FMODB

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

Last updated: 2024-07-23

All entries: 37478

Number of unique PDB entries: 7783

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FMODB ID: 89RQY

Calculation Name: 5XI8-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5XI8

Chain ID: A

ChEMBL ID:

UniProt ID: P66948

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 175
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1669881.178506
FMO2-HF: Nuclear repulsion 1602531.083581
FMO2-HF: Total energy -67350.094925
FMO2-MP2: Total energy -67549.555493


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(A:308:GLY)


Summations of interaction energy for fragment #1(A:308:GLY)
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.
-0.8861.9190.771-1.35-2.2250.003
Interaction energy analysis for fragmet #1(A:308:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.038 / 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].
3A310ALA00.0610.0373.5320.3141.4670.009-0.495-0.6670.000
4A311ALA0-0.005-0.0032.476-1.124-0.2890.757-0.630-0.9620.003
5A312GLN0-0.006-0.0133.401-0.1380.6090.006-0.221-0.5320.000
6A313TYR00.0750.0295.5880.4270.4270.0000.0000.0000.000
7A314GLY00.0390.0237.7260.1240.1240.0000.0000.0000.000
8A315ARG10.9130.9534.3600.0260.096-0.001-0.004-0.0640.000
9A316ALA00.0130.0089.6040.0270.0270.0000.0000.0000.000
10A317LEU00.0140.00111.6450.0440.0440.0000.0000.0000.000
11A318GLN00.0070.01212.8000.0040.0040.0000.0000.0000.000
12A319ALA0-0.039-0.01613.8360.0070.0070.0000.0000.0000.000
13A320MET0-0.005-0.00115.6410.0010.0010.0000.0000.0000.000
14A321GLU-1-0.945-0.96117.4780.0390.0390.0000.0000.0000.000
15A322ALA0-0.061-0.01918.6860.0100.0100.0000.0000.0000.000
16A323ASN0-0.025-0.02220.4760.0060.0060.0000.0000.0000.000
17A324LYS10.9300.97618.0390.0470.0470.0000.0000.0000.000
18A325TYR00.0780.02517.908-0.025-0.0250.0000.0000.0000.000
19A326ASP-1-0.947-0.97118.169-0.230-0.2300.0000.0000.0000.000
20A327GLU-1-0.929-0.96813.447-0.311-0.3110.0000.0000.0000.000
21A328ALA00.0400.01613.791-0.064-0.0640.0000.0000.0000.000
22A329ARG10.8010.87413.5790.1410.1410.0000.0000.0000.000
23A330LYS10.9090.94713.9730.2090.2090.0000.0000.0000.000
24A331THR0-0.025-0.0028.376-0.088-0.0880.0000.0000.0000.000
25A332LEU0-0.0010.0049.542-0.232-0.2320.0000.0000.0000.000
26A333GLN0-0.024-0.01811.6970.0010.0010.0000.0000.0000.000
27A334PRO0-0.008-0.0109.1130.0490.0490.0000.0000.0000.000
28A335LEU0-0.029-0.0016.061-0.120-0.1200.0000.0000.0000.000
29A336LEU00.0000.0049.8460.1130.1130.0000.0000.0000.000
30A337ALA0-0.023-0.01513.4470.0620.0620.0000.0000.0000.000
31A338ALA0-0.0110.00410.6810.0620.0620.0000.0000.0000.000
32A339GLU-1-0.918-0.95910.242-0.460-0.4600.0000.0000.0000.000
33A340PRO0-0.012-0.01413.9560.0150.0150.0000.0000.0000.000
34A341GLY0-0.036-0.03216.8770.0300.0300.0000.0000.0000.000
35A342ASN00.0090.01512.2330.0670.0670.0000.0000.0000.000
36A343ALA00.0260.00315.765-0.010-0.0100.0000.0000.0000.000
37A344TRP00.0740.03914.2320.0100.0100.0000.0000.0000.000
38A345TYR0-0.021-0.0148.538-0.085-0.0850.0000.0000.0000.000
39A346LEU0-0.030-0.01914.2640.0070.0070.0000.0000.0000.000
40A347ASP-1-0.859-0.89717.690-0.097-0.0970.0000.0000.0000.000
41A348LEU00.0560.03113.221-0.002-0.0020.0000.0000.0000.000
42A349ALA0-0.036-0.03617.0150.0070.0070.0000.0000.0000.000
43A350THR0-0.050-0.03818.1880.0170.0170.0000.0000.0000.000
44A351ASP-1-0.842-0.91019.832-0.093-0.0930.0000.0000.0000.000
45A352ILE0-0.049-0.03515.6360.0070.0070.0000.0000.0000.000
46A353ASP-1-0.789-0.87020.293-0.180-0.1800.0000.0000.0000.000
47A354LEU0-0.036-0.00723.0790.0120.0120.0000.0000.0000.000
48A355GLY00.0260.03323.8140.0110.0110.0000.0000.0000.000
49A356GLN0-0.027-0.01521.940-0.009-0.0090.0000.0000.0000.000
50A357ASN00.0000.01025.6400.0010.0010.0000.0000.0000.000
51A358LYS10.8430.93223.5870.1510.1510.0000.0000.0000.000
52A359ALA00.1000.04326.637-0.009-0.0090.0000.0000.0000.000
53A360ASN00.0130.00128.449-0.001-0.0010.0000.0000.0000.000
54A361GLU-1-0.897-0.95324.688-0.128-0.1280.0000.0000.0000.000
55A362ALA00.0100.00623.992-0.011-0.0110.0000.0000.0000.000
56A363ILE0-0.0050.00125.021-0.003-0.0030.0000.0000.0000.000
57A364ASN0-0.034-0.02427.1140.0060.0060.0000.0000.0000.000
58A365ARG10.8260.90519.4070.2070.2070.0000.0000.0000.000
59A366LEU00.0200.01822.497-0.003-0.0030.0000.0000.0000.000
60A367LYS10.9090.95224.6730.0900.0900.0000.0000.0000.000
61A368ASN0-0.050-0.00923.5030.0180.0180.0000.0000.0000.000
62A369ALA00.0180.02522.409-0.008-0.0080.0000.0000.0000.000
63A370ARG10.9410.94821.6250.1590.1590.0000.0000.0000.000
64A371ASP-1-0.886-0.94521.647-0.094-0.0940.0000.0000.0000.000
65A372LEU0-0.010-0.00124.5310.0090.0090.0000.0000.0000.000
66A373ARG10.8990.93726.2970.0850.0850.0000.0000.0000.000
67A374THR00.0010.00526.5400.0040.0040.0000.0000.0000.000
68A375ASN00.0490.04020.8130.0100.0100.0000.0000.0000.000
69A376PRO00.0600.01524.772-0.006-0.0060.0000.0000.0000.000
70A377VAL00.0760.04320.0380.0000.0000.0000.0000.0000.000
71A378LEU0-0.0220.00520.614-0.008-0.0080.0000.0000.0000.000
72A379GLN0-0.026-0.02124.0040.0050.0050.0000.0000.0000.000
73A380LEU00.0430.02926.1090.0000.0000.0000.0000.0000.000
74A381ASN0-0.035-0.04121.775-0.003-0.0030.0000.0000.0000.000
75A382LEU0-0.044-0.01525.410-0.002-0.0020.0000.0000.0000.000
76A383ALA00.004-0.00127.7350.0020.0020.0000.0000.0000.000
77A384ASN00.0730.03226.4650.0080.0080.0000.0000.0000.000
78A385ALA00.0230.00426.7800.0010.0010.0000.0000.0000.000
79A386TYR0-0.019-0.02928.780-0.001-0.0010.0000.0000.0000.000
80A387LEU0-0.011-0.00632.2370.0030.0030.0000.0000.0000.000
81A388GLN0-0.039-0.01329.5570.0040.0040.0000.0000.0000.000
82A389GLY0-0.045-0.02332.341-0.001-0.0010.0000.0000.0000.000
83A390GLY0-0.0290.00133.2130.0010.0010.0000.0000.0000.000
84A391GLN0-0.043-0.03034.5820.0050.0050.0000.0000.0000.000
85A392PRO00.0760.02736.252-0.001-0.0010.0000.0000.0000.000
86A393GLN00.0220.01838.0010.0030.0030.0000.0000.0000.000
87A394GLU-1-0.898-0.96534.993-0.051-0.0510.0000.0000.0000.000
88A395ALA0-0.013-0.00233.837-0.001-0.0010.0000.0000.0000.000
89A396ALA00.0800.03634.8390.0010.0010.0000.0000.0000.000
90A397ASN0-0.053-0.01836.9520.0050.0050.0000.0000.0000.000
91A398ILE0-0.096-0.04230.7550.0020.0020.0000.0000.0000.000
92A399LEU00.0200.00632.1680.0020.0020.0000.0000.0000.000
93A400ASN00.0150.02234.9340.0060.0060.0000.0000.0000.000
94A401ARG10.8770.95433.2390.0460.0460.0000.0000.0000.000
95A402TYR0-0.090-0.06627.9320.0000.0000.0000.0000.0000.000
96A403THR00.034-0.00433.1980.0030.0030.0000.0000.0000.000
97A404PHE0-0.065-0.01435.4940.0040.0040.0000.0000.0000.000
98A405ASN0-0.041-0.03032.8540.0060.0060.0000.0000.0000.000
99A406ASN0-0.083-0.03929.7910.0040.0040.0000.0000.0000.000
100A407LYS10.9150.94732.711-0.004-0.0040.0000.0000.0000.000
101A408ASP-1-0.852-0.91332.9990.0080.0080.0000.0000.0000.000
102A409ASP-1-0.827-0.88928.822-0.014-0.0140.0000.0000.0000.000
103A410SER00.0500.00431.867-0.002-0.0020.0000.0000.0000.000
104A411ASN00.0290.02827.682-0.002-0.0020.0000.0000.0000.000
105A412GLY0-0.0080.00231.273-0.005-0.0050.0000.0000.0000.000
106A413TRP00.001-0.02332.643-0.004-0.0040.0000.0000.0000.000
107A414ASP-1-0.895-0.93733.898-0.013-0.0130.0000.0000.0000.000
108A415LEU0-0.017-0.01529.747-0.003-0.0030.0000.0000.0000.000
109A416LEU0-0.037-0.01734.406-0.002-0.0020.0000.0000.0000.000
110A417ALA00.0110.00037.2230.0000.0000.0000.0000.0000.000
111A418GLN0-0.019-0.01534.0860.0010.0010.0000.0000.0000.000
112A419ALA0-0.011-0.00736.879-0.001-0.0010.0000.0000.0000.000
113A420GLU-1-0.813-0.92838.740-0.026-0.0260.0000.0000.0000.000
114A421ALA0-0.042-0.00741.8000.0010.0010.0000.0000.0000.000
115A422ALA0-0.059-0.02840.4040.0000.0000.0000.0000.0000.000
116A423LEU0-0.077-0.03640.629-0.001-0.0010.0000.0000.0000.000
117A424ASN0-0.073-0.02144.1870.0020.0020.0000.0000.0000.000
118A425ASN0-0.040-0.00944.0630.0020.0020.0000.0000.0000.000
119A426ARG10.9400.96846.3010.0150.0150.0000.0000.0000.000
120A427ASP-1-0.803-0.90247.915-0.015-0.0150.0000.0000.0000.000
121A428GLN00.0800.03743.8730.0020.0020.0000.0000.0000.000
122A429GLU-1-0.833-0.91043.169-0.017-0.0170.0000.0000.0000.000
123A430LEU0-0.091-0.05043.8650.0010.0010.0000.0000.0000.000
124A431ALA00.0300.01144.7640.0020.0020.0000.0000.0000.000
125A432ALA00.0120.01539.7100.0020.0020.0000.0000.0000.000
126A433ARG10.9010.93240.6090.0150.0150.0000.0000.0000.000
127A434ALA0-0.054-0.01842.4280.0020.0020.0000.0000.0000.000
128A435GLU-1-0.779-0.85939.835-0.002-0.0020.0000.0000.0000.000
129A436GLY00.0590.03538.3340.0020.0020.0000.0000.0000.000
130A437TYR0-0.049-0.04439.3200.0020.0020.0000.0000.0000.000
131A438ALA0-0.026-0.01541.7650.0020.0020.0000.0000.0000.000
132A439LEU0-0.0100.00535.2990.0030.0030.0000.0000.0000.000
133A440ALA0-0.0350.00237.8660.0030.0030.0000.0000.0000.000
134A441GLY00.0070.00239.5030.0010.0010.0000.0000.0000.000
135A442ARG10.8460.92542.487-0.004-0.0040.0000.0000.0000.000
136A443LEU00.0340.00644.090-0.002-0.0020.0000.0000.0000.000
137A444ASP-1-0.840-0.91146.9530.0040.0040.0000.0000.0000.000
138A445GLN00.0040.00347.1250.0000.0000.0000.0000.0000.000
139A446ALA00.0310.01445.117-0.001-0.0010.0000.0000.0000.000
140A447ILE00.0140.00747.001-0.001-0.0010.0000.0000.0000.000
141A448SER0-0.040-0.00550.274-0.001-0.0010.0000.0000.0000.000
142A449LEU0-0.001-0.01246.326-0.001-0.0010.0000.0000.0000.000
143A450MET00.0160.02345.099-0.002-0.0020.0000.0000.0000.000
144A451SER0-0.020-0.02149.6000.0000.0000.0000.0000.0000.000
145A452SER0-0.043-0.01751.941-0.001-0.0010.0000.0000.0000.000
146A453ALA00.0140.01849.146-0.001-0.0010.0000.0000.0000.000
147A454SER0-0.043-0.05951.210-0.001-0.0010.0000.0000.0000.000
148A455SER0-0.115-0.06353.4440.0000.0000.0000.0000.0000.000
149A456GLN00.0100.00152.160-0.001-0.0010.0000.0000.0000.000
150A457VAL0-0.0090.02551.453-0.001-0.0010.0000.0000.0000.000
151A458LYS10.9430.96954.8310.0120.0120.0000.0000.0000.000
152A459LEU00.0540.02457.3660.0000.0000.0000.0000.0000.000
153A460GLY0-0.007-0.00758.9510.0000.0000.0000.0000.0000.000
154A461SER0-0.072-0.03654.8320.0000.0000.0000.0000.0000.000
155A462LEU00.0360.00450.1990.0000.0000.0000.0000.0000.000
156A463GLN00.000-0.00547.1760.0020.0020.0000.0000.0000.000
157A464GLN00.1320.07051.1130.0000.0000.0000.0000.0000.000
158A465ALA00.0210.01653.3060.0010.0010.0000.0000.0000.000
159A466ARG10.9000.94946.6060.0130.0130.0000.0000.0000.000
160A467TYR0-0.010-0.02446.5910.0010.0010.0000.0000.0000.000
161A468ASP-1-0.809-0.89250.030-0.004-0.0040.0000.0000.0000.000
162A469ALA0-0.0080.00049.6930.0010.0010.0000.0000.0000.000
163A470ARG10.7750.84142.6240.0030.0030.0000.0000.0000.000
164A471ILE0-0.022-0.00548.0270.0010.0010.0000.0000.0000.000
165A472ASP-1-0.903-0.94350.6630.0010.0010.0000.0000.0000.000
166A473GLN0-0.033-0.02245.3550.0000.0000.0000.0000.0000.000
167A474LEU0-0.031-0.01544.6170.0020.0020.0000.0000.0000.000
168A475ARG10.9720.98747.9000.0000.0000.0000.0000.0000.000
169A476GLN0-0.018-0.01150.1050.0000.0000.0000.0000.0000.000
170A477LEU0-0.018-0.00443.2530.0020.0020.0000.0000.0000.000
171A478GLN0-0.006-0.03347.5500.0010.0010.0000.0000.0000.000
172A479GLU-1-0.912-0.94449.4230.0100.0100.0000.0000.0000.000
173A480ARG10.8660.93743.454-0.016-0.0160.0000.0000.0000.000
174A481PHE0-0.053-0.02642.8520.0020.0020.0000.0000.0000.000
175A482LYS10.8950.97648.784-0.008-0.0080.0000.0000.0000.000