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: 6N93Z

Calculation Name: 1FON-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1FON

Chain ID: A

ChEMBL ID:

UniProt ID: P05805

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 227
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2766092.89758
FMO2-HF: Nuclear repulsion 2677030.964885
FMO2-HF: Total energy -89061.932695
FMO2-MP2: Total energy -89318.03382


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:9:SER)


Summations of interaction energy for fragment #1(A:9:SER)
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.
-35.93-30.9457.231-5.585-6.6290.027
Interaction energy analysis for fragmet #1(A:9:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.005 / q_NPA : 0.008
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].
3A11SER0-0.056-0.0173.8030.9872.706-0.023-0.802-0.8940.004
4A12TRP00.0620.0296.1070.1310.1310.0000.0000.0000.000
5A13GLN0-0.062-0.0327.3910.4240.4240.0000.0000.0000.000
6A14VAL00.015-0.00711.485-0.058-0.0580.0000.0000.0000.000
7A15SER0-0.015-0.02015.1170.0910.0910.0000.0000.0000.000
8A16LEU0-0.0140.00318.144-0.038-0.0380.0000.0000.0000.000
9A17GLN00.030-0.01220.9480.0290.0290.0000.0000.0000.000
10A18TYR0-0.011-0.01024.391-0.010-0.0100.0000.0000.0000.000
11A19GLU-1-0.920-0.95628.115-0.098-0.0980.0000.0000.0000.000
12A20LYS10.8370.90731.0040.0260.0260.0000.0000.0000.000
13A21ASP-1-0.894-0.95433.257-0.032-0.0320.0000.0000.0000.000
14A22GLY0-0.0020.01434.900-0.001-0.0010.0000.0000.0000.000
15A23ALA00.0140.00230.275-0.007-0.0070.0000.0000.0000.000
16A24PHE00.0260.00926.2970.0080.0080.0000.0000.0000.000
17A25HIS0-0.053-0.01726.2360.0050.0050.0000.0000.0000.000
18A26HIS0-0.0380.00018.172-0.051-0.0510.0000.0000.0000.000
19A27THR0-0.073-0.03822.7920.0300.0300.0000.0000.0000.000
20A28CYS0-0.151-0.05620.5510.0460.0460.0000.0000.0000.000
21A29GLY00.0490.04516.331-0.035-0.0350.0000.0000.0000.000
22A30GLY00.0260.00815.3350.0010.0010.0000.0000.0000.000
23A31SER0-0.032-0.01312.925-0.025-0.0250.0000.0000.0000.000
24A32LEU00.0210.01913.0240.0320.0320.0000.0000.0000.000
25A33ILE0-0.014-0.00513.328-0.059-0.0590.0000.0000.0000.000
26A34ALA00.0140.00615.637-0.027-0.0270.0000.0000.0000.000
27A35PRO00.0320.01017.211-0.001-0.0010.0000.0000.0000.000
28A36ASP-1-0.824-0.90218.373-0.350-0.3500.0000.0000.0000.000
29A37TRP00.0430.04619.5120.0600.0600.0000.0000.0000.000
30A38VAL00.000-0.00217.123-0.039-0.0390.0000.0000.0000.000
31A39VAL00.0090.01517.0070.0350.0350.0000.0000.0000.000
32A40THR00.008-0.03417.8840.0200.0200.0000.0000.0000.000
33A41ALA00.0000.00320.1580.0090.0090.0000.0000.0000.000
34A42GLY00.0670.03222.913-0.018-0.0180.0000.0000.0000.000
35A43HIS10.7260.82223.522-0.108-0.1080.0000.0000.0000.000
36A45ILE00.0180.01624.948-0.013-0.0130.0000.0000.0000.000
37A46SER0-0.0010.02428.2220.0130.0130.0000.0000.0000.000
38A47THR00.032-0.00731.389-0.004-0.0040.0000.0000.0000.000
39A48SER0-0.017-0.00732.809-0.004-0.0040.0000.0000.0000.000
40A49ARG10.8710.94531.0780.0150.0150.0000.0000.0000.000
41A50THR00.0680.03630.784-0.001-0.0010.0000.0000.0000.000
42A51TYR0-0.017-0.02825.4850.0080.0080.0000.0000.0000.000
43A52GLN0-0.027-0.01023.981-0.015-0.0150.0000.0000.0000.000
44A53VAL0-0.012-0.01418.9970.0250.0250.0000.0000.0000.000
45A54VAL0-0.0050.00518.218-0.027-0.0270.0000.0000.0000.000
46A55LEU0-0.018-0.01515.0420.0280.0280.0000.0000.0000.000
47A56GLY00.0780.02213.5720.0420.0420.0000.0000.0000.000
48A57GLU-1-0.842-0.9278.703-2.281-2.2810.0000.0000.0000.000
49A58TYR0-0.021-0.0367.2790.4010.4010.0000.0000.0000.000
50A59ASP-1-0.793-0.9032.877-16.088-14.2300.211-1.094-0.974-0.011
51A60ARG10.8870.9111.911-20.179-18.9647.037-3.630-4.6220.034
52A61SER0-0.096-0.0473.7400.3680.5610.006-0.059-0.1390.000
53A62VAL0-0.011-0.0236.7110.2760.2760.0000.0000.0000.000
54A63LEU0-0.0080.0178.123-0.596-0.5960.0000.0000.0000.000
55A64GLU-1-0.934-0.9718.148-1.756-1.7560.0000.0000.0000.000
56A65GLY0-0.031-0.00511.0820.0190.0190.0000.0000.0000.000
57A66SER0-0.045-0.03314.5380.0980.0980.0000.0000.0000.000
58A67GLU-1-0.848-0.91716.326-0.431-0.4310.0000.0000.0000.000
59A68GLN0-0.069-0.03916.6380.0930.0930.0000.0000.0000.000
60A69VAL00.0430.02219.5470.0160.0160.0000.0000.0000.000
61A70ILE0-0.051-0.02720.4380.0010.0010.0000.0000.0000.000
62A71PRO00.0610.03923.8160.0190.0190.0000.0000.0000.000
63A72ILE00.0010.01823.486-0.017-0.0170.0000.0000.0000.000
64A73ASN0-0.029-0.01527.6370.0160.0160.0000.0000.0000.000
65A74ALA00.0500.02030.3860.0020.0020.0000.0000.0000.000
66A75GLY0-0.027-0.02631.935-0.001-0.0010.0000.0000.0000.000
67A76ASP-1-0.795-0.86527.644-0.172-0.1720.0000.0000.0000.000
68A77LEU0-0.085-0.03926.416-0.006-0.0060.0000.0000.0000.000
69A78PHE00.0310.00826.8750.0120.0120.0000.0000.0000.000
70A79VAL00.013-0.00527.2190.0050.0050.0000.0000.0000.000
71A80HIS00.0320.03427.9070.0010.0010.0000.0000.0000.000
72A81PRO00.0250.00029.6960.0050.0050.0000.0000.0000.000
73A82LEU0-0.024-0.02332.4820.0040.0040.0000.0000.0000.000
74A83TRP0-0.0190.02229.6980.0160.0160.0000.0000.0000.000
75A84ASN00.0680.02131.672-0.008-0.0080.0000.0000.0000.000
76A85SER00.0250.01132.0810.0060.0060.0000.0000.0000.000
77A86ASN0-0.099-0.04833.0290.0080.0080.0000.0000.0000.000
78A87CYS0-0.060-0.03632.1170.0070.0070.0000.0000.0000.000
79A88VAL00.0770.03628.539-0.001-0.0010.0000.0000.0000.000
80A89ALA00.0090.01130.2120.0060.0060.0000.0000.0000.000
81A91GLY00.0050.00828.796-0.002-0.0020.0000.0000.0000.000
82A92ASN0-0.002-0.01328.202-0.005-0.0050.0000.0000.0000.000
83A93ASP-1-0.726-0.79625.7180.0720.0720.0000.0000.0000.000
84A94ILE0-0.056-0.01421.7650.0150.0150.0000.0000.0000.000
85A95ALA00.0170.00323.349-0.003-0.0030.0000.0000.0000.000
86A96LEU00.0100.02621.600-0.003-0.0030.0000.0000.0000.000
87A97VAL0-0.042-0.02222.0770.0150.0150.0000.0000.0000.000
88A98LYS10.9180.96822.4460.1650.1650.0000.0000.0000.000
89A99LEU0-0.048-0.04419.0780.0140.0140.0000.0000.0000.000
90A100SER0-0.050-0.04323.807-0.004-0.0040.0000.0000.0000.000
91A101ARG10.8870.93323.0540.3670.3670.0000.0000.0000.000
92A102SER0-0.028-0.03321.140-0.001-0.0010.0000.0000.0000.000
93A103ALA0-0.020-0.00817.3980.0000.0000.0000.0000.0000.000
94A104GLN0-0.042-0.02317.8330.0450.0450.0000.0000.0000.000
95A105LEU00.0140.00013.270-0.025-0.0250.0000.0000.0000.000
96A106GLY0-0.0190.01412.747-0.195-0.1950.0000.0000.0000.000
97A107ASP-1-0.936-0.98112.087-1.290-1.2900.0000.0000.0000.000
98A108LYS10.8910.9647.3762.7162.7160.0000.0000.0000.000
99A109VAL0-0.045-0.0076.263-0.700-0.7000.0000.0000.0000.000
100A110GLN0-0.026-0.0036.9770.5120.5120.0000.0000.0000.000
101A111LEU0-0.023-0.0128.642-0.046-0.0460.0000.0000.0000.000
102A112ALA0-0.008-0.0019.9790.1030.1030.0000.0000.0000.000
103A113ASN0-0.014-0.02111.1050.0180.0180.0000.0000.0000.000
104A114LEU00.0570.03214.2360.0740.0740.0000.0000.0000.000
105A115PRO0-0.0210.00516.769-0.006-0.0060.0000.0000.0000.000
106A116PRO00.0100.00218.361-0.026-0.0260.0000.0000.0000.000
107A117ALA00.0650.01921.7870.0240.0240.0000.0000.0000.000
108A118GLY0-0.062-0.04724.6830.0070.0070.0000.0000.0000.000
109A119ASP-1-0.863-0.90519.7930.2220.2220.0000.0000.0000.000
110A120ILE0-0.060-0.00822.4750.0070.0070.0000.0000.0000.000
111A121LEU00.0260.01017.0780.0090.0090.0000.0000.0000.000
112A122PRO00.0120.01019.674-0.015-0.0150.0000.0000.0000.000
113A123ASN00.000-0.01821.3420.0250.0250.0000.0000.0000.000
114A124GLU-1-0.939-0.96520.7720.4250.4250.0000.0000.0000.000
115A125ALA0-0.0360.00317.2940.0680.0680.0000.0000.0000.000
116A126PRO00.0100.00412.8980.0170.0170.0000.0000.0000.000
117A127CYS00.0320.01811.0950.1970.1970.0000.0000.0000.000
118A128TYR0-0.003-0.0268.7550.2390.2390.0000.0000.0000.000
119A129ILE0-0.0220.00810.757-0.223-0.2230.0000.0000.0000.000
120A130SER00.008-0.0198.1090.3640.3640.0000.0000.0000.000
121A131GLY0-0.0020.00510.230-0.209-0.2090.0000.0000.0000.000
122A132TRP00.0410.00312.7970.1620.1620.0000.0000.0000.000
123A133GLY00.0010.00715.456-0.025-0.0250.0000.0000.0000.000
124A134ARG10.8560.91817.488-0.308-0.3080.0000.0000.0000.000
125A135LEU0-0.046-0.02019.467-0.028-0.0280.0000.0000.0000.000
126A136TYR0-0.033-0.02318.574-0.015-0.0150.0000.0000.0000.000
127A137THR00.023-0.00920.513-0.002-0.0020.0000.0000.0000.000
128A138GLY00.0800.05122.787-0.004-0.0040.0000.0000.0000.000
129A139GLY0-0.0420.00123.6200.0120.0120.0000.0000.0000.000
130A140PRO00.0010.00920.947-0.009-0.0090.0000.0000.0000.000
131A141LEU00.0100.01714.7740.0410.0410.0000.0000.0000.000
132A142PRO0-0.014-0.00615.378-0.001-0.0010.0000.0000.0000.000
133A143ASP-1-0.861-0.91014.081-0.371-0.3710.0000.0000.0000.000
134A144LYS10.8720.93011.393-0.407-0.4070.0000.0000.0000.000
135A145LEU0-0.0640.0037.2650.0380.0380.0000.0000.0000.000
136A146GLN0-0.016-0.01410.2130.3820.3820.0000.0000.0000.000
137A147GLN00.0420.0175.3351.7481.7480.0000.0000.0000.000
138A148ALA0-0.027-0.0059.6560.0370.0370.0000.0000.0000.000
139A149LEU0-0.0090.00911.681-0.033-0.0330.0000.0000.0000.000
140A150LEU0-0.038-0.03612.882-0.161-0.1610.0000.0000.0000.000
141A151PRO0-0.0020.00215.786-0.025-0.0250.0000.0000.0000.000
142A152THR0-0.021-0.01417.635-0.077-0.0770.0000.0000.0000.000
143A153VAL0-0.0060.01219.8690.0000.0000.0000.0000.0000.000
144A154ASP-1-0.762-0.87623.5930.2540.2540.0000.0000.0000.000
145A155TYR00.019-0.01325.386-0.009-0.0090.0000.0000.0000.000
146A156GLU-1-0.831-0.90428.2610.1810.1810.0000.0000.0000.000
147A157HIS10.8630.92027.494-0.281-0.2810.0000.0000.0000.000
148A158CYS0-0.067-0.00822.182-0.015-0.0150.0000.0000.0000.000
149A159SER0-0.009-0.01828.450-0.010-0.0100.0000.0000.0000.000
150A160GLN0-0.0070.00531.630-0.005-0.0050.0000.0000.0000.000
151A161TRP00.012-0.01433.6010.0030.0030.0000.0000.0000.000
152A162ASP-1-0.824-0.89634.1300.2110.2110.0000.0000.0000.000
153A163TRP0-0.054-0.02825.6020.0190.0190.0000.0000.0000.000
154A164TRP00.016-0.01826.333-0.020-0.0200.0000.0000.0000.000
155A165GLY0-0.0210.01231.241-0.016-0.0160.0000.0000.0000.000
156A166ILE00.002-0.01633.5230.0030.0030.0000.0000.0000.000
157A167THR0-0.041-0.01631.749-0.011-0.0110.0000.0000.0000.000
158A168VAL00.0100.00127.868-0.005-0.0050.0000.0000.0000.000
159A169LYS10.9090.92729.688-0.094-0.0940.0000.0000.0000.000
160A170LYS10.9280.94128.616-0.142-0.1420.0000.0000.0000.000
161A171THR0-0.0230.00926.9570.0060.0060.0000.0000.0000.000
162A172MET0-0.0420.02224.559-0.005-0.0050.0000.0000.0000.000
163A173VAL00.0420.02519.5020.0020.0020.0000.0000.0000.000
164A175ALA00.0670.03617.9280.0190.0190.0000.0000.0000.000
165A176GLY00.0150.00720.001-0.006-0.0060.0000.0000.0000.000
166A177GLY00.006-0.00120.674-0.032-0.0320.0000.0000.0000.000
167A178ASP-1-0.813-0.88822.8580.4700.4700.0000.0000.0000.000
168A179THR0-0.019-0.01522.2570.0220.0220.0000.0000.0000.000
169A180ARG10.8510.92916.595-0.708-0.7080.0000.0000.0000.000
170A181SER00.0150.01519.072-0.049-0.0490.0000.0000.0000.000
171A182GLY00.0500.00817.2680.0810.0810.0000.0000.0000.000
172A183CYS0-0.099-0.08018.177-0.040-0.0400.0000.0000.0000.000
173A184ASN00.0190.00513.6500.0730.0730.0000.0000.0000.000
174A185GLY00.0450.04414.4270.0150.0150.0000.0000.0000.000
175A186ASP-1-0.772-0.88915.4160.1590.1590.0000.0000.0000.000
176A187SER00.0340.02417.6990.0210.0210.0000.0000.0000.000
177A188GLY00.0680.01619.685-0.026-0.0260.0000.0000.0000.000
178A189GLY0-0.0170.00615.734-0.033-0.0330.0000.0000.0000.000
179A190PRO00.0230.02111.5220.0330.0330.0000.0000.0000.000
180A191LEU0-0.062-0.02213.0510.1240.1240.0000.0000.0000.000
181A192ASN0-0.010-0.0119.177-0.251-0.2510.0000.0000.0000.000
182A194PRO00.0120.0219.562-0.117-0.1170.0000.0000.0000.000
183A195ALA00.0070.00611.219-0.017-0.0170.0000.0000.0000.000
184A196ALA0-0.011-0.01613.5730.0580.0580.0000.0000.0000.000
185A197ASP-1-0.871-0.91714.2200.0840.0840.0000.0000.0000.000
186A198GLY00.0150.00711.293-0.031-0.0310.0000.0000.0000.000
187A199SER0-0.083-0.0499.4670.0460.0460.0000.0000.0000.000
188A200TRP00.005-0.0036.2700.3240.3240.0000.0000.0000.000
189A201GLN00.0470.01810.085-0.126-0.1260.0000.0000.0000.000
190A202VAL00.0070.00212.6540.1170.1170.0000.0000.0000.000
191A203HIS00.027-0.01814.051-0.005-0.0050.0000.0000.0000.000
192A204GLY0-0.036-0.02815.980-0.023-0.0230.0000.0000.0000.000
193A205VAL00.0150.02716.3820.0070.0070.0000.0000.0000.000
194A206THR0-0.086-0.05217.3180.0210.0210.0000.0000.0000.000
195A207SER0-0.057-0.05319.818-0.035-0.0350.0000.0000.0000.000
196A208PHE0-0.012-0.02623.586-0.013-0.0130.0000.0000.0000.000
197A209VAL00.0190.00423.0690.0320.0320.0000.0000.0000.000
198A210SER00.0420.01825.840-0.030-0.0300.0000.0000.0000.000
199A211ALA00.0220.01428.9820.0010.0010.0000.0000.0000.000
200A212PHE0-0.048-0.03130.660-0.006-0.0060.0000.0000.0000.000
201A213GLY00.0380.03527.1900.0060.0060.0000.0000.0000.000
202A215ASN00.021-0.00922.7360.0220.0220.0000.0000.0000.000
203A216THR00.0220.03124.008-0.026-0.0260.0000.0000.0000.000
204A217ILE00.009-0.01026.2080.0120.0120.0000.0000.0000.000
205A218LYS10.8200.90627.471-0.265-0.2650.0000.0000.0000.000
206A219LYS10.8220.92027.384-0.242-0.2420.0000.0000.0000.000
207A220PRO0-0.0210.00423.0180.0100.0100.0000.0000.0000.000
208A221THR00.0010.01119.750-0.033-0.0330.0000.0000.0000.000
209A222VAL00.0070.01122.0600.0180.0180.0000.0000.0000.000
210A223PHE00.005-0.01116.645-0.005-0.0050.0000.0000.0000.000
211A224THR0-0.025-0.02821.3170.0020.0020.0000.0000.0000.000
212A225ARG10.8830.92620.946-0.133-0.1330.0000.0000.0000.000
213A226VAL00.0430.02118.072-0.024-0.0240.0000.0000.0000.000
214A227SER00.001-0.00921.080-0.024-0.0240.0000.0000.0000.000
215A228ALA0-0.090-0.03622.451-0.009-0.0090.0000.0000.0000.000
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