Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: P4LRN

Calculation Name: 3ITF-A-Xray26

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3ITF

Chain ID: A

ChEMBL ID:

UniProt ID: P0AE85

Base Structure: X-ray

Registration Date: 2018-07-26

Reference:

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement Missing residues were capped by ACE, NME. Missing atoms were corrected by Structure prepareation by MOE.
Water Apo structure with with a 3 angstrom solvent shell.
Procedure Auto-FMO protocol ver. 1.20180227
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 227
LigandCharge
Software MIZUHO/ABINIT-MP 3.0
Total energy (hartree)
FMO2-HF: Electronic energy -1084309.029768
FMO2-HF: Nuclear repulsion 1027508.150133
FMO2-HF: Total energy -56800.879635
FMO2-MP2: Total energy -56958.269706


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:39:ACE)


Summations of interaction energy for fragment #1(A:39:ACE)
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.
3.112-2.17424.582-12.958-6.342-0.043
Interaction energy analysis for fragmet #1(A:39:ACE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.029 / q_NPA : -0.037
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].
3A41THR00.0980.0343.7751.1302.027-0.018-0.452-0.4270.000
4A42GLN00.0150.0227.3340.3140.3140.0000.0000.0000.000
5A43SER00.0220.0119.4310.0180.0180.0000.0000.0000.000
6A44HIS00.0580.03312.0940.0000.0000.0000.0000.0000.000
7A45MET0-0.0050.02214.9140.0290.0290.0000.0000.0000.000
8A46PHE00.0440.00616.0200.0380.0380.0000.0000.0000.000
9A47ASP-1-0.763-0.86718.034-0.259-0.2590.0000.0000.0000.000
10A48GLY0-0.003-0.00320.2810.0190.0190.0000.0000.0000.000
11A49ILE0-0.0030.01922.5610.0170.0170.0000.0000.0000.000
12A50SER0-0.009-0.00824.840-0.012-0.0120.0000.0000.0000.000
13A51LEU00.0140.01422.3350.0060.0060.0000.0000.0000.000
14A52THR00.0530.03427.0180.0040.0040.0000.0000.0000.000
15A53GLU-1-0.872-0.95727.464-0.142-0.1420.0000.0000.0000.000
16A54HIS00.0490.02127.103-0.014-0.0140.0000.0000.0000.000
17A55GLN0-0.003-0.00625.155-0.009-0.0090.0000.0000.0000.000
18A56ARG10.9450.96822.3510.1620.1620.0000.0000.0000.000
19A57GLN00.0510.03922.163-0.021-0.0210.0000.0000.0000.000
20A58GLN00.0410.03322.136-0.009-0.0090.0000.0000.0000.000
21A59MET0-0.002-0.00519.238-0.007-0.0070.0000.0000.0000.000
22A60ARG10.8280.92817.6800.1520.1520.0000.0000.0000.000
23A61ASP-1-0.794-0.88817.464-0.205-0.2050.0000.0000.0000.000
24A62LEU0-0.029-0.01316.701-0.013-0.0130.0000.0000.0000.000
25A63MET0-0.0030.00111.050-0.013-0.0130.0000.0000.0000.000
26A64GLN0-0.0090.01612.710-0.081-0.0810.0000.0000.0000.000
27A65GLN00.0410.03913.750-0.036-0.0360.0000.0000.0000.000
28A66ALA00.0270.01410.635-0.001-0.0010.0000.0000.0000.000
29A67ARG10.8450.9098.8020.7260.7260.0000.0000.0000.000
30A68HIS0-0.0070.0139.371-0.034-0.0340.0000.0000.0000.000
31A69GLU-1-0.832-0.90910.857-0.087-0.0870.0000.0000.0000.000
32A70GLN0-0.070-0.0273.283-1.988-1.7030.092-0.4160.039-0.003
33A71PRO00.0050.0176.206-0.137-0.1370.0000.0000.0000.000
34A72PRO00.0830.0414.884-0.298-0.273-0.001-0.002-0.0210.000
35A73VAL00.0620.0273.4590.2490.4290.007-0.048-0.1390.000
36A74ASN0-0.0150.0095.156-0.368-0.421-0.001-0.0040.0570.000
37A75VAL00.0780.0207.6910.0550.0550.0000.0000.0000.000
38A76SER00.0370.0249.952-0.016-0.0160.0000.0000.0000.000
39A77GLH0-0.017-0.0278.917-0.105-0.1050.0000.0000.0000.000
40A78LEU0-0.0080.0147.438-0.015-0.0150.0000.0000.0000.000
41A79GLU-1-0.816-0.88510.8840.1210.1210.0000.0000.0000.000
42A80THR0-0.024-0.00214.119-0.049-0.0490.0000.0000.0000.000
43A81MET00.0160.01012.805-0.055-0.0550.0000.0000.0000.000
44A82HIS00.0250.04414.682-0.024-0.0240.0000.0000.0000.000
45A83ARG10.8870.92016.332-0.205-0.2050.0000.0000.0000.000
46A84LEU0-0.0250.00317.253-0.018-0.0180.0000.0000.0000.000
47A85VAL00.002-0.00316.786-0.018-0.0180.0000.0000.0000.000
48A86THR0-0.035-0.01519.747-0.020-0.0200.0000.0000.0000.000
49A87ALA0-0.0290.01022.277-0.012-0.0120.0000.0000.0000.000
50A88GLU-1-0.889-0.93824.4090.0710.0710.0000.0000.0000.000
51A89ASN0-0.037-0.00527.592-0.008-0.0080.0000.0000.0000.000
52A90PHE0-0.0060.01020.6700.0120.0120.0000.0000.0000.000
53A91ASP-1-0.701-0.83123.6170.1500.1500.0000.0000.0000.000
54A92GLU-1-0.834-0.92221.9330.1700.1700.0000.0000.0000.000
55A93ASN0-0.012-0.00721.4310.0240.0240.0000.0000.0000.000
56A94ALA0-0.0010.01321.1150.0220.0220.0000.0000.0000.000
57A95VAL00.0240.00617.0950.0390.0390.0000.0000.0000.000
58A96ARG10.8660.92216.743-0.143-0.1430.0000.0000.0000.000
59A97ALA00.0260.02816.7490.0380.0380.0000.0000.0000.000
60A98GLN00.000-0.01213.2270.1050.1050.0000.0000.0000.000
61A99ALA00.0270.00212.3950.1000.1000.0000.0000.0000.000
62A100GLU-1-0.797-0.84711.9450.3860.3860.0000.0000.0000.000
63A101LYS10.9400.98512.585-0.374-0.3740.0000.0000.0000.000
64A102MET0-0.026-0.0128.3120.0400.0400.0000.0000.0000.000
65A103ALA00.0230.0227.8240.4110.4110.0000.0000.0000.000
66A104ASN00.015-0.0149.1080.0390.0390.0000.0000.0000.000
67A105GLU-1-0.738-0.8266.0401.1561.1560.0000.0000.0000.000
68A106GLN00.0290.0053.528-0.0380.7660.027-0.469-0.362-0.003
69A107ILE0-0.015-0.0035.725-0.331-0.3310.0000.0000.0000.000
70A108ALA00.0190.0198.209-0.162-0.1620.0000.0000.0000.000
71A109ARG10.7920.9462.0891.592-6.91818.677-7.209-2.958-0.007
72A110GLN00.0480.0296.259-0.606-0.6060.0000.0000.0000.000
73A111VAL00.0020.0088.093-0.148-0.1480.0000.0000.0000.000
74A112GLU-1-0.806-0.8539.128-0.111-0.1110.0000.0000.0000.000
75A113MET0-0.058-0.0377.174-0.141-0.1410.0000.0000.0000.000
76A114ALA0-0.0080.00110.172-0.033-0.0330.0000.0000.0000.000
77A115LYS10.9040.96513.094-0.016-0.0160.0000.0000.0000.000
78A116VAL00.0430.02511.709-0.003-0.0030.0000.0000.0000.000
79A117ARG10.8570.9098.4580.5770.5770.0000.0000.0000.000
80A118ASN0-0.017-0.00515.4920.0200.0200.0000.0000.0000.000
81A119GLN00.0200.02317.9200.0030.0030.0000.0000.0000.000
82A120MET0-0.023-0.01715.779-0.006-0.0060.0000.0000.0000.000
83A121TYR00.001-0.02419.5490.0060.0060.0000.0000.0000.000
84A122ARG10.8780.94721.3800.0690.0690.0000.0000.0000.000
85A123LEU00.0190.03721.9180.0090.0090.0000.0000.0000.000
86A124LEU0-0.070-0.00122.5640.0010.0010.0000.0000.0000.000
87A125THR00.0300.00126.2810.0060.0060.0000.0000.0000.000
88A126PRO00.0760.03528.693-0.004-0.0040.0000.0000.0000.000
89A127GLU-1-0.816-0.91230.033-0.063-0.0630.0000.0000.0000.000
90A128GLN00.0200.01226.5260.0000.0000.0000.0000.0000.000
91A129GLN0-0.0140.00125.0550.0010.0010.0000.0000.0000.000
92A130ALA00.0310.02225.918-0.001-0.0010.0000.0000.0000.000
93A131VAL00.0100.01526.3310.0010.0010.0000.0000.0000.000
94A132LEU0-0.033-0.00720.213-0.004-0.0040.0000.0000.0000.000
95A133ASN0-0.002-0.01522.984-0.009-0.0090.0000.0000.0000.000
96A134GLU-1-0.863-0.91724.516-0.055-0.0550.0000.0000.0000.000
97A135LYS10.9310.97223.0690.1160.1160.0000.0000.0000.000
98A136HIS0-0.025-0.00817.133-0.021-0.0210.0000.0000.0000.000
99A137GLN00.0090.01321.6780.0080.0080.0000.0000.0000.000
100A138GLN00.0810.04324.538-0.002-0.0020.0000.0000.0000.000
101A139ARG10.8710.92817.8400.1620.1620.0000.0000.0000.000
102A140MET0-0.096-0.05417.4030.0090.0090.0000.0000.0000.000
103A141GLU-1-0.807-0.88321.840-0.022-0.0220.0000.0000.0000.000
104A142GLN00.0550.04922.086-0.005-0.0050.0000.0000.0000.000
105A143LEU0-0.073-0.02718.0380.0040.0040.0000.0000.0000.000
106A144ARG10.8680.92822.5390.0230.0230.0000.0000.0000.000
107A145ASP-1-0.688-0.79326.012-0.030-0.0300.0000.0000.0000.000
108A146VAL00.012-0.00127.796-0.004-0.0040.0000.0000.0000.000
109A147THR0-0.0100.00629.296-0.003-0.0030.0000.0000.0000.000
110A148GLN0-0.062-0.04226.598-0.008-0.0080.0000.0000.0000.000
111A149TRP0-0.106-0.05920.939-0.010-0.0100.0000.0000.0000.000
112A150GLN-1-0.794-0.84927.476-0.030-0.0300.0000.0000.0000.000
113A4HOH0-0.027-0.0249.2340.0090.0090.0000.0000.0000.000
114A151HOH0-0.030-0.0197.4890.0160.0160.0000.0000.0000.000
115A152HOH0-0.071-0.05016.791-0.002-0.0020.0000.0000.0000.000
116A153HOH0-0.035-0.02026.1680.0020.0020.0000.0000.0000.000
117A155HOH00.0120.0027.034-0.073-0.0730.0000.0000.0000.000
118A156HOH0-0.021-0.01219.835-0.002-0.0020.0000.0000.0000.000
119A157HOH0-0.036-0.02015.1600.0100.0100.0000.0000.0000.000
120A158HOH0-0.031-0.02915.3820.0080.0080.0000.0000.0000.000
121A159HOH0-0.032-0.02814.553-0.017-0.0170.0000.0000.0000.000
122A160HOH0-0.017-0.01726.9210.0020.0020.0000.0000.0000.000
123A161HOH0-0.058-0.04516.6810.0000.0000.0000.0000.0000.000
124A162HOH00.0050.00223.0200.0020.0020.0000.0000.0000.000
125A163HOH0-0.013-0.01125.2180.0030.0030.0000.0000.0000.000
126A164HOH0-0.046-0.0322.3530.2890.5322.451-1.673-1.022-0.013
127A167HOH00.0140.00614.706-0.010-0.0100.0000.0000.0000.000
128A169HOH0-0.035-0.04528.4800.0020.0020.0000.0000.0000.000
129A170HOH0-0.018-0.02330.1030.0000.0000.0000.0000.0000.000
130A171HOH0-0.082-0.05325.4000.0000.0000.0000.0000.0000.000
131A172HOH0-0.081-0.06330.402-0.001-0.0010.0000.0000.0000.000
132A173HOH0-0.0040.01826.650-0.002-0.0020.0000.0000.0000.000
133A174HOH0-0.045-0.03022.5360.0060.0060.0000.0000.0000.000
134A177HOH0-0.030-0.02012.2130.0280.0280.0000.0000.0000.000
135A178HOH0-0.035-0.02927.0090.0030.0030.0000.0000.0000.000
136A179HOH00.0280.02211.3710.0110.0110.0000.0000.0000.000
137A180HOH00.009-0.0065.0750.3240.346-0.001-0.002-0.0190.000
138A182HOH00.0080.00322.2290.0030.0030.0000.0000.0000.000
139A183HOH0-0.012-0.00819.788-0.005-0.0050.0000.0000.0000.000
140A184HOH00.0220.01812.1780.0120.0120.0000.0000.0000.000
141A185HOH0-0.010-0.01222.493-0.002-0.0020.0000.0000.0000.000
142A188HOH0-0.062-0.03331.363-0.001-0.0010.0000.0000.0000.000
143A189HOH00.0030.01116.754-0.020-0.0200.0000.0000.0000.000
144A191HOH0-0.0070.00218.9900.0090.0090.0000.0000.0000.000
145A192HOH0-0.010-0.01917.182-0.008-0.0080.0000.0000.0000.000
146A193HOH0-0.031-0.02511.235-0.036-0.0360.0000.0000.0000.000
147A194HOH00.0040.01531.942-0.002-0.0020.0000.0000.0000.000
148A195HOH0-0.035-0.03321.460-0.009-0.0090.0000.0000.0000.000
149A198HOH0-0.0050.0043.7020.0850.3400.004-0.167-0.093-0.001
150A199HOH00.0080.00917.832-0.016-0.0160.0000.0000.0000.000
151A200HOH0-0.047-0.0349.1230.0430.0430.0000.0000.0000.000
152A202HOH0-0.010-0.0106.2400.1000.1000.0000.0000.0000.000
153A204HOH0-0.029-0.02020.5380.0060.0060.0000.0000.0000.000
154A205HOH0-0.007-0.01726.2290.0010.0010.0000.0000.0000.000
155A206HOH0-0.046-0.02326.172-0.001-0.0010.0000.0000.0000.000
156A207HOH0-0.033-0.04015.7750.0120.0120.0000.0000.0000.000
157A208HOH00.009-0.01016.071-0.015-0.0150.0000.0000.0000.000
158A210HOH0-0.033-0.05112.012-0.034-0.0340.0000.0000.0000.000
159A211HOH0-0.002-0.00110.544-0.021-0.0210.0000.0000.0000.000
160A216HOH0-0.037-0.0425.7570.4390.4390.0000.0000.0000.000
161A217HOH0-0.003-0.0025.5540.4680.4680.0000.0000.0000.000
162A218HOH0-0.002-0.00817.4020.0150.0150.0000.0000.0000.000
163A219HOH0-0.038-0.02521.409-0.005-0.0050.0000.0000.0000.000
164A220HOH0-0.036-0.02928.6480.0020.0020.0000.0000.0000.000
165A221HOH0-0.005-0.01527.174-0.003-0.0030.0000.0000.0000.000
166A223HOH0-0.050-0.07433.3340.0010.0010.0000.0000.0000.000
167A224HOH0-0.038-0.01830.3260.0010.0010.0000.0000.0000.000
168A225HOH0-0.035-0.02722.463-0.002-0.0020.0000.0000.0000.000
169A227HOH0-0.053-0.04618.436-0.004-0.0040.0000.0000.0000.000
170A228HOH0-0.033-0.02317.5630.0100.0100.0000.0000.0000.000
171A231HOH0-0.019-0.0362.925-0.862-0.3620.425-0.549-0.377-0.005
172A232HOH0-0.045-0.05412.499-0.007-0.0070.0000.0000.0000.000
173A235HOH0-0.032-0.0188.746-0.004-0.0040.0000.0000.0000.000
174A236HOH0-0.047-0.02733.4870.0010.0010.0000.0000.0000.000
175A237HOH00.0140.01415.543-0.005-0.0050.0000.0000.0000.000
176A238HOH00.005-0.00516.155-0.025-0.0250.0000.0000.0000.000
177A239HOH0-0.018-0.01213.7020.0080.0080.0000.0000.0000.000
178A241HOH00.0180.01327.7220.0010.0010.0000.0000.0000.000
179A242HOH0-0.035-0.02123.310-0.003-0.0030.0000.0000.0000.000
180A243HOH0-0.010-0.01125.963-0.001-0.0010.0000.0000.0000.000
181A244HOH0-0.009-0.01122.323-0.006-0.0060.0000.0000.0000.000
182A245HOH00.000-0.01128.370-0.002-0.0020.0000.0000.0000.000
183A247HOH00.0190.03531.4480.0010.0010.0000.0000.0000.000
184A248HOH0-0.010-0.00726.511-0.003-0.0030.0000.0000.0000.000
185A249HOH0-0.013-0.00816.9170.0010.0010.0000.0000.0000.000
186A251HOH0-0.044-0.02328.072-0.003-0.0030.0000.0000.0000.000
187A252HOH00.0250.01312.838-0.040-0.0400.0000.0000.0000.000
188A254HOH0-0.029-0.02231.2490.0020.0020.0000.0000.0000.000
189A255HOH0-0.010-0.00413.751-0.039-0.0390.0000.0000.0000.000
190A256HOH0-0.001-0.00823.300-0.002-0.0020.0000.0000.0000.000
191A258HOH00.0040.00526.777-0.002-0.0020.0000.0000.0000.000
192A259HOH0-0.010-0.01514.680-0.034-0.0340.0000.0000.0000.000
193A260HOH00.0280.01732.340-0.002-0.0020.0000.0000.0000.000
194A262HOH0-0.081-0.05532.1790.0010.0010.0000.0000.0000.000
195A263HOH00.0020.01215.366-0.025-0.0250.0000.0000.0000.000
196A264HOH0-0.014-0.01223.5750.0030.0030.0000.0000.0000.000
197A265HOH00.0050.00923.328-0.003-0.0030.0000.0000.0000.000
198A266HOH0-0.013-0.01118.587-0.006-0.0060.0000.0000.0000.000
199A267HOH0-0.029-0.01232.177-0.001-0.0010.0000.0000.0000.000
200A268HOH00.006-0.0057.357-0.058-0.0580.0000.0000.0000.000
201A269HOH0-0.060-0.05425.2430.0020.0020.0000.0000.0000.000
202A270HOH0-0.048-0.0269.959-0.016-0.0160.0000.0000.0000.000
203A273HOH00.0030.0135.3670.2380.2380.0000.0000.0000.000
204A275HOH00.0080.00617.511-0.010-0.0100.0000.0000.0000.000
205A277HOH0-0.028-0.03234.2060.0000.0000.0000.0000.0000.000
206A278HOH0-0.038-0.04319.714-0.006-0.0060.0000.0000.0000.000
207A280HOH0-0.012-0.00129.8980.0000.0000.0000.0000.0000.000
208A282HOH0-0.032-0.02421.649-0.001-0.0010.0000.0000.0000.000
209A284HOH0-0.064-0.0418.7900.0220.0220.0000.0000.0000.000
210A285HOH00.0000.00727.583-0.005-0.0050.0000.0000.0000.000
211A288HOH00.0300.01623.038-0.001-0.0010.0000.0000.0000.000
212A289HOH0-0.023-0.01927.0100.0000.0000.0000.0000.0000.000
213A294HOH0-0.034-0.01424.378-0.004-0.0040.0000.0000.0000.000
214A298HOH0-0.021-0.01934.4140.0010.0010.0000.0000.0000.000
215A301HOH0-0.019-0.02418.3570.0110.0110.0000.0000.0000.000
216A304HOH00.0330.02318.6130.0060.0060.0000.0000.0000.000
217A312HOH00.0370.0352.0630.3880.4542.920-1.967-1.020-0.011
218A313HOH0-0.020-0.01626.187-0.003-0.0030.0000.0000.0000.000
219A317HOH0-0.031-0.02511.320-0.067-0.0670.0000.0000.0000.000
220A318HOH0-0.016-0.01527.7160.0000.0000.0000.0000.0000.000
221A322HOH00.0120.0276.3910.2020.2020.0000.0000.0000.000
222A323HOH0-0.014-0.0356.6790.1580.1580.0000.0000.0000.000
223A324HOH0-0.033-0.02910.696-0.060-0.0600.0000.0000.0000.000
224A325HOH0-0.018-0.00922.8710.0010.0010.0000.0000.0000.000
225A326HOH00.0240.02913.441-0.006-0.0060.0000.0000.0000.000
226A337HOH0-0.034-0.02419.7200.0010.0010.0000.0000.0000.000
227B247HOH00.0370.02023.713-0.003-0.0030.0000.0000.0000.000