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: 85ZQY

Calculation Name: 3DMB-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3DMB

Chain ID: A

ChEMBL ID:

UniProt ID: Q8P8H7

Base Structure: X-ray

Registration Date: 2023-09-20

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 146
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1199026.369085
FMO2-HF: Nuclear repulsion 1143657.879779
FMO2-HF: Total energy -55368.489305
FMO2-MP2: Total energy -55530.549917


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:0:GLY)


Summations of interaction energy for fragment #1(A:0:GLY)
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.
-16.42-12.4956.063-5.23-4.757-0.048
Interaction energy analysis for fragmet #1(A:0:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.015 / q_NPA : 0.003
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].
3A2ALA0-0.003-0.0073.050-1.9390.4490.028-1.261-1.1550.003
4A3ASP-1-0.857-0.9112.049-16.333-14.9746.037-3.945-3.450-0.051
5A4PRO00.032-0.0074.6690.7120.721-0.001-0.0080.0000.000
6A5LYS10.8070.8857.1041.2041.2040.0000.0000.0000.000
7A6GLU-1-0.826-0.9194.992-0.848-0.679-0.001-0.016-0.1520.000
8A7LEU0-0.015-0.0047.0550.5560.5560.0000.0000.0000.000
9A8GLN00.0320.0199.3200.3330.3330.0000.0000.0000.000
10A9ASP-1-0.804-0.87510.177-0.713-0.7130.0000.0000.0000.000
11A10LYS10.8900.9457.4550.4780.4780.0000.0000.0000.000
12A11PHE00.0080.00712.4850.1130.1130.0000.0000.0000.000
13A12TRP00.0210.00115.0540.0870.0870.0000.0000.0000.000
14A13LYS10.9530.98214.7430.2190.2190.0000.0000.0000.000
15A14ALA00.0080.00916.6700.0420.0420.0000.0000.0000.000
16A15LEU0-0.006-0.00318.3850.0300.0300.0000.0000.0000.000
17A16LYS10.8660.94220.3710.1830.1830.0000.0000.0000.000
18A17SER0-0.035-0.02021.2820.0120.0120.0000.0000.0000.000
19A18ASP-1-0.841-0.92321.295-0.035-0.0350.0000.0000.0000.000
20A19ARG10.8840.95923.6700.1040.1040.0000.0000.0000.000
21A20THR0-0.026-0.00525.506-0.004-0.0040.0000.0000.0000.000
22A21VAL0-0.0110.00824.111-0.004-0.0040.0000.0000.0000.000
23A22MET0-0.0150.01226.5650.0050.0050.0000.0000.0000.000
24A23LEU00.005-0.00727.695-0.006-0.0060.0000.0000.0000.000
25A24GLY00.0290.01729.7600.0090.0090.0000.0000.0000.000
26A25LEU0-0.045-0.02930.679-0.009-0.0090.0000.0000.0000.000
27A26ASP-1-0.820-0.90629.619-0.084-0.0840.0000.0000.0000.000
28A27GLY0-0.038-0.02431.6190.0010.0010.0000.0000.0000.000
29A28VAL0-0.100-0.05334.0470.0020.0020.0000.0000.0000.000
30A29GLU-1-0.897-0.93036.350-0.026-0.0260.0000.0000.0000.000
31A30ASP-1-0.859-0.92237.897-0.032-0.0320.0000.0000.0000.000
32A31GLY00.0230.00334.646-0.004-0.0040.0000.0000.0000.000
33A32HIS0-0.054-0.05635.102-0.004-0.0040.0000.0000.0000.000
34A33ALA00.0000.00932.330-0.004-0.0040.0000.0000.0000.000
35A34ARG10.9040.94332.8530.0490.0490.0000.0000.0000.000
36A35PRO0-0.0180.00130.731-0.007-0.0070.0000.0000.0000.000
37A36MET0-0.017-0.00130.2910.0030.0030.0000.0000.0000.000
38A37THR00.006-0.00829.199-0.003-0.0030.0000.0000.0000.000
39A38ALA00.0150.01325.391-0.002-0.0020.0000.0000.0000.000
40A39GLN0-0.033-0.01427.0580.0110.0110.0000.0000.0000.000
41A40ILE00.0340.01821.285-0.002-0.0020.0000.0000.0000.000
42A41GLU-1-0.815-0.86025.638-0.121-0.1210.0000.0000.0000.000
43A42GLY00.0280.01923.708-0.015-0.0150.0000.0000.0000.000
44A43ASP-1-0.895-0.97419.572-0.177-0.1770.0000.0000.0000.000
45A44SER0-0.069-0.04317.093-0.031-0.0310.0000.0000.0000.000
46A45GLY00.0220.02018.7010.0180.0180.0000.0000.0000.000
47A46GLY00.0040.02220.3410.0220.0220.0000.0000.0000.000
48A47PRO0-0.007-0.01923.353-0.005-0.0050.0000.0000.0000.000
49A48ILE0-0.032-0.01022.102-0.003-0.0030.0000.0000.0000.000
50A49TRP00.0300.00526.1640.0120.0120.0000.0000.0000.000
51A50PHE00.0260.00126.7070.0000.0000.0000.0000.0000.000
52A51PHE00.0330.02331.9020.0010.0010.0000.0000.0000.000
53A52THR0-0.015-0.00935.2980.0040.0040.0000.0000.0000.000
54A53SER00.0540.03737.888-0.001-0.0010.0000.0000.0000.000
55A54LYS10.8310.88841.2770.0570.0570.0000.0000.0000.000
56A55ASP-1-0.849-0.90043.452-0.038-0.0380.0000.0000.0000.000
57A56ASN0-0.019-0.00936.6000.0040.0040.0000.0000.0000.000
58A57ALA00.027-0.00240.166-0.002-0.0020.0000.0000.0000.000
59A58LEU0-0.009-0.00234.276-0.001-0.0010.0000.0000.0000.000
60A59ILE00.0270.01738.305-0.002-0.0020.0000.0000.0000.000
61A60ALA0-0.022-0.00839.899-0.002-0.0020.0000.0000.0000.000
62A61MET0-0.044-0.01438.9020.0010.0010.0000.0000.0000.000
63A62LEU0-0.045-0.01435.048-0.003-0.0030.0000.0000.0000.000
64A63GLY00.0380.02037.792-0.003-0.0030.0000.0000.0000.000
65A64GLN0-0.046-0.02836.791-0.001-0.0010.0000.0000.0000.000
66A65GLY0-0.0070.00134.213-0.008-0.0080.0000.0000.0000.000
67A66ARG10.8950.97033.8620.0730.0730.0000.0000.0000.000
68A67ARG10.8830.93727.0930.1090.1090.0000.0000.0000.000
69A68VAL0-0.011-0.01027.7440.0110.0110.0000.0000.0000.000
70A69ILE00.0230.00924.395-0.014-0.0140.0000.0000.0000.000
71A70GLY00.003-0.00724.7450.0120.0120.0000.0000.0000.000
72A71ALA0-0.023-0.00723.409-0.013-0.0130.0000.0000.0000.000
73A72PHE00.011-0.00818.6060.0040.0040.0000.0000.0000.000
74A73SER00.0000.00420.3170.0050.0050.0000.0000.0000.000
75A74SER0-0.009-0.03218.115-0.004-0.0040.0000.0000.0000.000
76A75LYS10.8500.89320.3040.0540.0540.0000.0000.0000.000
77A76GLY0-0.018-0.00720.8980.0090.0090.0000.0000.0000.000
78A77HIS0-0.056-0.02420.4240.0260.0260.0000.0000.0000.000
79A78ASP-1-0.843-0.88515.3210.0450.0450.0000.0000.0000.000
80A79LEU0-0.013-0.00512.8650.0170.0170.0000.0000.0000.000
81A80PHE00.0080.00715.974-0.005-0.0050.0000.0000.0000.000
82A81ALA0-0.004-0.00816.479-0.029-0.0290.0000.0000.0000.000
83A82SER0-0.0210.01018.2520.0240.0240.0000.0000.0000.000
84A83ILE0-0.015-0.01619.755-0.032-0.0320.0000.0000.0000.000
85A84SER00.0450.03521.5760.0310.0310.0000.0000.0000.000
86A85GLY00.0560.01123.159-0.025-0.0250.0000.0000.0000.000
87A86SER0-0.042-0.00525.8830.0190.0190.0000.0000.0000.000
88A87LEU00.0120.01429.476-0.006-0.0060.0000.0000.0000.000
89A88ARG10.9210.94831.7570.1250.1250.0000.0000.0000.000
90A89GLU-1-0.774-0.85234.504-0.068-0.0680.0000.0000.0000.000
91A90ASP-1-0.874-0.94134.799-0.107-0.1070.0000.0000.0000.000
92A91THR00.016-0.00936.367-0.004-0.0040.0000.0000.0000.000
93A92ASP-1-0.842-0.91536.706-0.088-0.0880.0000.0000.0000.000
94A93PRO00.026-0.00338.157-0.002-0.0020.0000.0000.0000.000
95A94ALA00.0380.02237.8210.0010.0010.0000.0000.0000.000
96A95VAL0-0.033-0.02032.715-0.003-0.0030.0000.0000.0000.000
97A96VAL0-0.009-0.00834.983-0.001-0.0010.0000.0000.0000.000
98A97ASP-1-0.852-0.91737.048-0.065-0.0650.0000.0000.0000.000
99A98ARG10.7610.84631.7650.1160.1160.0000.0000.0000.000
100A99LEU0-0.018-0.00429.882-0.001-0.0010.0000.0000.0000.000
101A100TRP00.0210.02233.2250.0030.0030.0000.0000.0000.000
102A101ASN0-0.031-0.02632.8770.0040.0040.0000.0000.0000.000
103A102PRO00.0440.00635.9760.0020.0020.0000.0000.0000.000
104A103TYR0-0.0100.00432.5570.0020.0020.0000.0000.0000.000
105A104VAL0-0.016-0.00834.4440.0030.0030.0000.0000.0000.000
106A105ALA0-0.033-0.02537.0930.0020.0020.0000.0000.0000.000
107A106ALA0-0.007-0.00339.5860.0020.0020.0000.0000.0000.000
108A107TRP0-0.069-0.02436.3400.0040.0040.0000.0000.0000.000
109A108TYR0-0.063-0.03838.733-0.001-0.0010.0000.0000.0000.000
110A109GLU-1-0.898-0.94243.724-0.027-0.0270.0000.0000.0000.000
111A110GLY0-0.037-0.02047.2840.0010.0010.0000.0000.0000.000
112A111GLY0-0.029-0.01244.241-0.001-0.0010.0000.0000.0000.000
113A112LYS10.8150.87039.9750.0610.0610.0000.0000.0000.000
114A113ASP-1-0.919-0.94943.636-0.048-0.0480.0000.0000.0000.000
115A114ASP-1-0.888-0.93644.959-0.038-0.0380.0000.0000.0000.000
116A115PRO00.002-0.00845.707-0.002-0.0020.0000.0000.0000.000
117A116LYS10.7840.89345.9610.0340.0340.0000.0000.0000.000
118A117LEU00.0270.02039.834-0.001-0.0010.0000.0000.0000.000
119A118ALA0-0.055-0.03239.6840.0000.0000.0000.0000.0000.000
120A119LEU00.0010.01033.4880.0000.0000.0000.0000.0000.000
121A120LEU00.002-0.00833.153-0.001-0.0010.0000.0000.0000.000
122A121ARG10.7720.86029.5700.1340.1340.0000.0000.0000.000
123A122LEU00.0180.01225.2520.0040.0040.0000.0000.0000.000
124A123ASP-1-0.837-0.90326.544-0.168-0.1680.0000.0000.0000.000
125A124ALA0-0.030-0.02921.8170.0060.0060.0000.0000.0000.000
126A125ASP-1-0.872-0.91922.430-0.254-0.2540.0000.0000.0000.000
127A126HIS0-0.087-0.06417.850-0.027-0.0270.0000.0000.0000.000
128A127ALA00.026-0.00416.6090.0400.0400.0000.0000.0000.000
129A128GLN0-0.0370.01115.360-0.055-0.0550.0000.0000.0000.000
130A129ILE0-0.010-0.02012.3670.0310.0310.0000.0000.0000.000
131A130TRP0-0.016-0.00812.736-0.008-0.0080.0000.0000.0000.000
132A131LEU0-0.002-0.0048.752-0.025-0.0250.0000.0000.0000.000
133A132ASN0-0.058-0.01613.1380.0770.0770.0000.0000.0000.000
134A133GLY00.0080.00713.7040.0380.0380.0000.0000.0000.000
135A134SER0-0.024-0.02414.409-0.068-0.0680.0000.0000.0000.000
136A135SER00.0110.00215.9950.0580.0580.0000.0000.0000.000
137A136LEU0-0.031-0.00218.580-0.044-0.0440.0000.0000.0000.000
138A137LEU00.0190.00820.522-0.004-0.0040.0000.0000.0000.000
139A138ALA00.0160.00623.9890.0120.0120.0000.0000.0000.000
140A139GLY00.0150.00926.197-0.009-0.0090.0000.0000.0000.000
141A140ILE00.000-0.00728.016-0.010-0.0100.0000.0000.0000.000
142A141LYS10.9170.96031.692-0.151-0.1510.0000.0000.0000.000
143A142VAL00.0300.01534.070-0.006-0.0060.0000.0000.0000.000
144A143LEU0-0.0050.00336.7950.0020.0020.0000.0000.0000.000
145A144LEU00.010-0.00235.627-0.001-0.0010.0000.0000.0000.000
146A145GLY00.0170.01840.150-0.005-0.0050.0000.0000.0000.000