FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: MV21Z

Calculation Name: 5D1X-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5D1X

Chain ID: B

ChEMBL ID:

UniProt ID: Q2FZF0

Base Structure: X-ray

Registration Date: 2023-06-26

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 215
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2083148.130081
FMO2-HF: Nuclear repulsion 2002696.767749
FMO2-HF: Total energy -80451.362333
FMO2-MP2: Total energy -80685.866067


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:GLN)


Summations of interaction energy for fragment #1(B:1: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.
-4.727-1.6970.102-1.102-2.0290.003
Interaction energy analysis for fragmet #1(B:1:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.019 / q_NPA : -0.007
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].
3B3GLN0-0.001-0.0053.783-2.249-0.4830.003-0.651-1.1180.003
4B4LEU0-0.025-0.0166.143-0.510-0.5100.0000.0000.0000.000
5B5VAL00.0170.0129.6420.0270.0270.0000.0000.0000.000
6B6GLN0-0.026-0.04011.976-0.046-0.0460.0000.0000.0000.000
7B7SER0-0.002-0.00415.723-0.004-0.0040.0000.0000.0000.000
8B8GLY00.0120.02318.975-0.028-0.0280.0000.0000.0000.000
9B9SER0-0.053-0.04020.7030.0010.0010.0000.0000.0000.000
10B10GLU-1-0.887-0.92924.0930.1860.1860.0000.0000.0000.000
11B11VAL0-0.064-0.04226.8040.0020.0020.0000.0000.0000.000
12B12LYS10.9100.96429.296-0.159-0.1590.0000.0000.0000.000
13B13LYS10.9650.97933.020-0.099-0.0990.0000.0000.0000.000
14B14PRO00.027-0.01036.0510.0020.0020.0000.0000.0000.000
15B15GLY00.0380.04337.0240.0020.0020.0000.0000.0000.000
16B16SER0-0.064-0.01234.2660.0000.0000.0000.0000.0000.000
17B17SER00.035-0.00232.0010.0020.0020.0000.0000.0000.000
18B18VAL0-0.076-0.03626.621-0.006-0.0060.0000.0000.0000.000
19B19THR00.0490.02424.2240.0070.0070.0000.0000.0000.000
20B20LEU00.0050.02720.950-0.001-0.0010.0000.0000.0000.000
21B21SER00.013-0.01618.110-0.006-0.0060.0000.0000.0000.000
22B22CYS0-0.054-0.02413.5890.0350.0350.0000.0000.0000.000
23B23LYS10.9270.97910.994-0.141-0.1410.0000.0000.0000.000
24B24ALA00.0740.0519.0760.1640.1640.0000.0000.0000.000
25B25SER0-0.067-0.0376.071-0.353-0.3530.0000.0000.0000.000
26B26GLY00.0340.0012.9540.1200.3510.063-0.123-0.1710.000
27B27ASP-1-0.811-0.9043.8681.4761.8630.002-0.093-0.2950.000
28B28THR0-0.037-0.0056.556-0.226-0.2260.0000.0000.0000.000
29B29PHE00.011-0.00510.3670.1490.1490.0000.0000.0000.000
30B30ASN00.018-0.01311.7280.0900.0900.0000.0000.0000.000
31B31THR00.0210.00812.605-0.049-0.0490.0000.0000.0000.000
32B32HIS00.0030.0159.6240.1960.1960.0000.0000.0000.000
33B33THR00.0250.00713.948-0.082-0.0820.0000.0000.0000.000
34B34TYR0-0.066-0.04311.2960.1350.1350.0000.0000.0000.000
35B35SER00.000-0.00914.865-0.097-0.0970.0000.0000.0000.000
36B36TRP00.0180.01316.1310.0580.0580.0000.0000.0000.000
37B37VAL0-0.008-0.00717.690-0.024-0.0240.0000.0000.0000.000
38B38ARG10.8880.94819.592-0.217-0.2170.0000.0000.0000.000
39B39GLN0-0.004-0.00921.4190.0170.0170.0000.0000.0000.000
40B40ALA00.0560.03723.8040.0020.0020.0000.0000.0000.000
41B41PRO00.016-0.01826.4440.0120.0120.0000.0000.0000.000
42B42GLY00.0060.02327.261-0.011-0.0110.0000.0000.0000.000
43B43GLN0-0.035-0.01426.609-0.015-0.0150.0000.0000.0000.000
44B44ARG10.9670.97925.011-0.217-0.2170.0000.0000.0000.000
45B45LEU0-0.006-0.00418.728-0.003-0.0030.0000.0000.0000.000
46B46GLU-1-0.859-0.94222.6800.2310.2310.0000.0000.0000.000
47B47TRP0-0.006-0.00318.9270.0020.0020.0000.0000.0000.000
48B48ILE0-0.0150.00121.782-0.026-0.0260.0000.0000.0000.000
49B49GLY00.0880.02521.834-0.032-0.0320.0000.0000.0000.000
50B50GLY0-0.036-0.00719.6420.0440.0440.0000.0000.0000.000
51B51ILE0-0.016-0.00818.697-0.040-0.0400.0000.0000.0000.000
52B52MET00.0450.04217.8520.0650.0650.0000.0000.0000.000
53B52PRO0-0.040-0.02816.416-0.051-0.0510.0000.0000.0000.000
54B53ILE0-0.058-0.04618.640-0.039-0.0390.0000.0000.0000.000
55B54PHE00.0290.01520.434-0.020-0.0200.0000.0000.0000.000
56B55ALA0-0.0330.00322.591-0.014-0.0140.0000.0000.0000.000
57B56ALA00.0270.03023.477-0.012-0.0120.0000.0000.0000.000
58B57SER0-0.029-0.04323.1160.0270.0270.0000.0000.0000.000
59B58LYS10.9090.94324.164-0.222-0.2220.0000.0000.0000.000
60B59SER00.0510.01624.4520.0280.0280.0000.0000.0000.000
61B60ALA00.0020.01326.295-0.010-0.0100.0000.0000.0000.000
62B61PRO00.011-0.00527.674-0.009-0.0090.0000.0000.0000.000
63B62HIS0-0.018-0.00728.264-0.014-0.0140.0000.0000.0000.000
64B63LEU0-0.028-0.01527.316-0.006-0.0060.0000.0000.0000.000
65B64GLN0-0.049-0.02930.4010.0080.0080.0000.0000.0000.000
66B65ASP-1-0.898-0.93631.6340.1340.1340.0000.0000.0000.000
67B66ARG10.8210.89931.441-0.177-0.1770.0000.0000.0000.000
68B67LEU0-0.008-0.00625.0770.0080.0080.0000.0000.0000.000
69B68THR00.0560.04027.289-0.001-0.0010.0000.0000.0000.000
70B69ILE0-0.0080.00621.1040.0110.0110.0000.0000.0000.000
71B70THR00.0250.02623.201-0.007-0.0070.0000.0000.0000.000
72B71ALA00.0190.00118.2460.0330.0330.0000.0000.0000.000
73B72ASN0-0.0090.00618.727-0.043-0.0430.0000.0000.0000.000
74B73LYS10.9710.97417.033-0.105-0.1050.0000.0000.0000.000
75B74ALA00.0190.01916.173-0.012-0.0120.0000.0000.0000.000
76B75THR00.0090.01416.741-0.042-0.0420.0000.0000.0000.000
77B76ARG10.8850.9309.5880.0950.0950.0000.0000.0000.000
78B77THR0-0.026-0.00313.2170.0750.0750.0000.0000.0000.000
79B78ALA0-0.0020.00215.799-0.035-0.0350.0000.0000.0000.000
80B79TYR00.022-0.02517.4330.0120.0120.0000.0000.0000.000
81B80MET0-0.0120.01520.8440.0170.0170.0000.0000.0000.000
82B81GLU-1-0.932-0.96423.2170.1440.1440.0000.0000.0000.000
83B82LEU0-0.028-0.00726.8720.0010.0010.0000.0000.0000.000
84B82THR00.0210.00228.831-0.010-0.0100.0000.0000.0000.000
85B82SER00.015-0.00232.5910.0010.0010.0000.0000.0000.000
86B82LEU0-0.040-0.01329.6310.0030.0030.0000.0000.0000.000
87B83THR00.0480.02033.537-0.011-0.0110.0000.0000.0000.000
88B84SER00.0490.00333.2910.0060.0060.0000.0000.0000.000
89B85ASP-1-0.910-0.93032.6950.1650.1650.0000.0000.0000.000
90B86ASP-1-0.785-0.84729.7320.1960.1960.0000.0000.0000.000
91B87SER0-0.113-0.05428.2790.0140.0140.0000.0000.0000.000
92B88GLY00.0410.01426.190-0.003-0.0030.0000.0000.0000.000
93B89VAL0-0.044-0.00619.742-0.002-0.0020.0000.0000.0000.000
94B90TYR00.013-0.01320.6870.0030.0030.0000.0000.0000.000
95B91TYR0-0.036-0.01515.3600.0280.0280.0000.0000.0000.000
96B93ALA00.0420.01711.6240.0890.0890.0000.0000.0000.000
97B94ARG10.8600.9326.164-2.108-2.1080.0000.0000.0000.000
98B95ASP-1-0.853-0.95010.3210.8280.8280.0000.0000.0000.000
99B96GLY0-0.076-0.0318.6920.0640.0640.0000.0000.0000.000
100B97ARG10.9410.9648.867-1.266-1.2660.0000.0000.0000.000
101B98GLY00.0160.00810.943-0.159-0.1590.0000.0000.0000.000
102B99ALA00.0290.02213.777-0.018-0.0180.0000.0000.0000.000
103B100LEU0-0.036-0.02212.4660.0070.0070.0000.0000.0000.000
104B101GLN00.0250.0436.221-0.002-0.0020.0000.0000.0000.000
105B102TYR0-0.026-0.0243.288-0.4690.1770.034-0.235-0.4450.000
106B103TRP00.0440.0017.721-0.214-0.2140.0000.0000.0000.000
107B104GLY00.0110.0199.2160.1620.1620.0000.0000.0000.000
108B105GLN00.0210.01011.7150.0420.0420.0000.0000.0000.000
109B106GLY00.0260.02313.981-0.060-0.0600.0000.0000.0000.000
110B107THR0-0.079-0.05317.006-0.009-0.0090.0000.0000.0000.000
111B108LEU00.0290.02620.185-0.008-0.0080.0000.0000.0000.000
112B109VAL00.0470.02323.569-0.015-0.0150.0000.0000.0000.000
113B110THR0-0.022-0.01926.382-0.002-0.0020.0000.0000.0000.000
114B111VAL00.0160.01030.018-0.007-0.0070.0000.0000.0000.000
115B112SER00.0450.02233.126-0.004-0.0040.0000.0000.0000.000
116B113SER00.0380.00236.274-0.002-0.0020.0000.0000.0000.000
117B114ALA0-0.048-0.00239.069-0.006-0.0060.0000.0000.0000.000
118B119SER0-0.017-0.02138.2880.0060.0060.0000.0000.0000.000
119B120THR0-0.023-0.01635.4030.0040.0040.0000.0000.0000.000
120B121LYS10.9280.98237.559-0.083-0.0830.0000.0000.0000.000
121B122GLY00.0250.01337.9410.0060.0060.0000.0000.0000.000
122B123PRO00.0060.01036.863-0.001-0.0010.0000.0000.0000.000
123B124SER0-0.039-0.01739.685-0.007-0.0070.0000.0000.0000.000
124B125VAL0-0.010-0.01339.8870.0040.0040.0000.0000.0000.000
125B126PHE00.0230.00742.736-0.005-0.0050.0000.0000.0000.000
126B127PRO00.0320.00244.1850.0050.0050.0000.0000.0000.000
127B128LEU0-0.059-0.02742.372-0.001-0.0010.0000.0000.0000.000
128B129ALA00.0530.02145.8840.0010.0010.0000.0000.0000.000
129B130PRO00.0090.01247.2730.0000.0000.0000.0000.0000.000
130B136SER00.002-0.00549.620-0.002-0.0020.0000.0000.0000.000
131B137SER00.0680.04352.1040.0010.0010.0000.0000.0000.000
132B137LYS10.8350.92754.251-0.032-0.0320.0000.0000.0000.000
133B137SER00.024-0.00153.6080.0000.0000.0000.0000.0000.000
134B137THR0-0.009-0.01949.1570.0010.0010.0000.0000.0000.000
135B137SER0-0.037-0.02047.4610.0020.0020.0000.0000.0000.000
136B137GLY00.0600.04046.160-0.002-0.0020.0000.0000.0000.000
137B138GLY0-0.0230.00644.0830.0010.0010.0000.0000.0000.000
138B139THR0-0.057-0.07344.954-0.002-0.0020.0000.0000.0000.000
139B140ALA00.0580.02845.577-0.003-0.0030.0000.0000.0000.000
140B141ALA0-0.0440.00943.5170.0030.0030.0000.0000.0000.000
141B142LEU00.0210.04742.154-0.003-0.0030.0000.0000.0000.000
142B143GLY00.0530.00740.9400.0050.0050.0000.0000.0000.000
143B144CYS0-0.0800.01537.933-0.004-0.0040.0000.0000.0000.000
144B145LEU0-0.0060.00139.5980.0070.0070.0000.0000.0000.000
145B146VAL0-0.009-0.00436.363-0.005-0.0050.0000.0000.0000.000
146B147LYS10.9660.98638.937-0.074-0.0740.0000.0000.0000.000
147B148ASP-1-0.868-0.95641.0990.0810.0810.0000.0000.0000.000
148B149TYR0-0.035-0.00332.967-0.009-0.0090.0000.0000.0000.000
149B150PHE00.1020.04834.7690.0080.0080.0000.0000.0000.000
150B151PRO0-0.090-0.05331.145-0.007-0.0070.0000.0000.0000.000
151B152GLU-1-0.775-0.91629.1090.1670.1670.0000.0000.0000.000
152B153PRO0-0.053-0.00926.6770.0000.0000.0000.0000.0000.000
153B154VAL00.0400.02728.653-0.011-0.0110.0000.0000.0000.000
154B155THR0-0.040-0.01626.7500.0100.0100.0000.0000.0000.000
155B156VAL00.001-0.01129.973-0.012-0.0120.0000.0000.0000.000
156B157SER0-0.027-0.00731.3310.0050.0050.0000.0000.0000.000
157B158TRP00.0620.01633.106-0.008-0.0080.0000.0000.0000.000
158B159ASN00.0460.01135.6910.0000.0000.0000.0000.0000.000
159B160SER0-0.018-0.00834.158-0.006-0.0060.0000.0000.0000.000
160B161GLY0-0.030-0.01131.6670.0020.0020.0000.0000.0000.000
161B162ALA0-0.033-0.00732.1090.0020.0020.0000.0000.0000.000
162B163LEU0-0.023-0.00434.722-0.003-0.0030.0000.0000.0000.000
163B164THR00.0410.00929.6760.0040.0040.0000.0000.0000.000
164B165SER0-0.051-0.02432.5990.0100.0100.0000.0000.0000.000
165B166GLY00.0560.02534.418-0.005-0.0050.0000.0000.0000.000
166B167VAL0-0.042-0.01532.929-0.002-0.0020.0000.0000.0000.000
167B168HIS00.0180.01133.1650.0140.0140.0000.0000.0000.000
168B169THR0-0.013-0.02131.214-0.012-0.0120.0000.0000.0000.000
169B170PHE0-0.0260.00131.8490.0120.0120.0000.0000.0000.000
170B171PRO00.0150.00030.1510.0000.0000.0000.0000.0000.000
171B172ALA0-0.0060.01031.922-0.011-0.0110.0000.0000.0000.000
172B173VAL0-0.0090.00133.7970.0070.0070.0000.0000.0000.000
173B174LEU0-0.025-0.01435.668-0.006-0.0060.0000.0000.0000.000
174B175GLN0-0.029-0.01937.438-0.006-0.0060.0000.0000.0000.000
175B176SER00.0520.00241.0270.0030.0030.0000.0000.0000.000
176B177SER0-0.018-0.00843.5270.0020.0020.0000.0000.0000.000
177B178GLY00.0200.02539.645-0.002-0.0020.0000.0000.0000.000
178B179LEU0-0.091-0.03638.7660.0040.0040.0000.0000.0000.000
179B180TYR00.0200.00532.5720.0010.0010.0000.0000.0000.000
180B181SER0-0.051-0.02037.669-0.008-0.0080.0000.0000.0000.000
181B182LEU00.0530.03232.4750.0050.0050.0000.0000.0000.000
182B183SER00.013-0.00236.780-0.009-0.0090.0000.0000.0000.000
183B184SER00.0080.02934.6470.0040.0040.0000.0000.0000.000
184B185VAL00.038-0.00336.815-0.008-0.0080.0000.0000.0000.000
185B186VAL0-0.0010.00737.4050.0050.0050.0000.0000.0000.000
186B187THR0-0.034-0.01939.233-0.005-0.0050.0000.0000.0000.000
187B188VAL00.0620.00840.9410.0000.0000.0000.0000.0000.000
188B189PRO00.0450.04742.931-0.001-0.0010.0000.0000.0000.000
189B190SER00.017-0.00345.959-0.002-0.0020.0000.0000.0000.000
190B191SER0-0.031-0.03149.162-0.001-0.0010.0000.0000.0000.000
191B192SER0-0.015-0.03448.741-0.002-0.0020.0000.0000.0000.000
192B193LEU0-0.057-0.01645.208-0.003-0.0030.0000.0000.0000.000
193B194GLY00.0250.02948.9680.0020.0020.0000.0000.0000.000
194B195THR0-0.032-0.01149.4140.0000.0000.0000.0000.0000.000
195B196GLN00.0050.00542.6750.0020.0020.0000.0000.0000.000
196B197THR00.0280.02845.5940.0010.0010.0000.0000.0000.000
197B198TYR00.0300.00241.3160.0010.0010.0000.0000.0000.000
198B199ILE00.0130.00439.6230.0010.0010.0000.0000.0000.000
199B201ASN0-0.030-0.03534.779-0.004-0.0040.0000.0000.0000.000
200B202VAL00.0450.01634.5030.0080.0080.0000.0000.0000.000
201B203ASN0-0.029-0.02229.922-0.013-0.0130.0000.0000.0000.000
202B204HIS00.0560.01632.1490.0130.0130.0000.0000.0000.000
203B205LYS10.9060.95329.304-0.147-0.1470.0000.0000.0000.000
204B206PRO0-0.004-0.00632.019-0.005-0.0050.0000.0000.0000.000
205B207SER00.0020.01035.453-0.006-0.0060.0000.0000.0000.000
206B208ASN00.0120.01134.3100.0050.0050.0000.0000.0000.000
207B209THR0-0.021-0.01737.552-0.003-0.0030.0000.0000.0000.000
208B210LYS10.9340.96836.778-0.045-0.0450.0000.0000.0000.000
209B211VAL00.0340.02540.502-0.005-0.0050.0000.0000.0000.000
210B212ASP-1-0.806-0.88842.7450.0430.0430.0000.0000.0000.000
211B213LYN0-0.041-0.02542.2010.0000.0000.0000.0000.0000.000
212B214LYS10.8770.92846.133-0.039-0.0390.0000.0000.0000.000
213B215VAL0-0.001-0.00349.6530.0020.0020.0000.0000.0000.000
214B216GLU-1-0.916-0.96651.9740.0420.0420.0000.0000.0000.000
215B217PRO0-0.046-0.00855.1300.0000.0000.0000.0000.0000.000