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: M37JZ

Calculation Name: 4ZG0-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4ZG0

Chain ID: A

ChEMBL ID:

UniProt ID: Q8VHN8

Base Structure: X-ray

Registration Date: 2023-06-20

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 197
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2172216.837985
FMO2-HF: Nuclear repulsion 2095094.714961
FMO2-HF: Total energy -77122.123023
FMO2-MP2: Total energy -77346.476009


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:8:GLU)


Summations of interaction energy for fragment #1(A:8: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.
-145.851-151.82126.177-11.844-8.3630.085
Interaction energy analysis for fragmet #1(A:8:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.910 / q_NPA : -0.943
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].
3A10LYS10.9300.9663.572-25.455-23.8990.003-0.760-0.8000.002
4A11GLN00.0370.0195.195-6.904-6.9040.0000.0000.0000.000
5A12ILE0-0.069-0.0377.261-1.893-1.8930.0000.0000.0000.000
6A13SER00.008-0.02210.8770.5700.5700.0000.0000.0000.000
7A14ARG10.8300.88413.628-17.041-17.0410.0000.0000.0000.000
8A15GLU-1-0.762-0.86316.14916.57716.5770.0000.0000.0000.000
9A16GLU-1-0.894-0.91815.22617.36017.3600.0000.0000.0000.000
10A17ALA00.012-0.00714.660-0.513-0.5130.0000.0000.0000.000
11A18MET0-0.038-0.02816.480-0.668-0.6680.0000.0000.0000.000
12A19ARG10.8390.90018.481-16.518-16.5180.0000.0000.0000.000
13A20LEU0-0.074-0.00815.274-0.556-0.5560.0000.0000.0000.000
14A21GLY00.0480.02419.943-0.388-0.3880.0000.0000.0000.000
15A22PRO00.015-0.01222.2410.5090.5090.0000.0000.0000.000
16A23GLY0-0.0210.00722.857-0.132-0.1320.0000.0000.0000.000
17A24TRP00.0130.00813.7240.4180.4180.0000.0000.0000.000
18A25SER0-0.003-0.00918.181-0.403-0.4030.0000.0000.0000.000
19A26HIS00.0560.02417.5161.3521.3520.0000.0000.0000.000
20A27SER00.0010.00215.200-0.657-0.6570.0000.0000.0000.000
21A28CYS0-0.057-0.00416.2861.0781.0780.0000.0000.0000.000
22A29HIS0-0.020-0.00914.845-0.631-0.6310.0000.0000.0000.000
23A30ALA00.0480.01716.8060.5240.5240.0000.0000.0000.000
24A31MET0-0.0210.00214.5990.2370.2370.0000.0000.0000.000
25A32LEU00.0260.01417.224-0.308-0.3080.0000.0000.0000.000
26A33TYR00.017-0.01318.1900.0690.0690.0000.0000.0000.000
27A34ALA00.0410.03221.243-0.565-0.5650.0000.0000.0000.000
28A35ALA00.0480.02423.1060.5260.5260.0000.0000.0000.000
29A36ASN0-0.036-0.04124.734-0.911-0.9110.0000.0000.0000.000
30A37PRO00.0260.01526.5540.2640.2640.0000.0000.0000.000
31A38GLY00.0430.03529.039-0.351-0.3510.0000.0000.0000.000
32A39GLN00.002-0.01628.5580.4780.4780.0000.0000.0000.000
33A40LEU00.0310.02426.580-0.387-0.3870.0000.0000.0000.000
34A41PHE00.028-0.00129.715-0.096-0.0960.0000.0000.0000.000
35A42GLY00.0110.00932.918-0.289-0.2890.0000.0000.0000.000
36A43ARG10.8620.92331.515-9.364-9.3640.0000.0000.0000.000
37A44ILE0-0.0010.00524.9520.1320.1320.0000.0000.0000.000
38A45PRO00.0120.01225.4310.0180.0180.0000.0000.0000.000
39A46MET0-0.037-0.01924.4280.5650.5650.0000.0000.0000.000
40A47ARG10.8710.94418.152-16.146-16.1460.0000.0000.0000.000
41A48PHE00.0410.01019.839-0.051-0.0510.0000.0000.0000.000
42A49SER0-0.064-0.03022.003-0.608-0.6080.0000.0000.0000.000
43A50VAL00.0430.02116.699-0.140-0.1400.0000.0000.0000.000
44A51LEU00.0020.01620.127-0.104-0.1040.0000.0000.0000.000
45A52MET0-0.046-0.02013.7201.2281.2280.0000.0000.0000.000
46A53GLN00.0310.01019.211-1.220-1.2200.0000.0000.0000.000
47A54MET0-0.0070.01419.8410.9820.9820.0000.0000.0000.000
48A55ARG10.8260.89517.924-16.390-16.3900.0000.0000.0000.000
49A56PHE00.0530.01921.844-0.033-0.0330.0000.0000.0000.000
50A57ASP-1-0.825-0.88619.34915.08815.0880.0000.0000.0000.000
51A58GLY00.0040.00521.2480.1210.1210.0000.0000.0000.000
52A59LEU0-0.068-0.02415.3030.5860.5860.0000.0000.0000.000
53A60LEU00.014-0.00416.354-0.477-0.4770.0000.0000.0000.000
54A61GLY0-0.001-0.02215.0761.3851.3850.0000.0000.0000.000
55A62PHE00.0160.00412.092-0.854-0.8540.0000.0000.0000.000
56A63PRO00.0470.03016.884-0.116-0.1160.0000.0000.0000.000
57A64GLY00.017-0.00418.9520.7150.7150.0000.0000.0000.000
58A65GLY00.0250.01919.339-0.376-0.3760.0000.0000.0000.000
59A66PHE0-0.003-0.01118.0390.4590.4590.0000.0000.0000.000
60A67VAL0-0.059-0.02120.769-0.687-0.6870.0000.0000.0000.000
61A68ASP-1-0.785-0.87022.62511.77411.7740.0000.0000.0000.000
62A69ARG10.9130.94021.499-14.278-14.2780.0000.0000.0000.000
63A70ARG10.8130.89425.568-11.082-11.0820.0000.0000.0000.000
64A71PHE0-0.042-0.01928.551-0.402-0.4020.0000.0000.0000.000
65A72TRP00.0280.01526.401-0.151-0.1510.0000.0000.0000.000
66A73SER00.0350.00925.7900.4410.4410.0000.0000.0000.000
67A74LEU00.033-0.00418.852-0.011-0.0110.0000.0000.0000.000
68A75GLU-1-0.710-0.82021.66714.87714.8770.0000.0000.0000.000
69A76ASP-1-0.806-0.87123.76411.13111.1310.0000.0000.0000.000
70A77GLY0-0.014-0.00924.572-0.290-0.2900.0000.0000.0000.000
71A78LEU0-0.0070.00419.555-0.081-0.0810.0000.0000.0000.000
72A79ASN0-0.049-0.05823.110-0.239-0.2390.0000.0000.0000.000
73A80ARG10.9050.97825.843-12.068-12.0680.0000.0000.0000.000
74A81VAL0-0.0120.00022.840-0.333-0.3330.0000.0000.0000.000
75A82LEU0-0.011-0.02122.141-0.180-0.1800.0000.0000.0000.000
76A83GLY0-0.0080.00026.019-0.251-0.2510.0000.0000.0000.000
77A84LEU0-0.077-0.04129.305-0.417-0.4170.0000.0000.0000.000
78A85GLY00.1160.05227.816-0.396-0.3960.0000.0000.0000.000
79A86LEU0-0.092-0.03524.0590.3120.3120.0000.0000.0000.000
80A87GLY00.0770.06027.646-0.487-0.4870.0000.0000.0000.000
81A88GLY0-0.022-0.00727.4280.5030.5030.0000.0000.0000.000
82A89LEU0-0.028-0.02227.094-0.356-0.3560.0000.0000.0000.000
83A90ARG10.8340.89926.705-10.491-10.4910.0000.0000.0000.000
84A91LEU00.0110.02520.7950.0230.0230.0000.0000.0000.000
85A92THR0-0.049-0.05123.399-0.589-0.5890.0000.0000.0000.000
86A93GLU-1-0.813-0.90621.44815.54315.5430.0000.0000.0000.000
87A94ALA00.0460.02320.6240.7660.7660.0000.0000.0000.000
88A95ASP-1-0.781-0.83420.09014.30814.3080.0000.0000.0000.000
89A96TYR0-0.004-0.02013.8131.1991.1990.0000.0000.0000.000
90A97LEU0-0.032-0.01712.0320.2970.2970.0000.0000.0000.000
91A98SER0-0.012-0.0039.2962.4222.4220.0000.0000.0000.000
92A99SER00.001-0.00310.795-1.863-1.8630.0000.0000.0000.000
93A100HIS0-0.0010.0035.6984.0074.0070.0000.0000.0000.000
94A101LEU0-0.023-0.0059.183-2.741-2.7410.0000.0000.0000.000
95A102THR0-0.033-0.0288.2312.7492.7490.0000.0000.0000.000
96A103GLU-1-0.860-0.9096.39829.96529.9650.0000.0000.0000.000
97A104GLY0-0.0040.0208.812-1.177-1.1770.0000.0000.0000.000
98A105PRO00.005-0.01712.2030.4090.4090.0000.0000.0000.000
99A106HIS00.0040.00015.2490.2490.2490.0000.0000.0000.000
100A107ARG10.9070.95414.564-13.511-13.5110.0000.0000.0000.000
101A108VAL00.0140.02213.867-1.162-1.1620.0000.0000.0000.000
102A109VAL0-0.0190.00013.0461.6011.6010.0000.0000.0000.000
103A110ALA00.0170.00710.812-1.422-1.4220.0000.0000.0000.000
104A111HIS00.020-0.00311.8663.0503.0500.0000.0000.0000.000
105A112LEU0-0.056-0.02110.526-0.367-0.3670.0000.0000.0000.000
106A113TYR0-0.006-0.03713.8580.1590.1590.0000.0000.0000.000
107A114ALA0-0.032-0.02215.4580.6090.6090.0000.0000.0000.000
108A115ARG10.8130.89117.526-13.690-13.6900.0000.0000.0000.000
109A116GLN0-0.0090.00720.9500.2410.2410.0000.0000.0000.000
110A117LEU0-0.015-0.00622.556-0.517-0.5170.0000.0000.0000.000
111A118THR00.0480.00726.0160.2140.2140.0000.0000.0000.000
112A119LEU00.010-0.01326.8020.1750.1750.0000.0000.0000.000
113A120GLU-1-0.941-0.95828.8249.4319.4310.0000.0000.0000.000
114A121GLN00.0550.02129.1410.3020.3020.0000.0000.0000.000
115A122LEU0-0.026-0.00823.2870.0690.0690.0000.0000.0000.000
116A123HIS0-0.034-0.03427.399-0.185-0.1850.0000.0000.0000.000
117A124ALA00.0210.01130.328-0.160-0.1600.0000.0000.0000.000
118A125VAL0-0.0090.00425.662-0.118-0.1180.0000.0000.0000.000
119A126GLU-1-0.756-0.82926.92711.92311.9230.0000.0000.0000.000
120A127ILE0-0.003-0.00329.168-0.186-0.1860.0000.0000.0000.000
121A128SER0-0.076-0.04730.539-0.201-0.2010.0000.0000.0000.000
122A129ALA00.025-0.00228.032-0.149-0.1490.0000.0000.0000.000
123A130VAL0-0.031-0.01030.008-0.012-0.0120.0000.0000.0000.000
124A131HIS0-0.036-0.00532.347-0.380-0.3800.0000.0000.0000.000
125A132SER0-0.077-0.04329.180-0.250-0.2500.0000.0000.0000.000
126A133ARG10.8830.93232.028-9.531-9.5310.0000.0000.0000.000
127A134ASP-1-0.829-0.91026.72211.41311.4130.0000.0000.0000.000
128A135HIS0-0.054-0.01228.9820.4870.4870.0000.0000.0000.000
129A136GLY0-0.007-0.00329.643-0.414-0.4140.0000.0000.0000.000
130A137LEU0-0.056-0.02329.897-0.234-0.2340.0000.0000.0000.000
131A138GLU-1-0.902-0.95925.13811.22111.2210.0000.0000.0000.000
132A139VAL0-0.046-0.03123.7150.8010.8010.0000.0000.0000.000
133A140LEU00.0130.00925.218-0.483-0.4830.0000.0000.0000.000
134A141GLY00.0340.01925.695-0.398-0.3980.0000.0000.0000.000
135A142LEU0-0.023-0.00823.7800.6660.6660.0000.0000.0000.000
136A143VAL0-0.010-0.01120.769-0.386-0.3860.0000.0000.0000.000
137A144ARG10.8190.87121.926-11.605-11.6050.0000.0000.0000.000
138A145VAL0-0.015-0.00716.462-0.079-0.0790.0000.0000.0000.000
139A146PRO0-0.056-0.00519.691-0.345-0.3450.0000.0000.0000.000
140A147LEU00.049-0.00115.9730.8220.8220.0000.0000.0000.000
141A148TYR00.0290.03318.9340.3420.3420.0000.0000.0000.000
142A149THR0-0.035-0.03919.1380.9320.9320.0000.0000.0000.000
143A150GLN0-0.043-0.01521.513-0.362-0.3620.0000.0000.0000.000
144A151LYS10.9770.97124.028-10.278-10.2780.0000.0000.0000.000
145A152ASP-1-0.781-0.87224.85212.75912.7590.0000.0000.0000.000
146A153ARG10.9420.96721.012-13.574-13.5740.0000.0000.0000.000
147A154VAL00.0450.03420.4200.8820.8820.0000.0000.0000.000
148A155GLY00.0000.00120.9540.4010.4010.0000.0000.0000.000
149A156GLY00.018-0.00921.8950.2070.2070.0000.0000.0000.000
150A157PHE00.0230.00612.5810.2520.2520.0000.0000.0000.000
151A158PRO00.0180.01316.0370.8610.8610.0000.0000.0000.000
152A159ASN00.0340.02416.7740.4370.4370.0000.0000.0000.000
153A160PHE00.0410.02515.8110.0660.0660.0000.0000.0000.000
154A161LEU00.0120.00011.4870.6450.6450.0000.0000.0000.000
155A162SER0-0.062-0.03713.3910.6890.6890.0000.0000.0000.000
156A163ASN0-0.0250.00415.933-0.539-0.5390.0000.0000.0000.000
157A164ALA00.0410.03314.8071.1321.1320.0000.0000.0000.000
158A165PHE0-0.016-0.02012.134-0.040-0.0400.0000.0000.0000.000
159A166VAL00.0430.03211.9350.1510.1510.0000.0000.0000.000
160A167SER0-0.006-0.0207.4200.4860.4860.0000.0000.0000.000
161A168THR00.0340.0057.7823.7983.7980.0000.0000.0000.000
162A169ALA00.0160.0228.5102.1372.1370.0000.0000.0000.000
163A170LYS10.9300.9728.591-25.688-25.6880.0000.0000.0000.000
164A171TYR0-0.036-0.0521.568-36.617-44.46126.176-11.041-7.2910.083
165A172GLN00.024-0.0046.1771.2271.2270.0000.0000.0000.000
166A173LEU00.0060.0068.620-1.054-1.0540.0000.0000.0000.000
167A174LEU0-0.028-0.0177.030-1.543-1.5430.0000.0000.0000.000
168A175PHE0-0.016-0.0044.317-1.474-1.214-0.001-0.042-0.2160.000
169A176ALA00.0320.0086.974-3.038-3.0380.0000.0000.0000.000
170A177LEU0-0.003-0.02010.654-2.113-2.1130.0000.0000.0000.000
171A178LYS10.9260.9774.987-57.755-57.697-0.001-0.001-0.0560.000
172A179VAL00.0170.0129.480-2.286-2.2860.0000.0000.0000.000
173A180LEU0-0.023-0.01511.187-2.346-2.3460.0000.0000.0000.000
174A181ASN0-0.058-0.02513.583-1.732-1.7320.0000.0000.0000.000
175A182MET0-0.0070.02914.939-1.012-1.0120.0000.0000.0000.000
176A183MET0-0.048-0.01713.026-2.051-2.0510.0000.0000.0000.000
177A184PRO00.0600.03312.7541.8731.8730.0000.0000.0000.000
178A185SER00.0470.0038.0502.5542.5540.0000.0000.0000.000
179A186GLU-1-0.927-0.9469.73722.93322.9330.0000.0000.0000.000
180A187LYS10.8630.89912.336-18.054-18.0540.0000.0000.0000.000
181A188LEU0-0.039-0.0139.028-0.559-0.5590.0000.0000.0000.000
182A189ALA00.0170.0179.1560.4740.4740.0000.0000.0000.000
183A190GLU-1-0.814-0.89110.39017.44817.4480.0000.0000.0000.000
184A191ALA00.0030.00513.645-1.017-1.0170.0000.0000.0000.000
185A192LEU00.0440.0177.096-0.978-0.9780.0000.0000.0000.000
186A193ALA0-0.0050.01611.740-0.766-0.7660.0000.0000.0000.000
187A194SER0-0.038-0.03413.229-1.293-1.2930.0000.0000.0000.000
188A195ALA00.0020.00013.314-0.934-0.9340.0000.0000.0000.000
189A196THR0-0.014-0.02611.100-0.490-0.4900.0000.0000.0000.000
190A197GLU-1-0.854-0.90513.56515.17015.1700.0000.0000.0000.000
191A198LYS10.8890.93316.965-16.039-16.0390.0000.0000.0000.000
192A199GLN0-0.051-0.04713.3760.0810.0810.0000.0000.0000.000
193A200LYS10.8280.91314.622-18.157-18.1570.0000.0000.0000.000
194A201LYS10.7750.86018.957-13.505-13.5050.0000.0000.0000.000
195A202ALA0-0.035-0.01320.906-0.543-0.5430.0000.0000.0000.000
196A203LEU0-0.045-0.00319.201-0.215-0.2150.0000.0000.0000.000
197A204GLU-1-0.843-0.89722.57411.76411.7640.0000.0000.0000.000