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: 5J7KZ

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 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 302
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -4334631.288545
FMO2-HF: Nuclear repulsion 4218381.170932
FMO2-HF: Total energy -116250.117613
FMO2-MP2: Total energy -116588.491453


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.
-292.11-287.29532.242-16.593-20.466-0.157
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 : 0.894 / q_NPA : 0.946
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].
3A4ALA00.0650.0353.8783.0944.429-0.011-0.630-0.6940.002
4A5ILE0-0.056-0.0176.2380.6100.6100.0000.0000.0000.000
5A6VAL00.0560.0259.9591.2261.2260.0000.0000.0000.000
6A7GLY00.031-0.01012.6620.4860.4860.0000.0000.0000.000
7A8ALA0-0.036-0.00815.0480.8130.8130.0000.0000.0000.000
8A9GLY00.0310.01916.6400.7200.7200.0000.0000.0000.000
9A10ALA0-0.001-0.00717.910-0.672-0.6720.0000.0000.0000.000
10A11LEU00.0670.02716.332-0.463-0.4630.0000.0000.0000.000
11A12GLY00.0070.00814.289-0.892-0.8920.0000.0000.0000.000
12A13LEU0-0.006-0.00913.166-1.343-1.3430.0000.0000.0000.000
13A14TYR00.0090.00914.127-1.082-1.0820.0000.0000.0000.000
14A15TYR00.016-0.02812.244-0.511-0.5110.0000.0000.0000.000
15A16GLY00.0370.0229.367-1.856-1.8560.0000.0000.0000.000
16A17ALA00.010-0.0039.631-1.715-1.7150.0000.0000.0000.000
17A18LEU0-0.021-0.01811.914-0.605-0.6050.0000.0000.0000.000
18A19LEU00.0140.0186.636-0.929-0.9290.0000.0000.0000.000
19A20GLN00.0330.0067.272-2.390-2.3900.0000.0000.0000.000
20A21ARG10.8510.9468.27120.32220.3220.0000.0000.0000.000
21A22SER0-0.061-0.0337.8112.0672.0670.0000.0000.0000.000
22A23GLY0-0.035-0.0117.036-1.465-1.4650.0000.0000.0000.000
23A24GLU-1-0.848-0.9181.687-111.375-115.99819.286-7.656-7.007-0.102
24A25ASP-1-0.841-0.9202.079-29.401-28.4453.039-1.324-2.671-0.002
25A26VAL0-0.034-0.0112.630-0.4251.3760.897-1.204-1.495-0.016
26A27HIS00.0090.0102.6150.6021.6011.251-0.962-1.2890.003
27A28PHE0-0.001-0.0156.5080.5520.5520.0000.0000.0000.000
28A29LEU00.0360.02710.1410.7690.7690.0000.0000.0000.000
29A30LEU0-0.054-0.01212.2060.6630.6630.0000.0000.0000.000
30A31ARG10.9600.95915.63612.18812.1880.0000.0000.0000.000
31A32ARG10.9310.96219.04010.86210.8620.0000.0000.0000.000
32A33ASP-1-0.778-0.89520.378-12.918-12.9180.0000.0000.0000.000
33A34TYR00.0200.02114.784-0.006-0.0060.0000.0000.0000.000
34A35GLU-1-0.773-0.87618.530-12.447-12.4470.0000.0000.0000.000
35A36ALA0-0.052-0.01221.0890.1270.1270.0000.0000.0000.000
36A37ILE00.0340.01215.644-0.054-0.0540.0000.0000.0000.000
37A38ALA0-0.030-0.01617.149-0.393-0.3930.0000.0000.0000.000
38A39GLY0-0.0300.00118.0450.1050.1050.0000.0000.0000.000
39A40ASN0-0.090-0.05220.9280.5640.5640.0000.0000.0000.000
40A41GLY00.0240.04017.326-0.120-0.1200.0000.0000.0000.000
41A42LEU0-0.053-0.03014.3080.5070.5070.0000.0000.0000.000
42A43LYS10.8430.90518.39311.40011.4000.0000.0000.0000.000
43A44VAL0-0.004-0.00516.6010.0010.0010.0000.0000.0000.000
44A45PHE00.0070.01919.998-0.009-0.0090.0000.0000.0000.000
45A46SER00.017-0.03521.208-0.498-0.4980.0000.0000.0000.000
46A47ILE0-0.0320.00423.4910.2070.2070.0000.0000.0000.000
47A48ASN0-0.052-0.02520.4910.7330.7330.0000.0000.0000.000
48A49GLY0-0.0070.00222.555-0.243-0.2430.0000.0000.0000.000
49A50ASP-1-0.844-0.92321.691-12.486-12.4860.0000.0000.0000.000
50A51PHE0-0.065-0.03514.725-0.318-0.3180.0000.0000.0000.000
51A52THR00.007-0.00219.1130.3950.3950.0000.0000.0000.000
52A53LEU0-0.041-0.00812.825-0.508-0.5080.0000.0000.0000.000
53A54PRO0-0.001-0.01416.3370.1560.1560.0000.0000.0000.000
54A55HIS00.0230.01712.6861.0211.0210.0000.0000.0000.000
55A56VAL00.0290.01312.060-0.964-0.9640.0000.0000.0000.000
56A57LYS10.8060.8925.12232.29232.2920.0000.0000.0000.000
57A58GLY0-0.008-0.0029.640-0.713-0.7130.0000.0000.0000.000
58A59TYR0-0.011-0.0067.809-0.218-0.2180.0000.0000.0000.000
59A60ARG10.7730.84112.48713.13213.1320.0000.0000.0000.000
60A61ALA0-0.031-0.01014.1230.7460.7460.0000.0000.0000.000
61A62PRO00.0360.02211.216-0.751-0.7510.0000.0000.0000.000
62A63GLU-1-0.870-0.96210.434-16.150-16.1500.0000.0000.0000.000
63A64GLU-1-0.891-0.94111.684-15.850-15.8500.0000.0000.0000.000
64A65ILE0-0.100-0.0365.588-0.487-0.4870.0000.0000.0000.000
65A66GLY00.0160.0216.667-1.434-1.4340.0000.0000.0000.000
66A67PRO0-0.005-0.0196.690-1.345-1.3450.0000.0000.0000.000
67A68MET0-0.0350.0102.579-6.265-5.4741.925-0.607-2.109-0.007
68A69ASP-1-0.876-0.9242.200-58.996-55.9355.855-4.054-4.861-0.035
69A70LEU0-0.045-0.0293.9535.2655.6430.001-0.132-0.2470.000
70A71VAL00.0100.0105.599-1.153-1.220-0.001-0.0080.0760.000
71A72LEU00.0150.0108.1421.7691.7690.0000.0000.0000.000
72A73VAL00.0020.00410.9370.9270.9270.0000.0000.0000.000
73A74GLY00.028-0.00514.1120.4250.4250.0000.0000.0000.000
74A75LEU0-0.052-0.01916.5520.6600.6600.0000.0000.0000.000
75A76LYS10.8150.91718.72011.46111.4610.0000.0000.0000.000
76A77THR00.011-0.02322.4800.2760.2760.0000.0000.0000.000
77A78PHE0-0.021-0.00623.8900.0210.0210.0000.0000.0000.000
78A79ALA0-0.042-0.02221.5500.2560.2560.0000.0000.0000.000
79A80ASN00.0590.02721.108-0.635-0.6350.0000.0000.0000.000
80A81SER0-0.041-0.01221.907-0.297-0.2970.0000.0000.0000.000
81A82ARG10.8030.87619.80512.32112.3210.0000.0000.0000.000
82A83TYR00.003-0.03317.682-0.333-0.3330.0000.0000.0000.000
83A84GLU-1-0.845-0.89616.882-13.891-13.8910.0000.0000.0000.000
84A85GLU-1-0.765-0.87016.945-13.016-13.0160.0000.0000.0000.000
85A86LEU0-0.064-0.04015.087-0.465-0.4650.0000.0000.0000.000
86A87ILE00.0040.00311.817-0.963-0.9630.0000.0000.0000.000
87A88ARG10.8390.91412.23713.32713.3270.0000.0000.0000.000
88A89PRO0-0.029-0.01911.745-0.377-0.3770.0000.0000.0000.000
89A90LEU0-0.028-0.0027.569-0.651-0.6510.0000.0000.0000.000
90A91VAL0-0.062-0.0307.894-2.230-2.2300.0000.0000.0000.000
91A92GLU-1-0.828-0.9018.830-17.949-17.9490.0000.0000.0000.000
92A93GLU-1-1.019-1.01610.655-17.670-17.6700.0000.0000.0000.000
93A94GLY0-0.0020.0029.522-1.016-1.0160.0000.0000.0000.000
94A95THR0-0.063-0.0256.750-0.276-0.2760.0000.0000.0000.000
95A96GLN00.0160.0047.9994.9594.9590.0000.0000.0000.000
96A97ILE0-0.008-0.0158.933-1.696-1.6960.0000.0000.0000.000
97A98LEU00.0170.01110.8840.9970.9970.0000.0000.0000.000
98A99THR0-0.038-0.01612.6880.0870.0870.0000.0000.0000.000
99A100LEU00.003-0.00713.1550.2340.2340.0000.0000.0000.000
100A101GLN0-0.0350.01017.2390.2770.2770.0000.0000.0000.000
101A102ASN0-0.009-0.01420.365-0.066-0.0660.0000.0000.0000.000
102A103GLY00.0300.00724.047-0.055-0.0550.0000.0000.0000.000
103A104LEU0-0.0010.00725.218-0.382-0.3820.0000.0000.0000.000
104A105GLY00.0300.01025.3950.1560.1560.0000.0000.0000.000
105A106ASN0-0.034-0.01120.1680.0400.0400.0000.0000.0000.000
106A107GLU-1-0.701-0.85518.822-14.457-14.4570.0000.0000.0000.000
107A108GLU-1-0.809-0.87620.476-11.889-11.8890.0000.0000.0000.000
108A109ALA0-0.0150.00422.2420.0800.0800.0000.0000.0000.000
109A110LEU00.001-0.00615.770-0.123-0.1230.0000.0000.0000.000
110A111ALA00.0080.00718.114-0.341-0.3410.0000.0000.0000.000
111A112THR0-0.085-0.05819.7240.2160.2160.0000.0000.0000.000
112A113LEU0-0.030-0.01018.5240.3010.3010.0000.0000.0000.000
113A114PHE0-0.040-0.02414.884-0.167-0.1670.0000.0000.0000.000
114A115GLY00.0290.04116.442-0.508-0.5080.0000.0000.0000.000
115A116ALA00.022-0.00517.473-0.452-0.4520.0000.0000.0000.000
116A117GLU-1-0.826-0.93016.398-15.789-15.7890.0000.0000.0000.000
117A118ARG10.8510.91711.79118.09618.0960.0000.0000.0000.000
118A119ILE0-0.059-0.00713.355-1.268-1.2680.0000.0000.0000.000
119A120ILE0-0.021-0.01011.5620.5420.5420.0000.0000.0000.000
120A121GLY00.0270.02115.304-0.059-0.0590.0000.0000.0000.000
121A122GLY00.023-0.01616.272-0.390-0.3900.0000.0000.0000.000
122A123VAL0-0.038-0.01017.2120.2490.2490.0000.0000.0000.000
123A124ALA00.0190.00617.8790.1630.1630.0000.0000.0000.000
124A125PHE0-0.032-0.02319.8180.7020.7020.0000.0000.0000.000
125A126LEU0-0.0060.00518.800-0.224-0.2240.0000.0000.0000.000
126A127CYS0-0.0170.01822.5500.3640.3640.0000.0000.0000.000
127A128SER00.030-0.00422.106-0.352-0.3520.0000.0000.0000.000
128A129ASN0-0.0170.00424.1280.0840.0840.0000.0000.0000.000
129A130ARG10.8740.92020.74512.60812.6080.0000.0000.0000.000
130A131GLY00.0290.01024.2740.4010.4010.0000.0000.0000.000
131A132GLU-1-0.888-0.92626.269-9.870-9.8700.0000.0000.0000.000
132A133PRO0-0.087-0.06023.478-0.541-0.5410.0000.0000.0000.000
133A134GLY00.0510.02920.0060.0740.0740.0000.0000.0000.000
134A135GLU-1-0.864-0.91220.564-11.818-11.8180.0000.0000.0000.000
135A136VAL0-0.056-0.03717.6650.1110.1110.0000.0000.0000.000
136A137HIS0-0.005-0.00121.1050.0760.0760.0000.0000.0000.000
137A138HIS0-0.056-0.01421.285-0.037-0.0370.0000.0000.0000.000
138A139LEU00.014-0.00823.4080.1830.1830.0000.0000.0000.000
139A140GLY00.0440.01125.2270.4300.4300.0000.0000.0000.000
140A141ALA0-0.026-0.01124.137-0.376-0.3760.0000.0000.0000.000
141A142GLY00.0400.02020.074-0.192-0.1920.0000.0000.0000.000
142A143ARG10.9421.00918.41612.01012.0100.0000.0000.0000.000
143A144ILE00.007-0.00514.3050.3810.3810.0000.0000.0000.000
144A145ILE0-0.034-0.00718.3080.0660.0660.0000.0000.0000.000
145A146LEU00.0080.00512.8010.1800.1800.0000.0000.0000.000
146A147GLY00.0580.01517.2070.6900.6900.0000.0000.0000.000
147A148GLU-1-0.795-0.88016.814-16.906-16.9060.0000.0000.0000.000
148A149PHE0-0.030-0.02018.2130.9010.9010.0000.0000.0000.000
149A150LEU0-0.0140.00019.4230.8130.8130.0000.0000.0000.000
150A151PRO0-0.020-0.01319.695-0.676-0.6760.0000.0000.0000.000
151A152ARG10.7890.84619.65114.65514.6550.0000.0000.0000.000
152A153ASP-1-0.774-0.84417.714-15.881-15.8810.0000.0000.0000.000
153A154THR0-0.007-0.01417.182-0.924-0.9240.0000.0000.0000.000
154A155GLY0-0.0030.01115.535-0.567-0.5670.0000.0000.0000.000
155A156ARG10.9000.93411.80618.28518.2850.0000.0000.0000.000
156A157ILE0-0.0010.00811.808-1.266-1.2660.0000.0000.0000.000
157A158GLU-1-0.707-0.83213.523-18.108-18.1080.0000.0000.0000.000
158A159GLU-1-0.927-0.9599.418-27.830-27.8300.0000.0000.0000.000
159A160LEU00.0220.0127.544-2.243-2.2430.0000.0000.0000.000
160A161ALA00.007-0.0149.889-0.185-0.1850.0000.0000.0000.000
161A162ALA0-0.075-0.04010.6010.8120.8120.0000.0000.0000.000
162A163MET00.0110.0184.0101.8001.9840.000-0.016-0.1690.000
163A164PHE00.025-0.0058.3530.3560.3560.0000.0000.0000.000
164A165ARG10.7900.88211.33621.05521.0550.0000.0000.0000.000
165A166GLN0-0.048-0.0228.9210.9520.9520.0000.0000.0000.000
166A167ALA00.0170.0199.6430.6630.6630.0000.0000.0000.000
167A168GLY0-0.038-0.00911.1091.5111.5110.0000.0000.0000.000
168A169VAL0-0.065-0.03314.1431.3681.3680.0000.0000.0000.000
169A170ASP-1-0.906-0.96115.566-15.241-15.2410.0000.0000.0000.000
170A171CYS00.0120.02814.840-0.209-0.2090.0000.0000.0000.000
171A172ARG10.8080.90616.84915.26115.2610.0000.0000.0000.000
172A173THR00.019-0.02517.806-0.848-0.8480.0000.0000.0000.000
173A174THR0-0.060-0.02819.4920.8480.8480.0000.0000.0000.000
174A175ASP-1-0.889-0.93821.627-13.475-13.4750.0000.0000.0000.000
175A176ASP-1-0.821-0.91323.995-10.827-10.8270.0000.0000.0000.000
176A177LEU00.0040.00019.8380.1820.1820.0000.0000.0000.000
177A178LYS10.9120.97623.29310.62510.6250.0000.0000.0000.000
178A179ARG10.8230.87426.41610.22310.2230.0000.0000.0000.000
179A180ALA00.0420.02623.9490.1730.1730.0000.0000.0000.000
180A181ARG10.7330.83820.08813.70313.7030.0000.0000.0000.000
181A182TRP00.0200.00025.7860.2960.2960.0000.0000.0000.000
182A183GLU-1-0.830-0.90928.083-10.367-10.3670.0000.0000.0000.000
183A184LYS10.8840.97123.10712.89812.8980.0000.0000.0000.000
184A185LEU0-0.003-0.00427.8380.2290.2290.0000.0000.0000.000
185A186VAL0-0.0010.00630.3990.2890.2890.0000.0000.0000.000
186A187TRP00.0330.01829.0540.1000.1000.0000.0000.0000.000
187A188ASN0-0.050-0.04727.858-0.081-0.0810.0000.0000.0000.000
188A189ILE00.0250.01330.9480.1080.1080.0000.0000.0000.000
189A190PRO00.0030.00333.9410.1890.1890.0000.0000.0000.000
190A191PHE00.0480.02133.6710.2340.2340.0000.0000.0000.000
191A192ASN00.021-0.00129.652-0.035-0.0350.0000.0000.0000.000
192A193GLY00.0510.02833.3180.0570.0570.0000.0000.0000.000
193A194LEU0-0.017-0.02436.4310.1830.1830.0000.0000.0000.000
194A195CYS0-0.056-0.00935.5380.1310.1310.0000.0000.0000.000
195A196ALA00.0270.01934.5570.0880.0880.0000.0000.0000.000
196A197LEU0-0.036-0.01236.5840.1480.1480.0000.0000.0000.000
197A198LEU0-0.036-0.03540.0780.1860.1860.0000.0000.0000.000
198A199GLN0-0.054-0.01238.8600.1420.1420.0000.0000.0000.000
199A200GLN0-0.039-0.01839.3980.2290.2290.0000.0000.0000.000
200A201PRO00.0940.06036.883-0.105-0.1050.0000.0000.0000.000
201A202VAL00.012-0.00534.6550.2110.2110.0000.0000.0000.000
202A203ASN0-0.008-0.02237.7530.0890.0890.0000.0000.0000.000
203A204LEU0-0.003-0.00440.4460.2280.2280.0000.0000.0000.000
204A205ILE0-0.056-0.02240.0570.2050.2050.0000.0000.0000.000
205A206LEU0-0.013-0.01538.1450.1490.1490.0000.0000.0000.000
206A207ALA00.0040.01942.4930.1170.1170.0000.0000.0000.000
207A208ARG10.9440.98045.6926.6036.6030.0000.0000.0000.000
208A209ASP-1-0.815-0.90247.067-6.265-6.2650.0000.0000.0000.000
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