Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: G6LM1

Calculation Name: 5F9Q-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5F9Q

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-06-21

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 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 192
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1970797.711719
FMO2-HF: Nuclear repulsion 1896306.169138
FMO2-HF: Total energy -74491.54258
FMO2-MP2: Total energy -74706.781302


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:16:ASN)


Summations of interaction energy for fragment #1(A:16:ASN)
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.
-18.686-9.5156.028-4.682-10.518-0.005
Interaction energy analysis for fragmet #1(A:16:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.013 / q_NPA : -0.012
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].
3A18ILE0-0.027-0.0153.7491.5073.268-0.039-0.705-1.0180.003
4A19GLU-1-0.922-0.9636.5450.0700.0700.0000.0000.0000.000
5A20LEU0-0.042-0.01710.1720.0540.0540.0000.0000.0000.000
6A21PHE0-0.012-0.00712.5720.0180.0180.0000.0000.0000.000
7A22TYR00.0460.00916.409-0.050-0.0500.0000.0000.0000.000
8A23MET0-0.052-0.02317.7770.0350.0350.0000.0000.0000.000
9A24PRO00.0240.02122.1210.0020.0020.0000.0000.0000.000
10A25SER00.0440.02325.1420.0150.0150.0000.0000.0000.000
11A26ASP-1-0.833-0.93027.0380.1250.1250.0000.0000.0000.000
12A27GLU-1-0.968-0.98529.5960.0540.0540.0000.0000.0000.000
13A28GLU-1-0.842-0.90726.138-0.006-0.0060.0000.0000.0000.000
14A29LEU00.0310.00129.011-0.016-0.0160.0000.0000.0000.000
15A30THR0-0.129-0.06531.125-0.014-0.0140.0000.0000.0000.000
16A31ALA0-0.0110.00431.973-0.007-0.0070.0000.0000.0000.000
17A32ASN00.004-0.00829.909-0.015-0.0150.0000.0000.0000.000
18A33PRO00.0160.01032.1550.0040.0040.0000.0000.0000.000
19A34ASN0-0.086-0.07033.626-0.011-0.0110.0000.0000.0000.000
20A35ALA00.0570.05331.008-0.005-0.0050.0000.0000.0000.000
21A36LEU0-0.0330.00728.677-0.005-0.0050.0000.0000.0000.000
22A37GLN0-0.048-0.02725.694-0.001-0.0010.0000.0000.0000.000
23A38GLU-1-0.902-0.94724.6340.1390.1390.0000.0000.0000.000
24A39ALA00.008-0.02520.219-0.018-0.0180.0000.0000.0000.000
25A40SER0-0.071-0.00322.177-0.023-0.0230.0000.0000.0000.000
26A41PHE0-0.0030.01116.765-0.022-0.0220.0000.0000.0000.000
27A42THR00.0760.04120.513-0.019-0.0190.0000.0000.0000.000
28A43GLU-1-0.838-0.92520.571-0.386-0.3860.0000.0000.0000.000
29A44GLU-1-0.965-0.96920.683-0.395-0.3950.0000.0000.0000.000
30A45ASP-1-0.722-0.82818.470-0.365-0.3650.0000.0000.0000.000
31A46ILE0-0.052-0.02616.008-0.104-0.1040.0000.0000.0000.000
32A47ASN0-0.048-0.03515.908-0.191-0.1910.0000.0000.0000.000
33A48GLY00.0250.01117.411-0.080-0.0800.0000.0000.0000.000
34A49LEU00.003-0.01312.712-0.102-0.1020.0000.0000.0000.000
35A50LYS10.8570.93611.7701.6781.6780.0000.0000.0000.000
36A51GLY0-0.027-0.01013.238-0.176-0.1760.0000.0000.0000.000
37A52VAL0-0.0320.00111.6140.1110.1110.0000.0000.0000.000
38A53ASP-1-0.879-0.93711.814-1.695-1.6950.0000.0000.0000.000
39A54GLY00.0310.0288.6250.0770.0770.0000.0000.0000.000
40A55VAL0-0.073-0.0286.789-1.523-1.5230.0000.0000.0000.000
41A56LYS10.9831.0015.7105.6985.6980.0000.0000.0000.000
42A57GLN0-0.102-0.0737.6171.0241.0240.0000.0000.0000.000
43A58VAL00.0460.0408.627-0.257-0.2570.0000.0000.0000.000
44A59VAL0-0.055-0.0238.6620.1580.1580.0000.0000.0000.000
45A60ALA00.0270.01711.7470.1800.1800.0000.0000.0000.000
46A61SER0-0.020-0.03215.2170.0290.0290.0000.0000.0000.000
47A62ALA00.0430.03217.6850.0290.0290.0000.0000.0000.000
48A63VAL00.0000.01418.721-0.014-0.0140.0000.0000.0000.000
49A64LYS10.9280.95721.7850.0420.0420.0000.0000.0000.000
50A65SER00.0220.02025.4200.0020.0020.0000.0000.0000.000
51A66MET0-0.034-0.00827.633-0.017-0.0170.0000.0000.0000.000
52A67THR00.0260.01930.5780.0060.0060.0000.0000.0000.000
53A68ALA0-0.056-0.03030.953-0.014-0.0140.0000.0000.0000.000
54A69ARG10.9420.96733.033-0.003-0.0030.0000.0000.0000.000
55A70TYR00.001-0.01135.833-0.014-0.0140.0000.0000.0000.000
56A71HIS0-0.027-0.01037.6770.0070.0070.0000.0000.0000.000
57A72GLU-1-0.960-0.99141.4430.0130.0130.0000.0000.0000.000
58A73GLU-1-0.950-0.94737.6510.0360.0360.0000.0000.0000.000
59A74ASP-1-0.845-0.94036.5840.0180.0180.0000.0000.0000.000
60A75THR0-0.068-0.04731.2630.0150.0150.0000.0000.0000.000
61A76ASP-1-0.888-0.92030.9460.0730.0730.0000.0000.0000.000
62A77ILE0-0.071-0.05827.2210.0100.0100.0000.0000.0000.000
63A78THR00.001-0.00121.5620.0100.0100.0000.0000.0000.000
64A79LEU0-0.033-0.01424.349-0.014-0.0140.0000.0000.0000.000
65A80ASN00.014-0.00819.1870.0310.0310.0000.0000.0000.000
66A81GLY00.009-0.00121.353-0.030-0.0300.0000.0000.0000.000
67A82ILE0-0.015-0.01016.9640.0050.0050.0000.0000.0000.000
68A83ASN00.0710.01714.2590.0740.0740.0000.0000.0000.000
69A84SER00.007-0.00716.899-0.006-0.0060.0000.0000.0000.000
70A85GLY00.0570.02812.926-0.058-0.0580.0000.0000.0000.000
71A86TYR00.011-0.00211.686-0.123-0.1230.0000.0000.0000.000
72A87MET0-0.039-0.03212.1830.0720.0720.0000.0000.0000.000
73A88ASP-1-0.873-0.90710.306-2.142-2.1420.0000.0000.0000.000
74A89VAL0-0.029-0.0076.394-0.014-0.0140.0000.0000.0000.000
75A90LYS10.9210.9628.319-0.018-0.0180.0000.0000.0000.000
76A91LYS10.9090.9708.6460.5230.5230.0000.0000.0000.000
77A92LEU0-0.008-0.01911.9980.1290.1290.0000.0000.0000.000
78A93ASP-1-0.896-0.94615.329-0.241-0.2410.0000.0000.0000.000
79A94VAL0-0.030-0.01318.1830.0550.0550.0000.0000.0000.000
80A95GLN0-0.029-0.01221.768-0.009-0.0090.0000.0000.0000.000
81A96ASP-1-0.907-0.95124.502-0.068-0.0680.0000.0000.0000.000
82A97GLY0-0.010-0.01026.9900.0020.0020.0000.0000.0000.000
83A98ARG10.9270.95525.2070.2200.2200.0000.0000.0000.000
84A99THR00.0510.01919.2520.0320.0320.0000.0000.0000.000
85A100PHE0-0.031-0.01920.5920.0090.0090.0000.0000.0000.000
86A101THR0-0.028-0.01821.402-0.049-0.0490.0000.0000.0000.000
87A102ASP-1-0.813-0.92019.580-0.735-0.7350.0000.0000.0000.000
88A103ASN00.004-0.01422.2550.0070.0070.0000.0000.0000.000
89A104ASP-1-0.899-0.93524.320-0.284-0.2840.0000.0000.0000.000
90A105PHE00.006-0.00419.2360.0220.0220.0000.0000.0000.000
91A106LEU0-0.0030.01023.5730.0230.0230.0000.0000.0000.000
92A107SER0-0.086-0.05125.8040.0310.0310.0000.0000.0000.000
93A108GLY00.0330.02526.9070.0250.0250.0000.0000.0000.000
94A109LYS10.9170.96327.8960.2910.2910.0000.0000.0000.000
95A110ARG10.9420.97528.6660.1190.1190.0000.0000.0000.000
96A111ALA0-0.0020.00827.4700.0120.0120.0000.0000.0000.000
97A112GLY00.042-0.00625.782-0.011-0.0110.0000.0000.0000.000
98A113ILE0-0.0390.00021.5090.0020.0020.0000.0000.0000.000
99A114ILE00.0120.00523.5020.0170.0170.0000.0000.0000.000
100A115SER00.0460.00022.692-0.015-0.0150.0000.0000.0000.000
101A116LYS11.0301.00924.099-0.082-0.0820.0000.0000.0000.000
102A117LYS10.9701.00325.847-0.158-0.1580.0000.0000.0000.000
103A118MET0-0.0200.00726.353-0.008-0.0080.0000.0000.0000.000
104A119ALA00.0230.01328.427-0.009-0.0090.0000.0000.0000.000
105A120GLU-1-0.913-0.96130.1140.0770.0770.0000.0000.0000.000
106A121LYS10.8490.92131.240-0.107-0.1070.0000.0000.0000.000
107A122LEU00.0330.02631.911-0.003-0.0030.0000.0000.0000.000
108A123PHE00.0220.00532.212-0.008-0.0080.0000.0000.0000.000
109A124GLY0-0.0100.00535.151-0.004-0.0040.0000.0000.0000.000
110A125LYS10.9450.95734.531-0.013-0.0130.0000.0000.0000.000
111A126THR0-0.074-0.03436.445-0.006-0.0060.0000.0000.0000.000
112A127SER00.0310.01734.1320.0010.0010.0000.0000.0000.000
113A128PRO00.0600.02230.782-0.003-0.0030.0000.0000.0000.000
114A129LEU0-0.032-0.00229.104-0.007-0.0070.0000.0000.0000.000
115A130GLY00.0050.00832.7100.0050.0050.0000.0000.0000.000
116A131LYS10.8150.92134.4730.0560.0560.0000.0000.0000.000
117A132ILE0-0.019-0.00534.075-0.007-0.0070.0000.0000.0000.000
118A133VAL00.0120.00631.7410.0110.0110.0000.0000.0000.000
119A134TRP0-0.010-0.01933.860-0.014-0.0140.0000.0000.0000.000
120A135ALA00.0220.01430.3440.0140.0140.0000.0000.0000.000
121A136GLY00.0450.01732.408-0.010-0.0100.0000.0000.0000.000
122A137GLY0-0.013-0.00533.968-0.004-0.0040.0000.0000.0000.000
123A138GLN0-0.005-0.01232.945-0.019-0.0190.0000.0000.0000.000
124A139PRO0-0.0450.00633.9730.0040.0040.0000.0000.0000.000
125A140VAL00.012-0.01928.683-0.015-0.0150.0000.0000.0000.000
126A141GLU-1-0.921-0.95231.974-0.130-0.1300.0000.0000.0000.000
127A142VAL0-0.016-0.00328.546-0.015-0.0150.0000.0000.0000.000
128A143ILE0-0.015-0.01725.336-0.001-0.0010.0000.0000.0000.000
129A144GLY00.0250.00925.280-0.018-0.0180.0000.0000.0000.000
130A145VAL0-0.032-0.00925.6430.0160.0160.0000.0000.0000.000
131A146LEU00.004-0.01218.995-0.016-0.0160.0000.0000.0000.000
132A147LYS10.8860.95418.962-0.069-0.0690.0000.0000.0000.000
133A148GLU-1-0.981-0.99020.4180.1880.1880.0000.0000.0000.000
134A156GLY00.0220.00322.1170.0040.0040.0000.0000.0000.000
135A157LEU00.014-0.00221.2770.0010.0010.0000.0000.0000.000
136A158SER00.0050.02824.004-0.020-0.0200.0000.0000.0000.000
137A159GLU-1-0.799-0.88319.4960.1450.1450.0000.0000.0000.000
138A160MET0-0.019-0.00323.867-0.016-0.0160.0000.0000.0000.000
139A161TYR0-0.057-0.04517.161-0.013-0.0130.0000.0000.0000.000
140A162VAL00.023-0.00422.098-0.007-0.0070.0000.0000.0000.000
141A163PRO00.0020.01722.387-0.017-0.0170.0000.0000.0000.000
142A164PHE00.0360.01921.2020.0340.0340.0000.0000.0000.000
143A165ASN00.017-0.00623.1270.0450.0450.0000.0000.0000.000
144A166MET0-0.0520.00026.1750.0200.0200.0000.0000.0000.000
145A167LEU0-0.039-0.02923.9210.0270.0270.0000.0000.0000.000
146A168LYS10.8900.93527.0980.2890.2890.0000.0000.0000.000
147A169THR0-0.030-0.01529.5300.0170.0170.0000.0000.0000.000
148A170SER0-0.062-0.02031.0210.0150.0150.0000.0000.0000.000
149A171PHE0-0.053-0.04329.4840.0140.0140.0000.0000.0000.000
150A172GLY00.0290.03831.7280.0120.0120.0000.0000.0000.000
151A173THR0-0.099-0.06025.6060.0140.0140.0000.0000.0000.000
152A174ASN0-0.001-0.02527.260-0.033-0.0330.0000.0000.0000.000
153A175ASP-1-0.823-0.88223.500-0.176-0.1760.0000.0000.0000.000
154A176TYR0-0.056-0.04718.707-0.003-0.0030.0000.0000.0000.000
155A177SER00.035-0.00319.689-0.004-0.0040.0000.0000.0000.000
156A178ASN0-0.0060.01015.2670.0050.0050.0000.0000.0000.000
157A179VAL00.0760.03012.900-0.106-0.1060.0000.0000.0000.000
158A180SER0-0.034-0.0118.2510.3380.3380.0000.0000.0000.000
159A181VAL00.0280.0287.194-0.168-0.1680.0000.0000.0000.000
160A182GLN0-0.024-0.0223.2770.2050.6840.029-0.118-0.3890.000
161A183THR00.014-0.0042.595-4.706-2.1080.823-1.320-2.101-0.013
162A184GLU-1-0.938-0.9703.083-10.966-9.1410.149-1.024-0.950-0.009
163A185SER0-0.041-0.0272.577-3.609-2.6781.215-0.919-1.227-0.002
164A186ALA00.0420.0212.541-0.4311.0422.945-0.849-3.5690.014
165A187ASP-1-0.940-0.9673.3900.6960.3700.2050.577-0.4560.005
166A188GLN00.005-0.0065.854-1.163-1.1630.0000.0000.0000.000
167A189ILE0-0.0140.0172.461-0.564-0.1340.701-0.324-0.808-0.003
168A190LYS10.9540.9706.162-1.771-1.7710.0000.0000.0000.000
169A191SER00.0370.0179.6520.0160.0160.0000.0000.0000.000
170A192THR00.0550.0167.778-0.081-0.0810.0000.0000.0000.000
171A193GLY0-0.013-0.0109.0760.0180.0180.0000.0000.0000.000
172A194LYS10.9220.96110.1370.0520.0520.0000.0000.0000.000
173A195GLU-1-0.920-0.97013.287-0.709-0.7090.0000.0000.0000.000
174A196ALA00.0210.00911.7690.0240.0240.0000.0000.0000.000
175A197ALA00.0130.00213.7500.0620.0620.0000.0000.0000.000
176A198ARG10.8170.91415.7600.2100.2100.0000.0000.0000.000
177A199LEU00.0340.02816.5520.0180.0180.0000.0000.0000.000
178A200LEU0-0.0060.00215.6360.0270.0270.0000.0000.0000.000
179A201ASN0-0.001-0.00519.2950.0430.0430.0000.0000.0000.000
180A202ASP-1-0.839-0.91921.699-0.200-0.2000.0000.0000.0000.000
181A203ASN0-0.077-0.04220.6350.0100.0100.0000.0000.0000.000
182A204HIS10.7650.85922.1010.1890.1890.0000.0000.0000.000
183A205GLY0-0.0330.00725.4850.0200.0200.0000.0000.0000.000
184A206THR0-0.040-0.02323.4340.0130.0130.0000.0000.0000.000
185A207LYS10.8010.89524.903-0.070-0.0700.0000.0000.0000.000
186A208GLU-1-0.965-1.00721.6690.0870.0870.0000.0000.0000.000
187A209ALA00.0220.02521.4850.0410.0410.0000.0000.0000.000
188A210TYR0-0.045-0.04017.5690.0450.0450.0000.0000.0000.000
189A211GLN0-0.051-0.02316.0750.0590.0590.0000.0000.0000.000
190A212VAL00.0180.01510.4010.0070.0070.0000.0000.0000.000
191A213MET0-0.005-0.00710.161-0.033-0.0330.0000.0000.0000.000
192A214ASN0-0.023-0.00911.8800.1370.1370.0000.0000.0000.000