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: GYQN1

Calculation Name: 1BJM-A-Xray372

Preferred Name:

Target Type:

Ligand Name: pyroglutamic acid

ligand 3-letter code: PCA

PDB ID: 1BJM

Chain ID: A

ChEMBL ID:

UniProt ID:

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 -2153489.224781
FMO2-HF: Nuclear repulsion 2073403.294043
FMO2-HF: Total energy -80085.930739
FMO2-MP2: Total energy -80320.190195


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(A:1:PRO)


Summations of interaction energy for fragment #1(A:1:PRO)
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.
-1.4541.2951.461-1.435-2.775-0.001
Interaction energy analysis for fragmet #1(A:1:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.060 / q_NPA : 0.019
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].
3A3VAL00.0020.0202.188-1.3471.3001.462-1.422-2.687-0.001
4A4LEU00.0630.0435.1060.2430.345-0.001-0.013-0.0880.000
5A5THR0-0.036-0.0137.506-0.113-0.1130.0000.0000.0000.000
6A6GLN00.018-0.0139.8600.0270.0270.0000.0000.0000.000
7A7PRO0-0.0160.01011.877-0.018-0.0180.0000.0000.0000.000
8A8PRO00.0640.03213.435-0.022-0.0220.0000.0000.0000.000
9A9SER0-0.059-0.02714.4280.0270.0270.0000.0000.0000.000
10A10ALA00.0080.00317.830-0.020-0.0200.0000.0000.0000.000
11A11SER0-0.062-0.03820.2660.0130.0130.0000.0000.0000.000
12A12GLY00.003-0.00523.684-0.002-0.0020.0000.0000.0000.000
13A13THR00.008-0.00527.3700.0030.0030.0000.0000.0000.000
14A14PRO00.0910.01130.274-0.007-0.0070.0000.0000.0000.000
15A15GLY0-0.042-0.00131.4890.0030.0030.0000.0000.0000.000
16A16GLN0-0.0250.02328.4570.0040.0040.0000.0000.0000.000
17A17ARG10.9710.97826.9680.1770.1770.0000.0000.0000.000
18A18VAL0-0.0120.01021.9650.0000.0000.0000.0000.0000.000
19A19THR0-0.0180.00720.8960.0030.0030.0000.0000.0000.000
20A20ILE00.0070.02015.5560.0040.0040.0000.0000.0000.000
21A21SER0-0.024-0.01316.528-0.018-0.0180.0000.0000.0000.000
22A22CYS0-0.0050.01410.932-0.020-0.0200.0000.0000.0000.000
23A23SER0-0.0060.00012.5580.1210.1210.0000.0000.0000.000
24A24GLY00.0320.00311.307-0.198-0.1980.0000.0000.0000.000
25A25SER0-0.023-0.00711.4960.0840.0840.0000.0000.0000.000
26A26SER0-0.100-0.03913.308-0.003-0.0030.0000.0000.0000.000
27A27SER00.0740.03511.9560.0250.0250.0000.0000.0000.000
28A28ASN00.1430.0758.7130.0580.0580.0000.0000.0000.000
29A29ILE00.0520.01611.9620.0550.0550.0000.0000.0000.000
30A30GLY0-0.0140.00914.1860.0750.0750.0000.0000.0000.000
31A31GLU-1-0.997-0.98416.013-0.266-0.2660.0000.0000.0000.000
32A32ASN0-0.067-0.02813.5330.0580.0580.0000.0000.0000.000
33A33SER00.0440.03116.1540.0220.0220.0000.0000.0000.000
34A34VAL0-0.109-0.06314.317-0.049-0.0490.0000.0000.0000.000
35A35THR00.0160.02413.7340.0770.0770.0000.0000.0000.000
36A36TRP00.004-0.02014.511-0.083-0.0830.0000.0000.0000.000
37A37TYR0-0.024-0.03312.0450.0460.0460.0000.0000.0000.000
38A38GLN00.0110.02415.263-0.022-0.0220.0000.0000.0000.000
39A39HIS0-0.012-0.01912.7460.0060.0060.0000.0000.0000.000
40A40LEU00.0790.04816.3310.0010.0010.0000.0000.0000.000
41A41SER0-0.047-0.03016.7400.0020.0020.0000.0000.0000.000
42A42GLY0-0.101-0.04517.7490.0290.0290.0000.0000.0000.000
43A43THR00.0430.00017.826-0.019-0.0190.0000.0000.0000.000
44A44ALA0-0.0110.00916.4890.0100.0100.0000.0000.0000.000
45A45PRO00.0220.05213.519-0.004-0.0040.0000.0000.0000.000
46A46LYS11.0140.96015.7300.1880.1880.0000.0000.0000.000
47A47LEU0-0.035-0.00616.548-0.021-0.0210.0000.0000.0000.000
48A48LEU0-0.038-0.00318.7230.0300.0300.0000.0000.0000.000
49A49ILE00.003-0.01219.2590.0230.0230.0000.0000.0000.000
50A50TYR00.0450.02518.425-0.031-0.0310.0000.0000.0000.000
51A51GLU-1-0.892-0.94619.334-0.177-0.1770.0000.0000.0000.000
52A52ASP-1-0.824-0.91819.323-0.292-0.2920.0000.0000.0000.000
53A53ASN0-0.110-0.05820.5390.0020.0020.0000.0000.0000.000
54A54SER0-0.023-0.00723.4480.0190.0190.0000.0000.0000.000
55A55ARG10.8620.89923.4450.1500.1500.0000.0000.0000.000
56A56ALA00.0040.02322.2560.0120.0120.0000.0000.0000.000
57A57SER00.003-0.00724.3070.0090.0090.0000.0000.0000.000
58A58GLY00.0060.00027.3270.0010.0010.0000.0000.0000.000
59A59VAL0-0.079-0.03123.4800.0020.0020.0000.0000.0000.000
60A60SER00.012-0.00726.7780.0050.0050.0000.0000.0000.000
61A61ASP-1-0.872-0.94327.414-0.130-0.1300.0000.0000.0000.000
62A62ARG10.7570.85626.8190.1410.1410.0000.0000.0000.000
63A63PHE0-0.0110.01422.062-0.011-0.0110.0000.0000.0000.000
64A64SER0-0.0030.01524.7040.0050.0050.0000.0000.0000.000
65A65ALA00.0450.00720.608-0.016-0.0160.0000.0000.0000.000
66A66SER00.0040.00921.3910.0200.0200.0000.0000.0000.000
67A67LYS10.9200.94517.7790.3140.3140.0000.0000.0000.000
68A68SER0-0.030-0.03920.1040.0340.0340.0000.0000.0000.000
69A69GLY0-0.0160.02219.9250.0130.0130.0000.0000.0000.000
70A70THR00.0900.03916.626-0.019-0.0190.0000.0000.0000.000
71A71SER0-0.034-0.01315.576-0.069-0.0690.0000.0000.0000.000
72A72ALA00.0830.03616.0820.0250.0250.0000.0000.0000.000
73A73SER0-0.104-0.05017.609-0.013-0.0130.0000.0000.0000.000
74A74LEU00.0310.02818.2910.0210.0210.0000.0000.0000.000
75A75ALA0-0.038-0.03120.261-0.004-0.0040.0000.0000.0000.000
76A76ILE00.0380.01420.7580.0060.0060.0000.0000.0000.000
77A77SER0-0.032-0.05424.6960.0050.0050.0000.0000.0000.000
78A78GLY00.0480.01128.4580.0080.0080.0000.0000.0000.000
79A79LEU0-0.0870.00324.7760.0040.0040.0000.0000.0000.000
80A80GLN00.016-0.01127.6290.0170.0170.0000.0000.0000.000
81A81PRO00.0760.02526.954-0.011-0.0110.0000.0000.0000.000
82A82GLU-1-0.955-0.95926.218-0.097-0.0970.0000.0000.0000.000
83A83ASP-1-0.805-0.88323.483-0.164-0.1640.0000.0000.0000.000
84A84GLU-1-0.910-0.95921.957-0.149-0.1490.0000.0000.0000.000
85A85THR0-0.041-0.01818.1990.0190.0190.0000.0000.0000.000
86A86ASP-1-0.901-0.96213.814-0.310-0.3100.0000.0000.0000.000
87A87TYR0-0.036-0.05114.6840.0130.0130.0000.0000.0000.000
88A88TYR0-0.0190.0088.218-0.035-0.0350.0000.0000.0000.000
89A90ALA00.004-0.0169.924-0.152-0.1520.0000.0000.0000.000
90A91ALA00.0240.0309.9040.1320.1320.0000.0000.0000.000
91A92TRP0-0.068-0.06610.887-0.075-0.0750.0000.0000.0000.000
92A93ASP-1-0.730-0.84610.792-0.221-0.2210.0000.0000.0000.000
93A94ASP-1-0.914-0.9508.052-0.568-0.5680.0000.0000.0000.000
94A95SER0-0.047-0.0288.6760.1050.1050.0000.0000.0000.000
95A96LEU0-0.102-0.06911.209-0.045-0.0450.0000.0000.0000.000
96A97ASP-1-0.934-0.94913.316-0.111-0.1110.0000.0000.0000.000
97A98VAL0-0.049-0.0068.1260.0070.0070.0000.0000.0000.000
98A99ALA00.0040.0018.602-0.045-0.0450.0000.0000.0000.000
99A100VAL0-0.044-0.0304.925-0.205-0.2050.0000.0000.0000.000
100A101PHE00.021-0.0035.5510.1830.1830.0000.0000.0000.000
101A102GLY00.0340.0025.581-0.483-0.4830.0000.0000.0000.000
102A103THR0-0.076-0.0436.255-0.096-0.0960.0000.0000.0000.000
103A104GLY0-0.0130.0017.1930.1690.1690.0000.0000.0000.000
104A105THR0-0.080-0.04910.409-0.013-0.0130.0000.0000.0000.000
105A106LYS10.9600.99113.9580.1960.1960.0000.0000.0000.000
106A107VAL0-0.010-0.00316.7210.0050.0050.0000.0000.0000.000
107A108THR0-0.081-0.04120.1760.0170.0170.0000.0000.0000.000
108A109VAL00.0200.02823.228-0.008-0.0080.0000.0000.0000.000
109A110LEU0-0.079-0.03426.0650.0090.0090.0000.0000.0000.000
110A111GLY00.0580.02328.3260.0050.0050.0000.0000.0000.000
111A112GLN0-0.062-0.02629.2590.0130.0130.0000.0000.0000.000
112A113PRO00.0330.00929.913-0.008-0.0080.0000.0000.0000.000
113A114LYS10.9790.99624.8640.1640.1640.0000.0000.0000.000
114A115ALA0-0.029-0.00526.2730.0090.0090.0000.0000.0000.000
115A116ASN00.0190.02224.246-0.023-0.0230.0000.0000.0000.000
116A117PRO00.0410.02820.7990.0070.0070.0000.0000.0000.000
117A118THR00.0100.01323.931-0.006-0.0060.0000.0000.0000.000
118A119VAL0-0.010-0.01520.9360.0040.0040.0000.0000.0000.000
119A120THR0-0.034-0.01623.356-0.003-0.0030.0000.0000.0000.000
120A121LEU0-0.037-0.01420.9350.0040.0040.0000.0000.0000.000
121A122PHE0-0.027-0.01923.795-0.005-0.0050.0000.0000.0000.000
122A123PRO00.0370.05024.1670.0130.0130.0000.0000.0000.000
123A124PRO00.0580.02725.141-0.001-0.0010.0000.0000.0000.000
124A125SER0-0.0250.01027.301-0.007-0.0070.0000.0000.0000.000
125A126SER00.023-0.01330.7570.0060.0060.0000.0000.0000.000
126A127GLU-1-0.791-0.91033.0040.0650.0650.0000.0000.0000.000
127A128GLU-1-0.869-0.93725.8780.1420.1420.0000.0000.0000.000
128A129LEU0-0.002-0.00728.2000.0110.0110.0000.0000.0000.000
129A130GLN0-0.060-0.01530.8220.0020.0020.0000.0000.0000.000
130A131ALA0-0.048-0.00931.435-0.001-0.0010.0000.0000.0000.000
131A132ASN0-0.043-0.03029.6170.0050.0050.0000.0000.0000.000
132A133LYS10.9030.93325.116-0.145-0.1450.0000.0000.0000.000
133A134ALA00.0300.01024.660-0.017-0.0170.0000.0000.0000.000
134A135THR0-0.010-0.00220.6460.0350.0350.0000.0000.0000.000
135A136LEU0-0.062-0.01820.265-0.023-0.0230.0000.0000.0000.000
136A137VAL00.000-0.00920.4210.0180.0180.0000.0000.0000.000
137A138CYS0-0.039-0.02717.184-0.019-0.0190.0000.0000.0000.000
138A139LEU0-0.022-0.01919.987-0.002-0.0020.0000.0000.0000.000
139A140ILE00.0100.00817.387-0.017-0.0170.0000.0000.0000.000
140A141SER0-0.005-0.02921.7260.0050.0050.0000.0000.0000.000
141A142ASP-1-0.858-0.92524.721-0.047-0.0470.0000.0000.0000.000
142A143PHE00.0060.01419.581-0.010-0.0100.0000.0000.0000.000
143A144TYR00.0210.00824.2740.0070.0070.0000.0000.0000.000
144A145PRO00.0820.02321.2620.0050.0050.0000.0000.0000.000
145A146GLY00.0030.00620.9920.0010.0010.0000.0000.0000.000
146A147ALA0-0.017-0.01416.1600.0060.0060.0000.0000.0000.000
147A148VAL0-0.033-0.02015.339-0.004-0.0040.0000.0000.0000.000
148A149THR00.0130.02110.1370.0340.0340.0000.0000.0000.000
149A150VAL00.023-0.00111.8000.0180.0180.0000.0000.0000.000
150A151ALA00.0180.01710.827-0.009-0.0090.0000.0000.0000.000
151A152TRP00.0570.01212.133-0.007-0.0070.0000.0000.0000.000
152A153LYS10.8490.93313.3680.1430.1430.0000.0000.0000.000
153A154ALA00.0180.00415.8880.0110.0110.0000.0000.0000.000
154A155ASP-1-0.838-0.92318.5220.0520.0520.0000.0000.0000.000
155A156GLY0-0.0120.00218.427-0.008-0.0080.0000.0000.0000.000
156A157SER00.003-0.00415.404-0.031-0.0310.0000.0000.0000.000
157A158PRO0-0.031-0.00910.3530.0200.0200.0000.0000.0000.000
158A159VAL00.0280.01812.3040.0650.0650.0000.0000.0000.000
159A160LYS10.9060.9505.5860.2820.2820.0000.0000.0000.000
160A161ALA00.010-0.0129.0380.1520.1520.0000.0000.0000.000
161A162GLY00.0620.04011.253-0.132-0.1320.0000.0000.0000.000
162A163VAL0-0.033-0.01310.480-0.125-0.1250.0000.0000.0000.000
163A164GLU-1-0.873-0.91011.4320.7190.7190.0000.0000.0000.000
164A165THR0-0.040-0.00112.199-0.104-0.1040.0000.0000.0000.000
165A166THR0-0.0200.02614.0130.0190.0190.0000.0000.0000.000
166A167LYS10.9600.96414.563-0.050-0.0500.0000.0000.0000.000
167A168PRO00.0060.00416.2010.0120.0120.0000.0000.0000.000
168A169SER0-0.060-0.03119.514-0.001-0.0010.0000.0000.0000.000
169A170LYS10.9440.98122.9300.0540.0540.0000.0000.0000.000
170A171GLN00.0460.04225.5620.0110.0110.0000.0000.0000.000
171A172SER00.0550.00128.873-0.005-0.0050.0000.0000.0000.000
172A173ASN00.0050.00930.0040.0000.0000.0000.0000.0000.000
173A174ASN0-0.058-0.04030.441-0.006-0.0060.0000.0000.0000.000
174A175LYS10.8570.94227.3470.0510.0510.0000.0000.0000.000
175A176TYR0-0.025-0.01322.2640.0070.0070.0000.0000.0000.000
176A177ALA0-0.001-0.00823.162-0.003-0.0030.0000.0000.0000.000
177A178ALA0-0.004-0.00918.0150.0000.0000.0000.0000.0000.000
178A179SER00.0290.00518.6760.0020.0020.0000.0000.0000.000
179A180SER00.011-0.01413.8210.0220.0220.0000.0000.0000.000
180A181TYR00.0120.00116.331-0.040-0.0400.0000.0000.0000.000
181A182LEU00.0260.02415.3170.0410.0410.0000.0000.0000.000
182A183SER00.0280.01117.197-0.051-0.0510.0000.0000.0000.000
183A184LEU0-0.055-0.03318.5270.0290.0290.0000.0000.0000.000
184A185THR0-0.0670.00821.089-0.012-0.0120.0000.0000.0000.000
185A186PRO00.0900.04924.274-0.001-0.0010.0000.0000.0000.000
186A187GLU-1-0.864-0.94725.9650.1370.1370.0000.0000.0000.000
187A188GLN0-0.024-0.05519.656-0.006-0.0060.0000.0000.0000.000
188A189TRP00.0220.04422.684-0.008-0.0080.0000.0000.0000.000
189A190LYS10.8430.89124.373-0.086-0.0860.0000.0000.0000.000
190A191SER0-0.0550.00024.025-0.009-0.0090.0000.0000.0000.000
191A192HIS00.0430.08619.511-0.005-0.0050.0000.0000.0000.000
192A193ARG10.9040.93624.288-0.036-0.0360.0000.0000.0000.000
193A194SER0-0.095-0.05623.714-0.012-0.0120.0000.0000.0000.000
194A195TYR0-0.005-0.03918.6300.0070.0070.0000.0000.0000.000
195A196SER0-0.021-0.02318.797-0.002-0.0020.0000.0000.0000.000
196A198GLN0-0.007-0.01914.580-0.047-0.0470.0000.0000.0000.000
197A199VAL00.010-0.00315.026-0.020-0.0200.0000.0000.0000.000
198A200THR00.0050.00814.4130.0060.0060.0000.0000.0000.000
199A201HIS10.8160.88916.2370.1660.1660.0000.0000.0000.000
200A202GLU-1-0.813-0.91218.364-0.195-0.1950.0000.0000.0000.000
201A203GLY0-0.006-0.00819.6430.0260.0260.0000.0000.0000.000
202A204SER0-0.090-0.05121.314-0.005-0.0050.0000.0000.0000.000
203A205THR00.0470.00817.155-0.015-0.0150.0000.0000.0000.000
204A206VAL0-0.023-0.00319.6390.0170.0170.0000.0000.0000.000
205A207GLU-1-0.779-0.90318.804-0.131-0.1310.0000.0000.0000.000
206A208LYS10.8400.93720.6790.0520.0520.0000.0000.0000.000
207A209THR00.0890.04321.4030.0030.0030.0000.0000.0000.000
208A210VAL0-0.042-0.02223.320-0.001-0.0010.0000.0000.0000.000
209A211ALA00.0690.04824.5510.0060.0060.0000.0000.0000.000
210A212PRO00.0640.00826.104-0.002-0.0020.0000.0000.0000.000
211A213THR0-0.066-0.03728.592-0.003-0.0030.0000.0000.0000.000
212A214GLU-1-0.828-0.91330.7590.0510.0510.0000.0000.0000.000
213A215CYS0-0.039-0.01632.8150.0070.0070.0000.0000.0000.000
214A216SER0-0.0500.01331.8870.0030.0030.0000.0000.0000.000