FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: JLQ59

Calculation Name: 2E2L-B-Xray372

Preferred Name:

Target Type:

Ligand Name: formamide

ligand 3-letter code: ARF

PDB ID: 2E2L

Chain ID: B

ChEMBL ID:

UniProt ID: O25836

Base Structure: X-ray

Registration Date: 2023-06-22

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 322
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -4949405.863082
FMO2-HF: Nuclear repulsion 4822929.20958
FMO2-HF: Total energy -126476.653502
FMO2-MP2: Total energy -126846.553707


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(B:13:GLY)


Summations of interaction energy for fragment #1(B:13:GLY)
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.
-13.078-9.0346.909-5.994-4.961-0.022
Interaction energy analysis for fragmet #1(B:13:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.015 / 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].
3B15LEU00.0480.0513.8120.4612.453-0.018-1.120-0.8540.002
4B16VAL0-0.040-0.0256.9900.2060.2060.0000.0000.0000.000
5B17ALA00.019-0.0109.7080.1110.1110.0000.0000.0000.000
6B18ALA00.0040.00013.4060.0390.0390.0000.0000.0000.000
7B19ILE0-0.0070.00716.0760.0290.0290.0000.0000.0000.000
8B20GLN00.0480.02419.5710.0240.0240.0000.0000.0000.000
9B21PHE0-0.020-0.02122.4940.0100.0100.0000.0000.0000.000
10B22PRO0-0.0030.00524.8340.0210.0210.0000.0000.0000.000
11B23VAL0-0.030-0.00128.608-0.006-0.0060.0000.0000.0000.000
12B24PRO0-0.002-0.00330.4810.0110.0110.0000.0000.0000.000
13B25ILE0-0.0020.00734.1330.0030.0030.0000.0000.0000.000
14B26VAL00.0020.02034.143-0.003-0.0030.0000.0000.0000.000
15B27ASN0-0.048-0.02737.4390.0110.0110.0000.0000.0000.000
16B28SER0-0.033-0.02239.8880.0050.0050.0000.0000.0000.000
17B29ARG10.9280.94836.4900.1050.1050.0000.0000.0000.000
18B30LYS10.9760.98937.4050.1050.1050.0000.0000.0000.000
19B31ASP-1-0.831-0.91836.726-0.115-0.1150.0000.0000.0000.000
20B32ILE0-0.024-0.00132.763-0.008-0.0080.0000.0000.0000.000
21B33ASP-1-0.879-0.94532.452-0.149-0.1490.0000.0000.0000.000
22B34HIS0-0.030-0.00532.643-0.012-0.0120.0000.0000.0000.000
23B35ASN0-0.025-0.02129.905-0.014-0.0140.0000.0000.0000.000
24B36ILE00.0180.01728.316-0.018-0.0180.0000.0000.0000.000
25B37GLU-1-0.896-0.95927.768-0.238-0.2380.0000.0000.0000.000
26B38SER0-0.109-0.03928.367-0.023-0.0230.0000.0000.0000.000
27B39ILE00.0160.03522.934-0.024-0.0240.0000.0000.0000.000
28B40ILE00.0420.02023.428-0.041-0.0410.0000.0000.0000.000
29B41ARG10.9390.97123.8650.2000.2000.0000.0000.0000.000
30B42THR0-0.016-0.04021.280-0.016-0.0160.0000.0000.0000.000
31B43LEU0-0.0040.02418.443-0.041-0.0410.0000.0000.0000.000
32B44HIS00.0300.00619.194-0.088-0.0880.0000.0000.0000.000
33B45ALA0-0.028-0.01320.896-0.028-0.0280.0000.0000.0000.000
34B46THR0-0.038-0.04915.914-0.005-0.0050.0000.0000.0000.000
35B47LYS10.8620.94012.9301.1651.1650.0000.0000.0000.000
36B48ALA0-0.042-0.01416.985-0.039-0.0390.0000.0000.0000.000
37B49GLY0-0.023-0.00118.7840.0110.0110.0000.0000.0000.000
38B50TYR0-0.027-0.01413.206-0.005-0.0050.0000.0000.0000.000
39B51PRO00.0450.01714.081-0.121-0.1210.0000.0000.0000.000
40B52GLY00.001-0.00610.279-0.014-0.0140.0000.0000.0000.000
41B53VAL0-0.0330.0149.108-0.470-0.4700.0000.0000.0000.000
42B54GLU-1-0.889-0.9666.671-3.587-3.5870.0000.0000.0000.000
43B55LEU0-0.031-0.0049.8460.2510.2510.0000.0000.0000.000
44B56ILE00.0120.00911.3580.0030.0030.0000.0000.0000.000
45B57ILE0-0.021-0.01912.7150.0760.0760.0000.0000.0000.000
46B58PHE00.0140.00516.5910.0150.0150.0000.0000.0000.000
47B59PRO00.0030.00920.3870.0160.0160.0000.0000.0000.000
48B60GLU-1-0.711-0.83422.515-0.093-0.0930.0000.0000.0000.000
49B61TYR0-0.001-0.00925.1900.0020.0020.0000.0000.0000.000
50B62SER0-0.009-0.00824.5020.0020.0020.0000.0000.0000.000
51B63THR00.021-0.00326.932-0.008-0.0080.0000.0000.0000.000
52B64GLN0-0.006-0.02929.002-0.003-0.0030.0000.0000.0000.000
53B65GLY00.0100.01931.1370.0090.0090.0000.0000.0000.000
54B66LEU0-0.014-0.01830.9720.0030.0030.0000.0000.0000.000
55B67ASN0-0.006-0.01134.8160.0110.0110.0000.0000.0000.000
56B68THR00.0300.00037.4650.0000.0000.0000.0000.0000.000
57B69ALA00.0070.02039.5880.0040.0040.0000.0000.0000.000
58B70LYS10.8920.93640.8200.0750.0750.0000.0000.0000.000
59B71TRP0-0.0120.02233.984-0.004-0.0040.0000.0000.0000.000
60B72LEU00.0200.01937.238-0.002-0.0020.0000.0000.0000.000
61B73SER0-0.016-0.02639.7230.0020.0020.0000.0000.0000.000
62B74GLU-1-0.796-0.91639.678-0.071-0.0710.0000.0000.0000.000
63B75GLU-1-0.883-0.93439.634-0.089-0.0890.0000.0000.0000.000
64B76PHE00.021-0.00236.603-0.008-0.0080.0000.0000.0000.000
65B77LEU0-0.0260.02335.083-0.005-0.0050.0000.0000.0000.000
66B78LEU0-0.035-0.01531.0390.0010.0010.0000.0000.0000.000
67B79ASP-1-0.860-0.92233.057-0.087-0.0870.0000.0000.0000.000
68B80VAL0-0.0370.01126.697-0.013-0.0130.0000.0000.0000.000
69B81PRO00.019-0.01527.7210.0110.0110.0000.0000.0000.000
70B82GLY00.0580.00929.3220.0140.0140.0000.0000.0000.000
71B83LYS10.9070.94230.4340.1150.1150.0000.0000.0000.000
72B84GLU-1-0.803-0.91629.961-0.148-0.1480.0000.0000.0000.000
73B85THR00.0380.01626.013-0.010-0.0100.0000.0000.0000.000
74B86GLU-1-0.912-0.95525.610-0.230-0.2300.0000.0000.0000.000
75B87LEU0-0.0160.01326.892-0.017-0.0170.0000.0000.0000.000
76B88TYR0-0.014-0.02122.854-0.021-0.0210.0000.0000.0000.000
77B89ALA00.0350.02322.139-0.042-0.0420.0000.0000.0000.000
78B90LYS10.9290.96522.4410.2220.2220.0000.0000.0000.000
79B91ALA00.001-0.00122.913-0.021-0.0210.0000.0000.0000.000
80B92CYS0-0.0180.00318.365-0.045-0.0450.0000.0000.0000.000
81B93LYS10.9640.98718.5520.2400.2400.0000.0000.0000.000
82B94GLU-1-0.976-1.00220.237-0.347-0.3470.0000.0000.0000.000
83B95ALA0-0.0040.00618.239-0.015-0.0150.0000.0000.0000.000
84B96LYS10.7790.88215.4390.4560.4560.0000.0000.0000.000
85B97VAL0-0.032-0.01013.444-0.159-0.1590.0000.0000.0000.000
86B98TYR00.009-0.00410.8620.1820.1820.0000.0000.0000.000
87B99GLY00.0230.01114.011-0.043-0.0430.0000.0000.0000.000
88B100VAL0-0.028-0.00715.0710.0500.0500.0000.0000.0000.000
89B101PHE00.0290.00617.9240.0010.0010.0000.0000.0000.000
90B102SER00.0250.02321.7100.0240.0240.0000.0000.0000.000
91B103ILE0-0.0060.00324.720-0.007-0.0070.0000.0000.0000.000
92B104MET0-0.0420.00528.0550.0130.0130.0000.0000.0000.000
93B105GLU-1-0.687-0.83329.883-0.093-0.0930.0000.0000.0000.000
94B106ARG10.8260.89932.0880.0940.0940.0000.0000.0000.000
95B107ASN0-0.017-0.02534.882-0.001-0.0010.0000.0000.0000.000
96B108PRO00.003-0.00334.7880.0010.0010.0000.0000.0000.000
97B109ASP-1-0.856-0.92137.812-0.029-0.0290.0000.0000.0000.000
98B110SER00.007-0.00240.3310.0000.0000.0000.0000.0000.000
99B111ASN0-0.053-0.03142.6830.0010.0010.0000.0000.0000.000
100B112LYS10.8880.96038.3840.0260.0260.0000.0000.0000.000
101B113ASN00.0510.01238.208-0.005-0.0050.0000.0000.0000.000
102B114PRO0-0.0170.01435.0260.0020.0020.0000.0000.0000.000
103B115TYR00.0110.00530.6700.0070.0070.0000.0000.0000.000
104B116ASN0-0.006-0.01527.784-0.017-0.0170.0000.0000.0000.000
105B117THR0-0.007-0.02925.7370.0110.0110.0000.0000.0000.000
106B118ALA00.0020.01121.340-0.014-0.0140.0000.0000.0000.000
107B119ILE0-0.028-0.01521.3730.0190.0190.0000.0000.0000.000
108B120ILE00.003-0.00614.693-0.027-0.0270.0000.0000.0000.000
109B121ILE0-0.028-0.00917.6910.0370.0370.0000.0000.0000.000
110B122ASP-1-0.735-0.87315.323-0.482-0.4820.0000.0000.0000.000
111B123PRO00.0370.02713.3850.0460.0460.0000.0000.0000.000
112B124GLN0-0.091-0.05615.892-0.035-0.0350.0000.0000.0000.000
113B125GLY0-0.061-0.02119.4340.0420.0420.0000.0000.0000.000
114B126GLU-1-0.884-0.93820.169-0.190-0.1900.0000.0000.0000.000
115B127ILE0-0.043-0.02919.807-0.030-0.0300.0000.0000.0000.000
116B128ILE00.0010.01014.9330.0260.0260.0000.0000.0000.000
117B129LEU0-0.050-0.02216.7750.0390.0390.0000.0000.0000.000
118B130LYS10.8260.91319.8190.0780.0780.0000.0000.0000.000
119B131TYR0-0.039-0.04621.7780.0240.0240.0000.0000.0000.000
120B132ARG10.7480.85923.6850.0520.0520.0000.0000.0000.000
121B133LYS10.8020.88926.4500.0690.0690.0000.0000.0000.000
122B134LEU0-0.0090.01025.8130.0040.0040.0000.0000.0000.000
123B135PHE0-0.014-0.00527.4280.0060.0060.0000.0000.0000.000
124B136PRO00.0100.00929.769-0.004-0.0040.0000.0000.0000.000
125B137TRP0-0.0080.00130.9780.0050.0050.0000.0000.0000.000
126B138ASN00.0080.02632.671-0.008-0.0080.0000.0000.0000.000
127B139PRO0-0.019-0.02636.3570.0030.0030.0000.0000.0000.000
128B140ILE0-0.014-0.00835.313-0.002-0.0020.0000.0000.0000.000
129B141GLU-1-0.760-0.88331.520-0.062-0.0620.0000.0000.0000.000
130B142PRO0-0.0060.01135.9890.0050.0050.0000.0000.0000.000
131B143TRP0-0.035-0.03932.422-0.001-0.0010.0000.0000.0000.000
132B144TYR0-0.029-0.02035.0240.0080.0080.0000.0000.0000.000
133B145PRO00.0020.00232.456-0.005-0.0050.0000.0000.0000.000
134B146GLY0-0.003-0.01429.472-0.001-0.0010.0000.0000.0000.000
135B147ASP-1-0.855-0.92430.538-0.029-0.0290.0000.0000.0000.000
136B148LEU0-0.043-0.02126.3410.0040.0040.0000.0000.0000.000
137B149GLY00.0040.01425.8260.0040.0040.0000.0000.0000.000
138B150MET00.0320.00520.465-0.015-0.0150.0000.0000.0000.000
139B151PRO0-0.049-0.01020.6130.0260.0260.0000.0000.0000.000
140B152VAL00.020-0.00514.825-0.004-0.0040.0000.0000.0000.000
141B153CYS0-0.059-0.01714.0300.0050.0050.0000.0000.0000.000
142B154GLU-1-0.891-0.95012.1270.1180.1180.0000.0000.0000.000
143B155GLY00.0320.0169.934-0.036-0.0360.0000.0000.0000.000
144B156PRO00.0040.0226.9060.1230.1230.0000.0000.0000.000
145B157GLY00.0580.0263.438-0.1640.0120.023-0.063-0.1360.000
146B158GLY0-0.029-0.0153.5161.7402.4460.025-0.313-0.419-0.002
147B159SER0-0.064-0.0486.0610.4350.4350.0000.0000.0000.000
148B160LYS10.9290.9767.272-0.287-0.2870.0000.0000.0000.000
149B161LEU00.021-0.0039.3240.0560.0560.0000.0000.0000.000
150B162ALA00.0510.01812.4570.0280.0280.0000.0000.0000.000
151B163VAL0-0.0080.00515.534-0.018-0.0180.0000.0000.0000.000
152B164CYS0-0.0560.00518.0510.0230.0230.0000.0000.0000.000
153B165ILE00.008-0.01620.882-0.024-0.0240.0000.0000.0000.000
154B166SER00.011-0.02523.5910.0210.0210.0000.0000.0000.000
155B167HIS0-0.041-0.01324.9650.0180.0180.0000.0000.0000.000
156B168ASP-1-0.663-0.82724.094-0.015-0.0150.0000.0000.0000.000
157B169GLY0-0.019-0.02022.6230.0160.0160.0000.0000.0000.000
158B170MET0-0.048-0.01123.3390.0180.0180.0000.0000.0000.000
159B171ILE0-0.0210.01125.7960.0090.0090.0000.0000.0000.000
160B172PRO00.0270.01623.9330.0060.0060.0000.0000.0000.000
161B173GLU-1-0.834-0.92823.6860.1050.1050.0000.0000.0000.000
162B174LEU00.0000.00622.5900.0090.0090.0000.0000.0000.000
163B175ALA00.0120.00719.5630.0030.0030.0000.0000.0000.000
164B176ARG10.8750.93019.369-0.200-0.2000.0000.0000.0000.000
165B177GLU-1-0.904-0.95020.9740.1290.1290.0000.0000.0000.000
166B178ALA00.011-0.00417.2670.0070.0070.0000.0000.0000.000
167B179ALA0-0.022-0.01816.3070.0200.0200.0000.0000.0000.000
168B180TYR0-0.070-0.02417.3690.0480.0480.0000.0000.0000.000
169B181LYS10.8620.94019.305-0.059-0.0590.0000.0000.0000.000
170B182GLY0-0.011-0.00815.714-0.024-0.0240.0000.0000.0000.000
171B183CYS0-0.056-0.00213.0880.0810.0810.0000.0000.0000.000
172B184ASN00.0290.0028.563-0.186-0.1860.0000.0000.0000.000
173B185VAL0-0.0020.0027.2210.1000.1000.0000.0000.0000.000
174B186TYR00.029-0.02210.436-0.102-0.1020.0000.0000.0000.000
175B187ILE00.0110.00612.641-0.020-0.0200.0000.0000.0000.000
176B188ARG10.8100.88215.3170.0420.0420.0000.0000.0000.000
177B189ILE00.0160.01218.795-0.022-0.0220.0000.0000.0000.000
178B190SER0-0.007-0.04220.7540.0300.0300.0000.0000.0000.000
179B191GLY00.0230.02423.904-0.016-0.0160.0000.0000.0000.000
180B192TYR00.0580.00627.268-0.005-0.0050.0000.0000.0000.000
181B193SER00.0080.01627.3810.0060.0060.0000.0000.0000.000
182B194THR00.0340.02629.1000.0060.0060.0000.0000.0000.000
183B195GLN0-0.021-0.01431.3170.0100.0100.0000.0000.0000.000
184B196VAL0-0.042-0.02229.8310.0070.0070.0000.0000.0000.000
185B197ASN0-0.058-0.05226.6890.0070.0070.0000.0000.0000.000
186B198ASP-1-0.826-0.91126.7880.0040.0040.0000.0000.0000.000
187B199GLN0-0.003-0.02526.8080.0040.0040.0000.0000.0000.000
188B200TRP0-0.0070.02420.3660.0120.0120.0000.0000.0000.000
189B201ILE00.0660.04021.8920.0080.0080.0000.0000.0000.000
190B202LEU0-0.036-0.02021.9160.0210.0210.0000.0000.0000.000
191B203THR00.029-0.01222.9450.0170.0170.0000.0000.0000.000
192B204ASN00.0300.03018.3290.0220.0220.0000.0000.0000.000
193B205ARG10.9220.96917.952-0.120-0.1200.0000.0000.0000.000
194B206SER00.018-0.00219.0210.0360.0360.0000.0000.0000.000
195B207ASN0-0.040-0.03618.8210.0350.0350.0000.0000.0000.000
196B208ALA0-0.0040.02014.9880.0190.0190.0000.0000.0000.000
197B209TRP00.0420.01016.3110.0640.0640.0000.0000.0000.000
198B210HIS0-0.026-0.01318.4450.0430.0430.0000.0000.0000.000
199B211ASN0-0.028-0.02617.154-0.005-0.0050.0000.0000.0000.000
200B212LEU00.0050.03114.6250.0410.0410.0000.0000.0000.000
201B213MET0-0.068-0.01611.7190.1200.1200.0000.0000.0000.000
202B214TYR00.0310.0156.734-0.195-0.1950.0000.0000.0000.000
203B215THR0-0.067-0.02711.106-0.065-0.0650.0000.0000.0000.000
204B216VAL00.0110.01010.412-0.016-0.0160.0000.0000.0000.000
205B217SER0-0.010-0.01113.656-0.011-0.0110.0000.0000.0000.000
206B218VAL00.0100.01017.350-0.014-0.0140.0000.0000.0000.000
207B219ASN0-0.078-0.02319.6670.0240.0240.0000.0000.0000.000
208B220LEU00.0000.00623.460-0.020-0.0200.0000.0000.0000.000
209B221ALA0-0.0440.00125.7890.0150.0150.0000.0000.0000.000
210B222GLY00.0370.02627.3200.0100.0100.0000.0000.0000.000
211B223TYR0-0.013-0.03530.320-0.006-0.0060.0000.0000.0000.000
212B224ASP-1-0.830-0.91233.295-0.063-0.0630.0000.0000.0000.000
213B225ASN00.0150.02336.395-0.007-0.0070.0000.0000.0000.000
214B226VAL0-0.078-0.04237.0120.0010.0010.0000.0000.0000.000
215B227PHE00.0280.00635.944-0.002-0.0020.0000.0000.0000.000
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