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: QV7NY

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 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 198
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2255079.703797
FMO2-HF: Nuclear repulsion 2174645.958538
FMO2-HF: Total energy -80433.745259
FMO2-MP2: Total energy -80670.43519


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.
-11.025-19.16433.799-13.488-12.170.156
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 : -0.797 / q_NPA : -0.877
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-1-0.805-0.8873.86558.03160.908-0.002-1.214-1.6610.005
4A14ILE0-0.022-0.0104.795-9.364-9.2480.000-0.019-0.0960.000
5A22PHE0-0.050-0.05011.353-0.224-0.2240.0000.0000.0000.000
6A23GLN00.0100.00612.970-1.201-1.2010.0000.0000.0000.000
7A24GLY0-0.043-0.01615.171-1.014-1.0140.0000.0000.0000.000
8A25HIS00.0250.01614.483-0.993-0.9930.0000.0000.0000.000
9A26MET0-0.030-0.02417.837-1.340-1.3400.0000.0000.0000.000
10A27ALA00.0750.03618.0600.9000.9000.0000.0000.0000.000
11A28THR0-0.061-0.03219.609-1.067-1.0670.0000.0000.0000.000
12A29ASN0-0.019-0.00620.3830.3200.3200.0000.0000.0000.000
13A30LEU0-0.034-0.01316.7660.1240.1240.0000.0000.0000.000
14A31LYS10.8130.90121.002-15.055-15.0550.0000.0000.0000.000
15A32SER0-0.034-0.03217.240-0.006-0.0060.0000.0000.0000.000
16A33THR0-0.038-0.01719.267-0.256-0.2560.0000.0000.0000.000
17A34ALA00.0320.00716.0630.9810.9810.0000.0000.0000.000
18A35LYS10.7820.88017.996-15.446-15.4460.0000.0000.0000.000
19A36LEU00.0030.01617.6090.5840.5840.0000.0000.0000.000
20A37VAL0-0.031-0.01618.615-0.965-0.9650.0000.0000.0000.000
21A38LYS10.9370.96717.342-18.188-18.1880.0000.0000.0000.000
22A39PRO00.0090.00919.5210.5500.5500.0000.0000.0000.000
23A40ILE00.0490.02115.8710.1510.1510.0000.0000.0000.000
24A41GLN0-0.025-0.01217.954-1.287-1.2870.0000.0000.0000.000
25A42TYR0-0.025-0.03616.9440.9570.9570.0000.0000.0000.000
26A43ASP-1-0.882-0.94119.24913.19113.1910.0000.0000.0000.000
27A44GLU-1-0.952-0.96416.59616.01416.0140.0000.0000.0000.000
28A45VAL0-0.067-0.02816.5620.3210.3210.0000.0000.0000.000
29A46ILE0-0.026-0.00810.5870.6420.6420.0000.0000.0000.000
30A47GLU-1-0.788-0.88911.88318.05618.0560.0000.0000.0000.000
31A48VAL0-0.025-0.0279.2162.7102.7100.0000.0000.0000.000
32A49GLU-1-0.840-0.9087.32022.80422.8040.0000.0000.0000.000
33A50ARG10.8530.9425.282-30.685-30.6850.0000.0000.0000.000
34A51ILE00.0250.0139.5620.3220.3220.0000.0000.0000.000
35A52PHE0-0.017-0.0089.265-0.895-0.8950.0000.0000.0000.000
36A53ALA00.0570.0227.3342.0132.0130.0000.0000.0000.000
37A54ASP-1-0.829-0.8776.28024.98424.9840.0000.0000.0000.000
38A55PRO00.037-0.0158.931-0.026-0.0260.0000.0000.0000.000
39A56ALA00.0050.0219.820-0.871-0.8710.0000.0000.0000.000
40A57PHE00.0780.0387.245-0.996-0.9960.0000.0000.0000.000
41A58ILE0-0.018-0.0109.344-0.810-0.8100.0000.0000.0000.000
42A59GLU-1-0.766-0.85412.35813.70213.7020.0000.0000.0000.000
43A60GLN0-0.0180.00010.3120.4550.4550.0000.0000.0000.000
44A61HIS00.0180.0169.786-2.388-2.3880.0000.0000.0000.000
45A62ARG10.8400.88614.413-14.462-14.4620.0000.0000.0000.000
46A63GLN0-0.022-0.03117.190-1.153-1.1530.0000.0000.0000.000
47A64ARG10.8280.91614.735-18.758-18.7580.0000.0000.0000.000
48A65ILE0-0.063-0.01918.387-0.680-0.6800.0000.0000.0000.000
49A66LEU00.007-0.00720.668-0.649-0.6490.0000.0000.0000.000
50A67ALA0-0.018-0.00521.597-0.588-0.5880.0000.0000.0000.000
51A68SER0-0.062-0.02923.473-0.056-0.0560.0000.0000.0000.000
52A69PHE00.002-0.02023.367-0.390-0.3900.0000.0000.0000.000
53A70LYS10.8900.93326.281-9.622-9.6220.0000.0000.0000.000
54A71ASP-1-0.833-0.89427.5329.6099.6090.0000.0000.0000.000
55A72ALA0-0.038-0.01625.032-0.229-0.2290.0000.0000.0000.000
56A73LYS10.9520.97626.023-9.695-9.6950.0000.0000.0000.000
57A74GLU-1-0.748-0.86923.48212.11412.1140.0000.0000.0000.000
58A75SER0-0.017-0.02123.8110.2350.2350.0000.0000.0000.000
59A76ALA0-0.067-0.02324.4710.1140.1140.0000.0000.0000.000
60A77LEU00.0190.01720.5710.5720.5720.0000.0000.0000.000
61A78TYR0-0.023-0.04319.4020.6130.6130.0000.0000.0000.000
62A79HIS00.0130.03319.3090.3980.3980.0000.0000.0000.000
63A80GLU-1-0.771-0.88417.47317.08917.0890.0000.0000.0000.000
64A81LEU0-0.015-0.01314.6630.9260.9260.0000.0000.0000.000
65A82THR0-0.008-0.01114.3331.0691.0690.0000.0000.0000.000
66A83HIS0-0.051-0.04215.0090.5360.5360.0000.0000.0000.000
67A84ILE0-0.042-0.01311.3711.0341.0340.0000.0000.0000.000
68A85VAL00.0220.01410.2521.8931.8930.0000.0000.0000.000
69A86ILE0-0.013-0.00110.2751.4951.4950.0000.0000.0000.000
70A87LYS10.8210.88411.790-18.847-18.8470.0000.0000.0000.000
71A88ASP-1-0.865-0.9416.29537.69037.6900.0000.0000.0000.000
72A89ASN0-0.010-0.0106.8275.1745.1740.0000.0000.0000.000
73A90LEU0-0.0030.0097.8951.8511.8510.0000.0000.0000.000
74A91PHE00.013-0.0077.763-0.196-0.1960.0000.0000.0000.000
75A92SER0-0.028-0.0202.9645.7336.9250.070-0.615-0.6470.000
76A93CYS0-0.0130.0035.1205.6245.784-0.001-0.006-0.1520.000
77A94ALA00.0380.0167.098-1.045-1.0450.0000.0000.0000.000
78A95MET0-0.047-0.0136.214-3.936-3.9360.0000.0000.0000.000
79A96ASN0-0.061-0.0561.821-13.709-17.3148.824-2.634-2.5850.037
80A97ALA00.0010.0176.067-3.744-3.7440.0000.0000.0000.000
81A98ILE0-0.011-0.0149.818-2.592-2.5920.0000.0000.0000.000
82A99VAL00.006-0.0067.470-2.933-2.9330.0000.0000.0000.000
83A100GLY00.0170.01710.219-1.691-1.6910.0000.0000.0000.000
84A101TYR0-0.079-0.03612.411-2.825-2.8250.0000.0000.0000.000
85A102PHE0-0.029-0.02013.680-1.792-1.7920.0000.0000.0000.000
86A103GLU-1-0.813-0.87614.74415.90615.9060.0000.0000.0000.000
87A104PHE0-0.004-0.02111.8830.2750.2750.0000.0000.0000.000
88A105ASN0-0.062-0.02516.109-0.186-0.1860.0000.0000.0000.000
89A106ILE00.0360.01113.585-0.259-0.2590.0000.0000.0000.000
90A107ASP-1-0.744-0.87817.24113.97513.9750.0000.0000.0000.000
91A108GLU-1-0.802-0.88618.81914.86314.8630.0000.0000.0000.000
92A109ALA00.0120.00520.1230.2720.2720.0000.0000.0000.000
93A110GLU-1-0.763-0.86717.92816.81216.8120.0000.0000.0000.000
94A111LEU00.0160.01813.2000.6220.6220.0000.0000.0000.000
95A112LYS10.8140.88416.004-13.800-13.8000.0000.0000.0000.000
96A113ASN0-0.022-0.02318.587-0.146-0.1460.0000.0000.0000.000
97A114VAL0-0.0220.00212.758-0.245-0.2450.0000.0000.0000.000
98A115MET00.0020.01113.7660.6630.6630.0000.0000.0000.000
99A116GLU-1-0.865-0.91315.38014.39214.3920.0000.0000.0000.000
100A117GLY0-0.046-0.01817.209-0.472-0.4720.0000.0000.0000.000
101A118LEU00.0130.01111.101-0.018-0.0180.0000.0000.0000.000
102A119LYS10.8350.91714.792-19.068-19.0680.0000.0000.0000.000
103A120ARG10.8310.88917.373-15.301-15.3010.0000.0000.0000.000
104A121ASP-1-0.828-0.91213.92520.79620.7960.0000.0000.0000.000
105A122VAL0-0.052-0.02217.162-0.228-0.2280.0000.0000.0000.000
106A123ILE0-0.063-0.04012.9600.0330.0330.0000.0000.0000.000
107A124GLN0-0.0270.00411.3621.1931.1930.0000.0000.0000.000
108A125GLY00.0200.0038.543-0.640-0.6400.0000.0000.0000.000
109A126ALA00.0210.0559.5270.2400.2400.0000.0000.0000.000
110A127GLU-1-0.978-0.98711.43718.94118.9410.0000.0000.0000.000
111A128ASP-1-0.857-0.95314.18218.21818.2180.0000.0000.0000.000
112A129ASN00.005-0.00712.9342.2182.2180.0000.0000.0000.000
113A130THR00.010-0.0119.0711.0661.0660.0000.0000.0000.000
114A131VAL00.0370.0249.0503.4953.4950.0000.0000.0000.000
115A132GLN0-0.015-0.02611.081-0.451-0.4510.0000.0000.0000.000
116A133ALA0-0.0070.0017.3720.6950.6950.0000.0000.0000.000
117A134ILE00.0140.0045.3364.2454.2450.0000.0000.0000.000
118A135ALA00.0100.0007.323-0.270-0.2700.0000.0000.0000.000
119A136GLU-1-0.864-0.9469.78025.94625.9460.0000.0000.0000.000
120A137LYS10.7730.8801.803-142.483-151.36224.908-9.000-7.0290.114
121A138ILE00.0030.0067.460-2.554-2.5540.0000.0000.0000.000
122A139ILE0-0.013-0.0049.834-2.121-2.1210.0000.0000.0000.000
123A140LYS10.8800.9349.247-32.124-32.1240.0000.0000.0000.000
124A141LYS10.8240.9108.570-34.641-34.6410.0000.0000.0000.000
125A142ALA00.0110.02010.950-2.200-2.2000.0000.0000.0000.000
126A143LEU0-0.062-0.03414.360-1.707-1.7070.0000.0000.0000.000
127A144VAL00.0110.01211.811-1.574-1.5740.0000.0000.0000.000
128A145PHE00.027-0.00411.913-1.283-1.2830.0000.0000.0000.000
129A146ASN0-0.0130.00015.938-1.795-1.7950.0000.0000.0000.000
130A147HIS0-0.055-0.01817.795-1.561-1.5610.0000.0000.0000.000
131A148LEU00.039-0.00114.876-1.006-1.0060.0000.0000.0000.000
132A149GLN00.0200.00819.009-1.254-1.2540.0000.0000.0000.000
133A150LYS10.8620.94421.495-15.013-15.0130.0000.0000.0000.000
134A151GLU-1-0.811-0.87820.39215.26515.2650.0000.0000.0000.000
135A152TRP0-0.015-0.03015.679-0.732-0.7320.0000.0000.0000.000
136A153LYS10.7940.90323.342-12.693-12.6930.0000.0000.0000.000
137A154VAL0-0.018-0.00321.122-0.202-0.2020.0000.0000.0000.000
138A155GLU-1-0.827-0.90623.98712.52012.5200.0000.0000.0000.000
139A156ILE0-0.063-0.02822.302-0.107-0.1070.0000.0000.0000.000
140A157THR00.0440.01426.228-0.115-0.1150.0000.0000.0000.000
141A158ASP-1-0.790-0.89529.56210.35010.3500.0000.0000.0000.000
142A159GLU-1-0.854-0.92531.6309.3199.3190.0000.0000.0000.000
143A160VAL0-0.0030.00826.661-0.065-0.0650.0000.0000.0000.000
144A161VAL00.0250.02326.8190.1380.1380.0000.0000.0000.000
145A162LYS10.8680.91928.911-9.250-9.2500.0000.0000.0000.000
146A163ASN00.0020.01530.840-0.322-0.3220.0000.0000.0000.000
147A164VAL00.0200.01225.313-0.064-0.0640.0000.0000.0000.000
148A165ILE0-0.003-0.00428.6740.0260.0260.0000.0000.0000.000
149A166SER0-0.031-0.02730.175-0.259-0.2590.0000.0000.0000.000
150A167LEU00.0160.00529.881-0.107-0.1070.0000.0000.0000.000
151A168TYR0-0.054-0.02027.5920.0800.0800.0000.0000.0000.000
152A169TYR0-0.039-0.01429.691-0.151-0.1510.0000.0000.0000.000
153A170GLU-1-0.943-0.96533.2118.8858.8850.0000.0000.0000.000
154A171LYS10.8250.94125.275-11.832-11.8320.0000.0000.0000.000
155A172THR0-0.035-0.03729.4890.1810.1810.0000.0000.0000.000
156A173ASN0-0.035-0.02731.930-0.490-0.4900.0000.0000.0000.000
157A174GLN00.0230.02828.836-0.141-0.1410.0000.0000.0000.000
158A175SER00.0420.00733.8180.0260.0260.0000.0000.0000.000
159A176VAL00.0220.01030.5860.0430.0430.0000.0000.0000.000
160A177ARG10.8040.87332.557-8.114-8.1140.0000.0000.0000.000
161A178GLU-1-0.839-0.91831.9269.9269.9260.0000.0000.0000.000
162A179TYR00.012-0.00326.3710.2660.2660.0000.0000.0000.000
163A180LEU0-0.061-0.02931.2220.1350.1350.0000.0000.0000.000
164A181ASP-1-0.826-0.88433.8968.3958.3950.0000.0000.0000.000
165A182ASP-1-0.770-0.86332.5579.5499.5490.0000.0000.0000.000
166A183LYS10.8360.91231.002-9.991-9.9910.0000.0000.0000.000
167A184GLN00.012-0.00728.7430.3100.3100.0000.0000.0000.000
168A185LYS10.7770.88627.316-9.692-9.6920.0000.0000.0000.000
169A186PHE0-0.030-0.00427.0970.4090.4090.0000.0000.0000.000
170A187GLU-1-0.709-0.85026.56111.34711.3470.0000.0000.0000.000
171A188GLY00.0270.03423.3650.6100.6100.0000.0000.0000.000
172A189VAL0-0.005-0.00722.5180.6990.6990.0000.0000.0000.000
173A190ARG10.7280.82723.387-11.046-11.0460.0000.0000.0000.000
174A191THR0-0.017-0.01918.9110.4740.4740.0000.0000.0000.000
175A192ALA00.0040.00818.6020.8770.8770.0000.0000.0000.000
176A193LEU0-0.030-0.01918.5630.7000.7000.0000.0000.0000.000
177A194LEU0-0.0030.00419.1800.2690.2690.0000.0000.0000.000
178A195GLU-1-0.792-0.87711.88426.16526.1650.0000.0000.0000.000
179A196GLU-1-0.782-0.88615.23420.80920.8090.0000.0000.0000.000
180A197ARG10.8220.89716.744-13.862-13.8620.0000.0000.0000.000
181A198MET0-0.0010.00715.788-0.270-0.2700.0000.0000.0000.000
182A199VAL00.0220.02811.6300.7320.7320.0000.0000.0000.000
183A200LEU0-0.010-0.01014.0590.1750.1750.0000.0000.0000.000
184A201GLU-1-0.858-0.92016.94014.32114.3210.0000.0000.0000.000
185A202THR0-0.028-0.03511.743-0.139-0.1390.0000.0000.0000.000
186A203ILE0-0.041-0.01112.755-0.075-0.0750.0000.0000.0000.000
187A204ASN0-0.028-0.01014.945-0.688-0.6880.0000.0000.0000.000
188A205HIS10.8090.91417.259-16.713-16.7130.0000.0000.0000.000
189A206PHE00.0300.01914.468-0.068-0.0680.0000.0000.0000.000
190A207LYS10.8030.90617.059-15.010-15.0100.0000.0000.0000.000
191A208PHE00.003-0.00611.4450.9030.9030.0000.0000.0000.000
192A209HIS0-0.089-0.05314.735-2.186-2.1860.0000.0000.0000.000
193A210PHE00.019-0.00312.9771.3001.3000.0000.0000.0000.000
194A211ASN0-0.015-0.00212.430-2.659-2.6590.0000.0000.0000.000
195A212LEU0-0.030-0.02613.8670.2990.2990.0000.0000.0000.000
196A213THR0-0.118-0.07316.060-1.071-1.0710.0000.0000.0000.000
197A214GLY00.0050.00817.810-0.423-0.4230.0000.0000.0000.000
198A215GLN00.0100.02814.1340.6310.6310.0000.0000.0000.000