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: 3JM1L

Calculation Name: 3EXR-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3EXR

Chain ID: B

ChEMBL ID:

UniProt ID: Q93DA8

Base Structure: X-ray

Registration Date: 2023-09-23

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 218
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2499411.07955
FMO2-HF: Nuclear repulsion 2416983.038301
FMO2-HF: Total energy -82428.04125
FMO2-MP2: Total energy -82668.447727


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:4:GLN)


Summations of interaction energy for fragment #1(B:4: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.
-45.013-38.85611.99-8.601-9.545-0.016
Interaction energy analysis for fragmet #1(B:4:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.000 / 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].
3B6PRO00.0480.0312.580-8.895-5.2961.424-2.315-2.708-0.012
4B7ASN0-0.054-0.0243.120-1.950-0.6710.084-0.455-0.908-0.003
5B8LEU0-0.038-0.0084.7981.0021.092-0.001-0.007-0.0820.000
6B9GLN0-0.002-0.0286.864-1.040-1.0400.0000.0000.0000.000
7B10VAL0-0.037-0.0229.4350.3570.3570.0000.0000.0000.000
8B11ALA00.0560.03812.762-0.053-0.0530.0000.0000.0000.000
9B12LEU0-0.063-0.03815.9780.1220.1220.0000.0000.0000.000
10B13ASP-1-0.897-0.95818.840-0.521-0.5210.0000.0000.0000.000
11B14HIS00.003-0.00119.8380.0240.0240.0000.0000.0000.000
12B15SER00.0450.01824.259-0.004-0.0040.0000.0000.0000.000
13B16ASN0-0.035-0.02726.6850.0220.0220.0000.0000.0000.000
14B17LEU00.1130.06224.515-0.009-0.0090.0000.0000.0000.000
15B18LYS11.0030.99724.4930.1430.1430.0000.0000.0000.000
16B19GLY0-0.0120.01224.7150.0090.0090.0000.0000.0000.000
17B20ALA00.0720.03720.8110.0010.0010.0000.0000.0000.000
18B21ILE00.0190.01219.798-0.030-0.0300.0000.0000.0000.000
19B22THR0-0.034-0.03420.2220.0060.0060.0000.0000.0000.000
20B23ALA0-0.017-0.00119.0080.0220.0220.0000.0000.0000.000
21B24ALA00.0490.03715.9190.0010.0010.0000.0000.0000.000
22B25VAL00.002-0.00915.613-0.011-0.0110.0000.0000.0000.000
23B26SER0-0.106-0.06117.2400.0520.0520.0000.0000.0000.000
24B27VAL00.007-0.01913.1600.0800.0800.0000.0000.0000.000
25B28GLY00.0410.03211.9970.0010.0010.0000.0000.0000.000
26B29ASN00.026-0.00710.468-0.272-0.2720.0000.0000.0000.000
27B30GLU-1-0.848-0.8839.6220.5700.5700.0000.0000.0000.000
28B31VAL0-0.0340.0017.2920.3450.3450.0000.0000.0000.000
29B32ASP-1-0.757-0.8451.911-14.094-15.1336.835-2.938-2.858-0.045
30B33VAL0-0.011-0.0064.9320.0400.086-0.001-0.003-0.0420.000
31B34ILE0-0.014-0.0078.1330.5100.5100.0000.0000.0000.000
32B35GLU-1-0.836-0.91111.881-1.217-1.2170.0000.0000.0000.000
33B36ALA00.0150.00114.7570.1350.1350.0000.0000.0000.000
34B37GLY00.0710.03318.492-0.018-0.0180.0000.0000.0000.000
35B38THR0-0.010-0.03420.1080.0560.0560.0000.0000.0000.000
36B39VAL0-0.038-0.01923.2780.0390.0390.0000.0000.0000.000
37B40CYS0-0.054-0.00422.5310.0360.0360.0000.0000.0000.000
38B41LEU00.0200.00320.6000.0310.0310.0000.0000.0000.000
39B42LEU0-0.026-0.01924.7060.0250.0250.0000.0000.0000.000
40B43GLN0-0.088-0.03627.6350.0320.0320.0000.0000.0000.000
41B44VAL0-0.079-0.04524.8270.0260.0260.0000.0000.0000.000
42B45GLY00.0150.03027.2550.0090.0090.0000.0000.0000.000
43B46SER0-0.007-0.02023.502-0.007-0.0070.0000.0000.0000.000
44B47GLU-1-0.835-0.89323.084-0.340-0.3400.0000.0000.0000.000
45B48LEU0-0.003-0.00620.3920.0010.0010.0000.0000.0000.000
46B49VAL0-0.005-0.00817.660-0.024-0.0240.0000.0000.0000.000
47B50GLU-1-0.798-0.87718.718-0.439-0.4390.0000.0000.0000.000
48B51VAL0-0.043-0.02320.7750.0110.0110.0000.0000.0000.000
49B52LEU0-0.022-0.02016.0810.0190.0190.0000.0000.0000.000
50B53ARG10.7900.86412.0751.1691.1690.0000.0000.0000.000
51B54SER0-0.046-0.02517.1650.0290.0290.0000.0000.0000.000
52B55LEU0-0.092-0.03917.5830.0570.0570.0000.0000.0000.000
53B56PHE0-0.016-0.01312.4420.0530.0530.0000.0000.0000.000
54B57PRO00.0450.02413.494-0.167-0.1670.0000.0000.0000.000
55B58ASP-1-0.938-0.97011.013-0.688-0.6880.0000.0000.0000.000
56B59LYS10.7990.9107.4820.9090.9090.0000.0000.0000.000
57B60ILE00.0130.0215.4380.2830.2830.0000.0000.0000.000
58B61ILE0-0.017-0.0059.0170.1630.1630.0000.0000.0000.000
59B62VAL00.0080.00811.8280.0340.0340.0000.0000.0000.000
60B63ALA00.0290.01014.3680.1300.1300.0000.0000.0000.000
61B64ASP-1-0.729-0.83417.867-0.707-0.7070.0000.0000.0000.000
62B65THR0-0.017-0.02219.2730.0960.0960.0000.0000.0000.000
63B66LYS10.7810.89320.7720.6890.6890.0000.0000.0000.000
64B67CYS0-0.0380.01623.3900.0470.0470.0000.0000.0000.000
65B68ALA00.0530.01025.294-0.021-0.0210.0000.0000.0000.000
66B69ASP-1-0.843-0.92528.171-0.308-0.3080.0000.0000.0000.000
67B70ALA0-0.035-0.03329.075-0.020-0.0200.0000.0000.0000.000
68B71GLY00.043-0.00226.345-0.009-0.0090.0000.0000.0000.000
69B72GLY00.0070.01025.581-0.030-0.0300.0000.0000.0000.000
70B73THR00.001-0.00926.447-0.016-0.0160.0000.0000.0000.000
71B74VAL0-0.006-0.00324.352-0.003-0.0030.0000.0000.0000.000
72B75ALA00.0630.02922.012-0.023-0.0230.0000.0000.0000.000
73B76LYS10.8780.92622.4390.3580.3580.0000.0000.0000.000
74B77ASN0-0.024-0.02024.2870.0020.0020.0000.0000.0000.000
75B78ASN0-0.045-0.04420.4340.0070.0070.0000.0000.0000.000
76B79ALA00.0350.02019.419-0.038-0.0380.0000.0000.0000.000
77B80VAL0-0.012-0.01120.396-0.008-0.0080.0000.0000.0000.000
78B81ARG10.7220.85121.5330.4100.4100.0000.0000.0000.000
79B82GLY00.0490.02918.411-0.006-0.0060.0000.0000.0000.000
80B83ALA0-0.023-0.00616.005-0.114-0.1140.0000.0000.0000.000
81B84ASP-1-0.761-0.84011.452-1.590-1.5900.0000.0000.0000.000
82B85TRP00.0060.0027.003-0.091-0.0910.0000.0000.0000.000
83B86MET0-0.0010.01514.3460.1150.1150.0000.0000.0000.000
84B87THR0-0.003-0.01316.977-0.002-0.0020.0000.0000.0000.000
85B88CYS0-0.029-0.01118.9600.0690.0690.0000.0000.0000.000
86B89ILE0-0.0040.00921.801-0.038-0.0380.0000.0000.0000.000
87B90CYS00.0130.00923.7230.0120.0120.0000.0000.0000.000
88B91SER0-0.018-0.00224.9030.0100.0100.0000.0000.0000.000
89B92ALA0-0.0050.00925.7270.0320.0320.0000.0000.0000.000
90B93THR00.0220.02127.705-0.014-0.0140.0000.0000.0000.000
91B94ILE00.0730.02826.326-0.018-0.0180.0000.0000.0000.000
92B95PRO0-0.026-0.02727.658-0.021-0.0210.0000.0000.0000.000
93B96THR00.0040.01526.949-0.004-0.0040.0000.0000.0000.000
94B97MET00.0270.01523.486-0.033-0.0330.0000.0000.0000.000
95B98LYS10.9000.97623.6350.3750.3750.0000.0000.0000.000
96B99ALA0-0.032-0.01425.153-0.009-0.0090.0000.0000.0000.000
97B100ALA00.0020.00322.873-0.002-0.0020.0000.0000.0000.000
98B101ARG10.8380.88819.3130.6310.6310.0000.0000.0000.000
99B102LYS10.8710.92621.2600.4720.4720.0000.0000.0000.000
100B103ALA0-0.031-0.00723.8770.0160.0160.0000.0000.0000.000
101B104ILE0-0.034-0.00117.0150.0200.0200.0000.0000.0000.000
102B105GLU-1-0.779-0.88019.401-0.641-0.6410.0000.0000.0000.000
103B106ASP-1-0.889-0.92820.454-0.383-0.3830.0000.0000.0000.000
104B107ILE0-0.070-0.02620.7170.0390.0390.0000.0000.0000.000
105B108ASN0-0.044-0.03114.4450.0030.0030.0000.0000.0000.000
106B109PRO00.0310.01116.913-0.097-0.0970.0000.0000.0000.000
107B110ASP-1-0.933-0.95413.837-0.660-0.6600.0000.0000.0000.000
108B111LYS10.8190.8829.9981.3521.3520.0000.0000.0000.000
109B112GLY00.0130.02112.724-0.171-0.1710.0000.0000.0000.000
110B113GLU-1-0.812-0.85411.716-1.885-1.8850.0000.0000.0000.000
111B114ILE0-0.033-0.02615.5920.0510.0510.0000.0000.0000.000
112B115GLN0-0.014-0.02211.5810.1040.1040.0000.0000.0000.000
113B116VAL00.015-0.00116.5210.0960.0960.0000.0000.0000.000
114B117GLU-1-0.725-0.85918.863-0.745-0.7450.0000.0000.0000.000
115B118LEU0-0.059-0.01419.5590.0800.0800.0000.0000.0000.000
116B119TYR0-0.099-0.09721.5410.0430.0430.0000.0000.0000.000
117B120GLY00.0170.00325.7010.0080.0080.0000.0000.0000.000
118B121ASP-1-0.928-0.95728.064-0.305-0.3050.0000.0000.0000.000
119B122TRP0-0.037-0.01222.403-0.008-0.0080.0000.0000.0000.000
120B123THR0-0.045-0.06327.5360.0070.0070.0000.0000.0000.000
121B124TYR00.035-0.01221.681-0.006-0.0060.0000.0000.0000.000
122B125ASP-1-0.837-0.88625.173-0.343-0.3430.0000.0000.0000.000
123B126GLN00.0110.00626.675-0.029-0.0290.0000.0000.0000.000
124B127ALA00.0300.01121.504-0.026-0.0260.0000.0000.0000.000
125B128GLN0-0.019-0.02222.065-0.052-0.0520.0000.0000.0000.000
126B129GLN0-0.010-0.01023.681-0.014-0.0140.0000.0000.0000.000
127B130TRP0-0.001-0.00521.092-0.019-0.0190.0000.0000.0000.000
128B131LEU00.0420.03817.427-0.037-0.0370.0000.0000.0000.000
129B132ASP-1-0.866-0.91320.644-0.429-0.4290.0000.0000.0000.000
130B133ALA0-0.086-0.07422.9210.0450.0450.0000.0000.0000.000
131B134GLY0-0.024-0.01019.4570.0020.0020.0000.0000.0000.000
132B135ILE0-0.060-0.02417.897-0.081-0.0810.0000.0000.0000.000
133B136SER00.0640.03614.392-0.026-0.0260.0000.0000.0000.000
134B137GLN00.0080.01110.317-0.218-0.2180.0000.0000.0000.000
135B138ALA0-0.003-0.00214.5300.1830.1830.0000.0000.0000.000
136B139ILE0-0.0100.00014.113-0.153-0.1530.0000.0000.0000.000
137B140TYR00.010-0.01416.6210.1300.1300.0000.0000.0000.000
138B141HIS10.8080.88717.8780.6170.6170.0000.0000.0000.000
139B142GLN00.0010.02220.4760.0400.0400.0000.0000.0000.000
140B143SER0-0.045-0.04922.3970.0040.0040.0000.0000.0000.000
141B144ARG10.9000.94024.0010.3540.3540.0000.0000.0000.000
142B145ASP-1-0.892-0.95528.314-0.154-0.1540.0000.0000.0000.000
143B146ALA00.0600.05831.5590.0070.0070.0000.0000.0000.000
144B147LEU0-0.040-0.02127.084-0.004-0.0040.0000.0000.0000.000
145B148LEU00.006-0.00731.2790.0130.0130.0000.0000.0000.000
146B149ALA0-0.031-0.01633.010-0.007-0.0070.0000.0000.0000.000
147B150GLY00.0270.00929.149-0.015-0.0150.0000.0000.0000.000
148B151GLU-1-0.846-0.90526.150-0.069-0.0690.0000.0000.0000.000
149B152THR0-0.043-0.03622.354-0.035-0.0350.0000.0000.0000.000
150B153TRP0-0.046-0.04218.377-0.011-0.0110.0000.0000.0000.000
151B154GLY00.0530.04122.3100.0070.0070.0000.0000.0000.000
152B155GLU-1-0.750-0.88722.704-0.291-0.2910.0000.0000.0000.000
153B156LYS10.8020.90024.7690.1620.1620.0000.0000.0000.000
154B157ASP-1-0.762-0.83721.764-0.371-0.3710.0000.0000.0000.000
155B158LEU00.0700.04218.075-0.067-0.0670.0000.0000.0000.000
156B159ASN0-0.047-0.04619.806-0.056-0.0560.0000.0000.0000.000
157B160LYS10.8350.93821.5750.3430.3430.0000.0000.0000.000
158B161VAL00.0250.00515.339-0.042-0.0420.0000.0000.0000.000
159B162LYS10.8390.92116.7620.2360.2360.0000.0000.0000.000
160B163LYS11.0091.01617.4440.3230.3230.0000.0000.0000.000
161B164LEU0-0.054-0.02917.1900.0050.0050.0000.0000.0000.000
162B165ILE00.0260.01812.312-0.025-0.0250.0000.0000.0000.000
163B166GLU-1-0.963-0.98514.853-0.468-0.4680.0000.0000.0000.000
164B167MET0-0.100-0.04417.2910.0460.0460.0000.0000.0000.000
165B168GLY00.0180.01914.3060.0310.0310.0000.0000.0000.000
166B169PHE0-0.089-0.04613.804-0.103-0.1030.0000.0000.0000.000
167B170ARG10.7990.8528.5022.1222.1220.0000.0000.0000.000
168B171VAL0-0.028-0.01411.1150.0050.0050.0000.0000.0000.000
169B172SER00.0210.01311.385-0.318-0.3180.0000.0000.0000.000
170B173VAL0-0.031-0.00212.6230.2330.2330.0000.0000.0000.000
171B174THR00.012-0.01314.2020.0100.0100.0000.0000.0000.000
172B175GLY00.0270.01316.8170.0460.0460.0000.0000.0000.000
173B176GLY00.0460.01619.073-0.009-0.0090.0000.0000.0000.000
174B177LEU0-0.0390.02113.6470.0490.0490.0000.0000.0000.000
175B178SER0-0.016-0.02416.9460.0180.0180.0000.0000.0000.000
176B179VAL00.0680.01915.0030.0020.0020.0000.0000.0000.000
177B180ASP-1-0.909-0.95516.2850.2360.2360.0000.0000.0000.000
178B181THR00.002-0.01918.7590.0190.0190.0000.0000.0000.000
179B182LEU00.0090.02211.643-0.054-0.0540.0000.0000.0000.000
180B183LYS10.8530.91314.924-0.356-0.3560.0000.0000.0000.000
181B184LEU0-0.055-0.02016.702-0.017-0.0170.0000.0000.0000.000
182B185PHE0-0.016-0.01714.062-0.087-0.0870.0000.0000.0000.000
183B186GLU-1-0.834-0.91614.3360.2950.2950.0000.0000.0000.000
184B187GLY0-0.0110.00013.576-0.016-0.0160.0000.0000.0000.000
185B188VAL0-0.052-0.02713.530-0.082-0.0820.0000.0000.0000.000
186B189ASP-1-0.915-0.9467.642-2.278-2.2780.0000.0000.0000.000
187B190VAL0-0.052-0.02810.132-0.177-0.1770.0000.0000.0000.000
188B191PHE00.0420.0275.497-0.431-0.4310.0000.0000.0000.000
189B192THR0-0.021-0.0136.469-1.257-1.2570.0000.0000.0000.000
190B193PHE00.0430.0178.7550.3930.3930.0000.0000.0000.000
191B194ILE00.0070.00610.214-0.041-0.0410.0000.0000.0000.000
192B195ALA00.0250.02912.2830.1890.1890.0000.0000.0000.000
193B196GLY00.0920.02414.192-0.105-0.1050.0000.0000.0000.000
194B197ARG10.8250.87516.7850.2810.2810.0000.0000.0000.000
195B198GLY0-0.0080.00019.1650.0340.0340.0000.0000.0000.000
196B199ILE00.0070.00512.8470.0650.0650.0000.0000.0000.000
197B200THR00.0380.00216.6710.0280.0280.0000.0000.0000.000
198B201GLU-1-0.876-0.88918.566-0.176-0.1760.0000.0000.0000.000
199B202ALA0-0.0060.01919.4540.0270.0270.0000.0000.0000.000
200B203LYS10.9500.95121.479-0.129-0.1290.0000.0000.0000.000
201B204ASN0-0.025-0.01619.3750.0090.0090.0000.0000.0000.000
202B205PRO00.0320.03918.0990.0490.0490.0000.0000.0000.000
203B206ALA00.0730.04014.7460.0090.0090.0000.0000.0000.000
204B207GLY0-0.023-0.00714.2870.0950.0950.0000.0000.0000.000
205B208ALA0-0.019-0.01615.4460.0920.0920.0000.0000.0000.000
206B209ALA00.0110.00311.4860.0440.0440.0000.0000.0000.000
207B210ARG10.8420.89010.602-0.578-0.5780.0000.0000.0000.000
208B211ALA00.0330.01311.1760.2940.2940.0000.0000.0000.000
209B212PHE0-0.0100.00210.0220.0700.0700.0000.0000.0000.000
210B213LYS10.8390.8922.101-15.791-13.6093.649-2.883-2.9470.044
211B214ASP-1-0.909-0.9477.8052.8462.8460.0000.0000.0000.000
212B215GLU-1-0.747-0.84710.4650.7430.7430.0000.0000.0000.000
213B216ILE0-0.019-0.0095.934-0.061-0.0610.0000.0000.0000.000
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