Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: RY5V8

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 OptAll
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
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3012626.378042
FMO2-HF: Nuclear repulsion 2919151.870606
FMO2-HF: Total energy -93474.507436
FMO2-MP2: Total energy -93747.645046


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.
-4.752-0.860.814-2.07-2.638-0.012
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 : 0.036 / q_NPA : 0.015
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].
3B3GLN00.0150.0032.625-3.933-0.5310.810-1.909-2.304-0.012
4B4LEU00.0110.0094.5940.4590.549-0.001-0.014-0.0750.000
5B5VAL0-0.027-0.0208.3280.3360.3360.0000.0000.0000.000
6B6GLN0-0.003-0.01710.786-0.136-0.1360.0000.0000.0000.000
7B7SER00.0330.02814.3930.0720.0720.0000.0000.0000.000
8B8GLY00.0160.00817.6090.0210.0210.0000.0000.0000.000
9B9ALA0-0.005-0.00519.994-0.041-0.0410.0000.0000.0000.000
10B10GLU-1-0.805-0.90921.950-0.111-0.1110.0000.0000.0000.000
11B11VAL00.0000.00725.612-0.008-0.0080.0000.0000.0000.000
12B12LYS10.7450.87627.3110.1380.1380.0000.0000.0000.000
13B13LYS10.9911.00231.2590.0820.0820.0000.0000.0000.000
14B14PRO00.0390.01534.175-0.010-0.0100.0000.0000.0000.000
15B15GLY0-0.015-0.00135.9400.0060.0060.0000.0000.0000.000
16B16ALA0-0.024-0.01033.024-0.005-0.0050.0000.0000.0000.000
17B17SER0-0.014-0.02529.610-0.003-0.0030.0000.0000.0000.000
18B18VAL0-0.022-0.02224.2040.0190.0190.0000.0000.0000.000
19B19LYS10.9260.95823.4400.2320.2320.0000.0000.0000.000
20B20VAL0-0.0090.01918.1120.0160.0160.0000.0000.0000.000
21B21SER00.0280.00217.803-0.021-0.0210.0000.0000.0000.000
22B22CYS0-0.015-0.00712.998-0.028-0.0280.0000.0000.0000.000
23B23GLN0-0.0210.01511.7190.0090.0090.0000.0000.0000.000
24B24ALA0-0.011-0.0069.454-0.123-0.1230.0000.0000.0000.000
25B25SER0-0.022-0.0165.9670.2290.2290.0000.0000.0000.000
26B26GLY00.0480.0113.597-1.357-1.1190.006-0.131-0.1140.000
27B27TYR00.0110.0064.1550.4070.569-0.001-0.016-0.1450.000
28B28ARG10.9210.9557.5090.8750.8750.0000.0000.0000.000
29B29PHE00.0780.02511.1500.0600.0600.0000.0000.0000.000
30B30SER00.0100.00612.730-0.018-0.0180.0000.0000.0000.000
31B31HIS0-0.024-0.01814.2230.1670.1670.0000.0000.0000.000
32B32PHE0-0.0040.01111.682-0.038-0.0380.0000.0000.0000.000
33B33THR0-0.035-0.02315.0810.0200.0200.0000.0000.0000.000
34B34VAL0-0.016-0.00213.642-0.149-0.1490.0000.0000.0000.000
35B35HIS00.015-0.01215.6920.1970.1970.0000.0000.0000.000
36B36TRP0-0.010-0.01016.484-0.058-0.0580.0000.0000.0000.000
37B37VAL0-0.011-0.00917.9330.0420.0420.0000.0000.0000.000
38B38ARG10.7910.88719.4770.2820.2820.0000.0000.0000.000
39B39GLN0-0.019-0.00620.447-0.029-0.0290.0000.0000.0000.000
40B40ALA00.0330.02522.6130.0230.0230.0000.0000.0000.000
41B41PRO00.018-0.01325.804-0.007-0.0070.0000.0000.0000.000
42B42GLY00.0070.01026.5770.0050.0050.0000.0000.0000.000
43B43GLN0-0.047-0.00626.437-0.005-0.0050.0000.0000.0000.000
44B44ARG10.8970.93324.4310.2760.2760.0000.0000.0000.000
45B45PHE0-0.0160.00517.1110.0020.0020.0000.0000.0000.000
46B46GLU-1-0.765-0.86421.982-0.274-0.2740.0000.0000.0000.000
47B47TRP00.0360.01520.6810.0070.0070.0000.0000.0000.000
48B48MET0-0.035-0.02322.3520.0420.0420.0000.0000.0000.000
49B49GLY00.0580.00722.4620.0450.0450.0000.0000.0000.000
50B50TRP0-0.068-0.01619.733-0.074-0.0740.0000.0000.0000.000
51B51ILE00.0010.00119.0360.0690.0690.0000.0000.0000.000
52B52ASN00.0570.03318.956-0.126-0.1260.0000.0000.0000.000
53B53PRO00.002-0.01816.7080.0730.0730.0000.0000.0000.000
54B54TYR0-0.0400.00419.5450.0390.0390.0000.0000.0000.000
55B55ASN00.011-0.00820.7610.0320.0320.0000.0000.0000.000
56B56GLY00.0050.01923.4170.0370.0370.0000.0000.0000.000
57B57ASN0-0.024-0.01024.8760.0030.0030.0000.0000.0000.000
58B58LYS10.8640.91323.6920.3310.3310.0000.0000.0000.000
59B59GLU-1-0.838-0.90024.492-0.352-0.3520.0000.0000.0000.000
60B60PHE0-0.052-0.04025.106-0.025-0.0250.0000.0000.0000.000
61B61SER00.0030.02226.2560.0260.0260.0000.0000.0000.000
62B62ALA00.0540.01028.0690.0150.0150.0000.0000.0000.000
63B63LYS10.8140.89629.5520.2680.2680.0000.0000.0000.000
64B64PHE0-0.023-0.03527.0710.0120.0120.0000.0000.0000.000
65B65GLN00.0010.01029.9150.0050.0050.0000.0000.0000.000
66B66ASP-1-0.814-0.88031.244-0.181-0.1810.0000.0000.0000.000
67B67ARG10.7280.82830.7800.2150.2150.0000.0000.0000.000
68B68VAL0-0.0110.00225.3780.0030.0030.0000.0000.0000.000
69B69THR00.0060.00426.811-0.008-0.0080.0000.0000.0000.000
70B70PHE00.0400.03021.904-0.011-0.0110.0000.0000.0000.000
71B71THR0-0.019-0.02522.1120.0310.0310.0000.0000.0000.000
72B72ALA00.002-0.01319.179-0.048-0.0480.0000.0000.0000.000
73B73ASP-1-0.787-0.85119.656-0.359-0.3590.0000.0000.0000.000
74B74THR0-0.013-0.03117.500-0.056-0.0560.0000.0000.0000.000
75B75SER0-0.104-0.05417.380-0.015-0.0150.0000.0000.0000.000
76B76ALA00.0580.03616.5160.0110.0110.0000.0000.0000.000
77B77ASN0-0.0130.00111.260-0.004-0.0040.0000.0000.0000.000
78B78THR00.007-0.00913.666-0.134-0.1340.0000.0000.0000.000
79B79ALA00.0060.01515.4870.0740.0740.0000.0000.0000.000
80B80TYR0-0.012-0.03217.3140.0290.0290.0000.0000.0000.000
81B81MET0-0.0310.00719.9520.0000.0000.0000.0000.0000.000
82B82GLU-1-0.838-0.89022.152-0.191-0.1910.0000.0000.0000.000
83B83LEU00.0080.00325.563-0.008-0.0080.0000.0000.0000.000
84B84ARG10.8610.90527.8630.2030.2030.0000.0000.0000.000
85B85SER00.0120.00631.558-0.009-0.0090.0000.0000.0000.000
86B86LEU0-0.063-0.01728.596-0.003-0.0030.0000.0000.0000.000
87B87ARG10.9991.00532.5810.1850.1850.0000.0000.0000.000
88B88SER00.0840.03032.418-0.008-0.0080.0000.0000.0000.000
89B89ALA0-0.011-0.00131.926-0.002-0.0020.0000.0000.0000.000
90B90ASP-1-0.740-0.84128.546-0.220-0.2200.0000.0000.0000.000
91B91THR0-0.0080.00927.319-0.008-0.0080.0000.0000.0000.000
92B92ALA0-0.014-0.01124.044-0.003-0.0030.0000.0000.0000.000
93B93VAL0-0.0140.01318.2090.0210.0210.0000.0000.0000.000
94B94TYR0-0.011-0.02719.697-0.041-0.0410.0000.0000.0000.000
95B95TYR00.0180.00714.4320.0190.0190.0000.0000.0000.000
96B97ALA00.008-0.01511.765-0.085-0.0850.0000.0000.0000.000
97B98ARG10.7270.8478.5732.6552.6550.0000.0000.0000.000
98B99VAL0-0.0110.00611.8040.0210.0210.0000.0000.0000.000
99B100GLY00.0580.02111.922-0.234-0.2340.0000.0000.0000.000
100B101GLU-1-0.826-0.8989.978-1.971-1.9710.0000.0000.0000.000
101B102TRP0-0.085-0.02613.7740.0260.0260.0000.0000.0000.000
102B103GLY00.0140.00617.298-0.005-0.0050.0000.0000.0000.000
103B104TRP0-0.064-0.03718.6120.0340.0340.0000.0000.0000.000
104B105ASP-1-0.890-0.95021.423-0.368-0.3680.0000.0000.0000.000
105B106ASP-1-0.906-0.93619.279-0.720-0.7200.0000.0000.0000.000
106B107SER0-0.008-0.02922.8660.0420.0420.0000.0000.0000.000
107B108PRO0-0.017-0.02523.814-0.049-0.0490.0000.0000.0000.000
108B109TYR0-0.004-0.00222.0100.0380.0380.0000.0000.0000.000
109B110ASP-1-0.763-0.84921.357-0.533-0.5330.0000.0000.0000.000
110B111ASN00.0470.01816.4200.0600.0600.0000.0000.0000.000
111B112TYR0-0.049-0.01616.308-0.132-0.1320.0000.0000.0000.000
112B113TYR00.0130.02712.2280.0120.0120.0000.0000.0000.000
113B114MET0-0.0050.01913.902-0.056-0.0560.0000.0000.0000.000
114B115ASP-1-0.817-0.9029.323-2.824-2.8240.0000.0000.0000.000
115B116VAL0-0.0110.0025.372-0.335-0.3350.0000.0000.0000.000
116B117TRP0-0.015-0.0098.4280.4690.4690.0000.0000.0000.000
117B118GLY00.0210.0188.654-0.185-0.1850.0000.0000.0000.000
118B119LYS10.8820.9087.825-0.538-0.5380.0000.0000.0000.000
119B120GLY00.0180.02612.0990.0600.0600.0000.0000.0000.000
120B121THR0-0.031-0.01815.6020.0590.0590.0000.0000.0000.000
121B122THR0-0.009-0.01118.633-0.033-0.0330.0000.0000.0000.000
122B123VAL00.0070.01221.9690.0180.0180.0000.0000.0000.000
123B124ILE00.0210.01025.093-0.008-0.0080.0000.0000.0000.000
124B125VAL0-0.024-0.00928.5790.0070.0070.0000.0000.0000.000
125B126SER00.003-0.02431.6620.0030.0030.0000.0000.0000.000
126B127SER00.0020.00234.5890.0040.0040.0000.0000.0000.000
127B128GLY00.0520.01436.765-0.008-0.0080.0000.0000.0000.000
128B129GLY0-0.055-0.03436.626-0.005-0.0050.0000.0000.0000.000
129B130GLY00.0010.01437.4980.0010.0010.0000.0000.0000.000
130B131GLY00.0020.01137.094-0.002-0.0020.0000.0000.0000.000
131B142SER0-0.013-0.02636.3760.0020.0020.0000.0000.0000.000
132B143GLU-1-0.929-0.95732.232-0.256-0.2560.0000.0000.0000.000
133B144ILE0-0.0100.00028.5680.0080.0080.0000.0000.0000.000
134B145VAL00.0290.00929.493-0.019-0.0190.0000.0000.0000.000
135B146LEU00.0000.00424.3390.0110.0110.0000.0000.0000.000
136B147THR0-0.018-0.01028.0980.0090.0090.0000.0000.0000.000
137B148GLN0-0.011-0.02422.281-0.027-0.0270.0000.0000.0000.000
138B149ALA0-0.0020.01927.3530.0230.0230.0000.0000.0000.000
139B150PRO00.0960.03727.105-0.015-0.0150.0000.0000.0000.000
140B151GLY00.0410.03427.191-0.020-0.0200.0000.0000.0000.000
141B152THR0-0.067-0.05126.168-0.004-0.0040.0000.0000.0000.000
142B153LEU0-0.0040.00924.2280.0070.0070.0000.0000.0000.000
143B154SER00.0120.00225.3070.0030.0030.0000.0000.0000.000
144B155LEU00.0200.01924.672-0.005-0.0050.0000.0000.0000.000
145B156SER00.0160.00325.6590.0160.0160.0000.0000.0000.000
146B157PRO0-0.073-0.04622.323-0.013-0.0130.0000.0000.0000.000
147B158GLY00.0000.01123.1420.0160.0160.0000.0000.0000.000
148B159GLU-1-0.825-0.89724.905-0.079-0.0790.0000.0000.0000.000
149B160ARG10.9660.98924.3140.1730.1730.0000.0000.0000.000
150B161ALA00.0140.01222.0030.0080.0080.0000.0000.0000.000
151B162THR0-0.049-0.04023.747-0.015-0.0150.0000.0000.0000.000
152B163PHE0-0.017-0.00320.4990.0140.0140.0000.0000.0000.000
153B164SER00.0230.00425.046-0.008-0.0080.0000.0000.0000.000
154B165CYS0-0.059-0.02118.546-0.060-0.0600.0000.0000.0000.000
155B166ARG10.8460.90326.7140.2140.2140.0000.0000.0000.000
156B167SER00.013-0.01528.986-0.014-0.0140.0000.0000.0000.000
157B168SER00.004-0.00930.7020.0110.0110.0000.0000.0000.000
158B169HIS00.0440.04632.2550.0030.0030.0000.0000.0000.000
159B170SER00.0230.01231.687-0.014-0.0140.0000.0000.0000.000
160B171ILE0-0.0080.01926.0350.0050.0050.0000.0000.0000.000
161B172ARG10.9100.92528.3950.2270.2270.0000.0000.0000.000
162B173SER00.0330.02526.6890.0070.0070.0000.0000.0000.000
163B174ARG10.9270.96523.9200.3800.3800.0000.0000.0000.000
164B175ARG10.8510.93422.1700.4640.4640.0000.0000.0000.000
165B176VAL0-0.013-0.01821.7860.0120.0120.0000.0000.0000.000
166B177ALA0-0.022-0.00816.510-0.039-0.0390.0000.0000.0000.000
167B178TRP0-0.011-0.01116.6630.0910.0910.0000.0000.0000.000
168B179TYR00.006-0.01012.770-0.140-0.1400.0000.0000.0000.000
169B180GLN00.0030.00311.4560.0330.0330.0000.0000.0000.000
170B181HIS00.009-0.00712.716-0.073-0.0730.0000.0000.0000.000
171B182LYS10.8650.91912.4230.2920.2920.0000.0000.0000.000
172B183PRO00.0280.00114.549-0.002-0.0020.0000.0000.0000.000
173B184GLY00.0140.01715.7900.0560.0560.0000.0000.0000.000
174B185GLN0-0.046-0.02210.364-0.011-0.0110.0000.0000.0000.000
175B186ALA00.0370.0158.566-0.039-0.0390.0000.0000.0000.000
176B187PRO0-0.046-0.01210.151-0.055-0.0550.0000.0000.0000.000
177B188ARG10.9070.9587.5321.2591.2590.0000.0000.0000.000
178B189LEU00.0240.0189.4660.3160.3160.0000.0000.0000.000
179B190VAL0-0.032-0.01810.123-0.162-0.1620.0000.0000.0000.000
180B191ILE0-0.033-0.01412.7830.0310.0310.0000.0000.0000.000
181B192HIS00.0730.04413.7880.0860.0860.0000.0000.0000.000
182B193GLY00.0780.04416.8880.0430.0430.0000.0000.0000.000
183B194VAL0-0.094-0.04020.3850.0590.0590.0000.0000.0000.000
184B195SER0-0.002-0.01320.5520.0230.0230.0000.0000.0000.000
185B196ASN0-0.030-0.00716.9150.0810.0810.0000.0000.0000.000
186B197ARG10.8510.92713.3600.4700.4700.0000.0000.0000.000
187B198ALA00.0210.0219.8910.0030.0030.0000.0000.0000.000
188B199SER00.0450.0127.1390.2040.2040.0000.0000.0000.000
189B200GLY00.0070.0046.581-0.620-0.6200.0000.0000.0000.000
190B201ILE0-0.075-0.0277.6470.0400.0400.0000.0000.0000.000
191B202SER0-0.008-0.01710.8100.1270.1270.0000.0000.0000.000
192B203ASP-1-0.825-0.92313.963-0.311-0.3110.0000.0000.0000.000
193B204ARG10.7910.88814.1340.2160.2160.0000.0000.0000.000
194B205PHE0-0.0060.01314.2570.0010.0010.0000.0000.0000.000
195B206SER00.001-0.00817.497-0.011-0.0110.0000.0000.0000.000
196B207GLY00.0220.01719.7640.0160.0160.0000.0000.0000.000
197B208SER0-0.028-0.01721.0140.0210.0210.0000.0000.0000.000
198B209GLY00.0910.03224.513-0.007-0.0070.0000.0000.0000.000
199B210SER0-0.033-0.02227.516-0.005-0.0050.0000.0000.0000.000
200B211GLY00.0550.01929.9190.0100.0100.0000.0000.0000.000
201B212THR0-0.019-0.02330.873-0.014-0.0140.0000.0000.0000.000
202B213ASP-1-0.788-0.83329.978-0.227-0.2270.0000.0000.0000.000
203B214PHE00.0250.01224.748-0.008-0.0080.0000.0000.0000.000
204B215THR0-0.006-0.01124.8870.0080.0080.0000.0000.0000.000
205B216LEU00.0180.02917.687-0.040-0.0400.0000.0000.0000.000
206B217THR0-0.028-0.02820.9780.0620.0620.0000.0000.0000.000
207B218ILE00.0120.02117.946-0.046-0.0460.0000.0000.0000.000
208B219THR0-0.032-0.03220.6850.0410.0410.0000.0000.0000.000
209B220ARG10.8570.89820.6660.0880.0880.0000.0000.0000.000
210B221VAL0-0.0260.00419.855-0.028-0.0280.0000.0000.0000.000
211B222GLU-1-0.758-0.84916.8380.0100.0100.0000.0000.0000.000
212B223PRO0-0.032-0.03918.065-0.029-0.0290.0000.0000.0000.000
213B224GLU-1-0.807-0.88812.192-0.089-0.0890.0000.0000.0000.000
214B225ASP-1-0.757-0.86514.099-0.396-0.3960.0000.0000.0000.000
215B226PHE0-0.0250.01016.007-0.047-0.0470.0000.0000.0000.000
216B227ALA0-0.026-0.00715.5560.0110.0110.0000.0000.0000.000
217B228LEU0-0.0010.01017.3990.0290.0290.0000.0000.0000.000
218B229TYR00.008-0.01915.774-0.098-0.0980.0000.0000.0000.000
219B230TYR00.0230.02017.9080.0600.0600.0000.0000.0000.000
220B232GLN0-0.009-0.02018.290-0.043-0.0430.0000.0000.0000.000
221B233VAL00.0030.00821.243-0.004-0.0040.0000.0000.0000.000
222B234TYR0-0.031-0.02219.3370.0000.0000.0000.0000.0000.000
223B235GLY00.0380.00122.5020.0320.0320.0000.0000.0000.000
224B236ALA00.0100.03723.220-0.042-0.0420.0000.0000.0000.000
225B237SER00.0470.02224.964-0.024-0.0240.0000.0000.0000.000
226B238SER0-0.030-0.01326.2590.0220.0220.0000.0000.0000.000
227B239TYR0-0.024-0.03020.885-0.037-0.0370.0000.0000.0000.000
228B240THR0-0.053-0.02223.8510.0270.0270.0000.0000.0000.000
229B241PHE00.0700.01218.030-0.041-0.0410.0000.0000.0000.000
230B242GLY00.0390.02423.1440.0420.0420.0000.0000.0000.000
231B243GLN0-0.033-0.02823.997-0.031-0.0310.0000.0000.0000.000
232B244GLY00.0140.01122.6740.0030.0030.0000.0000.0000.000
233B245THR0-0.062-0.03522.3240.0210.0210.0000.0000.0000.000
234B246LYS10.8690.93721.6770.0720.0720.0000.0000.0000.000
235B247LEU0-0.0040.01419.1860.0190.0190.0000.0000.0000.000
236B248GLU-1-0.829-0.91621.067-0.074-0.0740.0000.0000.0000.000
237B249ARG10.9840.99422.344-0.053-0.0530.0000.0000.0000.000
238B250LYS10.8410.90524.7110.0570.0570.0000.0000.0000.000