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: ZVRNN

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 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 198
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2248461.519715
FMO2-HF: Nuclear repulsion 2168032.042017
FMO2-HF: Total energy -80429.477698
FMO2-MP2: Total energy -80666.320952


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.
36.40938.85112.849-6.936-8.3580.075
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 : -0.896 / q_NPA : -0.976
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-1-0.880-0.9233.24456.29059.3610.319-1.252-2.1380.007
4A14ILE0-0.088-0.0623.867-14.467-14.1490.022-0.158-0.1830.001
5A22PHE0-0.051-0.04910.646-0.045-0.0450.0000.0000.0000.000
6A23GLN00.0240.01112.204-0.658-0.6580.0000.0000.0000.000
7A24GLY0-0.0250.00314.694-0.929-0.9290.0000.0000.0000.000
8A25HIS00.0480.03412.860-1.872-1.8720.0000.0000.0000.000
9A26MET0-0.030-0.02217.301-1.271-1.2710.0000.0000.0000.000
10A27ALA00.1280.04317.3250.8680.8680.0000.0000.0000.000
11A28THR00.7010.80818.081-0.623-0.6230.0000.0000.0000.000
12A29ASN0-0.774-0.81920.473-0.967-0.9670.0000.0000.0000.000
13A30LEU0-0.076-0.04116.5290.0570.0570.0000.0000.0000.000
14A31LYS10.7980.89020.760-15.402-15.4020.0000.0000.0000.000
15A32SER00.0110.01816.7900.0090.0090.0000.0000.0000.000
16A33THR0-0.043-0.01918.671-0.326-0.3260.0000.0000.0000.000
17A34ALA00.0410.01515.8770.9020.9020.0000.0000.0000.000
18A35LYS10.9070.96217.660-14.437-14.4370.0000.0000.0000.000
19A36LEU00.0040.01518.0970.6240.6240.0000.0000.0000.000
20A37VAL0-0.0110.00618.921-0.926-0.9260.0000.0000.0000.000
21A38LYS10.9290.96519.321-16.454-16.4540.0000.0000.0000.000
22A39PRO00.0060.00320.4810.4860.4860.0000.0000.0000.000
23A40ILE00.0500.01217.0720.1820.1820.0000.0000.0000.000
24A41GLN0-0.029-0.01218.837-1.187-1.1870.0000.0000.0000.000
25A42TYR0-0.031-0.01418.5680.7440.7440.0000.0000.0000.000
26A43ASP-1-0.927-0.95719.93312.51612.5160.0000.0000.0000.000
27A44GLU-1-1.044-1.01417.91115.14115.1410.0000.0000.0000.000
28A45VAL0-0.052-0.03516.8410.4730.4730.0000.0000.0000.000
29A46ILE0-0.0200.00211.0850.4880.4880.0000.0000.0000.000
30A47GLU-1-0.851-0.90512.44716.39416.3940.0000.0000.0000.000
31A48VAL0-0.033-0.0329.8441.9871.9870.0000.0000.0000.000
32A49GLU-1-0.834-0.9327.86521.12421.1240.0000.0000.0000.000
33A50ARG10.8770.9485.843-28.567-28.5670.0000.0000.0000.000
34A51ILE00.0460.0229.7300.4650.4650.0000.0000.0000.000
35A52PHE0-0.073-0.0349.529-0.600-0.6000.0000.0000.0000.000
36A53ALA00.0960.0427.7871.6291.6290.0000.0000.0000.000
37A54ASP-1-0.871-0.8726.54128.27628.2760.0000.0000.0000.000
38A55PRO00.043-0.0069.4610.0820.0820.0000.0000.0000.000
39A56ALA00.0040.00710.216-0.704-0.7040.0000.0000.0000.000
40A57PHE00.0800.0568.048-0.835-0.8350.0000.0000.0000.000
41A58ILE00.000-0.01210.134-0.863-0.8630.0000.0000.0000.000
42A59GLU-1-0.737-0.83713.00414.21514.2150.0000.0000.0000.000
43A60GLN0-0.0330.00210.870-0.067-0.0670.0000.0000.0000.000
44A61HIS0-0.004-0.00410.588-2.354-2.3540.0000.0000.0000.000
45A62ARG10.8190.86215.138-15.091-15.0910.0000.0000.0000.000
46A63GLN0-0.022-0.02117.930-1.294-1.2940.0000.0000.0000.000
47A64ARG10.9440.98415.710-19.033-19.0330.0000.0000.0000.000
48A65ILE0-0.038-0.02118.257-0.507-0.5070.0000.0000.0000.000
49A66LEU00.003-0.00721.202-0.689-0.6890.0000.0000.0000.000
50A67ALA0-0.0080.00422.226-0.604-0.6040.0000.0000.0000.000
51A68SER0-0.051-0.01922.977-0.238-0.2380.0000.0000.0000.000
52A69PHE0-0.026-0.02123.538-0.458-0.4580.0000.0000.0000.000
53A70LYS10.9660.97627.062-10.005-10.0050.0000.0000.0000.000
54A71ASP-1-0.914-0.94528.3619.4679.4670.0000.0000.0000.000
55A72ALA0-0.070-0.01325.474-0.182-0.1820.0000.0000.0000.000
56A73LYS10.9700.98327.162-9.791-9.7910.0000.0000.0000.000
57A74GLU-1-0.834-0.93624.10712.01612.0160.0000.0000.0000.000
58A75SER0-0.017-0.03124.4460.2520.2520.0000.0000.0000.000
59A76ALA0-0.079-0.03124.8280.1580.1580.0000.0000.0000.000
60A77LEU00.0810.04520.4670.5080.5080.0000.0000.0000.000
61A78TYR00.0390.03319.8450.4800.4800.0000.0000.0000.000
62A79HIS00.0100.06719.4650.4830.4830.0000.0000.0000.000
63A80GLU-1-0.901-0.95318.56815.80615.8060.0000.0000.0000.000
64A81LEU0-0.013-0.02915.2710.9070.9070.0000.0000.0000.000
65A82THR0-0.033-0.07214.8070.9270.9270.0000.0000.0000.000
66A83HIS0-0.061-0.03515.0020.5530.5530.0000.0000.0000.000
67A84ILE0-0.050-0.01811.4331.0201.0200.0000.0000.0000.000
68A85VAL00.0110.01010.0221.8131.8130.0000.0000.0000.000
69A86ILE00.0010.00310.2321.3521.3520.0000.0000.0000.000
70A87LYS10.8530.92411.612-20.563-20.5630.0000.0000.0000.000
71A88ASP-1-0.849-0.9346.18437.56837.5680.0000.0000.0000.000
72A89ASN00.0110.0066.9704.7254.7250.0000.0000.0000.000
73A90LEU0-0.053-0.0368.0980.8780.8780.0000.0000.0000.000
74A91PHE0-0.014-0.0207.821-0.588-0.5880.0000.0000.0000.000
75A92SER00.0190.0162.9591.2471.7090.033-0.165-0.330-0.001
76A93CYS0-0.034-0.0085.7852.0742.0740.0000.0000.0000.000
77A94ALA00.0300.0227.511-1.161-1.1610.0000.0000.0000.000
78A95MET00.0040.0117.031-3.213-3.2130.0000.0000.0000.000
79A96ASN0-0.022-0.0293.4502.4622.7260.001-0.033-0.2340.000
80A97ALA0-0.0040.0217.635-1.827-1.8270.0000.0000.0000.000
81A98ILE00.004-0.00511.309-1.642-1.6420.0000.0000.0000.000
82A99VAL0-0.031-0.0227.921-1.885-1.8850.0000.0000.0000.000
83A100GLY00.0020.00610.912-0.617-0.6170.0000.0000.0000.000
84A101TYR0-0.085-0.03113.033-2.223-2.2230.0000.0000.0000.000
85A102PHE0-0.010-0.02613.983-1.394-1.3940.0000.0000.0000.000
86A103GLU-1-0.946-0.95615.08115.82715.8270.0000.0000.0000.000
87A104PHE00.001-0.02111.6500.3130.3130.0000.0000.0000.000
88A105ASN0-0.028-0.01215.542-0.185-0.1850.0000.0000.0000.000
89A106ILE00.003-0.00812.749-0.100-0.1000.0000.0000.0000.000
90A107ASP-1-0.779-0.88816.20214.55514.5550.0000.0000.0000.000
91A108GLU-1-0.793-0.88818.38315.15615.1560.0000.0000.0000.000
92A109ALA00.0230.00419.2250.5080.5080.0000.0000.0000.000
93A110GLU-1-0.856-0.94017.37717.91117.9110.0000.0000.0000.000
94A111LEU00.0240.01812.4020.6540.6540.0000.0000.0000.000
95A112LYS10.8320.89215.673-14.193-14.1930.0000.0000.0000.000
96A113ASN0-0.028-0.01818.279-0.252-0.2520.0000.0000.0000.000
97A114VAL0-0.0170.00112.346-0.201-0.2010.0000.0000.0000.000
98A115MET0-0.002-0.00413.4810.5930.5930.0000.0000.0000.000
99A116GLU-1-0.857-0.92115.00415.64815.6480.0000.0000.0000.000
100A117GLY0-0.141-0.06516.821-0.517-0.5170.0000.0000.0000.000
101A118LEU00.0350.01310.5700.1020.1020.0000.0000.0000.000
102A119LYS10.9010.97614.234-19.644-19.6440.0000.0000.0000.000
103A120ARG10.8640.91216.845-16.667-16.6670.0000.0000.0000.000
104A121ASP-1-0.904-0.93314.19821.71721.7170.0000.0000.0000.000
105A122VAL0-0.018-0.02515.9670.6530.6530.0000.0000.0000.000
106A123ILE0-0.043-0.02812.968-0.132-0.1320.0000.0000.0000.000
107A124GLN00.0070.03211.3841.2281.2280.0000.0000.0000.000
108A125GLY00.0450.0228.267-0.794-0.7940.0000.0000.0000.000
109A126ALA00.0200.0539.3420.2460.2460.0000.0000.0000.000
110A127GLU-1-0.995-0.99111.48519.73819.7380.0000.0000.0000.000
111A128ASP-1-0.904-0.98113.82119.00919.0090.0000.0000.0000.000
112A129ASN00.010-0.00811.6352.9462.9460.0000.0000.0000.000
113A130THR0-0.016-0.0298.7181.2501.2500.0000.0000.0000.000
114A131VAL00.0580.0278.8214.1284.1280.0000.0000.0000.000
115A132GLN0-0.033-0.02510.622-0.419-0.4190.0000.0000.0000.000
116A133ALA00.0050.0196.3530.8340.8340.0000.0000.0000.000
117A134ILE00.020-0.0065.4994.1694.1690.0000.0000.0000.000
118A135ALA0-0.001-0.0037.120-0.086-0.0860.0000.0000.0000.000
119A136GLU-1-0.914-0.9828.69029.22929.2290.0000.0000.0000.000
120A137LYS10.8860.9471.989-107.589-109.26212.474-5.328-5.4730.068
121A138ILE0-0.0180.0116.974-2.564-2.5640.0000.0000.0000.000
122A139ILE0-0.002-0.0029.055-2.391-2.3910.0000.0000.0000.000
123A140LYS10.9330.9747.987-34.813-34.8130.0000.0000.0000.000
124A141LYS10.9150.9918.000-35.050-35.0500.0000.0000.0000.000
125A142ALA0-0.0120.00610.294-2.504-2.5040.0000.0000.0000.000
126A143LEU0-0.041-0.03013.548-1.658-1.6580.0000.0000.0000.000
127A144VAL00.0030.00212.256-1.545-1.5450.0000.0000.0000.000
128A145PHE0-0.004-0.01112.249-1.174-1.1740.0000.0000.0000.000
129A146ASN0-0.027-0.01415.623-1.557-1.5570.0000.0000.0000.000
130A147HIS0-0.044-0.02017.916-1.188-1.1880.0000.0000.0000.000
131A148LEU00.0410.00715.854-0.980-0.9800.0000.0000.0000.000
132A149GLN00.0680.03419.542-1.199-1.1990.0000.0000.0000.000
133A150LYS10.8960.96321.210-13.557-13.5570.0000.0000.0000.000
134A151GLU-1-0.949-0.97222.37913.83713.8370.0000.0000.0000.000
135A152TRP0-0.004-0.01816.495-0.530-0.5300.0000.0000.0000.000
136A153LYS10.8760.95023.700-11.619-11.6190.0000.0000.0000.000
137A154VAL0-0.057-0.01721.422-0.093-0.0930.0000.0000.0000.000
138A155GLU-1-0.829-0.90224.03712.46812.4680.0000.0000.0000.000
139A156ILE0-0.068-0.01522.032-0.213-0.2130.0000.0000.0000.000
140A157THR00.0530.01925.807-0.042-0.0420.0000.0000.0000.000
141A158ASP-1-0.821-0.91029.09710.22110.2210.0000.0000.0000.000
142A159GLU-1-0.947-0.97231.2649.3969.3960.0000.0000.0000.000
143A160VAL00.0050.00426.040-0.011-0.0110.0000.0000.0000.000
144A161VAL00.0380.01526.7550.0910.0910.0000.0000.0000.000
145A162LYS10.9630.98028.197-9.157-9.1570.0000.0000.0000.000
146A163ASN00.0040.00630.652-0.194-0.1940.0000.0000.0000.000
147A164VAL00.0200.01724.871-0.016-0.0160.0000.0000.0000.000
148A165ILE0-0.022-0.01427.9920.0510.0510.0000.0000.0000.000
149A166SER0-0.040-0.02729.324-0.227-0.2270.0000.0000.0000.000
150A167LEU00.0220.00629.325-0.112-0.1120.0000.0000.0000.000
151A168TYR0-0.064-0.01726.6790.0320.0320.0000.0000.0000.000
152A169TYR0-0.046-0.03729.196-0.101-0.1010.0000.0000.0000.000
153A170GLU-1-0.964-0.96832.5748.7998.7990.0000.0000.0000.000
154A171LYS10.9150.96726.838-11.215-11.2150.0000.0000.0000.000
155A172THR0-0.038-0.00628.6530.0220.0220.0000.0000.0000.000
156A173ASN00.026-0.00831.465-0.256-0.2560.0000.0000.0000.000
157A174GLN0-0.048-0.01729.0390.0410.0410.0000.0000.0000.000
158A175SER00.019-0.00533.074-0.011-0.0110.0000.0000.0000.000
159A176VAL00.0740.04229.5830.2420.2420.0000.0000.0000.000
160A177ARG10.8700.93931.983-8.227-8.2270.0000.0000.0000.000
161A178GLU-1-0.881-0.95831.5199.9809.9800.0000.0000.0000.000
162A179TYR0-0.024-0.01825.8080.2530.2530.0000.0000.0000.000
163A180LEU0-0.067-0.03330.5560.0850.0850.0000.0000.0000.000
164A181ASP-1-0.938-0.97333.0808.6818.6810.0000.0000.0000.000
165A182ASP-1-0.790-0.90331.7869.4039.4030.0000.0000.0000.000
166A183LYS10.8430.92529.778-10.209-10.2090.0000.0000.0000.000
167A184GLN00.0200.01028.3250.2660.2660.0000.0000.0000.000
168A185LYS10.9440.98426.822-10.283-10.2830.0000.0000.0000.000
169A186PHE0-0.0210.01126.5180.4450.4450.0000.0000.0000.000
170A187GLU-1-0.806-0.89925.82811.72911.7290.0000.0000.0000.000
171A188GLY00.0080.00023.2580.5570.5570.0000.0000.0000.000
172A189VAL0-0.002-0.01322.0570.7430.7430.0000.0000.0000.000
173A190ARG10.7800.85422.679-11.142-11.1420.0000.0000.0000.000
174A191THR00.0030.00918.1730.3940.3940.0000.0000.0000.000
175A192ALA00.0130.00817.7760.6980.6980.0000.0000.0000.000
176A193LEU0-0.032-0.01818.0170.5930.5930.0000.0000.0000.000
177A194LEU00.007-0.00619.0120.1800.1800.0000.0000.0000.000
178A195GLU-1-0.841-0.92611.97624.76224.7620.0000.0000.0000.000
179A196GLU-1-0.817-0.91914.47721.19521.1950.0000.0000.0000.000
180A197ARG10.9100.96016.408-13.642-13.6420.0000.0000.0000.000
181A198MET00.0190.02015.439-0.455-0.4550.0000.0000.0000.000
182A199VAL00.0360.02811.4400.3280.3280.0000.0000.0000.000
183A200LEU0-0.038-0.02614.040-0.121-0.1210.0000.0000.0000.000
184A201GLU-1-0.938-0.98017.00313.94313.9430.0000.0000.0000.000
185A202THR0-0.006-0.00712.455-0.096-0.0960.0000.0000.0000.000
186A203ILE0-0.031-0.01312.629-0.330-0.3300.0000.0000.0000.000
187A204ASN0-0.075-0.03515.252-0.928-0.9280.0000.0000.0000.000
188A205HIS10.8010.91517.856-15.916-15.9160.0000.0000.0000.000
189A206PHE00.0790.03715.4370.2280.2280.0000.0000.0000.000
190A207LYS10.9490.99117.676-13.188-13.1880.0000.0000.0000.000
191A208PHE00.0200.00511.7420.5280.5280.0000.0000.0000.000
192A209HIS0-0.070-0.04715.425-1.839-1.8390.0000.0000.0000.000
193A210PHE0-0.015-0.01913.1591.0441.0440.0000.0000.0000.000
194A211ASN00.0150.02313.365-2.046-2.0460.0000.0000.0000.000
195A212LEU0-0.044-0.02414.5000.3170.3170.0000.0000.0000.000
196A213THR0-0.061-0.03216.746-0.445-0.4450.0000.0000.0000.000
197A214GLY00.022-0.00518.559-0.261-0.2610.0000.0000.0000.000
198A215GLN00.0100.02514.7021.2381.2380.0000.0000.0000.000