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: N9VRQ

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 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 192
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1975024.320902
FMO2-HF: Nuclear repulsion 1900531.228219
FMO2-HF: Total energy -74493.092683
FMO2-MP2: Total energy -74708.385933


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.
-30.119-18.8536.094-5.768-11.592-0.03
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 : -0.033 / q_NPA : -0.014
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].
3A18ILE00.0070.0083.874-0.5981.401-0.025-1.058-0.9170.001
4A19GLU-1-0.906-0.9487.078-0.185-0.1850.0000.0000.0000.000
5A20LEU0-0.032-0.01010.6470.0210.0210.0000.0000.0000.000
6A21PHE0-0.010-0.01312.7000.0460.0460.0000.0000.0000.000
7A22TYR0-0.012-0.02516.780-0.045-0.0450.0000.0000.0000.000
8A23MET0-0.053-0.02218.1170.0440.0440.0000.0000.0000.000
9A24PRO00.0320.02022.7340.0000.0000.0000.0000.0000.000
10A25SER00.0550.03125.8060.0140.0140.0000.0000.0000.000
11A26ASP-1-0.861-0.94627.6920.0090.0090.0000.0000.0000.000
12A27GLU-1-0.894-0.91629.621-0.055-0.0550.0000.0000.0000.000
13A28GLU-1-0.749-0.86325.916-0.131-0.1310.0000.0000.0000.000
14A29LEU0-0.025-0.02029.433-0.007-0.0070.0000.0000.0000.000
15A30THR0-0.090-0.07131.707-0.003-0.0030.0000.0000.0000.000
16A31ALA0-0.0230.00532.189-0.002-0.0020.0000.0000.0000.000
17A32ASN0-0.016-0.01529.961-0.001-0.0010.0000.0000.0000.000
18A33PRO00.0440.01132.5880.0000.0000.0000.0000.0000.000
19A34ASN0-0.096-0.05334.775-0.005-0.0050.0000.0000.0000.000
20A35ALA00.0320.02431.8110.0000.0000.0000.0000.0000.000
21A36LEU0-0.0120.01630.069-0.010-0.0100.0000.0000.0000.000
22A37GLN0-0.040-0.00225.7590.0040.0040.0000.0000.0000.000
23A38GLU-1-0.873-0.92224.772-0.011-0.0110.0000.0000.0000.000
24A39ALA00.008-0.03720.511-0.026-0.0260.0000.0000.0000.000
25A40SER0-0.089-0.03622.381-0.004-0.0040.0000.0000.0000.000
26A41PHE0-0.0050.00217.057-0.033-0.0330.0000.0000.0000.000
27A42THR00.0970.03420.829-0.005-0.0050.0000.0000.0000.000
28A43GLU-1-0.835-0.93220.810-0.360-0.3600.0000.0000.0000.000
29A44GLU-1-0.942-0.94320.995-0.414-0.4140.0000.0000.0000.000
30A45ASP-1-0.733-0.82418.663-0.443-0.4430.0000.0000.0000.000
31A46ILE0-0.056-0.02416.320-0.100-0.1000.0000.0000.0000.000
32A47ASN0-0.075-0.05916.076-0.156-0.1560.0000.0000.0000.000
33A48GLY00.0270.02217.313-0.076-0.0760.0000.0000.0000.000
34A49LEU00.016-0.01012.928-0.097-0.0970.0000.0000.0000.000
35A50LYS10.8130.89511.6611.4621.4620.0000.0000.0000.000
36A51GLY0-0.026-0.00713.847-0.094-0.0940.0000.0000.0000.000
37A52VAL0-0.041-0.00411.5730.0820.0820.0000.0000.0000.000
38A53ASP-1-0.866-0.94011.795-1.820-1.8200.0000.0000.0000.000
39A54GLY00.0050.0118.270-0.095-0.0950.0000.0000.0000.000
40A55VAL0-0.048-0.0196.693-1.523-1.5230.0000.0000.0000.000
41A56LYS10.8210.9225.8273.3433.3430.0000.0000.0000.000
42A57GLN0-0.102-0.0687.5830.8910.8910.0000.0000.0000.000
43A58VAL00.0690.0528.779-0.268-0.2680.0000.0000.0000.000
44A59VAL0-0.048-0.0218.6680.1840.1840.0000.0000.0000.000
45A60ALA00.0280.01811.9390.1110.1110.0000.0000.0000.000
46A61SER0-0.035-0.04115.5460.0610.0610.0000.0000.0000.000
47A62ALA00.0220.02118.1710.0020.0020.0000.0000.0000.000
48A63VAL00.0070.01219.0120.0100.0100.0000.0000.0000.000
49A64LYS10.9120.94522.0260.0580.0580.0000.0000.0000.000
50A65SER00.0160.01425.7540.0030.0030.0000.0000.0000.000
51A66MET0-0.047-0.00727.621-0.016-0.0160.0000.0000.0000.000
52A67THR00.0410.00930.9780.0060.0060.0000.0000.0000.000
53A68ALA0-0.058-0.02631.880-0.012-0.0120.0000.0000.0000.000
54A69ARG10.8470.89933.956-0.012-0.0120.0000.0000.0000.000
55A70TYR0-0.016-0.02236.655-0.011-0.0110.0000.0000.0000.000
56A71HIS0-0.018-0.01038.4920.0040.0040.0000.0000.0000.000
57A72GLU-1-0.942-0.97542.3480.0180.0180.0000.0000.0000.000
58A73GLU-1-0.942-0.94038.2740.0530.0530.0000.0000.0000.000
59A74ASP-1-0.783-0.87737.2270.0220.0220.0000.0000.0000.000
60A75THR0-0.077-0.06031.6990.0140.0140.0000.0000.0000.000
61A76ASP-1-0.863-0.89731.1410.0530.0530.0000.0000.0000.000
62A77ILE0-0.055-0.04527.7820.0130.0130.0000.0000.0000.000
63A78THR00.0070.00022.356-0.002-0.0020.0000.0000.0000.000
64A79LEU0-0.047-0.01924.8080.0020.0020.0000.0000.0000.000
65A80ASN00.0330.00319.991-0.014-0.0140.0000.0000.0000.000
66A81GLY00.0190.00022.065-0.011-0.0110.0000.0000.0000.000
67A82ILE0-0.014-0.00617.283-0.011-0.0110.0000.0000.0000.000
68A83ASN00.0410.01414.2740.0660.0660.0000.0000.0000.000
69A84SER00.007-0.02016.6410.0090.0090.0000.0000.0000.000
70A85GLY00.0160.00212.851-0.004-0.0040.0000.0000.0000.000
71A86TYR00.0550.00411.564-0.024-0.0240.0000.0000.0000.000
72A87MET0-0.032-0.02212.6310.1410.1410.0000.0000.0000.000
73A88ASP-1-0.837-0.8749.903-1.591-1.5910.0000.0000.0000.000
74A89VAL0-0.024-0.0056.3070.0850.0850.0000.0000.0000.000
75A90LYS10.9090.9698.9090.4240.4240.0000.0000.0000.000
76A91LYS10.9060.9639.472-0.464-0.4640.0000.0000.0000.000
77A92LEU0-0.001-0.01112.9190.0440.0440.0000.0000.0000.000
78A93ASP-1-0.821-0.90316.4060.1360.1360.0000.0000.0000.000
79A94VAL0-0.043-0.01719.0720.0130.0130.0000.0000.0000.000
80A95GLN0-0.077-0.03122.7030.0130.0130.0000.0000.0000.000
81A96ASP-1-0.864-0.91925.6300.0420.0420.0000.0000.0000.000
82A97GLY00.003-0.01327.633-0.001-0.0010.0000.0000.0000.000
83A98ARG10.7890.87025.9080.0990.0990.0000.0000.0000.000
84A99THR00.0550.01319.8800.0190.0190.0000.0000.0000.000
85A100PHE0-0.025-0.01120.967-0.007-0.0070.0000.0000.0000.000
86A101THR0-0.011-0.02521.527-0.030-0.0300.0000.0000.0000.000
87A102ASP-1-0.796-0.90519.278-0.550-0.5500.0000.0000.0000.000
88A103ASN00.0200.01122.0100.0050.0050.0000.0000.0000.000
89A104ASP-1-0.836-0.86224.694-0.189-0.1890.0000.0000.0000.000
90A105PHE00.0350.01519.4120.0110.0110.0000.0000.0000.000
91A106LEU0-0.0190.00923.4270.0110.0110.0000.0000.0000.000
92A107SER0-0.035-0.05625.5870.0230.0230.0000.0000.0000.000
93A108GLY00.0250.01027.0260.0190.0190.0000.0000.0000.000
94A109LYS10.8110.89528.0210.2140.2140.0000.0000.0000.000
95A110ARG10.8890.93028.7980.0860.0860.0000.0000.0000.000
96A111ALA0-0.0130.00028.0230.0110.0110.0000.0000.0000.000
97A112GLY00.036-0.00126.278-0.011-0.0110.0000.0000.0000.000
98A113ILE0-0.0410.00421.8280.0040.0040.0000.0000.0000.000
99A114ILE00.0090.00824.3540.0090.0090.0000.0000.0000.000
100A115SER00.034-0.00923.5870.0000.0000.0000.0000.0000.000
101A116LYS10.8440.89624.943-0.185-0.1850.0000.0000.0000.000
102A117LYS10.8900.95526.666-0.194-0.1940.0000.0000.0000.000
103A118MET0-0.032-0.00327.087-0.013-0.0130.0000.0000.0000.000
104A119ALA00.0150.00629.429-0.013-0.0130.0000.0000.0000.000
105A120GLU-1-0.849-0.93130.3630.1330.1330.0000.0000.0000.000
106A121LYS10.9250.94831.957-0.104-0.1040.0000.0000.0000.000
107A122LEU00.0160.03232.918-0.005-0.0050.0000.0000.0000.000
108A123PHE00.0150.00633.566-0.010-0.0100.0000.0000.0000.000
109A124GLY00.0150.03335.979-0.003-0.0030.0000.0000.0000.000
110A125LYS10.8680.91335.667-0.039-0.0390.0000.0000.0000.000
111A126THR0-0.051-0.02037.433-0.003-0.0030.0000.0000.0000.000
112A127SER00.0570.02834.4990.0010.0010.0000.0000.0000.000
113A128PRO00.0460.03031.740-0.008-0.0080.0000.0000.0000.000
114A129LEU00.0050.01730.055-0.009-0.0090.0000.0000.0000.000
115A130GLY00.0130.00933.1240.0010.0010.0000.0000.0000.000
116A131LYS10.7720.89234.9520.0070.0070.0000.0000.0000.000
117A132ILE0-0.009-0.00734.790-0.003-0.0030.0000.0000.0000.000
118A133VAL00.0240.01732.2580.0070.0070.0000.0000.0000.000
119A134TRP0-0.003-0.01734.864-0.014-0.0140.0000.0000.0000.000
120A135ALA00.0330.01830.8770.0090.0090.0000.0000.0000.000
121A136GLY00.0470.00932.979-0.011-0.0110.0000.0000.0000.000
122A137GLY0-0.019-0.00534.481-0.005-0.0050.0000.0000.0000.000
123A138GLN00.0320.02233.651-0.011-0.0110.0000.0000.0000.000
124A139PRO0-0.046-0.00334.6140.0040.0040.0000.0000.0000.000
125A140VAL0-0.005-0.01629.562-0.014-0.0140.0000.0000.0000.000
126A141GLU-1-0.817-0.88431.936-0.075-0.0750.0000.0000.0000.000
127A142VAL00.0160.00129.421-0.006-0.0060.0000.0000.0000.000
128A143ILE0-0.033-0.01325.0610.0010.0010.0000.0000.0000.000
129A144GLY00.0320.01026.435-0.006-0.0060.0000.0000.0000.000
130A145VAL0-0.046-0.01626.5660.0040.0040.0000.0000.0000.000
131A146LEU00.012-0.00620.141-0.001-0.0010.0000.0000.0000.000
132A147LYS10.8180.89419.267-0.288-0.2880.0000.0000.0000.000
133A148GLU-1-0.855-0.91321.2550.2580.2580.0000.0000.0000.000
134A156GLY00.0660.02422.4790.0050.0050.0000.0000.0000.000
135A157LEU00.0180.02321.309-0.020-0.0200.0000.0000.0000.000
136A158SER00.0100.02124.141-0.002-0.0020.0000.0000.0000.000
137A159GLU-1-0.829-0.89419.7740.1810.1810.0000.0000.0000.000
138A160MET00.0000.00124.5450.0000.0000.0000.0000.0000.000
139A161TYR0-0.031-0.02717.827-0.017-0.0170.0000.0000.0000.000
140A162VAL00.034-0.00522.713-0.001-0.0010.0000.0000.0000.000
141A163PRO0-0.0150.00322.707-0.021-0.0210.0000.0000.0000.000
142A164PHE00.0020.01321.5700.0200.0200.0000.0000.0000.000
143A165ASN00.028-0.00523.5810.0290.0290.0000.0000.0000.000
144A166MET0-0.0030.02726.5840.0160.0160.0000.0000.0000.000
145A167LEU00.0020.00124.8690.0210.0210.0000.0000.0000.000
146A168LYS10.8410.92426.4040.2740.2740.0000.0000.0000.000
147A169THR0-0.017-0.01529.8650.0080.0080.0000.0000.0000.000
148A170SER0-0.107-0.05431.7510.0110.0110.0000.0000.0000.000
149A171PHE0-0.041-0.03630.3210.0130.0130.0000.0000.0000.000
150A172GLY00.0490.04131.9570.0050.0050.0000.0000.0000.000
151A173THR0-0.069-0.02926.0070.0040.0040.0000.0000.0000.000
152A174ASN0-0.014-0.03827.369-0.022-0.0220.0000.0000.0000.000
153A175ASP-1-0.797-0.84223.684-0.231-0.2310.0000.0000.0000.000
154A176TYR0-0.077-0.05818.8750.0130.0130.0000.0000.0000.000
155A177SER00.034-0.00319.881-0.009-0.0090.0000.0000.0000.000
156A178ASN0-0.038-0.00815.5820.0130.0130.0000.0000.0000.000
157A179VAL00.0650.02413.478-0.032-0.0320.0000.0000.0000.000
158A180SER0-0.024-0.0038.8420.1220.1220.0000.0000.0000.000
159A181VAL00.0210.0197.436-0.012-0.0120.0000.0000.0000.000
160A182GLN00.011-0.0033.327-0.582-0.0920.029-0.139-0.3800.000
161A183THR00.008-0.0172.616-3.772-1.1120.794-1.392-2.061-0.015
162A184GLU-1-0.891-0.9372.685-13.163-10.4620.862-1.714-1.848-0.018
163A185SER0-0.062-0.0512.519-5.779-4.2952.453-1.778-2.160-0.009
164A186ALA00.0350.0192.693-1.843-0.2261.6690.144-3.4300.009
165A187ASP-1-0.915-0.9753.434-0.794-0.9580.1680.265-0.2690.004
166A188GLN00.0380.0355.607-1.224-1.2240.0000.0000.0000.000
167A189ILE0-0.0190.0102.959-0.4680.0110.144-0.096-0.527-0.002
168A190LYS10.8970.9546.211-1.170-1.1700.0000.0000.0000.000
169A191SER00.0190.0189.7550.0510.0510.0000.0000.0000.000
170A192THR00.019-0.0107.7400.0220.0220.0000.0000.0000.000
171A193GLY00.0210.0099.3120.0430.0430.0000.0000.0000.000
172A194LYS10.9370.96910.4090.3620.3620.0000.0000.0000.000
173A195GLU-1-0.893-0.95013.274-0.885-0.8850.0000.0000.0000.000
174A196ALA00.0300.00912.0750.0620.0620.0000.0000.0000.000
175A197ALA0-0.0010.00114.0640.0870.0870.0000.0000.0000.000
176A198ARG10.7450.84116.1180.3590.3590.0000.0000.0000.000
177A199LEU00.0330.02116.7510.0390.0390.0000.0000.0000.000
178A200LEU0-0.006-0.00715.9840.0330.0330.0000.0000.0000.000
179A201ASN00.0010.01219.5800.0690.0690.0000.0000.0000.000
180A202ASP-1-0.779-0.84622.147-0.307-0.3070.0000.0000.0000.000
181A203ASN0-0.063-0.04620.8740.0200.0200.0000.0000.0000.000
182A204HIS10.7760.86322.3980.2940.2940.0000.0000.0000.000
183A205GLY0-0.0340.00125.7990.0250.0250.0000.0000.0000.000
184A206THR0-0.065-0.03623.8120.0170.0170.0000.0000.0000.000
185A207LYS10.6960.81325.4840.0440.0440.0000.0000.0000.000
186A208GLU-1-0.906-0.96622.190-0.094-0.0940.0000.0000.0000.000
187A209ALA00.0010.02321.5010.0110.0110.0000.0000.0000.000
188A210TYR0-0.020-0.01818.3330.0200.0200.0000.0000.0000.000
189A211GLN0-0.050-0.04116.2450.0170.0170.0000.0000.0000.000
190A212VAL00.0100.00910.944-0.028-0.0280.0000.0000.0000.000
191A213MET00.0250.01610.0400.0510.0510.0000.0000.0000.000
192A214ASN0-0.053-0.02412.1820.1040.1040.0000.0000.0000.000