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: N231Q

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 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 -2151905.305922
FMO2-HF: Nuclear repulsion 2071814.099632
FMO2-HF: Total energy -80091.20629
FMO2-MP2: Total energy -80324.859002


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.
-4.322-1.0591.371-1.657-2.9760.003
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 : 0.052 / q_NPA : 0.008
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].
3A3VAL00.0040.0282.152-2.944-0.2451.372-1.364-2.7070.002
4A4LEU00.0220.0274.6340.5310.624-0.001-0.016-0.0760.000
5A5THR0-0.011-0.0017.5180.2700.2700.0000.0000.0000.000
6A6GLN00.029-0.0179.655-0.154-0.1540.0000.0000.0000.000
7A7PRO0-0.0250.01511.9850.0960.0960.0000.0000.0000.000
8A8PRO00.0390.02813.731-0.016-0.0160.0000.0000.0000.000
9A9SER0-0.053-0.05614.669-0.007-0.0070.0000.0000.0000.000
10A10ALA00.003-0.00418.062-0.004-0.0040.0000.0000.0000.000
11A11SER0-0.057-0.05020.669-0.007-0.0070.0000.0000.0000.000
12A12GLY00.014-0.00124.290-0.006-0.0060.0000.0000.0000.000
13A13THR0-0.0030.00127.9500.0020.0020.0000.0000.0000.000
14A14PRO00.0480.00330.861-0.002-0.0020.0000.0000.0000.000
15A15GLY0-0.0080.00532.077-0.002-0.0020.0000.0000.0000.000
16A16GLN0-0.0230.01528.225-0.002-0.0020.0000.0000.0000.000
17A17ARG10.9310.96826.008-0.018-0.0180.0000.0000.0000.000
18A18VAL00.0100.01322.6200.0060.0060.0000.0000.0000.000
19A19THR0-0.069-0.05321.431-0.014-0.0140.0000.0000.0000.000
20A20ILE00.0230.03015.9180.0190.0190.0000.0000.0000.000
21A21SER00.0180.00917.142-0.016-0.0160.0000.0000.0000.000
22A22CYS0-0.0310.00211.446-0.013-0.0130.0000.0000.0000.000
23A23SER0-0.001-0.00412.161-0.012-0.0120.0000.0000.0000.000
24A24GLY00.014-0.00210.962-0.014-0.0140.0000.0000.0000.000
25A25SER0-0.015-0.00411.8860.0720.0720.0000.0000.0000.000
26A26SER0-0.015-0.00113.6340.0000.0000.0000.0000.0000.000
27A27SER00.0220.00412.3810.0020.0020.0000.0000.0000.000
28A28ASN00.0430.0179.5980.0740.0740.0000.0000.0000.000
29A29ILE00.0090.00211.9750.0350.0350.0000.0000.0000.000
30A30GLY0-0.053-0.02614.6510.0320.0320.0000.0000.0000.000
31A31GLU-1-0.996-0.99716.666-0.198-0.1980.0000.0000.0000.000
32A32ASN00.0100.01914.6250.0390.0390.0000.0000.0000.000
33A33SER0-0.0170.00016.8790.0220.0220.0000.0000.0000.000
34A34VAL0-0.064-0.03713.918-0.039-0.0390.0000.0000.0000.000
35A35THR0-0.008-0.00614.8770.0430.0430.0000.0000.0000.000
36A36TRP0-0.013-0.00914.892-0.009-0.0090.0000.0000.0000.000
37A37TYR00.0340.01112.5710.0230.0230.0000.0000.0000.000
38A38GLN00.0110.00815.8170.0170.0170.0000.0000.0000.000
39A39HIS0-0.020-0.03312.472-0.042-0.0420.0000.0000.0000.000
40A40LEU00.0740.03816.1430.0310.0310.0000.0000.0000.000
41A41SER0-0.0170.00717.2050.0010.0010.0000.0000.0000.000
42A42GLY00.000-0.01718.2640.0020.0020.0000.0000.0000.000
43A43THR0-0.024-0.01117.8030.0000.0000.0000.0000.0000.000
44A44ALA00.003-0.00616.984-0.016-0.0160.0000.0000.0000.000
45A45PRO0-0.0010.03013.6290.0240.0240.0000.0000.0000.000
46A46LYS10.8800.92615.9720.0240.0240.0000.0000.0000.000
47A47LEU00.0170.01317.9260.0050.0050.0000.0000.0000.000
48A48LEU0-0.042-0.02119.0680.0160.0160.0000.0000.0000.000
49A49ILE0-0.017-0.01419.6800.0100.0100.0000.0000.0000.000
50A50TYR00.0250.01319.049-0.019-0.0190.0000.0000.0000.000
51A51GLU-1-0.880-0.95119.747-0.102-0.1020.0000.0000.0000.000
52A52ASP-1-0.761-0.89319.534-0.136-0.1360.0000.0000.0000.000
53A53ASN0-0.152-0.08820.7440.0210.0210.0000.0000.0000.000
54A54SER00.0220.02823.6550.0140.0140.0000.0000.0000.000
55A55ARG10.9030.95023.6970.0290.0290.0000.0000.0000.000
56A56ALA00.0070.01422.848-0.003-0.0030.0000.0000.0000.000
57A57SER00.006-0.01324.8860.0110.0110.0000.0000.0000.000
58A58GLY00.0110.00828.050-0.001-0.0010.0000.0000.0000.000
59A59VAL0-0.049-0.01023.9110.0070.0070.0000.0000.0000.000
60A60SER0-0.007-0.01527.1910.0000.0000.0000.0000.0000.000
61A61ASP-1-0.850-0.93828.162-0.015-0.0150.0000.0000.0000.000
62A62ARG10.7680.84627.020-0.013-0.0130.0000.0000.0000.000
63A63PHE0-0.0170.00823.1260.0040.0040.0000.0000.0000.000
64A64SER00.0040.00624.859-0.006-0.0060.0000.0000.0000.000
65A65ALA00.0190.00020.6910.0060.0060.0000.0000.0000.000
66A66SER0-0.0050.00921.2000.0020.0020.0000.0000.0000.000
67A67LYS10.8570.93018.1040.1700.1700.0000.0000.0000.000
68A68SER0-0.008-0.00320.1300.0080.0080.0000.0000.0000.000
69A69GLY00.0320.02420.1850.0090.0090.0000.0000.0000.000
70A70THR00.0250.00016.449-0.013-0.0130.0000.0000.0000.000
71A71SER0-0.043-0.00515.371-0.003-0.0030.0000.0000.0000.000
72A72ALA00.0780.02715.860-0.013-0.0130.0000.0000.0000.000
73A73SER0-0.075-0.04417.5110.0270.0270.0000.0000.0000.000
74A74LEU00.0330.03418.286-0.014-0.0140.0000.0000.0000.000
75A75ALA0-0.040-0.03320.2870.0190.0190.0000.0000.0000.000
76A76ILE00.0240.02321.445-0.008-0.0080.0000.0000.0000.000
77A77SER0-0.030-0.03825.4140.0080.0080.0000.0000.0000.000
78A78GLY00.0360.02029.168-0.004-0.0040.0000.0000.0000.000
79A79LEU0-0.084-0.01525.315-0.001-0.0010.0000.0000.0000.000
80A80GLN0-0.003-0.00228.064-0.003-0.0030.0000.0000.0000.000
81A81PRO00.0410.01727.3870.0030.0030.0000.0000.0000.000
82A82GLU-1-0.857-0.93526.3820.0340.0340.0000.0000.0000.000
83A83ASP-1-0.789-0.85823.8720.0190.0190.0000.0000.0000.000
84A84GLU-1-0.873-0.92822.3100.0940.0940.0000.0000.0000.000
85A85THR0-0.044-0.02618.354-0.005-0.0050.0000.0000.0000.000
86A86ASP-1-0.799-0.87113.9690.2380.2380.0000.0000.0000.000
87A87TYR0-0.039-0.04215.261-0.047-0.0470.0000.0000.0000.000
88A88TYR0-0.0080.0118.8770.0150.0150.0000.0000.0000.000
89A90ALA0-0.007-0.01610.362-0.053-0.0530.0000.0000.0000.000
90A91ALA00.0300.02410.3320.0880.0880.0000.0000.0000.000
91A92TRP0-0.062-0.02710.894-0.101-0.1010.0000.0000.0000.000
92A93ASP-1-0.753-0.87711.610-0.315-0.3150.0000.0000.0000.000
93A94ASP-1-0.881-0.9278.469-0.649-0.6490.0000.0000.0000.000
94A95SER0-0.074-0.0399.6000.0010.0010.0000.0000.0000.000
95A96LEU0-0.019-0.01911.235-0.036-0.0360.0000.0000.0000.000
96A97ASP-1-0.908-0.95013.280-0.301-0.3010.0000.0000.0000.000
97A98VAL0-0.062-0.0168.005-0.038-0.0380.0000.0000.0000.000
98A99ALA00.0170.0079.4430.0240.0240.0000.0000.0000.000
99A100VAL0-0.037-0.0225.708-0.302-0.3020.0000.0000.0000.000
100A101PHE00.014-0.0126.1130.2540.2540.0000.0000.0000.000
101A102GLY00.0360.0026.164-0.267-0.2670.0000.0000.0000.000
102A103THR0-0.087-0.0536.7260.1910.1910.0000.0000.0000.000
103A104GLY00.0070.0107.6440.0980.0980.0000.0000.0000.000
104A105THR0-0.069-0.04910.9860.0400.0400.0000.0000.0000.000
105A106LYS10.8320.90114.666-0.277-0.2770.0000.0000.0000.000
106A107VAL0-0.030-0.00217.3040.0020.0020.0000.0000.0000.000
107A108THR0-0.092-0.06120.6590.0140.0140.0000.0000.0000.000
108A109VAL00.0390.01723.782-0.004-0.0040.0000.0000.0000.000
109A110LEU0-0.076-0.05127.1430.0070.0070.0000.0000.0000.000
110A111GLY00.0340.02729.350-0.008-0.0080.0000.0000.0000.000
111A112GLN0-0.077-0.04728.733-0.008-0.0080.0000.0000.0000.000
112A113PRO00.0360.00430.4480.0030.0030.0000.0000.0000.000
113A114LYS10.8310.91023.790-0.119-0.1190.0000.0000.0000.000
114A115ALA0-0.0080.00926.782-0.008-0.0080.0000.0000.0000.000
115A116ASN00.0240.00224.8270.0230.0230.0000.0000.0000.000
116A117PRO00.0110.01721.379-0.007-0.0070.0000.0000.0000.000
117A118THR00.008-0.00924.473-0.004-0.0040.0000.0000.0000.000
118A119VAL0-0.040-0.01721.7460.0040.0040.0000.0000.0000.000
119A120THR0-0.020-0.00224.189-0.025-0.0250.0000.0000.0000.000
120A121LEU0-0.049-0.01721.5090.0180.0180.0000.0000.0000.000
121A122PHE0-0.018-0.00724.407-0.019-0.0190.0000.0000.0000.000
122A123PRO0-0.0010.00624.5790.0170.0170.0000.0000.0000.000
123A124PRO00.0230.01924.9260.0010.0010.0000.0000.0000.000
124A125SER0-0.022-0.02427.285-0.004-0.0040.0000.0000.0000.000
125A126SER0-0.010-0.01731.036-0.002-0.0020.0000.0000.0000.000
126A127GLU-1-0.813-0.89933.3810.0910.0910.0000.0000.0000.000
127A128GLU-1-0.784-0.85825.7760.1530.1530.0000.0000.0000.000
128A129LEU0-0.022-0.01027.8210.0000.0000.0000.0000.0000.000
129A130GLN0-0.040-0.02430.658-0.008-0.0080.0000.0000.0000.000
130A131ALA0-0.065-0.01631.062-0.005-0.0050.0000.0000.0000.000
131A132ASN0-0.057-0.03628.344-0.002-0.0020.0000.0000.0000.000
132A133LYS10.8480.90824.829-0.140-0.1400.0000.0000.0000.000
133A134ALA00.0240.00823.881-0.007-0.0070.0000.0000.0000.000
134A135THR0-0.061-0.05421.1610.0200.0200.0000.0000.0000.000
135A136LEU00.0020.02619.703-0.010-0.0100.0000.0000.0000.000
136A137VAL00.003-0.00520.6640.0290.0290.0000.0000.0000.000
137A138CYS0-0.021-0.00617.6300.0230.0230.0000.0000.0000.000
138A139LEU00.0170.01420.8520.0270.0270.0000.0000.0000.000
139A140ILE00.0160.00418.449-0.006-0.0060.0000.0000.0000.000
140A141SER00.030-0.01922.8220.0060.0060.0000.0000.0000.000
141A142ASP-1-0.807-0.87525.7130.1420.1420.0000.0000.0000.000
142A143PHE0-0.0050.01220.716-0.007-0.0070.0000.0000.0000.000
143A144TYR00.0370.00624.776-0.002-0.0020.0000.0000.0000.000
144A145PRO00.0740.02521.734-0.005-0.0050.0000.0000.0000.000
145A146GLY0-0.0070.00121.9360.0140.0140.0000.0000.0000.000
146A147ALA0-0.007-0.00816.7230.0180.0180.0000.0000.0000.000
147A148VAL0-0.030-0.00716.488-0.037-0.0370.0000.0000.0000.000
148A149THR00.0150.01210.6500.0800.0800.0000.0000.0000.000
149A150VAL00.028-0.00212.373-0.133-0.1330.0000.0000.0000.000
150A151ALA00.0150.01711.8910.1670.1670.0000.0000.0000.000
151A152TRP00.0390.00412.978-0.139-0.1390.0000.0000.0000.000
152A153LYS10.7950.88113.597-0.245-0.2450.0000.0000.0000.000
153A154ALA00.0510.02916.115-0.008-0.0080.0000.0000.0000.000
154A155ASP-1-0.761-0.86918.4320.1070.1070.0000.0000.0000.000
155A156GLY0-0.022-0.00418.853-0.015-0.0150.0000.0000.0000.000
156A157SER0-0.0010.00815.237-0.004-0.0040.0000.0000.0000.000
157A158PRO0-0.027-0.01710.4310.0290.0290.0000.0000.0000.000
158A159VAL00.008-0.00311.643-0.023-0.0230.0000.0000.0000.000
159A160LYS10.8640.9183.863-1.067-0.5960.000-0.277-0.1930.001
160A161ALA00.0080.0087.9630.1790.1790.0000.0000.0000.000
161A162GLY00.0480.01810.455-0.045-0.0450.0000.0000.0000.000
162A163VAL0-0.038-0.01110.560-0.049-0.0490.0000.0000.0000.000
163A164GLU-1-0.853-0.92511.9890.6570.6570.0000.0000.0000.000
164A165THR0-0.062-0.02513.101-0.054-0.0540.0000.0000.0000.000
165A166THR0-0.0120.02514.4990.0190.0190.0000.0000.0000.000
166A167LYS10.9790.97115.840-0.244-0.2440.0000.0000.0000.000
167A168PRO0-0.011-0.00717.033-0.036-0.0360.0000.0000.0000.000
168A169SER0-0.024-0.00420.146-0.020-0.0200.0000.0000.0000.000
169A170LYS10.8640.93923.621-0.112-0.1120.0000.0000.0000.000
170A171GLN00.0240.01225.969-0.014-0.0140.0000.0000.0000.000
171A172SER00.0390.01129.750-0.004-0.0040.0000.0000.0000.000
172A173ASN00.0130.01230.812-0.004-0.0040.0000.0000.0000.000
173A174ASN00.017-0.00631.3250.0000.0000.0000.0000.0000.000
174A175LYS10.8520.96727.825-0.101-0.1010.0000.0000.0000.000
175A176TYR0-0.005-0.00323.071-0.008-0.0080.0000.0000.0000.000
176A177ALA0-0.010-0.00623.920-0.003-0.0030.0000.0000.0000.000
177A178ALA0-0.009-0.01019.0070.0060.0060.0000.0000.0000.000
178A179SER00.0120.00019.799-0.017-0.0170.0000.0000.0000.000
179A180SER00.0130.00915.1960.0370.0370.0000.0000.0000.000
180A181TYR00.000-0.00716.780-0.055-0.0550.0000.0000.0000.000
181A182LEU00.0200.01514.9910.0610.0610.0000.0000.0000.000
182A183SER0-0.0090.00017.254-0.032-0.0320.0000.0000.0000.000
183A184LEU0-0.013-0.00718.1130.0110.0110.0000.0000.0000.000
184A185THR0-0.027-0.03720.738-0.006-0.0060.0000.0000.0000.000
185A186PRO00.020-0.00423.8460.0050.0050.0000.0000.0000.000
186A187GLU-1-0.824-0.89225.6030.0960.0960.0000.0000.0000.000
187A188GLN00.0290.03319.7740.0120.0120.0000.0000.0000.000
188A189TRP00.0020.01122.5570.0090.0090.0000.0000.0000.000
189A190LYS10.8210.88424.030-0.086-0.0860.0000.0000.0000.000
190A191SER0-0.051-0.02824.203-0.007-0.0070.0000.0000.0000.000
191A192HIS0-0.0160.01119.386-0.004-0.0040.0000.0000.0000.000
192A193ARG10.8700.91624.113-0.084-0.0840.0000.0000.0000.000
193A194SER0-0.100-0.06723.6180.0000.0000.0000.0000.0000.000
194A195TYR00.0530.01718.1020.0130.0130.0000.0000.0000.000
195A196SER0-0.059-0.05419.260-0.009-0.0090.0000.0000.0000.000
196A198GLN0-0.040-0.02616.091-0.016-0.0160.0000.0000.0000.000
197A199VAL00.0180.00116.3140.0650.0650.0000.0000.0000.000
198A200THR0-0.014-0.01515.246-0.038-0.0380.0000.0000.0000.000
199A201HIS10.8020.87117.060-0.180-0.1800.0000.0000.0000.000
200A202GLU-1-0.744-0.80418.5060.1140.1140.0000.0000.0000.000
201A203GLY00.0500.02519.964-0.024-0.0240.0000.0000.0000.000
202A204SER0-0.026-0.01321.8850.0000.0000.0000.0000.0000.000
203A205THR00.0480.01718.1480.0360.0360.0000.0000.0000.000
204A206VAL0-0.0270.00020.358-0.028-0.0280.0000.0000.0000.000
205A207GLU-1-0.758-0.83219.5830.2620.2620.0000.0000.0000.000
206A208LYS10.8300.91821.822-0.187-0.1870.0000.0000.0000.000
207A209THR00.0640.00722.1770.0270.0270.0000.0000.0000.000
208A210VAL0-0.0190.00523.481-0.013-0.0130.0000.0000.0000.000
209A211ALA00.0640.02224.9940.0040.0040.0000.0000.0000.000
210A212PRO00.0420.03725.866-0.001-0.0010.0000.0000.0000.000
211A213THR0-0.037-0.01928.463-0.007-0.0070.0000.0000.0000.000
212A214GLU-1-0.785-0.89430.6170.0850.0850.0000.0000.0000.000
213A215CYS0-0.0090.00432.588-0.002-0.0020.0000.0000.0000.000
214A216SER0-0.066-0.02531.816-0.004-0.0040.0000.0000.0000.000