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: 9MYY2

Calculation Name: 1AQK-L-Xray372

Preferred Name:

Target Type:

Ligand Name: pyroglutamic acid

ligand 3-letter code: PCA

PDB ID: 1AQK

Chain ID: L

ChEMBL ID:

UniProt ID: P01857

Base Structure: X-ray

Registration Date: 2023-09-26

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 OptAll
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 214
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1999968.435748
FMO2-HF: Nuclear repulsion 1920258.497538
FMO2-HF: Total energy -79709.93821
FMO2-MP2: Total energy -79942.89066


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(L:1:PCA)


Summations of interaction energy for fragment #1(L:1:PCA)
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.
-4.2752.0322.553-4.033-4.826-0.016
Interaction energy analysis for fragmet #1(L:1:PCA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.007 / q_NPA : -0.017
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].
3L3VAL00.0400.0173.852-1.2251.313-0.021-1.378-1.1400.004
4L4LEU00.0020.0007.2850.0630.0630.0000.0000.0000.000
5L5THR00.0200.00810.4980.1230.1230.0000.0000.0000.000
6L6GLN00.018-0.02213.760-0.014-0.0140.0000.0000.0000.000
7L7PRO00.0010.02717.146-0.006-0.0060.0000.0000.0000.000
8L8PRO00.0790.04620.6090.0060.0060.0000.0000.0000.000
9L9SER0-0.003-0.00521.6490.0210.0210.0000.0000.0000.000
10L10VAL0-0.045-0.02024.307-0.003-0.0030.0000.0000.0000.000
11L11SER0-0.038-0.05027.0020.0130.0130.0000.0000.0000.000
12L12GLY00.0280.01030.704-0.002-0.0020.0000.0000.0000.000
13L13ALA00.0150.01033.5950.0010.0010.0000.0000.0000.000
14L14PRO00.0400.00236.599-0.003-0.0030.0000.0000.0000.000
15L15GLY0-0.0100.00737.7710.0060.0060.0000.0000.0000.000
16L16GLN0-0.032-0.00733.2710.0060.0060.0000.0000.0000.000
17L17ARG10.9380.95727.7510.2300.2300.0000.0000.0000.000
18L18VAL0-0.0110.00228.3850.0000.0000.0000.0000.0000.000
19L19THR0-0.009-0.01623.8810.0170.0170.0000.0000.0000.000
20L20ILE0-0.0020.02120.274-0.002-0.0020.0000.0000.0000.000
21L21SER00.0120.01219.4590.0100.0100.0000.0000.0000.000
22L22CYS0-0.062-0.02414.190-0.038-0.0380.0000.0000.0000.000
23L23THR0-0.010-0.00213.7760.0670.0670.0000.0000.0000.000
24L24GLY00.0600.03010.122-0.151-0.1510.0000.0000.0000.000
25L25SER0-0.001-0.0126.7790.1440.1440.0000.0000.0000.000
26L26ASN00.034-0.0059.027-0.150-0.1500.0000.0000.0000.000
27L27SER00.0090.0253.712-0.826-0.6260.000-0.027-0.1720.000
28L28ASN00.0460.0215.6940.3160.3160.0000.0000.0000.000
29L29ILE00.0440.0267.6360.3610.3610.0000.0000.0000.000
30L30GLY0-0.052-0.03710.5230.2010.2010.0000.0000.0000.000
31L31ALA0-0.042-0.0078.3260.1380.1380.0000.0000.0000.000
32L32GLY00.0020.00910.4320.1620.1620.0000.0000.0000.000
33L33PHE0-0.043-0.0097.7920.0030.0030.0000.0000.0000.000
34L34THR00.0050.00211.857-0.051-0.0510.0000.0000.0000.000
35L35VAL0-0.012-0.00413.094-0.108-0.1080.0000.0000.0000.000
36L36HIS00.0090.01615.0680.0950.0950.0000.0000.0000.000
37L37TRP00.010-0.01116.614-0.087-0.0870.0000.0000.0000.000
38L38TYR0-0.007-0.01416.4570.0680.0680.0000.0000.0000.000
39L39GLN00.0480.02221.021-0.009-0.0090.0000.0000.0000.000
40L40HIS0-0.032-0.02522.823-0.012-0.0120.0000.0000.0000.000
41L41LEU00.0960.05124.806-0.003-0.0030.0000.0000.0000.000
42L42PRO00.0260.00025.0480.0120.0120.0000.0000.0000.000
43L43GLY0-0.0120.01826.9080.0050.0050.0000.0000.0000.000
44L44THR0-0.031-0.02528.3510.0200.0200.0000.0000.0000.000
45L45ALA00.0230.01825.495-0.018-0.0180.0000.0000.0000.000
46L46PRO0-0.011-0.01621.0130.0070.0070.0000.0000.0000.000
47L47LYS10.9160.97223.5660.2420.2420.0000.0000.0000.000
48L48LEU0-0.009-0.00520.502-0.021-0.0210.0000.0000.0000.000
49L49LEU0-0.060-0.02522.5060.0250.0250.0000.0000.0000.000
50L50ILE00.001-0.01221.2340.0220.0220.0000.0000.0000.000
51L51PHE00.0260.00619.583-0.039-0.0390.0000.0000.0000.000
52L52ALA00.019-0.00218.3960.0220.0220.0000.0000.0000.000
53L53ASN00.0060.00117.089-0.020-0.0200.0000.0000.0000.000
54L54THR0-0.024-0.02219.481-0.015-0.0150.0000.0000.0000.000
55L55ASN0-0.058-0.00322.6040.0370.0370.0000.0000.0000.000
56L56ARG10.8570.91924.1810.1520.1520.0000.0000.0000.000
57L57PRO0-0.0070.01125.2730.0170.0170.0000.0000.0000.000
58L58SER00.025-0.00527.9530.0000.0000.0000.0000.0000.000
59L59GLY00.0330.01531.7460.0030.0030.0000.0000.0000.000
60L60VAL0-0.075-0.01727.078-0.004-0.0040.0000.0000.0000.000
61L61PRO00.0030.00230.4810.0080.0080.0000.0000.0000.000
62L62ASP-1-0.810-0.92931.528-0.159-0.1590.0000.0000.0000.000
63L63ARG10.7430.84732.2780.1800.1800.0000.0000.0000.000
64L64PHE00.0190.02327.135-0.012-0.0120.0000.0000.0000.000
65L65SER00.000-0.00126.8730.0140.0140.0000.0000.0000.000
66L66GLY00.0410.01722.730-0.024-0.0240.0000.0000.0000.000
67L67SER0-0.024-0.01021.6490.0300.0300.0000.0000.0000.000
68L68LYS10.8880.92614.7300.4060.4060.0000.0000.0000.000
69L69SER0-0.0020.00318.5230.0540.0540.0000.0000.0000.000
70L70GLY00.0710.04317.107-0.051-0.0510.0000.0000.0000.000
71L71THR0-0.017-0.00612.1250.0610.0610.0000.0000.0000.000
72L72SER00.0200.00613.256-0.172-0.1720.0000.0000.0000.000
73L73ALA00.0120.00215.7960.0670.0670.0000.0000.0000.000
74L74SER0-0.023-0.01417.806-0.023-0.0230.0000.0000.0000.000
75L75LEU00.0190.04220.9720.0320.0320.0000.0000.0000.000
76L76ALA0-0.027-0.03022.788-0.001-0.0010.0000.0000.0000.000
77L77ILE00.0270.02526.1370.0080.0080.0000.0000.0000.000
78L78THR0-0.001-0.00829.3340.0070.0070.0000.0000.0000.000
79L79GLY00.0600.03133.1290.0000.0000.0000.0000.0000.000
80L80LEU0-0.078-0.02731.0280.0000.0000.0000.0000.0000.000
81L81GLN00.0270.02334.3140.0110.0110.0000.0000.0000.000
82L82ALA00.0450.02534.485-0.011-0.0110.0000.0000.0000.000
83L83GLU-1-0.871-0.95034.292-0.168-0.1680.0000.0000.0000.000
84L84ASP-1-0.757-0.84130.402-0.214-0.2140.0000.0000.0000.000
85L85GLU-1-0.824-0.88629.466-0.236-0.2360.0000.0000.0000.000
86L86ALA0-0.028-0.01126.7610.0030.0030.0000.0000.0000.000
87L87ASP-1-0.813-0.88322.555-0.361-0.3610.0000.0000.0000.000
88L88TYR0-0.051-0.04721.7790.0100.0100.0000.0000.0000.000
89L89TYR00.0100.02016.671-0.040-0.0400.0000.0000.0000.000
90L91GLN00.008-0.00511.9140.0090.0090.0000.0000.0000.000
91L92SER00.002-0.0069.5200.0570.0570.0000.0000.0000.000
92L93TYR00.0040.0108.0030.0390.0390.0000.0000.0000.000
93L94ASP-1-0.723-0.8342.700-6.475-3.9490.694-1.607-1.612-0.018
94L95SER00.0140.0044.149-0.543-0.321-0.001-0.034-0.1860.000
95L96SER0-0.020-0.0193.7000.1180.5880.004-0.143-0.332-0.001
96L97LEU0-0.055-0.0276.052-0.164-0.1640.0000.0000.0000.000
97L98SER0-0.007-0.0015.279-0.092-0.0920.0000.0000.0000.000
98L99ALA0-0.009-0.0127.136-0.222-0.2220.0000.0000.0000.000
99L100ARG10.7790.8852.2673.0443.3951.877-0.844-1.384-0.001
100L101PHE00.0550.0158.6470.1200.1200.0000.0000.0000.000
101L102GLY00.0080.00210.834-0.205-0.2050.0000.0000.0000.000
102L103GLY0-0.041-0.02513.0590.0710.0710.0000.0000.0000.000
103L104GLY00.0160.01515.1640.0660.0660.0000.0000.0000.000
104L105THR0-0.061-0.04918.407-0.017-0.0170.0000.0000.0000.000
105L106ARG10.7980.88021.6800.3230.3230.0000.0000.0000.000
106L107LEU0-0.042-0.01125.1940.0040.0040.0000.0000.0000.000
107L108THR0-0.009-0.01127.5910.0080.0080.0000.0000.0000.000
108L109VAL0-0.0040.01331.096-0.001-0.0010.0000.0000.0000.000
109L110LEU0-0.0190.00234.1750.0090.0090.0000.0000.0000.000
110L111GLY00.0470.00737.1750.0040.0040.0000.0000.0000.000
111L112GLN0-0.012-0.00237.1840.0080.0080.0000.0000.0000.000
112L113PRO0-0.0040.00741.762-0.003-0.0030.0000.0000.0000.000
113L114LYS10.8570.90942.1790.1380.1380.0000.0000.0000.000
114L115ALA00.0040.00743.2350.0060.0060.0000.0000.0000.000
115L116ALA00.0280.00543.713-0.007-0.0070.0000.0000.0000.000
116L117PRO0-0.0160.00243.2960.0000.0000.0000.0000.0000.000
117L118SER00.0180.02045.1710.0070.0070.0000.0000.0000.000
118L119VAL0-0.002-0.00945.687-0.005-0.0050.0000.0000.0000.000
119L120THR0-0.022-0.00347.5260.0070.0070.0000.0000.0000.000
120L121LEU0-0.024-0.00747.845-0.005-0.0050.0000.0000.0000.000
121L122PHE0-0.007-0.00148.8150.0040.0040.0000.0000.0000.000
122L123PRO00.0120.00750.267-0.003-0.0030.0000.0000.0000.000
123L124PRO00.0420.02350.948-0.001-0.0010.0000.0000.0000.000
124L125SER0-0.029-0.02452.3390.0020.0020.0000.0000.0000.000
125L126SER00.028-0.00654.5750.0000.0000.0000.0000.0000.000
126L127GLU-1-0.836-0.90054.742-0.066-0.0660.0000.0000.0000.000
127L128GLU-1-0.818-0.88548.718-0.085-0.0850.0000.0000.0000.000
128L129LEU00.001-0.00152.8800.0010.0010.0000.0000.0000.000
129L130GLN0-0.040-0.01555.1270.0030.0030.0000.0000.0000.000
130L131ALA0-0.057-0.01752.4280.0020.0020.0000.0000.0000.000
131L132ASN0-0.043-0.02652.1670.0000.0000.0000.0000.0000.000
132L133LYS10.8650.92447.0960.0750.0750.0000.0000.0000.000
133L134ALA00.0240.00449.1960.0030.0030.0000.0000.0000.000
134L135THR0-0.032-0.03844.770-0.005-0.0050.0000.0000.0000.000
135L136LEU0-0.0230.00947.3350.0020.0020.0000.0000.0000.000
136L137VAL00.0040.00044.683-0.006-0.0060.0000.0000.0000.000
137L138CYS0-0.058-0.01144.076-0.001-0.0010.0000.0000.0000.000
138L139LEU00.0090.01443.324-0.007-0.0070.0000.0000.0000.000
139L140ILE00.014-0.00140.6390.0040.0040.0000.0000.0000.000
140L141SER00.009-0.01141.948-0.005-0.0050.0000.0000.0000.000
141L142ASP-1-0.750-0.85942.884-0.118-0.1180.0000.0000.0000.000
142L143PHE00.0000.02037.3640.0020.0020.0000.0000.0000.000
143L144TYR00.014-0.00236.812-0.010-0.0100.0000.0000.0000.000
144L145PRO00.0490.01036.0490.0080.0080.0000.0000.0000.000
145L146GLY00.010-0.01534.8500.0070.0070.0000.0000.0000.000
146L147ALA0-0.011-0.00634.128-0.011-0.0110.0000.0000.0000.000
147L148VAL0-0.038-0.01235.6230.0110.0110.0000.0000.0000.000
148L149THR00.0140.01936.750-0.011-0.0110.0000.0000.0000.000
149L150VAL00.020-0.00538.5240.0080.0080.0000.0000.0000.000
150L151ALA0-0.0100.00439.796-0.004-0.0040.0000.0000.0000.000
151L152TRP00.0520.00842.0460.0070.0070.0000.0000.0000.000
152L153LYS10.8310.89545.1120.0920.0920.0000.0000.0000.000
153L154ALA00.0650.04548.2550.0010.0010.0000.0000.0000.000
154L155ASP-1-0.705-0.84150.873-0.069-0.0690.0000.0000.0000.000
155L156SER0-0.154-0.09252.0770.0010.0010.0000.0000.0000.000
156L157SER00.0150.02349.016-0.002-0.0020.0000.0000.0000.000
157L158PRO00.001-0.00244.383-0.001-0.0010.0000.0000.0000.000
158L159VAL0-0.0180.00044.5110.0030.0030.0000.0000.0000.000
159L160ASN00.000-0.01138.5630.0000.0000.0000.0000.0000.000
160L161ALA00.0230.01139.526-0.006-0.0060.0000.0000.0000.000
161L162GLY00.0460.02140.4170.0030.0030.0000.0000.0000.000
162L163VAL0-0.043-0.00838.7310.0010.0010.0000.0000.0000.000
163L164GLU-1-0.856-0.91835.077-0.172-0.1720.0000.0000.0000.000
164L165THR0-0.059-0.03835.7030.0080.0080.0000.0000.0000.000
165L166THR0-0.0160.01133.963-0.008-0.0080.0000.0000.0000.000
166L167LYS10.9920.99428.2370.2470.2470.0000.0000.0000.000
167L168PRO0-0.0050.00232.3630.0030.0030.0000.0000.0000.000
168L169SER0-0.019-0.01432.612-0.014-0.0140.0000.0000.0000.000
169L170LYS10.7940.89534.0460.2020.2020.0000.0000.0000.000
170L171GLN00.001-0.01835.9740.0010.0010.0000.0000.0000.000
171L172SER00.0360.00738.927-0.004-0.0040.0000.0000.0000.000
172L173ASN0-0.006-0.00840.553-0.005-0.0050.0000.0000.0000.000
173L174ASN00.015-0.00138.049-0.004-0.0040.0000.0000.0000.000
174L175LYS10.8470.94338.8280.1130.1130.0000.0000.0000.000
175L176TYR0-0.0090.01032.507-0.004-0.0040.0000.0000.0000.000
176L177ALA0-0.008-0.00137.9530.0090.0090.0000.0000.0000.000
177L178ALA0-0.008-0.01037.347-0.012-0.0120.0000.0000.0000.000
178L179SER0-0.040-0.02538.3320.0110.0110.0000.0000.0000.000
179L180SER0-0.023-0.00838.633-0.006-0.0060.0000.0000.0000.000
180L181TYR00.0220.00639.6600.0080.0080.0000.0000.0000.000
181L182LEU00.0080.01141.621-0.005-0.0050.0000.0000.0000.000
182L183SER0-0.020-0.00742.0070.0050.0050.0000.0000.0000.000
183L184LEU0-0.044-0.01944.680-0.001-0.0010.0000.0000.0000.000
184L185THR0-0.009-0.03547.8230.0000.0000.0000.0000.0000.000
185L186PRO00.0130.00350.589-0.001-0.0010.0000.0000.0000.000
186L187GLU-1-0.814-0.88953.492-0.065-0.0650.0000.0000.0000.000
187L188GLN00.0490.02447.5710.0000.0000.0000.0000.0000.000
188L189TRP00.0120.02152.373-0.001-0.0010.0000.0000.0000.000
189L190LYS10.9270.94753.6110.0600.0600.0000.0000.0000.000
190L191SER0-0.060-0.01355.3510.0020.0020.0000.0000.0000.000
191L192HIS0-0.057-0.01852.683-0.001-0.0010.0000.0000.0000.000
192L193LYS10.8970.94356.7760.0690.0690.0000.0000.0000.000
193L194SER0-0.061-0.06155.5490.0000.0000.0000.0000.0000.000
194L195TYR00.006-0.01149.265-0.002-0.0020.0000.0000.0000.000
195L196SER0-0.016-0.02350.0660.0020.0020.0000.0000.0000.000
196L198GLN0-0.045-0.03945.5740.0000.0000.0000.0000.0000.000
197L199VAL00.0120.00042.662-0.006-0.0060.0000.0000.0000.000
198L200THR00.005-0.01041.7580.0050.0050.0000.0000.0000.000
199L201HIS10.8120.88539.5890.1430.1430.0000.0000.0000.000
200L202GLU-1-0.841-0.91339.138-0.155-0.1550.0000.0000.0000.000
201L203GLY00.0020.00642.1660.0050.0050.0000.0000.0000.000
202L204SER0-0.0240.00544.5940.0070.0070.0000.0000.0000.000
203L205THR00.0230.00445.148-0.008-0.0080.0000.0000.0000.000
204L206VAL0-0.0210.00747.1280.0050.0050.0000.0000.0000.000
205L207GLU-1-0.752-0.84147.788-0.098-0.0980.0000.0000.0000.000
206L208LYS10.8400.92149.8570.0950.0950.0000.0000.0000.000
207L209THR00.038-0.00250.833-0.003-0.0030.0000.0000.0000.000
208L210VAL0-0.009-0.00152.0940.0020.0020.0000.0000.0000.000
209L211ALA00.0910.04254.883-0.001-0.0010.0000.0000.0000.000
210L212PRO0-0.0240.00156.3440.0010.0010.0000.0000.0000.000
211L213ALA0-0.050-0.03658.5170.0020.0020.0000.0000.0000.000
212L214GLU-1-0.931-0.95161.165-0.061-0.0610.0000.0000.0000.000
213L215CYS0-0.063-0.03563.1950.0000.0000.0000.0000.0000.000
214L216SER00.0030.00365.8060.0020.0020.0000.0000.0000.000