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: MN67Z

Calculation Name: 2YMQ-B-Xray372

Preferred Name:

Target Type:

Ligand Name: aspartic acid-4-carboxyethyl ester

ligand 3-letter code: ASL

PDB ID: 2YMQ

Chain ID: B

ChEMBL ID:

UniProt ID: R4GRT2

Base Structure: X-ray

Registration Date: 2023-09-20

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 225
LigandCharge ASL=-1
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2671621.108335
FMO2-HF: Nuclear repulsion 2585886.410008
FMO2-HF: Total energy -85734.698327
FMO2-MP2: Total energy -85986.832459


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:12:SER)


Summations of interaction energy for fragment #1(B:12:SER)
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.
-19.194-11.0166.303-5.845-8.639-0.046
Interaction energy analysis for fragmet #1(B:12:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.015 / q_NPA : -0.014
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].
3B14ILE0-0.025-0.0193.853-2.366-0.989-0.017-0.720-0.6410.002
4B15LEU0-0.024-0.0046.0190.1260.1260.0000.0000.0000.000
5B16VAL00.0220.0098.5200.1590.1590.0000.0000.0000.000
6B17PHE00.1200.1299.9100.0560.0560.0000.0000.0000.000
7B18ASL0-0.794-0.88514.4450.3240.3240.0000.0000.0000.000
8B19VAL-1-0.078-0.13218.695-0.435-0.4350.0000.0000.0000.000
9B20ASN0-0.0230.00620.160-0.013-0.0130.0000.0000.0000.000
10B21GLU-1-0.796-0.87322.970-0.271-0.2710.0000.0000.0000.000
11B22THR00.014-0.02317.212-0.021-0.0210.0000.0000.0000.000
12B23LEU0-0.013-0.00315.569-0.042-0.0420.0000.0000.0000.000
13B24LEU00.000-0.00619.5940.0020.0020.0000.0000.0000.000
14B25ASP-1-0.795-0.88323.207-0.271-0.2710.0000.0000.0000.000
15B26LEU00.0640.01426.1670.0240.0240.0000.0000.0000.000
16B27THR0-0.086-0.04628.6670.0260.0260.0000.0000.0000.000
17B28SER00.002-0.00129.6370.0200.0200.0000.0000.0000.000
18B29LEU00.006-0.02131.2060.0140.0140.0000.0000.0000.000
19B30SER0-0.021-0.01734.1790.0130.0130.0000.0000.0000.000
20B31PRO0-0.024-0.00936.1460.0090.0090.0000.0000.0000.000
21B32LEU00.0100.02337.5720.0070.0070.0000.0000.0000.000
22B33PHE0-0.007-0.01535.7220.0070.0070.0000.0000.0000.000
23B34GLU-1-0.945-0.97240.223-0.117-0.1170.0000.0000.0000.000
24B35ARG10.7840.88642.3750.1060.1060.0000.0000.0000.000
25B36VAL0-0.050-0.02043.1170.0050.0050.0000.0000.0000.000
26B37PHE0-0.031-0.02241.3010.0050.0050.0000.0000.0000.000
27B38GLY0-0.0040.01545.2100.0030.0030.0000.0000.0000.000
28B39ASP-1-0.794-0.90442.129-0.121-0.1210.0000.0000.0000.000
29B40ALA00.0350.01638.002-0.002-0.0020.0000.0000.0000.000
30B41LYS10.8330.90237.6120.1150.1150.0000.0000.0000.000
31B42VAL00.0300.02937.846-0.004-0.0040.0000.0000.0000.000
32B43LEU0-0.0050.01331.9740.0010.0010.0000.0000.0000.000
33B44ARG10.8490.90729.1090.2120.2120.0000.0000.0000.000
34B45GLU-1-0.820-0.87234.819-0.105-0.1050.0000.0000.0000.000
35B46TRP00.018-0.01332.420-0.005-0.0050.0000.0000.0000.000
36B47PHE00.0010.00527.0150.0000.0000.0000.0000.0000.000
37B48PRO0-0.002-0.00631.886-0.001-0.0010.0000.0000.0000.000
38B49GLU-1-0.847-0.92632.910-0.093-0.0930.0000.0000.0000.000
39B50LEU0-0.036-0.00231.2420.0070.0070.0000.0000.0000.000
40B51ILE0-0.0020.00027.9130.0040.0040.0000.0000.0000.000
41B52LEU00.0030.03631.1110.0070.0070.0000.0000.0000.000
42B53TYR00.028-0.00833.7940.0120.0120.0000.0000.0000.000
43B54SER0-0.073-0.04130.2880.0050.0050.0000.0000.0000.000
44B55GLN00.040-0.00228.450-0.005-0.0050.0000.0000.0000.000
45B56THR00.0040.01432.0000.0110.0110.0000.0000.0000.000
46B57LEU0-0.033-0.01534.3660.0090.0090.0000.0000.0000.000
47B58THR0-0.0050.00729.6060.0080.0080.0000.0000.0000.000
48B59LEU0-0.051-0.03332.9510.0090.0090.0000.0000.0000.000
49B60THR0-0.071-0.03634.8740.0070.0070.0000.0000.0000.000
50B61GLY0-0.0280.00435.7920.0050.0050.0000.0000.0000.000
51B62LEU0-0.047-0.01836.4850.0040.0040.0000.0000.0000.000
52B63TYR00.013-0.02129.928-0.007-0.0070.0000.0000.0000.000
53B64ARG10.8250.90334.3850.0570.0570.0000.0000.0000.000
54B65PRO00.0420.01531.935-0.006-0.0060.0000.0000.0000.000
55B66PHE00.0750.03828.4680.0000.0000.0000.0000.0000.000
56B67GLY00.0020.00131.341-0.002-0.0020.0000.0000.0000.000
57B68GLU-1-0.829-0.90233.272-0.062-0.0620.0000.0000.0000.000
58B69ILE00.0160.01132.7970.0030.0030.0000.0000.0000.000
59B70ALA0-0.007-0.01033.1110.0000.0000.0000.0000.0000.000
60B71ALA0-0.004-0.00635.172-0.001-0.0010.0000.0000.0000.000
61B72ALA00.0660.03638.5140.0020.0020.0000.0000.0000.000
62B73VAL00.004-0.00436.6680.0030.0030.0000.0000.0000.000
63B74PHE0-0.032-0.01438.3400.0000.0000.0000.0000.0000.000
64B75GLU-1-0.882-0.96040.026-0.074-0.0740.0000.0000.0000.000
65B76MET0-0.042-0.00140.5650.0040.0040.0000.0000.0000.000
66B77VAL00.0050.00139.4310.0020.0020.0000.0000.0000.000
67B78ALA00.016-0.00942.8320.0010.0010.0000.0000.0000.000
68B79ALA0-0.012-0.00645.2630.0030.0030.0000.0000.0000.000
69B80ASN0-0.008-0.00643.6710.0070.0070.0000.0000.0000.000
70B81HIS10.7440.85443.0450.0960.0960.0000.0000.0000.000
71B82GLN0-0.069-0.02647.7980.0030.0030.0000.0000.0000.000
72B83ALA00.0050.02146.9200.0020.0020.0000.0000.0000.000
73B84LYS10.9360.96048.5440.0640.0640.0000.0000.0000.000
74B85VAL00.0470.02544.383-0.004-0.0040.0000.0000.0000.000
75B86THR0-0.083-0.04546.6670.0050.0050.0000.0000.0000.000
76B87PRO00.040-0.01345.562-0.004-0.0040.0000.0000.0000.000
77B88ASP-1-0.862-0.92044.182-0.081-0.0810.0000.0000.0000.000
78B89ASP-1-0.779-0.87742.852-0.095-0.0950.0000.0000.0000.000
79B90ILE00.0080.02140.379-0.008-0.0080.0000.0000.0000.000
80B91ALA0-0.017-0.01239.324-0.006-0.0060.0000.0000.0000.000
81B92GLU-1-0.796-0.88738.522-0.126-0.1260.0000.0000.0000.000
82B93LEU00.0140.00535.293-0.011-0.0110.0000.0000.0000.000
83B94LYS10.9610.98834.7160.0880.0880.0000.0000.0000.000
84B95THR0-0.020-0.01233.571-0.008-0.0080.0000.0000.0000.000
85B96ARG10.8400.91132.9740.1360.1360.0000.0000.0000.000
86B97LEU00.0150.01029.498-0.014-0.0140.0000.0000.0000.000
87B98THR0-0.090-0.04428.859-0.012-0.0120.0000.0000.0000.000
88B99SER0-0.019-0.01728.869-0.001-0.0010.0000.0000.0000.000
89B100MET0-0.0410.01925.9880.0000.0000.0000.0000.0000.000
90B101PRO00.0420.03026.029-0.011-0.0110.0000.0000.0000.000
91B102ALA00.0590.01620.892-0.007-0.0070.0000.0000.0000.000
92B103TYR0-0.046-0.01721.2850.0330.0330.0000.0000.0000.000
93B104PRO0-0.002-0.01621.324-0.036-0.0360.0000.0000.0000.000
94B105ASP-1-0.779-0.89518.923-0.611-0.6110.0000.0000.0000.000
95B106VAL00.0070.01516.170-0.086-0.0860.0000.0000.0000.000
96B107ALA00.0390.02015.540-0.102-0.1020.0000.0000.0000.000
97B108PRO00.0030.00815.322-0.085-0.0850.0000.0000.0000.000
98B109ALA00.0230.01513.124-0.119-0.1190.0000.0000.0000.000
99B110LEU0-0.006-0.01111.079-0.276-0.2760.0000.0000.0000.000
100B111THR00.001-0.00110.421-0.178-0.1780.0000.0000.0000.000
101B112ARG10.8290.89710.2251.0851.0850.0000.0000.0000.000
102B113LEU0-0.029-0.0046.888-0.405-0.4050.0000.0000.0000.000
103B114GLN00.0010.0025.733-1.138-1.1380.0000.0000.0000.000
104B115ASP-1-0.926-0.9616.590-1.565-1.5650.0000.0000.0000.000
105B116ALA0-0.085-0.0344.3640.3920.475-0.001-0.025-0.0570.000
106B117GLY00.0130.0042.459-9.581-6.3330.808-2.087-1.969-0.023
107B118PHE0-0.058-0.0302.323-5.494-2.0483.120-2.714-3.854-0.024
108B119ARG10.8390.8883.0891.4980.9470.0320.787-0.267-0.001
109B120LEU0-0.0020.0016.058-0.202-0.2020.0000.0000.0000.000
110B121VAL00.0140.0109.0740.2400.2400.0000.0000.0000.000
111B122THR0-0.021-0.00612.303-0.074-0.0740.0000.0000.0000.000
112B123LEU00.0210.00915.5980.0640.0640.0000.0000.0000.000
113B124THR0-0.045-0.03118.150-0.014-0.0140.0000.0000.0000.000
114B125ASN00.072-0.00421.6170.0390.0390.0000.0000.0000.000
115B126SER0-0.030-0.02024.8050.0230.0230.0000.0000.0000.000
116B127ALA00.0130.00825.6210.0020.0020.0000.0000.0000.000
117B128PRO00.0050.00025.599-0.012-0.0120.0000.0000.0000.000
118B129SER0-0.041-0.02426.9250.0030.0030.0000.0000.0000.000
119B130PRO0-0.028-0.00328.0380.0020.0020.0000.0000.0000.000
120B131ALA00.0420.04427.331-0.012-0.0120.0000.0000.0000.000
121B132PRO0-0.044-0.02526.9840.0110.0110.0000.0000.0000.000
122B133SER00.0500.00223.298-0.006-0.0060.0000.0000.0000.000
123B134PRO00.014-0.00924.391-0.008-0.0080.0000.0000.0000.000
124B135LEU00.0500.02118.409-0.011-0.0110.0000.0000.0000.000
125B136GLU-1-0.848-0.92821.767-0.208-0.2080.0000.0000.0000.000
126B137LYS10.7830.88723.3520.1700.1700.0000.0000.0000.000
127B138ALA0-0.036-0.01122.6040.0020.0020.0000.0000.0000.000
128B139GLY0-0.0100.00322.480-0.020-0.0200.0000.0000.0000.000
129B140ILE0-0.004-0.00617.421-0.030-0.0300.0000.0000.0000.000
130B141ALA00.011-0.00816.950-0.053-0.0530.0000.0000.0000.000
131B142SER0-0.023-0.01716.829-0.019-0.0190.0000.0000.0000.000
132B143PHE00.0110.01212.5310.0250.0250.0000.0000.0000.000
133B144PHE0-0.040-0.01911.702-0.136-0.1360.0000.0000.0000.000
134B145GLU-1-0.804-0.8629.1240.1460.1460.0000.0000.0000.000
135B146ALA0-0.013-0.00813.0660.1060.1060.0000.0000.0000.000
136B147HIS0-0.0080.00215.333-0.082-0.0820.0000.0000.0000.000
137B148LEU00.0040.01215.9160.0470.0470.0000.0000.0000.000
138B149THR0-0.005-0.01519.432-0.027-0.0270.0000.0000.0000.000
139B150VAL00.0160.01222.5710.0210.0210.0000.0000.0000.000
140B151HIS00.0170.02224.7850.0120.0120.0000.0000.0000.000
141B152SER0-0.027-0.01224.5600.0040.0040.0000.0000.0000.000
142B153SER00.0220.01024.6700.0140.0140.0000.0000.0000.000
143B154GLN0-0.071-0.02527.2200.0030.0030.0000.0000.0000.000
144B155ARG10.9050.94727.9220.0100.0100.0000.0000.0000.000
145B156PHE0-0.0050.00026.969-0.006-0.0060.0000.0000.0000.000
146B157LYS10.7950.90119.8250.2940.2940.0000.0000.0000.000
147B158PRO0-0.024-0.00623.7800.0020.0020.0000.0000.0000.000
148B159HIS00.020-0.00224.7200.0130.0130.0000.0000.0000.000
149B160PRO00.0850.01723.286-0.006-0.0060.0000.0000.0000.000
150B161SER00.0100.00322.7320.0090.0090.0000.0000.0000.000
151B162VAL0-0.0070.02221.1240.0120.0120.0000.0000.0000.000
152B163TYR0-0.007-0.01117.9990.0110.0110.0000.0000.0000.000
153B164ASP-1-0.810-0.89518.2450.0800.0800.0000.0000.0000.000
154B165SER0-0.002-0.00819.4510.0310.0310.0000.0000.0000.000
155B166THR0-0.016-0.01515.3100.0040.0040.0000.0000.0000.000
156B167ALA0-0.006-0.01114.6140.0190.0190.0000.0000.0000.000
157B168GLU-1-0.954-0.96915.2560.2410.2410.0000.0000.0000.000
158B169THR0-0.071-0.03717.0720.0360.0360.0000.0000.0000.000
159B170LEU0-0.066-0.03711.633-0.005-0.0050.0000.0000.0000.000
160B171GLY0-0.0290.00712.5450.1240.1240.0000.0000.0000.000
161B172ALA0-0.039-0.01210.6030.1750.1750.0000.0000.0000.000
162B173LYS10.9570.96211.364-1.226-1.2260.0000.0000.0000.000
163B174PRO00.011-0.00311.6560.0090.0090.0000.0000.0000.000
164B175GLU-1-0.933-0.96910.1270.7040.7040.0000.0000.0000.000
165B176GLU-1-0.943-0.9647.4841.5741.5740.0000.0000.0000.000
166B177LEU0-0.0130.0107.443-0.304-0.3040.0000.0000.0000.000
167B178CYS0-0.0210.0008.8390.0390.0390.0000.0000.0000.000
168B179MET0-0.0260.02510.529-0.069-0.0690.0000.0000.0000.000
169B180ILE00.0390.0219.804-0.002-0.0020.0000.0000.0000.000
170B181ALA0-0.022-0.02614.1380.0680.0680.0000.0000.0000.000
171B182CYS0-0.0180.03017.835-0.006-0.0060.0000.0000.0000.000
172B183HIS10.8720.93120.7150.3350.3350.0000.0000.0000.000
173B184ILE00.0420.02820.905-0.010-0.0100.0000.0000.0000.000
174B185TRP00.0310.01022.3530.0010.0010.0000.0000.0000.000
175B186ASP-1-0.770-0.86620.034-0.284-0.2840.0000.0000.0000.000
176B187THR00.0140.00916.5530.0040.0040.0000.0000.0000.000
177B188ILE00.0090.01018.7240.0160.0160.0000.0000.0000.000
178B189GLY00.0250.00121.3940.0260.0260.0000.0000.0000.000
179B190ALA00.0130.00816.1850.0310.0310.0000.0000.0000.000
180B191GLN00.022-0.00716.2250.0020.0020.0000.0000.0000.000
181B192ALA0-0.036-0.00518.1730.0430.0430.0000.0000.0000.000
182B193ARG10.7420.85918.5100.0060.0060.0000.0000.0000.000
183B194GLY00.0050.00217.0650.0480.0480.0000.0000.0000.000
184B195TRP0-0.030-0.01213.3790.0080.0080.0000.0000.0000.000
185B196ARG10.9700.9819.5340.2400.2400.0000.0000.0000.000
186B197GLY0-0.016-0.01412.837-0.011-0.0110.0000.0000.0000.000
187B198GLY0-0.015-0.01812.825-0.043-0.0430.0000.0000.0000.000
188B199PHE00.001-0.01613.7320.0320.0320.0000.0000.0000.000
189B200VAL00.010-0.00216.111-0.041-0.0410.0000.0000.0000.000
190B201ALA0-0.015-0.00517.8820.0530.0530.0000.0000.0000.000
191B202ARG10.7720.87719.2960.4930.4930.0000.0000.0000.000
192B203PRO00.0470.00323.6040.0210.0210.0000.0000.0000.000
193B204HIS0-0.053-0.03127.2920.0130.0130.0000.0000.0000.000
194B205ASN0-0.068-0.03524.3610.0210.0210.0000.0000.0000.000
195B206THR0-0.001-0.00524.604-0.024-0.0240.0000.0000.0000.000
196B207PRO00.023-0.00522.0030.0100.0100.0000.0000.0000.000
197B208LEU00.0060.01224.3600.0160.0160.0000.0000.0000.000
198B209THR0-0.016-0.01225.300-0.004-0.0040.0000.0000.0000.000
199B210LEU00.003-0.00327.3450.0110.0110.0000.0000.0000.000
200B211ALA00.015-0.00628.025-0.004-0.0040.0000.0000.0000.000
201B212GLU-1-0.975-0.99128.115-0.049-0.0490.0000.0000.0000.000
202B213VAL00.0130.02624.5940.0060.0060.0000.0000.0000.000
203B214PRO0-0.059-0.01620.450-0.008-0.0080.0000.0000.0000.000
204B215GLN00.003-0.00519.3260.0030.0030.0000.0000.0000.000
205B216PRO0-0.013-0.01016.7560.0050.0050.0000.0000.0000.000
206B217ASP-1-0.859-0.92612.889-0.362-0.3620.0000.0000.0000.000
207B218PHE0-0.016-0.0018.994-0.084-0.0840.0000.0000.0000.000
208B219ILE0-0.007-0.01213.8250.0490.0490.0000.0000.0000.000
209B220GLY00.0050.02116.449-0.018-0.0180.0000.0000.0000.000
210B221ARG10.8020.84617.2060.4660.4660.0000.0000.0000.000
211B222ASP-1-0.861-0.91818.579-0.556-0.5560.0000.0000.0000.000
212B223MET00.006-0.00214.013-0.080-0.0800.0000.0000.0000.000
213B224GLY0-0.0160.00114.099-0.151-0.1510.0000.0000.0000.000
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215B226LEU00.000-0.01011.745-0.041-0.0410.0000.0000.0000.000
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