Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: YV6K2

Calculation Name: 2ZCX-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2ZCX

Chain ID: A

ChEMBL ID:

UniProt ID: Q9FBX0

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 205
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2163615.138964
FMO2-HF: Nuclear repulsion 2085938.608067
FMO2-HF: Total energy -77676.530896
FMO2-MP2: Total energy -77906.019911


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:19:GLN)


Summations of interaction energy for fragment #1(A:19:GLN)
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.
-19.074-14.5978.731-4.827-8.380.026
Interaction energy analysis for fragmet #1(A:19:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.066 / q_NPA : 0.020
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].
3A21LYS10.8780.9373.419-4.440-2.5370.011-0.823-1.0920.002
4A22GLN00.0320.0102.066-10.905-9.2416.382-2.823-5.2220.028
5A23GLN00.0630.0261.983-1.911-1.0012.338-1.181-2.066-0.004
6A24ARG10.8450.9305.7520.2310.2310.0000.0000.0000.000
7A25GLU-1-0.805-0.8997.3641.8521.8520.0000.0000.0000.000
8A26GLU-1-0.928-0.9577.567-1.918-1.9180.0000.0000.0000.000
9A27ALA00.0290.0119.636-0.028-0.0280.0000.0000.0000.000
10A28ILE0-0.052-0.03211.2470.0560.0560.0000.0000.0000.000
11A29LEU0-0.049-0.02211.0550.0240.0240.0000.0000.0000.000
12A30ASP-1-0.789-0.88213.678-0.536-0.5360.0000.0000.0000.000
13A31ALA00.0000.01015.4700.0150.0150.0000.0000.0000.000
14A32ALA0-0.041-0.03217.3860.0160.0160.0000.0000.0000.000
15A33ARG10.8070.87612.6070.1960.1960.0000.0000.0000.000
16A34GLU-1-0.930-0.95119.035-0.247-0.2470.0000.0000.0000.000
17A35LEU0-0.008-0.00621.3820.0180.0180.0000.0000.0000.000
18A36GLY0-0.002-0.02122.7970.0120.0120.0000.0000.0000.000
19A37THR0-0.080-0.05622.863-0.001-0.0010.0000.0000.0000.000
20A38GLU-1-0.912-0.92725.433-0.054-0.0540.0000.0000.0000.000
21A39ARG10.7860.88127.3710.0180.0180.0000.0000.0000.000
22A40GLY00.0140.03528.1660.0090.0090.0000.0000.0000.000
23A41ILE00.0240.00323.5830.0060.0060.0000.0000.0000.000
24A42ARG10.7390.85627.1070.0070.0070.0000.0000.0000.000
25A43GLU-1-0.813-0.90929.7170.0340.0340.0000.0000.0000.000
26A44ILE0-0.0210.01823.5850.0050.0050.0000.0000.0000.000
27A45THR00.002-0.00425.8510.0340.0340.0000.0000.0000.000
28A46LEU00.021-0.01118.990-0.010-0.0100.0000.0000.0000.000
29A47THR0-0.037-0.03621.5090.0170.0170.0000.0000.0000.000
30A48ASP-1-0.777-0.88223.4330.0540.0540.0000.0000.0000.000
31A49ILE00.0200.03317.688-0.016-0.0160.0000.0000.0000.000
32A50ALA0-0.041-0.02418.630-0.014-0.0140.0000.0000.0000.000
33A51ALA0-0.012-0.00919.491-0.010-0.0100.0000.0000.0000.000
34A52THR00.004-0.00719.327-0.023-0.0230.0000.0000.0000.000
35A53VAL0-0.014-0.00214.970-0.036-0.0360.0000.0000.0000.000
36A54GLY00.0300.03515.931-0.005-0.0050.0000.0000.0000.000
37A55MET0-0.107-0.05212.5220.0250.0250.0000.0000.0000.000
38A56HIS00.0740.03617.4480.0070.0070.0000.0000.0000.000
39A57LYS11.0241.00218.347-0.229-0.2290.0000.0000.0000.000
40A58SER0-0.006-0.00619.4940.0260.0260.0000.0000.0000.000
41A59ALA00.0060.00114.6280.0560.0560.0000.0000.0000.000
42A60LEU00.0540.02214.6080.0920.0920.0000.0000.0000.000
43A61LEU0-0.008-0.00415.3500.0560.0560.0000.0000.0000.000
44A62ARG10.8630.94413.210-0.777-0.7770.0000.0000.0000.000
45A63TYR0-0.116-0.0537.7830.1930.1930.0000.0000.0000.000
46A64PHE00.0540.01712.6310.0820.0820.0000.0000.0000.000
47A65GLU-1-0.812-0.87015.9220.4510.4510.0000.0000.0000.000
48A66THR0-0.014-0.02319.434-0.039-0.0390.0000.0000.0000.000
49A67ARG10.8480.90920.002-0.123-0.1230.0000.0000.0000.000
50A68GLU-1-0.825-0.89721.5170.2220.2220.0000.0000.0000.000
51A69GLN00.0180.01317.0120.0050.0050.0000.0000.0000.000
52A70ILE0-0.0140.00316.3150.0310.0310.0000.0000.0000.000
53A71PHE00.0590.01917.841-0.008-0.0080.0000.0000.0000.000
54A72LEU0-0.0110.02619.992-0.029-0.0290.0000.0000.0000.000
55A73LYS10.8890.94510.553-1.258-1.2580.0000.0000.0000.000
56A74ILE00.0160.00516.497-0.035-0.0350.0000.0000.0000.000
57A75THR0-0.020-0.02517.685-0.062-0.0620.0000.0000.0000.000
58A76ALA00.015-0.00316.805-0.033-0.0330.0000.0000.0000.000
59A77GLU-1-0.919-0.94912.5860.2630.2630.0000.0000.0000.000
60A78GLY00.0490.02816.272-0.064-0.0640.0000.0000.0000.000
61A79TRP00.010-0.00719.648-0.028-0.0280.0000.0000.0000.000
62A80LYS10.8650.93413.205-0.216-0.2160.0000.0000.0000.000
63A81GLU-1-0.839-0.87117.410-0.252-0.2520.0000.0000.0000.000
64A82TRP00.0370.00418.802-0.011-0.0110.0000.0000.0000.000
65A83SER0-0.014-0.02620.908-0.011-0.0110.0000.0000.0000.000
66A84ALA0-0.0090.00018.883-0.006-0.0060.0000.0000.0000.000
67A85GLU-1-0.757-0.84621.024-0.220-0.2200.0000.0000.0000.000
68A86LEU0-0.036-0.00923.5200.0000.0000.0000.0000.0000.000
69A87CYS0-0.034-0.03323.8810.0110.0110.0000.0000.0000.000
70A88ALA0-0.030-0.00923.5340.0000.0000.0000.0000.0000.000
71A89ARG10.8380.88725.5890.1900.1900.0000.0000.0000.000
72A90LEU00.006-0.00128.8220.0070.0070.0000.0000.0000.000
73A91ARG10.8200.90923.5070.1530.1530.0000.0000.0000.000
74A92GLU-1-0.905-0.95329.339-0.167-0.1670.0000.0000.0000.000
75A93LEU0-0.050-0.01432.3520.0050.0050.0000.0000.0000.000
76A94PRO0-0.030-0.01535.0550.0040.0040.0000.0000.0000.000
77A95GLY00.001-0.00238.0900.0030.0030.0000.0000.0000.000
78A96ALA0-0.002-0.00938.8550.0050.0050.0000.0000.0000.000
79A97ALA00.0000.00639.6180.0020.0020.0000.0000.0000.000
80A98PRO00.0600.02239.481-0.004-0.0040.0000.0000.0000.000
81A99ASP-1-0.795-0.90539.281-0.042-0.0420.0000.0000.0000.000
82A100ALA0-0.0360.00137.965-0.004-0.0040.0000.0000.0000.000
83A101VAL00.0450.02334.119-0.007-0.0070.0000.0000.0000.000
84A102GLY00.0130.00834.656-0.001-0.0010.0000.0000.0000.000
85A103GLN0-0.036-0.03035.100-0.003-0.0030.0000.0000.0000.000
86A104VAL00.0180.01730.813-0.006-0.0060.0000.0000.0000.000
87A105PHE00.0310.01230.931-0.006-0.0060.0000.0000.0000.000
88A106ALA0-0.021-0.00831.2500.0000.0000.0000.0000.0000.000
89A107ALA00.0320.01732.3140.0000.0000.0000.0000.0000.000
90A108THR0-0.066-0.03927.063-0.005-0.0050.0000.0000.0000.000
91A109LEU0-0.0040.00927.342-0.005-0.0050.0000.0000.0000.000
92A110ALA0-0.008-0.01129.0920.0010.0010.0000.0000.0000.000
93A111ALA0-0.004-0.00628.1350.0010.0010.0000.0000.0000.000
94A112ARG10.7010.80422.4050.1650.1650.0000.0000.0000.000
95A113PRO00.0690.03726.5270.0200.0200.0000.0000.0000.000
96A114LEU00.0420.02421.0410.0200.0200.0000.0000.0000.000
97A115PHE00.0120.00222.7720.0220.0220.0000.0000.0000.000
98A116CYS0-0.039-0.00624.4310.0250.0250.0000.0000.0000.000
99A117ASP-1-0.788-0.88727.4950.0170.0170.0000.0000.0000.000
100A118LEU0-0.070-0.02521.4170.0200.0200.0000.0000.0000.000
101A119LEU0-0.040-0.01825.5620.0280.0280.0000.0000.0000.000
102A120ALA0-0.017-0.00727.3880.0120.0120.0000.0000.0000.000
103A121GLN00.0300.02427.3420.0210.0210.0000.0000.0000.000
104A122ALA0-0.0050.00025.1490.0200.0200.0000.0000.0000.000
105A123PRO0-0.008-0.01726.4710.0240.0240.0000.0000.0000.000
106A124LEU00.0400.02529.4430.0090.0090.0000.0000.0000.000
107A125ASN0-0.015-0.01624.3660.0130.0130.0000.0000.0000.000
108A126LEU0-0.045-0.03124.9200.0290.0290.0000.0000.0000.000
109A127GLU-1-0.869-0.89925.9600.1630.1630.0000.0000.0000.000
110A128ARG10.8290.87328.949-0.160-0.1600.0000.0000.0000.000
111A129ASN0-0.0290.00026.3680.0100.0100.0000.0000.0000.000
112A130VAL0-0.0130.00021.1560.0240.0240.0000.0000.0000.000
113A131SER0-0.002-0.01720.435-0.003-0.0030.0000.0000.0000.000
114A132VAL00.0370.00322.5230.0130.0130.0000.0000.0000.000
115A133GLU-1-0.808-0.88519.8680.4680.4680.0000.0000.0000.000
116A134SER00.0150.01618.6240.0640.0640.0000.0000.0000.000
117A135VAL00.0200.01719.634-0.018-0.0180.0000.0000.0000.000
118A136ARG10.8440.90622.359-0.417-0.4170.0000.0000.0000.000
119A137SER0-0.014-0.02117.2990.0000.0000.0000.0000.0000.000
120A138PHE00.0250.01019.435-0.028-0.0280.0000.0000.0000.000
121A139LYS10.8610.94120.477-0.237-0.2370.0000.0000.0000.000
122A140ILE00.0380.01620.525-0.032-0.0320.0000.0000.0000.000
123A141ALA00.0170.00518.097-0.031-0.0310.0000.0000.0000.000
124A142THR0-0.040-0.03319.974-0.051-0.0510.0000.0000.0000.000
125A143LEU00.0160.00122.942-0.033-0.0330.0000.0000.0000.000
126A144ASP-1-0.842-0.88820.8240.1180.1180.0000.0000.0000.000
127A145GLU-1-0.792-0.85219.0430.0020.0020.0000.0000.0000.000
128A146VAL0-0.020-0.01122.850-0.026-0.0260.0000.0000.0000.000
129A147GLY00.0260.01925.917-0.014-0.0140.0000.0000.0000.000
130A148ARG10.7410.81819.502-0.059-0.0590.0000.0000.0000.000
131A149ILE00.0240.00424.708-0.015-0.0150.0000.0000.0000.000
132A150GLY00.0600.02227.454-0.007-0.0070.0000.0000.0000.000
133A151ALA0-0.066-0.02928.352-0.001-0.0010.0000.0000.0000.000
134A152GLU-1-0.748-0.84828.014-0.099-0.0990.0000.0000.0000.000
135A153LEU0-0.0070.00130.886-0.002-0.0020.0000.0000.0000.000
136A154ARG10.8140.89230.873-0.027-0.0270.0000.0000.0000.000
137A155ARG10.7850.89931.2960.0840.0840.0000.0000.0000.000
138A156LEU0-0.066-0.03832.751-0.003-0.0030.0000.0000.0000.000
139A157LEU0-0.029-0.02536.476-0.002-0.0020.0000.0000.0000.000
140A158GLY00.0060.02038.5540.0030.0030.0000.0000.0000.000
141A159VAL0-0.0230.00136.6710.0040.0040.0000.0000.0000.000
142A160ASP-1-0.757-0.87838.1350.0330.0330.0000.0000.0000.000
143A161GLU-1-0.902-0.93133.5140.0590.0590.0000.0000.0000.000
144A162THR0-0.052-0.04835.0750.0060.0060.0000.0000.0000.000
145A163GLN00.0690.02836.820-0.003-0.0030.0000.0000.0000.000
146A164ALA0-0.024-0.00233.114-0.004-0.0040.0000.0000.0000.000
147A165VAL0-0.015-0.01431.608-0.001-0.0010.0000.0000.0000.000
148A166ASP-1-0.871-0.93633.4690.0400.0400.0000.0000.0000.000
149A167VAL0-0.0220.00034.039-0.002-0.0020.0000.0000.0000.000
150A168ILE00.0100.00928.592-0.005-0.0050.0000.0000.0000.000
151A169ALA00.0030.01831.3460.0000.0000.0000.0000.0000.000
152A170THR0-0.020-0.01232.7180.0010.0010.0000.0000.0000.000
153A171ALA0-0.019-0.01232.228-0.003-0.0030.0000.0000.0000.000
154A172THR0-0.021-0.03227.874-0.001-0.0010.0000.0000.0000.000
155A173SER0-0.014-0.01830.6570.0030.0030.0000.0000.0000.000
156A174LEU0-0.034-0.00833.049-0.001-0.0010.0000.0000.0000.000
157A175ALA00.0180.00531.199-0.004-0.0040.0000.0000.0000.000
158A176GLY00.0490.02231.063-0.005-0.0050.0000.0000.0000.000
159A177ALA00.007-0.00231.812-0.002-0.0020.0000.0000.0000.000
160A178LEU0-0.043-0.03435.478-0.003-0.0030.0000.0000.0000.000
161A179TRP00.0390.00531.114-0.003-0.0030.0000.0000.0000.000
162A180GLN0-0.043-0.01231.4530.0040.0040.0000.0000.0000.000
163A181MET0-0.062-0.03135.335-0.001-0.0010.0000.0000.0000.000
164A182ALA0-0.0130.00535.830-0.002-0.0020.0000.0000.0000.000
165A183THR0-0.055-0.03633.133-0.005-0.0050.0000.0000.0000.000
166A184PRO00.0100.01336.4040.0040.0040.0000.0000.0000.000
167A185GLY00.0310.01337.9070.0040.0040.0000.0000.0000.000
168A186PRO00.012-0.00837.716-0.002-0.0020.0000.0000.0000.000
169A187HIS00.0560.03640.298-0.006-0.0060.0000.0000.0000.000
170A188ILE00.0250.01642.2560.0000.0000.0000.0000.0000.000
171A189GLN00.0520.03537.419-0.003-0.0030.0000.0000.0000.000
172A190THR0-0.040-0.02842.634-0.004-0.0040.0000.0000.0000.000
173A191LEU0-0.013-0.00545.5260.0000.0000.0000.0000.0000.000
174A192TYR00.011-0.00942.6950.0010.0010.0000.0000.0000.000
175A193ARG10.8360.91840.5500.0440.0440.0000.0000.0000.000
176A194SER0-0.070-0.02447.894-0.001-0.0010.0000.0000.0000.000
177A195ASP-1-0.767-0.85951.008-0.009-0.0090.0000.0000.0000.000
178A196PRO00.019-0.00452.0890.0000.0000.0000.0000.0000.000
179A197ARG10.8030.87353.7980.0070.0070.0000.0000.0000.000
180A198LEU0-0.024-0.00749.0350.0020.0020.0000.0000.0000.000
181A199ALA00.0440.03248.478-0.001-0.0010.0000.0000.0000.000
182A200HIS0-0.003-0.01247.618-0.003-0.0030.0000.0000.0000.000
183A201ALA0-0.024-0.00445.3680.0010.0010.0000.0000.0000.000
184A202VAL0-0.0080.00843.1600.0000.0000.0000.0000.0000.000
185A203VAL0-0.069-0.03838.6630.0000.0000.0000.0000.0000.000
186A204GLU-1-0.831-0.91739.014-0.059-0.0590.0000.0000.0000.000
187A205VAL00.0180.00433.7670.0020.0020.0000.0000.0000.000
188A206GLU-1-0.808-0.90834.956-0.088-0.0880.0000.0000.0000.000
189A207PRO00.0180.00336.7640.0040.0040.0000.0000.0000.000
190A208ARG10.8410.93639.8310.0240.0240.0000.0000.0000.000
191A209LEU00.0290.02433.2480.0040.0040.0000.0000.0000.000
192A210ASN00.0460.00937.9230.0050.0050.0000.0000.0000.000
193A211ARG10.8830.93038.7880.0400.0400.0000.0000.0000.000
194A212VAL0-0.0070.00940.0370.0030.0030.0000.0000.0000.000
195A213LEU00.0150.00834.7450.0040.0040.0000.0000.0000.000
196A214GLY00.0510.02438.9960.0010.0010.0000.0000.0000.000
197A215ALA0-0.049-0.02341.2770.0020.0020.0000.0000.0000.000
198A216LEU0-0.022-0.00538.4510.0020.0020.0000.0000.0000.000
199A217LEU00.012-0.00136.7010.0030.0030.0000.0000.0000.000
200A218ARG10.8480.91741.1160.0320.0320.0000.0000.0000.000
201A219GLY00.0020.00744.7590.0010.0010.0000.0000.0000.000
202A220ILE0-0.038-0.00440.1280.0040.0040.0000.0000.0000.000
203A221ALA00.0150.01543.1750.0010.0010.0000.0000.0000.000
204A222ASP-1-0.973-0.97644.786-0.021-0.0210.0000.0000.0000.000
205A223GLY0-0.117-0.07546.1480.0040.0040.0000.0000.0000.000