FMODB

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

Last updated: 2024-04-25

All entries: 37426

Number of unique PDB entries: 7782

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FMODB ID: R9148

Calculation Name: 5X7V-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5X7V

Chain ID: A

ChEMBL ID:

UniProt ID: Q9Y010

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 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 177
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1909656.527408
FMO2-HF: Nuclear repulsion 1835680.77439
FMO2-HF: Total energy -73975.753018
FMO2-MP2: Total energy -74192.230471


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:29:PHE)


Summations of interaction energy for fragment #1(A:29:PHE)
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.
-23.81-16.33410.249-8.307-9.417-0.051
Interaction energy analysis for fragmet #1(A:29:PHE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.014 / q_NPA : -0.011
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].
3A31GLN0-0.014-0.0082.249-5.616-2.9521.962-1.687-2.9390.007
4A32ASP-1-0.852-0.9382.306-19.010-14.9278.279-6.474-5.888-0.058
5A33PHE0-0.028-0.0103.7130.6591.3880.008-0.146-0.5900.000
6A34GLU-1-0.897-0.9525.8560.6990.6990.0000.0000.0000.000
7A35ASP-1-0.867-0.9146.912-1.213-1.2130.0000.0000.0000.000
8A36ILE0-0.0100.0027.0330.2120.2120.0000.0000.0000.000
9A37GLN0-0.051-0.0399.6130.1300.1300.0000.0000.0000.000
10A38LYS10.8360.9089.1470.6460.6460.0000.0000.0000.000
11A39ASP-1-0.925-0.96212.786-0.708-0.7080.0000.0000.0000.000
12A40ILE0-0.046-0.01811.5660.0600.0600.0000.0000.0000.000
13A41GLU-1-0.804-0.89015.390-0.092-0.0920.0000.0000.0000.000
14A42GLN0-0.028-0.02316.5730.0750.0750.0000.0000.0000.000
15A43LEU0-0.067-0.03217.1640.0320.0320.0000.0000.0000.000
16A44ASP-1-0.852-0.92418.944-0.205-0.2050.0000.0000.0000.000
17A45ILE0-0.060-0.03220.6890.0280.0280.0000.0000.0000.000
18A46LYS10.8710.92521.1640.3030.3030.0000.0000.0000.000
19A47CYS00.0090.02323.9570.0120.0120.0000.0000.0000.000
20A48ALA00.0320.00625.5580.0160.0160.0000.0000.0000.000
21A49HIS0-0.056-0.02027.4550.0110.0110.0000.0000.0000.000
22A50GLU-1-0.895-0.95028.934-0.147-0.1470.0000.0000.0000.000
23A51GLN00.002-0.01227.5210.0100.0100.0000.0000.0000.000
24A52MET00.0360.02731.5180.0120.0120.0000.0000.0000.000
25A53ASN0-0.053-0.01733.4320.0130.0130.0000.0000.0000.000
26A54ILE0-0.003-0.01234.5830.0060.0060.0000.0000.0000.000
27A55GLN00.0110.00234.5930.0080.0080.0000.0000.0000.000
28A56LYS10.9580.96936.8370.0640.0640.0000.0000.0000.000
29A57GLN00.0420.03139.2630.0060.0060.0000.0000.0000.000
30A58TYR0-0.027-0.03439.5680.0060.0060.0000.0000.0000.000
31A59ASP-1-0.807-0.88240.256-0.042-0.0420.0000.0000.0000.000
32A60GLU-1-0.944-0.98142.773-0.042-0.0420.0000.0000.0000.000
33A61LYS10.8270.92542.7220.0640.0640.0000.0000.0000.000
34A62LYS10.8660.92040.1970.0490.0490.0000.0000.0000.000
35A63LYS10.9590.99547.0380.0340.0340.0000.0000.0000.000
36A64PRO00.0340.01149.2660.0020.0020.0000.0000.0000.000
37A65LEU00.0110.01448.1240.0020.0020.0000.0000.0000.000
38A66PHE00.007-0.00945.0170.0020.0020.0000.0000.0000.000
39A67GLU-1-0.837-0.91551.157-0.019-0.0190.0000.0000.0000.000
40A68LYS10.7770.87954.4630.0240.0240.0000.0000.0000.000
41A69ARG10.8350.90849.0010.0210.0210.0000.0000.0000.000
42A70ASP-1-0.726-0.85753.860-0.016-0.0160.0000.0000.0000.000
43A71GLU-1-0.817-0.88556.446-0.020-0.0200.0000.0000.0000.000
44A72ILE0-0.070-0.04856.8040.0010.0010.0000.0000.0000.000
45A73ILE0-0.0080.01254.0760.0010.0010.0000.0000.0000.000
46A74GLN0-0.0010.00158.7170.0010.0010.0000.0000.0000.000
47A75LYS10.8540.94061.8840.0180.0180.0000.0000.0000.000
48A76ILE0-0.0220.00058.9370.0000.0000.0000.0000.0000.000
49A77PRO0-0.009-0.02061.8060.0010.0010.0000.0000.0000.000
50A78GLY00.0630.04262.1890.0000.0000.0000.0000.0000.000
51A79PHE00.0160.01653.8830.0010.0010.0000.0000.0000.000
52A80TRP00.0960.03551.1020.0000.0000.0000.0000.0000.000
53A81ALA00.0130.02755.8170.0010.0010.0000.0000.0000.000
54A82ASN0-0.037-0.03857.2330.0020.0020.0000.0000.0000.000
55A83THR0-0.023-0.01051.852-0.001-0.0010.0000.0000.0000.000
56A84LEU00.009-0.00950.9900.0000.0000.0000.0000.0000.000
57A85ARG10.9410.97851.6660.0010.0010.0000.0000.0000.000
58A86LYS10.8230.90052.8540.0080.0080.0000.0000.0000.000
59A87HIS0-0.001-0.01044.202-0.001-0.0010.0000.0000.0000.000
60A88PRO00.0310.00846.6880.0020.0020.0000.0000.0000.000
61A89ALA0-0.0170.00545.6250.0010.0010.0000.0000.0000.000
62A90LEU0-0.040-0.03647.7830.0010.0010.0000.0000.0000.000
63A91SER0-0.036-0.00151.0050.0000.0000.0000.0000.0000.000
64A92ASP-1-0.915-0.95452.8410.0090.0090.0000.0000.0000.000
65A93ILE0-0.0330.00253.4950.0010.0010.0000.0000.0000.000
66A94VAL0-0.030-0.01455.988-0.001-0.0010.0000.0000.0000.000
67A95PRO00.011-0.01059.529-0.001-0.0010.0000.0000.0000.000
68A96GLU-1-0.812-0.91962.2060.0070.0070.0000.0000.0000.000
69A97ASP-1-0.730-0.83757.0700.0060.0060.0000.0000.0000.000
70A98ILE0-0.048-0.04159.771-0.001-0.0010.0000.0000.0000.000
71A99ASP-1-0.897-0.93561.5300.0010.0010.0000.0000.0000.000
72A100ILE0-0.028-0.00961.305-0.001-0.0010.0000.0000.0000.000
73A101LEU00.0330.00856.272-0.001-0.0010.0000.0000.0000.000
74A102ASN0-0.049-0.02160.163-0.002-0.0020.0000.0000.0000.000
75A103HIS0-0.110-0.05662.686-0.001-0.0010.0000.0000.0000.000
76A104LEU0-0.0210.00255.2940.0000.0000.0000.0000.0000.000
77A105VAL0-0.060-0.03659.786-0.001-0.0010.0000.0000.0000.000
78A106LYS10.7260.82554.6980.0150.0150.0000.0000.0000.000
79A107LEU00.0340.03250.3040.0010.0010.0000.0000.0000.000
80A108ASP-1-0.809-0.88350.934-0.018-0.0180.0000.0000.0000.000
81A109LEU00.0370.02043.1030.0020.0020.0000.0000.0000.000
82A110LYS10.7600.87246.2940.0170.0170.0000.0000.0000.000
83A111ASP-1-0.716-0.88940.447-0.019-0.0190.0000.0000.0000.000
84A112ASN0-0.097-0.04038.1100.0000.0000.0000.0000.0000.000
85A113MET0-0.069-0.00539.620-0.003-0.0030.0000.0000.0000.000
86A114ASP-1-0.823-0.87036.332-0.014-0.0140.0000.0000.0000.000
87A115ASN0-0.087-0.05131.250-0.002-0.0020.0000.0000.0000.000
88A116ASN00.027-0.01132.111-0.006-0.0060.0000.0000.0000.000
89A117GLY00.0090.02734.0540.0050.0050.0000.0000.0000.000
90A118SER0-0.014-0.04636.2230.0050.0050.0000.0000.0000.000
91A119TYR00.011-0.01239.628-0.005-0.0050.0000.0000.0000.000
92A120LYS10.8640.93142.9450.0100.0100.0000.0000.0000.000
93A121ILE0-0.0220.00745.600-0.002-0.0020.0000.0000.0000.000
94A122THR0-0.045-0.02348.9560.0020.0020.0000.0000.0000.000
95A123PHE00.0070.00151.015-0.001-0.0010.0000.0000.0000.000
96A124ILE00.0000.00055.5150.0010.0010.0000.0000.0000.000
97A125PHE00.006-0.01257.9490.0000.0000.0000.0000.0000.000
98A126GLY00.0240.00461.8790.0000.0000.0000.0000.0000.000
99A127GLU-1-0.746-0.87865.226-0.003-0.0030.0000.0000.0000.000
100A128LYS10.9540.97768.4110.0040.0040.0000.0000.0000.000
101A129ALA00.0410.03664.3770.0010.0010.0000.0000.0000.000
102A130LYS10.8180.89066.4770.0030.0030.0000.0000.0000.000
103A131GLU-1-0.932-0.93768.5950.0020.0020.0000.0000.0000.000
104A132PHE00.0640.01265.5300.0010.0010.0000.0000.0000.000
105A133MET0-0.043-0.00560.2730.0010.0010.0000.0000.0000.000
106A134GLU-1-0.906-0.92264.0890.0010.0010.0000.0000.0000.000
107A135PRO00.0180.00360.4210.0010.0010.0000.0000.0000.000
108A136LEU00.005-0.00861.9360.0000.0000.0000.0000.0000.000
109A137THR00.0190.00957.090-0.001-0.0010.0000.0000.0000.000
110A138LEU0-0.031-0.00855.6880.0010.0010.0000.0000.0000.000
111A139VAL00.003-0.00752.055-0.002-0.0020.0000.0000.0000.000
112A140LYS10.9200.96946.629-0.010-0.0100.0000.0000.0000.000
113A141HIS0-0.114-0.06844.537-0.003-0.0030.0000.0000.0000.000
114A142VAL00.0080.01141.1900.0020.0020.0000.0000.0000.000
115A143THR0-0.002-0.00738.990-0.002-0.0020.0000.0000.0000.000
116A144PHE00.0500.01535.1670.0030.0030.0000.0000.0000.000
117A145ASP-1-0.867-0.89433.8490.0350.0350.0000.0000.0000.000
118A146ASN0-0.025-0.02829.5730.0040.0040.0000.0000.0000.000
119A147ASN0-0.074-0.04128.420-0.001-0.0010.0000.0000.0000.000
120A148GLN0-0.0020.00932.7290.0030.0030.0000.0000.0000.000
121A149GLU-1-0.922-0.96635.8470.0110.0110.0000.0000.0000.000
122A150LYS10.8470.90237.190-0.033-0.0330.0000.0000.0000.000
123A151VAL00.0180.01541.643-0.004-0.0040.0000.0000.0000.000
124A152VAL0-0.0250.00343.1760.0010.0010.0000.0000.0000.000
125A153GLU-1-0.834-0.91645.989-0.004-0.0040.0000.0000.0000.000
126A154CYS00.035-0.00349.4710.0000.0000.0000.0000.0000.000
127A155THR0-0.0470.01352.0430.0000.0000.0000.0000.0000.000
128A156ARG10.8970.96254.956-0.010-0.0100.0000.0000.0000.000
129A157ILE00.000-0.00456.664-0.001-0.0010.0000.0000.0000.000
130A158LYS10.8430.90659.905-0.003-0.0030.0000.0000.0000.000
131A159TRP00.0270.00159.023-0.001-0.0010.0000.0000.0000.000
132A160LYS10.8670.93964.807-0.002-0.0020.0000.0000.0000.000
133A161GLU-1-0.870-0.95068.1400.0090.0090.0000.0000.0000.000
134A162GLY0-0.034-0.01569.543-0.001-0.0010.0000.0000.0000.000
135A163LYS10.8100.90067.452-0.004-0.0040.0000.0000.0000.000
136A164ASN00.0120.00561.225-0.001-0.0010.0000.0000.0000.000
137A165PRO00.0580.03960.2570.0010.0010.0000.0000.0000.000
138A166ILE0-0.041-0.02656.9450.0010.0010.0000.0000.0000.000
139A167ALA0-0.065-0.02459.7050.0010.0010.0000.0000.0000.000
140A168ALA00.0020.01460.7710.0000.0000.0000.0000.0000.000
141A181PRO00.015-0.00653.7490.0000.0000.0000.0000.0000.000
142A182LYS10.7830.89154.902-0.010-0.0100.0000.0000.0000.000
143A183TRP00.0350.03249.7620.0010.0010.0000.0000.0000.000
144A184SER0-0.006-0.04054.865-0.001-0.0010.0000.0000.0000.000
145A185ILE00.0430.01752.0160.0010.0010.0000.0000.0000.000
146A186PHE0-0.061-0.04053.0130.0000.0000.0000.0000.0000.000
147A187GLU-1-0.827-0.91452.7650.0170.0170.0000.0000.0000.000
148A188TRP0-0.019-0.00445.8850.0000.0000.0000.0000.0000.000
149A189PHE0-0.050-0.02249.8840.0000.0000.0000.0000.0000.000
150A190THR0-0.020-0.03349.3260.0000.0000.0000.0000.0000.000
151A191THR0-0.006-0.02047.840-0.002-0.0020.0000.0000.0000.000
152A192ASP-1-0.924-0.93046.9050.0240.0240.0000.0000.0000.000
153A193GLU-1-0.842-0.92341.1830.0320.0320.0000.0000.0000.000
154A194LEU0-0.061-0.03644.169-0.001-0.0010.0000.0000.0000.000
155A195GLN0-0.043-0.03340.6440.0010.0010.0000.0000.0000.000
156A196ASP-1-0.918-0.95242.9300.0340.0340.0000.0000.0000.000
157A197LYS10.8500.91344.857-0.022-0.0220.0000.0000.0000.000
158A198PRO0-0.004-0.00345.0740.0000.0000.0000.0000.0000.000
159A199ASP-1-0.716-0.85842.1990.0080.0080.0000.0000.0000.000
160A200VAL0-0.020-0.02044.443-0.002-0.0020.0000.0000.0000.000
161A201GLY00.001-0.00544.949-0.003-0.0030.0000.0000.0000.000
162A202GLU-1-0.731-0.84837.775-0.005-0.0050.0000.0000.0000.000
163A203LEU0-0.0280.00041.674-0.003-0.0030.0000.0000.0000.000
164A204ILE0-0.014-0.00943.622-0.003-0.0030.0000.0000.0000.000
165A205ARG10.7880.88836.3350.0100.0100.0000.0000.0000.000
166A206ARG10.8360.91135.308-0.002-0.0020.0000.0000.0000.000
167A207GLU-1-0.881-0.93440.241-0.005-0.0050.0000.0000.0000.000
168A208ILE0-0.058-0.02142.684-0.002-0.0020.0000.0000.0000.000
169A209TRP0-0.0070.00644.4220.0000.0000.0000.0000.0000.000
170A210HIS0-0.014-0.01142.880-0.001-0.0010.0000.0000.0000.000
171A211ASN0-0.024-0.02945.0220.0000.0000.0000.0000.0000.000
172A212PRO00.0690.04847.5770.0010.0010.0000.0000.0000.000
173A213LEU00.0120.00750.2920.0020.0020.0000.0000.0000.000
174A214SER00.0200.00247.2210.0010.0010.0000.0000.0000.000
175A215TYR00.0330.07044.7120.0010.0010.0000.0000.0000.000
176A216TYR0-0.0020.00851.2830.0010.0010.0000.0000.0000.000
177A217LEU0-0.089-0.06752.3320.0020.0020.0000.0000.0000.000