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: 66K8Z

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 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 183
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2061853.03074
FMO2-HF: Nuclear repulsion 1983652.14822
FMO2-HF: Total energy -78200.88252
FMO2-MP2: Total energy -78417.685578


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.
-3.7570.8910.731-2.179-3.2-0.011
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 : -0.005 / q_NPA : -0.006
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].
3B14PRO00.0340.0083.8121.2753.029-0.023-0.769-0.9630.001
4B15CYS00.0260.0126.8710.4080.4080.0000.0000.0000.000
5B16LEU00.0250.0274.3810.0430.172-0.001-0.009-0.1180.000
6B17HIS0-0.0290.0166.7600.0350.0350.0000.0000.0000.000
7B18HIS00.0810.0328.117-0.052-0.0520.0000.0000.0000.000
8B19SER0-0.020-0.03010.304-0.085-0.0850.0000.0000.0000.000
9B20GLN0-0.017-0.0226.820-0.141-0.1410.0000.0000.0000.000
10B21ASN0-0.014-0.00711.674-0.023-0.0230.0000.0000.0000.000
11B22LEU00.0280.03113.870-0.041-0.0410.0000.0000.0000.000
12B23LEU00.0190.01814.803-0.017-0.0170.0000.0000.0000.000
13B24ARG10.8900.95212.169-0.482-0.4820.0000.0000.0000.000
14B25ALA00.0290.02217.313-0.019-0.0190.0000.0000.0000.000
15B26VAL00.0300.00219.707-0.015-0.0150.0000.0000.0000.000
16B27SER0-0.041-0.03119.416-0.018-0.0180.0000.0000.0000.000
17B28ASN0-0.001-0.00921.033-0.011-0.0110.0000.0000.0000.000
18B29MET0-0.0340.01523.352-0.004-0.0040.0000.0000.0000.000
19B30LEU0-0.003-0.00824.976-0.007-0.0070.0000.0000.0000.000
20B31GLN0-0.006-0.01625.593-0.009-0.0090.0000.0000.0000.000
21B32LYS10.9000.95725.614-0.110-0.1100.0000.0000.0000.000
22B33ALA00.0730.05129.655-0.005-0.0050.0000.0000.0000.000
23B34ARG10.9640.98930.039-0.052-0.0520.0000.0000.0000.000
24B35GLN0-0.084-0.05429.459-0.001-0.0010.0000.0000.0000.000
25B36THR0-0.068-0.04133.514-0.001-0.0010.0000.0000.0000.000
26B37LEU0-0.095-0.03534.606-0.003-0.0030.0000.0000.0000.000
27B38GLU-1-0.877-0.93337.1740.0370.0370.0000.0000.0000.000
28B39PHE0-0.0210.00739.688-0.002-0.0020.0000.0000.0000.000
29B40TYR0-0.041-0.05638.548-0.002-0.0020.0000.0000.0000.000
30B41PRO00.0440.02839.0860.0020.0020.0000.0000.0000.000
31B42CYS0-0.054-0.02331.1260.0010.0010.0000.0000.0000.000
32B43THR0-0.022-0.02534.6550.0050.0050.0000.0000.0000.000
33B44SER0-0.033-0.01632.390-0.003-0.0030.0000.0000.0000.000
34B45GLU-1-0.910-0.96029.8550.0250.0250.0000.0000.0000.000
35B46GLU-1-0.966-0.97433.9190.0090.0090.0000.0000.0000.000
36B47ILE0-0.082-0.05337.297-0.003-0.0030.0000.0000.0000.000
37B48ASP-1-0.926-0.95736.1000.0070.0070.0000.0000.0000.000
38B49HIS00.002-0.00331.9110.0050.0050.0000.0000.0000.000
39B50GLU-1-0.895-0.93332.353-0.020-0.0200.0000.0000.0000.000
40B51ASP-1-0.835-0.91327.404-0.034-0.0340.0000.0000.0000.000
41B52ILE0-0.026-0.01528.558-0.002-0.0020.0000.0000.0000.000
42B53THR0-0.061-0.05026.559-0.002-0.0020.0000.0000.0000.000
43B54LYS10.9320.97229.2060.0330.0330.0000.0000.0000.000
44B55ASP-1-0.852-0.91630.606-0.053-0.0530.0000.0000.0000.000
45B56LYS10.8530.94030.7460.0440.0440.0000.0000.0000.000
46B57THR00.0250.00925.178-0.005-0.0050.0000.0000.0000.000
47B58SER00.0290.03525.4530.0060.0060.0000.0000.0000.000
48B59THR0-0.034-0.04122.175-0.017-0.0170.0000.0000.0000.000
49B60VAL0-0.027-0.02622.429-0.007-0.0070.0000.0000.0000.000
50B61GLU-1-0.927-0.96424.497-0.110-0.1100.0000.0000.0000.000
51B62ALA00.0230.01022.529-0.002-0.0020.0000.0000.0000.000
52B63CYS0-0.0330.02317.858-0.009-0.0090.0000.0000.0000.000
53B64LEU0-0.0160.00718.005-0.008-0.0080.0000.0000.0000.000
54B65PRO00.004-0.00715.556-0.021-0.0210.0000.0000.0000.000
55B66LEU00.024-0.00415.0680.0130.0130.0000.0000.0000.000
56B67GLU-1-1.002-0.98616.354-0.107-0.1070.0000.0000.0000.000
57B68LEU0-0.006-0.00218.6300.0190.0190.0000.0000.0000.000
58B69THR0-0.0050.02020.5130.0220.0220.0000.0000.0000.000
59B70LYS10.8960.94422.0830.0840.0840.0000.0000.0000.000
60B71ASN0-0.048-0.05423.814-0.002-0.0020.0000.0000.0000.000
61B72GLU-1-0.752-0.84323.521-0.172-0.1720.0000.0000.0000.000
62B73SER0-0.038-0.04126.5830.0070.0070.0000.0000.0000.000
63B74CYS0-0.092-0.04827.9670.0080.0080.0000.0000.0000.000
64B75LEU00.0040.00929.8380.0010.0010.0000.0000.0000.000
65B76ASN00.0210.02324.8270.0100.0100.0000.0000.0000.000
66B77SER0-0.027-0.01928.198-0.002-0.0020.0000.0000.0000.000
67B78ARG10.7900.87327.4830.1090.1090.0000.0000.0000.000
68B79GLU-1-0.793-0.86525.881-0.124-0.1240.0000.0000.0000.000
69B80THR0-0.004-0.00725.7010.0010.0010.0000.0000.0000.000
70B81SER00.0100.00721.901-0.008-0.0080.0000.0000.0000.000
71B82PHE0-0.017-0.02621.580-0.002-0.0020.0000.0000.0000.000
72B83ILE00.0180.02714.9610.0110.0110.0000.0000.0000.000
73B84THR00.002-0.00617.8820.0350.0350.0000.0000.0000.000
74B85ASN0-0.037-0.02316.658-0.090-0.0900.0000.0000.0000.000
75B86GLY00.0380.03214.6460.0420.0420.0000.0000.0000.000
76B87SER00.002-0.00513.5380.0370.0370.0000.0000.0000.000
77B89LEU0-0.024-0.0218.5960.0560.0560.0000.0000.0000.000
78B90ALA00.0320.0433.861-0.498-0.3270.002-0.051-0.1220.000
79B91SER00.0660.0225.4840.2460.2460.0000.0000.0000.000
80B92ARG10.8900.9714.3321.2831.381-0.001-0.004-0.0920.000
81B93LYS10.9320.9449.8080.4890.4890.0000.0000.0000.000
82B94THR00.018-0.0029.5950.1210.1210.0000.0000.0000.000
83B95SER00.0070.00012.2520.0520.0520.0000.0000.0000.000
84B96PHE0-0.0120.00314.3590.0560.0560.0000.0000.0000.000
85B97MET00.0720.03016.255-0.002-0.0020.0000.0000.0000.000
86B98MET0-0.027-0.00114.523-0.008-0.0080.0000.0000.0000.000
87B99ALA00.0180.02317.3950.0070.0070.0000.0000.0000.000
88B100LEU00.0340.01818.9950.0130.0130.0000.0000.0000.000
89B102LEU0-0.002-0.02013.8770.0130.0130.0000.0000.0000.000
90B103SER0-0.0210.00517.9700.0330.0330.0000.0000.0000.000
91B104SER00.007-0.02521.4190.0200.0200.0000.0000.0000.000
92B105ILE00.0760.01617.0590.0180.0180.0000.0000.0000.000
93B106TYR0-0.063-0.02419.4450.0320.0320.0000.0000.0000.000
94B107GLU-1-0.726-0.84220.944-0.067-0.0670.0000.0000.0000.000
95B108ASP-1-0.787-0.89622.194-0.068-0.0680.0000.0000.0000.000
96B109LEU0-0.083-0.04518.4310.0200.0200.0000.0000.0000.000
97B110LYS10.8580.91822.5310.0970.0970.0000.0000.0000.000
98B111MET0-0.008-0.00125.5740.0070.0070.0000.0000.0000.000
99B112TYR0-0.010-0.03424.5510.0130.0130.0000.0000.0000.000
100B113GLN00.0150.03424.5190.0040.0040.0000.0000.0000.000
101B114VAL0-0.037-0.01326.4460.0080.0080.0000.0000.0000.000
102B115GLU-1-0.724-0.80929.613-0.003-0.0030.0000.0000.0000.000
103B116PHE00.0500.01225.0460.0050.0050.0000.0000.0000.000
104B117LYS10.9490.99229.2490.0040.0040.0000.0000.0000.000
105B118THR0-0.039-0.04230.5980.0010.0010.0000.0000.0000.000
106B119MET0-0.017-0.00431.0160.0010.0010.0000.0000.0000.000
107B120ASN00.0220.00430.8760.0040.0040.0000.0000.0000.000
108B121ALA00.0000.00733.0360.0020.0020.0000.0000.0000.000
109B122LYS10.8610.92635.889-0.008-0.0080.0000.0000.0000.000
110B123LEU0-0.006-0.02134.5110.0000.0000.0000.0000.0000.000
111B124LEU0-0.052-0.01033.7840.0020.0020.0000.0000.0000.000
112B125MET0-0.033-0.01437.5700.0000.0000.0000.0000.0000.000
113B126ASP-1-0.816-0.89540.2180.0250.0250.0000.0000.0000.000
114B127PRO00.0160.00741.7760.0020.0020.0000.0000.0000.000
115B128LYS10.8580.94343.044-0.028-0.0280.0000.0000.0000.000
116B129ARG10.9560.96338.558-0.042-0.0420.0000.0000.0000.000
117B130GLN0-0.0280.00038.8110.0010.0010.0000.0000.0000.000
118B131ILE00.0190.01431.5890.0030.0030.0000.0000.0000.000
119B132PHE00.012-0.00632.660-0.003-0.0030.0000.0000.0000.000
120B133LEU0-0.004-0.00726.8050.0050.0050.0000.0000.0000.000
121B134ASP-1-0.838-0.93024.9970.1220.1220.0000.0000.0000.000
122B135GLN00.0440.01624.4860.0100.0100.0000.0000.0000.000
123B136ASN00.0510.02419.7630.0050.0050.0000.0000.0000.000
124B137MET0-0.019-0.00620.9600.0120.0120.0000.0000.0000.000
125B138LEU0-0.041-0.02521.996-0.010-0.0100.0000.0000.0000.000
126B139ALA00.0080.01921.133-0.013-0.0130.0000.0000.0000.000
127B140VAL00.0240.01616.734-0.007-0.0070.0000.0000.0000.000
128B141ILE0-0.035-0.01617.446-0.007-0.0070.0000.0000.0000.000
129B142ASP-1-0.881-0.94219.963-0.014-0.0140.0000.0000.0000.000
130B143GLU-1-0.965-0.99715.7410.2110.2110.0000.0000.0000.000
131B144LEU0-0.025-0.01013.5830.0040.0040.0000.0000.0000.000
132B145MET00.000-0.00516.024-0.049-0.0490.0000.0000.0000.000
133B146GLN0-0.044-0.01317.260-0.019-0.0190.0000.0000.0000.000
134B147ALA0-0.041-0.00712.726-0.009-0.0090.0000.0000.0000.000
135B148LEU0-0.031-0.02513.995-0.102-0.1020.0000.0000.0000.000
136B149ASN0-0.065-0.04516.103-0.004-0.0040.0000.0000.0000.000
137B150PHE00.0420.02417.2960.0110.0110.0000.0000.0000.000
138B151ASN00.0000.01021.3990.0250.0250.0000.0000.0000.000
139B152SER0-0.006-0.01725.132-0.002-0.0020.0000.0000.0000.000
140B153GLU-1-0.926-0.94527.366-0.054-0.0540.0000.0000.0000.000
141B154THR0-0.074-0.07329.441-0.005-0.0050.0000.0000.0000.000
142B155VAL0-0.0040.01232.2840.0050.0050.0000.0000.0000.000
143B156PRO0-0.004-0.00732.929-0.001-0.0010.0000.0000.0000.000
144B157GLN00.002-0.02332.045-0.003-0.0030.0000.0000.0000.000
145B158LYS10.7800.89033.5430.0090.0090.0000.0000.0000.000
146B159SER0-0.023-0.01236.212-0.002-0.0020.0000.0000.0000.000
147B160SER00.002-0.00338.6630.0010.0010.0000.0000.0000.000
148B161LEU0-0.019-0.02436.958-0.001-0.0010.0000.0000.0000.000
149B162GLU-1-0.823-0.87240.893-0.001-0.0010.0000.0000.0000.000
150B163GLU-1-0.847-0.92439.5600.0020.0020.0000.0000.0000.000
151B164PRO0-0.039-0.01839.3850.0000.0000.0000.0000.0000.000
152B165ASP-1-0.778-0.89542.5440.0120.0120.0000.0000.0000.000
153B166PHE00.0290.01240.8970.0000.0000.0000.0000.0000.000
154B167TYR0-0.0070.00040.5380.0020.0020.0000.0000.0000.000
155B168LYS10.8390.90040.835-0.001-0.0010.0000.0000.0000.000
156B169THR0-0.037-0.04136.340-0.001-0.0010.0000.0000.0000.000
157B170LYS10.8180.89236.370-0.025-0.0250.0000.0000.0000.000
158B171ILE0-0.0040.01836.3210.0030.0030.0000.0000.0000.000
159B172LYS10.8870.93634.0890.0010.0010.0000.0000.0000.000
160B173LEU00.0240.00130.3170.0000.0000.0000.0000.0000.000
161B175ILE00.0440.03930.9620.0020.0020.0000.0000.0000.000
162B176LEU00.0270.01228.938-0.002-0.0020.0000.0000.0000.000
163B177LEU0-0.033-0.02225.9690.0000.0000.0000.0000.0000.000
164B178HIS00.0430.01925.7160.0060.0060.0000.0000.0000.000
165B179ALA00.0260.02726.0200.0000.0000.0000.0000.0000.000
166B180PHE0-0.002-0.00721.126-0.004-0.0040.0000.0000.0000.000
167B181ARG10.9430.97119.709-0.075-0.0750.0000.0000.0000.000
168B182ILE00.0020.00620.7770.0000.0000.0000.0000.0000.000
169B183ARG10.7930.88220.8800.0430.0430.0000.0000.0000.000
170B184ALA00.012-0.01417.809-0.015-0.0150.0000.0000.0000.000
171B185VAL0-0.045-0.02216.493-0.003-0.0030.0000.0000.0000.000
172B186THR0-0.019-0.01016.255-0.013-0.0130.0000.0000.0000.000
173B187ILE00.0240.02014.082-0.037-0.0370.0000.0000.0000.000
174B188ASP-1-0.799-0.89711.3070.0410.0410.0000.0000.0000.000
175B189ARG10.9200.95511.660-0.026-0.0260.0000.0000.0000.000
176B190VAL00.0320.02812.813-0.061-0.0610.0000.0000.0000.000
177B191MET0-0.009-0.0139.081-0.154-0.1540.0000.0000.0000.000
178B192SER0-0.009-0.0157.950-0.302-0.3020.0000.0000.0000.000
179B193TYR0-0.020-0.0028.264-0.093-0.0930.0000.0000.0000.000
180B194LEU00.005-0.0128.455-0.044-0.0440.0000.0000.0000.000
181B195ASN0-0.040-0.0082.922-5.177-3.3400.722-1.096-1.463-0.011
182B196ALA00.0170.0153.756-0.5430.1160.032-0.250-0.442-0.001
183B197SER0-0.097-0.0486.1450.2480.2480.0000.0000.0000.000