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: 2298R

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 OptH
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 -2062194.352823
FMO2-HF: Nuclear repulsion 1983994.859189
FMO2-HF: Total energy -78199.493633
FMO2-MP2: Total energy -78416.421328


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.
-3.771.2530.868-2.35-3.541-0.013
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 : -0.006 / q_NPA : -0.005
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].
3B14PRO00.0310.0053.8121.3383.098-0.023-0.774-0.9630.001
4B15CYS00.0060.0076.8710.4280.4280.0000.0000.0000.000
5B16LEU00.0310.0264.5420.0260.142-0.001-0.006-0.1100.000
6B17HIS0-0.0200.0146.7130.0790.0790.0000.0000.0000.000
7B18HIS00.0790.0308.071-0.073-0.0730.0000.0000.0000.000
8B19SER00.0160.00910.263-0.085-0.0850.0000.0000.0000.000
9B20GLN0-0.017-0.0127.604-0.131-0.1310.0000.0000.0000.000
10B21ASN0-0.0050.00211.636-0.007-0.0070.0000.0000.0000.000
11B22LEU00.0200.02813.829-0.037-0.0370.0000.0000.0000.000
12B23LEU00.0130.01414.930-0.015-0.0150.0000.0000.0000.000
13B24ARG10.9010.93212.051-0.465-0.4650.0000.0000.0000.000
14B25ALA00.0180.01417.279-0.018-0.0180.0000.0000.0000.000
15B26VAL00.0430.01319.667-0.015-0.0150.0000.0000.0000.000
16B27SER0-0.0190.00619.688-0.017-0.0170.0000.0000.0000.000
17B28ASN00.0240.00120.920-0.015-0.0150.0000.0000.0000.000
18B29MET0-0.0520.00923.318-0.004-0.0040.0000.0000.0000.000
19B30LEU0-0.005-0.01024.936-0.007-0.0070.0000.0000.0000.000
20B31GLN0-0.020-0.02125.546-0.007-0.0070.0000.0000.0000.000
21B32LYS10.9430.99025.405-0.114-0.1140.0000.0000.0000.000
22B33ALA00.0810.04529.618-0.005-0.0050.0000.0000.0000.000
23B34ARG10.9640.98930.090-0.055-0.0550.0000.0000.0000.000
24B35GLN0-0.080-0.05929.4520.0000.0000.0000.0000.0000.000
25B36THR0-0.074-0.02933.520-0.001-0.0010.0000.0000.0000.000
26B37LEU0-0.085-0.03635.118-0.004-0.0040.0000.0000.0000.000
27B38GLU-1-0.865-0.92437.1380.0400.0400.0000.0000.0000.000
28B39PHE0-0.035-0.00639.655-0.002-0.0020.0000.0000.0000.000
29B40TYR0-0.033-0.06238.614-0.003-0.0030.0000.0000.0000.000
30B41PRO00.0470.03339.0510.0020.0020.0000.0000.0000.000
31B42CYS0-0.048-0.01731.0850.0010.0010.0000.0000.0000.000
32B43THR0-0.021-0.02534.6100.0050.0050.0000.0000.0000.000
33B44SER0-0.039-0.01232.369-0.003-0.0030.0000.0000.0000.000
34B45GLU-1-0.912-0.96429.6780.0330.0330.0000.0000.0000.000
35B46GLU-1-0.963-0.96933.7660.0150.0150.0000.0000.0000.000
36B47ILE0-0.076-0.05937.155-0.003-0.0030.0000.0000.0000.000
37B48ASP-1-0.923-0.95435.8870.0110.0110.0000.0000.0000.000
38B49HIS0-0.010-0.01031.8820.0050.0050.0000.0000.0000.000
39B50GLU-1-0.911-0.93932.323-0.015-0.0150.0000.0000.0000.000
40B51ASP-1-0.913-0.98127.885-0.030-0.0300.0000.0000.0000.000
41B52ILE0-0.036-0.02128.434-0.003-0.0030.0000.0000.0000.000
42B53THR0-0.051-0.05326.462-0.002-0.0020.0000.0000.0000.000
43B54LYS10.9590.98829.1670.0250.0250.0000.0000.0000.000
44B55ASP-1-0.880-0.92430.573-0.050-0.0500.0000.0000.0000.000
45B56LYS10.8340.92730.6610.0410.0410.0000.0000.0000.000
46B57THR00.0490.02324.885-0.006-0.0060.0000.0000.0000.000
47B58SER00.0120.02625.6280.0070.0070.0000.0000.0000.000
48B59THR0-0.027-0.02821.905-0.014-0.0140.0000.0000.0000.000
49B60VAL0-0.021-0.01722.397-0.005-0.0050.0000.0000.0000.000
50B61GLU-1-0.919-0.96124.474-0.100-0.1000.0000.0000.0000.000
51B62ALA00.0150.00822.5640.0000.0000.0000.0000.0000.000
52B63CYS0-0.0470.02117.845-0.011-0.0110.0000.0000.0000.000
53B64LEU0-0.0150.00217.983-0.005-0.0050.0000.0000.0000.000
54B65PRO0-0.010-0.01215.693-0.022-0.0220.0000.0000.0000.000
55B66LEU00.027-0.00515.1230.0110.0110.0000.0000.0000.000
56B67GLU-1-1.008-0.99017.054-0.050-0.0500.0000.0000.0000.000
57B68LEU0-0.005-0.00218.8560.0150.0150.0000.0000.0000.000
58B69THR00.0000.02320.8910.0180.0180.0000.0000.0000.000
59B70LYS10.9090.94922.2850.0650.0650.0000.0000.0000.000
60B71ASN00.002-0.02324.019-0.013-0.0130.0000.0000.0000.000
61B72GLU-1-0.793-0.86523.879-0.155-0.1550.0000.0000.0000.000
62B73SER0-0.083-0.06226.7620.0060.0060.0000.0000.0000.000
63B74CYS0-0.090-0.05228.2340.0080.0080.0000.0000.0000.000
64B75LEU00.0040.01130.0460.0010.0010.0000.0000.0000.000
65B76ASN00.0240.02325.0400.0100.0100.0000.0000.0000.000
66B77SER0-0.022-0.01928.516-0.002-0.0020.0000.0000.0000.000
67B78ARG10.7840.86527.7020.1080.1080.0000.0000.0000.000
68B79GLU-1-0.781-0.86025.994-0.121-0.1210.0000.0000.0000.000
69B80THR0-0.002-0.00225.676-0.002-0.0020.0000.0000.0000.000
70B81SER00.0060.00721.970-0.007-0.0070.0000.0000.0000.000
71B82PHE0-0.029-0.03421.627-0.003-0.0030.0000.0000.0000.000
72B83ILE00.0200.02414.9890.0070.0070.0000.0000.0000.000
73B84THR00.0230.00517.8380.0350.0350.0000.0000.0000.000
74B85ASN0-0.058-0.03216.652-0.089-0.0890.0000.0000.0000.000
75B86GLY00.0420.03514.6370.0420.0420.0000.0000.0000.000
76B87SER00.0410.01313.5280.0260.0260.0000.0000.0000.000
77B89LEU00.007-0.0068.5610.0580.0580.0000.0000.0000.000
78B90ALA00.0290.0423.935-0.554-0.3970.001-0.045-0.1140.000
79B91SER00.041-0.0045.5050.3190.3190.0000.0000.0000.000
80B92ARG10.8870.9694.3951.0411.138-0.001-0.003-0.0930.000
81B93LYS10.9350.9549.8330.4200.4200.0000.0000.0000.000
82B94THR00.0250.0129.5870.1220.1220.0000.0000.0000.000
83B95SER00.0050.00412.3740.0420.0420.0000.0000.0000.000
84B96PHE0-0.0140.00114.4570.0530.0530.0000.0000.0000.000
85B97MET00.0800.03416.3590.0050.0050.0000.0000.0000.000
86B98MET0-0.0220.00514.587-0.007-0.0070.0000.0000.0000.000
87B99ALA00.0240.02617.5590.0050.0050.0000.0000.0000.000
88B100LEU00.0420.02219.1170.0110.0110.0000.0000.0000.000
89B102LEU00.006-0.01313.9480.0100.0100.0000.0000.0000.000
90B103SER0-0.0170.00917.8890.0270.0270.0000.0000.0000.000
91B104SER00.033-0.02221.3280.0170.0170.0000.0000.0000.000
92B105ILE00.0400.00216.6460.0190.0190.0000.0000.0000.000
93B106TYR0-0.047-0.01619.5310.0290.0290.0000.0000.0000.000
94B107GLU-1-0.811-0.92720.900-0.075-0.0750.0000.0000.0000.000
95B108ASP-1-0.793-0.91022.090-0.060-0.0600.0000.0000.0000.000
96B109LEU0-0.101-0.06118.9340.0210.0210.0000.0000.0000.000
97B110LYS10.9030.94822.4840.0940.0940.0000.0000.0000.000
98B111MET0-0.013-0.00225.5260.0080.0080.0000.0000.0000.000
99B112TYR00.040-0.00724.5000.0130.0130.0000.0000.0000.000
100B113GLN00.0080.03224.3070.0050.0050.0000.0000.0000.000
101B114VAL0-0.0160.01626.3980.0080.0080.0000.0000.0000.000
102B115GLU-1-0.801-0.88029.437-0.003-0.0030.0000.0000.0000.000
103B116PHE00.0470.01225.1920.0060.0060.0000.0000.0000.000
104B117LYS10.9400.98629.2960.0050.0050.0000.0000.0000.000
105B118THR0-0.033-0.02830.5500.0010.0010.0000.0000.0000.000
106B119MET0-0.025-0.01031.0900.0010.0010.0000.0000.0000.000
107B120ASN00.0280.00830.8450.0040.0040.0000.0000.0000.000
108B121ALA0-0.0060.00532.9890.0010.0010.0000.0000.0000.000
109B122LYS10.9260.96335.842-0.008-0.0080.0000.0000.0000.000
110B123LEU00.010-0.01334.4240.0000.0000.0000.0000.0000.000
111B124LEU0-0.055-0.01034.0270.0020.0020.0000.0000.0000.000
112B125MET0-0.035-0.01537.5500.0000.0000.0000.0000.0000.000
113B126ASP-1-0.872-0.95340.2010.0260.0260.0000.0000.0000.000
114B127PRO00.0060.00541.7320.0020.0020.0000.0000.0000.000
115B128LYS10.8760.95943.370-0.030-0.0300.0000.0000.0000.000
116B129ARG10.9660.96839.099-0.042-0.0420.0000.0000.0000.000
117B130GLN0-0.052-0.01138.5240.0010.0010.0000.0000.0000.000
118B131ILE00.0190.01531.6050.0030.0030.0000.0000.0000.000
119B132PHE00.003-0.01032.538-0.003-0.0030.0000.0000.0000.000
120B133LEU00.001-0.00926.6840.0050.0050.0000.0000.0000.000
121B134ASP-1-0.885-0.96324.6710.1200.1200.0000.0000.0000.000
122B135GLN00.0300.01624.6750.0110.0110.0000.0000.0000.000
123B136ASN00.0720.02419.642-0.003-0.0030.0000.0000.0000.000
124B137MET0-0.030-0.01320.9600.0110.0110.0000.0000.0000.000
125B138LEU0-0.033-0.02221.949-0.011-0.0110.0000.0000.0000.000
126B139ALA00.0180.02221.108-0.013-0.0130.0000.0000.0000.000
127B140VAL00.0040.01316.829-0.008-0.0080.0000.0000.0000.000
128B141ILE0-0.043-0.02417.398-0.009-0.0090.0000.0000.0000.000
129B142ASP-1-0.900-0.95219.914-0.021-0.0210.0000.0000.0000.000
130B143GLU-1-0.975-0.99815.7800.1970.1970.0000.0000.0000.000
131B144LEU0-0.033-0.01013.493-0.001-0.0010.0000.0000.0000.000
132B145MET0-0.015-0.01615.975-0.052-0.0520.0000.0000.0000.000
133B146GLN0-0.0050.00717.524-0.008-0.0080.0000.0000.0000.000
134B147ALA0-0.036-0.00712.723-0.013-0.0130.0000.0000.0000.000
135B148LEU0-0.065-0.04313.915-0.105-0.1050.0000.0000.0000.000
136B149ASN0-0.077-0.04716.063-0.003-0.0030.0000.0000.0000.000
137B150PHE00.0220.01517.1330.0110.0110.0000.0000.0000.000
138B151ASN00.0180.01921.2900.0210.0210.0000.0000.0000.000
139B152SER00.0110.00125.021-0.001-0.0010.0000.0000.0000.000
140B153GLU-1-0.893-0.92427.265-0.056-0.0560.0000.0000.0000.000
141B154THR0-0.076-0.05030.025-0.004-0.0040.0000.0000.0000.000
142B155VAL00.0420.03232.2010.0040.0040.0000.0000.0000.000
143B156PRO00.0160.05132.882-0.001-0.0010.0000.0000.0000.000
144B157GLN00.022-0.03032.098-0.002-0.0020.0000.0000.0000.000
145B158LYS10.7740.85233.7830.0110.0110.0000.0000.0000.000
146B159SER0-0.020-0.01135.979-0.002-0.0020.0000.0000.0000.000
147B160SER00.0040.00338.5510.0010.0010.0000.0000.0000.000
148B161LEU0-0.023-0.02836.906-0.001-0.0010.0000.0000.0000.000
149B162GLU-1-0.875-0.91640.8430.0000.0000.0000.0000.0000.000
150B163GLU-1-0.926-0.97039.9200.0000.0000.0000.0000.0000.000
151B164PRO0-0.012-0.01039.1780.0000.0000.0000.0000.0000.000
152B165ASP-1-0.812-0.92042.4990.0120.0120.0000.0000.0000.000
153B166PHE00.014-0.00140.7150.0010.0010.0000.0000.0000.000
154B167TYR0-0.028-0.02040.4950.0020.0020.0000.0000.0000.000
155B168LYS10.9050.97240.793-0.003-0.0030.0000.0000.0000.000
156B169THR0-0.009-0.01436.1470.0000.0000.0000.0000.0000.000
157B170LYS10.8730.94536.326-0.026-0.0260.0000.0000.0000.000
158B171ILE00.0020.02336.2800.0030.0030.0000.0000.0000.000
159B172LYS10.8950.95033.990-0.001-0.0010.0000.0000.0000.000
160B173LEU00.0240.00130.0390.0000.0000.0000.0000.0000.000
161B175ILE00.0500.04030.9240.0020.0020.0000.0000.0000.000
162B176LEU00.0260.01628.833-0.002-0.0020.0000.0000.0000.000
163B177LEU0-0.034-0.02126.0120.0010.0010.0000.0000.0000.000
164B178HIS00.0330.01225.6780.0050.0050.0000.0000.0000.000
165B179ALA00.0350.03225.9850.0000.0000.0000.0000.0000.000
166B180PHE0-0.008-0.00821.447-0.004-0.0040.0000.0000.0000.000
167B181ARG10.9440.96219.750-0.081-0.0810.0000.0000.0000.000
168B182ILE00.0120.01320.7430.0000.0000.0000.0000.0000.000
169B183ARG10.8590.93120.8060.0410.0410.0000.0000.0000.000
170B184ALA00.014-0.01217.721-0.015-0.0150.0000.0000.0000.000
171B185VAL0-0.032-0.02216.456-0.003-0.0030.0000.0000.0000.000
172B186THR0-0.032-0.01016.224-0.014-0.0140.0000.0000.0000.000
173B187ILE00.0340.01814.065-0.033-0.0330.0000.0000.0000.000
174B188ASP-1-0.850-0.93811.2320.0460.0460.0000.0000.0000.000
175B189ARG10.9060.95311.631-0.040-0.0400.0000.0000.0000.000
176B190VAL00.0300.02812.709-0.047-0.0470.0000.0000.0000.000
177B191MET0-0.013-0.0168.964-0.160-0.1600.0000.0000.0000.000
178B192SER0-0.010-0.0197.953-0.286-0.2860.0000.0000.0000.000
179B193TYR0-0.028-0.0098.191-0.041-0.0410.0000.0000.0000.000
180B194LEU00.004-0.0148.397-0.003-0.0030.0000.0000.0000.000
181B195ASN0-0.027-0.0022.856-5.587-3.4190.844-1.291-1.721-0.013
182B196ALA00.0140.0133.8100.0700.7360.049-0.231-0.483-0.001
183B197SER0-0.105-0.0526.3680.1010.160-0.0010.000-0.0570.000