FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: ZNY1N

Calculation Name: 3JUY-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3JUY

Chain ID: B

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-09-26

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 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 238
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3011032.246317
FMO2-HF: Nuclear repulsion 2917558.274404
FMO2-HF: Total energy -93473.971913
FMO2-MP2: Total energy -93747.017779


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:GLN)


Summations of interaction energy for fragment #1(B:1:GLN)
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.
-5.216-1.1810.587-2.036-2.586-0.011
Interaction energy analysis for fragmet #1(B:1:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.032 / q_NPA : 0.014
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].
3B3GLN0-0.019-0.0062.667-3.2270.5590.589-1.963-2.413-0.011
4B4LEU00.0070.0004.8840.0910.169-0.001-0.008-0.0680.000
5B5VAL0-0.024-0.0168.4930.4070.4070.0000.0000.0000.000
6B6GLN00.013-0.00210.999-0.115-0.1150.0000.0000.0000.000
7B7SER00.0420.03314.4750.0650.0650.0000.0000.0000.000
8B8GLY00.013-0.00117.8620.0290.0290.0000.0000.0000.000
9B9ALA0-0.030-0.01920.044-0.035-0.0350.0000.0000.0000.000
10B10GLU-1-0.785-0.88922.172-0.025-0.0250.0000.0000.0000.000
11B11VAL00.0110.01525.796-0.006-0.0060.0000.0000.0000.000
12B12LYS10.7590.87627.4430.0370.0370.0000.0000.0000.000
13B13LYS10.9931.00631.3410.0150.0150.0000.0000.0000.000
14B14PRO00.0350.01334.420-0.007-0.0070.0000.0000.0000.000
15B15GLY0-0.0090.00235.9460.0040.0040.0000.0000.0000.000
16B16ALA0-0.042-0.01733.127-0.005-0.0050.0000.0000.0000.000
17B17SER0-0.015-0.00930.173-0.002-0.0020.0000.0000.0000.000
18B18VAL0-0.020-0.01824.5230.0140.0140.0000.0000.0000.000
19B19LYS10.9080.95123.2830.1450.1450.0000.0000.0000.000
20B20VAL0-0.0120.00718.3880.0230.0230.0000.0000.0000.000
21B21SER00.0190.00418.337-0.027-0.0270.0000.0000.0000.000
22B22CYS0-0.042-0.01313.279-0.017-0.0170.0000.0000.0000.000
23B23GLN00.0110.01511.4870.0000.0000.0000.0000.0000.000
24B24ALA0-0.0040.0079.396-0.062-0.0620.0000.0000.0000.000
25B25SER0-0.005-0.0106.0460.0990.0990.0000.0000.0000.000
26B26GLY00.0510.0243.792-1.307-1.2600.000-0.0560.0090.000
27B27TYR00.0220.0024.4560.3650.489-0.001-0.009-0.1140.000
28B28ARG10.9320.9747.8350.7860.7860.0000.0000.0000.000
29B29PHE00.0740.02611.4100.0290.0290.0000.0000.0000.000
30B30SER00.015-0.00312.653-0.008-0.0080.0000.0000.0000.000
31B31HIS0-0.040-0.01914.0660.1190.1190.0000.0000.0000.000
32B32PHE00.0210.00211.469-0.069-0.0690.0000.0000.0000.000
33B33THR0-0.026-0.00514.8320.0350.0350.0000.0000.0000.000
34B34VAL0-0.018-0.00113.583-0.124-0.1240.0000.0000.0000.000
35B35HIS00.023-0.00915.5430.1540.1540.0000.0000.0000.000
36B36TRP0-0.013-0.01316.473-0.019-0.0190.0000.0000.0000.000
37B37VAL0-0.013-0.01517.6230.0170.0170.0000.0000.0000.000
38B38ARG10.8180.90919.3430.1760.1760.0000.0000.0000.000
39B39GLN0-0.043-0.02520.659-0.011-0.0110.0000.0000.0000.000
40B40ALA00.0250.02022.9110.0260.0260.0000.0000.0000.000
41B41PRO00.013-0.01225.868-0.006-0.0060.0000.0000.0000.000
42B42GLY0-0.0050.00926.5260.0000.0000.0000.0000.0000.000
43B43GLN0-0.0050.00326.408-0.011-0.0110.0000.0000.0000.000
44B44ARG10.8890.94624.7450.1880.1880.0000.0000.0000.000
45B45PHE0-0.0090.00017.4530.0030.0030.0000.0000.0000.000
46B46GLU-1-0.758-0.86122.664-0.179-0.1790.0000.0000.0000.000
47B47TRP00.0170.01220.5160.0130.0130.0000.0000.0000.000
48B48MET0-0.054-0.02522.1900.0310.0310.0000.0000.0000.000
49B49GLY00.0640.01122.2480.0290.0290.0000.0000.0000.000
50B50TRP0-0.067-0.01719.625-0.048-0.0480.0000.0000.0000.000
51B51ILE00.0070.00219.1310.0500.0500.0000.0000.0000.000
52B52ASN00.0400.01119.073-0.098-0.0980.0000.0000.0000.000
53B53PRO0-0.011-0.01316.7190.0590.0590.0000.0000.0000.000
54B54TYR0-0.0300.00219.7570.0380.0380.0000.0000.0000.000
55B55ASN00.023-0.00521.0590.0260.0260.0000.0000.0000.000
56B56GLY00.0000.01723.4050.0310.0310.0000.0000.0000.000
57B57ASN0-0.039-0.01424.6520.0110.0110.0000.0000.0000.000
58B58LYS10.8860.93023.7150.2510.2510.0000.0000.0000.000
59B59GLU-1-0.861-0.91524.496-0.277-0.2770.0000.0000.0000.000
60B60PHE0-0.031-0.02425.078-0.016-0.0160.0000.0000.0000.000
61B61SER00.0290.02926.6940.0140.0140.0000.0000.0000.000
62B62ALA00.0550.01028.3060.0110.0110.0000.0000.0000.000
63B63LYS10.8100.89929.6230.1720.1720.0000.0000.0000.000
64B64PHE0-0.015-0.03227.0010.0120.0120.0000.0000.0000.000
65B65GLN0-0.0170.00429.8160.0060.0060.0000.0000.0000.000
66B66ASP-1-0.835-0.89931.048-0.124-0.1240.0000.0000.0000.000
67B67ARG10.7150.82331.0060.1280.1280.0000.0000.0000.000
68B68VAL00.0080.01425.2890.0060.0060.0000.0000.0000.000
69B69THR00.0100.01426.796-0.010-0.0100.0000.0000.0000.000
70B70PHE00.0420.02622.098-0.005-0.0050.0000.0000.0000.000
71B71THR0-0.013-0.01522.5080.0120.0120.0000.0000.0000.000
72B72ALA00.003-0.01419.311-0.033-0.0330.0000.0000.0000.000
73B73ASP-1-0.813-0.89119.510-0.267-0.2670.0000.0000.0000.000
74B74THR0-0.002-0.02517.316-0.021-0.0210.0000.0000.0000.000
75B75SER0-0.090-0.02916.740-0.037-0.0370.0000.0000.0000.000
76B76ALA00.0590.03316.4330.0050.0050.0000.0000.0000.000
77B77ASN0-0.042-0.00910.5420.0410.0410.0000.0000.0000.000
78B78THR0-0.001-0.00713.516-0.084-0.0840.0000.0000.0000.000
79B79ALA0-0.0050.00715.9110.0340.0340.0000.0000.0000.000
80B80TYR0-0.014-0.03217.5830.0400.0400.0000.0000.0000.000
81B81MET0-0.0190.01120.377-0.007-0.0070.0000.0000.0000.000
82B82GLU-1-0.833-0.90722.197-0.105-0.1050.0000.0000.0000.000
83B83LEU0-0.015-0.00225.613-0.008-0.0080.0000.0000.0000.000
84B84ARG10.8860.92227.9390.1370.1370.0000.0000.0000.000
85B85SER0-0.001-0.00631.576-0.006-0.0060.0000.0000.0000.000
86B86LEU0-0.043-0.01328.622-0.002-0.0020.0000.0000.0000.000
87B87ARG11.0151.01532.6970.1090.1090.0000.0000.0000.000
88B88SER00.1230.04932.700-0.006-0.0060.0000.0000.0000.000
89B89ALA00.0020.00131.9020.0010.0010.0000.0000.0000.000
90B90ASP-1-0.808-0.87228.982-0.122-0.1220.0000.0000.0000.000
91B91THR00.0220.03327.6970.0000.0000.0000.0000.0000.000
92B92ALA0-0.006-0.01224.137-0.006-0.0060.0000.0000.0000.000
93B93VAL0-0.0190.01518.3670.0150.0150.0000.0000.0000.000
94B94TYR0-0.015-0.03619.846-0.048-0.0480.0000.0000.0000.000
95B95TYR00.0140.00214.5560.0340.0340.0000.0000.0000.000
96B97ALA00.020-0.01211.715-0.016-0.0160.0000.0000.0000.000
97B98ARG10.7500.8968.8042.3062.3060.0000.0000.0000.000
98B99VAL0-0.013-0.00811.832-0.054-0.0540.0000.0000.0000.000
99B100GLY00.0420.01111.867-0.222-0.2220.0000.0000.0000.000
100B101GLU-1-0.862-0.9349.781-1.960-1.9600.0000.0000.0000.000
101B102TRP0-0.066-0.02213.5110.0460.0460.0000.0000.0000.000
102B103GLY00.0230.01117.150-0.021-0.0210.0000.0000.0000.000
103B104TRP0-0.075-0.04518.4800.0400.0400.0000.0000.0000.000
104B105ASP-1-0.899-0.95121.319-0.371-0.3710.0000.0000.0000.000
105B106ASP-1-0.924-0.93819.406-0.659-0.6590.0000.0000.0000.000
106B107SER0-0.022-0.03622.9300.0440.0440.0000.0000.0000.000
107B108PRO0-0.008-0.02923.761-0.040-0.0400.0000.0000.0000.000
108B109TYR0-0.014-0.01821.7140.0310.0310.0000.0000.0000.000
109B110ASP-1-0.766-0.82821.308-0.479-0.4790.0000.0000.0000.000
110B111ASN00.0490.00816.2220.0540.0540.0000.0000.0000.000
111B112TYR0-0.047-0.02316.418-0.101-0.1010.0000.0000.0000.000
112B113TYR00.0130.02612.3270.0390.0390.0000.0000.0000.000
113B114MET0-0.029-0.01213.743-0.035-0.0350.0000.0000.0000.000
114B115ASP-1-0.814-0.8999.194-2.410-2.4100.0000.0000.0000.000
115B116VAL0-0.0230.0005.368-0.268-0.2680.0000.0000.0000.000
116B117TRP0-0.021-0.0098.3220.3640.3640.0000.0000.0000.000
117B118GLY00.0480.0328.7860.0650.0650.0000.0000.0000.000
118B119LYS10.8920.9098.622-1.275-1.2750.0000.0000.0000.000
119B120GLY00.0070.01812.4740.0120.0120.0000.0000.0000.000
120B121THR0-0.009-0.00715.8460.0630.0630.0000.0000.0000.000
121B122THR00.010-0.00318.746-0.036-0.0360.0000.0000.0000.000
122B123VAL00.0120.01821.9900.0140.0140.0000.0000.0000.000
123B124ILE00.0210.00425.244-0.010-0.0100.0000.0000.0000.000
124B125VAL0-0.034-0.01528.5180.0040.0040.0000.0000.0000.000
125B126SER0-0.022-0.01831.6700.0040.0040.0000.0000.0000.000
126B127SER00.025-0.01134.7390.0000.0000.0000.0000.0000.000
127B128GLY00.0260.00737.080-0.006-0.0060.0000.0000.0000.000
128B129GLY0-0.033-0.02236.820-0.005-0.0050.0000.0000.0000.000
129B130GLY0-0.0200.00737.7080.0030.0030.0000.0000.0000.000
130B131GLY00.0040.00737.119-0.001-0.0010.0000.0000.0000.000
131B142SER0-0.016-0.02536.9580.0030.0030.0000.0000.0000.000
132B143GLU-1-0.944-0.96032.777-0.186-0.1860.0000.0000.0000.000
133B144ILE0-0.020-0.01329.1620.0050.0050.0000.0000.0000.000
134B145VAL00.024-0.00330.479-0.007-0.0070.0000.0000.0000.000
135B146LEU0-0.020-0.00424.5780.0030.0030.0000.0000.0000.000
136B147THR00.0100.00628.5100.0170.0170.0000.0000.0000.000
137B148GLN0-0.010-0.01822.550-0.025-0.0250.0000.0000.0000.000
138B149ALA0-0.0080.03927.7000.0210.0210.0000.0000.0000.000
139B150PRO00.0990.02527.292-0.015-0.0150.0000.0000.0000.000
140B151GLY00.0440.02127.276-0.010-0.0100.0000.0000.0000.000
141B152THR0-0.065-0.04326.5650.0040.0040.0000.0000.0000.000
142B153LEU00.0090.01624.2480.0010.0010.0000.0000.0000.000
143B154SER00.019-0.00225.5020.0060.0060.0000.0000.0000.000
144B155LEU0-0.0030.01224.641-0.007-0.0070.0000.0000.0000.000
145B156SER0-0.007-0.01326.0450.0200.0200.0000.0000.0000.000
146B157PRO0-0.081-0.05322.286-0.012-0.0120.0000.0000.0000.000
147B158GLY00.0620.03723.5330.0140.0140.0000.0000.0000.000
148B159GLU-1-0.868-0.92924.988-0.065-0.0650.0000.0000.0000.000
149B160ARG11.0111.00624.5330.1620.1620.0000.0000.0000.000
150B161ALA0-0.0070.00422.0860.0110.0110.0000.0000.0000.000
151B162THR0-0.022-0.01523.572-0.022-0.0220.0000.0000.0000.000
152B163PHE0-0.018-0.00420.6630.0170.0170.0000.0000.0000.000
153B164SER00.0320.01024.762-0.014-0.0140.0000.0000.0000.000
154B165CYS0-0.079-0.02719.100-0.040-0.0400.0000.0000.0000.000
155B166ARG10.8440.89027.1220.1670.1670.0000.0000.0000.000
156B167SER0-0.009-0.03028.845-0.002-0.0020.0000.0000.0000.000
157B168SER00.0100.00030.5600.0070.0070.0000.0000.0000.000
158B169HIS00.0430.04332.4460.0020.0020.0000.0000.0000.000
159B170SER0-0.030-0.00931.988-0.007-0.0070.0000.0000.0000.000
160B171ILE0-0.0210.00326.095-0.001-0.0010.0000.0000.0000.000
161B172ARG10.9490.95228.6070.1960.1960.0000.0000.0000.000
162B173SER00.0390.02526.2750.0040.0040.0000.0000.0000.000
163B174ARG10.9500.97823.9430.3460.3460.0000.0000.0000.000
164B175ARG10.8610.93921.9840.3960.3960.0000.0000.0000.000
165B176VAL0-0.008-0.01021.8290.0160.0160.0000.0000.0000.000
166B177ALA0-0.0070.00116.504-0.041-0.0410.0000.0000.0000.000
167B178TRP0-0.008-0.01016.6590.0850.0850.0000.0000.0000.000
168B179TYR00.002-0.01213.291-0.126-0.1260.0000.0000.0000.000
169B180GLN00.0130.00311.5940.0370.0370.0000.0000.0000.000
170B181HIS00.011-0.00712.808-0.030-0.0300.0000.0000.0000.000
171B182LYS10.9170.96312.1250.0120.0120.0000.0000.0000.000
172B183PRO00.0280.01114.7340.0430.0430.0000.0000.0000.000
173B184GLY00.0070.00916.1530.0440.0440.0000.0000.0000.000
174B185GLN0-0.050-0.02710.6310.0380.0380.0000.0000.0000.000
175B186ALA00.0220.0078.728-0.097-0.0970.0000.0000.0000.000
176B187PRO0-0.034-0.00310.602-0.016-0.0160.0000.0000.0000.000
177B188ARG10.9370.9686.9691.1791.1790.0000.0000.0000.000
178B189LEU00.0020.0159.5010.2050.2050.0000.0000.0000.000
179B190VAL0-0.033-0.02010.261-0.159-0.1590.0000.0000.0000.000
180B191ILE0-0.016-0.00912.839-0.031-0.0310.0000.0000.0000.000
181B192HIS00.0520.03213.4380.1040.1040.0000.0000.0000.000
182B193GLY00.0940.05016.5820.0160.0160.0000.0000.0000.000
183B194VAL0-0.119-0.04719.9980.0460.0460.0000.0000.0000.000
184B195SER0-0.018-0.04320.2410.0250.0250.0000.0000.0000.000
185B196ASN0-0.0160.00816.5470.0640.0640.0000.0000.0000.000
186B197ARG10.8500.93312.9000.5600.5600.0000.0000.0000.000
187B198ALA00.0200.0219.653-0.019-0.0190.0000.0000.0000.000
188B199SER00.0710.0217.340-0.046-0.0460.0000.0000.0000.000
189B200GLY00.0130.0006.523-0.484-0.4840.0000.0000.0000.000
190B201ILE0-0.095-0.0297.5840.2350.2350.0000.0000.0000.000
191B202SER00.0090.00710.5380.1410.1410.0000.0000.0000.000
192B203ASP-1-0.865-0.95813.485-0.377-0.3770.0000.0000.0000.000
193B204ARG10.7900.89013.9640.2600.2600.0000.0000.0000.000
194B205PHE0-0.0160.00114.1420.0200.0200.0000.0000.0000.000
195B206SER00.0290.01217.450-0.037-0.0370.0000.0000.0000.000
196B207GLY00.0150.01419.4850.0190.0190.0000.0000.0000.000
197B208SER0-0.024-0.00421.1390.0090.0090.0000.0000.0000.000
198B209GLY00.0820.02824.4160.0030.0030.0000.0000.0000.000
199B210SER0-0.032-0.02027.364-0.009-0.0090.0000.0000.0000.000
200B211GLY00.0500.01829.6110.0110.0110.0000.0000.0000.000
201B212THR00.024-0.00130.880-0.010-0.0100.0000.0000.0000.000
202B213ASP-1-0.790-0.83530.031-0.181-0.1810.0000.0000.0000.000
203B214PHE0-0.004-0.00324.692-0.013-0.0130.0000.0000.0000.000
204B215THR00.001-0.01325.0480.0130.0130.0000.0000.0000.000
205B216LEU0-0.0140.01017.675-0.034-0.0340.0000.0000.0000.000
206B217THR0-0.021-0.02821.0010.0520.0520.0000.0000.0000.000
207B218ILE00.0060.01317.907-0.042-0.0420.0000.0000.0000.000
208B219THR0-0.043-0.03220.5590.0440.0440.0000.0000.0000.000
209B220ARG10.9120.93820.1700.1170.1170.0000.0000.0000.000
210B221VAL0-0.070-0.02220.015-0.018-0.0180.0000.0000.0000.000
211B222GLU-1-0.796-0.87216.720-0.034-0.0340.0000.0000.0000.000
212B223PRO0-0.025-0.03418.103-0.011-0.0110.0000.0000.0000.000
213B224GLU-1-0.816-0.90112.479-0.028-0.0280.0000.0000.0000.000
214B225ASP-1-0.772-0.88114.112-0.298-0.2980.0000.0000.0000.000
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217B228LEU0-0.033-0.00317.5060.0010.0010.0000.0000.0000.000
218B229TYR00.010-0.01615.797-0.071-0.0710.0000.0000.0000.000
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222B234TYR0-0.023-0.00919.2670.0100.0100.0000.0000.0000.000
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232B244GLY00.0160.00522.7020.0130.0130.0000.0000.0000.000
233B245THR0-0.075-0.04122.3650.0130.0130.0000.0000.0000.000
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235B247LEU00.0240.02119.6320.0060.0060.0000.0000.0000.000
236B248GLU-1-0.831-0.89621.3420.0010.0010.0000.0000.0000.000
237B249ARG10.9910.99522.145-0.094-0.0940.0000.0000.0000.000
238B250LYS10.8620.93424.7170.0050.0050.0000.0000.0000.000