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: R1398

Calculation Name: 3HMX-B-Xray312

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: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 1.20200116
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 184
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2067567.385472
FMO2-HF: Nuclear repulsion 1989216.983394
FMO2-HF: Total energy -78350.402078
FMO2-MP2: Total energy -78567.758647


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:11:ACE )


Summations of interaction energy for fragment #1(B:11:ACE )
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.
0.8652.3130.001-0.741-0.708-0.001
Interaction energy analysis for fragmet #1(B:11:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.011 / 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].
3B13PHE 00.0320.0053.6710.4791.817-0.001-0.681-0.656-0.001
4B14PRO 00.0240.0035.2120.3790.3790.0000.0000.0000.000
5B88CYS 00.0070.0077.7490.1510.1510.0000.0000.0000.000
6B16LEU 00.0310.0264.446-0.0460.0150.000-0.009-0.0520.000
7B17HIS 0-0.0270.0115.7700.1810.1810.0000.0000.0000.000
8B18HIS 00.0790.0316.9250.0490.0490.0000.0000.0000.000
9B19SER 00.0190.01110.074-0.029-0.0290.0000.0000.0000.000
10B20GLN 0-0.016-0.0135.6880.1880.1880.0000.0000.0000.000
11B21ASN 0-0.0110.00010.3060.0390.0390.0000.0000.0000.000
12B22LEU 00.0250.03012.153-0.039-0.0390.0000.0000.0000.000
13B23LEU 00.0090.01413.649-0.028-0.0280.0000.0000.0000.000
14B24ARG 10.9020.9329.727-0.569-0.5690.0000.0000.0000.000
15B25ALA 00.0150.01315.462-0.032-0.0320.0000.0000.0000.000
16B26VAL 00.0470.01517.909-0.023-0.0230.0000.0000.0000.000
17B27SER 0-0.0200.00618.161-0.021-0.0210.0000.0000.0000.000
18B28ASN 00.0230.00018.598-0.012-0.0120.0000.0000.0000.000
19B29MET 0-0.0520.00921.331-0.015-0.0150.0000.0000.0000.000
20B30LEU 0-0.006-0.01023.308-0.011-0.0110.0000.0000.0000.000
21B31GLN 0-0.021-0.02123.626-0.016-0.0160.0000.0000.0000.000
22B32LYS 10.9440.98923.232-0.136-0.1360.0000.0000.0000.000
23B33ALA 00.0820.04627.674-0.008-0.0080.0000.0000.0000.000
24B34ARG 10.9670.99128.430-0.102-0.1020.0000.0000.0000.000
25B35GLN 0-0.084-0.06127.266-0.002-0.0020.0000.0000.0000.000
26B36THR 0-0.078-0.03131.444-0.005-0.0050.0000.0000.0000.000
27B37LEU 0-0.082-0.03533.557-0.006-0.0060.0000.0000.0000.000
28B38GLU -1-0.867-0.92535.3740.0590.0590.0000.0000.0000.000
29B39PHE 0-0.037-0.00637.880-0.001-0.0010.0000.0000.0000.000
30B40TYR 0-0.031-0.06237.088-0.004-0.0040.0000.0000.0000.000
31B41PRO 00.0420.03137.5930.0030.0030.0000.0000.0000.000
32B174CYS 0-0.054-0.02129.9870.0070.0070.0000.0000.0000.000
33B43THR 0-0.015-0.02233.2310.0040.0040.0000.0000.0000.000
34B44SER 0-0.047-0.01231.300-0.004-0.0040.0000.0000.0000.000
35B45GLU -1-0.941-0.97828.5260.1010.1010.0000.0000.0000.000
36B46GLU -1-0.968-0.98732.9250.0650.0650.0000.0000.0000.000
37B47ILE 0-0.072-0.05236.047-0.005-0.0050.0000.0000.0000.000
38B48ASP -1-0.925-0.93334.9960.0610.0610.0000.0000.0000.000
39B49HIS 00.019-0.00831.3630.0080.0080.0000.0000.0000.000
40B50GLU -1-0.917-0.94431.8220.0470.0470.0000.0000.0000.000
41B51ASP -1-0.911-0.98027.9160.0720.0720.0000.0000.0000.000
42B52ILE 0-0.026-0.01528.218-0.006-0.0060.0000.0000.0000.000
43B53THR 0-0.048-0.05226.680-0.003-0.0030.0000.0000.0000.000
44B54LYS 10.9560.98829.587-0.049-0.0490.0000.0000.0000.000
45B55ASP -1-0.889-0.92831.0710.0320.0320.0000.0000.0000.000
46B56LYS 10.7110.90231.173-0.030-0.0300.0000.0000.0000.000
47B57THR 00.0450.02025.753-0.006-0.0060.0000.0000.0000.000
48B58SER 00.0130.02627.4450.0040.0040.0000.0000.0000.000
49B59THR 0-0.029-0.02922.4260.0000.0000.0000.0000.0000.000
50B60VAL 0-0.014-0.01323.2780.0060.0060.0000.0000.0000.000
51B61GLU -1-0.929-0.96625.3210.0220.0220.0000.0000.0000.000
52B62ALA 0-0.002-0.00224.5320.0010.0010.0000.0000.0000.000
53B101CYS 0-0.0420.02519.5360.0050.0050.0000.0000.0000.000
54B64LEU 0-0.0160.00119.1150.0170.0170.0000.0000.0000.000
55B65PRO 0-0.003-0.00616.919-0.012-0.0120.0000.0000.0000.000
56B66LEU 00.021-0.00718.478-0.003-0.0030.0000.0000.0000.000
57B67GLU -1-0.991-0.98219.6840.0390.0390.0000.0000.0000.000
58B68LEU 00.0000.00120.9130.0010.0010.0000.0000.0000.000
59B69THR 0-0.0200.01323.008-0.001-0.0010.0000.0000.0000.000
60B70LYS 10.9210.95625.124-0.022-0.0220.0000.0000.0000.000
61B71ASN 00.022-0.01527.125-0.008-0.0080.0000.0000.0000.000
62B72GLU -1-0.833-0.87628.103-0.007-0.0070.0000.0000.0000.000
63B73SER 0-0.049-0.03930.0140.0000.0000.0000.0000.0000.000
64B74CYS 0-0.061-0.03529.9050.0000.0000.0000.0000.0000.000
65B75LEU 00.0290.03927.5980.0010.0010.0000.0000.0000.000
66B76ASN 0-0.046-0.02431.682-0.005-0.0050.0000.0000.0000.000
67B77SER 0-0.0010.00331.468-0.001-0.0010.0000.0000.0000.000
68B78ARG 10.8510.87827.0550.0210.0210.0000.0000.0000.000
69B79GLU -1-0.906-0.92729.665-0.008-0.0080.0000.0000.0000.000
70B80THR 00.0340.02028.163-0.002-0.0020.0000.0000.0000.000
71B81SER 0-0.027-0.01225.5210.0000.0000.0000.0000.0000.000
72B82PHE 0-0.022-0.03225.154-0.006-0.0060.0000.0000.0000.000
73B83ILE 00.0190.02319.0140.0020.0020.0000.0000.0000.000
74B84THR 00.0210.00520.6900.0040.0040.0000.0000.0000.000
75B85ASN 0-0.058-0.03219.779-0.026-0.0260.0000.0000.0000.000
76B86GLY 00.0400.03417.4110.0060.0060.0000.0000.0000.000
77B87SER 00.0350.01215.6680.0160.0160.0000.0000.0000.000
78B89LEU 0-0.021-0.01611.9390.0360.0360.0000.0000.0000.000
79B90ALA 00.0220.0398.798-0.083-0.0830.0000.0000.0000.000
80B91SER 00.1910.07610.9380.0720.0720.0000.0000.0000.000
81B92ARG 10.6970.8519.8920.3550.3550.0000.0000.0000.000
82B93LYS 10.9930.99014.9250.0670.0670.0000.0000.0000.000
83B94THR 0-0.0070.00413.3730.0310.0310.0000.0000.0000.000
84B95SER 0-0.010-0.00716.4180.0090.0090.0000.0000.0000.000
85B96PHE 0-0.0070.00519.1220.0110.0110.0000.0000.0000.000
86B97MET 00.0500.00921.0240.0050.0050.0000.0000.0000.000
87B98MET 0-0.0130.01017.0430.0030.0030.0000.0000.0000.000
88B99ALA 00.0260.02820.4780.0060.0060.0000.0000.0000.000
89B100LEU 00.0410.02222.2500.0020.0020.0000.0000.0000.000
90B102LEU 00.014-0.00915.9350.0080.0080.0000.0000.0000.000
91B103SER 0-0.0160.01119.8470.0060.0060.0000.0000.0000.000
92B104SER 00.035-0.02223.3620.0060.0060.0000.0000.0000.000
93B105ILE 00.030-0.00117.5580.0080.0080.0000.0000.0000.000
94B106TYR 0-0.034-0.01120.1420.0110.0110.0000.0000.0000.000
95B107GLU -1-0.817-0.93021.5750.0170.0170.0000.0000.0000.000
96B108ASP -1-0.795-0.91222.4500.0640.0640.0000.0000.0000.000
97B109LEU 0-0.097-0.05918.7160.0070.0070.0000.0000.0000.000
98B110LYS 10.8940.94422.517-0.010-0.0100.0000.0000.0000.000
99B111MET 0-0.019-0.00925.641-0.002-0.0020.0000.0000.0000.000
100B112TYR 00.039-0.00324.1950.0020.0020.0000.0000.0000.000
101B113GLN 00.0000.02823.9260.0000.0000.0000.0000.0000.000
102B114VAL 0-0.004-0.01325.959-0.001-0.0010.0000.0000.0000.000
103B115GLU -1-0.868-0.91828.8790.0420.0420.0000.0000.0000.000
104B116PHE 00.0280.00124.4660.0000.0000.0000.0000.0000.000
105B117LYS 10.9290.98028.397-0.031-0.0310.0000.0000.0000.000
106B118THR 0-0.021-0.01729.688-0.003-0.0030.0000.0000.0000.000
107B119MET 0-0.025-0.01230.107-0.002-0.0020.0000.0000.0000.000
108B120ASN 00.0220.00429.5820.0020.0020.0000.0000.0000.000
109B121ALA 0-0.0070.00531.726-0.002-0.0020.0000.0000.0000.000
110B122LYS 10.9260.96334.681-0.033-0.0330.0000.0000.0000.000
111B123LEU 00.007-0.01432.901-0.001-0.0010.0000.0000.0000.000
112B124LEU 0-0.058-0.01132.6200.0000.0000.0000.0000.0000.000
113B125MET 0-0.038-0.01736.007-0.002-0.0020.0000.0000.0000.000
114B126ASP -1-0.870-0.95238.5960.0390.0390.0000.0000.0000.000
115B127PRO 00.0030.00340.0350.0010.0010.0000.0000.0000.000
116B128LYS 10.8730.95841.519-0.042-0.0420.0000.0000.0000.000
117B129ARG 10.9640.96837.118-0.041-0.0410.0000.0000.0000.000
118B130GLN 0-0.053-0.01236.749-0.002-0.0020.0000.0000.0000.000
119B131ILE 00.0190.01529.6920.0030.0030.0000.0000.0000.000
120B132PHE 00.003-0.01130.713-0.004-0.0040.0000.0000.0000.000
121B133LEU 00.005-0.00725.3180.0070.0070.0000.0000.0000.000
122B134ASP -1-0.886-0.96522.6300.1140.1140.0000.0000.0000.000
123B135GLN 00.0290.01623.1880.0120.0120.0000.0000.0000.000
124B136ASN 00.0710.02417.669-0.007-0.0070.0000.0000.0000.000
125B137MET 0-0.028-0.01219.4030.0090.0090.0000.0000.0000.000
126B138LEU 0-0.034-0.02120.699-0.002-0.0020.0000.0000.0000.000
127B139ALA 00.0170.02219.810-0.007-0.0070.0000.0000.0000.000
128B140VAL 00.0040.01315.423-0.004-0.0040.0000.0000.0000.000
129B141ILE 0-0.040-0.02216.5800.0060.0060.0000.0000.0000.000
130B142ASP -1-0.899-0.95219.2280.0150.0150.0000.0000.0000.000
131B143GLU -1-0.975-0.99815.0930.0850.0850.0000.0000.0000.000
132B144LEU 0-0.034-0.01013.318-0.008-0.0080.0000.0000.0000.000
133B145MET 0-0.016-0.01615.775-0.017-0.0170.0000.0000.0000.000
134B146GLN 0-0.0060.00717.849-0.011-0.0110.0000.0000.0000.000
135B147ALA 0-0.038-0.00913.304-0.021-0.0210.0000.0000.0000.000
136B148LEU 0-0.063-0.04314.754-0.029-0.0290.0000.0000.0000.000
137B149ASN 0-0.077-0.04617.074-0.002-0.0020.0000.0000.0000.000
138B150PHE 00.0250.01618.9180.0090.0090.0000.0000.0000.000
139B151ASN 00.0170.02022.8910.0040.0040.0000.0000.0000.000
140B152SER 00.0180.00626.5290.0030.0030.0000.0000.0000.000
141B153GLU -1-0.887-0.92128.5830.0000.0000.0000.0000.0000.000
142B154THR 0-0.089-0.05730.9550.0020.0020.0000.0000.0000.000
143B155VAL 0-0.0160.01332.9440.0000.0000.0000.0000.0000.000
144B156PRO 00.0780.04133.2030.0020.0020.0000.0000.0000.000
145B157GLN 00.1240.06831.3940.0020.0020.0000.0000.0000.000
146B158LYS 10.9160.90732.701-0.013-0.0130.0000.0000.0000.000
147B159SER 0-0.010-0.02636.007-0.001-0.0010.0000.0000.0000.000
148B160SER 0-0.014-0.00738.3080.0010.0010.0000.0000.0000.000
149B161LEU 00.0250.01636.6870.0020.0020.0000.0000.0000.000
150B162GLU -1-0.886-0.92140.4870.0310.0310.0000.0000.0000.000
151B163GLU -1-0.929-0.96539.3470.0320.0320.0000.0000.0000.000
152B164PRO 0-0.015-0.01238.3130.0000.0000.0000.0000.0000.000
153B165ASP -1-0.818-0.92541.6340.0330.0330.0000.0000.0000.000
154B166PHE 00.013-0.00239.3770.0020.0020.0000.0000.0000.000
155B167TYR 0-0.034-0.02339.1710.0030.0030.0000.0000.0000.000
156B168LYS 10.8970.96639.529-0.033-0.0330.0000.0000.0000.000
157B169THR 00.003-0.00735.0220.0030.0030.0000.0000.0000.000
158B170LYS 10.8710.94435.099-0.042-0.0420.0000.0000.0000.000
159B171ILE 0-0.0060.01834.9570.0040.0040.0000.0000.0000.000
160B172LYS 10.9020.95133.341-0.042-0.0420.0000.0000.0000.000
161B173LEU 00.0270.00328.7320.0040.0040.0000.0000.0000.000
162B175ILE 00.0550.03929.8440.0070.0070.0000.0000.0000.000
163B176LEU 00.0310.02028.0510.0040.0040.0000.0000.0000.000
164B177LEU 0-0.031-0.02024.6940.0080.0080.0000.0000.0000.000
165B178HIS 00.0250.00924.6320.0170.0170.0000.0000.0000.000
166B179ALA 00.0330.03125.2120.0100.0100.0000.0000.0000.000
167B180PHE 0-0.003-0.00520.8330.0080.0080.0000.0000.0000.000
168B181ARG 10.9420.96018.425-0.201-0.2010.0000.0000.0000.000
169B182ILE 00.0160.01720.0750.0220.0220.0000.0000.0000.000
170B183ARG 10.8580.93020.767-0.076-0.0760.0000.0000.0000.000
171B184ALA 00.012-0.01316.9750.0070.0070.0000.0000.0000.000
172B185VAL 0-0.037-0.02416.1170.0310.0310.0000.0000.0000.000
173B186THR 0-0.029-0.00915.8590.0200.0200.0000.0000.0000.000
174B187ILE 00.0340.01814.022-0.006-0.0060.0000.0000.0000.000
175B188ASP -1-0.851-0.93910.5920.5920.5920.0000.0000.0000.000
176B189ARG 10.9040.95211.502-0.163-0.1630.0000.0000.0000.000
177B190VAL 00.0260.02613.019-0.010-0.0100.0000.0000.0000.000
178B191MET 0-0.012-0.0159.464-0.048-0.0480.0000.0000.0000.000
179B192SER 0-0.010-0.0227.9390.0530.0530.0000.0000.0000.000
180B193TYR 0-0.039-0.0158.839-0.059-0.0590.0000.0000.0000.000
181B194LEU 00.017-0.00410.702-0.051-0.0510.0000.0000.0000.000
182B195ASN 0-0.033-0.0054.067-0.375-0.3260.002-0.0510.0000.000
183B196ALA 0-0.005-0.0057.050-0.200-0.2000.0000.0000.0000.000
184B197SER -1-0.948-0.9728.772-0.186-0.1860.0000.0000.0000.000