Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 6YNMZ

Calculation Name: 3H8N-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3H8N

Chain ID: A

ChEMBL ID:

UniProt ID: P43632

Base Structure: X-ray

Registration Date: 2023-09-21

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 193
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1985664.082218
FMO2-HF: Nuclear repulsion 1909302.717954
FMO2-HF: Total energy -76361.364263
FMO2-MP2: Total energy -76581.313428


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:6:ARG)


Summations of interaction energy for fragment #1(A:6: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.
-101.485-92.7776.86-4.54-11.032-0.03
Interaction energy analysis for fragmet #1(A:6:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.953 / q_NPA : 0.969
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].
3A8PRO0-0.013-0.0013.868-1.1960.229-0.012-0.612-0.8020.001
4A9SER0-0.0060.0126.7612.1862.1860.0000.0000.0000.000
5A10PHE0-0.046-0.0388.554-0.563-0.5630.0000.0000.0000.000
6A11LEU00.0160.01111.8320.9370.9370.0000.0000.0000.000
7A12ALA00.0250.01015.380-0.250-0.2500.0000.0000.0000.000
8A13LEU0-0.0300.00419.0500.3920.3920.0000.0000.0000.000
9A14PRO00.0510.00221.937-0.013-0.0130.0000.0000.0000.000
10A15GLY00.0330.01421.703-0.065-0.0650.0000.0000.0000.000
11A16HIS10.7860.85620.27612.54312.5430.0000.0000.0000.000
12A17LEU0-0.045-0.00122.0970.0990.0990.0000.0000.0000.000
13A18VAL00.0250.01225.7040.0310.0310.0000.0000.0000.000
14A19LYS10.8730.94028.1278.6748.6740.0000.0000.0000.000
15A20SER00.033-0.00331.347-0.268-0.2680.0000.0000.0000.000
16A21GLU-1-1.007-1.00232.569-8.436-8.4360.0000.0000.0000.000
17A22GLU-1-0.871-0.91130.273-9.938-9.9380.0000.0000.0000.000
18A23THR0-0.030-0.02726.837-0.098-0.0980.0000.0000.0000.000
19A24VAL0-0.0270.00022.2910.0830.0830.0000.0000.0000.000
20A25ILE0-0.014-0.00819.594-0.315-0.3150.0000.0000.0000.000
21A26LEU00.020-0.00317.188-0.135-0.1350.0000.0000.0000.000
22A27GLN00.0040.00515.147-0.974-0.9740.0000.0000.0000.000
23A28CYS0-0.064-0.02010.4440.4510.4510.0000.0000.0000.000
24A29TRP00.018-0.00210.0380.4140.4140.0000.0000.0000.000
25A30SER0-0.011-0.0185.542-3.530-3.5300.0000.0000.0000.000
26A31ASP-1-0.845-0.9097.037-26.559-26.5590.0000.0000.0000.000
27A32VAL0-0.082-0.0313.143-0.663-0.0150.033-0.141-0.540-0.001
28A33MET00.0150.0036.414-0.653-0.6530.0000.0000.0000.000
29A34PHE0-0.024-0.0072.081-8.423-7.1421.617-0.959-1.939-0.003
30A35GLU-1-0.797-0.8706.832-24.496-24.4960.0000.0000.0000.000
31A36HIS10.7290.8367.93929.04329.0430.0000.0000.0000.000
32A37PHE00.0340.0107.078-5.700-5.7000.0000.0000.0000.000
33A38LEU0-0.041-0.0258.7693.0133.0130.0000.0000.0000.000
34A39LEU00.0290.02510.479-1.419-1.4190.0000.0000.0000.000
35A40HIS0-0.048-0.05013.2270.9510.9510.0000.0000.0000.000
36A41ARG10.8390.94214.82613.61513.6150.0000.0000.0000.000
37A42GLU-1-0.820-0.90814.584-18.736-18.7360.0000.0000.0000.000
38A43GLY00.0300.00018.8440.6080.6080.0000.0000.0000.000
39A44LYS10.9230.94422.53510.47910.4790.0000.0000.0000.000
40A45PHE00.0240.01224.864-0.012-0.0120.0000.0000.0000.000
41A46ASN00.0210.03719.3500.4570.4570.0000.0000.0000.000
42A47ASN00.016-0.00119.2970.3640.3640.0000.0000.0000.000
43A48THR0-0.017-0.00213.464-0.615-0.6150.0000.0000.0000.000
44A49LEU0-0.0080.01515.1670.8900.8900.0000.0000.0000.000
45A50HIS00.0580.02611.440-2.386-2.3860.0000.0000.0000.000
46A51LEU0-0.012-0.00412.5831.5091.5090.0000.0000.0000.000
47A52ILE00.0020.00312.011-2.031-2.0310.0000.0000.0000.000
48A53GLY0-0.033-0.02011.8961.1801.1800.0000.0000.0000.000
49A54GLU-1-0.846-0.91411.514-22.151-22.1510.0000.0000.0000.000
50A55HIS00.0460.01210.245-2.324-2.3240.0000.0000.0000.000
51A56HIS0-0.095-0.04613.8201.9961.9960.0000.0000.0000.000
52A57ASP-1-0.898-0.95115.591-19.000-19.0000.0000.0000.0000.000
53A58GLY0-0.0040.00414.1021.0611.0610.0000.0000.0000.000
54A59VAL0-0.047-0.02411.598-1.266-1.2660.0000.0000.0000.000
55A60SER00.0280.0138.8980.7030.7030.0000.0000.0000.000
56A61LYS10.8620.90910.95817.90017.9000.0000.0000.0000.000
57A62ALA00.0260.02912.2140.5690.5690.0000.0000.0000.000
58A63ASN0-0.002-0.01213.8920.0980.0980.0000.0000.0000.000
59A64PHE00.0300.01012.5220.6650.6650.0000.0000.0000.000
60A65SER0-0.0040.00517.9620.3310.3310.0000.0000.0000.000
61A66ILE0-0.018-0.01219.638-0.199-0.1990.0000.0000.0000.000
62A67GLY00.0490.01723.2030.2550.2550.0000.0000.0000.000
63A68PRO00.008-0.00526.997-0.147-0.1470.0000.0000.0000.000
64A69MET0-0.0590.00425.482-0.219-0.2190.0000.0000.0000.000
65A70MET00.0500.01028.6000.4900.4900.0000.0000.0000.000
66A71PRO00.0640.02228.667-0.443-0.4430.0000.0000.0000.000
67A72VAL0-0.040-0.01127.211-0.308-0.3080.0000.0000.0000.000
68A73LEU0-0.048-0.02224.000-0.514-0.5140.0000.0000.0000.000
69A74ALA00.0180.03824.123-0.536-0.5360.0000.0000.0000.000
70A75GLY00.015-0.00522.789-0.012-0.0120.0000.0000.0000.000
71A76THR0-0.009-0.01417.1530.0030.0030.0000.0000.0000.000
72A77TYR0-0.036-0.03616.559-0.397-0.3970.0000.0000.0000.000
73A78ARG10.8220.89911.08620.86320.8630.0000.0000.0000.000
74A80TYR00.0260.0136.382-1.517-1.5170.0000.0000.0000.000
75A81GLY00.0590.0224.6185.5505.645-0.001-0.016-0.0780.000
76A82SER0-0.049-0.0442.826-19.293-17.2610.135-1.185-0.982-0.014
77A83VAL00.0850.0494.4354.0124.119-0.001-0.007-0.0990.000
78A84PRO0-0.028-0.0105.5884.5654.5650.0000.0000.0000.000
79A85HIS00.0310.0198.5080.1070.1070.0000.0000.0000.000
80A86SER00.0160.01410.618-1.484-1.4840.0000.0000.0000.000
81A87PRO0-0.014-0.01211.6631.0191.0190.0000.0000.0000.000
82A88TYR0-0.018-0.0207.508-0.245-0.2450.0000.0000.0000.000
83A89GLN0-0.021-0.0214.565-1.210-1.127-0.001-0.004-0.0780.000
84A90LEU0-0.041-0.0113.082-14.835-13.5330.041-0.671-0.673-0.006
85A91SER0-0.035-0.0142.420-8.832-6.4093.651-2.350-3.725-0.005
86A92ALA0-0.001-0.0022.1059.8459.0731.3991.426-2.053-0.002
87A93PRO00.0340.0164.114-3.319-3.235-0.001-0.021-0.0630.000
88A94SER00.0010.0117.110-0.022-0.0220.0000.0000.0000.000
89A95ASP-1-0.815-0.8978.799-20.933-20.9330.0000.0000.0000.000
90A96PRO0-0.030-0.00410.837-0.537-0.5370.0000.0000.0000.000
91A97LEU0-0.003-0.00214.4620.7040.7040.0000.0000.0000.000
92A98ASP-1-0.836-0.90317.066-14.232-14.2320.0000.0000.0000.000
93A99MET0-0.0170.02518.9930.4820.4820.0000.0000.0000.000
94A100VAL0-0.009-0.01122.7980.2300.2300.0000.0000.0000.000
95A101ILE00.0230.03526.2860.0140.0140.0000.0000.0000.000
96A102ILE00.005-0.00228.9320.3340.3340.0000.0000.0000.000
97A103GLY0-0.056-0.05731.5020.0590.0590.0000.0000.0000.000
98A104LEU00.0070.00933.4080.1910.1910.0000.0000.0000.000
99A105TYR00.012-0.00335.1320.3240.3240.0000.0000.0000.000
100A106GLU-1-0.837-0.88939.026-7.017-7.0170.0000.0000.0000.000
101A107LYS10.8390.91138.9516.9636.9630.0000.0000.0000.000
102A108PRO0-0.040-0.01436.8260.1860.1860.0000.0000.0000.000
103A109SER0-0.0040.00340.112-0.009-0.0090.0000.0000.0000.000
104A110LEU0-0.007-0.01336.184-0.140-0.1400.0000.0000.0000.000
105A111SER0-0.028-0.00840.0680.1730.1730.0000.0000.0000.000
106A112ALA00.0350.00140.395-0.174-0.1740.0000.0000.0000.000
107A113GLN00.0050.03141.5430.2530.2530.0000.0000.0000.000
108A114PRO00.0450.00742.061-0.148-0.1480.0000.0000.0000.000
109A115GLY00.0290.00243.4630.1390.1390.0000.0000.0000.000
110A116PRO0-0.016-0.01240.986-0.118-0.1180.0000.0000.0000.000
111A117THR00.0040.00640.725-0.180-0.1800.0000.0000.0000.000
112A118VAL0-0.0030.01238.7800.1260.1260.0000.0000.0000.000
113A119GLN00.0460.02441.2640.0150.0150.0000.0000.0000.000
114A120ALA00.019-0.00337.938-0.100-0.1000.0000.0000.0000.000
115A121GLY0-0.015-0.00237.3510.1450.1450.0000.0000.0000.000
116A122GLU-1-0.898-0.94338.278-6.700-6.7000.0000.0000.0000.000
117A123ASN0-0.011-0.01636.869-0.368-0.3680.0000.0000.0000.000
118A124VAL0-0.0050.01037.6900.1700.1700.0000.0000.0000.000
119A125THR0-0.013-0.01637.263-0.261-0.2610.0000.0000.0000.000
120A126LEU0-0.0020.01034.6390.1530.1530.0000.0000.0000.000
121A127SER0-0.022-0.03237.530-0.125-0.1250.0000.0000.0000.000
122A128CYS0-0.061-0.02432.550-0.112-0.1120.0000.0000.0000.000
123A129SER00.018-0.02238.7750.0220.0220.0000.0000.0000.000
124A130SER00.0570.02141.4730.0150.0150.0000.0000.0000.000
125A131ARG10.8570.90443.4186.2576.2570.0000.0000.0000.000
126A132SER00.0250.00742.1400.0680.0680.0000.0000.0000.000
127A133SER0-0.047-0.02642.6540.0030.0030.0000.0000.0000.000
128A134TYR0-0.058-0.04137.538-0.156-0.1560.0000.0000.0000.000
129A135ASP-1-0.792-0.89735.970-8.049-8.0490.0000.0000.0000.000
130A136MET0-0.090-0.02931.154-0.123-0.1230.0000.0000.0000.000
131A137TYR00.001-0.01734.046-0.033-0.0330.0000.0000.0000.000
132A138HIS10.8400.90428.2119.6399.6390.0000.0000.0000.000
133A139LEU00.0040.01230.6570.1210.1210.0000.0000.0000.000
134A140SER0-0.001-0.00827.228-0.298-0.2980.0000.0000.0000.000
135A141ARG10.8480.90226.9239.9589.9580.0000.0000.0000.000
136A142GLU-1-0.809-0.87727.318-9.092-9.0920.0000.0000.0000.000
137A143GLY00.0190.01125.7920.1310.1310.0000.0000.0000.000
138A144GLU-1-0.900-0.92622.802-10.858-10.8580.0000.0000.0000.000
139A145ALA0-0.012-0.02219.3750.0260.0260.0000.0000.0000.000
140A146HIS00.0000.00416.833-0.085-0.0850.0000.0000.0000.000
141A147GLU-1-0.802-0.88822.257-11.168-11.1680.0000.0000.0000.000
142A148ARG10.8430.92925.8219.1309.1300.0000.0000.0000.000
143A149ARG10.9340.96024.37311.15111.1510.0000.0000.0000.000
144A150LEU0-0.0020.00329.558-0.072-0.0720.0000.0000.0000.000
145A151PRO00.012-0.00732.7340.0080.0080.0000.0000.0000.000
146A152ALA0-0.0320.00235.3300.1160.1160.0000.0000.0000.000
147A153VAL00.000-0.00438.4680.0410.0410.0000.0000.0000.000
148A154ARG10.8750.95041.7596.3566.3560.0000.0000.0000.000
149A155SER0-0.002-0.01145.0050.1480.1480.0000.0000.0000.000
150A156ILE00.0720.01347.721-0.001-0.0010.0000.0000.0000.000
151A157ASN00.0290.00850.6730.0720.0720.0000.0000.0000.000
152A158GLY0-0.0130.00449.3350.0520.0520.0000.0000.0000.000
153A159THR0-0.0280.00445.164-0.015-0.0150.0000.0000.0000.000
154A160PHE00.0480.04641.7490.0510.0510.0000.0000.0000.000
155A161GLN0-0.009-0.00240.9400.0370.0370.0000.0000.0000.000
156A162ALA00.0250.02136.298-0.059-0.0590.0000.0000.0000.000
157A163ASP-1-0.813-0.87137.752-7.118-7.1180.0000.0000.0000.000
158A164PHE0-0.005-0.01531.282-0.161-0.1610.0000.0000.0000.000
159A165PRO0-0.0060.01334.5620.0630.0630.0000.0000.0000.000
160A166LEU00.0200.00032.406-0.292-0.2920.0000.0000.0000.000
161A167GLY00.0140.02231.894-0.318-0.3180.0000.0000.0000.000
162A168PRO0-0.0010.00132.5980.1540.1540.0000.0000.0000.000
163A169ALA0-0.009-0.00333.773-0.228-0.2280.0000.0000.0000.000
164A170THR00.0060.00330.7550.1040.1040.0000.0000.0000.000
165A171HIS0-0.015-0.02429.321-0.068-0.0680.0000.0000.0000.000
166A172GLY00.0350.02633.0560.0000.0000.0000.0000.0000.000
167A173GLY0-0.009-0.00732.155-0.324-0.3240.0000.0000.0000.000
168A174THR0-0.018-0.02132.8540.2850.2850.0000.0000.0000.000
169A175TYR00.0280.00830.815-0.397-0.3970.0000.0000.0000.000
170A176ARG10.8560.90432.3028.9528.9520.0000.0000.0000.000
171A178PHE00.0460.02529.8660.1520.1520.0000.0000.0000.000
172A179GLY00.0370.01333.901-0.031-0.0310.0000.0000.0000.000
173A180SER00.0010.00632.343-0.184-0.1840.0000.0000.0000.000
174A181PHE00.0450.02934.4970.1860.1860.0000.0000.0000.000
175A182ARG10.8750.93032.4098.7118.7110.0000.0000.0000.000
176A183ASP-1-0.940-0.97432.841-8.989-8.9890.0000.0000.0000.000
177A184ALA00.0520.03831.119-0.327-0.3270.0000.0000.0000.000
178A185PRO0-0.023-0.01527.5270.0280.0280.0000.0000.0000.000
179A186TYR0-0.051-0.02122.1440.0380.0380.0000.0000.0000.000
180A187GLU-1-0.821-0.90127.899-9.594-9.5940.0000.0000.0000.000
181A188TRP0-0.077-0.07326.2270.2540.2540.0000.0000.0000.000
182A189SER00.005-0.00432.694-0.002-0.0020.0000.0000.0000.000
183A190ASN0-0.034-0.01034.445-0.335-0.3350.0000.0000.0000.000
184A191SER00.003-0.01134.141-0.057-0.0570.0000.0000.0000.000
185A192SER0-0.0020.00735.6370.1140.1140.0000.0000.0000.000
186A193ASP-1-0.821-0.87737.493-7.256-7.2560.0000.0000.0000.000
187A194PRO0-0.007-0.01536.355-0.091-0.0910.0000.0000.0000.000
188A195LEU0-0.0030.01236.9150.2210.2210.0000.0000.0000.000
189A196LEU0-0.018-0.00736.451-0.194-0.1940.0000.0000.0000.000
190A197VAL00.0000.00735.9300.1940.1940.0000.0000.0000.000
191A198SER0-0.027-0.01636.803-0.177-0.1770.0000.0000.0000.000
192A199VAL0-0.006-0.00835.7590.0910.0910.0000.0000.0000.000
193A200THR0-0.033-0.00438.8410.0070.0070.0000.0000.0000.000