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: 6G63Z

Calculation Name: 2NN6-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2NN6

Chain ID: B

ChEMBL ID:

UniProt ID: Q9Y3B2

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 235
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2716158.946176
FMO2-HF: Nuclear repulsion 2626393.604395
FMO2-HF: Total energy -89765.341781
FMO2-MP2: Total energy -90024.999013


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:6:LEU)


Summations of interaction energy for fragment #1(B:6:LEU)
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.
-8.163-2.340.578-2.649-3.751-0.011
Interaction energy analysis for fragmet #1(B:6:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.001 / 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].
3B8ASP-1-0.822-0.9063.846-2.711-0.727-0.014-0.957-1.0120.003
4B9GLN0-0.035-0.0236.3780.5030.5030.0000.0000.0000.000
5B10GLY0-0.021-0.0039.6760.2480.2480.0000.0000.0000.000
6B11TYR0-0.121-0.0548.7650.3790.3790.0000.0000.0000.000
7B12ARG10.8200.8986.3290.2870.2870.0000.0000.0000.000
8B13VAL00.0330.0102.813-0.5380.2540.350-0.210-0.932-0.001
9B14ASP-1-0.823-0.9034.899-0.720-0.612-0.001-0.008-0.0990.000
10B15GLY0-0.020-0.0048.3040.2670.2670.0000.0000.0000.000
11B16ARG10.7120.85210.0650.8970.8970.0000.0000.0000.000
12B17ARG10.8840.91710.5950.6130.6130.0000.0000.0000.000
13B18ALA00.0530.0269.5700.0370.0370.0000.0000.0000.000
14B19GLY00.0360.01611.1050.0980.0980.0000.0000.0000.000
15B20GLU-1-0.862-0.90214.369-0.560-0.5600.0000.0000.0000.000
16B21LEU00.0380.02514.955-0.057-0.0570.0000.0000.0000.000
17B22ARG10.7470.84913.9260.2640.2640.0000.0000.0000.000
18B23LYS10.8590.90916.3530.5080.5080.0000.0000.0000.000
19B24ILE00.0300.02919.9480.0120.0120.0000.0000.0000.000
20B25GLN0-0.060-0.01922.3020.0090.0090.0000.0000.0000.000
21B26ALA00.028-0.00325.6270.0050.0050.0000.0000.0000.000
22B27ARG10.8550.93928.4840.0780.0780.0000.0000.0000.000
23B28MET00.0700.04232.0080.0010.0010.0000.0000.0000.000
24B29GLY00.0450.03134.325-0.001-0.0010.0000.0000.0000.000
25B30VAL0-0.123-0.04733.5220.0010.0010.0000.0000.0000.000
26B31PHE0-0.019-0.03034.9420.0040.0040.0000.0000.0000.000
27B32ALA00.0670.03039.5000.0010.0010.0000.0000.0000.000
28B33GLN0-0.066-0.02542.6360.0000.0000.0000.0000.0000.000
29B34ALA0-0.018-0.03540.7600.0030.0030.0000.0000.0000.000
30B35ASP-1-0.908-0.95241.535-0.038-0.0380.0000.0000.0000.000
31B36GLY00.0490.04338.967-0.003-0.0030.0000.0000.0000.000
32B37SER0-0.079-0.05936.0620.0040.0040.0000.0000.0000.000
33B38ALA00.004-0.00731.461-0.006-0.0060.0000.0000.0000.000
34B39TYR0-0.037-0.02626.0090.0110.0110.0000.0000.0000.000
35B40ILE0-0.014-0.01524.479-0.009-0.0090.0000.0000.0000.000
36B41GLU-1-0.777-0.86622.116-0.111-0.1110.0000.0000.0000.000
37B42GLN00.0480.02218.1520.0050.0050.0000.0000.0000.000
38B43GLY00.0240.01417.616-0.025-0.0250.0000.0000.0000.000
39B44ASN0-0.046-0.04916.7750.0180.0180.0000.0000.0000.000
40B45THR00.0040.01617.8280.0340.0340.0000.0000.0000.000
41B46LYS10.8020.92019.7950.0980.0980.0000.0000.0000.000
42B47ALA00.0270.01423.4810.0160.0160.0000.0000.0000.000
43B48LEU0-0.046-0.02726.195-0.009-0.0090.0000.0000.0000.000
44B49ALA00.0150.01329.9990.0050.0050.0000.0000.0000.000
45B50VAL0-0.042-0.02632.074-0.004-0.0040.0000.0000.0000.000
46B51VAL0-0.0130.00335.8990.0030.0030.0000.0000.0000.000
47B52TYR0-0.0440.00038.2760.0000.0000.0000.0000.0000.000
48B53GLY00.1020.04441.9820.0000.0000.0000.0000.0000.000
49B54PRO0-0.049-0.04543.5810.0030.0030.0000.0000.0000.000
50B55HIS0-0.0300.00143.8120.0030.0030.0000.0000.0000.000
51B56GLU-1-0.796-0.88047.959-0.013-0.0130.0000.0000.0000.000
52B57ILE00.0140.00347.7450.0010.0010.0000.0000.0000.000
53B58ARG10.9050.94047.4000.0140.0140.0000.0000.0000.000
54B59GLY00.0050.00847.6360.0010.0010.0000.0000.0000.000
55B60SER0-0.045-0.04447.3460.0000.0000.0000.0000.0000.000
56B61ARG10.8600.91349.3810.0110.0110.0000.0000.0000.000
57B62ALA00.0020.02451.223-0.001-0.0010.0000.0000.0000.000
58B63ARG10.9460.98143.2780.0030.0030.0000.0000.0000.000
59B64ALA00.0500.00948.416-0.001-0.0010.0000.0000.0000.000
60B65LEU00.0280.01443.8850.0000.0000.0000.0000.0000.000
61B66PRO0-0.008-0.00648.407-0.001-0.0010.0000.0000.0000.000
62B67ASP-1-0.807-0.89847.310-0.026-0.0260.0000.0000.0000.000
63B68ARG10.8400.91041.5860.0300.0300.0000.0000.0000.000
64B69ALA00.0180.01743.5230.0020.0020.0000.0000.0000.000
65B70LEU0-0.062-0.04442.8510.0000.0000.0000.0000.0000.000
66B71VAL00.0100.00836.779-0.002-0.0020.0000.0000.0000.000
67B72ASN0-0.045-0.01537.7110.0050.0050.0000.0000.0000.000
68B73CYS00.0080.01732.662-0.005-0.0050.0000.0000.0000.000
69B74GLN0-0.054-0.02932.9350.0050.0050.0000.0000.0000.000
70B75TYR-1-0.852-0.93923.072-0.021-0.0210.0000.0000.0000.000
71B76SER-1-0.784-0.87828.6430.0120.0120.0000.0000.0000.000
72B77SER-1-0.755-0.87123.8860.0200.0200.0000.0000.0000.000
73B78ALA00.0170.01326.1690.0080.0080.0000.0000.0000.000
74B79THR0-0.073-0.04225.4060.0090.0090.0000.0000.0000.000
75B80PHE0-0.030-0.03824.0730.0130.0130.0000.0000.0000.000
76B81SER0-0.067-0.01422.610-0.005-0.0050.0000.0000.0000.000
77B82THR00.0420.01819.261-0.007-0.0070.0000.0000.0000.000
78B83GLY00.0300.01517.298-0.003-0.0030.0000.0000.0000.000
79B84GLU-1-0.875-0.93418.2930.2400.2400.0000.0000.0000.000
80B85ARG10.9260.96821.310-0.094-0.0940.0000.0000.0000.000
81B86LYS10.7830.88221.185-0.180-0.1800.0000.0000.0000.000
82B87ARG10.8830.92926.191-0.088-0.0880.0000.0000.0000.000
83B88ARG00.1460.06923.3840.0160.0160.0000.0000.0000.000
84B89PRO0-0.0050.01829.334-0.001-0.0010.0000.0000.0000.000
85B90HIS0-0.016-0.02331.2730.0040.0040.0000.0000.0000.000
86B91GLY0-0.028-0.00927.7230.0040.0040.0000.0000.0000.000
87B92ASP-1-0.835-0.92627.7940.0410.0410.0000.0000.0000.000
88B93ARG10.9130.96427.789-0.072-0.0720.0000.0000.0000.000
89B94LYS11.0601.03219.969-0.111-0.1110.0000.0000.0000.000
90B95SER00.0790.05125.925-0.006-0.0060.0000.0000.0000.000
91B96CYS0-0.107-0.05427.852-0.008-0.0080.0000.0000.0000.000
92B97GLU-1-0.920-0.96125.2870.0270.0270.0000.0000.0000.000
93B98MET00.0560.03622.159-0.014-0.0140.0000.0000.0000.000
94B99GLY00.0210.00526.704-0.010-0.0100.0000.0000.0000.000
95B100LEU0-0.066-0.03930.211-0.006-0.0060.0000.0000.0000.000
96B101GLN00.013-0.01024.004-0.003-0.0030.0000.0000.0000.000
97B102LEU0-0.019-0.00126.585-0.011-0.0110.0000.0000.0000.000
98B103ARG10.8200.87329.5200.0140.0140.0000.0000.0000.000
99B104GLN00.0000.01130.409-0.008-0.0080.0000.0000.0000.000
100B105THR0-0.031-0.02228.075-0.004-0.0040.0000.0000.0000.000
101B106PHE00.0220.01230.143-0.003-0.0030.0000.0000.0000.000
102B107GLU-1-0.816-0.88534.497-0.026-0.0260.0000.0000.0000.000
103B108ALA0-0.0260.01033.9290.0010.0010.0000.0000.0000.000
104B109ALA0-0.018-0.01834.594-0.002-0.0020.0000.0000.0000.000
105B110ILE00.0180.00636.564-0.002-0.0020.0000.0000.0000.000
106B111LEU0-0.004-0.00638.7120.0030.0030.0000.0000.0000.000
107B112THR00.0310.02640.6830.0020.0020.0000.0000.0000.000
108B113GLN0-0.075-0.04643.3980.0010.0010.0000.0000.0000.000
109B114LEU0-0.0050.00545.9730.0010.0010.0000.0000.0000.000
110B115HIS00.0220.00943.7900.0000.0000.0000.0000.0000.000
111B116PRO00.0440.03247.7160.0010.0010.0000.0000.0000.000
112B117ARG10.8830.93849.2800.0160.0160.0000.0000.0000.000
113B118SER0-0.0340.00546.8040.0010.0010.0000.0000.0000.000
114B119GLN0-0.096-0.08042.2190.0020.0020.0000.0000.0000.000
115B120ILE00.0070.02739.3960.0000.0000.0000.0000.0000.000
116B121ASP-1-0.803-0.86638.882-0.021-0.0210.0000.0000.0000.000
117B122ILE00.033-0.00433.534-0.002-0.0020.0000.0000.0000.000
118B123TYR0-0.106-0.06334.0080.0030.0030.0000.0000.0000.000
119B124VAL00.004-0.01528.046-0.007-0.0070.0000.0000.0000.000
120B125GLN0-0.067-0.04028.7570.0070.0070.0000.0000.0000.000
121B126VAL00.018-0.00222.218-0.012-0.0120.0000.0000.0000.000
122B127LEU0-0.022-0.01825.5320.0120.0120.0000.0000.0000.000
123B128GLN0-0.058-0.04419.972-0.006-0.0060.0000.0000.0000.000
124B129ALA00.0150.01318.836-0.021-0.0210.0000.0000.0000.000
125B130ASP-1-0.846-0.95813.742-0.150-0.1500.0000.0000.0000.000
126B131GLY00.0690.05314.055-0.049-0.0490.0000.0000.0000.000
127B132GLY00.0250.01715.121-0.034-0.0340.0000.0000.0000.000
128B133THR0-0.007-0.01117.022-0.007-0.0070.0000.0000.0000.000
129B134TYR00.0840.03620.005-0.005-0.0050.0000.0000.0000.000
130B135ALA00.0200.01119.8960.0000.0000.0000.0000.0000.000
131B136ALA0-0.023-0.00821.221-0.003-0.0030.0000.0000.0000.000
132B137CYS0-0.018-0.00822.9040.0020.0020.0000.0000.0000.000
133B138VAL00.0370.02725.1300.0040.0040.0000.0000.0000.000
134B139ASN00.0220.02523.3160.0070.0070.0000.0000.0000.000
135B140ALA0-0.001-0.00226.8790.0030.0030.0000.0000.0000.000
136B141ALA00.0400.00928.7310.0040.0040.0000.0000.0000.000
137B142THR0-0.027-0.01929.8250.0040.0040.0000.0000.0000.000
138B143LEU0-0.043-0.03228.9970.0010.0010.0000.0000.0000.000
139B144ALA00.0000.00832.6460.0030.0030.0000.0000.0000.000
140B145VAL00.009-0.00934.7150.0050.0050.0000.0000.0000.000
141B146LEU0-0.045-0.03333.7410.0010.0010.0000.0000.0000.000
142B147ASP-1-0.873-0.92236.725-0.059-0.0590.0000.0000.0000.000
143B148ALA00.0390.02738.5430.0020.0020.0000.0000.0000.000
144B149GLY0-0.059-0.01640.3730.0020.0020.0000.0000.0000.000
145B150ILE0-0.034-0.01039.7850.0010.0010.0000.0000.0000.000
146B151PRO0-0.031-0.00340.297-0.004-0.0040.0000.0000.0000.000
147B152MET0-0.003-0.01834.1130.0020.0020.0000.0000.0000.000
148B153ARG10.8500.90636.9510.0550.0550.0000.0000.0000.000
149B154ASP-1-0.786-0.89333.392-0.110-0.1100.0000.0000.0000.000
150B155PHE0-0.025-0.01130.5450.0020.0020.0000.0000.0000.000
151B156VAL0-0.017-0.01028.896-0.010-0.0100.0000.0000.0000.000
152B157CYS0-0.040-0.00625.687-0.003-0.0030.0000.0000.0000.000
153B158ALA00.0230.02223.0310.0020.0020.0000.0000.0000.000
154B159CYS0-0.058-0.03118.979-0.026-0.0260.0000.0000.0000.000
155B160SER00.0510.02615.1530.0280.0280.0000.0000.0000.000
156B161ALA0-0.043-0.01614.026-0.048-0.0480.0000.0000.0000.000
157B162GLY00.0580.02410.9230.0840.0840.0000.0000.0000.000
158B163PHE0-0.055-0.02010.390-0.118-0.1180.0000.0000.0000.000
159B164VAL00.0340.0063.849-0.0510.1990.002-0.033-0.2190.000
160B165ASP-1-0.832-0.9003.059-6.700-4.0110.241-1.441-1.489-0.013
161B166GLY0-0.039-0.0105.7770.1460.1460.0000.0000.0000.000
162B167THR0-0.087-0.0448.2140.0730.0730.0000.0000.0000.000
163B168ALA00.0260.00510.2070.0050.0050.0000.0000.0000.000
164B169LEU0-0.036-0.0156.341-0.047-0.0470.0000.0000.0000.000
165B170ALA00.0330.01311.0830.1220.1220.0000.0000.0000.000
166B171ASP-1-0.840-0.91913.480-0.426-0.4260.0000.0000.0000.000
167B172LEU00.0010.0069.258-0.079-0.0790.0000.0000.0000.000
168B173SER0-0.015-0.0179.5390.1150.1150.0000.0000.0000.000
169B174HIS0-0.039-0.02610.7670.0310.0310.0000.0000.0000.000
170B175VAL0-0.017-0.0095.4620.1520.1520.0000.0000.0000.000
171B176GLU-1-0.776-0.8605.734-0.429-0.4290.0000.0000.0000.000
172B177GLU-1-0.831-0.9046.7010.0110.0110.0000.0000.0000.000
173B178ALA0-0.090-0.0317.9850.0430.0430.0000.0000.0000.000
174B179ALA00.0180.0224.8490.2980.2980.0000.0000.0000.000
175B180GLY0-0.051-0.0336.295-0.042-0.0420.0000.0000.0000.000
176B181GLY00.0270.0188.874-0.079-0.0790.0000.0000.0000.000
177B182PRO0-0.046-0.0107.677-0.026-0.0260.0000.0000.0000.000
178B183GLN0-0.014-0.03710.891-0.101-0.1010.0000.0000.0000.000
179B184LEU00.0070.00913.2260.0440.0440.0000.0000.0000.000
180B185ALA00.004-0.00716.492-0.037-0.0370.0000.0000.0000.000
181B186LEU0-0.0060.00419.1950.0190.0190.0000.0000.0000.000
182B187ALA00.0060.00322.743-0.010-0.0100.0000.0000.0000.000
183B188LEU0-0.034-0.01725.6580.0070.0070.0000.0000.0000.000
184B189LEU00.0350.02227.7310.0000.0000.0000.0000.0000.000
185B190PRO00.020-0.00529.1440.0000.0000.0000.0000.0000.000
186B191ALA0-0.029-0.01730.897-0.002-0.0020.0000.0000.0000.000
187B192SER0-0.053-0.03233.7070.0040.0040.0000.0000.0000.000
188B193GLY0-0.030-0.01630.035-0.005-0.0050.0000.0000.0000.000
189B194GLN0-0.019-0.00429.7850.0000.0000.0000.0000.0000.000
190B195ILE00.0240.00825.769-0.004-0.0040.0000.0000.0000.000
191B196ALA0-0.046-0.01828.7250.0080.0080.0000.0000.0000.000
192B197LEU0-0.0060.01024.6590.0080.0080.0000.0000.0000.000
193B198LEU0-0.032-0.02422.002-0.016-0.0160.0000.0000.0000.000
194B199GLU-1-0.810-0.88421.902-0.020-0.0200.0000.0000.0000.000
195B200MET0-0.049-0.01717.373-0.023-0.0230.0000.0000.0000.000
196B201ASP-1-0.895-0.93016.7460.0090.0090.0000.0000.0000.000
197B202ALA00.0040.00713.7220.0280.0280.0000.0000.0000.000
198B203ARG10.9030.94113.105-0.133-0.1330.0000.0000.0000.000
199B204LEU0-0.042-0.02413.5730.0120.0120.0000.0000.0000.000
200B205HIS0-0.048-0.04215.2010.0320.0320.0000.0000.0000.000
201B206GLU-1-0.884-0.95417.283-0.083-0.0830.0000.0000.0000.000
202B207ASP-1-0.777-0.86718.326-0.169-0.1690.0000.0000.0000.000
203B208HIS0-0.047-0.03414.823-0.055-0.0550.0000.0000.0000.000
204B209LEU00.0340.02916.909-0.033-0.0330.0000.0000.0000.000
205B210GLU-1-0.889-0.94219.353-0.179-0.1790.0000.0000.0000.000
206B211ARG10.7960.89015.4630.2370.2370.0000.0000.0000.000
207B212VAL0-0.001-0.01413.897-0.037-0.0370.0000.0000.0000.000
208B213LEU00.0140.01316.654-0.002-0.0020.0000.0000.0000.000
209B214GLU-1-0.877-0.94320.247-0.204-0.2040.0000.0000.0000.000
210B215ALA0-0.059-0.01315.836-0.011-0.0110.0000.0000.0000.000
211B216ALA00.008-0.00317.927-0.009-0.0090.0000.0000.0000.000
212B217ALA00.0270.01219.0870.0140.0140.0000.0000.0000.000
213B218GLN0-0.052-0.04620.8380.0300.0300.0000.0000.0000.000
214B219ALA00.0380.02218.3520.0080.0080.0000.0000.0000.000
215B220ALA00.0340.01220.4640.0120.0120.0000.0000.0000.000
216B221ARG10.8930.95223.4450.1870.1870.0000.0000.0000.000
217B222ASP-1-0.838-0.90021.321-0.288-0.2880.0000.0000.0000.000
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