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

tag_button

FMODB ID: YV3V2

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 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 181
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1794307.312173
FMO2-HF: Nuclear repulsion 1721605.623339
FMO2-HF: Total energy -72701.688834
FMO2-MP2: Total energy -72912.76384


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.
-22.022-12.15211.185-7.511-13.543-0.051
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 : 0.013
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].
3B3ILE00.0080.0083.8010.0811.803-0.021-0.881-0.8210.003
4B4LEU0-0.026-0.0096.3110.3110.3110.0000.0000.0000.000
5B5SER0-0.013-0.01010.091-0.222-0.2220.0000.0000.0000.000
6B6LYS10.9060.96012.7820.1580.1580.0000.0000.0000.000
7B7ILE00.0150.00014.904-0.052-0.0520.0000.0000.0000.000
8B8ALA00.0120.01318.7800.0390.0390.0000.0000.0000.000
9B9ASP-1-0.799-0.87921.989-0.021-0.0210.0000.0000.0000.000
10B10LEU0-0.0210.00624.0810.0150.0150.0000.0000.0000.000
11B11VAL0-0.010-0.00424.7560.0060.0060.0000.0000.0000.000
12B12ARG10.8670.91827.391-0.067-0.0670.0000.0000.0000.000
13B13ILE00.0070.00629.4220.0110.0110.0000.0000.0000.000
14B14PRO0-0.002-0.01131.124-0.008-0.0080.0000.0000.0000.000
15B15PRO00.0770.04334.3590.0060.0060.0000.0000.0000.000
16B16ASP-1-0.922-0.96535.4420.0930.0930.0000.0000.0000.000
17B17GLN0-0.041-0.04229.5330.0200.0200.0000.0000.0000.000
18B18PHE0-0.0120.00733.8930.0060.0060.0000.0000.0000.000
19B19HIS0-0.038-0.00936.0680.0030.0030.0000.0000.0000.000
20B20ARG10.9060.95830.273-0.153-0.1530.0000.0000.0000.000
21B21ASP-1-0.817-0.90729.0540.1740.1740.0000.0000.0000.000
22B22THR00.0480.02429.4800.0060.0060.0000.0000.0000.000
23B23ILE00.0700.02925.278-0.002-0.0020.0000.0000.0000.000
24B24SER0-0.057-0.03125.1390.0140.0140.0000.0000.0000.000
25B25ALA00.011-0.00925.2070.0130.0130.0000.0000.0000.000
26B26ILE0-0.010-0.00223.7790.0010.0010.0000.0000.0000.000
27B27THR00.0330.00019.9720.0010.0010.0000.0000.0000.000
28B28HIS0-0.0310.01621.1930.0310.0310.0000.0000.0000.000
29B29GLN0-0.006-0.02322.3960.0120.0120.0000.0000.0000.000
30B30LEU00.0030.02219.451-0.012-0.0120.0000.0000.0000.000
31B31ASN00.0340.02116.9110.0370.0370.0000.0000.0000.000
32B32ASN0-0.015-0.00718.7850.0160.0160.0000.0000.0000.000
33B33LYS10.8060.88020.541-0.009-0.0090.0000.0000.0000.000
34B34PHE0-0.031-0.03515.495-0.031-0.0310.0000.0000.0000.000
35B35ALA0-0.0030.00314.4950.0090.0090.0000.0000.0000.000
36B36ASN0-0.039-0.01612.3910.0430.0430.0000.0000.0000.000
37B37LYS10.8950.95613.464-0.203-0.2030.0000.0000.0000.000
38B38ILE0-0.001-0.00712.523-0.014-0.0140.0000.0000.0000.000
39B39ILE0-0.0060.00313.0940.0350.0350.0000.0000.0000.000
40B40PRO00.035-0.00514.225-0.111-0.1110.0000.0000.0000.000
41B41ASN0-0.026-0.01615.635-0.015-0.0150.0000.0000.0000.000
42B42VAL0-0.0270.00611.071-0.081-0.0810.0000.0000.0000.000
43B43GLY00.0930.0299.296-0.296-0.2960.0000.0000.0000.000
44B44LEU0-0.0120.0217.9610.1620.1620.0000.0000.0000.000
45B45CYS0-0.0150.0218.3650.0100.0100.0000.0000.0000.000
46B46ILE00.016-0.0016.5770.1160.1160.0000.0000.0000.000
47B47THR0-0.008-0.02210.5940.0220.0220.0000.0000.0000.000
48B48ILE0-0.052-0.01913.036-0.054-0.0540.0000.0000.0000.000
49B49TYR0-0.051-0.01512.8300.0390.0390.0000.0000.0000.000
50B50ASP-1-0.792-0.89414.9410.2900.2900.0000.0000.0000.000
51B51LEU00.0110.00218.516-0.045-0.0450.0000.0000.0000.000
52B52LEU0-0.049-0.02818.272-0.001-0.0010.0000.0000.0000.000
53B53THR00.004-0.01022.214-0.009-0.0090.0000.0000.0000.000
54B54VAL0-0.036-0.01325.609-0.002-0.0020.0000.0000.0000.000
55B55GLU-1-0.873-0.91528.3630.0020.0020.0000.0000.0000.000
56B56GLU-1-0.933-0.96931.6890.0500.0500.0000.0000.0000.000
57B57GLY0-0.017-0.01334.183-0.005-0.0050.0000.0000.0000.000
58B58GLN00.0030.02035.000-0.002-0.0020.0000.0000.0000.000
59B59LEU00.034-0.00736.5220.0020.0020.0000.0000.0000.000
60B60LYS10.9040.97734.635-0.023-0.0230.0000.0000.0000.000
61B61PRO0-0.007-0.01339.8980.0030.0030.0000.0000.0000.000
62B62GLY0-0.0110.00341.8000.0000.0000.0000.0000.0000.000
63B63ASP-1-0.772-0.87037.2400.0480.0480.0000.0000.0000.000
64B64GLY00.0220.02039.516-0.001-0.0010.0000.0000.0000.000
65B65SER0-0.072-0.05134.6330.0030.0030.0000.0000.0000.000
66B66SER00.0060.00933.824-0.005-0.0050.0000.0000.0000.000
67B67TYR0-0.062-0.05531.8960.0040.0040.0000.0000.0000.000
68B68ILE00.0270.00229.308-0.002-0.0020.0000.0000.0000.000
69B69ASN0-0.0210.00228.038-0.001-0.0010.0000.0000.0000.000
70B70VAL0-0.002-0.01623.0710.0100.0100.0000.0000.0000.000
71B71THR0-0.003-0.00221.005-0.027-0.0270.0000.0000.0000.000
72B72PHE0-0.027-0.02516.9640.0290.0290.0000.0000.0000.000
73B73ARG10.8940.94713.892-0.292-0.2920.0000.0000.0000.000
74B74ALA0-0.006-0.01413.2190.0660.0660.0000.0000.0000.000
75B75VAL00.0430.0227.661-0.140-0.1400.0000.0000.0000.000
76B76VAL0-0.003-0.0117.8510.1410.1410.0000.0000.0000.000
77B77PHE0-0.008-0.0152.789-2.734-2.2742.411-0.719-2.1520.002
78B78LYS10.7600.8534.1302.2522.471-0.001-0.032-0.1860.000
79B79PRO00.0170.0332.598-2.000-0.6030.411-0.497-1.3110.000
80B80PHE0-0.026-0.0143.6921.8092.2730.012-0.073-0.4030.000
81B81LEU0-0.012-0.0215.8100.0040.0040.0000.0000.0000.000
82B82GLY00.0080.0089.1810.1770.1770.0000.0000.0000.000
83B83GLU-1-0.863-0.9302.560-20.445-14.4843.521-4.559-4.922-0.055
84B84ILE00.016-0.0046.3010.4990.4990.0000.0000.0000.000
85B85VAL0-0.0190.0022.231-0.166-1.6834.666-0.534-2.614-0.002
86B86THR0-0.022-0.0203.3300.8111.0630.006-0.044-0.2140.000
87B87GLY00.0030.0004.4670.1910.278-0.001-0.014-0.0730.000
88B88TRP0-0.032-0.0027.030-0.038-0.0380.0000.0000.0000.000
89B89ILE00.0180.02910.740-0.013-0.0130.0000.0000.0000.000
90B90SER00.0000.00113.5530.0290.0290.0000.0000.0000.000
91B91LYS10.9410.95615.1730.0620.0620.0000.0000.0000.000
92B92CYS00.0040.03317.513-0.050-0.0500.0000.0000.0000.000
93B93THR0-0.095-0.05619.7160.0320.0320.0000.0000.0000.000
94B94ALA00.0910.03721.932-0.017-0.0170.0000.0000.0000.000
95B95GLU-1-0.874-0.92621.867-0.180-0.1800.0000.0000.0000.000
96B96GLY0-0.018-0.03118.510-0.042-0.0420.0000.0000.0000.000
97B97ILE00.0010.00914.3250.0490.0490.0000.0000.0000.000
98B98LYS10.8230.91913.8680.0030.0030.0000.0000.0000.000
99B99VAL00.0210.0068.2860.0550.0550.0000.0000.0000.000
100B100SER0-0.0220.0029.5950.0630.0630.0000.0000.0000.000
101B101LEU0-0.014-0.0223.597-0.733-0.0930.183-0.146-0.6760.001
102B102LEU00.005-0.0086.9670.4120.4120.0000.0000.0000.000
103B103GLY00.0230.02410.2300.1780.1780.0000.0000.0000.000
104B104ILE0-0.063-0.0215.450-0.0770.031-0.001-0.009-0.0990.000
105B105PHE00.020-0.0067.368-0.325-0.3250.0000.0000.0000.000
106B106ASP-1-0.844-0.9379.2000.4070.4070.0000.0000.0000.000
107B107ASP-1-0.926-0.94911.244-0.212-0.2120.0000.0000.0000.000
108B108ILE00.0130.0135.945-0.181-0.1810.0000.0000.0000.000
109B109PHE0-0.037-0.01110.1900.1250.1250.0000.0000.0000.000
110B110ILE00.0180.03610.767-0.141-0.1410.0000.0000.0000.000
111B111PRO00.0110.01714.0960.0790.0790.0000.0000.0000.000
112B112GLN00.0850.04317.791-0.044-0.0440.0000.0000.0000.000
113B113ASN0-0.070-0.02518.9740.0150.0150.0000.0000.0000.000
114B114MET0-0.077-0.04715.104-0.041-0.0410.0000.0000.0000.000
115B115LEU0-0.0050.00316.586-0.046-0.0460.0000.0000.0000.000
116B116PHE00.0700.03517.604-0.016-0.0160.0000.0000.0000.000
117B117GLU-1-0.947-0.97220.734-0.252-0.2520.0000.0000.0000.000
118B118GLY00.0370.01824.1740.0170.0170.0000.0000.0000.000
119B119CYS0-0.117-0.03121.6210.0170.0170.0000.0000.0000.000
120B120TYR00.0040.00723.777-0.008-0.0080.0000.0000.0000.000
121B121TYR00.003-0.00423.2110.0040.0040.0000.0000.0000.000
122B122THR00.0160.01525.5320.0020.0020.0000.0000.0000.000
123B123PRO0-0.033-0.02227.0220.0070.0070.0000.0000.0000.000
124B124GLU-1-0.975-0.98228.775-0.049-0.0490.0000.0000.0000.000
125B125GLU-1-0.836-0.92726.987-0.058-0.0580.0000.0000.0000.000
126B126SER0-0.083-0.03523.5430.0100.0100.0000.0000.0000.000
127B127ALA00.0130.00322.0630.0000.0000.0000.0000.0000.000
128B128TRP0-0.059-0.03020.123-0.016-0.0160.0000.0000.0000.000
129B129ILE0-0.0060.00621.837-0.001-0.0010.0000.0000.0000.000
130B130TRP00.026-0.02120.097-0.028-0.0280.0000.0000.0000.000
131B131PRO0-0.0210.00523.6410.0130.0130.0000.0000.0000.000
132B132MET0-0.003-0.01924.923-0.025-0.0250.0000.0000.0000.000
133B133ASP-1-0.907-0.93627.863-0.136-0.1360.0000.0000.0000.000
134B134GLU-1-0.931-0.97731.581-0.093-0.0930.0000.0000.0000.000
135B135GLU-1-0.936-0.93232.051-0.080-0.0800.0000.0000.0000.000
136B136THR0-0.049-0.03327.8020.0070.0070.0000.0000.0000.000
137B137LYS10.8390.90427.0700.0770.0770.0000.0000.0000.000
138B138LEU00.0000.01221.5820.0160.0160.0000.0000.0000.000
139B139TYR00.001-0.03222.267-0.019-0.0190.0000.0000.0000.000
140B140PHE0-0.062-0.02615.805-0.001-0.0010.0000.0000.0000.000
141B141ASP-1-0.802-0.90718.524-0.034-0.0340.0000.0000.0000.000
142B142VAL0-0.040-0.05917.300-0.007-0.0070.0000.0000.0000.000
143B143ASN0-0.090-0.05315.2030.0400.0400.0000.0000.0000.000
144B144GLU-1-0.864-0.91915.0390.0970.0970.0000.0000.0000.000
145B145LYS10.8980.94910.436-0.363-0.3630.0000.0000.0000.000
146B146ILE00.022-0.0049.761-0.033-0.0330.0000.0000.0000.000
147B147ARG10.8210.9098.3480.3530.3530.0000.0000.0000.000
148B148PHE00.043-0.0035.5390.0550.0550.0000.0000.0000.000
149B149ARG10.8790.9057.8490.8600.8600.0000.0000.0000.000
150B150ILE0-0.012-0.0044.7160.2120.289-0.001-0.003-0.0720.000
151B151GLU-1-0.759-0.8378.576-1.122-1.1220.0000.0000.0000.000
152B152ARG10.9020.94212.0840.7630.7630.0000.0000.0000.000
153B153GLU-1-0.743-0.8409.293-1.827-1.8270.0000.0000.0000.000
154B154VAL0-0.046-0.02212.0210.1210.1210.0000.0000.0000.000
155B155PHE00.0020.01011.6540.0370.0370.0000.0000.0000.000
156B156VAL0-0.039-0.02816.2270.0280.0280.0000.0000.0000.000
157B157ASP-1-0.930-0.95719.483-0.199-0.1990.0000.0000.0000.000
158B158VAL0-0.035-0.00820.8620.0290.0290.0000.0000.0000.000
159B190LYS10.9641.00320.0510.1440.1440.0000.0000.0000.000
160B191PRO0-0.015-0.02220.6980.0140.0140.0000.0000.0000.000
161B192PRO00.0280.00215.8020.0240.0240.0000.0000.0000.000
162B193ALA00.0190.00516.769-0.044-0.0440.0000.0000.0000.000
163B194TYR0-0.038-0.0407.962-0.067-0.0670.0000.0000.0000.000
164B195ALA00.0030.01112.0070.1150.1150.0000.0000.0000.000
165B196LEU0-0.009-0.0016.509-0.130-0.1300.0000.0000.0000.000
166B197LEU0-0.023-0.01510.6370.1690.1690.0000.0000.0000.000
167B198GLY00.015-0.00210.280-0.257-0.2570.0000.0000.0000.000
168B199SER0-0.050-0.06510.9250.1800.1800.0000.0000.0000.000
169B200CYS0-0.043-0.02812.113-0.048-0.0480.0000.0000.0000.000
170B201GLN0-0.0170.00614.6570.0370.0370.0000.0000.0000.000
171B202THR0-0.031-0.01615.5340.0000.0000.0000.0000.0000.000
172B203ASP-1-0.861-0.92116.540-0.371-0.3710.0000.0000.0000.000
173B204GLY0-0.010-0.01315.248-0.056-0.0560.0000.0000.0000.000
174B205MET0-0.135-0.06711.240-0.101-0.1010.0000.0000.0000.000
175B206GLY00.0590.01312.6630.0690.0690.0000.0000.0000.000
176B207LEU0-0.0140.01812.861-0.036-0.0360.0000.0000.0000.000
177B208VAL0-0.024-0.01610.707-0.012-0.0120.0000.0000.0000.000
178B209SER0-0.045-0.02313.867-0.004-0.0040.0000.0000.0000.000
179B210TRP00.026-0.00116.919-0.004-0.0040.0000.0000.0000.000
180B211TRP00.0200.02415.661-0.008-0.0080.0000.0000.0000.000
181B212GLU-1-0.905-0.92913.089-0.033-0.0330.0000.0000.0000.000