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: KGY63

Calculation Name: 3HN2-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3HN2

Chain ID: A

ChEMBL ID:

UniProt ID: Q39SB2

Base Structure: X-ray

Registration Date: 2023-09-24

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 302
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -4316200.86549
FMO2-HF: Nuclear repulsion 4199953.415439
FMO2-HF: Total energy -116247.450052
FMO2-MP2: Total energy -116585.696696


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:2:ARG)


Summations of interaction energy for fragment #1(A:2:ARG)
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.
-275.497-264.69923.112-15.081-18.827-0.087
Interaction energy analysis for fragmet #1(A:2:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.951 / q_NPA : 0.979
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].
3A4ALA00.0740.0393.8032.8094.475-0.017-0.805-0.8450.002
4A5ILE0-0.075-0.0276.8420.6010.6010.0000.0000.0000.000
5A6VAL00.0710.02210.0741.3991.3990.0000.0000.0000.000
6A7GLY00.033-0.00513.2400.4290.4290.0000.0000.0000.000
7A8ALA0-0.0310.00415.0380.7120.7120.0000.0000.0000.000
8A9GLY00.0050.00716.2940.7900.7900.0000.0000.0000.000
9A10ALA0-0.018-0.02718.070-0.484-0.4840.0000.0000.0000.000
10A11LEU00.0380.02915.529-0.143-0.1430.0000.0000.0000.000
11A12GLY00.0150.00113.693-0.895-0.8950.0000.0000.0000.000
12A13LEU00.0040.00512.584-1.412-1.4120.0000.0000.0000.000
13A14TYR00.0360.02213.545-1.188-1.1880.0000.0000.0000.000
14A15TYR00.025-0.02911.653-0.322-0.3220.0000.0000.0000.000
15A16GLY00.0420.0288.949-1.919-1.9190.0000.0000.0000.000
16A17ALA00.000-0.0099.255-1.965-1.9650.0000.0000.0000.000
17A18LEU0-0.031-0.01811.737-0.537-0.5370.0000.0000.0000.000
18A19LEU00.0070.0046.046-0.815-0.8150.0000.0000.0000.000
19A20GLN00.0380.0186.635-3.692-3.6920.0000.0000.0000.000
20A21ARG10.8820.9627.70320.28120.2810.0000.0000.0000.000
21A22SER0-0.069-0.0338.1550.8950.8950.0000.0000.0000.000
22A23GLY0-0.0230.0045.785-1.640-1.6400.0000.0000.0000.000
23A24GLU-1-0.882-0.9491.799-89.461-86.9906.565-4.124-4.912-0.035
24A25ASP-1-0.923-0.9711.695-32.374-34.46210.495-3.708-4.6980.007
25A26VAL00.0000.0022.246-4.045-2.0102.689-2.292-2.432-0.040
26A27HIS0-0.018-0.0092.6412.2513.2610.538-0.585-0.9630.004
27A28PHE0-0.002-0.0136.7450.6440.6440.0000.0000.0000.000
28A29LEU00.0240.01810.2770.7540.7540.0000.0000.0000.000
29A30LEU0-0.046-0.01112.8290.5310.5310.0000.0000.0000.000
30A31ARG10.9690.97416.03212.11712.1170.0000.0000.0000.000
31A32ARG10.9030.93919.52710.87410.8740.0000.0000.0000.000
32A33ASP-1-0.837-0.92619.790-12.906-12.9060.0000.0000.0000.000
33A34TYR00.0060.01015.372-0.081-0.0810.0000.0000.0000.000
34A35GLU-1-0.929-0.97818.801-11.447-11.4470.0000.0000.0000.000
35A36ALA0-0.016-0.00521.5670.0740.0740.0000.0000.0000.000
36A37ILE0-0.011-0.01415.683-0.096-0.0960.0000.0000.0000.000
37A38ALA0-0.013-0.00117.062-0.577-0.5770.0000.0000.0000.000
38A39GLY0-0.045-0.00718.0530.0170.0170.0000.0000.0000.000
39A40ASN0-0.037-0.03220.9690.0610.0610.0000.0000.0000.000
40A41GLY00.0300.05617.021-0.321-0.3210.0000.0000.0000.000
41A42LEU0-0.053-0.03014.1450.6790.6790.0000.0000.0000.000
42A43LYS10.9320.95718.16411.70611.7060.0000.0000.0000.000
43A44VAL0-0.015-0.00616.3680.0980.0980.0000.0000.0000.000
44A45PHE0-0.0110.00219.7250.0270.0270.0000.0000.0000.000
45A46SER0-0.018-0.02520.654-0.454-0.4540.0000.0000.0000.000
46A47ILE00.0170.02423.0600.3510.3510.0000.0000.0000.000
47A48ASN0-0.074-0.03920.4770.7940.7940.0000.0000.0000.000
48A49GLY00.0010.00621.651-0.454-0.4540.0000.0000.0000.000
49A50ASP-1-0.808-0.90721.273-12.914-12.9140.0000.0000.0000.000
50A51PHE0-0.065-0.04014.343-0.299-0.2990.0000.0000.0000.000
51A52THR00.005-0.00318.9860.3580.3580.0000.0000.0000.000
52A53LEU0-0.029-0.00412.430-0.474-0.4740.0000.0000.0000.000
53A54PRO0-0.014-0.00915.8140.4450.4450.0000.0000.0000.000
54A55HIS00.0480.02411.2771.4531.4530.0000.0000.0000.000
55A56VAL00.009-0.00511.564-1.279-1.2790.0000.0000.0000.000
56A57LYS10.8920.9625.98631.38331.3830.0000.0000.0000.000
57A58GLY00.0110.0169.818-0.711-0.7110.0000.0000.0000.000
58A59TYR0-0.0010.0008.560-0.279-0.2790.0000.0000.0000.000
59A60ARG10.9300.95613.46412.92612.9260.0000.0000.0000.000
60A61ALA0-0.0110.00915.5780.5210.5210.0000.0000.0000.000
61A62PRO00.0360.01212.549-0.722-0.7220.0000.0000.0000.000
62A63GLU-1-0.904-0.97412.103-14.912-14.9120.0000.0000.0000.000
63A64GLU-1-0.955-0.98413.339-14.957-14.9570.0000.0000.0000.000
64A65ILE0-0.077-0.0267.176-0.436-0.4360.0000.0000.0000.000
65A66GLY00.0150.0238.380-0.863-0.8630.0000.0000.0000.000
66A67PRO00.000-0.0147.681-0.703-0.7030.0000.0000.0000.000
67A68MET0-0.0210.0073.646-2.580-1.7790.044-0.240-0.6040.000
68A69ASP-1-0.888-0.9282.302-57.179-53.1532.779-3.026-3.780-0.026
69A70LEU0-0.047-0.0343.7754.1704.7910.003-0.243-0.3800.001
70A71VAL00.0060.0075.514-0.512-0.576-0.001-0.0070.0730.000
71A72LEU00.0240.0098.0201.6091.6090.0000.0000.0000.000
72A73VAL00.0100.00610.4810.9060.9060.0000.0000.0000.000
73A74GLY0-0.020-0.03313.9170.2770.2770.0000.0000.0000.000
74A75LEU0-0.063-0.03216.0190.7370.7370.0000.0000.0000.000
75A76LYS10.9590.99618.77512.15012.1500.0000.0000.0000.000
76A77THR00.001-0.02422.4300.2060.2060.0000.0000.0000.000
77A78PHE0-0.0070.00123.8900.1160.1160.0000.0000.0000.000
78A79ALA0-0.066-0.03222.0220.2920.2920.0000.0000.0000.000
79A80ASN00.0670.01621.563-0.650-0.6500.0000.0000.0000.000
80A81SER0-0.030-0.00522.439-0.225-0.2250.0000.0000.0000.000
81A82ARG10.9010.95320.92711.82611.8260.0000.0000.0000.000
82A83TYR0-0.004-0.03618.046-0.380-0.3800.0000.0000.0000.000
83A84GLU-1-0.963-0.97817.302-12.662-12.6620.0000.0000.0000.000
84A85GLU-1-0.889-0.95917.728-12.610-12.6100.0000.0000.0000.000
85A86LEU0-0.048-0.03015.763-0.354-0.3540.0000.0000.0000.000
86A87ILE00.0080.00411.875-0.813-0.8130.0000.0000.0000.000
87A88ARG10.9740.99312.36413.00113.0010.0000.0000.0000.000
88A89PRO0-0.013-0.01012.905-0.285-0.2850.0000.0000.0000.000
89A90LEU0-0.0140.0048.269-0.450-0.4500.0000.0000.0000.000
90A91VAL0-0.099-0.0418.170-1.769-1.7690.0000.0000.0000.000
91A92GLU-1-0.835-0.9128.764-17.392-17.3920.0000.0000.0000.000
92A93GLU-1-1.029-1.03110.594-17.728-17.7280.0000.0000.0000.000
93A94GLY00.0190.01110.054-0.681-0.6810.0000.0000.0000.000
94A95THR0-0.052-0.0106.737-0.931-0.9310.0000.0000.0000.000
95A96GLN0-0.006-0.0127.5234.4224.4220.0000.0000.0000.000
96A97ILE0-0.014-0.0158.724-1.599-1.5990.0000.0000.0000.000
97A98LEU00.0000.01210.0341.0261.0260.0000.0000.0000.000
98A99THR0-0.0010.00812.1100.0890.0890.0000.0000.0000.000
99A100LEU00.011-0.01013.1890.2570.2570.0000.0000.0000.000
100A101GLN0-0.0240.01216.8300.5670.5670.0000.0000.0000.000
101A102ASN00.0210.01219.826-0.260-0.2600.0000.0000.0000.000
102A103GLY00.0050.00623.4520.1470.1470.0000.0000.0000.000
103A104LEU00.0160.00124.607-0.407-0.4070.0000.0000.0000.000
104A105GLY00.0100.01225.2880.0490.0490.0000.0000.0000.000
105A106ASN00.002-0.00720.2300.1830.1830.0000.0000.0000.000
106A107GLU-1-0.823-0.92618.676-14.352-14.3520.0000.0000.0000.000
107A108GLU-1-0.853-0.93920.095-12.105-12.1050.0000.0000.0000.000
108A109ALA0-0.0250.00821.9410.1290.1290.0000.0000.0000.000
109A110LEU00.0230.00615.9040.0350.0350.0000.0000.0000.000
110A111ALA00.0010.00918.165-0.386-0.3860.0000.0000.0000.000
111A112THR0-0.078-0.05319.9120.2420.2420.0000.0000.0000.000
112A113LEU0-0.080-0.03518.8170.1850.1850.0000.0000.0000.000
113A114PHE0-0.042-0.02915.313-0.105-0.1050.0000.0000.0000.000
114A115GLY00.0590.03217.460-0.081-0.0810.0000.0000.0000.000
115A116ALA00.0260.00117.189-0.653-0.6530.0000.0000.0000.000
116A117GLU-1-0.893-0.94316.694-14.778-14.7780.0000.0000.0000.000
117A118ARG10.8960.96711.66017.50117.5010.0000.0000.0000.000
118A119ILE0-0.068-0.00812.811-1.327-1.3270.0000.0000.0000.000
119A120ILE00.0120.00211.0440.4490.4490.0000.0000.0000.000
120A121GLY00.0180.00714.648-0.100-0.1000.0000.0000.0000.000
121A122GLY00.0330.00215.962-0.272-0.2720.0000.0000.0000.000
122A123VAL0-0.035-0.00416.8700.3670.3670.0000.0000.0000.000
123A124ALA00.0550.02517.543-0.210-0.2100.0000.0000.0000.000
124A125PHE0-0.052-0.03619.5970.7080.7080.0000.0000.0000.000
125A126LEU00.015-0.00118.131-0.252-0.2520.0000.0000.0000.000
126A127CYS0-0.0180.02222.1610.4180.4180.0000.0000.0000.000
127A128SER00.023-0.00821.661-0.387-0.3870.0000.0000.0000.000
128A129ASN00.0210.03923.6260.0540.0540.0000.0000.0000.000
129A130ARG10.9240.93121.27112.37612.3760.0000.0000.0000.000
130A131GLY0-0.051-0.03123.7570.3630.3630.0000.0000.0000.000
131A132GLU-1-0.818-0.89624.732-9.664-9.6640.0000.0000.0000.000
132A133PRO0-0.119-0.06723.158-0.337-0.3370.0000.0000.0000.000
133A134GLY00.0520.03819.652-0.063-0.0630.0000.0000.0000.000
134A135GLU-1-0.908-0.94720.657-11.843-11.8430.0000.0000.0000.000
135A136VAL0-0.064-0.04317.3480.1890.1890.0000.0000.0000.000
136A137HIS00.0290.02420.746-0.032-0.0320.0000.0000.0000.000
137A138HIS0-0.087-0.05620.392-0.133-0.1330.0000.0000.0000.000
138A139LEU00.023-0.00622.5160.1440.1440.0000.0000.0000.000
139A140GLY00.0370.01324.2710.4360.4360.0000.0000.0000.000
140A141ALA0-0.036-0.02023.333-0.352-0.3520.0000.0000.0000.000
141A142GLY00.0580.03619.316-0.337-0.3370.0000.0000.0000.000
142A143ARG10.9561.01417.92611.98811.9880.0000.0000.0000.000
143A144ILE00.009-0.00213.9550.4420.4420.0000.0000.0000.000
144A145ILE0-0.034-0.01617.762-0.060-0.0600.0000.0000.0000.000
145A146LEU0-0.013-0.00312.2100.2360.2360.0000.0000.0000.000
146A147GLY00.0500.01216.4910.4940.4940.0000.0000.0000.000
147A148GLU-1-0.842-0.93016.447-16.960-16.9600.0000.0000.0000.000
148A149PHE0-0.039-0.02017.7230.8860.8860.0000.0000.0000.000
149A150LEU0-0.007-0.00919.0710.7800.7800.0000.0000.0000.000
150A151PRO0-0.031-0.00119.377-0.624-0.6240.0000.0000.0000.000
151A152ARG10.8830.94319.64513.41613.4160.0000.0000.0000.000
152A153ASP-1-0.862-0.92116.824-16.966-16.9660.0000.0000.0000.000
153A154THR0-0.008-0.02017.265-0.082-0.0820.0000.0000.0000.000
154A155GLY00.0530.03314.500-0.712-0.7120.0000.0000.0000.000
155A156ARG10.9770.97411.35017.74517.7450.0000.0000.0000.000
156A157ILE00.0000.00411.100-1.615-1.6150.0000.0000.0000.000
157A158GLU-1-0.946-0.99713.019-18.213-18.2130.0000.0000.0000.000
158A159GLU-1-0.969-0.9838.472-29.577-29.5770.0000.0000.0000.000
159A160LEU00.0050.0036.937-2.684-2.6840.0000.0000.0000.000
160A161ALA0-0.004-0.0109.226-0.278-0.2780.0000.0000.0000.000
161A162ALA0-0.066-0.03810.5580.6330.6330.0000.0000.0000.000
162A163MET00.0170.0173.2531.5301.8500.017-0.051-0.2860.000
163A164PHE00.022-0.0048.288-0.268-0.2680.0000.0000.0000.000
164A165ARG10.8810.94010.70520.68220.6820.0000.0000.0000.000
165A166GLN0-0.047-0.0199.3830.6150.6150.0000.0000.0000.000
166A167ALA0-0.0100.0159.1200.4490.4490.0000.0000.0000.000
167A168GLY0-0.049-0.01910.9681.3911.3910.0000.0000.0000.000
168A169VAL0-0.051-0.02212.9161.4981.4980.0000.0000.0000.000
169A170ASP-1-0.944-0.97115.149-15.265-15.2650.0000.0000.0000.000
170A171CYS00.0070.01414.3000.1390.1390.0000.0000.0000.000
171A172ARG10.9170.96216.42714.79214.7920.0000.0000.0000.000
172A173THR00.011-0.01516.356-1.055-1.0550.0000.0000.0000.000
173A174THR0-0.059-0.02518.6980.8160.8160.0000.0000.0000.000
174A175ASP-1-0.829-0.90420.650-13.563-13.5630.0000.0000.0000.000
175A176ASP-1-0.889-0.96223.178-10.717-10.7170.0000.0000.0000.000
176A177LEU0-0.017-0.00119.4280.1430.1430.0000.0000.0000.000
177A178LYS10.9590.97722.72810.64810.6480.0000.0000.0000.000
178A179ARG10.8570.92925.71710.21010.2100.0000.0000.0000.000
179A180ALA00.0570.03523.2890.2210.2210.0000.0000.0000.000
180A181ARG10.8000.90219.24513.97713.9770.0000.0000.0000.000
181A182TRP00.012-0.00925.3970.2840.2840.0000.0000.0000.000
182A183GLU-1-0.879-0.93627.090-10.642-10.6420.0000.0000.0000.000
183A184LYS10.8930.96222.80212.71312.7130.0000.0000.0000.000
184A185LEU0-0.010-0.00727.6610.1510.1510.0000.0000.0000.000
185A186VAL00.0010.00730.1610.3180.3180.0000.0000.0000.000
186A187TRP00.015-0.00629.2340.0910.0910.0000.0000.0000.000
187A188ASN0-0.004-0.04626.2960.1730.1730.0000.0000.0000.000
188A189ILE00.0020.01830.5620.1260.1260.0000.0000.0000.000
189A190PRO0-0.015-0.00233.7060.1880.1880.0000.0000.0000.000
190A191PHE00.0320.00933.0630.2080.2080.0000.0000.0000.000
191A192ASN00.0380.00129.089-0.143-0.1430.0000.0000.0000.000
192A193GLY00.0420.02932.5280.0400.0400.0000.0000.0000.000
193A194LEU0-0.025-0.02835.7190.1710.1710.0000.0000.0000.000
194A195CYS0-0.0410.00135.0120.1820.1820.0000.0000.0000.000
195A196ALA00.0610.04434.2050.0870.0870.0000.0000.0000.000
196A197LEU0-0.0260.00136.2190.1480.1480.0000.0000.0000.000
197A198LEU0-0.066-0.05039.6590.1930.1930.0000.0000.0000.000
198A199GLN0-0.033-0.00738.5070.0240.0240.0000.0000.0000.000
199A200GLN0-0.057-0.01839.0260.1330.1330.0000.0000.0000.000
200A201PRO00.0950.05136.438-0.140-0.1400.0000.0000.0000.000
201A202VAL00.010-0.01333.8910.2160.2160.0000.0000.0000.000
202A203ASN00.0470.02137.1040.0250.0250.0000.0000.0000.000
203A204LEU0-0.024-0.00539.8000.2170.2170.0000.0000.0000.000
204A205ILE0-0.0070.00438.7910.1960.1960.0000.0000.0000.000
205A206LEU0-0.013-0.01837.7150.1500.1500.0000.0000.0000.000
206A207ALA0-0.0050.02341.9590.1110.1110.0000.0000.0000.000
207A208ARG10.9570.98045.1676.5076.5070.0000.0000.0000.000
208A209ASP-1-0.798-0.89946.620-6.261-6.2610.0000.0000.0000.000
209A210VAL0-0.060-0.05748.002-0.101-0.1010.0000.0000.0000.000
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