0000.000
182A185ASP-1-0.787-0.87123.2880.0060.0060.0000.0000.0000.000
183A186ALA0-0.065-0.03020.2120.0180.0180.0000.0000.0000.000
184A187LEU0-0.0110.00214.175-0.031-0.0310.0000.0000.0000.000
185A188ILE00.0010.00016.1830.0440.0440.0000.0000.0000.000
186A189GLU-1-0.756-0.8709.478-0.258-0.2580.0000.0000.0000.000
187A190ILE00.000-0.00713.1070.1100.1100.0000.0000.0000.000
188A191PRO0-0.050-0.0268.093-0.052-0.0520.0000.0000.0000.000
189A192ASP-1-0.822-0.89210.2240.1240.1240.0000.0000.0000.000
190A193SER00.008-0.0196.2160.1990.1990.0000.0000.0000.000
191A194LEU0-0.080-0.0446.5790.1050.1050.0000.0000.0000.000
192A195ASP-1-0.882-0.9059.7860.1870.1870.0000.0000.0000.000
193A196PHE0-0.022-0.0228.867-0.062-0.0620.0000.0000.0000.000
194A197SER0-0.070-0.03013.799-0.137-0.1370.0000.0000.0000.000