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: ZYK1N

Calculation Name: 3HMX-B-Xray372

Preferred Name: Interleukin-12

Target Type: PROTEIN COMPLEX

Ligand Name: 2-acetamido-2-deoxy-beta-d-glucopyranose

ligand 3-letter code: NAG

PDB ID: 3HMX

Chain ID: B

ChEMBL ID: CHEMBL2364153

UniProt ID: P29459

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 183
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2070447.973693
FMO2-HF: Nuclear repulsion 1992245.94987
FMO2-HF: Total energy -78202.023823
FMO2-MP2: Total energy -78418.75889


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(B:12:MET)


Summations of interaction energy for fragment #1(B:12:MET)
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.
-6.253-2.313.617-2.884-4.673-0.026
Interaction energy analysis for fragmet #1(B:12:MET)
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 : -0.013
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].
3B14PRO00.0350.0093.8681.4632.911-0.014-0.621-0.8120.001
4B15CYS0-0.042-0.0196.8300.3720.3720.0000.0000.0000.000
5B16LEU00.0090.0103.875-0.1300.0650.000-0.025-0.1690.000
6B17HIS0-0.0330.0106.7730.0600.0600.0000.0000.0000.000
7B18HIS00.0700.0338.121-0.102-0.1020.0000.0000.0000.000
8B19SER0-0.025-0.0269.722-0.104-0.1040.0000.0000.0000.000
9B20GLN0-0.004-0.0166.750-0.174-0.1740.0000.0000.0000.000
10B21ASN0-0.014-0.00511.439-0.022-0.0220.0000.0000.0000.000
11B22LEU00.0390.03213.762-0.047-0.0470.0000.0000.0000.000
12B23LEU00.0140.01314.299-0.022-0.0220.0000.0000.0000.000
13B24ARG10.8820.94612.154-0.547-0.5470.0000.0000.0000.000
14B25ALA00.0120.00417.119-0.025-0.0250.0000.0000.0000.000
15B26VAL00.0340.00919.334-0.018-0.0180.0000.0000.0000.000
16B27SER0-0.021-0.02419.253-0.022-0.0220.0000.0000.0000.000
17B28ASN0-0.020-0.01220.718-0.017-0.0170.0000.0000.0000.000
18B29MET0-0.0010.04023.0590.0000.0000.0000.0000.0000.000
19B30LEU00.0190.00624.888-0.007-0.0070.0000.0000.0000.000
20B31GLN00.023-0.00225.169-0.012-0.0120.0000.0000.0000.000
21B32LYS10.8360.91625.250-0.124-0.1240.0000.0000.0000.000
22B33ALA00.0500.04429.459-0.005-0.0050.0000.0000.0000.000
23B34ARG10.9600.96429.402-0.065-0.0650.0000.0000.0000.000
24B35GLN0-0.104-0.04829.662-0.002-0.0020.0000.0000.0000.000
25B36THR0-0.037-0.03433.177-0.001-0.0010.0000.0000.0000.000
26B37LEU0-0.077-0.03334.190-0.004-0.0040.0000.0000.0000.000
27B38GLU-1-0.883-0.94036.9800.0420.0420.0000.0000.0000.000
28B39PHE0-0.008-0.00639.371-0.002-0.0020.0000.0000.0000.000
29B40TYR0-0.014-0.02837.967-0.003-0.0030.0000.0000.0000.000
30B41PRO00.0810.05038.2610.0030.0030.0000.0000.0000.000
31B42CYS0-0.070-0.02230.5210.0030.0030.0000.0000.0000.000
32B43THR0-0.065-0.04633.7750.0060.0060.0000.0000.0000.000
33B44SER0-0.050-0.02632.058-0.003-0.0030.0000.0000.0000.000
34B45GLU-1-0.885-0.95429.0370.0310.0310.0000.0000.0000.000
35B46GLU-1-0.949-0.96032.9590.0110.0110.0000.0000.0000.000
36B47ILE0-0.089-0.05736.485-0.003-0.0030.0000.0000.0000.000
37B48ASP-1-0.915-0.95335.7410.0080.0080.0000.0000.0000.000
38B49HIS0-0.008-0.01031.4090.0060.0060.0000.0000.0000.000
39B50GLU-1-0.890-0.93231.777-0.027-0.0270.0000.0000.0000.000
40B51ASP-1-0.817-0.88326.672-0.040-0.0400.0000.0000.0000.000
41B52ILE0-0.009-0.01328.055-0.005-0.0050.0000.0000.0000.000
42B53THR0-0.014-0.02126.011-0.001-0.0010.0000.0000.0000.000
43B54LYS10.8190.90929.1740.0440.0440.0000.0000.0000.000
44B55ASP-1-0.820-0.89830.804-0.063-0.0630.0000.0000.0000.000
45B56LYS10.8630.94130.0250.0570.0570.0000.0000.0000.000
46B57THR00.0260.00924.712-0.006-0.0060.0000.0000.0000.000
47B58SER00.0500.04024.7070.0070.0070.0000.0000.0000.000
48B59THR0-0.049-0.04221.500-0.018-0.0180.0000.0000.0000.000
49B60VAL0-0.014-0.03122.130-0.013-0.0130.0000.0000.0000.000
50B61GLU-1-0.936-0.96224.414-0.132-0.1320.0000.0000.0000.000
51B62ALA00.0310.00922.290-0.001-0.0010.0000.0000.0000.000
52B63CYS0-0.0730.01017.509-0.017-0.0170.0000.0000.0000.000
53B64LEU00.0130.01717.543-0.014-0.0140.0000.0000.0000.000
54B65PRO00.022-0.00215.355-0.026-0.0260.0000.0000.0000.000
55B66LEU00.0550.02215.1050.0260.0260.0000.0000.0000.000
56B67GLU-1-0.875-0.90614.708-0.242-0.2420.0000.0000.0000.000
57B68LEU0-0.032-0.00918.6650.0260.0260.0000.0000.0000.000
58B69THR0-0.0040.00619.9360.0280.0280.0000.0000.0000.000
59B70LYS10.9000.94521.6690.1130.1130.0000.0000.0000.000
60B71ASN0-0.049-0.04623.1150.0070.0070.0000.0000.0000.000
61B72GLU-1-0.777-0.86623.392-0.208-0.2080.0000.0000.0000.000
62B73SER0-0.042-0.03426.4140.0080.0080.0000.0000.0000.000
63B74CYS0-0.065-0.03426.8410.0110.0110.0000.0000.0000.000
64B75LEU0-0.0160.00329.4360.0050.0050.0000.0000.0000.000
65B76ASN0-0.0100.00224.7120.0120.0120.0000.0000.0000.000
66B77SER0-0.011-0.01128.081-0.003-0.0030.0000.0000.0000.000
67B78ARG10.8120.89926.9960.1340.1340.0000.0000.0000.000
68B79GLU-1-0.806-0.88525.523-0.153-0.1530.0000.0000.0000.000
69B80THR00.007-0.01524.5160.0070.0070.0000.0000.0000.000
70B81SER00.0020.01121.781-0.008-0.0080.0000.0000.0000.000
71B82PHE0-0.032-0.02221.560-0.009-0.0090.0000.0000.0000.000
72B83ILE00.0130.01514.9400.0110.0110.0000.0000.0000.000
73B84THR00.0120.00618.0390.0350.0350.0000.0000.0000.000
74B85ASN0-0.029-0.02416.561-0.107-0.1070.0000.0000.0000.000
75B86GLY00.0140.02115.0660.0550.0550.0000.0000.0000.000
76B87SER00.031-0.00713.4250.0420.0420.0000.0000.0000.000
77B89LEU00.0500.0218.806-0.064-0.0640.0000.0000.0000.000
78B90ALA00.0260.0204.317-0.446-0.333-0.001-0.025-0.0870.000
79B91SER00.002-0.0355.6780.3220.3220.0000.0000.0000.000
80B92ARG10.8400.9304.1351.7091.827-0.001-0.006-0.1110.000
81B93LYS10.8840.9389.6370.5960.5960.0000.0000.0000.000
82B94THR00.0490.0379.2490.0460.0460.0000.0000.0000.000
83B95SER0-0.030-0.01311.9700.0700.0700.0000.0000.0000.000
84B96PHE00.0090.02314.5710.0620.0620.0000.0000.0000.000
85B97MET00.0700.03016.465-0.012-0.0120.0000.0000.0000.000
86B98MET0-0.022-0.00514.286-0.014-0.0140.0000.0000.0000.000
87B99ALA00.0240.01917.0050.0010.0010.0000.0000.0000.000
88B100LEU00.0310.01818.3330.0180.0180.0000.0000.0000.000
89B102LEU00.008-0.02013.4210.0200.0200.0000.0000.0000.000
90B103SER0-0.0050.01217.4420.0410.0410.0000.0000.0000.000
91B104SER0-0.023-0.02420.8890.0290.0290.0000.0000.0000.000
92B105ILE00.043-0.00516.4280.0250.0250.0000.0000.0000.000
93B106TYR0-0.052-0.03019.0950.0380.0380.0000.0000.0000.000
94B107GLU-1-0.734-0.83220.583-0.082-0.0820.0000.0000.0000.000
95B108ASP-1-0.756-0.86621.456-0.084-0.0840.0000.0000.0000.000
96B109LEU0-0.056-0.02317.6470.0240.0240.0000.0000.0000.000
97B110LYS10.8470.91521.8350.1250.1250.0000.0000.0000.000
98B111MET0-0.015-0.00924.8610.0090.0090.0000.0000.0000.000
99B112TYR0-0.024-0.05323.9790.0160.0160.0000.0000.0000.000
100B113GLN0-0.046-0.01023.9590.0050.0050.0000.0000.0000.000
101B114VAL0-0.032-0.01825.6340.0100.0100.0000.0000.0000.000
102B115GLU-1-0.713-0.81729.081-0.004-0.0040.0000.0000.0000.000
103B116PHE00.023-0.00424.7480.0070.0070.0000.0000.0000.000
104B117LYS10.9600.99028.8490.0070.0070.0000.0000.0000.000
105B118THR0-0.044-0.02930.2400.0010.0010.0000.0000.0000.000
106B119MET0-0.0150.00130.5290.0010.0010.0000.0000.0000.000
107B120ASN00.0500.01530.5530.0040.0040.0000.0000.0000.000
108B121ALA0-0.0140.00032.8000.0020.0020.0000.0000.0000.000
109B122LYS10.8470.93135.634-0.008-0.0080.0000.0000.0000.000
110B123LEU00.019-0.00834.6030.0000.0000.0000.0000.0000.000
111B124LEU0-0.058-0.03233.2830.0020.0020.0000.0000.0000.000
112B125MET0-0.027-0.00537.2050.0000.0000.0000.0000.0000.000
113B126ASP-1-0.791-0.87439.8020.0280.0280.0000.0000.0000.000
114B127PRO0-0.007-0.01041.5600.0030.0030.0000.0000.0000.000
115B128LYS10.8460.93342.533-0.034-0.0340.0000.0000.0000.000
116B129ARG10.9730.97538.470-0.047-0.0470.0000.0000.0000.000
117B130GLN0-0.040-0.00438.4560.0010.0010.0000.0000.0000.000
118B131ILE00.0060.00231.2620.0040.0040.0000.0000.0000.000
119B132PHE00.010-0.00232.431-0.005-0.0050.0000.0000.0000.000
120B133LEU0-0.011-0.00726.1540.0050.0050.0000.0000.0000.000
121B134ASP-1-0.826-0.92924.6180.1400.1400.0000.0000.0000.000
122B135GLN00.0270.00823.9700.0090.0090.0000.0000.0000.000
123B136ASN00.0500.02919.3430.0090.0090.0000.0000.0000.000
124B137MET0-0.0230.00220.6360.0130.0130.0000.0000.0000.000
125B138LEU0-0.054-0.03621.447-0.010-0.0100.0000.0000.0000.000
126B139ALA0-0.0070.01620.560-0.015-0.0150.0000.0000.0000.000
127B140VAL00.0480.01316.250-0.011-0.0110.0000.0000.0000.000
128B141ILE0-0.041-0.01817.081-0.013-0.0130.0000.0000.0000.000
129B142ASP-1-0.841-0.91619.168-0.024-0.0240.0000.0000.0000.000
130B143GLU-1-0.923-0.97415.4980.2330.2330.0000.0000.0000.000
131B144LEU0-0.026-0.01912.910-0.018-0.0180.0000.0000.0000.000
132B145MET0-0.0120.00615.453-0.057-0.0570.0000.0000.0000.000
133B146GLN0-0.037-0.02617.232-0.033-0.0330.0000.0000.0000.000
134B147ALA0-0.0220.00512.523-0.020-0.0200.0000.0000.0000.000
135B148LEU0-0.012-0.00413.751-0.125-0.1250.0000.0000.0000.000
136B149ASN0-0.049-0.02016.055-0.002-0.0020.0000.0000.0000.000
137B150PHE00.010-0.00217.2200.0190.0190.0000.0000.0000.000
138B151ASN00.0060.01121.4920.0280.0280.0000.0000.0000.000
139B152SER0-0.031-0.01324.945-0.003-0.0030.0000.0000.0000.000
140B153GLU-1-0.913-0.95027.211-0.065-0.0650.0000.0000.0000.000
141B154THR0-0.072-0.06828.968-0.006-0.0060.0000.0000.0000.000
142B155VAL0-0.0130.01231.8330.0060.0060.0000.0000.0000.000
143B156PRO00.0340.00233.093-0.001-0.0010.0000.0000.0000.000
144B157GLN0-0.012-0.01132.365-0.004-0.0040.0000.0000.0000.000
145B158LYS10.7760.89433.4520.0150.0150.0000.0000.0000.000
146B159SER0-0.011-0.01235.593-0.002-0.0020.0000.0000.0000.000
147B160SER0-0.002-0.01538.1040.0010.0010.0000.0000.0000.000
148B161LEU0-0.047-0.01736.746-0.001-0.0010.0000.0000.0000.000
149B162GLU-1-0.843-0.88140.794-0.003-0.0030.0000.0000.0000.000
150B163GLU-1-0.797-0.91038.7420.0000.0000.0000.0000.0000.000
151B164PRO0-0.062-0.01338.3550.0000.0000.0000.0000.0000.000
152B165ASP-1-0.759-0.88141.6900.0130.0130.0000.0000.0000.000
153B166PHE00.0290.01240.5370.0000.0000.0000.0000.0000.000
154B167TYR0-0.0250.00339.9490.0020.0020.0000.0000.0000.000
155B168LYS10.8590.89040.1570.0000.0000.0000.0000.0000.000
156B169THR0-0.063-0.05335.744-0.001-0.0010.0000.0000.0000.000
157B170LYS10.8260.89735.944-0.030-0.0300.0000.0000.0000.000
158B171ILE00.0010.01035.7090.0030.0030.0000.0000.0000.000
159B172LYS10.8980.94633.4650.0010.0010.0000.0000.0000.000
160B173LEU00.005-0.01530.1870.0000.0000.0000.0000.0000.000
161B175ILE00.0370.04430.3450.0030.0030.0000.0000.0000.000
162B176LEU00.0290.00128.679-0.002-0.0020.0000.0000.0000.000
163B177LEU0-0.041-0.02425.6790.0010.0010.0000.0000.0000.000
164B178HIS00.0380.01925.3240.0080.0080.0000.0000.0000.000
165B179ALA00.0360.03125.3590.0000.0000.0000.0000.0000.000
166B180PHE00.0060.00020.630-0.004-0.0040.0000.0000.0000.000
167B181ARG10.9260.95619.675-0.085-0.0850.0000.0000.0000.000
168B182ILE0-0.005-0.00320.3020.0040.0040.0000.0000.0000.000
169B183ARG10.7720.85720.0710.0540.0540.0000.0000.0000.000
170B184ALA00.0220.00217.061-0.020-0.0200.0000.0000.0000.000
171B185VAL0-0.024-0.01015.7770.0000.0000.0000.0000.0000.000
172B186THR0-0.034-0.01716.009-0.014-0.0140.0000.0000.0000.000
173B187ILE00.0220.01613.426-0.044-0.0440.0000.0000.0000.000
174B188ASP-1-0.794-0.87010.6140.0400.0400.0000.0000.0000.000
175B189ARG10.9210.96011.221-0.039-0.0390.0000.0000.0000.000
176B190VAL00.0310.02712.750-0.063-0.0630.0000.0000.0000.000
177B191MET0-0.016-0.0188.564-0.175-0.1750.0000.0000.0000.000
178B192SER0-0.003-0.0227.314-0.411-0.4110.0000.0000.0000.000
179B193TYR0-0.094-0.0727.656-0.148-0.1480.0000.0000.0000.000
180B194LEU00.012-0.0078.226-0.057-0.0570.0000.0000.0000.000
181B195ASN0-0.038-0.0162.438-6.807-5.6253.591-1.831-2.942-0.025
182B196ALA00.0080.0143.449-1.177-0.2900.042-0.376-0.552-0.002
183B197SER0-0.021-0.0025.7610.1250.1250.0000.0000.0000.000