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

tag_button

FMODB ID: 1N84Z

Calculation Name: 3A1Y-G-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3A1Y

Chain ID: G

ChEMBL ID:

UniProt ID: O74109

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 211
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1979436.710832
FMO2-HF: Nuclear repulsion 1896385.228828
FMO2-HF: Total energy -83051.482004
FMO2-MP2: Total energy -83294.582234


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(G:1:MET)


Summations of interaction energy for fragment #1(G:1:MET)
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.
-3.020.245-0.021-1.568-1.676-0.002
Interaction energy analysis for fragmet #1(G:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.040 / q_NPA : -0.039
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].
3G3HIS0-0.0170.0053.422-2.0750.925-0.019-1.538-1.443-0.002
4G4VAL0-0.010-0.0134.9360.2210.2210.0000.0000.0000.000
5G5ALA0-0.0170.0036.097-0.340-0.3400.0000.0000.0000.000
6G6GLU-1-0.914-0.9445.100-1.562-1.553-0.001-0.005-0.0030.000
7G7TRP0-0.017-0.0177.5900.1230.1230.0000.0000.0000.000
8G8LYS10.9460.9529.2950.4700.4700.0000.0000.0000.000
9G9LYS10.9300.96012.3430.1860.1860.0000.0000.0000.000
10G10LYS10.8820.9454.2190.4380.694-0.001-0.025-0.2300.000
11G11GLU-1-0.728-0.8506.697-0.592-0.5920.0000.0000.0000.000
12G12VAL0-0.037-0.0159.9820.0680.0680.0000.0000.0000.000
13G13GLU-1-0.898-0.95010.5360.0790.0790.0000.0000.0000.000
14G14GLU-1-0.807-0.8919.2510.2990.2990.0000.0000.0000.000
15G15LEU0-0.011-0.01311.8430.0140.0140.0000.0000.0000.000
16G16ALA00.0260.01014.3210.0130.0130.0000.0000.0000.000
17G17LYS10.8330.90911.119-0.169-0.1690.0000.0000.0000.000
18G18LEU0-0.0130.01313.9510.0020.0020.0000.0000.0000.000
19G19ILE00.0380.00316.7920.0010.0010.0000.0000.0000.000
20G20LYS10.8130.90619.6520.0080.0080.0000.0000.0000.000
21G21SER0-0.061-0.03419.1070.0100.0100.0000.0000.0000.000
22G22TYR0-0.046-0.02318.2880.0080.0080.0000.0000.0000.000
23G23PRO0-0.0060.01523.185-0.007-0.0070.0000.0000.0000.000
24G24VAL00.0060.01125.427-0.005-0.0050.0000.0000.0000.000
25G25ILE0-0.039-0.02721.4080.0010.0010.0000.0000.0000.000
26G26ALA00.0150.01122.803-0.001-0.0010.0000.0000.0000.000
27G27LEU00.0100.01222.115-0.008-0.0080.0000.0000.0000.000
28G28VAL00.0360.00221.4260.0080.0080.0000.0000.0000.000
29G29ASP-1-0.735-0.83421.934-0.066-0.0660.0000.0000.0000.000
30G30VAL0-0.057-0.04717.4270.0080.0080.0000.0000.0000.000
31G31SER0-0.128-0.08520.7600.0080.0080.0000.0000.0000.000
32G32SER00.0220.02222.2790.0060.0060.0000.0000.0000.000
33G33MET0-0.0340.00420.5550.0080.0080.0000.0000.0000.000
34G34PRO00.0110.00219.823-0.002-0.0020.0000.0000.0000.000
35G35ALA00.0250.00614.9810.0030.0030.0000.0000.0000.000
36G36TYR00.0060.00416.4480.0000.0000.0000.0000.0000.000
37G37PRO00.0500.01018.2130.0010.0010.0000.0000.0000.000
38G38LEU00.0660.04415.873-0.003-0.0030.0000.0000.0000.000
39G39SER0-0.064-0.03714.291-0.012-0.0120.0000.0000.0000.000
40G40GLN00.009-0.00116.2440.0130.0130.0000.0000.0000.000
41G41MET00.0920.05119.6290.0020.0020.0000.0000.0000.000
42G42ARG10.8670.94413.1730.0650.0650.0000.0000.0000.000
43G43ARG10.7670.86617.045-0.096-0.0960.0000.0000.0000.000
44G44LEU00.0730.04418.4560.0020.0020.0000.0000.0000.000
45G45ILE00.0250.01119.563-0.001-0.0010.0000.0000.0000.000
46G46ARG10.8900.95412.431-0.086-0.0860.0000.0000.0000.000
47G47GLU-1-0.880-0.91919.8220.0860.0860.0000.0000.0000.000
48G48ASN0-0.038-0.02122.893-0.004-0.0040.0000.0000.0000.000
49G49GLY00.0220.02423.182-0.005-0.0050.0000.0000.0000.000
50G50GLY00.0510.01720.877-0.003-0.0030.0000.0000.0000.000
51G51LEU0-0.091-0.05014.7340.0110.0110.0000.0000.0000.000
52G52LEU00.0420.03616.290-0.009-0.0090.0000.0000.0000.000
53G53ARG10.7530.8529.962-0.047-0.0470.0000.0000.0000.000
54G54VAL00.0410.01412.0380.0250.0250.0000.0000.0000.000
55G55SER00.0270.01312.036-0.076-0.0760.0000.0000.0000.000
56G56ARG10.8380.90014.0380.1880.1880.0000.0000.0000.000
57G57ASN00.0600.03317.235-0.009-0.0090.0000.0000.0000.000
58G58THR0-0.020-0.03112.7330.0250.0250.0000.0000.0000.000
59G59LEU00.0330.02515.7190.0040.0040.0000.0000.0000.000
60G60ILE00.0140.03417.5350.0160.0160.0000.0000.0000.000
61G61GLU-1-0.847-0.94316.155-0.147-0.1470.0000.0000.0000.000
62G62LEU00.0560.02320.2560.0130.0130.0000.0000.0000.000
63G63ALA00.0660.02822.3550.0100.0100.0000.0000.0000.000
64G64ILE0-0.046-0.03418.5480.0040.0040.0000.0000.0000.000
65G65LYN0-0.048-0.01316.7180.0180.0180.0000.0000.0000.000
66G66LYS10.8200.92822.5340.0510.0510.0000.0000.0000.000
67G67ALA0-0.0010.00124.7550.0050.0050.0000.0000.0000.000
68G68ALA0-0.060-0.02422.7270.0050.0050.0000.0000.0000.000
69G69LYN00.0390.02424.1810.0070.0070.0000.0000.0000.000
70G70GLU-1-0.912-0.94627.908-0.020-0.0200.0000.0000.0000.000
71G71LEU00.0270.02327.460-0.004-0.0040.0000.0000.0000.000
72G72GLY00.0620.02730.868-0.004-0.0040.0000.0000.0000.000
73G73LYS10.8600.92123.7740.0380.0380.0000.0000.0000.000
74G74PRO0-0.090-0.02526.016-0.003-0.0030.0000.0000.0000.000
75G75GLU-1-0.909-0.97426.383-0.095-0.0950.0000.0000.0000.000
76G76LEU0-0.092-0.04127.8760.0040.0040.0000.0000.0000.000
77G77GLU-1-0.916-0.95330.839-0.039-0.0390.0000.0000.0000.000
78G78LYN0-0.047-0.01128.7330.0050.0050.0000.0000.0000.000
79G79LEU0-0.0120.00332.4280.0010.0010.0000.0000.0000.000
80G80VAL00.030-0.00532.156-0.001-0.0010.0000.0000.0000.000
81G81GLU-1-0.867-0.93723.927-0.091-0.0910.0000.0000.0000.000
82G82TYR00.0430.02727.855-0.005-0.0050.0000.0000.0000.000
83G83ILE0-0.040-0.02220.6070.0000.0000.0000.0000.0000.000
84G84ASP-1-0.735-0.87624.272-0.070-0.0700.0000.0000.0000.000
85G85ARG10.8930.93823.1930.0730.0730.0000.0000.0000.000
86G86GLY0-0.006-0.00820.907-0.014-0.0140.0000.0000.0000.000
87G87ALA0-0.0150.00920.506-0.002-0.0020.0000.0000.0000.000
88G88GLY0-0.0020.00717.823-0.027-0.0270.0000.0000.0000.000
89G89ILE0-0.020-0.01316.4330.0090.0090.0000.0000.0000.000
90G90LEU0-0.020-0.00517.543-0.001-0.0010.0000.0000.0000.000
91G91VAL00.0090.01617.9150.0000.0000.0000.0000.0000.000
92G92THR00.046-0.00420.6960.0110.0110.0000.0000.0000.000
93G93ASN00.008-0.00823.232-0.004-0.0040.0000.0000.0000.000
94G94MET0-0.073-0.01426.276-0.002-0.0020.0000.0000.0000.000
95G95ASN00.0490.01128.198-0.004-0.0040.0000.0000.0000.000
96G96PRO00.0430.02229.8150.0010.0010.0000.0000.0000.000
97G97PHE00.0470.04030.857-0.001-0.0010.0000.0000.0000.000
98G98LYS10.8200.90630.725-0.016-0.0160.0000.0000.0000.000
99G99LEU00.0270.00924.7820.0020.0020.0000.0000.0000.000
100G100TYR00.0490.02328.5330.0010.0010.0000.0000.0000.000
101G101LYN00.0940.06030.5690.0010.0010.0000.0000.0000.000
102G102PHE0-0.047-0.02324.3030.0020.0020.0000.0000.0000.000
103G103LEU00.011-0.00624.1930.0020.0020.0000.0000.0000.000
104G104GLN0-0.058-0.02327.773-0.002-0.0020.0000.0000.0000.000
105G105GLN0-0.011-0.01231.1430.0020.0020.0000.0000.0000.000
106G106ASN0-0.067-0.03126.9790.0070.0070.0000.0000.0000.000
107G107ARG10.8190.90726.6430.0000.0000.0000.0000.0000.000
108G108GLN00.0520.01726.6630.0020.0020.0000.0000.0000.000
109G109PRO0-0.088-0.05322.9750.0020.0020.0000.0000.0000.000
110G183GLN0-0.008-0.02732.0450.0020.0020.0000.0000.0000.000
111G184PRO0-0.011-0.00532.5620.0010.0010.0000.0000.0000.000
112G185LEU0-0.034-0.00529.272-0.003-0.0030.0000.0000.0000.000
113G186GLU-1-0.889-0.94329.4780.0250.0250.0000.0000.0000.000
114G187VAL0-0.053-0.02624.690-0.004-0.0040.0000.0000.0000.000
115G188GLY00.0440.00924.8290.0060.0060.0000.0000.0000.000
116G189LEU0-0.018-0.00320.440-0.005-0.0050.0000.0000.0000.000
117G190ASP-1-0.781-0.85224.520-0.008-0.0080.0000.0000.0000.000
118G191VAL0-0.032-0.03326.183-0.006-0.0060.0000.0000.0000.000
119G192LEU0-0.047-0.01424.8710.0010.0010.0000.0000.0000.000
120G193ALA00.019-0.00227.3090.0010.0010.0000.0000.0000.000
121G194VAL0-0.042-0.01926.857-0.002-0.0020.0000.0000.0000.000
122G195TYR00.0300.02726.526-0.002-0.0020.0000.0000.0000.000
123G196GLU-1-0.793-0.91427.7580.0060.0060.0000.0000.0000.000
124G197ASP-1-0.953-0.97530.119-0.007-0.0070.0000.0000.0000.000
125G198GLY00.0190.01131.6570.0000.0000.0000.0000.0000.000
126G199ILE0-0.019-0.00432.827-0.003-0.0030.0000.0000.0000.000
127G200VAL0-0.024-0.02630.133-0.001-0.0010.0000.0000.0000.000
128G201TYR0-0.046-0.02631.6060.0010.0010.0000.0000.0000.000
129G202THR0-0.001-0.03331.642-0.002-0.0020.0000.0000.0000.000
130G203PRO0-0.006-0.02731.3410.0030.0030.0000.0000.0000.000
131G204ASP-1-0.852-0.90133.732-0.016-0.0160.0000.0000.0000.000
132G205VAL0-0.0050.00436.2540.0020.0020.0000.0000.0000.000
133G206LEU0-0.036-0.02531.3660.0020.0020.0000.0000.0000.000
134G207ALA0-0.054-0.01135.6350.0030.0030.0000.0000.0000.000
135G208ILE0-0.019-0.00837.7070.0000.0000.0000.0000.0000.000
136G209ASP-1-0.836-0.90440.3170.0030.0030.0000.0000.0000.000
137G210GLU-1-0.921-0.98241.6010.0090.0090.0000.0000.0000.000
138G211GLN0-0.066-0.02743.7230.0010.0010.0000.0000.0000.000
139G212GLU-1-0.931-0.97146.590-0.002-0.0020.0000.0000.0000.000
140G213TYR00.0240.00643.6710.0000.0000.0000.0000.0000.000
141G214ILE0-0.0090.00147.1170.0000.0000.0000.0000.0000.000
142G215ASP-1-0.814-0.90449.5410.0040.0040.0000.0000.0000.000
143G216MET0-0.041-0.02450.0280.0000.0000.0000.0000.0000.000
144G217LEU0-0.0050.01249.9730.0000.0000.0000.0000.0000.000
145G218GLN0-0.007-0.01352.6730.0000.0000.0000.0000.0000.000
146G219LYS10.8150.89755.195-0.003-0.0030.0000.0000.0000.000
147G220ALA00.0140.01555.1350.0000.0000.0000.0000.0000.000
148G221TYR00.0080.00856.7600.0000.0000.0000.0000.0000.000
149G222MET00.0180.00258.5190.0000.0000.0000.0000.0000.000
150G223HIS00.0000.00359.3630.0000.0000.0000.0000.0000.000
151G224ALA00.0030.00860.4930.0000.0000.0000.0000.0000.000
152G225PHE00.0160.00862.4140.0000.0000.0000.0000.0000.000
153G226ASN0-0.018-0.02364.3840.0000.0000.0000.0000.0000.000
154G227LEU0-0.0080.01164.7820.0000.0000.0000.0000.0000.000
155G228ALA00.0240.00966.4710.0000.0000.0000.0000.0000.000
156G229VAL00.020-0.00168.2200.0000.0000.0000.0000.0000.000
157G230ASN0-0.091-0.06769.5930.0000.0000.0000.0000.0000.000
158G231ILE0-0.048-0.01469.2780.0000.0000.0000.0000.0000.000
159G232ALA0-0.033-0.01372.9290.0000.0000.0000.0000.0000.000
160G233TYR00.0140.01066.4890.0000.0000.0000.0000.0000.000
161G234PRO0-0.023-0.00370.2020.0000.0000.0000.0000.0000.000
162G235THR00.0280.02366.0080.0000.0000.0000.0000.0000.000
163G236PRO0-0.001-0.00666.3760.0000.0000.0000.0000.0000.000
164G237GLU-1-0.871-0.93762.8710.0070.0070.0000.0000.0000.000
165G238THR0-0.027-0.03466.2310.0000.0000.0000.0000.0000.000
166G239ILE00.0010.00169.1470.0000.0000.0000.0000.0000.000
167G240GLU-1-0.900-0.95171.9570.0070.0070.0000.0000.0000.000
168G241ALA00.0250.01370.5330.0000.0000.0000.0000.0000.000
169G242ILE0-0.0200.00471.4010.0000.0000.0000.0000.0000.000
170G243ILE0-0.013-0.00674.5730.0000.0000.0000.0000.0000.000
171G244GLN0-0.015-0.01273.2410.0000.0000.0000.0000.0000.000
172G245LYS10.9160.97074.039-0.003-0.0030.0000.0000.0000.000
173G246ALA0-0.0030.00276.9520.0000.0000.0000.0000.0000.000
174G247PHE0-0.001-0.00580.1180.0000.0000.0000.0000.0000.000
175G248LEU00.0040.00978.0110.0000.0000.0000.0000.0000.000
176G249ASN00.000-0.00178.7450.0000.0000.0000.0000.0000.000
177G250ALA00.0070.00881.8220.0000.0000.0000.0000.0000.000
178G251LYS10.8340.90983.956-0.004-0.0040.0000.0000.0000.000
179G252THR0-0.028-0.03082.2950.0000.0000.0000.0000.0000.000
180G253VAL00.006-0.00184.7940.0000.0000.0000.0000.0000.000
181G254ALA0-0.0060.00287.1260.0000.0000.0000.0000.0000.000
182G255ILE0-0.041-0.02986.3210.0000.0000.0000.0000.0000.000
183G256GLU-1-0.844-0.87786.8310.0020.0020.0000.0000.0000.000
184G257ALA0-0.029-0.00589.5700.0000.0000.0000.0000.0000.000
185G258GLY0-0.028-0.00892.4380.0000.0000.0000.0000.0000.000
186G259TYR0-0.045-0.02393.0530.0000.0000.0000.0000.0000.000
187G260ILE0-0.002-0.01093.5230.0000.0000.0000.0000.0000.000
188G261THR00.006-0.00491.2400.0000.0000.0000.0000.0000.000
189G262LYS10.9720.98490.786-0.004-0.0040.0000.0000.0000.000
190G263GLU-1-0.874-0.92787.6910.0040.0040.0000.0000.0000.000
191G264THR00.0230.00588.2070.0000.0000.0000.0000.0000.000
192G265ILE00.0210.01390.3390.0000.0000.0000.0000.0000.000
193G266GLN00.0090.00489.5180.0000.0000.0000.0000.0000.000
194G267ASP-1-0.777-0.88486.3840.0040.0040.0000.0000.0000.000
195G268ILE0-0.0110.00189.5220.0000.0000.0000.0000.0000.000
196G269ILE0-0.001-0.00792.6910.0000.0000.0000.0000.0000.000
197G270GLY00.0190.01590.8730.0000.0000.0000.0000.0000.000
198G271ARG10.7500.82786.913-0.002-0.0020.0000.0000.0000.000
199G272ALA00.0200.01492.2480.0000.0000.0000.0000.0000.000
200G273PHE00.0080.00593.3890.0000.0000.0000.0000.0000.000
201G274ARG10.9710.98088.575-0.003-0.0030.0000.0000.0000.000
202G275ALA00.0100.01493.4470.0000.0000.0000.0000.0000.000
203G276MET0-0.0230.00195.7380.0000.0000.0000.0000.0000.000
204G277LEU00.028-0.00393.9110.0000.0000.0000.0000.0000.000
205G278LEU0-0.016-0.00593.0260.0000.0000.0000.0000.0000.000
206G279LEU0-0.001-0.00396.1890.0000.0000.0000.0000.0000.000
207G280ALA00.009-0.00299.6120.0000.0000.0000.0000.0000.000
208G281GLN0-0.050-0.02994.9810.0000.0000.0000.0000.0000.000
209G282GLN0-0.068-0.02297.7550.0000.0000.0000.0000.0000.000
210G283LEU0-0.049-0.010101.5650.0000.0000.0000.0000.0000.000
211G284PRO0-0.025-0.006103.1930.0000.0000.0000.0000.0000.000