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: 43V6N

Calculation Name: 4C47-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4C47

Chain ID: A

ChEMBL ID:

UniProt ID: Q8ZL65

Base Structure: X-ray

Registration Date: 2023-06-19

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 191
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1674107.02924
FMO2-HF: Nuclear repulsion 1598163.902585
FMO2-HF: Total energy -75943.126655
FMO2-MP2: Total energy -76166.942545


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:23:ASP)


Summations of interaction energy for fragment #1(A:23:ASP)
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.
-17.004-10.680.92-3.453-3.7910.029
Interaction energy analysis for fragmet #1(A:23:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.848 / q_NPA : -0.917
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].
3A25PHE0-0.039-0.0192.536-24.267-18.0360.920-3.398-3.7530.029
4A26ALA0-0.009-0.0014.131-0.793-0.7000.000-0.055-0.0380.000
5A27ASP-1-0.784-0.8926.71828.37428.3740.0000.0000.0000.000
6A28LYS10.8220.8897.465-23.802-23.8020.0000.0000.0000.000
7A29HIS0-0.047-0.03610.399-1.672-1.6720.0000.0000.0000.000
8A30LEU00.0260.0059.939-1.487-1.4870.0000.0000.0000.000
9A31VAL0-0.006-0.01210.790-1.364-1.3640.0000.0000.0000.000
10A32GLU-1-0.857-0.92013.27916.25616.2560.0000.0000.0000.000
11A33GLU-1-0.873-0.91114.86514.89914.8990.0000.0000.0000.000
12A34MET0-0.046-0.02713.901-0.529-0.5290.0000.0000.0000.000
13A35LYS10.9460.98917.046-16.147-16.1470.0000.0000.0000.000
14A36GLU-1-0.771-0.87519.33012.18212.1820.0000.0000.0000.000
15A37GLN00.0180.01020.221-0.520-0.5200.0000.0000.0000.000
16A38GLN0-0.0070.00120.889-0.326-0.3260.0000.0000.0000.000
17A39LYS10.8050.88022.693-13.297-13.2970.0000.0000.0000.000
18A40GLU-1-0.875-0.91124.98510.56510.5650.0000.0000.0000.000
19A41GLN0-0.041-0.03221.955-0.446-0.4460.0000.0000.0000.000
20A42GLU-1-0.843-0.91226.7029.8559.8550.0000.0000.0000.000
21A43THR0-0.043-0.02528.624-0.513-0.5130.0000.0000.0000.000
22A44LYS10.8400.90427.712-10.647-10.6470.0000.0000.0000.000
23A45ILE00.0280.02028.250-0.337-0.3370.0000.0000.0000.000
24A46ASN0-0.035-0.03132.019-0.540-0.5400.0000.0000.0000.000
25A47LEU0-0.053-0.01734.648-0.331-0.3310.0000.0000.0000.000
26A48LEU00.0170.00033.149-0.290-0.2900.0000.0000.0000.000
27A49GLU-1-0.827-0.90135.6068.1228.1220.0000.0000.0000.000
28A50LYS10.8490.93238.238-7.442-7.4420.0000.0000.0000.000
29A51GLN0-0.030-0.02938.695-0.098-0.0980.0000.0000.0000.000
30A52GLN00.007-0.00640.419-0.078-0.0780.0000.0000.0000.000
31A53LYS10.8930.94239.387-7.949-7.9490.0000.0000.0000.000
32A54GLU-1-0.842-0.91244.3936.5886.5880.0000.0000.0000.000
33A55GLN0-0.039-0.02242.531-0.202-0.2020.0000.0000.0000.000
34A56GLU-1-0.861-0.91545.6486.5266.5260.0000.0000.0000.000
35A57ALA0-0.008-0.00347.870-0.164-0.1640.0000.0000.0000.000
36A58LYS10.8360.90048.030-6.498-6.4980.0000.0000.0000.000
37A59ILE00.0460.02347.977-0.152-0.1520.0000.0000.0000.000
38A60ASN00.0210.01551.891-0.177-0.1770.0000.0000.0000.000
39A61LEU0-0.048-0.01353.769-0.149-0.1490.0000.0000.0000.000
40A62LEU00.0120.00353.457-0.132-0.1320.0000.0000.0000.000
41A63GLU-1-0.851-0.91654.1505.6515.6510.0000.0000.0000.000
42A64LYS10.8620.91556.180-5.644-5.6440.0000.0000.0000.000
43A65GLN00.0100.01558.993-0.115-0.1150.0000.0000.0000.000
44A66GLN00.0230.01358.054-0.117-0.1170.0000.0000.0000.000
45A67ALA00.0310.01561.764-0.093-0.0930.0000.0000.0000.000
46A68THR0-0.024-0.02463.709-0.119-0.1190.0000.0000.0000.000
47A69ILE00.0280.02163.075-0.109-0.1090.0000.0000.0000.000
48A70ILE00.0120.02763.268-0.103-0.1030.0000.0000.0000.000
49A71ASN0-0.005-0.00667.347-0.136-0.1360.0000.0000.0000.000
50A72THR0-0.007-0.01169.566-0.104-0.1040.0000.0000.0000.000
51A73THR00.003-0.01969.003-0.079-0.0790.0000.0000.0000.000
52A74LYS10.9650.98571.110-4.454-4.4540.0000.0000.0000.000
53A75LYS10.8350.91873.453-4.339-4.3390.0000.0000.0000.000
54A76VAL00.0310.01874.274-0.068-0.0680.0000.0000.0000.000
55A77THR00.0410.01574.050-0.035-0.0350.0000.0000.0000.000
56A78GLU-1-0.808-0.88176.9213.7773.7770.0000.0000.0000.000
57A79VAL0-0.036-0.01779.618-0.063-0.0630.0000.0000.0000.000
58A80VAL00.0420.01578.626-0.055-0.0550.0000.0000.0000.000
59A81GLY00.0440.03180.916-0.044-0.0440.0000.0000.0000.000
60A82ARG10.8250.88782.138-3.853-3.8530.0000.0000.0000.000
61A83VAL0-0.022-0.00584.735-0.055-0.0550.0000.0000.0000.000
62A84GLU-1-0.789-0.87283.2893.7503.7500.0000.0000.0000.000
63A85ARG10.8190.88783.434-3.767-3.7670.0000.0000.0000.000
64A86LYS10.9450.97288.227-3.512-3.5120.0000.0000.0000.000
65A87GLN00.0140.00887.161-0.007-0.0070.0000.0000.0000.000
66A88ARG10.8340.89684.400-3.700-3.7000.0000.0000.0000.000
67A89LEU0-0.093-0.03191.779-0.023-0.0230.0000.0000.0000.000
68A90PHE0-0.027-0.00394.535-0.036-0.0360.0000.0000.0000.000
69A91ASP-1-0.885-0.93791.0103.4563.4560.0000.0000.0000.000
70A92TYR0-0.068-0.05691.0230.0070.0070.0000.0000.0000.000
71A93THR0-0.007-0.01696.8360.0120.0120.0000.0000.0000.000
72A94GLU-1-0.836-0.88792.2913.4503.4500.0000.0000.0000.000
73A95LEU0-0.0180.00197.142-0.007-0.0070.0000.0000.0000.000
74A96ASP-1-0.738-0.84799.0033.1863.1860.0000.0000.0000.000
75A97PRO00.0210.018100.794-0.024-0.0240.0000.0000.0000.000
76A98SER0-0.023-0.021102.844-0.030-0.0300.0000.0000.0000.000
77A99GLN0-0.076-0.041102.272-0.022-0.0220.0000.0000.0000.000
78A100THR0-0.021-0.017103.5540.0140.0140.0000.0000.0000.000
79A101HIS00.0040.002106.099-0.027-0.0270.0000.0000.0000.000
80A102TYR00.0050.003109.053-0.001-0.0010.0000.0000.0000.000
81A103PHE0-0.040-0.013104.2040.0310.0310.0000.0000.0000.000
82A104ILE00.0180.004103.677-0.028-0.0280.0000.0000.0000.000
83A105ILE00.0260.026100.7480.0330.0330.0000.0000.0000.000
84A106ASN00.009-0.003101.040-0.029-0.0290.0000.0000.0000.000
85A107ASN00.0720.02898.4000.0090.0090.0000.0000.0000.000
86A108GLY0-0.0100.00198.6370.0260.0260.0000.0000.0000.000
87A109ASN0-0.109-0.05299.9650.0010.0010.0000.0000.0000.000
88A110ILE00.0580.027102.733-0.033-0.0330.0000.0000.0000.000
89A111GLY0-0.0100.002103.7670.0330.0330.0000.0000.0000.000
90A112LEU00.0080.003105.780-0.034-0.0340.0000.0000.0000.000
91A113ALA0-0.007-0.008106.6080.0300.0300.0000.0000.0000.000
92A114GLY00.0410.017108.737-0.015-0.0150.0000.0000.0000.000
93A115ARG10.7890.879109.691-2.737-2.7370.0000.0000.0000.000
94A116ILE00.0020.001105.855-0.014-0.0140.0000.0000.0000.000
95A117LEU0-0.063-0.021110.529-0.012-0.0120.0000.0000.0000.000
96A118SER0-0.045-0.050112.570-0.014-0.0140.0000.0000.0000.000
97A119ILE0-0.015-0.021106.6190.0250.0250.0000.0000.0000.000
98A120GLU-1-0.767-0.848110.0062.8082.8080.0000.0000.0000.000
99A121PRO0-0.036-0.027108.9950.0330.0330.0000.0000.0000.000
100A122ILE0-0.019-0.002107.194-0.031-0.0310.0000.0000.0000.000
101A123ASP-1-0.825-0.914107.2943.0003.0000.0000.0000.0000.000
102A124ASN0-0.0130.001100.6690.0260.0260.0000.0000.0000.000
103A125GLY00.0090.008103.5820.0320.0320.0000.0000.0000.000
104A126SER00.002-0.020104.453-0.027-0.0270.0000.0000.0000.000
105A127VAL0-0.021-0.014106.5870.0130.0130.0000.0000.0000.000
106A128ILE0-0.0100.011104.480-0.015-0.0150.0000.0000.0000.000
107A129HIS00.0530.046108.9540.0040.0040.0000.0000.0000.000
108A130LEU0-0.022-0.022108.2700.0130.0130.0000.0000.0000.000
109A131ASP-1-0.764-0.842112.2672.7262.7260.0000.0000.0000.000
110A132LEU0-0.005-0.007107.8340.0310.0310.0000.0000.0000.000
111A133VAL00.0000.006111.167-0.029-0.0290.0000.0000.0000.000
112A134ASN00.0240.006110.8050.0570.0570.0000.0000.0000.000
113A135LEU0-0.042-0.024107.773-0.025-0.0250.0000.0000.0000.000
114A136LEU0-0.0180.000107.503-0.001-0.0010.0000.0000.0000.000
115A137SER0-0.029-0.025111.564-0.013-0.0130.0000.0000.0000.000
116A138ILE00.0230.011110.606-0.026-0.0260.0000.0000.0000.000
117A139PRO00.0010.001113.3030.0230.0230.0000.0000.0000.000
118A140VAL0-0.0140.008109.1480.0190.0190.0000.0000.0000.000
119A141SER00.010-0.020110.950-0.009-0.0090.0000.0000.0000.000
120A142ASN0-0.025-0.009108.3230.0040.0040.0000.0000.0000.000
121A143LEU00.0100.025105.6320.0330.0330.0000.0000.0000.000
122A144ALA00.0430.043103.041-0.016-0.0160.0000.0000.0000.000
123A145PHE0-0.003-0.002101.9830.0240.0240.0000.0000.0000.000
124A146ASN0-0.0210.00296.6030.0040.0040.0000.0000.0000.000
125A147MET00.001-0.00798.446-0.011-0.0110.0000.0000.0000.000
126A148THR0-0.021-0.02592.9940.0340.0340.0000.0000.0000.000
127A149TRP0-0.017-0.00996.455-0.013-0.0130.0000.0000.0000.000
128A150GLY00.0340.00895.3610.0310.0310.0000.0000.0000.000
129A151THR00.0550.02693.296-0.026-0.0260.0000.0000.0000.000
130A152LYS10.8500.91894.680-3.244-3.2440.0000.0000.0000.000
131A153LYS10.9230.97887.721-3.542-3.5420.0000.0000.0000.000
132A154PRO0-0.0100.01087.311-0.009-0.0090.0000.0000.0000.000
133A155SER00.021-0.00587.9180.0010.0010.0000.0000.0000.000
134A156GLU-1-0.848-0.91181.2773.8943.8940.0000.0000.0000.000
135A157ALA00.026-0.00480.104-0.012-0.0120.0000.0000.0000.000
136A158LYS10.8700.92579.282-3.863-3.8630.0000.0000.0000.000
137A159ASP-1-0.798-0.90180.5113.7893.7890.0000.0000.0000.000
138A160LEU0-0.0260.00382.907-0.040-0.0400.0000.0000.0000.000
139A161PRO0-0.029-0.01980.057-0.032-0.0320.0000.0000.0000.000
140A162ARG10.9260.94780.084-3.868-3.8680.0000.0000.0000.000
141A163TRP00.0270.00885.066-0.003-0.0030.0000.0000.0000.000
142A164LYS10.9480.96582.475-3.802-3.8020.0000.0000.0000.000
143A165GLN0-0.040-0.01982.075-0.014-0.0140.0000.0000.0000.000
144A166LEU0-0.022-0.00287.361-0.016-0.0160.0000.0000.0000.000
145A167LEU0-0.090-0.01790.416-0.043-0.0430.0000.0000.0000.000
146A168LEU0-0.0040.01492.6370.0120.0120.0000.0000.0000.000
147A169ASN00.015-0.02093.917-0.012-0.0120.0000.0000.0000.000
148A170THR0-0.028-0.00796.0090.0000.0000.0000.0000.0000.000
149A171LYS10.8650.93197.181-3.212-3.2120.0000.0000.0000.000
150A172MET0-0.039-0.017100.221-0.012-0.0120.0000.0000.0000.000
151A173ASP-1-0.841-0.936103.1833.0863.0860.0000.0000.0000.000
152A174SER0-0.083-0.059105.467-0.032-0.0320.0000.0000.0000.000
153A175THR00.0350.012109.0590.0130.0130.0000.0000.0000.000
154A176ILE0-0.044-0.016111.534-0.030-0.0300.0000.0000.0000.000
155A177GLU-1-0.838-0.902112.2962.7522.7520.0000.0000.0000.000
156A178LEU0-0.051-0.027110.286-0.015-0.0150.0000.0000.0000.000
157A179LEU00.0780.027114.2280.0110.0110.0000.0000.0000.000
158A180PRO0-0.0030.000115.3360.0090.0090.0000.0000.0000.000
159A181GLY0-0.022-0.005115.397-0.026-0.0260.0000.0000.0000.000
160A182ALA0-0.019-0.010116.989-0.014-0.0140.0000.0000.0000.000
161A183TRP0-0.028-0.029112.5420.0310.0310.0000.0000.0000.000
162A184THR0-0.009-0.004114.884-0.034-0.0340.0000.0000.0000.000
163A185ASN0-0.057-0.034114.4920.0250.0250.0000.0000.0000.000
164A186VAL00.002-0.004109.5400.0040.0040.0000.0000.0000.000
165A187THR00.0070.000110.713-0.008-0.0080.0000.0000.0000.000
166A188LEU0-0.013-0.011104.5430.0180.0180.0000.0000.0000.000
167A189THR00.001-0.007106.308-0.006-0.0060.0000.0000.0000.000
168A190LEU0-0.028-0.006101.8530.0260.0260.0000.0000.0000.000
169A191LYS10.8540.898102.402-3.019-3.0190.0000.0000.0000.000
170A192GLY00.0210.00399.4540.0310.0310.0000.0000.0000.000
171A193VAL0-0.015-0.00598.3330.0310.0310.0000.0000.0000.000
172A194SER00.0190.028101.048-0.018-0.0180.0000.0000.0000.000
173A195PRO00.0710.024103.3600.0310.0310.0000.0000.0000.000
174A196ASN0-0.0060.016102.8890.0000.0000.0000.0000.0000.000
175A197ASN0-0.054-0.03999.4230.0340.0340.0000.0000.0000.000
176A198LEU00.0000.00799.4040.0430.0430.0000.0000.0000.000
177A199LYS10.8740.93198.499-3.129-3.1290.0000.0000.0000.000
178A200TYR0-0.094-0.07893.1690.0330.0330.0000.0000.0000.000
179A201LEU00.0200.00997.684-0.012-0.0120.0000.0000.0000.000
180A202LYS10.8170.91391.344-3.433-3.4330.0000.0000.0000.000
181A203ILE00.0180.00597.411-0.010-0.0100.0000.0000.0000.000
182A204GLY00.0650.02397.8600.0110.0110.0000.0000.0000.000
183A205ILE0-0.037-0.00698.905-0.011-0.0110.0000.0000.0000.000
184A206ASP-1-0.805-0.89598.4253.2623.2620.0000.0000.0000.000
185A207MET00.0170.00699.632-0.039-0.0390.0000.0000.0000.000
186A208GLU-1-0.956-0.95698.3443.2093.2090.0000.0000.0000.000
187A209ASN0-0.042-0.029100.936-0.025-0.0250.0000.0000.0000.000
188A210VAL0-0.0190.004104.409-0.034-0.0340.0000.0000.0000.000
189A211ILE0-0.031-0.009106.3820.0030.0030.0000.0000.0000.000
190A212PHE00.005-0.013105.387-0.001-0.0010.0000.0000.0000.000
191A213ASP-1-0.951-0.969111.0422.7322.7320.0000.0000.0000.000