FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37478

Number of unique PDB entries: 7783

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FMODB ID: GNZZ1

Calculation Name: 1WYZ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1WYZ

Chain ID: A

ChEMBL ID:

UniProt ID: Q8A031

Base Structure: X-ray

Registration Date: 2023-06-19

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 226
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2613909.680425
FMO2-HF: Nuclear repulsion 2525250.724441
FMO2-HF: Total energy -88658.955984
FMO2-MP2: Total energy -88918.938089


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:2:GLU)


Summations of interaction energy for fragment #1(A:2:GLU)
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.
-60.797-58.89719.936-12.091-9.7440.074
Interaction energy analysis for fragmet #1(A:2:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.890 / q_NPA : -0.928
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].
3A4ALA0-0.036-0.0413.804-6.487-4.835-0.005-0.680-0.9670.003
4A5LEU00.0340.0125.4371.7341.7340.0000.0000.0000.000
5A6TYR00.002-0.0401.656-36.330-39.55719.835-9.932-6.6770.061
6A7LEU0-0.059-0.0368.054-2.303-2.3030.0000.0000.0000.000
7A8LEU0-0.001-0.0188.3060.4530.4530.0000.0000.0000.000
8A9PRO0-0.0230.01512.172-1.490-1.4900.0000.0000.0000.000
9A10VAL00.0290.00615.3240.7360.7360.0000.0000.0000.000
10A11THR0-0.028-0.02117.9600.0120.0120.0000.0000.0000.000
11A12LEU0-0.023-0.01521.224-0.244-0.2440.0000.0000.0000.000
12A13GLY00.029-0.00524.245-0.511-0.5110.0000.0000.0000.000
13A14ASP-1-1.008-0.98225.14711.81511.8150.0000.0000.0000.000
14A15THR0-0.020-0.00424.387-0.175-0.1750.0000.0000.0000.000
15A16PRO0-0.0050.00123.6970.4000.4000.0000.0000.0000.000
16A17LEU00.0680.01416.9320.2490.2490.0000.0000.0000.000
17A18GLU-1-0.923-0.96918.91215.69715.6970.0000.0000.0000.000
18A19GLN0-0.066-0.03219.950-0.089-0.0890.0000.0000.0000.000
19A20VAL0-0.034-0.03420.023-0.229-0.2290.0000.0000.0000.000
20A21LEU0-0.0180.00015.1650.5870.5870.0000.0000.0000.000
21A22PRO00.0010.00913.083-0.290-0.2900.0000.0000.0000.000
22A23SER00.0580.01513.2460.7690.7690.0000.0000.0000.000
23A24TYR0-0.0080.0064.884-1.308-1.199-0.001-0.005-0.1030.000
24A25ASN00.014-0.0128.3595.5055.5050.0000.0000.0000.000
25A26THR00.0230.0109.0481.7181.7180.0000.0000.0000.000
26A27GLU-1-0.967-0.9856.66334.70834.7080.0000.0000.0000.000
27A28ILE00.0300.0193.6070.3041.4320.022-0.426-0.7240.003
28A29ILE0-0.033-0.0095.144-0.128-0.139-0.001-0.0020.0140.000
29A30ARG10.8190.8828.031-27.923-27.9230.0000.0000.0000.000
30A31GLY0-0.0240.0085.162-1.964-1.896-0.001-0.003-0.0630.000
31A32ILE0-0.085-0.0364.955-2.963-2.870-0.001-0.003-0.0890.000
32A33ARG10.9690.9877.367-30.405-30.4050.0000.0000.0000.000
33A34HIS00.0200.01210.293-1.103-1.1030.0000.0000.0000.000
34A35PHE00.0420.01110.2181.7641.7640.0000.0000.0000.000
35A36ILE0-0.0190.00213.223-1.663-1.6630.0000.0000.0000.000
36A37VAL0-0.013-0.02415.7260.4790.4790.0000.0000.0000.000
37A38GLU-1-0.804-0.89218.15014.34114.3410.0000.0000.0000.000
38A39ASP-1-0.754-0.89220.88812.06612.0660.0000.0000.0000.000
39A40VAL0-0.0090.00620.1230.4590.4590.0000.0000.0000.000
40A41ARG10.8860.94721.358-11.175-11.1750.0000.0000.0000.000
41A42SER0-0.007-0.00822.3600.3660.3660.0000.0000.0000.000
42A43ALA00.0680.04117.4000.4400.4400.0000.0000.0000.000
43A44ARG10.8740.94417.894-14.383-14.3830.0000.0000.0000.000
44A45ARG10.8840.92819.223-12.090-12.0900.0000.0000.0000.000
45A46PHE00.0650.03314.0900.0150.0150.0000.0000.0000.000
46A47LEU00.0270.01012.8700.3480.3480.0000.0000.0000.000
47A48LYS10.7440.87216.090-17.060-17.0600.0000.0000.0000.000
48A49LYN0-0.0040.01719.018-0.140-0.1400.0000.0000.0000.000
49A50VAL0-0.0360.00012.6450.1590.1590.0000.0000.0000.000
50A51ASP-1-0.796-0.89214.01022.26422.2640.0000.0000.0000.000
51A52ARG10.9450.97716.103-15.831-15.8310.0000.0000.0000.000
52A53GLU-1-0.901-0.95615.79115.87215.8720.0000.0000.0000.000
53A54ILE0-0.050-0.00811.5730.1460.1460.0000.0000.0000.000
54A55ASP-1-0.809-0.90315.34615.04215.0420.0000.0000.0000.000
55A56ILE0-0.060-0.02716.9180.4530.4530.0000.0000.0000.000
56A57ASP-1-0.898-0.94718.47313.58113.5810.0000.0000.0000.000
57A58SER0-0.034-0.01014.716-0.054-0.0540.0000.0000.0000.000
58A59LEU0-0.069-0.05916.2700.8110.8110.0000.0000.0000.000
59A60THR0-0.0050.00314.967-0.316-0.3160.0000.0000.0000.000
60A61PHE0-0.036-0.01316.2060.3980.3980.0000.0000.0000.000
61A62TYR00.0190.00915.521-0.892-0.8920.0000.0000.0000.000
62A63PRO0-0.014-0.01118.9870.3870.3870.0000.0000.0000.000
63A64LEU0-0.0040.02119.252-0.213-0.2130.0000.0000.0000.000
64A65ASN00.0320.00122.038-0.433-0.4330.0000.0000.0000.000
65A66LYS10.9660.96124.605-10.511-10.5110.0000.0000.0000.000
66A67HIS0-0.013-0.00926.668-0.324-0.3240.0000.0000.0000.000
67A68THR0-0.0090.02323.017-0.243-0.2430.0000.0000.0000.000
68A69SER00.0640.03925.6670.0420.0420.0000.0000.0000.000
69A70PRO00.009-0.02823.1070.5340.5340.0000.0000.0000.000
70A71GLU-1-0.937-0.96922.55112.70612.7060.0000.0000.0000.000
71A72ASP-1-0.858-0.94223.21412.36412.3640.0000.0000.0000.000
72A73ILE0-0.023-0.01018.4320.7130.7130.0000.0000.0000.000
73A74SER00.0250.02218.7291.2881.2880.0000.0000.0000.000
74A75GLY0-0.045-0.03018.4840.6560.6560.0000.0000.0000.000
75A76TYR0-0.040-0.03817.3900.4730.4730.0000.0000.0000.000
76A77LEU00.0250.00813.8251.2961.2960.0000.0000.0000.000
77A78LYS10.9340.98113.750-13.225-13.2250.0000.0000.0000.000
78A79PRO00.0290.01411.7580.2720.2720.0000.0000.0000.000
79A80LEU00.0300.0317.7651.0541.0540.0000.0000.0000.000
80A81ALA0-0.094-0.04510.3020.9420.9420.0000.0000.0000.000
81A82GLY0-0.027-0.00912.367-0.600-0.6000.0000.0000.0000.000
82A83GLY0-0.0190.0018.504-0.417-0.4170.0000.0000.0000.000
83A84ALA0-0.051-0.0176.6973.5233.5230.0000.0000.0000.000
84A85SER00.0280.0022.845-8.982-7.0930.090-1.026-0.9530.007
85A86MET0-0.065-0.0115.861-3.500-3.5000.0000.0000.0000.000
86A87GLY00.0330.0197.9243.2263.2260.0000.0000.0000.000
87A88VAL0-0.046-0.0209.874-2.299-2.2990.0000.0000.0000.000
88A89ILE00.0000.00013.2910.7920.7920.0000.0000.0000.000
89A90SER00.019-0.00315.627-0.481-0.4810.0000.0000.0000.000
90A91GLU-1-1.000-0.99819.14713.05413.0540.0000.0000.0000.000
91A99ASP-1-0.876-0.95422.43612.72212.7220.0000.0000.0000.000
92A100PRO0-0.0210.00021.7980.1340.1340.0000.0000.0000.000
93A101GLY00.0700.03018.2780.3710.3710.0000.0000.0000.000
94A102ALA0-0.035-0.02717.4310.8330.8330.0000.0000.0000.000
95A103ASP-1-0.894-0.95519.01113.18413.1840.0000.0000.0000.000
96A104VAL0-0.020-0.01215.1390.0640.0640.0000.0000.0000.000
97A105VAL00.0040.00713.5770.7000.7000.0000.0000.0000.000
98A106ALA0-0.0060.00515.3900.1640.1640.0000.0000.0000.000
99A107ILE0-0.033-0.00218.036-0.292-0.2920.0000.0000.0000.000
100A108ALA00.0480.01512.572-0.070-0.0700.0000.0000.0000.000
101A109GLN0-0.016-0.01212.3570.2040.2040.0000.0000.0000.000
102A110ARG10.9200.97915.062-12.826-12.8260.0000.0000.0000.000
103A111GLN0-0.058-0.02715.5130.1480.1480.0000.0000.0000.000
104A112LYS10.8800.92812.398-19.063-19.0630.0000.0000.0000.000
105A113LEU00.0260.02810.4491.0751.0750.0000.0000.0000.000
106A114LYS10.9490.9764.142-35.917-35.814-0.001-0.008-0.0930.000
107A115VAL00.0280.0177.5801.4441.4440.0000.0000.0000.000
108A116ILE0-0.040-0.0224.318-1.119-1.023-0.001-0.006-0.0890.000
109A117PRO00.0040.0147.6011.4031.4030.0000.0000.0000.000
110A118LEU00.0130.0157.4280.5830.5830.0000.0000.0000.000
111A119VAL0-0.014-0.01911.355-1.775-1.7750.0000.0000.0000.000
112A120GLY00.0710.02414.7510.8580.8580.0000.0000.0000.000
113A121PRO0-0.0160.02317.261-0.628-0.6280.0000.0000.0000.000
114A122SER00.0610.01820.964-0.176-0.1760.0000.0000.0000.000
115A123SER00.0680.02522.803-0.254-0.2540.0000.0000.0000.000
116A124ILE00.0090.01624.756-0.531-0.5310.0000.0000.0000.000
117A125ILE00.030-0.00121.210-0.437-0.4370.0000.0000.0000.000
118A126LEU00.0300.02123.950-0.321-0.3210.0000.0000.0000.000
119A127SER0-0.008-0.01926.932-0.520-0.5200.0000.0000.0000.000
120A128VAL0-0.025-0.00828.250-0.385-0.3850.0000.0000.0000.000
121A129MET0-0.038-0.01625.607-0.171-0.1710.0000.0000.0000.000
122A130ALA00.0260.02329.877-0.270-0.2700.0000.0000.0000.000
123A131SER0-0.055-0.02532.714-0.390-0.3900.0000.0000.0000.000
124A132GLY00.0270.01933.812-0.333-0.3330.0000.0000.0000.000
125A133PHE0-0.081-0.05534.342-0.325-0.3250.0000.0000.0000.000
126A134ASN0-0.014-0.00932.9420.3900.3900.0000.0000.0000.000
127A135GLY00.1080.04229.5610.1120.1120.0000.0000.0000.000
128A136GLN0-0.065-0.02428.0680.5700.5700.0000.0000.0000.000
129A137SER0-0.002-0.00829.7100.0470.0470.0000.0000.0000.000
130A138PHE0-0.004-0.00424.960-0.368-0.3680.0000.0000.0000.000
131A139ALA00.0280.02229.3640.2400.2400.0000.0000.0000.000
132A140PHE00.0400.01527.016-0.300-0.3000.0000.0000.0000.000
133A141HIS0-0.015-0.03729.607-0.036-0.0360.0000.0000.0000.000
134A142GLY00.0330.03130.411-0.094-0.0940.0000.0000.0000.000
135A143TYR00.0210.02530.797-0.300-0.3000.0000.0000.0000.000
136A144LEU0-0.013-0.01134.374-0.081-0.0810.0000.0000.0000.000
137A145PRO00.000-0.01237.6040.0080.0080.0000.0000.0000.000
138A146ILE00.0470.01938.841-0.138-0.1380.0000.0000.0000.000
139A147GLU-1-0.921-0.95342.1626.7326.7320.0000.0000.0000.000
140A148PRO00.0820.01145.5180.0650.0650.0000.0000.0000.000
141A149GLY00.0270.03247.684-0.047-0.0470.0000.0000.0000.000
142A150GLU-1-0.860-0.95243.1437.0617.0610.0000.0000.0000.000
143A151ARG10.7520.85540.812-7.492-7.4920.0000.0000.0000.000
144A152ALA0-0.0020.00743.5760.0930.0930.0000.0000.0000.000
145A153LYS10.9410.98144.978-6.790-6.7900.0000.0000.0000.000
146A154LYS10.9080.97935.539-8.502-8.5020.0000.0000.0000.000
147A155LEU00.0220.01540.4790.0970.0970.0000.0000.0000.000
148A156LYS10.8490.91242.302-6.542-6.5420.0000.0000.0000.000
149A157THR0-0.011-0.01240.608-0.039-0.0390.0000.0000.0000.000
150A158LEU0-0.036-0.01636.4110.0770.0770.0000.0000.0000.000
151A159GLU-1-0.719-0.83739.5486.9176.9170.0000.0000.0000.000
152A160GLN0-0.041-0.03242.0690.0250.0250.0000.0000.0000.000
153A161ARG10.9020.94035.905-8.509-8.5090.0000.0000.0000.000
154A162VAL0-0.0380.00838.3340.0830.0830.0000.0000.0000.000
155A163TYR0-0.100-0.08439.6050.0220.0220.0000.0000.0000.000
156A164ALA0-0.033-0.00341.082-0.065-0.0650.0000.0000.0000.000
157A165GLU-1-0.802-0.88935.4178.4878.4870.0000.0000.0000.000
158A166SER0-0.038-0.00836.6130.1110.1110.0000.0000.0000.000
159A167GLN00.0060.02532.5760.1850.1850.0000.0000.0000.000
160A168THR0-0.013-0.01532.557-0.316-0.3160.0000.0000.0000.000
161A169GLN0-0.035-0.01633.2170.2590.2590.0000.0000.0000.000
162A170LEU00.006-0.00229.352-0.131-0.1310.0000.0000.0000.000
163A171PHE0-0.009-0.01232.5090.0590.0590.0000.0000.0000.000
164A172ILE00.0220.00929.580-0.053-0.0530.0000.0000.0000.000
165A173GLU-1-0.741-0.89233.5248.0218.0210.0000.0000.0000.000
166A174THR0-0.0210.00935.0540.1930.1930.0000.0000.0000.000
167A175PRO00.045-0.00534.338-0.247-0.2470.0000.0000.0000.000
168A176TYR00.0340.01637.076-0.192-0.1920.0000.0000.0000.000
169A177ARG10.8770.94839.798-7.660-7.6600.0000.0000.0000.000
170A178ASN00.0000.00736.765-0.081-0.0810.0000.0000.0000.000
171A179HIS00.0500.00940.749-0.164-0.1640.0000.0000.0000.000
172A180LYS10.8510.91944.236-6.932-6.9320.0000.0000.0000.000
173A181MET0-0.0270.00639.733-0.065-0.0650.0000.0000.0000.000
174A182ILE00.0160.01842.192-0.062-0.0620.0000.0000.0000.000
175A183GLU-1-0.838-0.90444.2956.2526.2520.0000.0000.0000.000
176A184ASP-1-0.786-0.88844.7366.8496.8490.0000.0000.0000.000
177A185ILE0-0.023-0.01241.008-0.084-0.0840.0000.0000.0000.000
178A186LEU0-0.012-0.01344.921-0.097-0.0970.0000.0000.0000.000
179A187GLN0-0.068-0.03548.068-0.200-0.2000.0000.0000.0000.000
180A188ASN0-0.046-0.03346.831-0.178-0.1780.0000.0000.0000.000
181A189CYS0-0.065-0.00944.4910.0330.0330.0000.0000.0000.000
182A190ARG10.8670.93745.353-6.872-6.8720.0000.0000.0000.000
183A191PRO00.0320.00348.0150.1050.1050.0000.0000.0000.000
184A192GLN00.008-0.02048.5290.1410.1410.0000.0000.0000.000
185A193THR0-0.038-0.00742.7940.0790.0790.0000.0000.0000.000
186A194LYS10.9300.96941.376-7.469-7.4690.0000.0000.0000.000
187A195LEU00.0290.01239.4510.1290.1290.0000.0000.0000.000
188A196CYS0-0.057-0.00136.431-0.030-0.0300.0000.0000.0000.000
189A197ILE00.0080.01337.2090.1310.1310.0000.0000.0000.000
190A198ALA00.0690.02132.824-0.019-0.0190.0000.0000.0000.000
191A199ALA0-0.011-0.02933.5750.1870.1870.0000.0000.0000.000
192A200ASN00.0320.01731.5390.1470.1470.0000.0000.0000.000
193A201ILE00.0070.00627.6500.0710.0710.0000.0000.0000.000
194A202THR0-0.039-0.02524.7590.6200.6200.0000.0000.0000.000
195A203CYS0-0.027-0.01427.8160.2100.2100.0000.0000.0000.000
196A204GLU-1-0.883-0.94229.80710.41610.4160.0000.0000.0000.000
197A205GLY0-0.0150.02132.498-0.323-0.3230.0000.0000.0000.000
198A206GLU-1-0.928-0.98230.62610.25510.2550.0000.0000.0000.000
199A207PHE0-0.026-0.00734.113-0.364-0.3640.0000.0000.0000.000
200A208ILE00.0220.00731.5290.1120.1120.0000.0000.0000.000
201A209GLN00.0310.04436.183-0.202-0.2020.0000.0000.0000.000
202A210THR0-0.005-0.02437.8780.0310.0310.0000.0000.0000.000
203A211ARG10.8230.89340.276-7.232-7.2320.0000.0000.0000.000
204A212THR00.0140.01643.6600.1050.1050.0000.0000.0000.000
205A213VAL00.0460.03445.077-0.032-0.0320.0000.0000.0000.000
206A214LYS10.8560.90447.081-6.148-6.1480.0000.0000.0000.000
207A215ASP-1-0.856-0.92648.5056.2576.2570.0000.0000.0000.000
208A216TRP0-0.049-0.02341.542-0.025-0.0250.0000.0000.0000.000
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