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: NNLYQ

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 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. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2491036.368202
FMO2-HF: Nuclear repulsion 2408609.535115
FMO2-HF: Total energy -82426.833087
FMO2-MP2: Total energy -82667.171396


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.
-25.77-18.8350.905-3.483-4.359-0.004
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 : 0.010 / q_NPA : 0.000
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].
3B6PRO00.0540.0413.255-8.624-5.0260.576-1.887-2.288-0.001
4B7ASN0-0.045-0.0232.869-5.413-3.8090.272-0.755-1.122-0.008
5B8LEU0-0.036-0.0104.5691.4731.541-0.001-0.006-0.0610.000
6B9GLN00.009-0.0137.293-0.716-0.7160.0000.0000.0000.000
7B10VAL0-0.034-0.0209.7300.3310.3310.0000.0000.0000.000
8B11ALA00.0500.02313.125-0.070-0.0700.0000.0000.0000.000
9B12LEU0-0.087-0.04216.2380.1420.1420.0000.0000.0000.000
10B13ASP-1-0.878-0.94819.195-0.666-0.6660.0000.0000.0000.000
11B14HIS00.000-0.00620.5610.0310.0310.0000.0000.0000.000
12B15SER00.0430.01124.900-0.009-0.0090.0000.0000.0000.000
13B16ASN0-0.003-0.01827.3060.0120.0120.0000.0000.0000.000
14B17LEU00.1290.07025.252-0.016-0.0160.0000.0000.0000.000
15B18LYS10.9730.98225.3080.1750.1750.0000.0000.0000.000
16B19GLY0-0.013-0.00125.3880.0060.0060.0000.0000.0000.000
17B20ALA00.0550.02221.424-0.004-0.0040.0000.0000.0000.000
18B21ILE00.0300.01520.634-0.025-0.0250.0000.0000.0000.000
19B22THR0-0.028-0.01921.1160.0110.0110.0000.0000.0000.000
20B23ALA0-0.0060.00319.5630.0210.0210.0000.0000.0000.000
21B24ALA00.0440.03416.750-0.002-0.0020.0000.0000.0000.000
22B25VAL00.0000.00016.463-0.003-0.0030.0000.0000.0000.000
23B26SER0-0.118-0.06618.0860.0500.0500.0000.0000.0000.000
24B27VAL00.005-0.01613.8570.0720.0720.0000.0000.0000.000
25B28GLY00.0350.03212.820-0.023-0.0230.0000.0000.0000.000
26B29ASN00.005-0.02111.368-0.196-0.1960.0000.0000.0000.000
27B30GLU-1-0.923-0.96010.4600.6850.6850.0000.0000.0000.000
28B31VAL0-0.051-0.0078.1390.1020.1020.0000.0000.0000.000
29B32ASP-1-0.771-0.8783.955-4.077-3.7290.002-0.133-0.216-0.001
30B33VAL0-0.027-0.0086.068-0.068-0.0680.0000.0000.0000.000
31B34ILE0-0.006-0.0028.8750.3910.3910.0000.0000.0000.000
32B35GLU-1-0.847-0.92312.593-1.243-1.2430.0000.0000.0000.000
33B36ALA0-0.026-0.01515.2190.1360.1360.0000.0000.0000.000
34B37GLY00.0900.03718.933-0.030-0.0300.0000.0000.0000.000
35B38THR0-0.039-0.04520.5090.0610.0610.0000.0000.0000.000
36B39VAL0-0.037-0.01023.6040.0420.0420.0000.0000.0000.000
37B40CYS0-0.0170.00623.0570.0390.0390.0000.0000.0000.000
38B41LEU00.0060.00021.1520.0410.0410.0000.0000.0000.000
39B42LEU0-0.029-0.02225.2230.0330.0330.0000.0000.0000.000
40B43GLN0-0.086-0.01928.0890.0340.0340.0000.0000.0000.000
41B44VAL0-0.070-0.04225.7320.0280.0280.0000.0000.0000.000
42B45GLY00.0100.01927.9620.0150.0150.0000.0000.0000.000
43B46SER00.025-0.00724.519-0.009-0.0090.0000.0000.0000.000
44B47GLU-1-0.927-0.95624.023-0.347-0.3470.0000.0000.0000.000
45B48LEU00.002-0.00221.295-0.002-0.0020.0000.0000.0000.000
46B49VAL0-0.003-0.00818.524-0.022-0.0220.0000.0000.0000.000
47B50GLU-1-0.826-0.89719.567-0.441-0.4410.0000.0000.0000.000
48B51VAL0-0.051-0.02921.4990.0140.0140.0000.0000.0000.000
49B52LEU0-0.024-0.02516.9190.0240.0240.0000.0000.0000.000
50B53ARG10.8220.88313.1081.0991.0990.0000.0000.0000.000
51B54SER0-0.033-0.02117.6980.0210.0210.0000.0000.0000.000
52B55LEU0-0.057-0.02918.3240.0470.0470.0000.0000.0000.000
53B56PHE0-0.022-0.02113.3730.0690.0690.0000.0000.0000.000
54B57PRO00.0160.00814.294-0.151-0.1510.0000.0000.0000.000
55B58ASP-1-0.964-0.95511.652-0.543-0.5430.0000.0000.0000.000
56B59LYS10.8500.9247.9260.6890.6890.0000.0000.0000.000
57B60ILE0-0.020-0.0015.9370.1680.1680.0000.0000.0000.000
58B61ILE00.0020.0439.7630.1190.1190.0000.0000.0000.000
59B62VAL00.0140.00912.018-0.012-0.0120.0000.0000.0000.000
60B63ALA00.002-0.00414.5880.1480.1480.0000.0000.0000.000
61B64ASP-1-0.735-0.86418.113-0.847-0.8470.0000.0000.0000.000
62B65THR0-0.002-0.02619.4290.0910.0910.0000.0000.0000.000
63B66LYS10.7920.90221.0630.8110.8110.0000.0000.0000.000
64B67CYS0-0.0230.01423.3130.0650.0650.0000.0000.0000.000
65B68ALA00.0580.01525.293-0.023-0.0230.0000.0000.0000.000
66B69ASP-1-0.867-0.94828.268-0.353-0.3530.0000.0000.0000.000
67B70ALA0-0.049-0.02429.276-0.017-0.0170.0000.0000.0000.000
68B71GLY00.0430.01126.580-0.014-0.0140.0000.0000.0000.000
69B72GLY00.0210.01425.931-0.030-0.0300.0000.0000.0000.000
70B73THR0-0.019-0.01527.076-0.009-0.0090.0000.0000.0000.000
71B74VAL00.0140.00324.353-0.003-0.0030.0000.0000.0000.000
72B75ALA00.0530.02422.428-0.026-0.0260.0000.0000.0000.000
73B76LYS10.9951.00922.8520.3550.3550.0000.0000.0000.000
74B77ASN0-0.041-0.03024.7210.0080.0080.0000.0000.0000.000
75B78ASN0-0.018-0.02820.8810.0080.0080.0000.0000.0000.000
76B79ALA00.0440.03020.023-0.036-0.0360.0000.0000.0000.000
77B80VAL0-0.061-0.03321.0760.0020.0020.0000.0000.0000.000
78B81ARG10.8300.91222.0430.4460.4460.0000.0000.0000.000
79B82GLY00.0310.02319.0960.0130.0130.0000.0000.0000.000
80B83ALA0-0.034-0.01516.520-0.093-0.0930.0000.0000.0000.000
81B84ASP-1-0.745-0.85812.130-1.554-1.5540.0000.0000.0000.000
82B85TRP00.0180.0097.115-0.108-0.1080.0000.0000.0000.000
83B86MET0-0.0200.02014.4580.1380.1380.0000.0000.0000.000
84B87THR00.0100.01117.100-0.008-0.0080.0000.0000.0000.000
85B88CYS0-0.041-0.01318.9870.1100.1100.0000.0000.0000.000
86B89ILE0-0.0060.00321.769-0.048-0.0480.0000.0000.0000.000
87B90CYS00.0150.01023.6260.0200.0200.0000.0000.0000.000
88B91SER0-0.039-0.01224.9260.0140.0140.0000.0000.0000.000
89B92ALA00.0060.01326.1430.0390.0390.0000.0000.0000.000
90B93THR00.0090.01227.648-0.017-0.0170.0000.0000.0000.000
91B94ILE00.0640.02626.165-0.021-0.0210.0000.0000.0000.000
92B95PRO0-0.016-0.02827.559-0.025-0.0250.0000.0000.0000.000
93B96THR00.0270.02226.8550.0030.0030.0000.0000.0000.000
94B97MET00.0390.01823.505-0.034-0.0340.0000.0000.0000.000
95B98LYS10.9340.97623.7170.4180.4180.0000.0000.0000.000
96B99ALA0-0.043-0.02125.294-0.007-0.0070.0000.0000.0000.000
97B100ALA0-0.001-0.00322.8220.0030.0030.0000.0000.0000.000
98B101ARG10.8290.90419.5750.7380.7380.0000.0000.0000.000
99B102LYS10.9380.96821.3160.4970.4970.0000.0000.0000.000
100B103ALA0-0.0060.00923.8470.0140.0140.0000.0000.0000.000
101B104ILE0-0.025-0.01317.5970.0270.0270.0000.0000.0000.000
102B105GLU-1-0.857-0.93618.684-0.808-0.8080.0000.0000.0000.000
103B106ASP-1-0.999-0.99320.365-0.410-0.4100.0000.0000.0000.000
104B107ILE0-0.058-0.02621.1560.0340.0340.0000.0000.0000.000
105B108ASN0-0.065-0.03414.8280.0270.0270.0000.0000.0000.000
106B109PRO00.0360.01717.256-0.114-0.1140.0000.0000.0000.000
107B110ASP-1-0.943-0.95913.934-0.732-0.7320.0000.0000.0000.000
108B111LYS10.8250.89710.2621.5621.5620.0000.0000.0000.000
109B112GLY0-0.0110.01313.039-0.191-0.1910.0000.0000.0000.000
110B113GLU-1-0.806-0.87911.686-2.225-2.2250.0000.0000.0000.000
111B114ILE0-0.052-0.02715.5890.0500.0500.0000.0000.0000.000
112B115GLN0-0.007-0.01211.9460.1060.1060.0000.0000.0000.000
113B116VAL00.0120.00216.4830.1220.1220.0000.0000.0000.000
114B117GLU-1-0.798-0.90118.684-0.995-0.9950.0000.0000.0000.000
115B118LEU0-0.038-0.01619.6680.0920.0920.0000.0000.0000.000
116B119TYR0-0.053-0.04422.2060.0090.0090.0000.0000.0000.000
117B120GLY00.009-0.00325.7000.0090.0090.0000.0000.0000.000
118B121ASP-1-0.933-0.96128.067-0.369-0.3690.0000.0000.0000.000
119B122TRP0-0.0180.00422.7060.0000.0000.0000.0000.0000.000
120B123THR00.018-0.00627.9310.0050.0050.0000.0000.0000.000
121B124TYR00.051-0.01222.244-0.035-0.0350.0000.0000.0000.000
122B125ASP-1-0.868-0.91925.211-0.393-0.3930.0000.0000.0000.000
123B126GLN0-0.016-0.01527.018-0.033-0.0330.0000.0000.0000.000
124B127ALA00.006-0.01221.678-0.026-0.0260.0000.0000.0000.000
125B128GLN00.0080.00122.040-0.065-0.0650.0000.0000.0000.000
126B129GLN0-0.006-0.01123.6630.0080.0080.0000.0000.0000.000
127B130TRP00.003-0.00121.185-0.017-0.0170.0000.0000.0000.000
128B131LEU00.0340.02817.205-0.032-0.0320.0000.0000.0000.000
129B132ASP-1-0.879-0.91920.429-0.511-0.5110.0000.0000.0000.000
130B133ALA0-0.140-0.07123.1760.0460.0460.0000.0000.0000.000
131B134GLY0-0.006-0.01419.6860.0110.0110.0000.0000.0000.000
132B135ILE0-0.055-0.01518.212-0.080-0.0800.0000.0000.0000.000
133B136SER00.0750.03414.243-0.025-0.0250.0000.0000.0000.000
134B137GLN00.0370.03710.788-0.317-0.3170.0000.0000.0000.000
135B138ALA0-0.001-0.00214.5000.2250.2250.0000.0000.0000.000
136B139ILE0-0.0040.00614.068-0.185-0.1850.0000.0000.0000.000
137B140TYR0-0.032-0.04816.4850.1610.1610.0000.0000.0000.000
138B141HIS10.8030.87817.8950.7630.7630.0000.0000.0000.000
139B142GLN00.0440.03320.4360.0640.0640.0000.0000.0000.000
140B143SER0-0.065-0.05122.1270.0160.0160.0000.0000.0000.000
141B144ARG10.8950.93723.5900.4750.4750.0000.0000.0000.000
142B145ASP-1-0.896-0.95128.046-0.212-0.2120.0000.0000.0000.000
143B146ALA00.0430.04431.1570.0110.0110.0000.0000.0000.000
144B147LEU0-0.050-0.02527.005-0.004-0.0040.0000.0000.0000.000
145B148LEU00.015-0.00131.1510.0170.0170.0000.0000.0000.000
146B149ALA0-0.048-0.03433.071-0.007-0.0070.0000.0000.0000.000
147B150GLY00.012-0.01129.657-0.015-0.0150.0000.0000.0000.000
148B151GLU-1-0.902-0.93725.706-0.164-0.1640.0000.0000.0000.000
149B152THR0-0.022-0.00322.041-0.008-0.0080.0000.0000.0000.000
150B153TRP0-0.072-0.04518.351-0.010-0.0100.0000.0000.0000.000
151B154GLY00.0790.03522.6070.0180.0180.0000.0000.0000.000
152B155GLU-1-0.897-0.97124.069-0.314-0.3140.0000.0000.0000.000
153B156LYS10.8130.91324.4840.2190.2190.0000.0000.0000.000
154B157ASP-1-0.762-0.83821.966-0.494-0.4940.0000.0000.0000.000
155B158LEU00.0400.02418.633-0.078-0.0780.0000.0000.0000.000
156B159ASN0-0.004-0.00519.637-0.067-0.0670.0000.0000.0000.000
157B160LYS10.8970.96221.0830.4370.4370.0000.0000.0000.000
158B161VAL00.0190.01115.757-0.050-0.0500.0000.0000.0000.000
159B162LYS10.9700.98316.3400.3260.3260.0000.0000.0000.000
160B163LYS10.9891.01617.0660.4100.4100.0000.0000.0000.000
161B164LEU0-0.052-0.03317.3850.0030.0030.0000.0000.0000.000
162B165ILE00.0280.01711.835-0.029-0.0290.0000.0000.0000.000
163B166GLU-1-0.952-0.98214.329-0.580-0.5800.0000.0000.0000.000
164B167MET0-0.114-0.05516.4960.0440.0440.0000.0000.0000.000
165B168GLY00.0160.02214.3100.0610.0610.0000.0000.0000.000
166B169PHE0-0.086-0.04014.044-0.100-0.1000.0000.0000.0000.000
167B170ARG10.8210.8888.2532.7012.7010.0000.0000.0000.000
168B171VAL0-0.002-0.00711.3010.0900.0900.0000.0000.0000.000
169B172SER00.0210.01311.267-0.402-0.4020.0000.0000.0000.000
170B173VAL0-0.0040.01212.4180.2860.2860.0000.0000.0000.000
171B174THR00.0320.00214.028-0.004-0.0040.0000.0000.0000.000
172B175GLY00.0190.01116.6920.0680.0680.0000.0000.0000.000
173B176GLY00.0290.00219.175-0.004-0.0040.0000.0000.0000.000
174B177LEU0-0.0240.01113.5910.0280.0280.0000.0000.0000.000
175B178SER0-0.016-0.01916.8960.0320.0320.0000.0000.0000.000
176B179VAL00.0730.02915.041-0.023-0.0230.0000.0000.0000.000
177B180ASP-1-0.915-0.96416.4300.1020.1020.0000.0000.0000.000
178B181THR0-0.033-0.03818.3890.0120.0120.0000.0000.0000.000
179B182LEU00.0350.03511.972-0.050-0.0500.0000.0000.0000.000
180B183LYS10.9440.97015.349-0.147-0.1470.0000.0000.0000.000
181B184LEU0-0.049-0.01817.2160.0030.0030.0000.0000.0000.000
182B185PHE0-0.014-0.01114.498-0.079-0.0790.0000.0000.0000.000
183B186GLU-1-0.918-0.95414.0720.1230.1230.0000.0000.0000.000
184B187GLY0-0.019-0.00913.246-0.023-0.0230.0000.0000.0000.000
185B188VAL0-0.057-0.02813.240-0.067-0.0670.0000.0000.0000.000
186B189ASP-1-0.932-0.9607.351-2.700-2.7000.0000.0000.0000.000
187B190VAL0-0.052-0.0249.565-0.295-0.2950.0000.0000.0000.000
188B191PHE00.0480.0265.752-0.512-0.5120.0000.0000.0000.000
189B192THR0-0.048-0.0256.309-1.561-1.5610.0000.0000.0000.000
190B193PHE00.0330.0178.3850.5420.5420.0000.0000.0000.000
191B194ILE00.0200.01110.106-0.091-0.0910.0000.0000.0000.000
192B195ALA0-0.0040.00212.7210.2120.2120.0000.0000.0000.000
193B196GLY00.1160.04214.723-0.075-0.0750.0000.0000.0000.000
194B197ARG10.8160.89217.5230.3300.3300.0000.0000.0000.000
195B198GLY00.0010.01819.3010.0430.0430.0000.0000.0000.000
196B199ILE00.0370.00713.2660.0680.0680.0000.0000.0000.000
197B200THR0-0.017-0.01917.2340.0650.0650.0000.0000.0000.000
198B201GLU-1-0.870-0.91919.218-0.209-0.2090.0000.0000.0000.000
199B202ALA0-0.0130.01120.0190.0340.0340.0000.0000.0000.000
200B203LYS10.9670.96821.913-0.071-0.0710.0000.0000.0000.000
201B204ASN0-0.015-0.01520.056-0.009-0.0090.0000.0000.0000.000
202B205PRO00.0470.04018.7290.0360.0360.0000.0000.0000.000
203B206ALA00.0910.05215.608-0.011-0.0110.0000.0000.0000.000
204B207GLY0-0.050-0.02914.9250.0720.0720.0000.0000.0000.000
205B208ALA0-0.017-0.00916.0220.0710.0710.0000.0000.0000.000
206B209ALA00.0150.00411.8900.0070.0070.0000.0000.0000.000
207B210ARG10.9240.96611.370-0.549-0.5490.0000.0000.0000.000
208B211ALA00.0070.00311.8790.2100.2100.0000.0000.0000.000
209B212PHE0-0.008-0.00110.2720.0690.0690.0000.0000.0000.000
210B213LYS10.8730.9302.712-2.732-1.4150.056-0.702-0.6720.006
211B214ASP-1-0.945-0.9798.4272.1902.1900.0000.0000.0000.000
212B215GLU-1-0.794-0.87110.8070.7150.7150.0000.0000.0000.000
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