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

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FMODB ID: R8NY8

Calculation Name: 1ZXJ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1ZXJ

Chain ID: A

ChEMBL ID:

UniProt ID: P75223

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 OptHSide
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 198
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2249086.436277
FMO2-HF: Nuclear repulsion 2168654.79594
FMO2-HF: Total energy -80431.640337
FMO2-MP2: Total energy -80668.468935


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:11:ASP)


Summations of interaction energy for fragment #1(A:11:ASP)
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.
0.31199999999997-3.32727.482-12.376-11.4680.143
Interaction energy analysis for fragmet #1(A:11:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.838 / q_NPA : -0.906
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].
3A13ASP-1-0.832-0.9133.53164.75268.2880.047-1.463-2.1200.007
4A14ILE0-0.045-0.0254.379-10.612-10.3800.003-0.076-0.1580.000
5A22PHE0-0.052-0.03911.135-0.222-0.2220.0000.0000.0000.000
6A23GLN00.0130.00212.633-1.158-1.1580.0000.0000.0000.000
7A24GLY0-0.0150.00615.180-0.932-0.9320.0000.0000.0000.000
8A25HIS00.0210.01813.546-1.501-1.5010.0000.0000.0000.000
9A26MET0-0.036-0.02517.703-1.206-1.2060.0000.0000.0000.000
10A27ALA00.065-0.01517.7170.8560.8560.0000.0000.0000.000
11A28THR00.6470.72818.414-0.388-0.3880.0000.0000.0000.000
12A29ASN0-0.636-0.67620.683-0.816-0.8160.0000.0000.0000.000
13A30LEU0-0.061-0.02816.6540.0800.0800.0000.0000.0000.000
14A31LYS10.7960.88620.881-15.128-15.1280.0000.0000.0000.000
15A32SER0-0.027-0.02717.0860.0080.0080.0000.0000.0000.000
16A33THR0-0.042-0.02419.117-0.266-0.2660.0000.0000.0000.000
17A34ALA00.0400.01715.7700.8940.8940.0000.0000.0000.000
18A35LYS10.7750.87817.635-15.434-15.4340.0000.0000.0000.000
19A36LEU00.0150.01817.5080.7080.7080.0000.0000.0000.000
20A37VAL0-0.030-0.00418.288-0.974-0.9740.0000.0000.0000.000
21A38LYS10.9410.97218.329-17.419-17.4190.0000.0000.0000.000
22A39PRO00.0210.00919.6410.5170.5170.0000.0000.0000.000
23A40ILE00.0460.01515.8270.2100.2100.0000.0000.0000.000
24A41GLN0-0.036-0.02117.802-1.363-1.3630.0000.0000.0000.000
25A42TYR0-0.036-0.03917.2600.8060.8060.0000.0000.0000.000
26A43ASP-1-0.872-0.92619.30213.08313.0830.0000.0000.0000.000
27A44GLU-1-1.013-0.99017.33815.81215.8120.0000.0000.0000.000
28A45VAL0-0.056-0.03416.8860.5460.5460.0000.0000.0000.000
29A46ILE0-0.0140.00211.0850.6120.6120.0000.0000.0000.000
30A47GLU-1-0.813-0.89312.15117.43617.4360.0000.0000.0000.000
31A48VAL0-0.046-0.0419.7352.4152.4150.0000.0000.0000.000
32A49GLU-1-0.823-0.9067.49122.50322.5030.0000.0000.0000.000
33A50ARG10.8720.9446.103-29.237-29.2370.0000.0000.0000.000
34A51ILE00.0310.0179.7070.5160.5160.0000.0000.0000.000
35A52PHE0-0.040-0.0169.836-0.702-0.7020.0000.0000.0000.000
36A53ALA00.0720.0287.9641.7901.7900.0000.0000.0000.000
37A54ASP-1-0.867-0.8996.27525.10125.1010.0000.0000.0000.000
38A55PRO00.047-0.0089.1560.1170.1170.0000.0000.0000.000
39A56ALA00.0100.0149.570-0.628-0.6280.0000.0000.0000.000
40A57PHE00.0720.0457.585-0.825-0.8250.0000.0000.0000.000
41A58ILE0-0.013-0.0129.697-0.643-0.6430.0000.0000.0000.000
42A59GLU-1-0.766-0.86312.77013.65813.6580.0000.0000.0000.000
43A60GLN0-0.0220.00410.6980.2250.2250.0000.0000.0000.000
44A61HIS00.0320.02310.517-2.268-2.2680.0000.0000.0000.000
45A62ARG10.8480.89014.879-14.438-14.4380.0000.0000.0000.000
46A63GLN0-0.033-0.03117.521-1.202-1.2020.0000.0000.0000.000
47A64ARG10.8920.95815.532-18.506-18.5060.0000.0000.0000.000
48A65ILE0-0.060-0.02918.531-0.584-0.5840.0000.0000.0000.000
49A66LEU0-0.005-0.00921.032-0.657-0.6570.0000.0000.0000.000
50A67ALA0-0.0110.00722.240-0.589-0.5890.0000.0000.0000.000
51A68SER0-0.034-0.01423.498-0.093-0.0930.0000.0000.0000.000
52A69PHE0-0.011-0.02723.807-0.396-0.3960.0000.0000.0000.000
53A70LYS10.9240.96026.902-9.693-9.6930.0000.0000.0000.000
54A71ASP-1-0.885-0.93028.0849.4319.4310.0000.0000.0000.000
55A72ALA0-0.046-0.00525.319-0.189-0.1890.0000.0000.0000.000
56A73LYS10.9620.97827.026-9.718-9.7180.0000.0000.0000.000
57A74GLU-1-0.762-0.87924.11911.91811.9180.0000.0000.0000.000
58A75SER0-0.022-0.03324.5020.2500.2500.0000.0000.0000.000
59A76ALA0-0.068-0.02325.0230.1910.1910.0000.0000.0000.000
60A77LEU00.0660.03920.8720.5300.5300.0000.0000.0000.000
61A78TYR0-0.025-0.02419.9570.5680.5680.0000.0000.0000.000
62A79HIS00.0240.04219.7190.4540.4540.0000.0000.0000.000
63A80GLU-1-0.860-0.93418.38616.42216.4220.0000.0000.0000.000
64A81LEU0-0.015-0.03315.3770.8760.8760.0000.0000.0000.000
65A82THR0-0.025-0.03015.0710.9770.9770.0000.0000.0000.000
66A83HIS0-0.074-0.05415.4640.5760.5760.0000.0000.0000.000
67A84ILE0-0.053-0.01911.7101.1041.1040.0000.0000.0000.000
68A85VAL00.0210.01410.6031.8841.8840.0000.0000.0000.000
69A86ILE00.0010.00610.5921.5811.5810.0000.0000.0000.000
70A87LYS10.8480.91311.792-19.133-19.1330.0000.0000.0000.000
71A88ASP-1-0.844-0.9276.74936.72836.7280.0000.0000.0000.000
72A89ASN00.010-0.0017.1345.2665.2660.0000.0000.0000.000
73A90LEU0-0.038-0.0248.2161.5801.5800.0000.0000.0000.000
74A91PHE0-0.016-0.0257.923-0.571-0.5710.0000.0000.0000.000
75A92SER00.0040.0093.1774.9275.3990.017-0.189-0.3000.000
76A93CYS0-0.0140.0025.5634.8634.977-0.001-0.004-0.1090.000
77A94ALA00.0210.0137.585-1.404-1.4040.0000.0000.0000.000
78A95MET0-0.0250.0086.198-3.858-3.8580.0000.0000.0000.000
79A96ASN0-0.063-0.0542.448-9.244-7.2860.655-1.084-1.5300.018
80A97ALA00.0090.0296.546-2.744-2.7440.0000.0000.0000.000
81A98ILE00.007-0.00810.318-2.159-2.1590.0000.0000.0000.000
82A99VAL0-0.027-0.0177.414-2.586-2.5860.0000.0000.0000.000
83A100GLY00.0160.01110.201-0.977-0.9770.0000.0000.0000.000
84A101TYR0-0.088-0.03412.275-2.616-2.6160.0000.0000.0000.000
85A102PHE0-0.004-0.02113.565-1.567-1.5670.0000.0000.0000.000
86A103GLU-1-0.854-0.89214.82915.82615.8260.0000.0000.0000.000
87A104PHE00.003-0.01311.7560.0550.0550.0000.0000.0000.000
88A105ASN0-0.038-0.01415.769-0.310-0.3100.0000.0000.0000.000
89A106ILE00.008-0.00913.201-0.118-0.1180.0000.0000.0000.000
90A107ASP-1-0.765-0.88016.73814.37414.3740.0000.0000.0000.000
91A108GLU-1-0.796-0.88818.68614.84614.8460.0000.0000.0000.000
92A109ALA00.0240.01019.5260.4570.4570.0000.0000.0000.000
93A110GLU-1-0.814-0.88817.40017.21417.2140.0000.0000.0000.000
94A111LEU00.0250.01712.6010.6490.6490.0000.0000.0000.000
95A112LYS10.8150.87715.702-13.988-13.9880.0000.0000.0000.000
96A113ASN0-0.033-0.01618.294-0.282-0.2820.0000.0000.0000.000
97A114VAL0-0.0180.00112.476-0.197-0.1970.0000.0000.0000.000
98A115MET00.0040.01113.4170.7640.7640.0000.0000.0000.000
99A116GLU-1-0.881-0.93515.12314.70514.7050.0000.0000.0000.000
100A117GLY0-0.116-0.04917.151-0.490-0.4900.0000.0000.0000.000
101A118LEU00.0300.02010.9420.1460.1460.0000.0000.0000.000
102A119LYS10.8580.94614.529-18.759-18.7590.0000.0000.0000.000
103A120ARG10.8630.91017.060-16.029-16.0290.0000.0000.0000.000
104A121ASP-1-0.919-0.93914.28620.56020.5600.0000.0000.0000.000
105A122VAL0-0.011-0.02215.9930.5330.5330.0000.0000.0000.000
106A123ILE0-0.051-0.03012.8110.0510.0510.0000.0000.0000.000
107A124GLN00.0310.03211.3081.2711.2710.0000.0000.0000.000
108A125GLY00.0420.0198.199-0.675-0.6750.0000.0000.0000.000
109A126ALA00.0110.0529.2520.0490.0490.0000.0000.0000.000
110A127GLU-1-0.976-0.99111.26818.92718.9270.0000.0000.0000.000
111A128ASP-1-0.845-0.95013.82018.16318.1630.0000.0000.0000.000
112A129ASN0-0.010-0.00912.1262.4572.4570.0000.0000.0000.000
113A130THR00.008-0.0208.6411.3521.3520.0000.0000.0000.000
114A131VAL00.0450.0248.8143.7803.7800.0000.0000.0000.000
115A132GLN0-0.016-0.02610.625-0.368-0.3680.0000.0000.0000.000
116A133ALA0-0.0110.0077.1120.7250.7250.0000.0000.0000.000
117A134ILE00.016-0.0055.1223.8713.8710.0000.0000.0000.000
118A135ALA00.003-0.0057.1550.2740.2740.0000.0000.0000.000
119A136GLU-1-0.880-0.9559.30327.81127.8110.0000.0000.0000.000
120A137LYS10.7810.8771.829-143.964-153.91526.761-9.560-7.2510.118
121A138ILE0-0.0200.0026.995-1.816-1.8160.0000.0000.0000.000
122A139ILE00.0070.0039.278-2.070-2.0700.0000.0000.0000.000
123A140LYS10.8870.9508.632-34.232-34.2320.0000.0000.0000.000
124A141LYS10.8890.9608.208-35.345-35.3450.0000.0000.0000.000
125A142ALA0-0.0100.00810.456-2.512-2.5120.0000.0000.0000.000
126A143LEU0-0.033-0.03313.762-1.662-1.6620.0000.0000.0000.000
127A144VAL00.0010.00211.660-1.555-1.5550.0000.0000.0000.000
128A145PHE00.000-0.01312.145-1.225-1.2250.0000.0000.0000.000
129A146ASN0-0.032-0.01815.693-1.689-1.6890.0000.0000.0000.000
130A147HIS0-0.027-0.00917.436-1.365-1.3650.0000.0000.0000.000
131A148LEU00.0370.00315.033-1.005-1.0050.0000.0000.0000.000
132A149GLN00.0630.04219.105-1.300-1.3000.0000.0000.0000.000
133A150LYS10.9110.96721.159-14.318-14.3180.0000.0000.0000.000
134A151GLU-1-0.845-0.89321.05414.88914.8890.0000.0000.0000.000
135A152TRP0-0.063-0.06615.701-0.638-0.6380.0000.0000.0000.000
136A153LYS10.8300.93523.243-12.440-12.4400.0000.0000.0000.000
137A154VAL0-0.026-0.01421.502-0.114-0.1140.0000.0000.0000.000
138A155GLU-1-0.854-0.92024.22412.41412.4140.0000.0000.0000.000
139A156ILE0-0.064-0.01722.495-0.187-0.1870.0000.0000.0000.000
140A157THR00.0590.02026.255-0.103-0.1030.0000.0000.0000.000
141A158ASP-1-0.788-0.90529.58410.30810.3080.0000.0000.0000.000
142A159GLU-1-0.895-0.94431.7519.3239.3230.0000.0000.0000.000
143A160VAL00.0120.01326.597-0.033-0.0330.0000.0000.0000.000
144A161VAL00.0350.02026.7050.0790.0790.0000.0000.0000.000
145A162LYS10.8990.94628.730-9.199-9.1990.0000.0000.0000.000
146A163ASN0-0.0030.00431.176-0.282-0.2820.0000.0000.0000.000
147A164VAL00.0100.00825.297-0.034-0.0340.0000.0000.0000.000
148A165ILE0-0.010-0.00928.5720.0260.0260.0000.0000.0000.000
149A166SER0-0.033-0.02529.908-0.238-0.2380.0000.0000.0000.000
150A167LEU00.0260.00829.943-0.107-0.1070.0000.0000.0000.000
151A168TYR0-0.066-0.02627.3700.0930.0930.0000.0000.0000.000
152A169TYR0-0.043-0.02129.803-0.105-0.1050.0000.0000.0000.000
153A170GLU-1-0.962-0.97033.1828.7998.7990.0000.0000.0000.000
154A171LYS10.8870.96426.249-11.544-11.5440.0000.0000.0000.000
155A172THR0-0.046-0.02229.3740.0780.0780.0000.0000.0000.000
156A173ASN0-0.027-0.02431.853-0.461-0.4610.0000.0000.0000.000
157A174GLN0-0.0060.00329.285-0.063-0.0630.0000.0000.0000.000
158A175SER00.0280.00233.668-0.025-0.0250.0000.0000.0000.000
159A176VAL00.0800.04530.4480.2330.2330.0000.0000.0000.000
160A177ARG10.8130.88832.570-8.130-8.1300.0000.0000.0000.000
161A178GLU-1-0.842-0.92532.0329.8969.8960.0000.0000.0000.000
162A179TYR00.002-0.01626.1250.2340.2340.0000.0000.0000.000
163A180LEU0-0.064-0.02431.1100.0920.0920.0000.0000.0000.000
164A181ASP-1-0.826-0.89533.6308.4418.4410.0000.0000.0000.000
165A182ASP-1-0.780-0.88432.4489.5589.5580.0000.0000.0000.000
166A183LYS10.8560.91630.649-10.079-10.0790.0000.0000.0000.000
167A184GLN00.0050.00628.7350.3340.3340.0000.0000.0000.000
168A185LYS10.8160.90227.333-9.717-9.7170.0000.0000.0000.000
169A186PHE0-0.0350.00327.0390.4390.4390.0000.0000.0000.000
170A187GLU-1-0.775-0.86026.29911.53311.5330.0000.0000.0000.000
171A188GLY00.0220.00823.7420.5690.5690.0000.0000.0000.000
172A189VAL0-0.019-0.02322.5690.7150.7150.0000.0000.0000.000
173A190ARG10.7380.83123.210-11.100-11.1000.0000.0000.0000.000
174A191THR0-0.0070.00018.7120.4360.4360.0000.0000.0000.000
175A192ALA00.0340.02318.3060.7330.7330.0000.0000.0000.000
176A193LEU0-0.034-0.01818.5490.6170.6170.0000.0000.0000.000
177A194LEU0-0.008-0.01019.3930.2220.2220.0000.0000.0000.000
178A195GLU-1-0.839-0.91612.04325.83725.8370.0000.0000.0000.000
179A196GLU-1-0.802-0.90715.10420.93320.9330.0000.0000.0000.000
180A197ARG10.8250.90716.920-14.072-14.0720.0000.0000.0000.000
181A198MET00.0250.02515.686-0.233-0.2330.0000.0000.0000.000
182A199VAL00.0300.03611.8750.5290.5290.0000.0000.0000.000
183A200LEU0-0.022-0.01614.385-0.010-0.0100.0000.0000.0000.000
184A201GLU-1-0.862-0.92617.20214.15514.1550.0000.0000.0000.000
185A202THR0-0.018-0.02611.931-0.060-0.0600.0000.0000.0000.000
186A203ILE0-0.036-0.01412.843-0.292-0.2920.0000.0000.0000.000
187A204ASN0-0.051-0.01815.293-0.838-0.8380.0000.0000.0000.000
188A205HIS10.8040.91317.625-16.650-16.6500.0000.0000.0000.000
189A206PHE00.0640.03214.7120.2510.2510.0000.0000.0000.000
190A207LYS10.8360.92717.540-14.541-14.5410.0000.0000.0000.000
191A208PHE00.011-0.00411.8600.6750.6750.0000.0000.0000.000
192A209HIS0-0.069-0.04515.303-2.082-2.0820.0000.0000.0000.000
193A210PHE0-0.016-0.01613.4491.2041.2040.0000.0000.0000.000
194A211ASN0-0.009-0.00212.781-2.401-2.4010.0000.0000.0000.000
195A212LEU0-0.033-0.01814.2460.2630.2630.0000.0000.0000.000
196A213THR0-0.079-0.04316.563-0.513-0.5130.0000.0000.0000.000
197A214GLY00.0300.00418.390-0.293-0.2930.0000.0000.0000.000
198A215GLN0-0.0020.02414.3421.2771.2770.0000.0000.0000.000