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: 17Q8Z

Calculation Name: 5HA8-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5HA8

Chain ID: A

ChEMBL ID:

UniProt ID: A0A0K0

Base Structure: X-ray

Registration Date: 2023-09-20

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 175
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1786796.718338
FMO2-HF: Nuclear repulsion 1720123.810007
FMO2-HF: Total energy -66672.908331
FMO2-MP2: Total energy -66868.921623


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:PRO)


Summations of interaction energy for fragment #1(A:4:PRO)
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.
-1.878-0.321-0.019-0.596-0.9420.002
Interaction energy analysis for fragmet #1(A:4:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.026 / q_NPA : -0.040
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].
3A6ARG10.9200.9623.8150.5521.986-0.018-0.564-0.8520.002
4A7THR00.0150.0086.3120.2290.2290.0000.0000.0000.000
5A8VAL00.0210.0149.738-0.005-0.0050.0000.0000.0000.000
6A9VAL00.0000.00612.9050.0580.0580.0000.0000.0000.000
7A10LEU0-0.026-0.01216.416-0.017-0.0170.0000.0000.0000.000
8A11ALA00.0220.00218.6140.0340.0340.0000.0000.0000.000
9A12ILE0-0.029-0.03621.554-0.005-0.0050.0000.0000.0000.000
10A13ASP-1-0.700-0.85624.642-0.128-0.1280.0000.0000.0000.000
11A14LEU0-0.0210.01725.7680.0130.0130.0000.0000.0000.000
12A15GLN0-0.007-0.01229.224-0.002-0.0020.0000.0000.0000.000
13A16ALA00.0340.00832.1170.0070.0070.0000.0000.0000.000
14A17GLY0-0.008-0.00835.6330.0060.0060.0000.0000.0000.000
15A18VAL0-0.124-0.05331.9870.0030.0030.0000.0000.0000.000
16A19THR0-0.010-0.03931.9750.0020.0020.0000.0000.0000.000
17A20PRO00.0200.02534.8060.0060.0060.0000.0000.0000.000
18A21GLY0-0.042-0.01138.5530.0000.0000.0000.0000.0000.000
19A22CYS0-0.096-0.02734.7440.0020.0020.0000.0000.0000.000
20A23PHE00.0340.00534.4520.0020.0020.0000.0000.0000.000
21A24ASP-1-0.806-0.88433.574-0.029-0.0290.0000.0000.0000.000
22A25GLU-1-0.787-0.87534.282-0.056-0.0560.0000.0000.0000.000
23A26GLU-1-0.922-0.96033.728-0.038-0.0380.0000.0000.0000.000
24A27GLY00.0210.00733.436-0.002-0.0020.0000.0000.0000.000
25A28VAL0-0.044-0.03128.842-0.002-0.0020.0000.0000.0000.000
26A29LEU00.0120.01028.954-0.008-0.0080.0000.0000.0000.000
27A30SER0-0.036-0.01129.389-0.007-0.0070.0000.0000.0000.000
28A31ARG10.7530.86026.9460.0270.0270.0000.0000.0000.000
29A32ALA00.0200.01124.871-0.005-0.0050.0000.0000.0000.000
30A33ALA00.0150.00824.501-0.014-0.0140.0000.0000.0000.000
31A34ALA0-0.0060.00025.257-0.007-0.0070.0000.0000.0000.000
32A35LEU0-0.041-0.02118.9900.0020.0020.0000.0000.0000.000
33A36VAL00.0150.00820.506-0.016-0.0160.0000.0000.0000.000
34A37GLU-1-0.855-0.91720.897-0.128-0.1280.0000.0000.0000.000
35A38ARG10.7990.88318.0040.0210.0210.0000.0000.0000.000
36A39ALA0-0.025-0.01116.8440.0010.0010.0000.0000.0000.000
37A40ARG10.7650.83416.5810.1360.1360.0000.0000.0000.000
38A41ALA0-0.045-0.02018.251-0.006-0.0060.0000.0000.0000.000
39A42GLY0-0.033-0.00915.7170.0170.0170.0000.0000.0000.000
40A43GLY0-0.038-0.01113.709-0.019-0.0190.0000.0000.0000.000
41A44VAL0-0.087-0.04211.986-0.089-0.0890.0000.0000.0000.000
42A45PRO0-0.014-0.00711.5280.0460.0460.0000.0000.0000.000
43A46VAL00.0350.01814.468-0.005-0.0050.0000.0000.0000.000
44A47VAL0-0.015-0.00815.985-0.005-0.0050.0000.0000.0000.000
45A48TRP0-0.009-0.02218.7500.0240.0240.0000.0000.0000.000
46A49VAL0-0.016-0.00621.665-0.014-0.0140.0000.0000.0000.000
47A50HIS00.0100.01124.1260.0090.0090.0000.0000.0000.000
48A51HIS00.0260.00827.864-0.014-0.0140.0000.0000.0000.000
49A52ASP-1-0.717-0.84130.354-0.132-0.1320.0000.0000.0000.000
50A53PRO0-0.085-0.04932.6580.0070.0070.0000.0000.0000.000
51A54VAL0-0.0330.00533.4380.0060.0060.0000.0000.0000.000
52A55GLY00.0220.01836.0500.0060.0060.0000.0000.0000.000
53A56VAL0-0.0310.00134.0470.0000.0000.0000.0000.0000.000
54A57GLY0-0.016-0.00436.0940.0040.0040.0000.0000.0000.000
55A58THR0-0.065-0.03937.9590.0050.0050.0000.0000.0000.000
56A59PRO00.036-0.00337.419-0.005-0.0050.0000.0000.0000.000
57A60GLU-1-0.862-0.93136.972-0.072-0.0720.0000.0000.0000.000
58A61TRP0-0.067-0.03529.759-0.006-0.0060.0000.0000.0000.000
59A62GLU-1-0.867-0.94132.391-0.126-0.1260.0000.0000.0000.000
60A63LEU0-0.024-0.00527.1230.0030.0030.0000.0000.0000.000
61A64ALA00.0070.01531.3220.0070.0070.0000.0000.0000.000
62A65ALA00.0040.02232.081-0.004-0.0040.0000.0000.0000.000
63A66PRO0-0.022-0.02531.3810.0030.0030.0000.0000.0000.000
64A67LEU0-0.010-0.01326.872-0.004-0.0040.0000.0000.0000.000
65A68HIS0-0.014-0.01227.9300.0040.0040.0000.0000.0000.000
66A69ARG10.8850.95123.5090.2000.2000.0000.0000.0000.000
67A70ALA0-0.016-0.00522.5760.0130.0130.0000.0000.0000.000
68A71GLU-1-0.910-0.97123.469-0.184-0.1840.0000.0000.0000.000
69A72GLY0-0.026-0.01420.126-0.008-0.0080.0000.0000.0000.000
70A73GLU-1-0.742-0.81318.851-0.250-0.2500.0000.0000.0000.000
71A74PRO00.0020.00917.2040.0320.0320.0000.0000.0000.000
72A75LEU0-0.013-0.00620.5170.0080.0080.0000.0000.0000.000
73A76VAL0-0.021-0.00920.1440.0000.0000.0000.0000.0000.000
74A77ARG10.8370.89723.4150.1610.1610.0000.0000.0000.000
75A78LYS10.7830.89925.3770.1410.1410.0000.0000.0000.000
76A79ASN00.0530.00927.9230.0160.0160.0000.0000.0000.000
77A80TYR0-0.0100.00028.9430.0160.0160.0000.0000.0000.000
78A81ARG10.9350.96228.5570.0730.0730.0000.0000.0000.000
79A82ASP-1-0.765-0.87623.238-0.198-0.1980.0000.0000.0000.000
80A83SER00.026-0.01822.0540.0010.0010.0000.0000.0000.000
81A84PHE0-0.0020.00916.573-0.016-0.0160.0000.0000.0000.000
82A85ALA0-0.099-0.03822.076-0.004-0.0040.0000.0000.0000.000
83A86ASP-1-0.941-0.97325.538-0.155-0.1550.0000.0000.0000.000
84A87THR0-0.017-0.02022.617-0.004-0.0040.0000.0000.0000.000
85A88THR00.0580.02621.146-0.004-0.0040.0000.0000.0000.000
86A89LEU0-0.0070.01117.853-0.037-0.0370.0000.0000.0000.000
87A90ARG10.7990.85312.1780.5870.5870.0000.0000.0000.000
88A91GLU-1-0.893-0.94715.033-0.412-0.4120.0000.0000.0000.000
89A92THR0-0.011-0.01315.339-0.043-0.0430.0000.0000.0000.000
90A93LEU0-0.024-0.02312.611-0.060-0.0600.0000.0000.0000.000
91A94ASP-1-0.807-0.88210.821-0.981-0.9810.0000.0000.0000.000
92A95GLU-1-0.960-0.95910.551-0.720-0.7200.0000.0000.0000.000
93A96LEU0-0.080-0.03810.829-0.043-0.0430.0000.0000.0000.000
94A97GLY00.0090.0117.008-0.190-0.1900.0000.0000.0000.000
95A98ALA0-0.080-0.0386.274-0.638-0.6380.0000.0000.0000.000
96A99THR00.0350.0044.217-0.381-0.258-0.001-0.032-0.0900.000
97A100HIS0-0.033-0.0117.6380.4740.4740.0000.0000.0000.000
98A101LEU00.0080.01010.125-0.044-0.0440.0000.0000.0000.000
99A102VAL00.0030.00013.7300.0920.0920.0000.0000.0000.000
100A103ILE0-0.004-0.00416.060-0.012-0.0120.0000.0000.0000.000
101A104THR0-0.034-0.02819.5080.0330.0330.0000.0000.0000.000
102A105GLY00.0380.00322.836-0.020-0.0200.0000.0000.0000.000
103A106ALA0-0.0150.01225.9140.0160.0160.0000.0000.0000.000
104A107GLN00.0550.01028.993-0.012-0.0120.0000.0000.0000.000
105A108SER00.014-0.02228.288-0.007-0.0070.0000.0000.0000.000
106A109ASP-1-0.819-0.88928.379-0.059-0.0590.0000.0000.0000.000
107A110PHE0-0.021-0.02030.288-0.001-0.0010.0000.0000.0000.000
108A111CYS00.0060.00927.288-0.002-0.0020.0000.0000.0000.000
109A112VAL00.0260.04823.989-0.014-0.0140.0000.0000.0000.000
110A113ARG10.9680.99424.0020.0450.0450.0000.0000.0000.000
111A114THR0-0.064-0.05624.5160.0010.0010.0000.0000.0000.000
112A115THR00.0420.03220.543-0.013-0.0130.0000.0000.0000.000
113A116MET0-0.0190.00819.715-0.020-0.0200.0000.0000.0000.000
114A117GLN0-0.022-0.01919.364-0.001-0.0010.0000.0000.0000.000
115A118ARG10.7900.88519.8910.2340.2340.0000.0000.0000.000
116A119ALA00.0290.00615.941-0.020-0.0200.0000.0000.0000.000
117A120ALA00.000-0.00715.594-0.028-0.0280.0000.0000.0000.000
118A121ALA0-0.044-0.01516.2720.0040.0040.0000.0000.0000.000
119A122GLU-1-0.853-0.90215.303-0.336-0.3360.0000.0000.0000.000
120A123GLY0-0.0070.00712.806-0.056-0.0560.0000.0000.0000.000
121A124TYR0-0.067-0.02310.6030.0430.0430.0000.0000.0000.000
122A125ASP-1-0.771-0.8568.3710.2560.2560.0000.0000.0000.000
123A126VAL0-0.049-0.03411.572-0.109-0.1090.0000.0000.0000.000
124A127THR0-0.002-0.01714.3100.0940.0940.0000.0000.0000.000
125A128LEU0-0.046-0.00216.774-0.038-0.0380.0000.0000.0000.000
126A129VAL00.0470.00819.8760.0270.0270.0000.0000.0000.000
127A130SER0-0.067-0.03821.992-0.002-0.0020.0000.0000.0000.000
128A131ASP-1-0.741-0.85225.189-0.020-0.0200.0000.0000.0000.000
129A132ALA00.0340.02224.276-0.002-0.0020.0000.0000.0000.000
130A133HIS10.8580.92025.1410.0350.0350.0000.0000.0000.000
131A134THR0-0.003-0.03227.6940.0100.0100.0000.0000.0000.000
132A135THR0-0.027-0.03731.313-0.009-0.0090.0000.0000.0000.000
133A136VAL00.0420.03434.0150.0040.0040.0000.0000.0000.000
134A137ASP-1-0.845-0.92337.817-0.025-0.0250.0000.0000.0000.000
135A138THR0-0.032-0.01338.472-0.002-0.0020.0000.0000.0000.000
136A139GLU-1-0.875-0.94041.390-0.019-0.0190.0000.0000.0000.000
137A140TRP0-0.036-0.01141.940-0.004-0.0040.0000.0000.0000.000
138A141GLU-1-0.928-0.96643.103-0.020-0.0200.0000.0000.0000.000
139A142GLY0-0.029-0.00446.2750.0020.0020.0000.0000.0000.000
140A143VAL0-0.048-0.01943.4200.0020.0020.0000.0000.0000.000
141A144ARG10.9120.93644.0730.0150.0150.0000.0000.0000.000
142A145ILE0-0.061-0.02336.8890.0030.0030.0000.0000.0000.000
143A146SER00.0630.02639.732-0.003-0.0030.0000.0000.0000.000
144A147GLY00.0720.01736.4410.0000.0000.0000.0000.0000.000
145A148GLU-1-0.957-0.97035.046-0.009-0.0090.0000.0000.0000.000
146A149GLN00.0250.00434.8940.0000.0000.0000.0000.0000.000
147A150ILE00.0040.01932.3010.0020.0020.0000.0000.0000.000
148A151VAL0-0.0060.01829.923-0.002-0.0020.0000.0000.0000.000
149A152ALA00.0210.00330.0130.0020.0020.0000.0000.0000.000
150A153HIS00.0070.00030.6230.0080.0080.0000.0000.0000.000
151A154THR0-0.036-0.03926.2840.0000.0000.0000.0000.0000.000
152A155ASN00.0250.01025.961-0.007-0.0070.0000.0000.0000.000
153A156MET0-0.0400.00126.0100.0110.0110.0000.0000.0000.000
154A157TYR00.0120.00624.2590.0060.0060.0000.0000.0000.000
155A158PHE00.027-0.00918.0350.0060.0060.0000.0000.0000.000
156A159SER0-0.064-0.03621.9050.0150.0150.0000.0000.0000.000
157A160GLY00.0020.00222.9700.0240.0240.0000.0000.0000.000
158A161LEU0-0.0370.00619.7070.0050.0050.0000.0000.0000.000
159A162ARG10.8350.89818.871-0.090-0.0900.0000.0000.0000.000
160A163TYR00.0670.03516.287-0.025-0.0250.0000.0000.0000.000
161A164PRO0-0.038-0.01716.1510.0410.0410.0000.0000.0000.000
162A165GLY0-0.009-0.00912.670-0.033-0.0330.0000.0000.0000.000
163A166GLN0-0.050-0.01710.8970.0600.0600.0000.0000.0000.000
164A167GLU-1-0.886-0.92211.7110.5370.5370.0000.0000.0000.000
165A168PHE0-0.027-0.02213.376-0.076-0.0760.0000.0000.0000.000
166A169VAL00.0020.00115.1150.0340.0340.0000.0000.0000.000
167A170ILE0-0.038-0.00217.897-0.039-0.0390.0000.0000.0000.000
168A171ALA00.007-0.00819.2020.0230.0230.0000.0000.0000.000
169A172THR0-0.014-0.01221.186-0.015-0.0150.0000.0000.0000.000
170A173HIS00.014-0.04221.4650.0020.0020.0000.0000.0000.000
171A174ASP-1-0.849-0.89521.5600.0130.0130.0000.0000.0000.000
172A175HIS10.8030.89420.855-0.034-0.0340.0000.0000.0000.000
173A176VAL00.0160.03615.9500.0300.0300.0000.0000.0000.000
174A177ALA00.0110.01113.110-0.013-0.0130.0000.0000.0000.000
175A178LEU00.0070.00811.680-0.038-0.0380.0000.0000.0000.000