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: 76ZMK

Calculation Name: 1QDL-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1QDL

Chain ID: B

ChEMBL ID:

UniProt ID: Q06128

Base Structure: X-ray

Registration Date: 2023-09-23

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 195
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2314598.548963
FMO2-HF: Nuclear repulsion 2239094.355933
FMO2-HF: Total energy -75504.19303
FMO2-MP2: Total energy -75729.401672


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.
-9.292-3.8453.295-2.921-5.823-0.011
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 : -0.032 / 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].
3B3LEU00.0150.0052.989-2.5441.3050.251-1.925-2.175-0.006
4B4THR0-0.014-0.0284.6570.9631.089-0.001-0.021-0.1050.000
5B5LEU00.0080.0137.7630.1490.1490.0000.0000.0000.000
6B6ILE0-0.028-0.0379.6950.1960.1960.0000.0000.0000.000
7B7ILE00.0110.00212.5640.0490.0490.0000.0000.0000.000
8B8ASP-1-0.759-0.88615.554-0.395-0.3950.0000.0000.0000.000
9B9ASN0-0.054-0.01917.5500.0290.0290.0000.0000.0000.000
10B10TYR0-0.061-0.07320.7800.0490.0490.0000.0000.0000.000
11B11ASP-1-0.773-0.91620.364-0.320-0.3200.0000.0000.0000.000
12B12SER0-0.071-0.03721.1750.0090.0090.0000.0000.0000.000
13B13PHE0-0.065-0.03321.1780.0320.0320.0000.0000.0000.000
14B14VAL00.0370.02415.380-0.015-0.0150.0000.0000.0000.000
15B15TYR00.0360.00513.518-0.066-0.0660.0000.0000.0000.000
16B16ASN0-0.035-0.00815.8420.0370.0370.0000.0000.0000.000
17B17ILE0-0.011-0.00914.0840.0160.0160.0000.0000.0000.000
18B18ALA00.0110.00411.395-0.049-0.0490.0000.0000.0000.000
19B19GLN0-0.018-0.00311.4260.0250.0250.0000.0000.0000.000
20B20ILE00.0180.02213.3950.0560.0560.0000.0000.0000.000
21B21VAL0-0.020-0.0138.6270.0150.0150.0000.0000.0000.000
22B22GLY00.0250.0108.562-0.043-0.0430.0000.0000.0000.000
23B23GLU-1-0.912-0.9269.6190.1760.1760.0000.0000.0000.000
24B24LEU0-0.119-0.05311.8420.0780.0780.0000.0000.0000.000
25B25GLY0-0.027-0.0118.235-0.097-0.0970.0000.0000.0000.000
26B26SER0-0.054-0.0185.9380.1960.1960.0000.0000.0000.000
27B27TYR00.015-0.0082.384-1.521-0.1923.047-0.956-3.421-0.005
28B28PRO0-0.038-0.0084.353-1.044-0.991-0.001-0.016-0.0350.000
29B29ILE00.001-0.0054.7920.0920.182-0.001-0.003-0.0870.000
30B30VAL0-0.029-0.0147.9970.0360.0360.0000.0000.0000.000
31B31ILE0-0.0010.00711.7660.0470.0470.0000.0000.0000.000
32B32ARG10.9010.94714.1430.3630.3630.0000.0000.0000.000
33B33ASN0-0.102-0.05217.861-0.010-0.0100.0000.0000.0000.000
34B34ASP-1-0.810-0.88519.893-0.392-0.3920.0000.0000.0000.000
35B35GLU-1-0.868-0.92917.267-0.472-0.4720.0000.0000.0000.000
36B36ILE0-0.023-0.00713.258-0.019-0.0190.0000.0000.0000.000
37B37SER0-0.021-0.00417.3480.0050.0050.0000.0000.0000.000
38B38ILE00.0850.02917.268-0.067-0.0670.0000.0000.0000.000
39B39LYS10.8020.87517.5630.5290.5290.0000.0000.0000.000
40B40GLY0-0.022-0.00815.584-0.055-0.0550.0000.0000.0000.000
41B41ILE00.0260.00912.964-0.114-0.1140.0000.0000.0000.000
42B42GLU-1-0.788-0.88712.552-0.901-0.9010.0000.0000.0000.000
43B43ARG10.8770.93712.4720.5610.5610.0000.0000.0000.000
44B44ILE0-0.052-0.0197.5300.0470.0470.0000.0000.0000.000
45B45ASP-1-0.972-0.9737.944-2.539-2.5390.0000.0000.0000.000
46B46PRO0-0.038-0.0077.572-0.587-0.5870.0000.0000.0000.000
47B47ASP-1-0.794-0.8775.653-6.098-6.0980.0000.0000.0000.000
48B48ARG10.7410.8247.6193.1493.1490.0000.0000.0000.000
49B49LEU0-0.006-0.00510.766-0.141-0.1410.0000.0000.0000.000
50B50ILE0-0.010-0.00213.0670.1760.1760.0000.0000.0000.000
51B51ILE0-0.032-0.00115.042-0.005-0.0050.0000.0000.0000.000
52B52SER00.0440.01117.3090.0470.0470.0000.0000.0000.000
53B53PRO0-0.0170.00418.8890.0170.0170.0000.0000.0000.000
54B54GLY00.0700.03022.009-0.022-0.0220.0000.0000.0000.000
55B55PRO0-0.040-0.00524.6270.0160.0160.0000.0000.0000.000
56B56GLY00.0340.01427.824-0.011-0.0110.0000.0000.0000.000
57B57THR0-0.086-0.08629.890-0.010-0.0100.0000.0000.0000.000
58B58PRO00.018-0.00127.391-0.006-0.0060.0000.0000.0000.000
59B59GLU-1-0.903-0.93728.834-0.230-0.2300.0000.0000.0000.000
60B60LYS10.7750.88531.1180.2420.2420.0000.0000.0000.000
61B61ARG10.8950.91124.3790.3890.3890.0000.0000.0000.000
62B62GLU-1-0.884-0.92227.000-0.253-0.2530.0000.0000.0000.000
63B63ASP-1-0.758-0.86526.943-0.263-0.2630.0000.0000.0000.000
64B64ILE0-0.039-0.01224.042-0.021-0.0210.0000.0000.0000.000
65B65GLY00.0450.03722.653-0.047-0.0470.0000.0000.0000.000
66B66VAL0-0.080-0.05918.4610.0150.0150.0000.0000.0000.000
67B67SER00.028-0.00620.191-0.057-0.0570.0000.0000.0000.000
68B68LEU0-0.023-0.01421.238-0.021-0.0210.0000.0000.0000.000
69B69ASP-1-0.844-0.89822.422-0.441-0.4410.0000.0000.0000.000
70B70VAL00.0300.02516.944-0.018-0.0180.0000.0000.0000.000
71B71ILE0-0.009-0.00319.791-0.032-0.0320.0000.0000.0000.000
72B72LYS10.8830.94721.6470.3760.3760.0000.0000.0000.000
73B73TYR0-0.044-0.03521.4850.0250.0250.0000.0000.0000.000
74B74LEU00.0300.01315.3280.0120.0120.0000.0000.0000.000
75B75GLY00.0430.01617.739-0.059-0.0590.0000.0000.0000.000
76B76LYS10.7640.87919.7270.4450.4450.0000.0000.0000.000
77B77ARG10.9130.93416.0120.6530.6530.0000.0000.0000.000
78B78THR00.0720.06712.484-0.015-0.0150.0000.0000.0000.000
79B79PRO0-0.026-0.01413.3000.1430.1430.0000.0000.0000.000
80B80ILE0-0.0140.00314.889-0.100-0.1000.0000.0000.0000.000
81B81LEU0-0.0180.00016.8120.1000.1000.0000.0000.0000.000
82B82GLY00.008-0.00618.014-0.037-0.0370.0000.0000.0000.000
83B83VAL00.032-0.00419.3710.0410.0410.0000.0000.0000.000
84B84CYS0-0.0050.00422.0670.0070.0070.0000.0000.0000.000
85B85LEU00.0330.03924.032-0.005-0.0050.0000.0000.0000.000
86B86GLY00.0700.02921.668-0.002-0.0020.0000.0000.0000.000
87B87HIS0-0.043-0.00822.663-0.034-0.0340.0000.0000.0000.000
88B88GLN00.0360.01124.8890.0160.0160.0000.0000.0000.000
89B89ALA00.0090.00424.0030.0140.0140.0000.0000.0000.000
90B90ILE00.0050.00721.0480.0090.0090.0000.0000.0000.000
91B91GLY00.0410.00325.2790.0110.0110.0000.0000.0000.000
92B92TYR0-0.029-0.01528.9320.0130.0130.0000.0000.0000.000
93B93ALA0-0.063-0.04026.2900.0140.0140.0000.0000.0000.000
94B94PHE0-0.022-0.02725.0000.0030.0030.0000.0000.0000.000
95B95GLY00.0110.00630.4510.0170.0170.0000.0000.0000.000
96B96ALA0-0.0380.01732.1620.0190.0190.0000.0000.0000.000
97B97LYS10.8440.88433.9580.1840.1840.0000.0000.0000.000
98B98ILE0-0.0240.00230.853-0.008-0.0080.0000.0000.0000.000
99B99ARG10.7250.82634.7210.1920.1920.0000.0000.0000.000
100B100ARG10.9890.99036.0340.1460.1460.0000.0000.0000.000
101B101ALA0-0.0050.00935.9350.0020.0020.0000.0000.0000.000
102B102ARG10.8110.88237.9730.1630.1630.0000.0000.0000.000
103B103LYS10.9080.95839.5590.1270.1270.0000.0000.0000.000
104B104VAL00.0390.01936.269-0.009-0.0090.0000.0000.0000.000
105B105PHE0-0.024-0.00933.8800.0110.0110.0000.0000.0000.000
106B106HIS00.0210.01732.668-0.020-0.0200.0000.0000.0000.000
107B107GLY00.0750.02531.0630.0100.0100.0000.0000.0000.000
108B108LYS10.8230.92232.1100.1400.1400.0000.0000.0000.000
109B109ILE00.0150.00331.150-0.013-0.0130.0000.0000.0000.000
110B110SER0-0.101-0.06432.6560.0050.0050.0000.0000.0000.000
111B111ASN0-0.013-0.02133.176-0.001-0.0010.0000.0000.0000.000
112B112ILE00.0090.00829.6240.0000.0000.0000.0000.0000.000
113B113ILE00.0290.00532.9010.0070.0070.0000.0000.0000.000
114B114LEU0-0.027-0.01028.440-0.011-0.0110.0000.0000.0000.000
115B115VAL0-0.038-0.04032.4330.0140.0140.0000.0000.0000.000
116B116ASN0-0.033-0.01429.9240.0050.0050.0000.0000.0000.000
117B117ASN00.0150.00732.5010.0170.0170.0000.0000.0000.000
118B118SER00.0100.00430.9320.0110.0110.0000.0000.0000.000
119B119PRO0-0.007-0.00727.678-0.013-0.0130.0000.0000.0000.000
120B120LEU00.0380.02325.101-0.014-0.0140.0000.0000.0000.000
121B121SER00.0000.00519.9660.0370.0370.0000.0000.0000.000
122B122LEU00.0190.01419.4800.0110.0110.0000.0000.0000.000
123B123TYR00.017-0.00221.6760.0090.0090.0000.0000.0000.000
124B124TYR00.0510.03122.1940.0400.0400.0000.0000.0000.000
125B125GLY0-0.005-0.01423.937-0.001-0.0010.0000.0000.0000.000
126B126ILE0-0.064-0.01523.8470.0160.0160.0000.0000.0000.000
127B127ALA00.0010.00227.4370.0060.0060.0000.0000.0000.000
128B128LYS10.9190.93131.1110.1150.1150.0000.0000.0000.000
129B129GLU-1-0.840-0.90033.236-0.135-0.1350.0000.0000.0000.000
130B130PHE0-0.046-0.01527.5390.0110.0110.0000.0000.0000.000
131B131LYS10.9230.95731.4020.1190.1190.0000.0000.0000.000
132B132ALA00.0480.01027.685-0.008-0.0080.0000.0000.0000.000
133B133THR0-0.015-0.00127.6600.0140.0140.0000.0000.0000.000
134B134ARG10.8130.88628.4080.1680.1680.0000.0000.0000.000
135B135TYR00.0440.01727.1090.0250.0250.0000.0000.0000.000
136B136HIS00.0280.01529.300-0.010-0.0100.0000.0000.0000.000
137B137SER00.005-0.01431.5360.0110.0110.0000.0000.0000.000
138B138LEU0-0.046-0.00932.1660.0130.0130.0000.0000.0000.000
139B139VAL0-0.0070.01232.468-0.008-0.0080.0000.0000.0000.000
140B140VAL00.0270.02129.8050.0000.0000.0000.0000.0000.000
141B141ASP-1-0.809-0.89833.197-0.176-0.1760.0000.0000.0000.000
142B142GLU-1-0.828-0.89036.283-0.187-0.1870.0000.0000.0000.000
143B143VAL0-0.0040.00132.396-0.009-0.0090.0000.0000.0000.000
144B144HIS10.8120.90435.0070.2530.2530.0000.0000.0000.000
145B145ARG10.9190.94133.3950.2190.2190.0000.0000.0000.000
146B146PRO0-0.001-0.00329.4250.0120.0120.0000.0000.0000.000
147B147LEU0-0.0140.00727.443-0.016-0.0160.0000.0000.0000.000
148B148ILE0-0.024-0.01329.8090.0260.0260.0000.0000.0000.000
149B149VAL00.0100.00630.117-0.018-0.0180.0000.0000.0000.000
150B150ASP-1-0.822-0.89927.618-0.321-0.3210.0000.0000.0000.000
151B151ALA0-0.0050.00429.9310.0130.0130.0000.0000.0000.000
152B152ILE0-0.0100.00631.796-0.005-0.0050.0000.0000.0000.000
153B153SER0-0.045-0.01434.7520.0050.0050.0000.0000.0000.000
154B154ALA00.0230.01735.9530.0050.0050.0000.0000.0000.000
155B155GLU-1-0.778-0.87137.137-0.142-0.1420.0000.0000.0000.000
156B156ASP-1-0.814-0.90937.601-0.156-0.1560.0000.0000.0000.000
157B157ASN00.0080.02138.7650.0060.0060.0000.0000.0000.000
158B158GLU-1-0.700-0.82735.509-0.173-0.1730.0000.0000.0000.000
159B159ILE00.0340.00831.461-0.001-0.0010.0000.0000.0000.000
160B160MET0-0.042-0.01130.071-0.004-0.0040.0000.0000.0000.000
161B161ALA0-0.016-0.00227.069-0.019-0.0190.0000.0000.0000.000
162B162ILE0-0.0360.00626.8380.0280.0280.0000.0000.0000.000
163B163HIS10.9150.93924.6610.3260.3260.0000.0000.0000.000
164B164HIS00.0240.03624.7890.0320.0320.0000.0000.0000.000
165B165GLU-1-0.851-0.91226.317-0.273-0.2730.0000.0000.0000.000
166B166GLU-1-0.825-0.92125.334-0.387-0.3870.0000.0000.0000.000
167B167TYR0-0.057-0.01821.866-0.028-0.0280.0000.0000.0000.000
168B168PRO00.0220.03417.6710.0440.0440.0000.0000.0000.000
169B169ILE0-0.018-0.00419.013-0.066-0.0660.0000.0000.0000.000
170B170TYR00.003-0.02620.2080.0910.0910.0000.0000.0000.000
171B171GLY00.0230.02921.737-0.041-0.0410.0000.0000.0000.000
172B172VAL0-0.0110.00122.3150.0320.0320.0000.0000.0000.000
173B173GLN0-0.007-0.04424.873-0.009-0.0090.0000.0000.0000.000
174B174PHE0-0.018-0.02224.7400.0100.0100.0000.0000.0000.000
175B175HIS00.027-0.01323.469-0.021-0.0210.0000.0000.0000.000
176B176PRO0-0.0530.00120.2810.0370.0370.0000.0000.0000.000
177B177GLU-1-0.746-0.88318.678-0.314-0.3140.0000.0000.0000.000
178B178SER0-0.0210.01620.6650.0380.0380.0000.0000.0000.000
179B179VAL00.0720.02424.1980.0030.0030.0000.0000.0000.000
180B180GLY0-0.047-0.02125.9760.0130.0130.0000.0000.0000.000
181B181THR0-0.060-0.05624.9030.0100.0100.0000.0000.0000.000
182B182SER00.0230.02025.193-0.008-0.0080.0000.0000.0000.000
183B183LEU0-0.019-0.01825.0620.0020.0020.0000.0000.0000.000
184B184GLY00.0230.01122.805-0.024-0.0240.0000.0000.0000.000
185B185TYR00.010-0.01916.013-0.066-0.0660.0000.0000.0000.000
186B186LYS10.9430.98218.7660.1480.1480.0000.0000.0000.000
187B187ILE0-0.0020.00019.805-0.033-0.0330.0000.0000.0000.000
188B188LEU00.0430.01715.707-0.056-0.0560.0000.0000.0000.000
189B189TYR00.0360.01915.126-0.103-0.1030.0000.0000.0000.000
190B190ASN0-0.078-0.05215.611-0.046-0.0460.0000.0000.0000.000
191B191PHE0-0.001-0.00613.791-0.028-0.0280.0000.0000.0000.000
192B192LEU00.000-0.00210.149-0.106-0.1060.0000.0000.0000.000
193B193ASN0-0.035-0.02011.974-0.142-0.1420.0000.0000.0000.000
194B194ARG10.8450.92213.6980.3830.3830.0000.0000.0000.000
195B195VAL0-0.0290.01214.6980.0260.0260.0000.0000.0000.000