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: 8NJ2Y

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 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 -2153120.992215
FMO2-HF: Nuclear repulsion 2073032.078575
FMO2-HF: Total energy -80088.91364
FMO2-MP2: Total energy -80322.916033


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.
-3.109-0.3350.801-1.255-2.319-0.002
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 : 0.067 / q_NPA : 0.009
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].
3A3VAL00.0060.0212.340-1.5070.9050.803-1.113-2.102-0.002
4A4LEU00.0470.0425.1960.2370.318-0.001-0.012-0.0680.000
5A5THR0-0.036-0.0097.738-0.021-0.0210.0000.0000.0000.000
6A6GLN00.022-0.0209.768-0.043-0.0430.0000.0000.0000.000
7A7PRO0-0.0080.01211.8450.0360.0360.0000.0000.0000.000
8A8PRO00.0610.03913.522-0.026-0.0260.0000.0000.0000.000
9A9SER0-0.055-0.04814.4390.0080.0080.0000.0000.0000.000
10A10ALA0-0.002-0.00318.039-0.010-0.0100.0000.0000.0000.000
11A11SER0-0.029-0.03520.6170.0050.0050.0000.0000.0000.000
12A12GLY0-0.028-0.02324.022-0.001-0.0010.0000.0000.0000.000
13A13THR00.007-0.00627.7140.0030.0030.0000.0000.0000.000
14A14PRO00.0950.01130.584-0.005-0.0050.0000.0000.0000.000
15A15GLY0-0.047-0.00531.7360.0020.0020.0000.0000.0000.000
16A16GLN0-0.0200.02728.8080.0020.0020.0000.0000.0000.000
17A17ARG10.9690.97127.0200.0980.0980.0000.0000.0000.000
18A18VAL0-0.0080.01022.1720.0030.0030.0000.0000.0000.000
19A19THR0-0.041-0.01021.350-0.004-0.0040.0000.0000.0000.000
20A20ILE00.0160.02916.0180.0120.0120.0000.0000.0000.000
21A21SER00.0060.00217.110-0.015-0.0150.0000.0000.0000.000
22A22CYS0-0.0170.02611.209-0.016-0.0160.0000.0000.0000.000
23A23SER00.006-0.00212.8000.0640.0640.0000.0000.0000.000
24A24GLY00.0190.00011.376-0.124-0.1240.0000.0000.0000.000
25A25SER0-0.0140.00511.7130.0910.0910.0000.0000.0000.000
26A26SER0-0.068-0.02013.4180.0020.0020.0000.0000.0000.000
27A27SER00.0580.02212.0330.0200.0200.0000.0000.0000.000
28A28ASN00.0520.0199.1790.0210.0210.0000.0000.0000.000
29A29ILE00.0490.01412.1210.0350.0350.0000.0000.0000.000
30A30GLY0-0.0030.00414.3430.0520.0520.0000.0000.0000.000
31A31GLU-1-1.003-0.99416.556-0.232-0.2320.0000.0000.0000.000
32A32ASN0-0.055-0.01214.0080.0350.0350.0000.0000.0000.000
33A33SER0-0.025-0.00616.3280.0270.0270.0000.0000.0000.000
34A34VAL0-0.081-0.05714.018-0.046-0.0460.0000.0000.0000.000
35A35THR00.0550.02914.2860.0630.0630.0000.0000.0000.000
36A36TRP0-0.030-0.03314.707-0.054-0.0540.0000.0000.0000.000
37A37TYR0-0.012-0.02212.1260.0550.0550.0000.0000.0000.000
38A38GLN00.0340.03315.396-0.001-0.0010.0000.0000.0000.000
39A39HIS0-0.031-0.03312.588-0.019-0.0190.0000.0000.0000.000
40A40LEU00.0760.04616.4520.0130.0130.0000.0000.0000.000
41A41SER0-0.0260.01017.144-0.006-0.0060.0000.0000.0000.000
42A42GLY0-0.089-0.06218.1740.0210.0210.0000.0000.0000.000
43A43THR00.035-0.00618.219-0.013-0.0130.0000.0000.0000.000
44A44ALA00.0080.01416.7820.0030.0030.0000.0000.0000.000
45A45PRO00.0090.04913.8230.0130.0130.0000.0000.0000.000
46A46LYS10.9460.93315.9520.1600.1600.0000.0000.0000.000
47A47LEU0-0.015-0.00217.559-0.010-0.0100.0000.0000.0000.000
48A48LEU0-0.0180.00718.8560.0230.0230.0000.0000.0000.000
49A49ILE0-0.007-0.02419.3950.0180.0180.0000.0000.0000.000
50A50TYR00.0480.03218.714-0.029-0.0290.0000.0000.0000.000
51A51GLU-1-0.882-0.93619.764-0.155-0.1550.0000.0000.0000.000
52A52ASP-1-0.779-0.90319.238-0.235-0.2350.0000.0000.0000.000
53A53ASN0-0.131-0.08020.7010.0090.0090.0000.0000.0000.000
54A54SER00.0040.02323.6900.0180.0180.0000.0000.0000.000
55A55ARG10.8940.92623.7500.1040.1040.0000.0000.0000.000
56A56ALA00.0030.01822.6030.0060.0060.0000.0000.0000.000
57A57SER00.003-0.00624.6520.0110.0110.0000.0000.0000.000
58A58GLY00.005-0.00127.710-0.001-0.0010.0000.0000.0000.000
59A59VAL0-0.074-0.02123.6210.0040.0040.0000.0000.0000.000
60A60SER00.010-0.00726.8760.0040.0040.0000.0000.0000.000
61A61ASP-1-0.873-0.95127.593-0.091-0.0910.0000.0000.0000.000
62A62ARG10.7140.83226.7830.0850.0850.0000.0000.0000.000
63A63PHE0-0.022-0.00522.541-0.005-0.0050.0000.0000.0000.000
64A64SER00.0110.02124.9410.0030.0030.0000.0000.0000.000
65A65ALA00.0290.00220.936-0.008-0.0080.0000.0000.0000.000
66A66SER0-0.0060.00421.7420.0130.0130.0000.0000.0000.000
67A67LYS10.8660.93018.1470.2480.2480.0000.0000.0000.000
68A68SER0-0.016-0.01320.2290.0200.0200.0000.0000.0000.000
69A69GLY00.0160.01620.0610.0120.0120.0000.0000.0000.000
70A70THR00.0460.02216.748-0.018-0.0180.0000.0000.0000.000
71A71SER0-0.050-0.01315.696-0.043-0.0430.0000.0000.0000.000
72A72ALA00.0960.04016.2800.0060.0060.0000.0000.0000.000
73A73SER0-0.088-0.05018.0390.0040.0040.0000.0000.0000.000
74A74LEU00.0280.03518.2800.0060.0060.0000.0000.0000.000
75A75ALA0-0.029-0.03720.5950.0050.0050.0000.0000.0000.000
76A76ILE00.0390.01220.891-0.001-0.0010.0000.0000.0000.000
77A77SER0-0.032-0.03824.9910.0070.0070.0000.0000.0000.000
78A78GLY00.0580.00928.7640.0020.0020.0000.0000.0000.000
79A79LEU0-0.0940.00325.0110.0020.0020.0000.0000.0000.000
80A80GLN00.0220.00427.8590.0080.0080.0000.0000.0000.000
81A81PRO00.0700.02227.119-0.006-0.0060.0000.0000.0000.000
82A82GLU-1-0.899-0.93726.364-0.051-0.0510.0000.0000.0000.000
83A83ASP-1-0.793-0.87723.685-0.099-0.0990.0000.0000.0000.000
84A84GLU-1-0.854-0.90922.139-0.051-0.0510.0000.0000.0000.000
85A85THR0-0.087-0.05018.3390.0060.0060.0000.0000.0000.000
86A86ASP-1-0.829-0.88913.922-0.083-0.0830.0000.0000.0000.000
87A87TYR0-0.032-0.04714.881-0.010-0.0100.0000.0000.0000.000
88A88TYR0-0.0180.0088.5490.0160.0160.0000.0000.0000.000
89A90ALA00.003-0.01910.131-0.118-0.1180.0000.0000.0000.000
90A91ALA00.0160.02510.0810.1090.1090.0000.0000.0000.000
91A92TRP0-0.073-0.05511.063-0.092-0.0920.0000.0000.0000.000
92A93ASP-1-0.766-0.85710.944-0.309-0.3090.0000.0000.0000.000
93A94ASP-1-0.854-0.9328.180-0.627-0.6270.0000.0000.0000.000
94A95SER0-0.058-0.0189.2880.0450.0450.0000.0000.0000.000
95A96LEU0-0.061-0.06211.100-0.039-0.0390.0000.0000.0000.000
96A97ASP-1-0.886-0.92613.340-0.242-0.2420.0000.0000.0000.000
97A98VAL0-0.054-0.0188.536-0.023-0.0230.0000.0000.0000.000
98A99ALA0-0.002-0.0039.1660.0050.0050.0000.0000.0000.000
99A100VAL0-0.038-0.0205.412-0.246-0.2460.0000.0000.0000.000
100A101PHE00.021-0.0055.6750.2020.2020.0000.0000.0000.000
101A102GLY00.0440.0065.887-0.342-0.3420.0000.0000.0000.000
102A103THR0-0.089-0.0586.596-0.031-0.0310.0000.0000.0000.000
103A104GLY0-0.0160.0067.5620.1590.1590.0000.0000.0000.000
104A105THR0-0.071-0.04410.6750.0270.0270.0000.0000.0000.000
105A106LYS10.8530.90414.2680.0390.0390.0000.0000.0000.000
106A107VAL0-0.031-0.01516.9670.0080.0080.0000.0000.0000.000
107A108THR0-0.077-0.04620.4400.0100.0100.0000.0000.0000.000
108A109VAL00.0130.02423.481-0.005-0.0050.0000.0000.0000.000
109A110LEU0-0.064-0.03226.3940.0070.0070.0000.0000.0000.000
110A111GLY00.0430.02228.620-0.001-0.0010.0000.0000.0000.000
111A112GLN0-0.098-0.05928.3480.0060.0060.0000.0000.0000.000
112A113PRO00.0320.01030.002-0.004-0.0040.0000.0000.0000.000
113A114LYS10.8510.91923.7030.0450.0450.0000.0000.0000.000
114A115ALA0-0.021-0.00426.2330.0010.0010.0000.0000.0000.000
115A116ASN00.0140.01124.335-0.002-0.0020.0000.0000.0000.000
116A117PRO00.0090.01720.8390.0010.0010.0000.0000.0000.000
117A118THR00.0100.01324.036-0.007-0.0070.0000.0000.0000.000
118A119VAL0-0.014-0.01820.9980.0090.0090.0000.0000.0000.000
119A120THR0-0.0070.00023.612-0.016-0.0160.0000.0000.0000.000
120A121LEU0-0.042-0.01021.4500.0130.0130.0000.0000.0000.000
121A122PHE0-0.0170.00024.207-0.016-0.0160.0000.0000.0000.000
122A123PRO00.0380.04124.6300.0210.0210.0000.0000.0000.000
123A124PRO00.0450.02725.623-0.003-0.0030.0000.0000.0000.000
124A125SER0-0.0040.01327.829-0.010-0.0100.0000.0000.0000.000
125A126SER00.011-0.00931.2720.0050.0050.0000.0000.0000.000
126A127GLU-1-0.809-0.91933.7240.0970.0970.0000.0000.0000.000
127A128GLU-1-0.837-0.90426.3170.1900.1900.0000.0000.0000.000
128A129LEU00.0150.00128.1470.0090.0090.0000.0000.0000.000
129A130GLN0-0.060-0.01631.000-0.002-0.0020.0000.0000.0000.000
130A131ALA0-0.056-0.02031.849-0.004-0.0040.0000.0000.0000.000
131A132ASN0-0.057-0.02928.6670.0000.0000.0000.0000.0000.000
132A133LYS10.8330.88625.617-0.177-0.1770.0000.0000.0000.000
133A134ALA00.0540.02624.451-0.016-0.0160.0000.0000.0000.000
134A135THR0-0.039-0.02921.3610.0360.0360.0000.0000.0000.000
135A136LEU0-0.0290.01220.294-0.027-0.0270.0000.0000.0000.000
136A137VAL00.000-0.01420.9420.0290.0290.0000.0000.0000.000
137A138CYS0-0.048-0.03017.4570.0060.0060.0000.0000.0000.000
138A139LEU0-0.009-0.00820.3690.0120.0120.0000.0000.0000.000
139A140ILE00.011-0.00117.629-0.012-0.0120.0000.0000.0000.000
140A141SER00.004-0.03422.0030.0030.0030.0000.0000.0000.000
141A142ASP-1-0.852-0.91424.9610.0510.0510.0000.0000.0000.000
142A143PHE00.0090.01920.062-0.006-0.0060.0000.0000.0000.000
143A144TYR00.0340.01124.2730.0030.0030.0000.0000.0000.000
144A145PRO00.0480.00721.3280.0000.0000.0000.0000.0000.000
145A146GLY00.0040.00621.1610.0080.0080.0000.0000.0000.000
146A147ALA00.0100.00716.0210.0100.0100.0000.0000.0000.000
147A148VAL0-0.058-0.03115.704-0.020-0.0200.0000.0000.0000.000
148A149THR00.0170.0219.9310.0600.0600.0000.0000.0000.000
149A150VAL00.020-0.00112.028-0.057-0.0570.0000.0000.0000.000
150A151ALA00.0180.02011.0890.1040.1040.0000.0000.0000.000
151A152TRP00.0490.00712.348-0.104-0.1040.0000.0000.0000.000
152A153LYS10.7990.88513.640-0.083-0.0830.0000.0000.0000.000
153A154ALA00.0350.01016.123-0.004-0.0040.0000.0000.0000.000
154A155ASP-1-0.787-0.89818.4740.1240.1240.0000.0000.0000.000
155A156GLY0-0.0070.00218.501-0.014-0.0140.0000.0000.0000.000
156A157SER0-0.0080.00215.178-0.032-0.0320.0000.0000.0000.000
157A158PRO0-0.018-0.00810.4400.0280.0280.0000.0000.0000.000
158A159VAL00.0070.01412.3960.0140.0140.0000.0000.0000.000
159A160LYS10.8790.9273.965-0.943-0.662-0.001-0.130-0.1490.000
160A161ALA00.011-0.0119.1290.1550.1550.0000.0000.0000.000
161A162GLY00.0610.03910.989-0.127-0.1270.0000.0000.0000.000
162A163VAL0-0.047-0.01910.962-0.131-0.1310.0000.0000.0000.000
163A164GLU-1-0.865-0.90512.0010.8230.8230.0000.0000.0000.000
164A165THR0-0.020-0.02312.583-0.097-0.0970.0000.0000.0000.000
165A166THR0-0.0450.01214.1450.0110.0110.0000.0000.0000.000
166A167LYS10.9750.97614.933-0.147-0.1470.0000.0000.0000.000
167A168PRO00.0090.00016.570-0.010-0.0100.0000.0000.0000.000
168A169SER0-0.040-0.01419.737-0.012-0.0120.0000.0000.0000.000
169A170LYS10.8770.93923.146-0.023-0.0230.0000.0000.0000.000
170A171GLN00.0450.03425.528-0.001-0.0010.0000.0000.0000.000
171A172SER00.0420.00629.078-0.006-0.0060.0000.0000.0000.000
172A173ASN00.003-0.00130.215-0.004-0.0040.0000.0000.0000.000
173A174ASN0-0.008-0.00730.675-0.006-0.0060.0000.0000.0000.000
174A175LYS10.8880.97327.317-0.026-0.0260.0000.0000.0000.000
175A176TYR0-0.037-0.02822.5790.0000.0000.0000.0000.0000.000
176A177ALA00.0110.01223.494-0.002-0.0020.0000.0000.0000.000
177A178ALA0-0.004-0.01618.3470.0030.0030.0000.0000.0000.000
178A179SER00.0230.00219.117-0.012-0.0120.0000.0000.0000.000
179A180SER00.0140.02514.8030.0170.0170.0000.0000.0000.000
180A181TYR00.000-0.00816.898-0.053-0.0530.0000.0000.0000.000
181A182LEU00.0270.02715.4630.0640.0640.0000.0000.0000.000
182A183SER00.0120.00117.621-0.048-0.0480.0000.0000.0000.000
183A184LEU0-0.039-0.02318.5080.0300.0300.0000.0000.0000.000
184A185THR0-0.027-0.04121.005-0.007-0.0070.0000.0000.0000.000
185A186PRO00.0580.03124.0030.0040.0040.0000.0000.0000.000
186A187GLU-1-0.832-0.90225.9370.1530.1530.0000.0000.0000.000
187A188GLN0-0.0220.00519.5050.0080.0080.0000.0000.0000.000
188A189TRP0-0.0050.01022.4960.0020.0020.0000.0000.0000.000
189A190LYS10.8610.89424.270-0.114-0.1140.0000.0000.0000.000
190A191SER0-0.050-0.01824.109-0.009-0.0090.0000.0000.0000.000
191A192HIS0-0.0120.01119.412-0.002-0.0020.0000.0000.0000.000
192A193ARG10.8770.92524.171-0.090-0.0900.0000.0000.0000.000
193A194SER0-0.095-0.05324.012-0.011-0.0110.0000.0000.0000.000
194A195TYR00.0350.01418.4230.0140.0140.0000.0000.0000.000
195A196SER0-0.026-0.05119.269-0.009-0.0090.0000.0000.0000.000
196A198GLN0-0.037-0.04314.861-0.045-0.0450.0000.0000.0000.000
197A199VAL00.004-0.00415.1570.0280.0280.0000.0000.0000.000
198A200THR00.0080.01714.398-0.035-0.0350.0000.0000.0000.000
199A201HIS10.8280.88916.2140.0010.0010.0000.0000.0000.000
200A202GLU-1-0.734-0.82518.209-0.053-0.0530.0000.0000.0000.000
201A203GLY00.0290.00719.4040.0080.0080.0000.0000.0000.000
202A204SER0-0.054-0.01221.075-0.001-0.0010.0000.0000.0000.000
203A205THR00.0490.00017.080-0.002-0.0020.0000.0000.0000.000
204A206VAL0-0.029-0.00219.633-0.004-0.0040.0000.0000.0000.000
205A207GLU-1-0.736-0.83018.5600.1040.1040.0000.0000.0000.000
206A208LYS10.8110.91320.768-0.090-0.0900.0000.0000.0000.000
207A209THR00.0810.04021.6190.0200.0200.0000.0000.0000.000
208A210VAL0-0.037-0.01323.385-0.010-0.0100.0000.0000.0000.000
209A211ALA00.0790.05024.8710.0100.0100.0000.0000.0000.000
210A212PRO00.0450.02026.272-0.004-0.0040.0000.0000.0000.000
211A213THR0-0.028-0.01228.913-0.008-0.0080.0000.0000.0000.000
212A214GLU-1-0.835-0.92331.1800.0890.0890.0000.0000.0000.000
213A215CYS0-0.038-0.00233.2510.0030.0030.0000.0000.0000.000
214A216SER0-0.055-0.00632.076-0.001-0.0010.0000.0000.0000.000