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: 2JM6R

Calculation Name: 1AD0-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1AD0

Chain ID: B

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-06-26

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 218
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2287487.450936
FMO2-HF: Nuclear repulsion 2203623.489615
FMO2-HF: Total energy -83863.961322
FMO2-MP2: Total energy -84107.947838


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:1:GLU)


Summations of interaction energy for fragment #1(B:1:GLU)
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.
-73.548-67.1960.908-3.229-4.0290.018
Interaction energy analysis for fragmet #1(B:1:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.947 / q_NPA : -0.986
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].
3B3GLN00.0090.0062.703-15.705-9.9890.866-2.955-3.6270.018
4B4LEU0-0.037-0.0234.817-5.177-5.105-0.001-0.008-0.0620.000
5B5LEU00.0300.0208.4440.5790.5790.0000.0000.0000.000
6B6GLU-1-0.771-0.88610.92421.13221.1320.0000.0000.0000.000
7B7SER0-0.040-0.01914.562-0.180-0.1800.0000.0000.0000.000
8B8GLY00.021-0.00217.636-0.288-0.2880.0000.0000.0000.000
9B9GLY0-0.0090.00820.647-0.668-0.6680.0000.0000.0000.000
10B10GLY00.0350.00622.4700.1470.1470.0000.0000.0000.000
11B11LEU0-0.046-0.01325.709-0.047-0.0470.0000.0000.0000.000
12B12VAL0-0.026-0.00928.492-0.041-0.0410.0000.0000.0000.000
13B13GLN00.0510.02531.160-0.175-0.1750.0000.0000.0000.000
14B14PRO0-0.005-0.02534.3540.1300.1300.0000.0000.0000.000
15B15GLY0-0.0070.00335.112-0.229-0.2290.0000.0000.0000.000
16B16GLY0-0.037-0.00633.908-0.102-0.1020.0000.0000.0000.000
17B17SER0-0.031-0.04030.8010.0140.0140.0000.0000.0000.000
18B18LEU0-0.014-0.00424.7770.0070.0070.0000.0000.0000.000
19B19ARG10.9180.97223.359-12.649-12.6490.0000.0000.0000.000
20B20LEU00.0050.02019.6110.2550.2550.0000.0000.0000.000
21B21SER0-0.054-0.03618.042-0.132-0.1320.0000.0000.0000.000
22B22CYS0-0.065-0.02912.8010.2050.2050.0000.0000.0000.000
23B23ALA00.0140.02812.383-0.615-0.6150.0000.0000.0000.000
24B24THR0-0.042-0.0329.1311.7391.7390.0000.0000.0000.000
25B25SER00.012-0.0036.3330.0430.0430.0000.0000.0000.000
26B26GLY00.0850.0403.1782.0442.3170.035-0.184-0.1230.000
27B27PHE0-0.035-0.0253.7291.9972.2880.008-0.082-0.2170.000
28B28THR00.0140.0126.582-0.735-0.7350.0000.0000.0000.000
29B29PHE00.0840.05410.238-1.445-1.4450.0000.0000.0000.000
30B30THR0-0.046-0.04912.061-0.657-0.6570.0000.0000.0000.000
31B31ASP-1-0.864-0.93313.01116.42316.4230.0000.0000.0000.000
32B32TYR0-0.024-0.01110.309-0.031-0.0310.0000.0000.0000.000
33B33TYR0-0.0040.02714.617-0.637-0.6370.0000.0000.0000.000
34B34MET0-0.0280.00211.8321.0161.0160.0000.0000.0000.000
35B35ASN00.030-0.00115.804-1.926-1.9260.0000.0000.0000.000
36B36TRP00.0290.01416.6481.0321.0320.0000.0000.0000.000
37B37VAL00.0100.00917.962-0.841-0.8410.0000.0000.0000.000
38B38ARG10.8120.91219.082-10.823-10.8230.0000.0000.0000.000
39B39GLN00.0350.01520.3570.3160.3160.0000.0000.0000.000
40B40ALA00.0780.05222.7130.0270.0270.0000.0000.0000.000
41B41PRO00.0770.02625.2680.0580.0580.0000.0000.0000.000
42B42GLY0-0.028-0.01725.628-0.362-0.3620.0000.0000.0000.000
43B43LYS10.8150.91926.668-11.300-11.3000.0000.0000.0000.000
44B44GLY00.0430.01425.0220.4000.4000.0000.0000.0000.000
45B45LEU0-0.006-0.00219.0820.1700.1700.0000.0000.0000.000
46B46GLU-1-0.809-0.89422.83510.75010.7500.0000.0000.0000.000
47B47TRP0-0.041-0.01120.5220.1120.1120.0000.0000.0000.000
48B48LEU0-0.022-0.01822.164-0.537-0.5370.0000.0000.0000.000
49B49GLY00.0640.00022.261-0.632-0.6320.0000.0000.0000.000
50B50PHE0-0.056-0.02320.0670.7320.7320.0000.0000.0000.000
51B51ILE0-0.0140.00719.477-0.646-0.6460.0000.0000.0000.000
52B52GLY00.030-0.00119.7680.7630.7630.0000.0000.0000.000
53B52ASN00.0330.02117.488-0.357-0.3570.0000.0000.0000.000
54B52LYS10.8850.96519.097-12.672-12.6720.0000.0000.0000.000
55B52ALA00.005-0.00521.182-0.146-0.1460.0000.0000.0000.000
56B53ASN0-0.001-0.03423.105-0.579-0.5790.0000.0000.0000.000
57B54GLY0-0.069-0.03224.330-0.201-0.2010.0000.0000.0000.000
58B55TYR0-0.016-0.00620.1170.1410.1410.0000.0000.0000.000
59B56THR00.1040.05123.881-0.210-0.2100.0000.0000.0000.000
60B57THR0-0.042-0.01524.1720.4340.4340.0000.0000.0000.000
61B58GLU-1-0.901-0.93725.12510.17010.1700.0000.0000.0000.000
62B59TYR0-0.001-0.00225.3220.5550.5550.0000.0000.0000.000
63B60SER00.0460.03827.209-0.357-0.3570.0000.0000.0000.000
64B61ALA00.019-0.02028.755-0.096-0.0960.0000.0000.0000.000
65B62SER0-0.040-0.01629.251-0.154-0.1540.0000.0000.0000.000
66B63VAL00.0390.02126.692-0.058-0.0580.0000.0000.0000.000
67B64LYS10.9640.99230.130-9.312-9.3120.0000.0000.0000.000
68B65GLY0-0.012-0.00131.602-0.284-0.2840.0000.0000.0000.000
69B66ARG10.7830.89930.975-9.867-9.8670.0000.0000.0000.000
70B67PHE00.003-0.01225.7490.1740.1740.0000.0000.0000.000
71B68THR0-0.037-0.01426.829-0.277-0.2770.0000.0000.0000.000
72B69ILE0-0.0060.00920.9060.3570.3570.0000.0000.0000.000
73B70SER0-0.034-0.01922.118-0.403-0.4030.0000.0000.0000.000
74B71ARG10.8030.89015.715-15.632-15.6320.0000.0000.0000.000
75B72ASP-1-0.816-0.90118.83513.38313.3830.0000.0000.0000.000
76B73LYS10.9580.96516.917-13.668-13.6680.0000.0000.0000.000
77B74SER0-0.088-0.04916.2780.7010.7010.0000.0000.0000.000
78B75LYS10.9850.99516.419-13.995-13.9950.0000.0000.0000.000
79B76SER0-0.0030.01211.8131.1121.1120.0000.0000.0000.000
80B77THR0-0.0010.00313.3031.4431.4430.0000.0000.0000.000
81B78LEU0-0.035-0.01215.446-1.112-1.1120.0000.0000.0000.000
82B79TYR0-0.019-0.03317.2770.2600.2600.0000.0000.0000.000
83B80LEU00.0130.01220.330-0.270-0.2700.0000.0000.0000.000
84B81GLN0-0.035-0.01822.4600.1550.1550.0000.0000.0000.000
85B82MET0-0.0080.00524.098-0.162-0.1620.0000.0000.0000.000
86B82ASN00.1000.04727.8620.0920.0920.0000.0000.0000.000
87B82THR00.008-0.00131.6430.0600.0600.0000.0000.0000.000
88B82LEU0-0.0060.00828.353-0.014-0.0140.0000.0000.0000.000
89B83GLN00.0210.00832.130-0.451-0.4510.0000.0000.0000.000
90B84ALA00.0800.03432.0200.3280.3280.0000.0000.0000.000
91B85GLU-1-0.895-0.96131.8709.2199.2190.0000.0000.0000.000
92B86ASP-1-0.790-0.86828.46310.52710.5270.0000.0000.0000.000
93B87SER0-0.0110.01527.1210.5230.5230.0000.0000.0000.000
94B88ALA0-0.025-0.02823.831-0.141-0.1410.0000.0000.0000.000
95B89ILE00.0070.03118.244-0.015-0.0150.0000.0000.0000.000
96B90TYR0-0.037-0.04519.437-0.220-0.2200.0000.0000.0000.000
97B91TYR00.007-0.00714.4510.6660.6660.0000.0000.0000.000
98B93THR00.003-0.01812.3131.0401.0400.0000.0000.0000.000
99B94ARG10.8010.8717.712-27.221-27.2210.0000.0000.0000.000
100B95ASP-1-0.785-0.90412.51915.95815.9580.0000.0000.0000.000
101B96ARG10.9090.96911.886-19.075-19.0750.0000.0000.0000.000
102B97GLY0-0.012-0.02513.655-0.030-0.0300.0000.0000.0000.000
103B98LEU0-0.023-0.00716.9860.0820.0820.0000.0000.0000.000
104B99ARG10.9020.95720.312-11.918-11.9180.0000.0000.0000.000
105B100PHE0-0.035-0.00116.755-0.320-0.3200.0000.0000.0000.000
106B100TYR00.0270.00113.1270.0490.0490.0000.0000.0000.000
107B100PHE0-0.003-0.00714.5070.2470.2470.0000.0000.0000.000
108B101ASP-1-0.773-0.87110.09824.87124.8710.0000.0000.0000.000
109B102TYR0-0.0080.0055.2273.0743.0740.0000.0000.0000.000
110B103TRP00.007-0.0159.007-3.036-3.0360.0000.0000.0000.000
111B104GLY00.0740.0578.8542.9412.9410.0000.0000.0000.000
112B105GLN0-0.036-0.03410.2260.7380.7380.0000.0000.0000.000
113B106GLY0-0.0030.00712.463-1.518-1.5180.0000.0000.0000.000
114B107THR0-0.047-0.02315.576-0.141-0.1410.0000.0000.0000.000
115B108LEU0-0.015-0.01618.391-0.421-0.4210.0000.0000.0000.000
116B109VAL0-0.0050.00721.905-0.179-0.1790.0000.0000.0000.000
117B110THR0-0.043-0.02524.895-0.135-0.1350.0000.0000.0000.000
118B111VAL00.0070.01128.365-0.133-0.1330.0000.0000.0000.000
119B112SER0-0.018-0.01931.420-0.299-0.2990.0000.0000.0000.000
120B113SER00.0530.02234.3880.1180.1180.0000.0000.0000.000
121B114ALA0-0.047-0.00135.700-0.164-0.1640.0000.0000.0000.000
122B115SER00.018-0.00735.7010.0950.0950.0000.0000.0000.000
123B116THR0-0.027-0.01530.8800.0240.0240.0000.0000.0000.000
124B117LYS10.9150.97033.040-8.671-8.6710.0000.0000.0000.000
125B118GLY00.0520.03031.4490.2810.2810.0000.0000.0000.000
126B119PRO0-0.042-0.01529.460-0.275-0.2750.0000.0000.0000.000
127B120SER0-0.023-0.00132.722-0.149-0.1490.0000.0000.0000.000
128B121VAL0-0.006-0.01430.3740.1200.1200.0000.0000.0000.000
129B122PHE0-0.012-0.00933.506-0.205-0.2050.0000.0000.0000.000
130B123PRO0-0.0050.00234.7440.2790.2790.0000.0000.0000.000
131B124LEU0-0.0270.00033.278-0.220-0.2200.0000.0000.0000.000
132B125ALA00.0320.00535.7660.2260.2260.0000.0000.0000.000
133B126PRO00.0180.02338.169-0.160-0.1600.0000.0000.0000.000
134B127CYS0-0.008-0.01741.027-0.027-0.0270.0000.0000.0000.000
135B128SER0-0.018-0.00744.254-0.130-0.1300.0000.0000.0000.000
136B129ARG10.9580.97540.891-7.562-7.5620.0000.0000.0000.000
137B130SER00.0310.02342.2790.0290.0290.0000.0000.0000.000
138B131THR0-0.010-0.02343.3790.1350.1350.0000.0000.0000.000
139B132SER0-0.0110.01244.7180.0090.0090.0000.0000.0000.000
140B133GLU-1-0.909-0.94340.6307.7947.7940.0000.0000.0000.000
141B134SER00.0160.00038.3420.0570.0570.0000.0000.0000.000
142B135THR0-0.082-0.03533.6660.3270.3270.0000.0000.0000.000
143B136ALA00.0540.04135.549-0.200-0.2000.0000.0000.0000.000
144B137ALA0-0.003-0.00933.5220.3330.3330.0000.0000.0000.000
145B138LEU0-0.0120.00432.295-0.264-0.2640.0000.0000.0000.000
146B139GLY00.057-0.01330.9870.2860.2860.0000.0000.0000.000
147B140CYS0-0.094-0.02226.9450.1480.1480.0000.0000.0000.000
148B141LEU00.0190.01731.4080.2040.2040.0000.0000.0000.000
149B142VAL0-0.018-0.00828.231-0.185-0.1850.0000.0000.0000.000
150B143LYS10.9540.96731.577-8.303-8.3030.0000.0000.0000.000
151B144ASP-1-0.867-0.94734.4728.4508.4500.0000.0000.0000.000
152B145TYR0-0.0040.00527.761-0.109-0.1090.0000.0000.0000.000
153B146PHE00.0060.02631.2340.0240.0240.0000.0000.0000.000
154B147PRO00.0200.00627.608-0.155-0.1550.0000.0000.0000.000
155B148GLU-1-0.798-0.89825.31012.30612.3060.0000.0000.0000.000
156B149PRO0-0.007-0.01821.231-0.016-0.0160.0000.0000.0000.000
157B150VAL0-0.001-0.01624.146-0.142-0.1420.0000.0000.0000.000
158B151THR0-0.046-0.01919.0660.7740.7740.0000.0000.0000.000
159B152VAL0-0.002-0.01121.831-0.623-0.6230.0000.0000.0000.000
160B153SER00.0020.00720.2280.6460.6460.0000.0000.0000.000
161B154TRP0-0.0040.01422.233-0.826-0.8260.0000.0000.0000.000
162B155ASN0-0.021-0.02523.5410.1900.1900.0000.0000.0000.000
163B156SER00.000-0.01621.9030.1280.1280.0000.0000.0000.000
164B157GLY00.0130.01819.0310.6800.6800.0000.0000.0000.000
165B158ALA0-0.027-0.00219.5090.4680.4680.0000.0000.0000.000
166B159LEU0-0.076-0.03021.849-0.172-0.1720.0000.0000.0000.000
167B160THR00.0350.00318.094-0.108-0.1080.0000.0000.0000.000
168B161SER00.000-0.00121.2800.0000.0000.0000.0000.0000.000
169B162GLY00.0650.02523.290-0.399-0.3990.0000.0000.0000.000
170B163VAL0-0.063-0.02722.739-0.466-0.4660.0000.0000.0000.000
171B164HIS00.0240.01823.8840.6280.6280.0000.0000.0000.000
172B165THR0-0.047-0.02923.322-0.313-0.3130.0000.0000.0000.000
173B166PHE0-0.007-0.00624.8800.3060.3060.0000.0000.0000.000
174B167PRO00.0030.00526.3720.1780.1780.0000.0000.0000.000
175B168ALA00.0080.00927.313-0.433-0.4330.0000.0000.0000.000
176B169VAL0-0.0030.01429.622-0.043-0.0430.0000.0000.0000.000
177B170LEU0-0.028-0.01933.1540.0100.0100.0000.0000.0000.000
178B171GLN0-0.051-0.03434.876-0.373-0.3730.0000.0000.0000.000
179B172SER00.0190.00638.0930.0650.0650.0000.0000.0000.000
180B173SER0-0.001-0.00639.715-0.057-0.0570.0000.0000.0000.000
181B173GLY00.0070.00537.632-0.016-0.0160.0000.0000.0000.000
182B174LEU0-0.040-0.00435.0980.2480.2480.0000.0000.0000.000
183B175TYR00.0360.00730.893-0.136-0.1360.0000.0000.0000.000
184B176SER0-0.011-0.01732.684-0.206-0.2060.0000.0000.0000.000
185B177LEU0-0.0110.01326.308-0.004-0.0040.0000.0000.0000.000
186B178SER00.0380.01430.585-0.244-0.2440.0000.0000.0000.000
187B179SER00.0000.00825.5360.3150.3150.0000.0000.0000.000
188B180VAL00.0340.01228.251-0.339-0.3390.0000.0000.0000.000
189B181VAL00.0070.00426.6610.5310.5310.0000.0000.0000.000
190B182THR0-0.0190.00028.817-0.326-0.3260.0000.0000.0000.000
191B183VAL00.0040.00029.6510.3850.3850.0000.0000.0000.000
192B184PRO00.0390.02531.884-0.280-0.2800.0000.0000.0000.000
193B185SER00.0920.01434.8240.0950.0950.0000.0000.0000.000
194B186SER0-0.062-0.02537.344-0.074-0.0740.0000.0000.0000.000
195B187SER0-0.024-0.02134.2540.1010.1010.0000.0000.0000.000
196B188LEU0-0.0050.00935.8420.0980.0980.0000.0000.0000.000
197B189GLY00.0050.00738.007-0.250-0.2500.0000.0000.0000.000
198B190THR0-0.041-0.00536.646-0.189-0.1890.0000.0000.0000.000
199B191LYS10.9470.98328.294-10.968-10.9680.0000.0000.0000.000
200B192THR0-0.057-0.03332.101-0.029-0.0290.0000.0000.0000.000
201B193TYR00.0570.02129.5630.4940.4940.0000.0000.0000.000
202B194THR00.0170.00228.641-0.512-0.5120.0000.0000.0000.000
203B196ASN0-0.008-0.02923.3010.1190.1190.0000.0000.0000.000
204B197VAL00.0090.00224.0430.5690.5690.0000.0000.0000.000
205B198ASP-1-0.902-0.96021.89813.79213.7920.0000.0000.0000.000
206B199HIS00.0420.02824.0200.2220.2220.0000.0000.0000.000
207B200LYS10.9810.97418.313-16.421-16.4210.0000.0000.0000.000
208B201PRO0-0.0080.01124.021-0.258-0.2580.0000.0000.0000.000
209B202SER0-0.007-0.00426.658-0.410-0.4100.0000.0000.0000.000
210B203ASN0-0.052-0.01426.8150.0030.0030.0000.0000.0000.000
211B204THR0-0.005-0.00927.772-0.400-0.4000.0000.0000.0000.000
212B205LYS10.9400.98322.481-13.225-13.2250.0000.0000.0000.000
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214B207ASP-1-0.843-0.91126.52712.44512.4450.0000.0000.0000.000
215B208LYS10.9290.97129.301-9.411-9.4110.0000.0000.0000.000
216B209ARG10.9180.94531.414-9.063-9.0630.0000.0000.0000.000
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218B211GLU-1-0.918-0.95834.7488.1468.1460.0000.0000.0000.000