FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: NN5MQ

Calculation Name: 5D06-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5D06

Chain ID: A

ChEMBL ID:

UniProt ID: Q6FSK0

Base Structure: X-ray

Registration Date: 2023-09-24

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 1526
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -58417744.373577
FMO2-HF: Nuclear repulsion 57806562.636004
FMO2-HF: Total energy -611181.737573
FMO2-MP2: Total energy -612967.325905


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:3:ALA)


Summations of interaction energy for fragment #1(A:3:ALA)
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.
-7.362-1.4292.519-3.758-4.694-0.019
Interaction energy analysis for fragmet #1(A:3:ALA)
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].
3A5ARG10.8880.9303.782-3.338-1.105-0.031-1.119-1.0830.001
4A6THR00.004-0.0026.547-0.284-0.2840.0000.0000.0000.000
5A7LEU0-0.0130.0019.2160.0100.0100.0000.0000.0000.000
6A8LEU0-0.017-0.01212.788-0.041-0.0410.0000.0000.0000.000
7A9LEU0-0.002-0.01015.6110.0270.0270.0000.0000.0000.000
8A10ARG10.8820.92918.879-0.026-0.0260.0000.0000.0000.000
9A11LEU0-0.0190.00121.7120.0130.0130.0000.0000.0000.000
10A12SER00.001-0.00824.829-0.008-0.0080.0000.0000.0000.000
11A13ASP-1-0.771-0.88828.318-0.010-0.0100.0000.0000.0000.000
12A14SER00.006-0.01430.906-0.003-0.0030.0000.0000.0000.000
13A15GLY0-0.003-0.02127.6390.0030.0030.0000.0000.0000.000
14A16GLU-1-0.857-0.89326.9270.0390.0390.0000.0000.0000.000
15A17PRO00.0330.02323.601-0.006-0.0060.0000.0000.0000.000
16A18VAL00.0000.00224.1530.0010.0010.0000.0000.0000.000
17A19THR0-0.028-0.01023.9320.0080.0080.0000.0000.0000.000
18A20SER00.003-0.00621.259-0.012-0.0120.0000.0000.0000.000
19A21CYS0-0.045-0.02422.579-0.007-0.0070.0000.0000.0000.000
20A22SER0-0.0110.00725.3110.0000.0000.0000.0000.0000.000
21A23TYR0-0.025-0.03821.6280.0010.0010.0000.0000.0000.000
22A24GLY00.0190.01727.4710.0020.0020.0000.0000.0000.000
23A25GLN0-0.038-0.02029.1580.0030.0030.0000.0000.0000.000
24A26GLY00.0270.00227.0450.0050.0050.0000.0000.0000.000
25A27VAL00.0170.00723.515-0.007-0.0070.0000.0000.0000.000
26A28LEU0-0.0070.00720.6550.0090.0090.0000.0000.0000.000
27A29THR0-0.006-0.01219.2150.0070.0070.0000.0000.0000.000
28A30LEU0-0.0090.00713.3570.0000.0000.0000.0000.0000.000
29A31PRO00.0060.01112.807-0.007-0.0070.0000.0000.0000.000
30A32SER0-0.0120.00113.7450.1070.1070.0000.0000.0000.000
31A33LEU00.016-0.0038.951-0.011-0.0110.0000.0000.0000.000
32A34PRO0-0.0180.02210.525-0.023-0.0230.0000.0000.0000.000
33A35LEU00.0140.0079.0850.2860.2860.0000.0000.0000.000
34A36PRO00.0210.0014.778-0.298-0.209-0.001-0.005-0.0820.000
35A37GLN0-0.052-0.0277.054-0.379-0.3790.0000.0000.0000.000
36A38GLY00.0300.0229.315-0.137-0.1370.0000.0000.0000.000
37A39LYS10.8760.9435.545-0.375-0.3750.0000.0000.0000.000
38A40LYS10.8710.92410.463-0.180-0.1800.0000.0000.0000.000
39A41LEU00.004-0.00511.6220.0450.0450.0000.0000.0000.000
40A42GLY00.0430.01711.885-0.062-0.0620.0000.0000.0000.000
41A43ASP-1-0.886-0.9379.3800.2370.2370.0000.0000.0000.000
42A44MET0-0.038-0.0152.758-0.949-0.3360.134-0.278-0.4690.002
43A45PRO00.0030.0096.4350.1040.1040.0000.0000.0000.000
44A46VAL0-0.044-0.0136.9160.3420.3420.0000.0000.0000.000
45A47TYR0-0.022-0.0458.2660.3870.3870.0000.0000.0000.000
46A48THR0-0.033-0.0118.763-0.108-0.1080.0000.0000.0000.000
47A49VAL0-0.007-0.00510.4710.0060.0060.0000.0000.0000.000
48A50LYS10.8730.90011.4830.2000.2000.0000.0000.0000.000
49A51LEU00.0020.01715.1980.0180.0180.0000.0000.0000.000
50A52ALA00.0270.01718.910-0.021-0.0210.0000.0000.0000.000
51A53ILE0-0.034-0.02720.7530.0150.0150.0000.0000.0000.000
52A54PRO00.0330.02224.348-0.009-0.0090.0000.0000.0000.000
53A55ALA00.0720.04226.9610.0030.0030.0000.0000.0000.000
54A56GLY0-0.052-0.02128.4770.0040.0040.0000.0000.0000.000
55A57SER0-0.034-0.00129.2740.0050.0050.0000.0000.0000.000
56A58PRO0-0.018-0.01232.065-0.002-0.0020.0000.0000.0000.000
57A59VAL00.0370.02128.762-0.001-0.0010.0000.0000.0000.000
58A60THR0-0.061-0.04628.073-0.002-0.0020.0000.0000.0000.000
59A61ARG10.7810.88830.3710.0090.0090.0000.0000.0000.000
60A62ASP-1-0.902-0.96532.541-0.018-0.0180.0000.0000.0000.000
61A63GLY00.0130.02729.8130.0040.0040.0000.0000.0000.000
62A64LEU0-0.077-0.05527.030-0.005-0.0050.0000.0000.0000.000
63A65ILE00.0260.00721.4620.0070.0070.0000.0000.0000.000
64A66TRP00.004-0.01624.500-0.005-0.0050.0000.0000.0000.000
65A67THR00.0430.00219.7830.0100.0100.0000.0000.0000.000
66A68ASN0-0.0160.00623.110-0.001-0.0010.0000.0000.0000.000
67A69CYS00.0060.01217.6410.0160.0160.0000.0000.0000.000
68A70PRO0-0.042-0.02518.244-0.019-0.0190.0000.0000.0000.000
69A71PRO0-0.032-0.01117.3920.0060.0060.0000.0000.0000.000
70A72ASP-1-0.827-0.91514.9630.0080.0080.0000.0000.0000.000
71A73PHE0-0.021-0.00714.3100.0180.0180.0000.0000.0000.000
72A74SER0-0.042-0.02316.2260.0050.0050.0000.0000.0000.000
73A75THR0-0.113-0.04419.473-0.006-0.0060.0000.0000.0000.000
74A76GLN00.0390.01720.3720.0150.0150.0000.0000.0000.000
75A77PHE0-0.016-0.00521.427-0.009-0.0090.0000.0000.0000.000
76A78ASP-1-0.887-0.95423.0660.0520.0520.0000.0000.0000.000
77A79ARG10.7670.87025.913-0.096-0.0960.0000.0000.0000.000
78A80GLU-1-0.857-0.94827.5100.0460.0460.0000.0000.0000.000
79A81LYS10.8820.96225.616-0.034-0.0340.0000.0000.0000.000
80A82PHE0-0.017-0.01125.4620.0050.0050.0000.0000.0000.000
81A83TYR00.007-0.00922.507-0.012-0.0120.0000.0000.0000.000
82A84LYS10.8790.94824.4740.0060.0060.0000.0000.0000.000
83A85LYS10.9190.96517.1630.0290.0290.0000.0000.0000.000
84A86ILE0-0.030-0.01823.3990.0050.0050.0000.0000.0000.000
85A87ILE00.0280.03023.832-0.008-0.0080.0000.0000.0000.000
86A88LYS10.8450.91822.9300.0810.0810.0000.0000.0000.000
87A89THR0-0.021-0.01726.050-0.003-0.0030.0000.0000.0000.000
88A90SER00.0480.02427.839-0.004-0.0040.0000.0000.0000.000
89A91PHE0-0.069-0.03629.6820.0050.0050.0000.0000.0000.000
90A92HIS0-0.048-0.03229.1720.0050.0050.0000.0000.0000.000
91A93GLU-1-0.884-0.94324.400-0.091-0.0910.0000.0000.0000.000
92A94ASP-1-0.848-0.90922.773-0.043-0.0430.0000.0000.0000.000
93A95ASP-1-0.824-0.89721.912-0.089-0.0890.0000.0000.0000.000
94A96HIS0-0.008-0.02217.0360.0130.0130.0000.0000.0000.000
95A97ILE0-0.035-0.02017.964-0.012-0.0120.0000.0000.0000.000
96A98ASP-1-0.827-0.88812.254-0.185-0.1850.0000.0000.0000.000
97A99LEU0-0.054-0.03814.806-0.001-0.0010.0000.0000.0000.000
98A100ASP-1-0.843-0.90210.294-0.078-0.0780.0000.0000.0000.000
99A101ILE0-0.016-0.00911.511-0.007-0.0070.0000.0000.0000.000
100A102TYR00.0440.01011.1050.0980.0980.0000.0000.0000.000
101A103VAL00.005-0.00112.9780.0450.0450.0000.0000.0000.000
102A104PRO00.0050.02715.357-0.017-0.0170.0000.0000.0000.000
103A105GLY00.0170.00917.289-0.033-0.0330.0000.0000.0000.000
104A106THR0-0.0170.00220.2640.0140.0140.0000.0000.0000.000
105A107TYR0-0.041-0.02617.270-0.033-0.0330.0000.0000.0000.000
106A108CYS0-0.058-0.03621.542-0.005-0.0050.0000.0000.0000.000
107A109PHE00.0310.00821.907-0.006-0.0060.0000.0000.0000.000
108A110TYR0-0.0110.00724.2750.0040.0040.0000.0000.0000.000
109A111LEU00.0250.02424.995-0.005-0.0050.0000.0000.0000.000
110A112SER00.0100.01128.5590.0030.0030.0000.0000.0000.000
111A113PHE0-0.0010.00930.838-0.004-0.0040.0000.0000.0000.000
112A114LYS10.8180.91533.3760.0150.0150.0000.0000.0000.000
113A115ASN0-0.005-0.01236.839-0.002-0.0020.0000.0000.0000.000
114A116ASP-1-0.779-0.87439.279-0.007-0.0070.0000.0000.0000.000
115A117LYS10.7940.88041.767-0.002-0.0020.0000.0000.0000.000
116A118ASP-1-0.819-0.90041.508-0.011-0.0110.0000.0000.0000.000
117A119GLU-1-0.835-0.89341.7050.0020.0020.0000.0000.0000.000
118A120LEU0-0.034-0.01234.709-0.001-0.0010.0000.0000.0000.000
119A121GLU-1-0.888-0.94136.3480.0100.0100.0000.0000.0000.000
120A122THR00.004-0.01932.993-0.002-0.0020.0000.0000.0000.000
121A123THR0-0.0090.02329.5840.0000.0000.0000.0000.0000.000
122A124ARG10.8610.89031.335-0.038-0.0380.0000.0000.0000.000
123A125LYS10.8980.97128.280-0.050-0.0500.0000.0000.0000.000
124A126PHE00.0200.00925.2830.0020.0020.0000.0000.0000.000
125A127TYR00.007-0.01523.885-0.004-0.0040.0000.0000.0000.000
126A128PHE00.0110.00516.743-0.005-0.0050.0000.0000.0000.000
127A129VAL00.0150.01920.4870.0010.0010.0000.0000.0000.000
128A130VAL0-0.031-0.01114.3240.0240.0240.0000.0000.0000.000
129A131LEU00.0190.00317.292-0.019-0.0190.0000.0000.0000.000
130A132PRO00.0130.01816.7150.0470.0470.0000.0000.0000.000
131A133ILE0-0.020-0.01413.3640.0170.0170.0000.0000.0000.000
132A134LEU00.0040.00817.018-0.043-0.0430.0000.0000.0000.000
133A135SER00.0060.00317.8580.0300.0300.0000.0000.0000.000
134A136VAL0-0.023-0.00519.919-0.021-0.0210.0000.0000.0000.000
135A137ASN0-0.035-0.00322.300-0.024-0.0240.0000.0000.0000.000
136A138ASP-1-0.896-0.95817.8020.2310.2310.0000.0000.0000.000
137A139LYS10.8760.93017.640-0.145-0.1450.0000.0000.0000.000
138A140PHE00.019-0.00615.355-0.008-0.0080.0000.0000.0000.000
139A141ILE0-0.004-0.00217.510-0.025-0.0250.0000.0000.0000.000
140A142PRO00.0210.01617.2100.0170.0170.0000.0000.0000.000
141A143LEU00.0110.00918.841-0.032-0.0320.0000.0000.0000.000
142A144ASN00.0520.00220.931-0.026-0.0260.0000.0000.0000.000
143A145SER0-0.030-0.01122.134-0.010-0.0100.0000.0000.0000.000
144A146ILE0-0.033-0.00323.2690.0000.0000.0000.0000.0000.000
145A147ALA00.0120.01525.936-0.009-0.0090.0000.0000.0000.000
146A148MET0-0.002-0.01829.568-0.001-0.0010.0000.0000.0000.000
147A149GLN0-0.0120.00131.824-0.009-0.0090.0000.0000.0000.000
148A150SER00.0050.01635.4010.0010.0010.0000.0000.0000.000
149A151VAL0-0.026-0.02637.550-0.005-0.0050.0000.0000.0000.000
150A152VAL00.0520.02540.1420.0010.0010.0000.0000.0000.000
151A153SER00.018-0.00442.114-0.003-0.0030.0000.0000.0000.000
152A154LYS10.7650.88643.667-0.048-0.0480.0000.0000.0000.000
153A155TRP00.008-0.01146.447-0.001-0.0010.0000.0000.0000.000
154A156MET0-0.0200.00740.3680.0010.0010.0000.0000.0000.000
155A157GLY00.0390.02846.0240.0000.0000.0000.0000.0000.000
156A158PRO0-0.041-0.01847.4510.0020.0020.0000.0000.0000.000
157A159THR00.006-0.01447.111-0.001-0.0010.0000.0000.0000.000
158A160ILE00.0970.03641.1130.0020.0020.0000.0000.0000.000
159A161LYS10.8390.92441.330-0.056-0.0560.0000.0000.0000.000
160A162ASP-1-0.816-0.89444.3690.0460.0460.0000.0000.0000.000
161A163TRP00.0200.00140.4360.0040.0040.0000.0000.0000.000
162A164GLU-1-0.840-0.91738.8480.0670.0670.0000.0000.0000.000
163A165LYS10.8590.92640.698-0.052-0.0520.0000.0000.0000.000
164A166VAL0-0.0070.00240.4760.0010.0010.0000.0000.0000.000
165A167PHE00.041-0.00336.7490.0020.0020.0000.0000.0000.000
166A168ALA00.0290.02137.2180.0040.0040.0000.0000.0000.000
167A169ARG10.9040.95838.619-0.057-0.0570.0000.0000.0000.000
168A170VAL00.0060.00735.3410.0010.0010.0000.0000.0000.000
169A171ALA00.0420.02133.8240.0040.0040.0000.0000.0000.000
170A172SER0-0.093-0.04034.0660.0020.0020.0000.0000.0000.000
171A173LYS10.7330.85135.917-0.073-0.0730.0000.0000.0000.000
172A174LYS10.8040.87828.158-0.123-0.1230.0000.0000.0000.000
173A175TYR0-0.010-0.02030.6540.0060.0060.0000.0000.0000.000
174A176ASN00.0220.00625.360-0.005-0.0050.0000.0000.0000.000
175A177MET0-0.018-0.00125.8710.0080.0080.0000.0000.0000.000
176A178ILE0-0.0060.00829.809-0.009-0.0090.0000.0000.0000.000
177A179HIS0-0.058-0.04732.5330.0070.0070.0000.0000.0000.000
178A180PHE0-0.015-0.02334.380-0.006-0.0060.0000.0000.0000.000
179A181THR00.0960.04237.1270.0000.0000.0000.0000.0000.000
180A182PRO0-0.031-0.01839.0600.0020.0020.0000.0000.0000.000
181A183LEU0-0.035-0.01837.907-0.004-0.0040.0000.0000.0000.000
182A184GLN00.0180.00838.536-0.003-0.0030.0000.0000.0000.000
183A185HIS00.0310.02443.0570.0000.0000.0000.0000.0000.000
184A186ARG10.8700.92745.380-0.051-0.0510.0000.0000.0000.000
185A187GLY00.0410.01448.310-0.002-0.0020.0000.0000.0000.000
186A188GLU-1-0.919-0.94551.1110.0320.0320.0000.0000.0000.000
187A189SER0-0.028-0.01953.103-0.001-0.0010.0000.0000.0000.000
188A190ASN0-0.040-0.02850.6560.0020.0020.0000.0000.0000.000
189A191SER00.0660.04748.7240.0030.0030.0000.0000.0000.000
190A192PRO0-0.048-0.02644.0730.0000.0000.0000.0000.0000.000
191A193TYR00.010-0.02440.1360.0020.0020.0000.0000.0000.000
192A194SER00.0300.02045.0450.0000.0000.0000.0000.0000.000
193A195ILE0-0.044-0.02741.919-0.001-0.0010.0000.0000.0000.000
194A196TYR00.0160.02246.280-0.001-0.0010.0000.0000.0000.000
195A197ASP-1-0.833-0.93045.3250.0440.0440.0000.0000.0000.000
196A198GLN00.015-0.00140.996-0.001-0.0010.0000.0000.0000.000
197A199LEU0-0.027-0.02540.5000.0030.0030.0000.0000.0000.000
198A200GLU-1-0.993-0.96741.6880.0430.0430.0000.0000.0000.000
199A201PHE00.0440.00936.9730.0000.0000.0000.0000.0000.000
200A202ASP-1-0.767-0.86042.9040.0450.0450.0000.0000.0000.000
201A203PRO00.0560.02745.7700.0000.0000.0000.0000.0000.000
202A204THR0-0.115-0.07548.259-0.002-0.0020.0000.0000.0000.000
203A205VAL0-0.066-0.01844.244-0.001-0.0010.0000.0000.0000.000
204A206PHE00.0090.00740.3040.0010.0010.0000.0000.0000.000
205A207LYS10.8490.91044.191-0.044-0.0440.0000.0000.0000.000
206A208SER0-0.018-0.00841.3390.0000.0000.0000.0000.0000.000
207A209GLU-1-0.734-0.86335.2140.0720.0720.0000.0000.0000.000
208A210LYS10.8080.89536.106-0.061-0.0610.0000.0000.0000.000
209A211GLU-1-0.874-0.93237.4070.0540.0540.0000.0000.0000.000
210A212VAL00.0220.01036.2690.0020.0020.0000.0000.0000.000
211A213ALA00.0270.01033.0910.0050.0050.0000.0000.0000.000
212A214ASP-1-0.823-0.89733.3260.0750.0750.0000.0000.0000.000
213A215MET0-0.054-0.00834.8030.0000.0000.0000.0000.0000.000
214A216VAL0-0.013-0.00730.7530.0020.0020.0000.0000.0000.000
215A217GLU-1-0.815-0.90027.4960.1380.1380.0000.0000.0000.000
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