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: V5VK1

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 OptH
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 -2374314.471098
FMO2-HF: Nuclear repulsion 2295583.468469
FMO2-HF: Total energy -78731.002629
FMO2-MP2: Total energy -78963.502194


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.
-38.374-29.73717.173-11.398-14.411-0.023
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 : -0.015 / q_NPA : -0.010
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].
3A6PHE00.0420.0222.866-4.565-0.8980.251-2.024-1.8940.012
4A7TYR0-0.107-0.0762.109-5.895-4.4924.753-2.630-3.5270.029
5A8ASN00.0850.0341.958-18.594-19.6939.491-4.479-3.913-0.063
6A9PRO00.0340.0173.3150.9781.3750.015-0.092-0.3190.000
7A10GLN00.0130.0126.3170.4640.4640.0000.0000.0000.000
8A11LYS10.9760.9988.5190.7080.7080.0000.0000.0000.000
9A12MET0-0.0040.0299.0820.1560.1560.0000.0000.0000.000
10A13LEU00.023-0.0138.6390.1080.1080.0000.0000.0000.000
11A14SER0-0.090-0.05712.0440.0650.0650.0000.0000.0000.000
12A15TYR0-0.026-0.01114.3310.0460.0460.0000.0000.0000.000
13A16ASP-1-0.932-0.95815.835-0.085-0.0850.0000.0000.0000.000
14A17ARG10.8320.92817.1400.1020.1020.0000.0000.0000.000
15A18ILE00.0530.03217.8810.0190.0190.0000.0000.0000.000
16A19LEU0-0.0060.00519.0600.0340.0340.0000.0000.0000.000
17A20ASN0-0.036-0.02714.167-0.066-0.0660.0000.0000.0000.000
18A21PHE00.0220.01415.2830.0580.0580.0000.0000.0000.000
19A22VAL0-0.0050.0078.853-0.030-0.0300.0000.0000.0000.000
20A23ILE0-0.016-0.01712.2810.1090.1090.0000.0000.0000.000
21A24GLY00.0300.01212.918-0.012-0.0120.0000.0000.0000.000
22A25ALA0-0.027-0.0119.1520.1150.1150.0000.0000.0000.000
23A26ARG11.0121.01510.090-0.702-0.7020.0000.0000.0000.000
24A27GLY00.0380.0088.3430.4990.4990.0000.0000.0000.000
25A28ILE00.0810.0334.1870.2330.347-0.001-0.023-0.0910.000
26A29GLY0-0.0050.0042.767-1.294-0.1451.212-1.179-1.1810.008
27A30LYS10.9010.9682.969-5.611-5.2170.2260.472-1.091-0.005
28A31SER00.0440.0075.608-0.318-0.3180.0000.0000.0000.000
29A32TYR0-0.048-0.0232.414-1.347-0.2290.775-0.726-1.168-0.004
30A33ALA00.0390.0082.471-1.359-0.0830.439-0.667-1.0470.000
31A34MET0-0.058-0.0263.667-0.947-0.8080.013-0.045-0.1080.000
32A35LYS10.8600.9556.611-1.282-1.2820.0000.0000.0000.000
33A36VAL00.0660.0214.907-0.289-0.2890.0000.0000.0000.000
34A37TYR00.002-0.0017.418-0.426-0.4260.0000.0000.0000.000
35A38PRO00.0190.0038.837-0.225-0.2250.0000.0000.0000.000
36A39ILE00.0000.01810.581-0.110-0.1100.0000.0000.0000.000
37A40ASN0-0.005-0.0138.465-0.249-0.2490.0000.0000.0000.000
38A41ARG10.8040.89712.006-0.040-0.0400.0000.0000.0000.000
39A42PHE00.0050.01514.446-0.043-0.0430.0000.0000.0000.000
40A43ILE0-0.026-0.00913.853-0.034-0.0340.0000.0000.0000.000
41A44LYS10.8830.95012.1990.2180.2180.0000.0000.0000.000
42A45TYR0-0.024-0.02415.519-0.033-0.0330.0000.0000.0000.000
43A46GLY00.0150.02319.1370.0020.0020.0000.0000.0000.000
44A47GLU-1-0.830-0.87017.2230.0190.0190.0000.0000.0000.000
45A48GLN0-0.007-0.02118.0910.0200.0200.0000.0000.0000.000
46A49PHE0-0.017-0.01614.8080.0120.0120.0000.0000.0000.000
47A50ILE00.0080.00417.293-0.006-0.0060.0000.0000.0000.000
48A51TYR0-0.0160.00312.6380.0020.0020.0000.0000.0000.000
49A52VAL00.009-0.00716.356-0.037-0.0370.0000.0000.0000.000
50A53ARG10.8690.94715.468-0.485-0.4850.0000.0000.0000.000
51A54ARG10.7670.85219.315-0.320-0.3200.0000.0000.0000.000
52A55TYR0-0.013-0.03322.475-0.032-0.0320.0000.0000.0000.000
53A56LYS10.9900.97922.986-0.150-0.1500.0000.0000.0000.000
54A57PRO00.0120.01123.8400.0090.0090.0000.0000.0000.000
55A58GLU-1-0.813-0.90619.3790.3770.3770.0000.0000.0000.000
56A59LEU0-0.025-0.01818.3600.0380.0380.0000.0000.0000.000
57A60ALA0-0.017-0.00520.703-0.016-0.0160.0000.0000.0000.000
58A61LYS10.9680.98118.965-0.403-0.4030.0000.0000.0000.000
59A62VAL00.0300.01917.5420.0310.0310.0000.0000.0000.000
60A63SER00.0260.00318.2110.0110.0110.0000.0000.0000.000
61A64ASN0-0.016-0.01116.444-0.039-0.0390.0000.0000.0000.000
62A65TYR0-0.029-0.00412.2420.0850.0850.0000.0000.0000.000
63A66PHE00.061-0.00412.4980.0920.0920.0000.0000.0000.000
64A67ASN00.0060.00612.831-0.034-0.0340.0000.0000.0000.000
65A68ASP-1-0.926-0.9568.0220.9820.9820.0000.0000.0000.000
66A69VAL0-0.005-0.0167.1070.0030.0030.0000.0000.0000.000
67A70ALA00.0070.0099.248-0.099-0.0990.0000.0000.0000.000
68A71GLN00.005-0.00510.063-0.088-0.0880.0000.0000.0000.000
69A72GLU-1-0.908-0.9385.035-0.614-0.535-0.001-0.005-0.0720.000
70A73PHE0-0.113-0.0579.338-0.068-0.0680.0000.0000.0000.000
71A74PRO00.0440.03312.9010.0330.0330.0000.0000.0000.000
72A75ASP-1-0.923-0.94915.623-0.081-0.0810.0000.0000.0000.000
73A76HIS10.7740.85215.5550.0000.0000.0000.0000.0000.000
74A77GLU-1-0.870-0.91917.5910.1080.1080.0000.0000.0000.000
75A78LEU0-0.033-0.01813.5460.0160.0160.0000.0000.0000.000
76A79VAL00.0210.00617.9380.0050.0050.0000.0000.0000.000
77A80VAL0-0.001-0.00118.1290.0120.0120.0000.0000.0000.000
78A81LYS10.9510.97920.951-0.132-0.1320.0000.0000.0000.000
79A82GLY00.0000.00624.547-0.004-0.0040.0000.0000.0000.000
80A83ARG10.7780.86522.171-0.181-0.1810.0000.0000.0000.000
81A84ARG10.9360.98221.926-0.134-0.1340.0000.0000.0000.000
82A85PHE00.0100.00616.8730.0100.0100.0000.0000.0000.000
83A86TYR0-0.024-0.03219.763-0.021-0.0210.0000.0000.0000.000
84A87ILE00.0440.02715.7790.0210.0210.0000.0000.0000.000
85A88ASP-1-0.780-0.86519.7650.0260.0260.0000.0000.0000.000
86A89GLY0-0.029-0.01422.163-0.012-0.0120.0000.0000.0000.000
87A90LYS10.9290.96723.201-0.029-0.0290.0000.0000.0000.000
88A91LEU0-0.032-0.01222.4560.0150.0150.0000.0000.0000.000
89A92ALA00.0290.02018.351-0.012-0.0120.0000.0000.0000.000
90A93GLY00.0600.01618.3010.0100.0100.0000.0000.0000.000
91A94TRP0-0.036-0.00719.367-0.012-0.0120.0000.0000.0000.000
92A95ALA00.0280.02218.8350.0300.0300.0000.0000.0000.000
93A96ILE00.0070.00119.966-0.030-0.0300.0000.0000.0000.000
94A97PRO0-0.017-0.00821.4640.0190.0190.0000.0000.0000.000
95A98LEU00.0340.01222.806-0.020-0.0200.0000.0000.0000.000
96A99SER00.017-0.01024.586-0.013-0.0130.0000.0000.0000.000
97A100VAL0-0.120-0.06027.170-0.013-0.0130.0000.0000.0000.000
98A101TRP00.0780.03226.0040.0000.0000.0000.0000.0000.000
99A102GLN00.0340.01128.013-0.002-0.0020.0000.0000.0000.000
100A103SER0-0.009-0.01531.265-0.007-0.0070.0000.0000.0000.000
101A104GLU-1-0.870-0.91826.4640.1570.1570.0000.0000.0000.000
102A105LYS10.9010.95329.092-0.099-0.0990.0000.0000.0000.000
103A106SER0-0.0260.00930.757-0.006-0.0060.0000.0000.0000.000
104A107ASN0-0.060-0.01828.785-0.012-0.0120.0000.0000.0000.000
105A108ALA00.0270.01629.678-0.003-0.0030.0000.0000.0000.000
106A109TYR0-0.050-0.05624.1600.0150.0150.0000.0000.0000.000
107A110PRO0-0.061-0.02525.719-0.004-0.0040.0000.0000.0000.000
108A111ASN00.0080.00022.741-0.014-0.0140.0000.0000.0000.000
109A112VAL00.0050.02219.6140.0080.0080.0000.0000.0000.000
110A113SER00.009-0.01317.8090.0000.0000.0000.0000.0000.000
111A114THR0-0.013-0.00913.003-0.005-0.0050.0000.0000.0000.000
112A115ILE0-0.0050.00016.4570.0200.0200.0000.0000.0000.000
113A116VAL0-0.0060.00310.9420.0030.0030.0000.0000.0000.000
114A117PHE0-0.004-0.00914.053-0.008-0.0080.0000.0000.0000.000
115A118ASP-1-0.831-0.93111.9220.9280.9280.0000.0000.0000.000
116A119GLU-1-0.901-0.95514.1020.5270.5270.0000.0000.0000.000
117A120PHE0-0.0070.00015.920-0.063-0.0630.0000.0000.0000.000
118A121ILE0-0.0280.00618.148-0.055-0.0550.0000.0000.0000.000
119A122ARG10.9340.95420.301-0.237-0.2370.0000.0000.0000.000
120A123GLU-1-0.935-0.93817.7550.5070.5070.0000.0000.0000.000
121A124LYS10.9390.93819.965-0.346-0.3460.0000.0000.0000.000
122A125ASP-1-0.957-0.97423.9430.2060.2060.0000.0000.0000.000
123A126ASN00.0870.03526.880-0.022-0.0220.0000.0000.0000.000
124A127SER00.0180.03627.4090.0170.0170.0000.0000.0000.000
125A128ASN0-0.079-0.04428.043-0.019-0.0190.0000.0000.0000.000
126A129TYR0-0.002-0.00623.2120.0220.0220.0000.0000.0000.000
127A130ILE0-0.0020.00625.959-0.010-0.0100.0000.0000.0000.000
128A131PRO00.0420.01229.198-0.001-0.0010.0000.0000.0000.000
129A132ASN00.0130.00031.5820.0000.0000.0000.0000.0000.000
130A133GLU-1-0.685-0.78923.8450.2280.2280.0000.0000.0000.000
131A134VAL00.0190.01425.7830.0060.0060.0000.0000.0000.000
132A135SER00.0300.00926.918-0.003-0.0030.0000.0000.0000.000
133A136ALA0-0.0150.00727.299-0.005-0.0050.0000.0000.0000.000
134A137LEU00.010-0.00220.5370.0010.0010.0000.0000.0000.000
135A138LEU00.0510.01824.616-0.003-0.0030.0000.0000.0000.000
136A139ASN00.0400.04126.516-0.003-0.0030.0000.0000.0000.000
137A140LEU0-0.0300.00022.097-0.005-0.0050.0000.0000.0000.000
138A141MET0-0.018-0.01921.8240.0040.0040.0000.0000.0000.000
139A142ASP-1-0.866-0.93624.2960.0570.0570.0000.0000.0000.000
140A143THR0-0.152-0.06627.473-0.008-0.0080.0000.0000.0000.000
141A144VAL0-0.050-0.03422.608-0.004-0.0040.0000.0000.0000.000
142A145PHE0-0.040-0.01019.091-0.001-0.0010.0000.0000.0000.000
143A146ARG10.9871.00124.967-0.030-0.0300.0000.0000.0000.000
144A147ASN0-0.001-0.02226.057-0.006-0.0060.0000.0000.0000.000
145A148ARG10.8970.91824.4260.0100.0100.0000.0000.0000.000
146A149GLU-1-0.907-0.93822.996-0.079-0.0790.0000.0000.0000.000
147A150ARG10.9330.96219.2180.1160.1160.0000.0000.0000.000
148A151VAL00.0190.02619.1060.0170.0170.0000.0000.0000.000
149A152ARG10.8960.95513.3730.0020.0020.0000.0000.0000.000
150A153CYS0-0.030-0.01516.8660.0530.0530.0000.0000.0000.000
151A154ILE0-0.010-0.02110.964-0.026-0.0260.0000.0000.0000.000
152A155CYS0-0.027-0.01013.9100.0590.0590.0000.0000.0000.000
153A156LEU0-0.012-0.0029.0620.0100.0100.0000.0000.0000.000
154A157SER00.0490.02012.851-0.055-0.0550.0000.0000.0000.000
155A158ASN0-0.004-0.01511.4060.0030.0030.0000.0000.0000.000
156A159ALA0-0.041-0.01114.089-0.051-0.0510.0000.0000.0000.000
157A160VAL00.0580.00616.4410.0260.0260.0000.0000.0000.000
158A161SER0-0.0180.00218.617-0.040-0.0400.0000.0000.0000.000
159A162VAL00.0350.01321.0840.0040.0040.0000.0000.0000.000
160A163VAL00.0310.02222.790-0.017-0.0170.0000.0000.0000.000
161A164ASN00.0090.00521.3210.0030.0030.0000.0000.0000.000
162A165PRO00.0390.00024.715-0.014-0.0140.0000.0000.0000.000
163A166TYR00.019-0.01422.252-0.016-0.0160.0000.0000.0000.000
164A167PHE00.003-0.00118.525-0.009-0.0090.0000.0000.0000.000
165A168LEU0-0.0010.00724.358-0.016-0.0160.0000.0000.0000.000
166A169PHE0-0.051-0.01627.310-0.011-0.0110.0000.0000.0000.000
167A170PHE0-0.019-0.02623.959-0.007-0.0070.0000.0000.0000.000
168A171ASN0-0.0280.00427.282-0.007-0.0070.0000.0000.0000.000
169A172LEU0-0.035-0.01521.816-0.008-0.0080.0000.0000.0000.000
170A173VAL00.018-0.00625.0960.0160.0160.0000.0000.0000.000
171A174PRO0-0.052-0.01520.631-0.012-0.0120.0000.0000.0000.000
172A175ASP-1-0.832-0.93522.3780.0390.0390.0000.0000.0000.000
173A176VAL00.010-0.01120.081-0.003-0.0030.0000.0000.0000.000
174A177ASN0-0.0030.00219.6050.0260.0260.0000.0000.0000.000
175A178LYS10.8600.94719.031-0.010-0.0100.0000.0000.0000.000
176A179ARG10.8670.9377.5690.5190.5190.0000.0000.0000.000
177A180PHE00.012-0.01911.2620.0100.0100.0000.0000.0000.000
178A181ASN0-0.0150.01816.491-0.013-0.0130.0000.0000.0000.000
179A182VAL00.014-0.00218.6760.0100.0100.0000.0000.0000.000
180A183TYR00.0430.01720.7810.0100.0100.0000.0000.0000.000
181A184ASP-1-0.869-0.92822.733-0.037-0.0370.0000.0000.0000.000
182A185ASP-1-0.841-0.91023.303-0.005-0.0050.0000.0000.0000.000
183A186ALA0-0.050-0.03020.3240.0170.0170.0000.0000.0000.000
184A187LEU0-0.0200.00014.335-0.030-0.0300.0000.0000.0000.000
185A188ILE00.0050.00716.2850.0410.0410.0000.0000.0000.000
186A189GLU-1-0.752-0.8619.558-0.351-0.3510.0000.0000.0000.000
187A190ILE00.008-0.00413.1420.1030.1030.0000.0000.0000.000
188A191PRO0-0.070-0.0378.106-0.063-0.0630.0000.0000.0000.000
189A192ASP-1-0.872-0.92910.2260.1010.1010.0000.0000.0000.000
190A193SER0-0.012-0.0256.1510.1900.1900.0000.0000.0000.000
191A194LEU0-0.076-0.0476.7700.1320.1320.0000.0000.0000.000
192A195ASP-1-0.906-0.9339.7300.1740.1740.0000.0000.0000.000
193A196PHE0-0.034-0.0278.921-0.064-0.0640.0000.0000.0000.000
194A197SER0-0.0390.00513.716-0.105-0.1050.0000.0000.0000.000