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: L7LL9

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 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 214
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1997651.117152
FMO2-HF: Nuclear repulsion 1917942.280013
FMO2-HF: Total energy -79708.837139
FMO2-MP2: Total energy -79941.699451


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.
-3.6242.2436.163-5.98-6.049-0.024
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 : -0.010 / 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].
3L3VAL00.0360.0013.755-1.9401.436-0.040-1.874-1.4620.006
4L4LEU00.0210.0127.0480.0860.0860.0000.0000.0000.000
5L5THR00.0100.01010.2490.1030.1030.0000.0000.0000.000
6L6GLN00.015-0.02213.556-0.025-0.0250.0000.0000.0000.000
7L7PRO0-0.0070.02416.8170.0020.0020.0000.0000.0000.000
8L8PRO00.1040.05720.0340.0080.0080.0000.0000.0000.000
9L9SER0-0.0050.00021.3820.0220.0220.0000.0000.0000.000
10L10VAL0-0.024-0.01424.1360.0000.0000.0000.0000.0000.000
11L11SER0-0.012-0.02126.8580.0140.0140.0000.0000.0000.000
12L12GLY00.0170.01530.468-0.004-0.0040.0000.0000.0000.000
13L13ALA0-0.0240.00333.0350.0020.0020.0000.0000.0000.000
14L14PRO00.1210.03436.071-0.004-0.0040.0000.0000.0000.000
15L15GLY0-0.051-0.01937.3430.0050.0050.0000.0000.0000.000
16L16GLN0-0.021-0.00233.0030.0070.0070.0000.0000.0000.000
17L17ARG10.9430.96628.0800.2320.2320.0000.0000.0000.000
18L18VAL0-0.035-0.00527.8570.0000.0000.0000.0000.0000.000
19L19THR00.004-0.01323.8580.0130.0130.0000.0000.0000.000
20L20ILE0-0.0030.01420.099-0.005-0.0050.0000.0000.0000.000
21L21SER00.0330.01518.9900.0120.0120.0000.0000.0000.000
22L22CYS0-0.047-0.00313.827-0.048-0.0480.0000.0000.0000.000
23L23THR0-0.0080.00213.7640.0450.0450.0000.0000.0000.000
24L24GLY00.0530.02110.233-0.145-0.1450.0000.0000.0000.000
25L25SER00.007-0.0166.9590.1060.1060.0000.0000.0000.000
26L26ASN00.001-0.0229.152-0.089-0.0890.0000.0000.0000.000
27L27SER00.0160.0153.930-0.889-0.737-0.001-0.018-0.1330.000
28L28ASN00.0630.0515.9970.5310.5310.0000.0000.0000.000
29L29ILE00.0240.0147.6940.3990.3990.0000.0000.0000.000
30L30GLY0-0.050-0.03010.5380.2080.2080.0000.0000.0000.000
31L31ALA0-0.029-0.0038.9200.1600.1600.0000.0000.0000.000
32L32GLY00.0030.00610.9120.1410.1410.0000.0000.0000.000
33L33PHE0-0.053-0.0117.7670.0020.0020.0000.0000.0000.000
34L34THR00.0150.00311.927-0.032-0.0320.0000.0000.0000.000
35L35VAL0-0.052-0.02512.882-0.107-0.1070.0000.0000.0000.000
36L36HIS00.0290.03614.8840.0880.0880.0000.0000.0000.000
37L37TRP00.026-0.00116.293-0.087-0.0870.0000.0000.0000.000
38L38TYR0-0.011-0.00816.0690.0670.0670.0000.0000.0000.000
39L39GLN00.0360.01020.701-0.008-0.0080.0000.0000.0000.000
40L40HIS0-0.073-0.06122.376-0.010-0.0100.0000.0000.0000.000
41L41LEU00.1090.06124.359-0.009-0.0090.0000.0000.0000.000
42L42PRO00.0540.02324.3440.0150.0150.0000.0000.0000.000
43L43GLY0-0.0470.01026.3420.0060.0060.0000.0000.0000.000
44L44THR0-0.011-0.04227.7060.0210.0210.0000.0000.0000.000
45L45ALA00.0120.03125.102-0.017-0.0170.0000.0000.0000.000
46L46PRO0-0.022-0.02220.6300.0060.0060.0000.0000.0000.000
47L47LYS10.9370.97923.3890.2430.2430.0000.0000.0000.000
48L48LEU00.0060.01320.216-0.024-0.0240.0000.0000.0000.000
49L49LEU0-0.054-0.03422.2620.0240.0240.0000.0000.0000.000
50L50ILE00.012-0.01521.1780.0220.0220.0000.0000.0000.000
51L51PHE00.006-0.00819.501-0.041-0.0410.0000.0000.0000.000
52L52ALA00.0360.00418.1150.0250.0250.0000.0000.0000.000
53L53ASN0-0.019-0.00816.978-0.019-0.0190.0000.0000.0000.000
54L54THR0-0.021-0.02419.528-0.009-0.0090.0000.0000.0000.000
55L55ASN0-0.043-0.00122.3990.0420.0420.0000.0000.0000.000
56L56ARG10.8690.93623.9450.1630.1630.0000.0000.0000.000
57L57PRO00.0050.02525.0620.0170.0170.0000.0000.0000.000
58L58SER00.0500.02427.8730.0020.0020.0000.0000.0000.000
59L59GLY00.008-0.00731.190-0.001-0.0010.0000.0000.0000.000
60L60VAL0-0.062-0.02527.013-0.002-0.0020.0000.0000.0000.000
61L61PRO0-0.005-0.01130.3490.0060.0060.0000.0000.0000.000
62L62ASP-1-0.823-0.93130.817-0.166-0.1660.0000.0000.0000.000
63L63ARG10.7380.84631.9100.1830.1830.0000.0000.0000.000
64L64PHE00.0180.02626.464-0.013-0.0130.0000.0000.0000.000
65L65SER00.0190.00926.4660.0120.0120.0000.0000.0000.000
66L66GLY00.0260.01922.484-0.020-0.0200.0000.0000.0000.000
67L67SER0-0.034-0.00521.7620.0260.0260.0000.0000.0000.000
68L68LYS10.8960.93214.7280.4740.4740.0000.0000.0000.000
69L69SER00.0010.00418.5340.0510.0510.0000.0000.0000.000
70L70GLY00.0740.04717.162-0.046-0.0460.0000.0000.0000.000
71L71THR0-0.006-0.00312.4340.0260.0260.0000.0000.0000.000
72L72SER00.018-0.00113.683-0.144-0.1440.0000.0000.0000.000
73L73ALA00.001-0.00715.9930.0680.0680.0000.0000.0000.000
74L74SER0-0.017-0.01717.482-0.019-0.0190.0000.0000.0000.000
75L75LEU00.0070.02320.4680.0220.0220.0000.0000.0000.000
76L76ALA0-0.047-0.02422.7560.0010.0010.0000.0000.0000.000
77L77ILE00.0400.02625.9450.0050.0050.0000.0000.0000.000
78L78THR0-0.025-0.01729.1210.0080.0080.0000.0000.0000.000
79L79GLY00.0600.03032.8050.0010.0010.0000.0000.0000.000
80L80LEU0-0.073-0.03030.4300.0000.0000.0000.0000.0000.000
81L81GLN00.0160.01933.9890.0120.0120.0000.0000.0000.000
82L82ALA00.0490.03334.112-0.011-0.0110.0000.0000.0000.000
83L83GLU-1-0.849-0.93734.102-0.166-0.1660.0000.0000.0000.000
84L84ASP-1-0.797-0.85730.149-0.214-0.2140.0000.0000.0000.000
85L85GLU-1-0.840-0.90029.274-0.231-0.2310.0000.0000.0000.000
86L86ALA0-0.055-0.02326.6380.0050.0050.0000.0000.0000.000
87L87ASP-1-0.810-0.88222.005-0.357-0.3570.0000.0000.0000.000
88L88TYR0-0.042-0.03621.4000.0120.0120.0000.0000.0000.000
89L89TYR0-0.0140.01816.174-0.031-0.0310.0000.0000.0000.000
90L91GLN00.009-0.00611.4850.0340.0340.0000.0000.0000.000
91L92SER0-0.013-0.0279.2530.0410.0410.0000.0000.0000.000
92L93TYR00.0050.0057.6340.0480.0480.0000.0000.0000.000
93L94ASP-1-0.698-0.8422.411-7.355-4.7432.020-2.364-2.268-0.029
94L95SER00.0600.0315.0410.1060.208-0.001-0.003-0.0980.000
95L96SER0-0.085-0.0444.2780.8231.060-0.001-0.024-0.2120.000
96L97LEU0-0.071-0.0296.693-0.024-0.0240.0000.0000.0000.000
97L98SER00.0010.0295.4440.0330.0330.0000.0000.0000.000
98L99ALA0-0.002-0.0197.390-0.157-0.1570.0000.0000.0000.000
99L100ARG10.8030.8892.0353.2522.6404.186-1.697-1.876-0.001
100L101PHE00.0340.0168.2580.1090.1090.0000.0000.0000.000
101L102GLY00.0230.02110.669-0.172-0.1720.0000.0000.0000.000
102L103GLY0-0.021-0.01712.6210.0650.0650.0000.0000.0000.000
103L104GLY00.0230.01714.9760.0630.0630.0000.0000.0000.000
104L105THR0-0.083-0.04818.231-0.017-0.0170.0000.0000.0000.000
105L106ARG10.8460.88521.2720.3190.3190.0000.0000.0000.000
106L107LEU0-0.061-0.03524.6340.0020.0020.0000.0000.0000.000
107L108THR0-0.032-0.02827.2780.0130.0130.0000.0000.0000.000
108L109VAL00.0150.01430.786-0.001-0.0010.0000.0000.0000.000
109L110LEU0-0.021-0.01233.8010.0100.0100.0000.0000.0000.000
110L111GLY00.0550.01236.6380.0030.0030.0000.0000.0000.000
111L112GLN0-0.0210.00136.4820.0070.0070.0000.0000.0000.000
112L113PRO0-0.0040.00341.125-0.004-0.0040.0000.0000.0000.000
113L114LYS10.8590.91041.8310.1330.1330.0000.0000.0000.000
114L115ALA0-0.009-0.00142.7700.0060.0060.0000.0000.0000.000
115L116ALA0-0.006-0.00643.274-0.006-0.0060.0000.0000.0000.000
116L117PRO00.0180.00742.9350.0010.0010.0000.0000.0000.000
117L118SER00.0120.02644.9310.0060.0060.0000.0000.0000.000
118L119VAL00.011-0.00745.157-0.004-0.0040.0000.0000.0000.000
119L120THR0-0.012-0.01247.0120.0060.0060.0000.0000.0000.000
120L121LEU0-0.052-0.00947.414-0.004-0.0040.0000.0000.0000.000
121L122PHE00.0060.00448.4670.0040.0040.0000.0000.0000.000
122L123PRO00.0270.01949.688-0.003-0.0030.0000.0000.0000.000
123L124PRO00.0350.02250.6150.0000.0000.0000.0000.0000.000
124L125SER00.0570.03752.0540.0030.0030.0000.0000.0000.000
125L126SER00.040-0.00854.2920.0000.0000.0000.0000.0000.000
126L127GLU-1-0.902-0.94354.656-0.057-0.0570.0000.0000.0000.000
127L128GLU-1-0.827-0.88948.116-0.075-0.0750.0000.0000.0000.000
128L129LEU00.0170.00052.5050.0010.0010.0000.0000.0000.000
129L130GLN0-0.068-0.02454.5920.0030.0030.0000.0000.0000.000
130L131ALA0-0.079-0.02752.1300.0020.0020.0000.0000.0000.000
131L132ASN0-0.037-0.03352.0680.0000.0000.0000.0000.0000.000
132L133LYS10.8730.93346.7640.0640.0640.0000.0000.0000.000
133L134ALA0-0.008-0.00448.7570.0020.0020.0000.0000.0000.000
134L135THR0-0.007-0.02644.502-0.004-0.0040.0000.0000.0000.000
135L136LEU0-0.061-0.01146.4320.0020.0020.0000.0000.0000.000
136L137VAL00.018-0.00444.053-0.005-0.0050.0000.0000.0000.000
137L138CYS0-0.074-0.00943.450-0.002-0.0020.0000.0000.0000.000
138L139LEU0-0.001-0.00842.940-0.006-0.0060.0000.0000.0000.000
139L140ILE00.0240.01240.2860.0030.0030.0000.0000.0000.000
140L141SER0-0.004-0.01041.468-0.006-0.0060.0000.0000.0000.000
141L142ASP-1-0.777-0.89042.731-0.113-0.1130.0000.0000.0000.000
142L143PHE00.0160.02337.1820.0020.0020.0000.0000.0000.000
143L144TYR00.008-0.00536.140-0.010-0.0100.0000.0000.0000.000
144L145PRO00.0520.00835.6880.0080.0080.0000.0000.0000.000
145L146GLY0-0.0010.00234.3500.0070.0070.0000.0000.0000.000
146L147ALA00.001-0.00333.740-0.009-0.0090.0000.0000.0000.000
147L148VAL0-0.049-0.02335.1360.0100.0100.0000.0000.0000.000
148L149THR00.0250.02136.248-0.010-0.0100.0000.0000.0000.000
149L150VAL00.019-0.00138.1010.0070.0070.0000.0000.0000.000
150L151ALA0-0.018-0.00239.616-0.002-0.0020.0000.0000.0000.000
151L152TRP00.0830.02041.5160.0070.0070.0000.0000.0000.000
152L153LYS10.8440.90344.6560.0850.0850.0000.0000.0000.000
153L154ALA00.0400.04847.8080.0010.0010.0000.0000.0000.000
154L155ASP-1-0.800-0.89950.432-0.062-0.0620.0000.0000.0000.000
155L156SER0-0.049-0.02951.951-0.001-0.0010.0000.0000.0000.000
156L157SER0-0.0120.00548.498-0.001-0.0010.0000.0000.0000.000
157L158PRO0-0.007-0.00943.847-0.001-0.0010.0000.0000.0000.000
158L159VAL00.0030.00543.8350.0010.0010.0000.0000.0000.000
159L160ASN0-0.006-0.01937.918-0.001-0.0010.0000.0000.0000.000
160L161ALA0-0.022-0.00639.185-0.006-0.0060.0000.0000.0000.000
161L162GLY00.0560.02739.4360.0040.0040.0000.0000.0000.000
162L163VAL0-0.010-0.00238.2320.0020.0020.0000.0000.0000.000
163L164GLU-1-0.904-0.94034.407-0.151-0.1510.0000.0000.0000.000
164L165THR00.0040.00435.1660.0080.0080.0000.0000.0000.000
165L166THR0-0.033-0.00233.466-0.006-0.0060.0000.0000.0000.000
166L167LYS10.9780.99027.5700.2300.2300.0000.0000.0000.000
167L168PRO0-0.004-0.00531.8490.0070.0070.0000.0000.0000.000
168L169SER0-0.021-0.01532.317-0.014-0.0140.0000.0000.0000.000
169L170LYS10.8020.90233.5310.1980.1980.0000.0000.0000.000
170L171GLN00.0390.01235.3970.0020.0020.0000.0000.0000.000
171L172SER00.007-0.01238.498-0.003-0.0030.0000.0000.0000.000
172L173ASN00.0050.00940.033-0.004-0.0040.0000.0000.0000.000
173L174ASN0-0.002-0.01637.352-0.007-0.0070.0000.0000.0000.000
174L175LYS10.8540.95338.8310.1110.1110.0000.0000.0000.000
175L176TYR0-0.017-0.01032.169-0.003-0.0030.0000.0000.0000.000
176L177ALA00.0050.01237.4360.0080.0080.0000.0000.0000.000
177L178ALA0-0.015-0.01536.981-0.011-0.0110.0000.0000.0000.000
178L179SER0-0.018-0.01337.6730.0100.0100.0000.0000.0000.000
179L180SER0-0.024-0.01338.027-0.005-0.0050.0000.0000.0000.000
180L181TYR00.0180.00839.1990.0070.0070.0000.0000.0000.000
181L182LEU00.0120.01740.841-0.004-0.0040.0000.0000.0000.000
182L183SER0-0.030-0.00841.9260.0040.0040.0000.0000.0000.000
183L184LEU0-0.016-0.00744.2070.0000.0000.0000.0000.0000.000
184L185THR0-0.038-0.04147.3540.0010.0010.0000.0000.0000.000
185L186PRO00.0360.00250.018-0.001-0.0010.0000.0000.0000.000
186L187GLU-1-0.826-0.90153.084-0.055-0.0550.0000.0000.0000.000
187L188GLN00.0410.02247.3820.0000.0000.0000.0000.0000.000
188L189TRP00.0180.02252.2030.0000.0000.0000.0000.0000.000
189L190LYS10.9270.94253.4610.0520.0520.0000.0000.0000.000
190L191SER0-0.0230.00754.9900.0020.0020.0000.0000.0000.000
191L192HIS0-0.105-0.03952.177-0.001-0.0010.0000.0000.0000.000
192L193LYS10.9150.93755.9460.0630.0630.0000.0000.0000.000
193L194SER0-0.025-0.02054.8490.0010.0010.0000.0000.0000.000
194L195TYR0-0.010-0.01848.545-0.002-0.0020.0000.0000.0000.000
195L196SER00.018-0.00449.5490.0020.0020.0000.0000.0000.000
196L198GLN0-0.060-0.05644.949-0.001-0.0010.0000.0000.0000.000
197L199VAL00.0110.00642.189-0.005-0.0050.0000.0000.0000.000
198L200THR00.0150.00441.2820.0040.0040.0000.0000.0000.000
199L201HIS10.8300.89239.1760.1370.1370.0000.0000.0000.000
200L202GLU-1-0.856-0.90338.458-0.151-0.1510.0000.0000.0000.000
201L203GLY00.019-0.00141.5990.0040.0040.0000.0000.0000.000
202L204SER0-0.0300.00544.3300.0070.0070.0000.0000.0000.000
203L205THR00.0290.00644.811-0.007-0.0070.0000.0000.0000.000
204L206VAL0-0.0190.01246.7160.0050.0050.0000.0000.0000.000
205L207GLU-1-0.761-0.85847.547-0.089-0.0890.0000.0000.0000.000
206L208LYS10.8350.92949.3650.0880.0880.0000.0000.0000.000
207L209THR00.022-0.01250.791-0.002-0.0020.0000.0000.0000.000
208L210VAL0-0.021-0.01151.6760.0010.0010.0000.0000.0000.000
209L211ALA00.0750.04254.449-0.001-0.0010.0000.0000.0000.000
210L212PRO0-0.020-0.01256.2400.0010.0010.0000.0000.0000.000
211L213ALA00.007-0.00158.2660.0010.0010.0000.0000.0000.000
212L214GLU-1-0.974-0.95260.564-0.055-0.0550.0000.0000.0000.000
213L215CYS0-0.058-0.05262.6190.0010.0010.0000.0000.0000.000
214L216SER00.0130.02265.0110.0010.0010.0000.0000.0000.000