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

tag_button

FMODB ID: 37NNL

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 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 214
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1997385.976376
FMO2-HF: Nuclear repulsion 1917679.551236
FMO2-HF: Total energy -79706.42514
FMO2-MP2: Total energy -79939.581325


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.
-2.2360.33713.208-8.392-7.391-0.013
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 : -0.004 / 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].
3L3VAL00.0640.0063.755-3.1261.114-0.043-2.356-1.8420.010
4L4LEU00.0200.0117.0490.1080.1080.0000.0000.0000.000
5L5THR00.0020.01310.2400.0580.0580.0000.0000.0000.000
6L6GLN00.020-0.03313.551-0.017-0.0170.0000.0000.0000.000
7L7PRO00.0030.02216.814-0.007-0.0070.0000.0000.0000.000
8L8PRO00.1010.04919.6200.0110.0110.0000.0000.0000.000
9L9SER0-0.071-0.02821.3630.0260.0260.0000.0000.0000.000
10L10VAL00.0290.00924.1520.0000.0000.0000.0000.0000.000
11L11SER00.0460.02426.8580.0090.0090.0000.0000.0000.000
12L12GLY00.0040.00530.467-0.002-0.0020.0000.0000.0000.000
13L13ALA0-0.027-0.00533.0300.0020.0020.0000.0000.0000.000
14L14PRO00.1360.05036.063-0.003-0.0030.0000.0000.0000.000
15L15GLY0-0.063-0.02837.3360.0040.0040.0000.0000.0000.000
16L16GLN0-0.0070.00732.9270.0060.0060.0000.0000.0000.000
17L17ARG10.9760.98428.6630.1680.1680.0000.0000.0000.000
18L18VAL0-0.042-0.00827.900-0.001-0.0010.0000.0000.0000.000
19L19THR0-0.010-0.01423.8890.0110.0110.0000.0000.0000.000
20L20ILE00.0030.00320.087-0.007-0.0070.0000.0000.0000.000
21L21SER00.0220.01018.822-0.003-0.0030.0000.0000.0000.000
22L22CYS0-0.041-0.01213.847-0.034-0.0340.0000.0000.0000.000
23L23THR0-0.020-0.00513.9170.0500.0500.0000.0000.0000.000
24L24GLY00.0550.02510.203-0.116-0.1160.0000.0000.0000.000
25L25SER00.0190.0017.1570.0730.0730.0000.0000.0000.000
26L26ASN00.028-0.0199.197-0.062-0.0620.0000.0000.0000.000
27L27SER0-0.0030.0023.928-0.546-0.400-0.001-0.019-0.1270.000
28L28ASN00.0290.0325.4830.3380.3380.0000.0000.0000.000
29L29ILE00.0010.0107.6380.2900.2900.0000.0000.0000.000
30L30GLY0-0.026-0.02210.5420.1440.1440.0000.0000.0000.000
31L31ALA0-0.044-0.0068.7890.1180.1180.0000.0000.0000.000
32L32GLY0-0.009-0.00310.8220.1170.1170.0000.0000.0000.000
33L33PHE0-0.054-0.0127.5520.0090.0090.0000.0000.0000.000
34L34THR00.0190.00211.879-0.035-0.0350.0000.0000.0000.000
35L35VAL0-0.031-0.00612.850-0.073-0.0730.0000.0000.0000.000
36L36HIS00.0110.03114.8560.0610.0610.0000.0000.0000.000
37L37TRP00.0290.00116.282-0.069-0.0690.0000.0000.0000.000
38L38TYR0-0.008-0.02916.0170.0520.0520.0000.0000.0000.000
39L39GLN0-0.008-0.02920.705-0.010-0.0100.0000.0000.0000.000
40L40HIS0-0.074-0.04822.354-0.010-0.0100.0000.0000.0000.000
41L41LEU00.1460.08324.378-0.010-0.0100.0000.0000.0000.000
42L42PRO00.0560.03824.6090.0120.0120.0000.0000.0000.000
43L43GLY0-0.045-0.00126.2380.0050.0050.0000.0000.0000.000
44L44THR0-0.061-0.08327.5690.0170.0170.0000.0000.0000.000
45L45ALA00.0280.03224.930-0.015-0.0150.0000.0000.0000.000
46L46PRO0-0.042-0.02920.5280.0070.0070.0000.0000.0000.000
47L47LYS11.0051.02423.4090.1740.1740.0000.0000.0000.000
48L48LEU0-0.0090.00620.338-0.019-0.0190.0000.0000.0000.000
49L49LEU0-0.030-0.02822.2590.0170.0170.0000.0000.0000.000
50L50ILE0-0.012-0.02120.8970.0180.0180.0000.0000.0000.000
51L51PHE00.017-0.00819.486-0.028-0.0280.0000.0000.0000.000
52L52ALA00.0310.00718.0880.0190.0190.0000.0000.0000.000
53L53ASN0-0.031-0.01317.106-0.013-0.0130.0000.0000.0000.000
54L54THR0-0.010-0.01719.492-0.011-0.0110.0000.0000.0000.000
55L55ASN0-0.0290.00122.5200.0270.0270.0000.0000.0000.000
56L56ARG10.9180.99523.9210.1160.1160.0000.0000.0000.000
57L57PRO00.0210.03425.0340.0130.0130.0000.0000.0000.000
58L58SER00.0490.02727.8580.0000.0000.0000.0000.0000.000
59L59GLY00.001-0.01031.1810.0000.0000.0000.0000.0000.000
60L60VAL0-0.070-0.02627.004-0.004-0.0040.0000.0000.0000.000
61L61PRO00.005-0.01030.3390.0050.0050.0000.0000.0000.000
62L62ASP-1-0.896-0.97730.801-0.111-0.1110.0000.0000.0000.000
63L63ARG10.8590.89831.8870.1370.1370.0000.0000.0000.000
64L64PHE00.0050.03626.532-0.009-0.0090.0000.0000.0000.000
65L65SER0-0.025-0.02026.4370.0100.0100.0000.0000.0000.000
66L66GLY00.0410.02422.453-0.017-0.0170.0000.0000.0000.000
67L67SER0-0.037-0.00921.7330.0210.0210.0000.0000.0000.000
68L68LYS10.9750.96715.4380.2550.2550.0000.0000.0000.000
69L69SER0-0.0200.00018.4780.0400.0400.0000.0000.0000.000
70L70GLY00.0690.04317.185-0.036-0.0360.0000.0000.0000.000
71L71THR00.0050.00412.5420.0270.0270.0000.0000.0000.000
72L72SER00.005-0.00513.637-0.112-0.1120.0000.0000.0000.000
73L73ALA0-0.008-0.00815.9490.0570.0570.0000.0000.0000.000
74L74SER0-0.055-0.03217.445-0.023-0.0230.0000.0000.0000.000
75L75LEU00.0390.03520.4390.0190.0190.0000.0000.0000.000
76L76ALA0-0.052-0.02522.734-0.002-0.0020.0000.0000.0000.000
77L77ILE00.0420.02526.1360.0050.0050.0000.0000.0000.000
78L78THR0-0.040-0.03429.1050.0010.0010.0000.0000.0000.000
79L79GLY00.0440.02132.7870.0020.0020.0000.0000.0000.000
80L80LEU0-0.082-0.03130.6390.0010.0010.0000.0000.0000.000
81L81GLN00.0500.02333.9960.0090.0090.0000.0000.0000.000
82L82ALA00.0460.03134.114-0.008-0.0080.0000.0000.0000.000
83L83GLU-1-0.875-0.94634.111-0.130-0.1300.0000.0000.0000.000
84L84ASP-1-0.855-0.89530.192-0.161-0.1610.0000.0000.0000.000
85L85GLU-1-0.863-0.92229.280-0.183-0.1830.0000.0000.0000.000
86L86ALA0-0.059-0.03226.6890.0030.0030.0000.0000.0000.000
87L87ASP-1-0.838-0.91421.878-0.300-0.3000.0000.0000.0000.000
88L88TYR0-0.034-0.01821.4060.0140.0140.0000.0000.0000.000
89L89TYR0-0.0120.02016.074-0.030-0.0300.0000.0000.0000.000
90L91GLN00.0280.03811.6830.0100.0100.0000.0000.0000.000
91L92SER0-0.021-0.0459.0260.0550.0550.0000.0000.0000.000
92L93TYR00.0060.0037.6640.0100.0100.0000.0000.0000.000
93L94ASP-1-0.710-0.8532.649-5.446-2.1911.030-2.357-1.928-0.028
94L95SER00.0360.0024.8330.4070.4070.0000.0000.0000.000
95L96SER0-0.049-0.0084.6171.0861.287-0.001-0.010-0.1900.000
96L97LEU0-0.072-0.0307.030-0.195-0.1950.0000.0000.0000.000
97L98SER00.0290.0475.3530.0590.0590.0000.0000.0000.000
98L99ALA0-0.015-0.0187.398-0.072-0.0720.0000.0000.0000.000
99L100ARG10.7700.8741.7723.890-1.37912.223-3.650-3.3040.005
100L101PHE00.0280.0178.2750.0920.0920.0000.0000.0000.000
101L102GLY00.0150.02010.660-0.148-0.1480.0000.0000.0000.000
102L103GLY0-0.024-0.01812.6310.0470.0470.0000.0000.0000.000
103L104GLY00.0180.02114.9680.0480.0480.0000.0000.0000.000
104L105THR0-0.067-0.03318.220-0.015-0.0150.0000.0000.0000.000
105L106ARG10.8620.91421.2810.2750.2750.0000.0000.0000.000
106L107LEU0-0.070-0.04224.6470.0010.0010.0000.0000.0000.000
107L108THR0-0.053-0.03927.2840.0100.0100.0000.0000.0000.000
108L109VAL0-0.0030.00330.794-0.001-0.0010.0000.0000.0000.000
109L110LEU0-0.017-0.01133.8050.0070.0070.0000.0000.0000.000
110L111GLY00.0410.00336.6420.0030.0030.0000.0000.0000.000
111L112GLN0-0.0050.03736.4060.0060.0060.0000.0000.0000.000
112L113PRO00.0100.01641.128-0.003-0.0030.0000.0000.0000.000
113L114LYS10.8940.94642.2470.1120.1120.0000.0000.0000.000
114L115ALA0-0.026-0.00942.7920.0050.0050.0000.0000.0000.000
115L116ALA0-0.017-0.01143.310-0.006-0.0060.0000.0000.0000.000
116L117PRO00.0310.00442.5480.0010.0010.0000.0000.0000.000
117L118SER00.0260.04144.9740.0050.0050.0000.0000.0000.000
118L119VAL0-0.031-0.02645.134-0.004-0.0040.0000.0000.0000.000
119L120THR0-0.018-0.01547.0620.0050.0050.0000.0000.0000.000
120L121LEU0-0.056-0.01047.620-0.004-0.0040.0000.0000.0000.000
121L122PHE00.0030.00348.6720.0030.0030.0000.0000.0000.000
122L123PRO00.0260.02149.758-0.003-0.0030.0000.0000.0000.000
123L124PRO00.0500.01650.9320.0000.0000.0000.0000.0000.000
124L125SER00.0440.03452.1250.0020.0020.0000.0000.0000.000
125L126SER00.048-0.00354.3470.0000.0000.0000.0000.0000.000
126L127GLU-1-0.908-0.95254.397-0.053-0.0530.0000.0000.0000.000
127L128GLU-1-0.856-0.87747.954-0.074-0.0740.0000.0000.0000.000
128L129LEU00.0100.00052.5620.0000.0000.0000.0000.0000.000
129L130GLN0-0.073-0.02954.6660.0020.0020.0000.0000.0000.000
130L131ALA0-0.087-0.02952.1290.0020.0020.0000.0000.0000.000
131L132ASN0-0.022-0.01951.8960.0000.0000.0000.0000.0000.000
132L133LYS10.9050.93646.4340.0650.0650.0000.0000.0000.000
133L134ALA0-0.007-0.00148.8570.0020.0020.0000.0000.0000.000
134L135THR0-0.023-0.04544.702-0.004-0.0040.0000.0000.0000.000
135L136LEU0-0.050-0.00646.5060.0030.0030.0000.0000.0000.000
136L137VAL00.014-0.00344.534-0.005-0.0050.0000.0000.0000.000
137L138CYS0-0.0660.00443.356-0.001-0.0010.0000.0000.0000.000
138L139LEU0-0.002-0.01342.999-0.006-0.0060.0000.0000.0000.000
139L140ILE00.0360.01440.5280.0030.0030.0000.0000.0000.000
140L141SER0-0.032-0.02441.499-0.004-0.0040.0000.0000.0000.000
141L142ASP-1-0.844-0.92942.696-0.095-0.0950.0000.0000.0000.000
142L143PHE0-0.020-0.00437.2300.0010.0010.0000.0000.0000.000
143L144TYR0-0.027-0.06336.146-0.009-0.0090.0000.0000.0000.000
144L145PRO00.0590.00536.1070.0070.0070.0000.0000.0000.000
145L146GLY0-0.0110.00934.3780.0060.0060.0000.0000.0000.000
146L147ALA00.0090.00133.758-0.009-0.0090.0000.0000.0000.000
147L148VAL0-0.045-0.02235.1420.0090.0090.0000.0000.0000.000
148L149THR00.0230.01936.189-0.008-0.0080.0000.0000.0000.000
149L150VAL00.017-0.00137.9960.0070.0070.0000.0000.0000.000
150L151ALA0-0.023-0.00739.473-0.003-0.0030.0000.0000.0000.000
151L152TRP00.0810.02641.3030.0070.0070.0000.0000.0000.000
152L153LYS10.8520.92244.5150.0810.0810.0000.0000.0000.000
153L154ALA00.0540.04647.6090.0010.0010.0000.0000.0000.000
154L155ASP-1-0.833-0.93450.241-0.061-0.0610.0000.0000.0000.000
155L156SER0-0.050-0.03651.669-0.001-0.0010.0000.0000.0000.000
156L157SER00.005-0.00348.276-0.002-0.0020.0000.0000.0000.000
157L158PRO0-0.035-0.02243.6860.0000.0000.0000.0000.0000.000
158L159VAL0-0.0010.02043.2950.0010.0010.0000.0000.0000.000
159L160ASN00.012-0.01437.468-0.001-0.0010.0000.0000.0000.000
160L161ALA0-0.041-0.01239.005-0.005-0.0050.0000.0000.0000.000
161L162GLY00.0590.02839.3520.0040.0040.0000.0000.0000.000
162L163VAL00.0050.00537.7760.0030.0030.0000.0000.0000.000
163L164GLU-1-0.915-0.94034.679-0.145-0.1450.0000.0000.0000.000
164L165THR00.0100.00835.2560.0090.0090.0000.0000.0000.000
165L166THR0-0.0200.00933.537-0.006-0.0060.0000.0000.0000.000
166L167LYS10.9690.97927.9110.2060.2060.0000.0000.0000.000
167L168PRO00.009-0.00432.1140.0050.0050.0000.0000.0000.000
168L169SER0-0.042-0.02532.335-0.011-0.0110.0000.0000.0000.000
169L170LYS10.8840.95532.9190.1680.1680.0000.0000.0000.000
170L171GLN00.0650.01635.3740.0000.0000.0000.0000.0000.000
171L172SER00.012-0.00738.460-0.001-0.0010.0000.0000.0000.000
172L173ASN0-0.0120.01639.970-0.003-0.0030.0000.0000.0000.000
173L174ASN0-0.022-0.02637.347-0.005-0.0050.0000.0000.0000.000
174L175LYS10.9320.99538.8090.0940.0940.0000.0000.0000.000
175L176TYR0-0.026-0.01332.328-0.003-0.0030.0000.0000.0000.000
176L177ALA00.0490.03337.4510.0070.0070.0000.0000.0000.000
177L178ALA0-0.041-0.02936.978-0.010-0.0100.0000.0000.0000.000
178L179SER00.0360.01237.7230.0090.0090.0000.0000.0000.000
179L180SER0-0.072-0.04438.090-0.005-0.0050.0000.0000.0000.000
180L181TYR00.0100.01139.2550.0070.0070.0000.0000.0000.000
181L182LEU00.0180.01440.935-0.004-0.0040.0000.0000.0000.000
182L183SER0-0.028-0.00742.3000.0050.0050.0000.0000.0000.000
183L184LEU0-0.004-0.00244.305-0.001-0.0010.0000.0000.0000.000
184L185THR0-0.041-0.01547.4000.0010.0010.0000.0000.0000.000
185L186PRO00.057-0.00250.068-0.001-0.0010.0000.0000.0000.000
186L187GLU-1-0.845-0.91653.430-0.055-0.0550.0000.0000.0000.000
187L188GLN00.0340.00847.799-0.001-0.0010.0000.0000.0000.000
188L189TRP00.0240.02252.2240.0000.0000.0000.0000.0000.000
189L190LYS10.8890.92253.4610.0540.0540.0000.0000.0000.000
190L191SER0-0.0240.00555.1110.0010.0010.0000.0000.0000.000
191L192HIS0-0.073-0.01951.893-0.001-0.0010.0000.0000.0000.000
192L193LYS10.9530.97955.8030.0600.0600.0000.0000.0000.000
193L194SER0-0.053-0.02854.7090.0000.0000.0000.0000.0000.000
194L195TYR00.0280.00648.390-0.001-0.0010.0000.0000.0000.000
195L196SER00.0350.03749.3750.0020.0020.0000.0000.0000.000
196L198GLN0-0.021-0.03544.7350.0000.0000.0000.0000.0000.000
197L199VAL00.002-0.00142.481-0.005-0.0050.0000.0000.0000.000
198L200THR00.0330.02340.8280.0030.0030.0000.0000.0000.000
199L201HIS10.8190.88739.2220.1200.1200.0000.0000.0000.000
200L202GLU-1-0.904-0.94538.399-0.130-0.1300.0000.0000.0000.000
201L203GLY00.015-0.00241.4380.0040.0040.0000.0000.0000.000
202L204SER00.0110.01244.1460.0060.0060.0000.0000.0000.000
203L205THR00.0120.00244.660-0.006-0.0060.0000.0000.0000.000
204L206VAL0-0.0230.00446.6240.0040.0040.0000.0000.0000.000
205L207GLU-1-0.849-0.93847.464-0.083-0.0830.0000.0000.0000.000
206L208LYS10.8860.96349.3470.0790.0790.0000.0000.0000.000
207L209THR00.025-0.03250.761-0.002-0.0020.0000.0000.0000.000
208L210VAL0-0.038-0.01451.7660.0020.0020.0000.0000.0000.000
209L211ALA00.0830.04554.436-0.002-0.0020.0000.0000.0000.000
210L212PRO0-0.036-0.02455.9650.0010.0010.0000.0000.0000.000
211L213ALA00.0180.01258.3180.0010.0010.0000.0000.0000.000
212L214GLU-1-0.968-0.95060.216-0.053-0.0530.0000.0000.0000.000
213L215CYS0-0.040-0.05162.6480.0010.0010.0000.0000.0000.000
214L216SER0-0.0140.01365.0980.0010.0010.0000.0000.0000.000