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: G6MZ1

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 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 175
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1790611.682868
FMO2-HF: Nuclear repulsion 1723938.6767
FMO2-HF: Total energy -66673.006168
FMO2-MP2: Total energy -66869.005371


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.
-1.43-0.012000000000001-0.012-0.549-0.8580.002
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 : -0.041
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].
3A6ARG10.8990.9563.8710.5741.886-0.011-0.522-0.7790.002
4A7THR00.0250.0086.3490.2220.2220.0000.0000.0000.000
5A8VAL00.0230.0159.765-0.061-0.0610.0000.0000.0000.000
6A9VAL0-0.0040.00412.9060.0570.0570.0000.0000.0000.000
7A10LEU0-0.027-0.01016.532-0.025-0.0250.0000.0000.0000.000
8A11ALA00.016-0.00418.8040.0310.0310.0000.0000.0000.000
9A12ILE0-0.013-0.02021.818-0.003-0.0030.0000.0000.0000.000
10A13ASP-1-0.700-0.84624.816-0.103-0.1030.0000.0000.0000.000
11A14LEU0-0.0160.01825.6160.0110.0110.0000.0000.0000.000
12A15GLN0-0.016-0.01229.289-0.002-0.0020.0000.0000.0000.000
13A16ALA00.0280.00132.2950.0060.0060.0000.0000.0000.000
14A17GLY0-0.004-0.00335.8050.0060.0060.0000.0000.0000.000
15A18VAL0-0.118-0.04832.0900.0010.0010.0000.0000.0000.000
16A19THR0-0.024-0.04332.1070.0010.0010.0000.0000.0000.000
17A20PRO0-0.0110.00434.8810.0050.0050.0000.0000.0000.000
18A21GLY0-0.020-0.00138.7050.0010.0010.0000.0000.0000.000
19A22CYS0-0.101-0.03534.7040.0020.0020.0000.0000.0000.000
20A23PHE00.013-0.00334.3840.0020.0020.0000.0000.0000.000
21A24ASP-1-0.768-0.87133.638-0.010-0.0100.0000.0000.0000.000
22A25GLU-1-0.784-0.85534.184-0.041-0.0410.0000.0000.0000.000
23A26GLU-1-0.908-0.95533.610-0.023-0.0230.0000.0000.0000.000
24A27GLY00.0130.00733.368-0.001-0.0010.0000.0000.0000.000
25A28VAL0-0.044-0.03628.8900.0000.0000.0000.0000.0000.000
26A29LEU00.0120.00828.848-0.005-0.0050.0000.0000.0000.000
27A30SER0-0.032-0.00529.294-0.005-0.0050.0000.0000.0000.000
28A31ARG10.7300.84326.9040.0060.0060.0000.0000.0000.000
29A32ALA00.0260.00924.813-0.001-0.0010.0000.0000.0000.000
30A33ALA00.0070.00524.484-0.012-0.0120.0000.0000.0000.000
31A34ALA0-0.006-0.00225.066-0.005-0.0050.0000.0000.0000.000
32A35LEU0-0.049-0.02318.9970.0050.0050.0000.0000.0000.000
33A36VAL00.0210.01620.344-0.011-0.0110.0000.0000.0000.000
34A37GLU-1-0.836-0.91120.890-0.099-0.0990.0000.0000.0000.000
35A38ARG10.7740.87118.019-0.024-0.0240.0000.0000.0000.000
36A39ALA0-0.032-0.00816.6340.0040.0040.0000.0000.0000.000
37A40ARG10.7450.82116.6870.1080.1080.0000.0000.0000.000
38A41ALA0-0.036-0.01918.558-0.007-0.0070.0000.0000.0000.000
39A42GLY0-0.024-0.00315.5270.0190.0190.0000.0000.0000.000
40A43GLY0-0.044-0.01613.655-0.013-0.0130.0000.0000.0000.000
41A44VAL0-0.080-0.03111.809-0.081-0.0810.0000.0000.0000.000
42A45PRO0-0.014-0.00711.7770.0410.0410.0000.0000.0000.000
43A46VAL00.0330.01714.7360.0030.0030.0000.0000.0000.000
44A47VAL0-0.017-0.00716.105-0.008-0.0080.0000.0000.0000.000
45A48TRP00.007-0.01718.9910.0220.0220.0000.0000.0000.000
46A49VAL0-0.029-0.02221.867-0.016-0.0160.0000.0000.0000.000
47A50HIS00.0000.00924.4140.0080.0080.0000.0000.0000.000
48A51HIS00.0080.00128.175-0.013-0.0130.0000.0000.0000.000
49A52ASP-1-0.716-0.83930.485-0.117-0.1170.0000.0000.0000.000
50A53PRO0-0.078-0.04932.7670.0070.0070.0000.0000.0000.000
51A54VAL0-0.0330.00733.6350.0050.0050.0000.0000.0000.000
52A55GLY00.0160.01736.2640.0050.0050.0000.0000.0000.000
53A56VAL0-0.036-0.00233.8200.0010.0010.0000.0000.0000.000
54A57GLY0-0.0090.00036.0850.0030.0030.0000.0000.0000.000
55A58THR0-0.066-0.04237.9140.0040.0040.0000.0000.0000.000
56A59PRO00.007-0.01237.433-0.004-0.0040.0000.0000.0000.000
57A60GLU-1-0.851-0.93237.022-0.059-0.0590.0000.0000.0000.000
58A61TRP0-0.059-0.02930.192-0.003-0.0030.0000.0000.0000.000
59A62GLU-1-0.833-0.93232.220-0.110-0.1100.0000.0000.0000.000
60A63LEU0-0.027-0.00327.4470.0030.0030.0000.0000.0000.000
61A64ALA0-0.0080.00331.5420.0060.0060.0000.0000.0000.000
62A65ALA00.0130.01432.058-0.002-0.0020.0000.0000.0000.000
63A66PRO0-0.010-0.01531.2950.0030.0030.0000.0000.0000.000
64A67LEU0-0.027-0.00726.746-0.004-0.0040.0000.0000.0000.000
65A68HIS0-0.018-0.01328.3290.0020.0020.0000.0000.0000.000
66A69ARG10.8900.95623.6990.1740.1740.0000.0000.0000.000
67A70ALA0-0.029-0.01123.1780.0120.0120.0000.0000.0000.000
68A71GLU-1-0.889-0.95724.041-0.170-0.1700.0000.0000.0000.000
69A72GLY0-0.044-0.02320.759-0.008-0.0080.0000.0000.0000.000
70A73GLU-1-0.737-0.82019.458-0.205-0.2050.0000.0000.0000.000
71A74PRO00.0010.00317.2530.0260.0260.0000.0000.0000.000
72A75LEU0-0.014-0.00520.5760.0100.0100.0000.0000.0000.000
73A76VAL0-0.0140.00620.1790.0030.0030.0000.0000.0000.000
74A77ARG10.8400.89023.4190.1460.1460.0000.0000.0000.000
75A78LYS10.7930.89225.4840.1150.1150.0000.0000.0000.000
76A79ASN00.0610.01928.0430.0140.0140.0000.0000.0000.000
77A80TYR0-0.031-0.01028.8390.0150.0150.0000.0000.0000.000
78A81ARG10.9410.96728.8740.0610.0610.0000.0000.0000.000
79A82ASP-1-0.777-0.87823.401-0.172-0.1720.0000.0000.0000.000
80A83SER00.029-0.01021.9640.0010.0010.0000.0000.0000.000
81A84PHE00.0140.01916.295-0.017-0.0170.0000.0000.0000.000
82A85ALA0-0.069-0.03121.889-0.003-0.0030.0000.0000.0000.000
83A86ASP-1-0.923-0.96825.454-0.137-0.1370.0000.0000.0000.000
84A87THR0-0.024-0.02222.366-0.003-0.0030.0000.0000.0000.000
85A88THR00.0620.03421.037-0.004-0.0040.0000.0000.0000.000
86A89LEU0-0.0180.01117.710-0.034-0.0340.0000.0000.0000.000
87A90ARG10.7760.83812.0460.5380.5380.0000.0000.0000.000
88A91GLU-1-0.883-0.94614.868-0.375-0.3750.0000.0000.0000.000
89A92THR0-0.018-0.02315.135-0.045-0.0450.0000.0000.0000.000
90A93LEU0-0.023-0.01912.610-0.042-0.0420.0000.0000.0000.000
91A94ASP-1-0.786-0.86410.544-0.896-0.8960.0000.0000.0000.000
92A95GLU-1-0.941-0.95510.430-0.661-0.6610.0000.0000.0000.000
93A96LEU0-0.071-0.03311.159-0.033-0.0330.0000.0000.0000.000
94A97GLY0-0.0110.0027.120-0.132-0.1320.0000.0000.0000.000
95A98ALA0-0.066-0.0306.183-0.600-0.6000.0000.0000.0000.000
96A99THR00.010-0.0104.533-0.396-0.290-0.001-0.027-0.0790.000
97A100HIS0-0.036-0.0067.8980.4210.4210.0000.0000.0000.000
98A101LEU00.0110.01210.188-0.036-0.0360.0000.0000.0000.000
99A102VAL00.0070.00413.8050.0820.0820.0000.0000.0000.000
100A103ILE0-0.016-0.00616.113-0.017-0.0170.0000.0000.0000.000
101A104THR0-0.027-0.03319.5280.0300.0300.0000.0000.0000.000
102A105GLY00.036-0.00122.875-0.018-0.0180.0000.0000.0000.000
103A106ALA00.0130.01925.9930.0150.0150.0000.0000.0000.000
104A107GLN00.0480.01128.756-0.012-0.0120.0000.0000.0000.000
105A108SER0-0.008-0.02428.431-0.006-0.0060.0000.0000.0000.000
106A109ASP-1-0.786-0.88528.326-0.043-0.0430.0000.0000.0000.000
107A110PHE0-0.042-0.02830.656-0.002-0.0020.0000.0000.0000.000
108A111CYS0-0.0010.00627.506-0.002-0.0020.0000.0000.0000.000
109A112VAL00.0240.04723.977-0.012-0.0120.0000.0000.0000.000
110A113ARG10.9390.97124.0240.0320.0320.0000.0000.0000.000
111A114THR0-0.065-0.05024.5680.0000.0000.0000.0000.0000.000
112A115THR00.0470.03120.701-0.013-0.0130.0000.0000.0000.000
113A116MET0-0.0180.00719.852-0.018-0.0180.0000.0000.0000.000
114A117GLN0-0.024-0.01119.6590.0050.0050.0000.0000.0000.000
115A118ARG10.7630.86420.1510.2120.2120.0000.0000.0000.000
116A119ALA00.0280.00316.306-0.019-0.0190.0000.0000.0000.000
117A120ALA0-0.003-0.00115.629-0.029-0.0290.0000.0000.0000.000
118A121ALA0-0.035-0.01016.325-0.001-0.0010.0000.0000.0000.000
119A122GLU-1-0.836-0.89115.615-0.315-0.3150.0000.0000.0000.000
120A123GLY0-0.0110.00612.904-0.076-0.0760.0000.0000.0000.000
121A124TYR0-0.060-0.02110.5300.0190.0190.0000.0000.0000.000
122A125ASP-1-0.780-0.8728.1270.3530.3530.0000.0000.0000.000
123A126VAL0-0.040-0.03011.437-0.099-0.0990.0000.0000.0000.000
124A127THR0-0.009-0.02714.2260.0830.0830.0000.0000.0000.000
125A128LEU0-0.0350.00116.794-0.034-0.0340.0000.0000.0000.000
126A129VAL00.0430.01219.7770.0260.0260.0000.0000.0000.000
127A130SER0-0.066-0.05321.917-0.007-0.0070.0000.0000.0000.000
128A131ASP-1-0.738-0.84925.0390.0080.0080.0000.0000.0000.000
129A132ALA00.0360.02524.237-0.002-0.0020.0000.0000.0000.000
130A133HIS10.8290.91025.1820.0100.0100.0000.0000.0000.000
131A134THR0-0.011-0.02527.5330.0090.0090.0000.0000.0000.000
132A135THR0-0.016-0.03231.209-0.009-0.0090.0000.0000.0000.000
133A136VAL00.0500.04034.0240.0040.0040.0000.0000.0000.000
134A137ASP-1-0.843-0.92237.858-0.013-0.0130.0000.0000.0000.000
135A138THR0-0.037-0.01538.628-0.002-0.0020.0000.0000.0000.000
136A139GLU-1-0.858-0.92741.605-0.011-0.0110.0000.0000.0000.000
137A140TRP0-0.048-0.02341.968-0.004-0.0040.0000.0000.0000.000
138A141GLU-1-0.923-0.96243.426-0.015-0.0150.0000.0000.0000.000
139A142GLY0-0.0040.01146.3750.0020.0020.0000.0000.0000.000
140A143VAL0-0.068-0.03243.6120.0020.0020.0000.0000.0000.000
141A144ARG10.8840.91744.1320.0080.0080.0000.0000.0000.000
142A145ILE0-0.054-0.02036.9480.0030.0030.0000.0000.0000.000
143A146SER00.0830.03839.710-0.003-0.0030.0000.0000.0000.000
144A147GLY00.0440.00636.2130.0000.0000.0000.0000.0000.000
145A148GLU-1-0.956-0.96934.7520.0040.0040.0000.0000.0000.000
146A149GLN00.0290.01034.7550.0010.0010.0000.0000.0000.000
147A150ILE00.0060.01732.2490.0030.0030.0000.0000.0000.000
148A151VAL0-0.0120.01429.8460.0000.0000.0000.0000.0000.000
149A152ALA00.0340.00929.8670.0040.0040.0000.0000.0000.000
150A153HIS00.010-0.00230.4270.0080.0080.0000.0000.0000.000
151A154THR0-0.047-0.05026.1730.0000.0000.0000.0000.0000.000
152A155ASN00.0480.01725.842-0.004-0.0040.0000.0000.0000.000
153A156MET0-0.0360.00725.9250.0120.0120.0000.0000.0000.000
154A157TYR00.0160.01024.5060.0060.0060.0000.0000.0000.000
155A158PHE00.025-0.01118.1240.0040.0040.0000.0000.0000.000
156A159SER0-0.062-0.04121.9100.0170.0170.0000.0000.0000.000
157A160GLY0-0.0060.00323.0680.0230.0230.0000.0000.0000.000
158A161LEU0-0.0340.00619.6380.0030.0030.0000.0000.0000.000
159A162ARG10.8250.89518.455-0.105-0.1050.0000.0000.0000.000
160A163TYR00.0630.03416.111-0.025-0.0250.0000.0000.0000.000
161A164PRO0-0.056-0.03115.9730.0440.0440.0000.0000.0000.000
162A165GLY00.0100.00212.566-0.033-0.0330.0000.0000.0000.000
163A166GLN0-0.066-0.03110.6620.0500.0500.0000.0000.0000.000
164A167GLU-1-0.882-0.91611.3250.6830.6830.0000.0000.0000.000
165A168PHE0-0.005-0.01412.992-0.086-0.0860.0000.0000.0000.000
166A169VAL00.0010.00615.1490.0280.0280.0000.0000.0000.000
167A170ILE0-0.034-0.00917.946-0.039-0.0390.0000.0000.0000.000
168A171ALA00.0160.00719.4640.0200.0200.0000.0000.0000.000
169A172THR0-0.012-0.01021.472-0.015-0.0150.0000.0000.0000.000
170A173HIS00.015-0.02721.6420.0080.0080.0000.0000.0000.000
171A174ASP-1-0.833-0.88521.7980.0450.0450.0000.0000.0000.000
172A175HIS10.7930.88820.604-0.067-0.0670.0000.0000.0000.000
173A176VAL00.0310.03715.9470.0350.0350.0000.0000.0000.000
174A177ALA00.0090.00912.845-0.015-0.0150.0000.0000.0000.000
175A178LEU00.0160.01012.033-0.033-0.0330.0000.0000.0000.000