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: 1745Z

Calculation Name: 3CDK-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3CDK

Chain ID: B

ChEMBL ID:

UniProt ID: P42315

Base Structure: X-ray

Registration Date: 2023-06-21

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 213
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2339124.869901
FMO2-HF: Nuclear repulsion 2256199.940377
FMO2-HF: Total energy -82924.929524
FMO2-MP2: Total energy -83159.035469


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.
-5.6931.7131.766-3.618-5.552-1.7347234759768E-18
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 : 0.060 / q_NPA : 0.005
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].
3B3GLU-1-0.861-0.9213.290-1.6321.542-0.016-1.492-1.666-0.001
4B4ALA00.0160.0152.647-0.2960.4940.434-0.377-0.8470.000
5B5ARG11.0260.9933.2480.3931.2790.059-0.207-0.7370.000
6B6LYS10.9700.9956.0010.5720.5720.0000.0000.0000.000
7B7ARG10.7890.8676.9890.7470.7470.0000.0000.0000.000
8B8MET0-0.0340.0016.0760.1400.1400.0000.0000.0000.000
9B9VAL00.0270.0049.9320.0670.0670.0000.0000.0000.000
10B10LYS10.8580.92311.9640.1660.1660.0000.0000.0000.000
11B11ARG10.7200.82313.4270.1260.1260.0000.0000.0000.000
12B12ALA00.0180.01414.4700.0270.0270.0000.0000.0000.000
13B13VAL00.0330.02716.2580.0170.0170.0000.0000.0000.000
14B14GLN0-0.041-0.02118.2060.0010.0010.0000.0000.0000.000
15B15GLU-1-0.767-0.87119.517-0.042-0.0420.0000.0000.0000.000
16B16ILE0-0.010-0.00320.6680.0080.0080.0000.0000.0000.000
17B17LYS10.8790.92823.7330.0410.0410.0000.0000.0000.000
18B18ASP-1-0.826-0.93227.182-0.028-0.0280.0000.0000.0000.000
19B19GLY0-0.011-0.00229.7820.0020.0020.0000.0000.0000.000
20B20MET0-0.096-0.00626.5540.0010.0010.0000.0000.0000.000
21B21ASN00.0230.01628.502-0.001-0.0010.0000.0000.0000.000
22B22VAL0-0.035-0.03622.2420.0010.0010.0000.0000.0000.000
23B23ASN0-0.023-0.00321.4920.0020.0020.0000.0000.0000.000
24B24LEU0-0.0110.00017.6400.0010.0010.0000.0000.0000.000
25B25GLY00.0510.03316.8740.0020.0020.0000.0000.0000.000
26B26ILE00.029-0.00213.578-0.011-0.0110.0000.0000.0000.000
27B27GLY0-0.031-0.01110.7020.0190.0190.0000.0000.0000.000
28B28MET0-0.027-0.0327.985-0.056-0.0560.0000.0000.0000.000
29B29PRO00.0120.00310.168-0.031-0.0310.0000.0000.0000.000
30B30THR00.0470.03513.754-0.011-0.0110.0000.0000.0000.000
31B31LEU0-0.030-0.0189.218-0.017-0.0170.0000.0000.0000.000
32B32VAL0-0.018-0.01513.602-0.001-0.0010.0000.0000.0000.000
33B33ALA00.0370.02016.0630.0050.0050.0000.0000.0000.000
34B34ASN0-0.037-0.01815.4630.0160.0160.0000.0000.0000.000
35B35GLU-1-0.909-0.93915.552-0.098-0.0980.0000.0000.0000.000
36B36ILE00.0070.00318.597-0.003-0.0030.0000.0000.0000.000
37B37PRO0-0.020-0.01521.7360.0030.0030.0000.0000.0000.000
38B38ASP-1-0.836-0.92124.223-0.037-0.0370.0000.0000.0000.000
39B39GLY0-0.106-0.05027.7010.0030.0030.0000.0000.0000.000
40B40VAL0-0.087-0.04125.5280.0030.0030.0000.0000.0000.000
41B41HIS00.0060.01727.713-0.001-0.0010.0000.0000.0000.000
42B42VAL0-0.0040.01225.1670.0010.0010.0000.0000.0000.000
43B43MET00.0050.01028.1230.0000.0000.0000.0000.0000.000
44B44LEU00.010-0.00422.1750.0000.0000.0000.0000.0000.000
45B45GLN0-0.034-0.04025.2110.0010.0010.0000.0000.0000.000
46B46SER00.0420.00023.923-0.003-0.0030.0000.0000.0000.000
47B47GLU-1-0.871-0.93221.955-0.008-0.0080.0000.0000.0000.000
48B48ASN0-0.089-0.03525.0770.0020.0020.0000.0000.0000.000
49B49GLY0-0.011-0.01227.2650.0010.0010.0000.0000.0000.000
50B50LEU00.0220.01626.9930.0000.0000.0000.0000.0000.000
51B51LEU0-0.035-0.00628.104-0.001-0.0010.0000.0000.0000.000
52B52GLY00.031-0.00428.1020.0010.0010.0000.0000.0000.000
53B53ILE0-0.021-0.01222.3000.0000.0000.0000.0000.0000.000
54B54GLY00.0210.01425.354-0.001-0.0010.0000.0000.0000.000
55B55PRO0-0.026-0.01922.189-0.002-0.0020.0000.0000.0000.000
56B56TYR0-0.065-0.04916.801-0.001-0.0010.0000.0000.0000.000
57B57PRO00.0140.04222.8840.0010.0010.0000.0000.0000.000
58B58LEU0-0.052-0.03125.353-0.001-0.0010.0000.0000.0000.000
59B59GLU-1-0.933-0.97625.382-0.019-0.0190.0000.0000.0000.000
60B60GLY0-0.046-0.02727.4510.0020.0020.0000.0000.0000.000
61B61THR0-0.102-0.05529.5920.0020.0020.0000.0000.0000.000
62B62GLU-1-0.892-0.93926.492-0.021-0.0210.0000.0000.0000.000
63B63ASP-1-0.849-0.93128.462-0.012-0.0120.0000.0000.0000.000
64B64ALA0-0.064-0.03528.675-0.001-0.0010.0000.0000.0000.000
65B65ASP-1-0.968-0.96729.536-0.010-0.0100.0000.0000.0000.000
66B66LEU0-0.031-0.01327.7230.0000.0000.0000.0000.0000.000
67B67ILE0-0.005-0.01823.777-0.002-0.0020.0000.0000.0000.000
68B68ASN00.0220.00418.7370.0060.0060.0000.0000.0000.000
69B69ALA00.0690.03319.9650.0020.0020.0000.0000.0000.000
70B70GLY0-0.088-0.05717.5910.0060.0060.0000.0000.0000.000
71B71LYS10.7980.90118.4390.0070.0070.0000.0000.0000.000
72B72GLU-1-0.829-0.87515.989-0.074-0.0740.0000.0000.0000.000
73B73THR00.0300.02920.7410.0030.0030.0000.0000.0000.000
74B74ILE0-0.041-0.02521.804-0.005-0.0050.0000.0000.0000.000
75B75THR00.007-0.00224.3170.0040.0040.0000.0000.0000.000
76B76GLU-1-0.879-0.90026.895-0.018-0.0180.0000.0000.0000.000
77B77VAL0-0.008-0.00627.7090.0000.0000.0000.0000.0000.000
78B78THR0-0.016-0.03730.4920.0020.0020.0000.0000.0000.000
79B79GLY0-0.013-0.00533.602-0.001-0.0010.0000.0000.0000.000
80B80ALA0-0.0180.01031.6420.0010.0010.0000.0000.0000.000
81B81SER0-0.022-0.01132.8160.0020.0020.0000.0000.0000.000
82B82TYR0-0.002-0.03230.535-0.001-0.0010.0000.0000.0000.000
83B83PHE0-0.032-0.01030.4350.0010.0010.0000.0000.0000.000
84B84ASP-1-0.806-0.90033.295-0.003-0.0030.0000.0000.0000.000
85B85SER00.040-0.00930.6300.0000.0000.0000.0000.0000.000
86B86ALA0-0.061-0.02731.7190.0010.0010.0000.0000.0000.000
87B87GLU-1-0.871-0.94234.379-0.004-0.0040.0000.0000.0000.000
88B88SER0-0.043-0.02328.404-0.001-0.0010.0000.0000.0000.000
89B89PHE0-0.032-0.04325.6160.0000.0000.0000.0000.0000.000
90B90ALA00.0000.02230.7540.0010.0010.0000.0000.0000.000
91B91MET00.0230.02430.8020.0000.0000.0000.0000.0000.000
92B92ILE0-0.052-0.02126.0950.0000.0000.0000.0000.0000.000
93B93ARG10.8640.91329.333-0.005-0.0050.0000.0000.0000.000
94B94GLY0-0.054-0.01531.3530.0010.0010.0000.0000.0000.000
95B95GLY00.0270.02931.3700.0000.0000.0000.0000.0000.000
96B96HIS0-0.040-0.03232.315-0.002-0.0020.0000.0000.0000.000
97B97ILE0-0.0200.00025.688-0.002-0.0020.0000.0000.0000.000
98B98ASP-1-0.777-0.90128.328-0.015-0.0150.0000.0000.0000.000
99B99LEU0-0.040-0.01621.7670.0000.0000.0000.0000.0000.000
100B100ALA00.0450.02921.459-0.002-0.0020.0000.0000.0000.000
101B101ILE0-0.0080.00515.8650.0020.0020.0000.0000.0000.000
102B102LEU00.005-0.00915.8360.0000.0000.0000.0000.0000.000
103B103GLY00.0620.03111.8170.0020.0020.0000.0000.0000.000
104B104GLY00.0310.00111.146-0.023-0.0230.0000.0000.0000.000
105B105MET0-0.116-0.05810.6690.0810.0810.0000.0000.0000.000
106B106GLU-1-0.712-0.83912.0750.2220.2220.0000.0000.0000.000
107B107VAL0-0.013-0.00414.821-0.022-0.0220.0000.0000.0000.000
108B108SER0-0.012-0.02717.4910.0060.0060.0000.0000.0000.000
109B109GLU-1-0.785-0.90220.8820.0280.0280.0000.0000.0000.000
110B110GLN0-0.042-0.02523.493-0.010-0.0100.0000.0000.0000.000
111B111GLY00.0380.02722.097-0.005-0.0050.0000.0000.0000.000
112B112ASP-1-0.846-0.88922.1240.0420.0420.0000.0000.0000.000
113B113LEU00.003-0.00115.8000.0100.0100.0000.0000.0000.000
114B114ALA00.0580.03817.160-0.009-0.0090.0000.0000.0000.000
115B115ASN0-0.091-0.04714.0450.0230.0230.0000.0000.0000.000
116B116TRP00.0730.02914.989-0.006-0.0060.0000.0000.0000.000
117B117MET0-0.046-0.01616.998-0.007-0.0070.0000.0000.0000.000
118B118ILE00.0110.00512.5240.0130.0130.0000.0000.0000.000
119B119PRO00.0140.01316.775-0.012-0.0120.0000.0000.0000.000
120B120GLY00.0220.01419.3940.0070.0070.0000.0000.0000.000
121B121LYS10.9780.97613.071-0.166-0.1660.0000.0000.0000.000
122B122MET0-0.070-0.05714.489-0.008-0.0080.0000.0000.0000.000
123B123VAL00.0580.03817.404-0.006-0.0060.0000.0000.0000.000
124B124LYS10.9340.98815.830-0.028-0.0280.0000.0000.0000.000
125B125GLY00.0410.01519.204-0.007-0.0070.0000.0000.0000.000
126B126MET00.003-0.00619.0220.0030.0030.0000.0000.0000.000
127B127GLY0-0.029-0.01120.588-0.002-0.0020.0000.0000.0000.000
128B128GLY00.1080.04421.8250.0010.0010.0000.0000.0000.000
129B129ALA0-0.007-0.00118.931-0.001-0.0010.0000.0000.0000.000
130B130MET00.006-0.00420.934-0.001-0.0010.0000.0000.0000.000
131B131ASP-1-0.852-0.89823.7500.0090.0090.0000.0000.0000.000
132B132LEU00.0580.01421.980-0.001-0.0010.0000.0000.0000.000
133B133VAL0-0.097-0.04320.856-0.001-0.0010.0000.0000.0000.000
134B134ASN0-0.073-0.05923.7230.0000.0000.0000.0000.0000.000
135B135GLY00.0160.03126.958-0.001-0.0010.0000.0000.0000.000
136B136ALA0-0.027-0.00624.921-0.002-0.0020.0000.0000.0000.000
137B137LYS10.8150.92527.0490.0140.0140.0000.0000.0000.000
138B138ARG10.8230.90622.5800.0290.0290.0000.0000.0000.000
139B139ILE00.0010.00420.806-0.002-0.0020.0000.0000.0000.000
140B140VAL0-0.001-0.00517.366-0.001-0.0010.0000.0000.0000.000
141B141VAL00.0200.01614.2100.0030.0030.0000.0000.0000.000
142B142ILE0-0.0280.00211.602-0.015-0.0150.0000.0000.0000.000
143B143MET0-0.085-0.0449.6730.0440.0440.0000.0000.0000.000
144B144GLU-1-0.809-0.8894.0413.2415.1020.140-0.942-1.059-0.008
145B145HIS00.0610.0257.797-0.008-0.0080.0000.0000.0000.000
146B146VAL00.0180.0138.496-0.056-0.0560.0000.0000.0000.000
147B147ASN0-0.033-0.0107.1010.4730.4730.0000.0000.0000.000
148B148LYS10.7850.8522.968-7.886-7.1911.149-0.600-1.2430.009
149B149HIS0-0.010-0.0137.591-0.143-0.1430.0000.0000.0000.000
150B150GLY00.0180.02310.111-0.103-0.1030.0000.0000.0000.000
151B151GLU-1-0.909-0.94011.4070.1060.1060.0000.0000.0000.000
152B152SER0-0.042-0.04311.7730.1020.1020.0000.0000.0000.000
153B153LYS10.8180.9017.962-0.593-0.5930.0000.0000.0000.000
154B154VAL0-0.0030.00313.417-0.022-0.0220.0000.0000.0000.000
155B155LYS10.8630.92515.903-0.192-0.1920.0000.0000.0000.000
156B156LYS10.8700.94419.346-0.037-0.0370.0000.0000.0000.000
157B157THR00.010-0.00522.682-0.007-0.0070.0000.0000.0000.000
158B158CYS0-0.060-0.00918.4750.0050.0050.0000.0000.0000.000
159B159SER0-0.076-0.06317.853-0.010-0.0100.0000.0000.0000.000
160B160LEU0-0.049-0.02814.486-0.002-0.0020.0000.0000.0000.000
161B161PRO0-0.022-0.02419.118-0.009-0.0090.0000.0000.0000.000
162B162LEU00.0340.01919.7290.0080.0080.0000.0000.0000.000
163B163THR0-0.039-0.05718.3210.0000.0000.0000.0000.0000.000
164B164GLY00.0440.01621.090-0.008-0.0080.0000.0000.0000.000
165B165GLN0-0.044-0.01623.2250.0030.0030.0000.0000.0000.000
166B166LYS10.8680.92425.235-0.027-0.0270.0000.0000.0000.000
167B167VAL00.0070.00521.975-0.003-0.0030.0000.0000.0000.000
168B168VAL0-0.050-0.01419.240-0.004-0.0040.0000.0000.0000.000
169B169HIS00.0540.04422.198-0.004-0.0040.0000.0000.0000.000
170B170ARG10.7610.84418.8570.0390.0390.0000.0000.0000.000
171B171LEU0-0.034-0.01314.2170.0080.0080.0000.0000.0000.000
172B172ILE0-0.033-0.00712.683-0.015-0.0150.0000.0000.0000.000
173B173THR00.020-0.00910.4950.0060.0060.0000.0000.0000.000
174B174ASP-1-0.889-0.9616.389-0.381-0.3810.0000.0000.0000.000
175B175LEU0-0.023-0.0188.680-0.097-0.0970.0000.0000.0000.000
176B176ALA00.0360.00811.4610.0040.0040.0000.0000.0000.000
177B177VAL0-0.0120.01514.3460.0070.0070.0000.0000.0000.000
178B178PHE00.0390.00115.5870.0020.0020.0000.0000.0000.000
179B179ASP-1-0.757-0.83619.640-0.030-0.0300.0000.0000.0000.000
180B180PHE0-0.013-0.01520.1190.0040.0040.0000.0000.0000.000
181B181VAL0-0.025-0.01525.235-0.002-0.0020.0000.0000.0000.000
182B182ASN0-0.033-0.02729.0060.0000.0000.0000.0000.0000.000
183B183GLY00.0110.01028.4720.0000.0000.0000.0000.0000.000
184B184ARG10.9460.99527.5890.0090.0090.0000.0000.0000.000
185B185MET00.0660.04919.8130.0000.0000.0000.0000.0000.000
186B186THR0-0.065-0.04523.615-0.001-0.0010.0000.0000.0000.000
187B187LEU0-0.0260.00618.333-0.001-0.0010.0000.0000.0000.000
188B188THR0-0.003-0.02620.378-0.001-0.0010.0000.0000.0000.000
189B189GLU-1-0.791-0.84218.528-0.087-0.0870.0000.0000.0000.000
190B190LEU0-0.010-0.00316.1950.0070.0070.0000.0000.0000.000
191B191GLN0-0.035-0.00811.317-0.049-0.0490.0000.0000.0000.000
192B192ASP-1-0.828-0.90412.063-0.251-0.2510.0000.0000.0000.000
193B193GLY0-0.081-0.03111.7210.0250.0250.0000.0000.0000.000
194B194VAL0-0.0050.02511.7870.0200.0200.0000.0000.0000.000
195B195THR00.0310.00414.4800.0270.0270.0000.0000.0000.000
196B196ILE00.027-0.00717.603-0.003-0.0030.0000.0000.0000.000
197B197GLU-1-0.918-0.95019.962-0.040-0.0400.0000.0000.0000.000
198B198GLU-1-0.799-0.87312.144-0.264-0.2640.0000.0000.0000.000
199B199VAL0-0.004-0.01115.3050.0100.0100.0000.0000.0000.000
200B200TYR0-0.0050.01417.0720.0200.0200.0000.0000.0000.000
201B201GLU-1-0.939-0.96117.480-0.053-0.0530.0000.0000.0000.000
202B202LYS10.7800.86910.7000.2600.2600.0000.0000.0000.000
203B203THR0-0.082-0.06915.1640.0420.0420.0000.0000.0000.000
204B204GLU-1-0.777-0.84216.9700.1330.1330.0000.0000.0000.000
205B205ALA0-0.104-0.05719.525-0.008-0.0080.0000.0000.0000.000
206B206ASP-1-0.785-0.88521.5050.0120.0120.0000.0000.0000.000
207B207PHE0-0.037-0.04620.3730.0000.0000.0000.0000.0000.000
208B208ALA0-0.044-0.01124.528-0.003-0.0030.0000.0000.0000.000
209B209VAL00.0290.01323.930-0.001-0.0010.0000.0000.0000.000
210B210SER0-0.049-0.02925.0050.0050.0050.0000.0000.0000.000
211B211GLN0-0.0070.00126.844-0.002-0.0020.0000.0000.0000.000
212B212SER0-0.042-0.01427.7330.0000.0000.0000.0000.0000.000
213B213VAL0-0.012-0.02721.263-0.002-0.0020.0000.0000.0000.000