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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: 1NJQZ

Calculation Name: 4XAH-A-Xray372

Preferred Name:

Target Type:

Ligand Name: s,s-(2-hydroxyethyl)thiocysteine

ligand 3-letter code: CME

PDB ID: 4XAH

Chain ID: A

ChEMBL ID:

UniProt ID: Q03705

Base Structure: X-ray

Registration Date: 2023-09-20

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 177
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1988122.720745
FMO2-HF: Nuclear repulsion 1915688.376228
FMO2-HF: Total energy -72434.344518
FMO2-MP2: Total energy -72641.375402


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:1:MET)


Summations of interaction energy for fragment #1(A: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.
-35.702-34.22539.074-15.369-25.18-0.072
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.063 / q_NPA : -0.019
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].
3A3VAL0-0.002-0.0202.301-1.951-0.3802.713-1.492-2.792-0.008
4A4SER0-0.034-0.0024.7060.2650.335-0.001-0.018-0.0510.000
5A5ILE00.0540.0178.3410.1610.1610.0000.0000.0000.000
6A6ILE00.0270.02311.386-0.027-0.0270.0000.0000.0000.000
7A7PRO00.0320.00414.9310.0570.0570.0000.0000.0000.000
8A8GLN00.0070.02117.9060.0160.0160.0000.0000.0000.000
9A9PHE0-0.082-0.04816.0670.0290.0290.0000.0000.0000.000
10A10PRO00.0380.02215.055-0.023-0.0230.0000.0000.0000.000
11A11ASP-1-0.927-0.96114.042-0.015-0.0150.0000.0000.0000.000
12A12ILE0-0.081-0.03211.5890.0480.0480.0000.0000.0000.000
13A13LYS10.8370.9057.205-0.267-0.2670.0000.0000.0000.000
14A14VAL0-0.007-0.0197.3400.1510.1510.0000.0000.0000.000
15A15SER00.0030.0232.208-0.224-0.4852.327-0.694-1.3720.002
16A16LEU0-0.032-0.0203.4550.6791.1350.004-0.034-0.4260.000
17A17ALA00.0370.0182.410-5.217-2.6171.614-1.929-2.285-0.015
18A18LEU00.0080.0083.6630.8500.9490.013-0.010-0.1020.000
19A19PHE00.0220.0095.580-0.428-0.4280.0000.0000.0000.000
20A20GLU-1-0.816-0.9088.946-0.523-0.5230.0000.0000.0000.000
21A21GLN0-0.055-0.04612.1300.1500.1500.0000.0000.0000.000
22A22VAL0-0.001-0.00112.3650.0690.0690.0000.0000.0000.000
23A23LYS10.8700.93215.0120.2150.2150.0000.0000.0000.000
24A24ASN0-0.010-0.02715.091-0.027-0.0270.0000.0000.0000.000
25A25ALA00.0590.04116.6090.0290.0290.0000.0000.0000.000
26A26LYS10.9050.93817.5720.0650.0650.0000.0000.0000.000
27A27GLU-1-0.840-0.89018.2110.1510.1510.0000.0000.0000.000
28A28ILE00.0190.02613.1610.0160.0160.0000.0000.0000.000
29A29ARG10.8620.90717.1270.1000.1000.0000.0000.0000.000
30A30SER0-0.105-0.05919.4750.0100.0100.0000.0000.0000.000
31A31LYS10.8870.92519.102-0.159-0.1590.0000.0000.0000.000
32A32MET0-0.0080.02116.8630.0120.0120.0000.0000.0000.000
33A33SER0-0.007-0.00518.1980.0060.0060.0000.0000.0000.000
34A34GLU-1-0.797-0.87419.5030.1840.1840.0000.0000.0000.000
35A35LEU00.0580.01414.8650.0290.0290.0000.0000.0000.000
36A36SER00.0080.02814.5510.0570.0570.0000.0000.0000.000
37A37THR0-0.062-0.03614.9030.0050.0050.0000.0000.0000.000
38A38SER0-0.057-0.01211.6250.0430.0430.0000.0000.0000.000
39A39PHE00.058-0.0036.6640.0200.0200.0000.0000.0000.000
40A40ALA0-0.021-0.00410.840-0.032-0.0320.0000.0000.0000.000
41A41PHE00.0290.00010.122-0.055-0.0550.0000.0000.0000.000
42A42ILE00.0070.00012.3070.0570.0570.0000.0000.0000.000
43A43ASP-1-0.759-0.86513.267-0.434-0.4340.0000.0000.0000.000
44A44PRO00.0210.00312.2540.0030.0030.0000.0000.0000.000
45A45ARG10.7940.86814.5700.3010.3010.0000.0000.0000.000
46A46LEU0-0.038-0.01917.5210.0300.0300.0000.0000.0000.000
47A47VAL0-0.052-0.02812.7740.0130.0130.0000.0000.0000.000
48A48CYS00.0230.02214.612-0.049-0.0490.0000.0000.0000.000
49A49SER0-0.008-0.01114.057-0.026-0.0260.0000.0000.0000.000
50A50GLY00.020-0.00111.298-0.044-0.0440.0000.0000.0000.000
51A51GLU-1-0.852-0.89012.038-0.504-0.5040.0000.0000.0000.000
52A52GLN00.0270.01115.4160.0260.0260.0000.0000.0000.000
53A53MET0-0.0010.01210.4340.0720.0720.0000.0000.0000.000
54A54TYR00.027-0.0147.9420.0620.0620.0000.0000.0000.000
55A55SER00.0010.00213.9490.0980.0980.0000.0000.0000.000
56A56ALA00.0450.03115.8580.0620.0620.0000.0000.0000.000
57A57ILE0-0.023-0.00810.1840.0680.0680.0000.0000.0000.000
58A58TYR0-0.026-0.03014.3760.0630.0630.0000.0000.0000.000
59A59LYS10.8580.92116.9030.3050.3050.0000.0000.0000.000
60A60THR0-0.012-0.04815.9850.0420.0420.0000.0000.0000.000
61A61LEU0-0.024-0.01013.7410.0450.0450.0000.0000.0000.000
62A62ILE00.0130.00818.1070.0360.0360.0000.0000.0000.000
63A63GLU-1-0.843-0.92021.556-0.122-0.1220.0000.0000.0000.000
64A64VAL0-0.042-0.03719.0380.0250.0250.0000.0000.0000.000
65A65LYS10.8870.96420.7720.1000.1000.0000.0000.0000.000
66A66TYR0-0.020-0.01522.5700.0090.0090.0000.0000.0000.000
67A67ASN0-0.031-0.00925.3960.0190.0190.0000.0000.0000.000
68A68LYS10.8550.90325.4040.0810.0810.0000.0000.0000.000
69A69MET0-0.0360.02619.784-0.015-0.0150.0000.0000.0000.000
70A70ARG10.8740.92623.1260.1130.1130.0000.0000.0000.000
71A71THR0-0.068-0.06420.6630.0090.0090.0000.0000.0000.000
72A72ARG10.9130.93220.478-0.038-0.0380.0000.0000.0000.000
73A73ASN00.0260.03315.999-0.002-0.0020.0000.0000.0000.000
74A74LEU00.1050.05113.745-0.018-0.0180.0000.0000.0000.000
75A75ASN00.0070.01111.327-0.110-0.1100.0000.0000.0000.000
76A76SER0-0.037-0.04413.876-0.041-0.0410.0000.0000.0000.000
77A77GLU-1-0.770-0.83617.489-0.128-0.1280.0000.0000.0000.000
78A78CYS00.0070.01914.235-0.045-0.0450.0000.0000.0000.000
79A79VAL00.0170.01115.531-0.034-0.0340.0000.0000.0000.000
80A80LEU0-0.063-0.04917.518-0.001-0.0010.0000.0000.0000.000
81A81CME0-0.089-0.02518.3470.0130.0130.0000.0000.0000.000
82A82LEU00.0500.02715.498-0.006-0.0060.0000.0000.0000.000
83A83SER00.0140.02619.1410.0000.0000.0000.0000.0000.000
84A84PRO00.0400.03522.1460.0200.0200.0000.0000.0000.000
85A85THR0-0.092-0.07224.7420.0250.0250.0000.0000.0000.000
86A86SER00.0510.01226.196-0.001-0.0010.0000.0000.0000.000
87A87ASN00.0020.02127.1890.0150.0150.0000.0000.0000.000
88A88ILE00.0770.03920.072-0.010-0.0100.0000.0000.0000.000
89A89SER0-0.026-0.02423.227-0.008-0.0080.0000.0000.0000.000
90A90ASP-1-0.779-0.85525.023-0.153-0.1530.0000.0000.0000.000
91A91ALA00.0140.01121.419-0.014-0.0140.0000.0000.0000.000
92A92PHE00.021-0.01016.900-0.022-0.0220.0000.0000.0000.000
93A93LEU0-0.046-0.00921.211-0.010-0.0100.0000.0000.0000.000
94A94LYS10.8580.91623.0690.1540.1540.0000.0000.0000.000
95A95PHE00.0610.02017.991-0.007-0.0070.0000.0000.0000.000
96A96GLY00.0230.02217.101-0.044-0.0440.0000.0000.0000.000
97A97ILE0-0.036-0.00414.532-0.010-0.0100.0000.0000.0000.000
98A98LYS10.7980.86317.5580.3020.3020.0000.0000.0000.000
99A99ASP-1-0.800-0.89119.769-0.079-0.0790.0000.0000.0000.000
100A100ASP-1-0.788-0.86021.891-0.211-0.2110.0000.0000.0000.000
101A101SER0-0.0030.00816.541-0.008-0.0080.0000.0000.0000.000
102A102SER00.0020.00616.6510.0060.0060.0000.0000.0000.000
103A103GLN0-0.017-0.00412.8110.0230.0230.0000.0000.0000.000
104A104LEU0-0.073-0.0349.4860.1050.1050.0000.0000.0000.000
105A105ILE00.0480.0388.141-0.206-0.2060.0000.0000.0000.000
106A106CYS0-0.049-0.0196.2360.3670.3670.0000.0000.0000.000
107A107LEU00.0140.0086.275-0.322-0.3220.0000.0000.0000.000
108A108LYS10.8440.9216.154-0.269-0.2690.0000.0000.0000.000
109A109PHE00.0300.0096.993-0.198-0.1980.0000.0000.0000.000
110A110HIS0-0.036-0.0344.3420.1700.245-0.001-0.004-0.0700.000
111A111THR00.013-0.0159.408-0.085-0.0850.0000.0000.0000.000
112A112ASN00.0030.01012.115-0.047-0.0470.0000.0000.0000.000
113A113THR0-0.032-0.0057.7050.0170.0170.0000.0000.0000.000
114A114ASP-1-0.824-0.90410.8210.4220.4220.0000.0000.0000.000
115A115ASP-1-0.861-0.9298.8680.3700.3700.0000.0000.0000.000
116A116VAL0-0.047-0.0133.103-0.3020.0470.046-0.084-0.311-0.001
117A117ASP-1-0.795-0.8845.8432.8272.8270.0000.0000.0000.000
118A118LYS10.9070.9232.273-5.901-4.6783.165-1.079-3.3100.005
119A119GLU-1-0.779-0.8663.5487.5037.5940.7110.664-1.465-0.010
120A120GLN0-0.035-0.0086.197-0.775-0.761-0.001-0.003-0.0090.000
121A121LEU0-0.011-0.0112.471-1.865-0.9791.140-0.402-1.624-0.001
122A122ARG10.8270.8601.987-11.252-15.09313.879-4.848-5.1890.018
123A123THR0-0.0100.0035.240-1.298-1.2710.000-0.015-0.0120.000
124A124ILE0-0.0150.0088.295-0.450-0.4500.0000.0000.0000.000
125A125MET0-0.020-0.0202.524-1.520-1.7942.608-0.513-1.8210.002
126A126THR0-0.016-0.0237.260-0.487-0.4870.0000.0000.0000.000
127A127SER0-0.041-0.0179.476-0.199-0.1990.0000.0000.0000.000
128A128ILE0-0.050-0.01711.188-0.144-0.1440.0000.0000.0000.000
129A129VAL0-0.024-0.0149.229-0.111-0.1110.0000.0000.0000.000
130A130LYS10.8320.91511.364-0.197-0.1970.0000.0000.0000.000
131A131GLY00.015-0.00511.998-0.037-0.0370.0000.0000.0000.000
132A132GLN0-0.019-0.00110.0380.1050.1050.0000.0000.0000.000
133A133GLU-1-0.789-0.8651.817-14.098-16.13010.858-4.860-3.966-0.064
134A134ILE0-0.030-0.0155.9220.2710.2710.0000.0000.0000.000
135A135GLU-1-0.861-0.9193.973-3.288-3.051-0.001-0.022-0.2140.000
136A136PHE0-0.009-0.0113.9550.8281.0150.000-0.026-0.1610.000
137A137ASN00.003-0.0165.6080.0840.0840.0000.0000.0000.000
138A138ASP-1-0.748-0.8929.011-0.938-0.9380.0000.0000.0000.000
139A139ASP-1-0.848-0.88612.507-0.656-0.6560.0000.0000.0000.000
140A140ASN00.005-0.0108.3130.3770.3770.0000.0000.0000.000
141A141LEU0-0.038-0.01010.1110.1020.1020.0000.0000.0000.000
142A142SER0-0.068-0.05112.8170.1440.1440.0000.0000.0000.000
143A143ARG10.7960.88512.3680.9140.9140.0000.0000.0000.000
144A144PHE0-0.053-0.03411.9960.0660.0660.0000.0000.0000.000
145A145TYR0-0.0090.01516.6120.0310.0310.0000.0000.0000.000
146A146ASP-1-0.825-0.91818.329-0.254-0.2540.0000.0000.0000.000
147A147GLU-1-0.778-0.89222.001-0.278-0.2780.0000.0000.0000.000
148A148ALA0-0.0170.00524.2560.0200.0200.0000.0000.0000.000
149A149LEU00.015-0.00221.8480.0220.0220.0000.0000.0000.000
150A150ILE00.0230.00619.6050.0160.0160.0000.0000.0000.000
151A151ARG10.7120.83923.8630.2420.2420.0000.0000.0000.000
152A152LYS10.8660.93627.4740.2090.2090.0000.0000.0000.000
153A153ILE0-0.037-0.01323.6290.0160.0160.0000.0000.0000.000
154A154TYR0-0.021-0.05020.141-0.005-0.0050.0000.0000.0000.000
155A155LYS10.8290.93926.1580.1870.1870.0000.0000.0000.000
156A156LEU00.0060.01825.3970.0070.0070.0000.0000.0000.000
157A157SER00.011-0.01829.7920.0070.0070.0000.0000.0000.000
158A158ASP-1-0.838-0.92732.505-0.191-0.1910.0000.0000.0000.000
159A159ASP-1-0.906-0.92333.995-0.150-0.1500.0000.0000.0000.000
160A160PHE0-0.030-0.00726.8720.0010.0010.0000.0000.0000.000
161A161LYS10.8810.93131.3930.1720.1720.0000.0000.0000.000
162A162PRO0-0.0080.01726.3940.0050.0050.0000.0000.0000.000
163A163GLN00.000-0.01828.567-0.001-0.0010.0000.0000.0000.000
164A164ASP-1-0.797-0.88523.366-0.375-0.3750.0000.0000.0000.000
165A165VAL00.0400.02818.3200.0090.0090.0000.0000.0000.000
166A166ASN0-0.023-0.02520.209-0.049-0.0490.0000.0000.0000.000
167A167GLY0-0.019-0.01421.8250.0080.0080.0000.0000.0000.000
168A168LEU0-0.018-0.01621.5280.0170.0170.0000.0000.0000.000
169A169SER0-0.009-0.03818.708-0.012-0.0120.0000.0000.0000.000
170A170ARG10.9911.00020.6620.2750.2750.0000.0000.0000.000
171A171ALA00.0020.00223.2050.0150.0150.0000.0000.0000.000
172A172LEU0-0.028-0.01319.7460.0200.0200.0000.0000.0000.000
173A173VAL00.0140.00118.9150.0080.0080.0000.0000.0000.000
174A174ASP-1-1.017-0.99921.474-0.224-0.2240.0000.0000.0000.000
175A175ALA00.0110.00224.6730.0140.0140.0000.0000.0000.000
176A176ILE0-0.097-0.02918.8290.0160.0160.0000.0000.0000.000
177A177GLN0-0.028-0.00322.5780.0210.0210.0000.0000.0000.000