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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: XMM1Z

Calculation Name: 1RTT-A-Xray13

Preferred Name:

Target Type:

Ligand Name: sulfate ion

ligand 3-letter code: SO4

PDB ID: 1RTT

Chain ID: A

ChEMBL ID:

UniProt ID: Q9I4D4

Base Structure: X-ray

Registration Date: 2018-03-01

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 No
Procedure Auto-FMO protocol ver. 1.20181228
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 177
LigandCharge SO4=-2
Software MIZUHO/ABINIT-MP 3.0
Total energy (hartree)
FMO2-HF: Electronic energy -1758333.102512
FMO2-HF: Nuclear repulsion 1692144.032249
FMO2-HF: Total energy -66189.070263
FMO2-MP2: Total energy -66383.964457


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:6:ACE)


Summations of interaction energy for fragment #1(A:6: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.
-1.191-1.5693.652-1.756-1.518-0.017
Interaction energy analysis for fragmet #1(A:6:ACE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.035 / q_NPA : -0.032
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].
3A8LYS10.9000.9503.8801.6532.343-0.009-0.295-0.3860.000
4A9VAL00.0450.0226.4710.0660.0660.0000.0000.0000.000
5A10LEU00.0120.0129.6330.1340.1340.0000.0000.0000.000
6A11GLY0-0.012-0.01012.9240.0000.0000.0000.0000.0000.000
7A12ILE0-0.006-0.01615.4940.0330.0330.0000.0000.0000.000
8A13SER00.029-0.00519.0440.0000.0000.0000.0000.0000.000
9A14GLY0-0.018-0.01922.0290.0030.0030.0000.0000.0000.000
10A15SER0-0.062-0.06125.3740.0100.0100.0000.0000.0000.000
11A16LEU00.0420.01626.2950.0000.0000.0000.0000.0000.000
12A17ARG10.8080.92828.6350.0500.0500.0000.0000.0000.000
13A18SER00.039-0.00128.481-0.004-0.0040.0000.0000.0000.000
14A19GLY00.0050.00328.0810.0010.0010.0000.0000.0000.000
15A20SER0-0.077-0.05226.451-0.003-0.0030.0000.0000.0000.000
16A21TYR00.0770.01026.2220.0020.0020.0000.0000.0000.000
17A22ASN00.003-0.01523.966-0.012-0.0120.0000.0000.0000.000
18A23SER00.0470.02021.945-0.015-0.0150.0000.0000.0000.000
19A24ALA00.0100.02421.231-0.001-0.0010.0000.0000.0000.000
20A25ALA00.0100.00121.4170.0030.0030.0000.0000.0000.000
21A26LEU0-0.015-0.00616.834-0.007-0.0070.0000.0000.0000.000
22A27GLN00.0000.00016.636-0.013-0.0130.0000.0000.0000.000
23A28GLU-1-0.854-0.93617.2780.0000.0000.0000.0000.0000.000
24A29ALA0-0.009-0.00815.1910.0070.0070.0000.0000.0000.000
25A30ILE0-0.041-0.01212.096-0.013-0.0130.0000.0000.0000.000
26A31GLY0-0.036-0.01212.1330.0340.0340.0000.0000.0000.000
27A32LEU0-0.072-0.04014.0880.0250.0250.0000.0000.0000.000
28A33VAL0-0.021-0.0018.802-0.045-0.0450.0000.0000.0000.000
29A34PRO0-0.0160.0047.6900.1030.1030.0000.0000.0000.000
30A35PRO00.023-0.0147.3960.0340.0340.0000.0000.0000.000
31A36GLY00.000-0.0033.240-0.275-0.1440.072-0.097-0.1060.000
32A37MET0-0.0230.0162.557-0.438-1.7273.590-1.359-0.941-0.017
33A38SER0-0.054-0.0224.9390.5140.604-0.001-0.005-0.0850.000
34A39ILE00.0450.0166.938-0.239-0.2390.0000.0000.0000.000
35A40GLU-1-0.979-0.98010.222-0.051-0.0510.0000.0000.0000.000
36A41LEU0-0.007-0.00412.197-0.046-0.0460.0000.0000.0000.000
37A42ALA00.0080.00815.8850.0120.0120.0000.0000.0000.000
38A43ASP-1-0.872-0.91018.213-0.049-0.0490.0000.0000.0000.000
39A44ILE0-0.003-0.02221.7190.0000.0000.0000.0000.0000.000
40A45SER0-0.069-0.05724.3430.0060.0060.0000.0000.0000.000
41A46GLY0-0.0040.00726.6090.0050.0050.0000.0000.0000.000
42A47ILE0-0.074-0.03224.2910.0010.0010.0000.0000.0000.000
43A48PRO00.0100.02028.6550.0020.0020.0000.0000.0000.000
44A49LEU00.0270.00031.780-0.006-0.0060.0000.0000.0000.000
45A50TYR0-0.055-0.05631.9050.0010.0010.0000.0000.0000.000
46A51ASN00.0200.00034.0470.0030.0030.0000.0000.0000.000
47A52GLU-1-0.828-0.89936.198-0.070-0.0700.0000.0000.0000.000
48A53ASP-1-0.890-0.94537.234-0.045-0.0450.0000.0000.0000.000
49A54VAL0-0.077-0.03834.4630.0020.0020.0000.0000.0000.000
50A55TYR0-0.011-0.03230.4450.0000.0000.0000.0000.0000.000
51A56ALA0-0.022-0.00334.052-0.001-0.0010.0000.0000.0000.000
52A57LEU0-0.069-0.02936.4800.0020.0020.0000.0000.0000.000
53A58GLY0-0.0050.00532.4830.0020.0020.0000.0000.0000.000
54A59PHE0-0.040-0.02227.768-0.001-0.0010.0000.0000.0000.000
55A60PRO00.0120.01229.6580.0040.0040.0000.0000.0000.000
56A61PRO00.0820.02627.446-0.007-0.0070.0000.0000.0000.000
57A62ALA00.0000.00625.280-0.005-0.0050.0000.0000.0000.000
58A63VAL0-0.002-0.00124.119-0.010-0.0100.0000.0000.0000.000
59A64GLU-1-0.941-0.95723.572-0.083-0.0830.0000.0000.0000.000
60A65ARG10.9650.98416.6660.0630.0630.0000.0000.0000.000
61A66PHE00.0170.00219.116-0.016-0.0160.0000.0000.0000.000
62A67ARG10.8800.92118.9500.1040.1040.0000.0000.0000.000
63A68GLU-1-0.955-0.97318.092-0.154-0.1540.0000.0000.0000.000
64A69GLN0-0.045-0.03015.019-0.020-0.0200.0000.0000.0000.000
65A70ILE0-0.028-0.00714.111-0.061-0.0610.0000.0000.0000.000
66A71ARG10.9470.97114.7950.1250.1250.0000.0000.0000.000
67A72ALA0-0.053-0.03311.813-0.037-0.0370.0000.0000.0000.000
68A73ALA0-0.0350.01110.109-0.104-0.1040.0000.0000.0000.000
69A74ASP-1-0.816-0.8906.281-2.108-2.1080.0000.0000.0000.000
70A75ALA0-0.018-0.0159.4790.0920.0920.0000.0000.0000.000
71A76LEU0-0.0140.00011.5580.0480.0480.0000.0000.0000.000
72A77LEU00.0280.01414.130-0.001-0.0010.0000.0000.0000.000
73A78PHE00.0000.00115.8410.0330.0330.0000.0000.0000.000
74A79ALA00.0350.02019.5600.0040.0040.0000.0000.0000.000
75A80THR00.003-0.02321.7410.0110.0110.0000.0000.0000.000
76A81PRO0-0.0060.01425.1830.0040.0040.0000.0000.0000.000
77A82GLU-1-0.810-0.89528.425-0.078-0.0780.0000.0000.0000.000
78A83TYR0-0.025-0.01731.3250.0050.0050.0000.0000.0000.000
79A84ASN0-0.037-0.02934.7360.0000.0000.0000.0000.0000.000
80A85TYR0-0.033-0.02835.9290.0000.0000.0000.0000.0000.000
81A86SER00.0740.06933.249-0.005-0.0050.0000.0000.0000.000
82A87MET00.0420.02128.282-0.001-0.0010.0000.0000.0000.000
83A88ALA00.0070.02829.1880.0060.0060.0000.0000.0000.000
84A89GLY00.0340.00030.237-0.005-0.0050.0000.0000.0000.000
85A90VAL00.0220.01128.115-0.002-0.0020.0000.0000.0000.000
86A91LEU00.0500.03223.405-0.003-0.0030.0000.0000.0000.000
87A92LYS10.8250.89826.6570.0930.0930.0000.0000.0000.000
88A93ASN00.0300.01628.854-0.001-0.0010.0000.0000.0000.000
89A94ALA00.0080.00924.8130.0000.0000.0000.0000.0000.000
90A95ILE0-0.003-0.00523.609-0.006-0.0060.0000.0000.0000.000
91A96ASP-1-0.808-0.89525.610-0.103-0.1030.0000.0000.0000.000
92A97TRP0-0.016-0.01627.490-0.001-0.0010.0000.0000.0000.000
93A98ALA0-0.016-0.01622.6240.0010.0010.0000.0000.0000.000
94A99SER0-0.057-0.02324.274-0.008-0.0080.0000.0000.0000.000
95A100ARG10.9170.98026.0230.0850.0850.0000.0000.0000.000
96A101PRO00.0070.02827.178-0.008-0.0080.0000.0000.0000.000
97A102PRO00.010-0.00126.5950.0060.0060.0000.0000.0000.000
98A103GLU-1-0.907-0.97123.305-0.145-0.1450.0000.0000.0000.000
99A104GLN0-0.0170.01322.951-0.017-0.0170.0000.0000.0000.000
100A105PRO00.024-0.00918.555-0.010-0.0100.0000.0000.0000.000
101A106PHE0-0.026-0.01618.198-0.035-0.0350.0000.0000.0000.000
102A107SER0-0.023-0.00918.918-0.029-0.0290.0000.0000.0000.000
103A108GLY00.0550.03218.389-0.021-0.0210.0000.0000.0000.000
104A109LYS10.7950.90713.1440.4500.4500.0000.0000.0000.000
105A110PRO00.0230.03312.0780.0690.0690.0000.0000.0000.000
106A111ALA00.010-0.01314.388-0.032-0.0320.0000.0000.0000.000
107A112ALA00.0170.01415.7740.0220.0220.0000.0000.0000.000
108A113ILE0-0.011-0.00417.2610.0070.0070.0000.0000.0000.000
109A114LEU0-0.0050.01818.4820.0080.0080.0000.0000.0000.000
110A115GLY00.0580.01921.8650.0000.0000.0000.0000.0000.000
111A116ALA0-0.0240.00224.8590.0050.0050.0000.0000.0000.000
112A117SER00.007-0.00427.3080.0030.0030.0000.0000.0000.000
113A118ALA00.0410.03431.0270.0020.0020.0000.0000.0000.000
114A119GLY0-0.012-0.00934.1490.0030.0030.0000.0000.0000.000
115A120ARG11.0000.97734.2110.0430.0430.0000.0000.0000.000
116A121PHE0-0.025-0.03933.8560.0000.0000.0000.0000.0000.000
117A122GLY00.0720.05330.273-0.005-0.0050.0000.0000.0000.000
118A123THR0-0.045-0.00727.495-0.011-0.0110.0000.0000.0000.000
119A124ALA00.0790.02929.357-0.006-0.0060.0000.0000.0000.000
120A125ARG10.8300.89730.4140.0590.0590.0000.0000.0000.000
121A126ALA0-0.0120.00329.125-0.002-0.0020.0000.0000.0000.000
122A127GLN0-0.016-0.01625.167-0.014-0.0140.0000.0000.0000.000
123A128TYR0-0.053-0.05027.144-0.006-0.0060.0000.0000.0000.000
124A129HIS0-0.028-0.02929.5300.0000.0000.0000.0000.0000.000
125A130LEU00.0200.00122.9280.0000.0000.0000.0000.0000.000
126A131ARG10.8970.93522.7110.1680.1680.0000.0000.0000.000
127A132GLN0-0.0030.01626.362-0.004-0.0040.0000.0000.0000.000
128A133THR0-0.026-0.02226.1270.0030.0030.0000.0000.0000.000
129A134LEU0-0.015-0.02521.442-0.001-0.0010.0000.0000.0000.000
130A135VAL00.0060.02024.280-0.010-0.0100.0000.0000.0000.000
131A136PHE0-0.049-0.02126.514-0.002-0.0020.0000.0000.0000.000
132A137LEU0-0.062-0.02423.1240.0020.0020.0000.0000.0000.000
133A138ASP-1-0.885-0.93822.705-0.236-0.2360.0000.0000.0000.000
134A139VAL0-0.0200.00818.370-0.023-0.0230.0000.0000.0000.000
135A140HIS0-0.016-0.01017.8980.0300.0300.0000.0000.0000.000
136A141PRO0-0.045-0.02017.779-0.041-0.0410.0000.0000.0000.000
137A142LEU00.0210.02115.3050.0270.0270.0000.0000.0000.000
138A143ASN0-0.012-0.01619.1740.0260.0260.0000.0000.0000.000
139A144LYS10.8920.96720.9420.1480.1480.0000.0000.0000.000
140A145PRO00.0440.01818.560-0.020-0.0200.0000.0000.0000.000
141A146GLU-1-0.845-0.92021.196-0.140-0.1400.0000.0000.0000.000
142A147VAL00.0260.00920.5850.0120.0120.0000.0000.0000.000
143A148MET0-0.046-0.00923.7780.0010.0010.0000.0000.0000.000
144A149ILE00.0190.01523.7770.0080.0080.0000.0000.0000.000
145A150SER0-0.013-0.01627.9600.0010.0010.0000.0000.0000.000
146A151SER0-0.046-0.01631.7130.0040.0040.0000.0000.0000.000
147A152ALA00.037-0.00429.4180.0030.0030.0000.0000.0000.000
148A153GLN00.0230.01630.820-0.001-0.0010.0000.0000.0000.000
149A154ASN0-0.045-0.03033.2260.0060.0060.0000.0000.0000.000
150A155ALA0-0.0110.01027.9630.0020.0020.0000.0000.0000.000
151A156PHE0-0.003-0.00523.767-0.002-0.0020.0000.0000.0000.000
152A157ASP-1-0.854-0.92128.206-0.002-0.0020.0000.0000.0000.000
153A158ALA0-0.049-0.02430.333-0.002-0.0020.0000.0000.0000.000
154A159GLN0-0.075-0.05624.6150.0030.0030.0000.0000.0000.000
155A160GLY00.020-0.00625.039-0.006-0.0060.0000.0000.0000.000
156A161ARG10.9681.01523.728-0.021-0.0210.0000.0000.0000.000
157A162LEU0-0.023-0.01321.371-0.005-0.0050.0000.0000.0000.000
158A163LEU0-0.027-0.02124.9240.0060.0060.0000.0000.0000.000
159A164ASP-1-0.888-0.93626.611-0.047-0.0470.0000.0000.0000.000
160A165ASP-1-0.817-0.93624.501-0.019-0.0190.0000.0000.0000.000
161A166LYS10.9721.00423.7340.0570.0570.0000.0000.0000.000
162A167ALA0-0.055-0.04323.666-0.011-0.0110.0000.0000.0000.000
163A168ARG10.9140.96019.989-0.007-0.0070.0000.0000.0000.000
164A169GLU-1-0.902-0.94319.157-0.056-0.0560.0000.0000.0000.000
165A170LEU0-0.053-0.02519.042-0.019-0.0190.0000.0000.0000.000
166A171ILE00.000-0.00916.374-0.028-0.0280.0000.0000.0000.000
167A172GLN0-0.0060.00814.770-0.039-0.0390.0000.0000.0000.000
168A173GLN0-0.008-0.01714.373-0.023-0.0230.0000.0000.0000.000
169A174GLN0-0.060-0.04115.269-0.039-0.0390.0000.0000.0000.000
170A175LEU00.0350.02211.112-0.073-0.0730.0000.0000.0000.000
171A176GLN00.014-0.00510.482-0.097-0.0970.0000.0000.0000.000
172A177ALA0-0.032-0.00711.550-0.044-0.0440.0000.0000.0000.000
173A178LEU0-0.039-0.02410.692-0.029-0.0290.0000.0000.0000.000
174A179GLN0-0.057-0.0265.233-0.008-0.0080.0000.0000.0000.000
175A180LEU0-0.081-0.0288.352-0.086-0.0860.0000.0000.0000.000
176A181NME0-0.0070.00310.9450.0000.0000.0000.0000.0000.000
177A194SO4-2-1.640-1.75227.944-0.126-0.1260.0000.0000.0000.000