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: 5J7NZ

Calculation Name: 2CKZ-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2CKZ

Chain ID: B

ChEMBL ID:

UniProt ID: P35718

Base Structure: X-ray

Registration Date: 2023-09-24

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 181
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1794706.586565
FMO2-HF: Nuclear repulsion 1722006.354428
FMO2-HF: Total energy -72700.232137
FMO2-MP2: Total energy -72911.457982


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(B:1:MET)


Summations of interaction energy for fragment #1(B:1:MET)
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.
-22.706-11.43411.13-7.83-14.571-0.057
Interaction energy analysis for fragmet #1(B:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.003 / q_NPA : 0.015
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].
3B3ILE00.0050.0053.801-0.2091.572-0.021-0.911-0.8480.003
4B4LEU0-0.035-0.0106.3190.2820.2820.0000.0000.0000.000
5B5SER0-0.020-0.01510.099-0.238-0.2380.0000.0000.0000.000
6B6LYS10.9140.96312.7890.0930.0930.0000.0000.0000.000
7B7ILE00.0130.00214.845-0.060-0.0600.0000.0000.0000.000
8B8ALA00.0060.00818.6890.0390.0390.0000.0000.0000.000
9B9ASP-1-0.810-0.89721.944-0.009-0.0090.0000.0000.0000.000
10B10LEU0-0.0310.00123.9720.0160.0160.0000.0000.0000.000
11B11VAL0-0.015-0.00724.6990.0050.0050.0000.0000.0000.000
12B12ARG10.9310.96327.297-0.076-0.0760.0000.0000.0000.000
13B13ILE00.0020.00429.1590.0100.0100.0000.0000.0000.000
14B14PRO0-0.020-0.02731.011-0.010-0.0100.0000.0000.0000.000
15B15PRO00.1000.04934.2860.0070.0070.0000.0000.0000.000
16B16ASP-1-0.932-0.96535.4450.0980.0980.0000.0000.0000.000
17B17GLN0-0.062-0.05930.1070.0210.0210.0000.0000.0000.000
18B18PHE0-0.0140.01833.8320.0070.0070.0000.0000.0000.000
19B19HIS0-0.040-0.01336.0020.0030.0030.0000.0000.0000.000
20B20ARG10.9100.96830.011-0.163-0.1630.0000.0000.0000.000
21B21ASP-1-0.832-0.92029.2650.2020.2020.0000.0000.0000.000
22B22THR00.0690.02029.4210.0070.0070.0000.0000.0000.000
23B23ILE00.0570.02725.203-0.001-0.0010.0000.0000.0000.000
24B24SER0-0.045-0.01325.0860.0180.0180.0000.0000.0000.000
25B25ALA00.011-0.00625.1500.0130.0130.0000.0000.0000.000
26B26ILE0-0.0010.00123.5960.0000.0000.0000.0000.0000.000
27B27THR00.0240.00219.8580.0020.0020.0000.0000.0000.000
28B28HIS0-0.0410.00521.1260.0330.0330.0000.0000.0000.000
29B29GLN0-0.004-0.02422.3310.0100.0100.0000.0000.0000.000
30B30LEU0-0.0060.02219.242-0.015-0.0150.0000.0000.0000.000
31B31ASN00.0560.02416.7740.0330.0330.0000.0000.0000.000
32B32ASN0-0.013-0.00618.7190.0150.0150.0000.0000.0000.000
33B33LYS10.8020.89920.337-0.022-0.0220.0000.0000.0000.000
34B34PHE0-0.053-0.04215.374-0.037-0.0370.0000.0000.0000.000
35B35ALA00.0190.00914.4430.0110.0110.0000.0000.0000.000
36B36ASN0-0.045-0.01812.3380.0260.0260.0000.0000.0000.000
37B37LYS10.9170.97413.413-0.192-0.1920.0000.0000.0000.000
38B38ILE00.0220.00212.2810.0030.0030.0000.0000.0000.000
39B39ILE0-0.0220.00112.5930.0400.0400.0000.0000.0000.000
40B40PRO00.046-0.00214.113-0.114-0.1140.0000.0000.0000.000
41B41ASN00.004-0.01515.603-0.013-0.0130.0000.0000.0000.000
42B42VAL0-0.074-0.02410.923-0.087-0.0870.0000.0000.0000.000
43B43GLY00.0830.0189.185-0.296-0.2960.0000.0000.0000.000
44B44LEU0-0.0010.0347.7850.1590.1590.0000.0000.0000.000
45B45CYS0-0.0470.0138.2750.1160.1160.0000.0000.0000.000
46B46ILE00.0440.0016.6270.1010.1010.0000.0000.0000.000
47B47THR0-0.001-0.01510.536-0.003-0.0030.0000.0000.0000.000
48B48ILE0-0.050-0.01612.962-0.036-0.0360.0000.0000.0000.000
49B49TYR0-0.052-0.01613.0510.1110.1110.0000.0000.0000.000
50B50ASP-1-0.803-0.91414.8780.3920.3920.0000.0000.0000.000
51B51LEU00.0220.00918.447-0.046-0.0460.0000.0000.0000.000
52B52LEU0-0.073-0.03918.1690.0020.0020.0000.0000.0000.000
53B53THR0-0.003-0.01022.222-0.012-0.0120.0000.0000.0000.000
54B54VAL0-0.013-0.00625.618-0.001-0.0010.0000.0000.0000.000
55B55GLU-1-0.926-0.95028.3650.0220.0220.0000.0000.0000.000
56B56GLU-1-0.936-0.97031.6700.0650.0650.0000.0000.0000.000
57B57GLY0-0.015-0.01134.088-0.005-0.0050.0000.0000.0000.000
58B58GLN0-0.0070.01234.920-0.005-0.0050.0000.0000.0000.000
59B59LEU00.031-0.00736.4250.0020.0020.0000.0000.0000.000
60B60LYS10.9390.98835.177-0.026-0.0260.0000.0000.0000.000
61B61PRO0-0.014-0.01639.8020.0030.0030.0000.0000.0000.000
62B62GLY0-0.0140.00041.697-0.001-0.0010.0000.0000.0000.000
63B63ASP-1-0.823-0.89737.0820.0490.0490.0000.0000.0000.000
64B64GLY00.0240.02339.4290.0000.0000.0000.0000.0000.000
65B65SER0-0.094-0.08134.5520.0040.0040.0000.0000.0000.000
66B66SER0-0.0030.01033.858-0.005-0.0050.0000.0000.0000.000
67B67TYR0-0.026-0.03831.8210.0040.0040.0000.0000.0000.000
68B68ILE00.0240.00029.120-0.002-0.0020.0000.0000.0000.000
69B69ASN00.0140.02127.914-0.003-0.0030.0000.0000.0000.000
70B70VAL00.009-0.00522.9380.0110.0110.0000.0000.0000.000
71B71THR0-0.005-0.00121.116-0.025-0.0250.0000.0000.0000.000
72B72PHE0-0.028-0.02616.7490.0300.0300.0000.0000.0000.000
73B73ARG10.9050.95813.603-0.394-0.3940.0000.0000.0000.000
74B74ALA00.005-0.00613.0490.0570.0570.0000.0000.0000.000
75B75VAL00.0520.0237.717-0.130-0.1300.0000.0000.0000.000
76B76VAL0-0.010-0.0137.6860.1170.1170.0000.0000.0000.000
77B77PHE00.004-0.0062.075-1.863-1.2782.937-0.656-2.8660.002
78B78LYS10.8410.9224.0141.7542.001-0.001-0.037-0.2090.000
79B79PRO00.0210.0342.618-2.183-0.6240.448-0.567-1.4400.000
80B80PHE0-0.0030.0143.6831.6722.1430.016-0.052-0.4350.000
81B81LEU00.014-0.0115.799-0.047-0.0470.0000.0000.0000.000
82B82GLY0-0.046-0.0169.1790.2270.2270.0000.0000.0000.000
83B83GLU-1-0.848-0.9362.471-20.661-14.2243.552-4.930-5.059-0.059
84B84ILE00.008-0.0076.5100.4380.4380.0000.0000.0000.000
85B85VAL0-0.0100.0082.305-0.611-0.8332.755-0.453-2.080-0.002
86B86THR0-0.041-0.0353.9181.0151.1680.000-0.030-0.1240.000
87B87GLY00.0080.0084.524-0.109-0.020-0.001-0.011-0.0770.000
88B88TRP0-0.0250.0036.7880.0870.0870.0000.0000.0000.000
89B89ILE00.0360.02510.370-0.047-0.0470.0000.0000.0000.000
90B90SER0-0.002-0.00112.8280.0620.0620.0000.0000.0000.000
91B91LYS10.9350.94914.4190.1860.1860.0000.0000.0000.000
92B92CYS00.0380.05616.801-0.064-0.0640.0000.0000.0000.000
93B93THR0-0.114-0.02119.3170.0440.0440.0000.0000.0000.000
94B94ALA00.0870.02321.392-0.020-0.0200.0000.0000.0000.000
95B95GLU-1-0.890-0.96321.525-0.249-0.2490.0000.0000.0000.000
96B96GLY0-0.030-0.04018.182-0.043-0.0430.0000.0000.0000.000
97B97ILE00.0130.01414.0920.0530.0530.0000.0000.0000.000
98B98LYS10.8940.95812.9430.1530.1530.0000.0000.0000.000
99B99VAL00.0070.0017.3960.0670.0670.0000.0000.0000.000
100B100SER0-0.022-0.0048.5230.0690.0690.0000.0000.0000.000
101B101LEU00.003-0.0142.386-0.575-0.4891.446-0.180-1.352-0.001
102B102LEU00.014-0.0056.0340.5220.5220.0000.0000.0000.000
103B103GLY00.0120.0199.4560.2070.2070.0000.0000.0000.000
104B104ILE0-0.062-0.0185.0770.1090.1090.0000.0000.0000.000
105B105PHE00.027-0.0016.172-0.243-0.2430.0000.0000.0000.000
106B106ASP-1-0.867-0.9448.1180.0240.0240.0000.0000.0000.000
107B107ASP-1-0.972-0.97610.145-0.375-0.3750.0000.0000.0000.000
108B108ILE00.0090.0165.211-0.199-0.1990.0000.0000.0000.000
109B109PHE0-0.053-0.0209.4330.1680.1680.0000.0000.0000.000
110B110ILE00.0140.03210.719-0.144-0.1440.0000.0000.0000.000
111B111PRO0-0.0160.00813.8800.0930.0930.0000.0000.0000.000
112B112GLN00.0980.05017.541-0.048-0.0480.0000.0000.0000.000
113B113ASN0-0.037-0.01119.3140.0020.0020.0000.0000.0000.000
114B114MET0-0.081-0.04614.524-0.028-0.0280.0000.0000.0000.000
115B115LEU0-0.008-0.00416.519-0.049-0.0490.0000.0000.0000.000
116B116PHE00.0540.03417.529-0.014-0.0140.0000.0000.0000.000
117B117GLU-1-0.945-0.97320.898-0.276-0.2760.0000.0000.0000.000
118B118GLY00.0400.02124.3590.0200.0200.0000.0000.0000.000
119B119CYS0-0.111-0.03221.6700.0150.0150.0000.0000.0000.000
120B120TYR00.0000.00223.841-0.004-0.0040.0000.0000.0000.000
121B121TYR00.0100.00422.6900.0040.0040.0000.0000.0000.000
122B122THR00.0340.02125.2130.0120.0120.0000.0000.0000.000
123B123PRO0-0.048-0.03426.5370.0040.0040.0000.0000.0000.000
124B124GLU-1-0.977-0.98228.196-0.084-0.0840.0000.0000.0000.000
125B125GLU-1-0.885-0.95126.591-0.095-0.0950.0000.0000.0000.000
126B126SER0-0.097-0.05622.8140.0060.0060.0000.0000.0000.000
127B127ALA00.0390.02221.653-0.009-0.0090.0000.0000.0000.000
128B128TRP0-0.075-0.04219.797-0.010-0.0100.0000.0000.0000.000
129B129ILE00.0150.01821.661-0.003-0.0030.0000.0000.0000.000
130B130TRP00.019-0.02220.589-0.029-0.0290.0000.0000.0000.000
131B131PRO0-0.038-0.00523.6870.0160.0160.0000.0000.0000.000
132B132MET0-0.007-0.01625.278-0.025-0.0250.0000.0000.0000.000
133B133ASP-1-0.886-0.92928.036-0.149-0.1490.0000.0000.0000.000
134B134GLU-1-0.962-0.98731.795-0.113-0.1130.0000.0000.0000.000
135B135GLU-1-0.980-1.00731.864-0.109-0.1090.0000.0000.0000.000
136B136THR0-0.024-0.00928.3870.0070.0070.0000.0000.0000.000
137B137LYS10.8880.96427.1840.1090.1090.0000.0000.0000.000
138B138LEU00.0100.01821.8860.0150.0150.0000.0000.0000.000
139B139TYR00.032-0.00622.262-0.022-0.0220.0000.0000.0000.000
140B140PHE0-0.062-0.02415.833-0.006-0.0060.0000.0000.0000.000
141B141ASP-1-0.794-0.91918.476-0.113-0.1130.0000.0000.0000.000
142B142VAL0-0.060-0.06217.058-0.024-0.0240.0000.0000.0000.000
143B143ASN0-0.070-0.04214.8450.0380.0380.0000.0000.0000.000
144B144GLU-1-0.879-0.92114.9940.0240.0240.0000.0000.0000.000
145B145LYS10.9090.93910.686-0.373-0.3730.0000.0000.0000.000
146B146ILE00.0120.0119.725-0.004-0.0040.0000.0000.0000.000
147B147ARG10.8880.9588.6910.3570.3570.0000.0000.0000.000
148B148PHE00.043-0.0125.2100.1090.1090.0000.0000.0000.000
149B149ARG11.0040.9957.9340.9280.9280.0000.0000.0000.000
150B150ILE0-0.025-0.0114.5400.1670.253-0.001-0.003-0.0810.000
151B151GLU-1-0.881-0.9598.703-1.076-1.0760.0000.0000.0000.000
152B152ARG10.9080.94511.7680.8550.8550.0000.0000.0000.000
153B153GLU-1-0.863-0.9288.910-1.984-1.9840.0000.0000.0000.000
154B154VAL0-0.035-0.01911.8960.1520.1520.0000.0000.0000.000
155B155PHE0-0.0080.01211.4410.0430.0430.0000.0000.0000.000
156B156VAL0-0.027-0.02116.0760.0320.0320.0000.0000.0000.000
157B157ASP-1-0.954-0.96319.201-0.220-0.2200.0000.0000.0000.000
158B158VAL0-0.025-0.00720.5210.0280.0280.0000.0000.0000.000
159B190LYS10.9570.99718.7520.2430.2430.0000.0000.0000.000
160B191PRO0-0.020-0.02619.7320.0210.0210.0000.0000.0000.000
161B192PRO00.0320.00314.8180.0340.0340.0000.0000.0000.000
162B193ALA00.0290.01016.458-0.047-0.0470.0000.0000.0000.000
163B194TYR0-0.011-0.0167.591-0.096-0.0960.0000.0000.0000.000
164B195ALA00.0150.01710.9630.0880.0880.0000.0000.0000.000
165B196LEU0-0.016-0.0075.767-0.148-0.1480.0000.0000.0000.000
166B197LEU0-0.027-0.0109.8390.1650.1650.0000.0000.0000.000
167B198GLY00.022-0.00110.214-0.263-0.2630.0000.0000.0000.000
168B199SER0-0.014-0.02010.8450.1890.1890.0000.0000.0000.000
169B200CYS0-0.044-0.03412.307-0.064-0.0640.0000.0000.0000.000
170B201GLN0-0.010-0.00214.8080.0320.0320.0000.0000.0000.000
171B202THR0-0.040-0.01315.4820.0090.0090.0000.0000.0000.000
172B203ASP-1-0.858-0.92616.514-0.373-0.3730.0000.0000.0000.000
173B204GLY0-0.017-0.02515.473-0.050-0.0500.0000.0000.0000.000
174B205MET0-0.144-0.06411.326-0.118-0.1180.0000.0000.0000.000
175B206GLY00.0470.01612.9540.0740.0740.0000.0000.0000.000
176B207LEU0-0.0100.01913.156-0.052-0.0520.0000.0000.0000.000
177B208VAL0-0.003-0.01011.345-0.005-0.0050.0000.0000.0000.000
178B209SER0-0.062-0.03114.4190.0100.0100.0000.0000.0000.000
179B210TRP00.0430.01217.452-0.003-0.0030.0000.0000.0000.000
180B211TRP00.0320.03916.484-0.005-0.0050.0000.0000.0000.000
181B212GLU-1-0.999-0.98414.7840.0570.0570.0000.0000.0000.000