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: 3JQ5L

Calculation Name: 2G7L-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2G7L

Chain ID: A

ChEMBL ID:

UniProt ID: Q93JG8

Base Structure: X-ray

Registration Date: 2023-09-21

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 204
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1990709.54738
FMO2-HF: Nuclear repulsion 1914821.973687
FMO2-HF: Total energy -75887.573694
FMO2-MP2: Total energy -76112.421353


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:16:LYS)


Summations of interaction energy for fragment #1(A:16:LYS)
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.
-43.005-41.768-0.007-0.582-0.6470.002
Interaction energy analysis for fragmet #1(A:16:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.993 / q_NPA : 0.991
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].
3A18ALA00.0170.0083.908-1.407-0.170-0.007-0.582-0.6470.002
4A19LEU00.0240.0206.4743.0093.0090.0000.0000.0000.000
5A20SER00.0110.0058.2041.1681.1680.0000.0000.0000.000
6A21ARG10.8200.86611.95413.38713.3870.0000.0000.0000.000
7A22ARG10.9220.96012.95117.47217.4720.0000.0000.0000.000
8A23TRP00.0410.0295.811-0.078-0.0780.0000.0000.0000.000
9A24ILE00.0170.02112.0360.2950.2950.0000.0000.0000.000
10A25VAL00.0300.00513.9140.5420.5420.0000.0000.0000.000
11A26ASP-1-0.827-0.90515.424-14.568-14.5680.0000.0000.0000.000
12A27THR0-0.035-0.03013.1440.3640.3640.0000.0000.0000.000
13A28ALA0-0.021-0.01015.6860.4510.4510.0000.0000.0000.000
14A29VAL00.0240.01018.5010.5720.5720.0000.0000.0000.000
15A30ALA0-0.012-0.00317.4020.4970.4970.0000.0000.0000.000
16A31LEU00.0060.00117.9750.4330.4330.0000.0000.0000.000
17A32MET0-0.041-0.01920.0320.4720.4720.0000.0000.0000.000
18A33ARG10.8880.94522.98110.47710.4770.0000.0000.0000.000
19A34ALA0-0.0080.01321.2460.3180.3180.0000.0000.0000.000
20A35GLU-1-0.848-0.89920.991-12.243-12.2430.0000.0000.0000.000
21A36GLY0-0.0060.01024.8140.2770.2770.0000.0000.0000.000
22A37LEU00.018-0.01525.022-0.009-0.0090.0000.0000.0000.000
23A38GLU-1-0.812-0.88725.218-10.392-10.3920.0000.0000.0000.000
24A39LYS10.8070.88722.42010.32310.3230.0000.0000.0000.000
25A40VAL0-0.0080.00620.247-0.646-0.6460.0000.0000.0000.000
26A41THR0-0.019-0.01120.3780.1040.1040.0000.0000.0000.000
27A42MET00.0280.01117.634-0.503-0.5030.0000.0000.0000.000
28A43ARG10.9530.97816.42212.42612.4260.0000.0000.0000.000
29A44ARG10.7080.80916.30213.36113.3610.0000.0000.0000.000
30A45LEU00.0400.01114.499-0.536-0.5360.0000.0000.0000.000
31A46ALA0-0.014-0.00712.137-0.833-0.8330.0000.0000.0000.000
32A47GLN0-0.025-0.01811.157-0.590-0.5900.0000.0000.0000.000
33A48GLU-1-0.810-0.86412.414-16.071-16.0710.0000.0000.0000.000
34A49LEU0-0.080-0.0408.848-0.405-0.4050.0000.0000.0000.000
35A50ASP-1-0.928-0.9486.049-28.764-28.7640.0000.0000.0000.000
36A51THR0-0.020-0.0047.174-1.977-1.9770.0000.0000.0000.000
37A52GLY00.0250.0169.1761.7401.7400.0000.0000.0000.000
38A53PRO00.012-0.02112.705-0.295-0.2950.0000.0000.0000.000
39A54ALA0-0.0100.00014.6500.3740.3740.0000.0000.0000.000
40A55SER0-0.008-0.0169.9490.4500.4500.0000.0000.0000.000
41A56LEU00.0020.00111.982-0.105-0.1050.0000.0000.0000.000
42A57TYR0-0.012-0.01314.3620.5370.5370.0000.0000.0000.000
43A58VAL0-0.0210.00213.8920.7480.7480.0000.0000.0000.000
44A59TYR0-0.029-0.02510.9640.8250.8250.0000.0000.0000.000
45A60VAL00.0110.00716.7530.6380.6380.0000.0000.0000.000
46A61ALA00.0470.03719.328-0.138-0.1380.0000.0000.0000.000
47A62ASN0-0.013-0.01621.9100.3210.3210.0000.0000.0000.000
48A63THR00.0430.00922.964-0.272-0.2720.0000.0000.0000.000
49A64ALA00.0410.04024.0000.0430.0430.0000.0000.0000.000
50A65GLU-1-0.736-0.84722.662-12.127-12.1270.0000.0000.0000.000
51A66LEU0-0.002-0.00118.775-0.160-0.1600.0000.0000.0000.000
52A67HIS00.0000.00122.2000.2860.2860.0000.0000.0000.000
53A68ALA00.0530.03625.2720.1660.1660.0000.0000.0000.000
54A69ALA0-0.007-0.00621.6250.1380.1380.0000.0000.0000.000
55A70VAL0-0.028-0.02221.755-0.035-0.0350.0000.0000.0000.000
56A71LEU0-0.0010.00023.7620.1690.1690.0000.0000.0000.000
57A72ASP-1-0.796-0.91424.971-10.315-10.3150.0000.0000.0000.000
58A73ALA0-0.017-0.00322.7540.1260.1260.0000.0000.0000.000
59A74LEU0-0.019-0.00324.8330.1530.1530.0000.0000.0000.000
60A75LEU0-0.015-0.00727.9690.2960.2960.0000.0000.0000.000
61A76GLY0-0.033-0.01127.9860.1470.1470.0000.0000.0000.000
62A77GLU-1-0.989-0.99928.926-8.989-8.9890.0000.0000.0000.000
63A78VAL0-0.033-0.00731.4950.2420.2420.0000.0000.0000.000
64A79ASP-1-0.825-0.89434.729-7.483-7.4830.0000.0000.0000.000
65A80LEU0-0.048-0.03334.2950.2100.2100.0000.0000.0000.000
66A81THR0-0.0120.00237.9220.0230.0230.0000.0000.0000.000
67A82GLY00.0060.01240.2380.1730.1730.0000.0000.0000.000
68A83ALA00.016-0.00442.193-0.080-0.0800.0000.0000.0000.000
69A84GLY0-0.034-0.02544.1040.0270.0270.0000.0000.0000.000
70A85ALA0-0.0110.01747.3330.0670.0670.0000.0000.0000.000
71A86GLU-1-0.923-0.96448.698-5.764-5.7640.0000.0000.0000.000
72A87GLU-1-0.863-0.93147.708-6.391-6.3910.0000.0000.0000.000
73A88ASP-1-0.850-0.90950.520-5.613-5.6130.0000.0000.0000.000
74A89TRP0-0.002-0.00748.518-0.114-0.1140.0000.0000.0000.000
75A90ARG10.7810.87948.2895.5495.5490.0000.0000.0000.000
76A91GLU-1-0.944-0.97349.396-6.023-6.0230.0000.0000.0000.000
77A92GLN00.0870.03745.198-0.201-0.2010.0000.0000.0000.000
78A93LEU00.0140.00643.579-0.153-0.1530.0000.0000.0000.000
79A94ARG10.8280.89543.9775.8355.8350.0000.0000.0000.000
80A95ALA00.0030.02243.913-0.088-0.0880.0000.0000.0000.000
81A96VAL00.0480.02839.361-0.114-0.1140.0000.0000.0000.000
82A97LEU00.0120.00639.278-0.176-0.1760.0000.0000.0000.000
83A98THR0-0.057-0.02140.571-0.040-0.0400.0000.0000.0000.000
84A99SER0-0.016-0.03337.762-0.098-0.0980.0000.0000.0000.000
85A100TYR0-0.003-0.02033.813-0.266-0.2660.0000.0000.0000.000
86A101THR0-0.014-0.03736.114-0.138-0.1380.0000.0000.0000.000
87A102LEU0-0.031-0.01138.074-0.031-0.0310.0000.0000.0000.000
88A103VAL00.0380.02231.757-0.062-0.0620.0000.0000.0000.000
89A104LEU0-0.048-0.01733.321-0.181-0.1810.0000.0000.0000.000
90A105PHE0-0.026-0.02834.8220.0270.0270.0000.0000.0000.000
91A106ALA0-0.0390.00133.7370.0470.0470.0000.0000.0000.000
92A107HIS0-0.020-0.01529.252-0.252-0.2520.0000.0000.0000.000
93A108PRO00.0810.05132.458-0.189-0.1890.0000.0000.0000.000
94A109GLN0-0.056-0.03330.0590.2310.2310.0000.0000.0000.000
95A110LEU00.0090.00026.793-0.145-0.1450.0000.0000.0000.000
96A111ALA00.0530.03430.530-0.050-0.0500.0000.0000.0000.000
97A112ARG10.8370.90733.6137.9167.9160.0000.0000.0000.000
98A113SER0-0.040-0.04028.7710.0990.0990.0000.0000.0000.000
99A114ALA00.0230.01931.080-0.100-0.1000.0000.0000.0000.000
100A115LEU0-0.052-0.02132.1110.1140.1140.0000.0000.0000.000
101A116VAL0-0.094-0.03131.1610.0970.0970.0000.0000.0000.000
102A117ALA0-0.029-0.03228.444-0.092-0.0920.0000.0000.0000.000
103A118ARG10.8610.92229.7968.0978.0970.0000.0000.0000.000
104A119PRO0-0.034-0.02127.782-0.257-0.2570.0000.0000.0000.000
105A120SER0-0.023-0.01325.1870.1690.1690.0000.0000.0000.000
106A121GLY0-0.0180.00325.401-0.272-0.2720.0000.0000.0000.000
107A122GLU-1-0.847-0.94125.760-9.573-9.5730.0000.0000.0000.000
108A123ASN0-0.039-0.00726.0710.5320.5320.0000.0000.0000.000
109A124TYR00.0600.01729.1670.4170.4170.0000.0000.0000.000
110A125LEU0-0.017-0.00528.9700.3200.3200.0000.0000.0000.000
111A126ARG10.9000.94529.7479.5819.5810.0000.0000.0000.000
112A127LEU0-0.0030.01133.3670.2760.2760.0000.0000.0000.000
113A128VAL0-0.016-0.02334.6050.2790.2790.0000.0000.0000.000
114A129GLU-1-0.908-0.93736.169-7.566-7.5660.0000.0000.0000.000
115A130ARG10.7830.87037.6607.2457.2450.0000.0000.0000.000
116A131VAL0-0.003-0.01739.2970.2380.2380.0000.0000.0000.000
117A132LEU0-0.021-0.01539.2830.2350.2350.0000.0000.0000.000
118A133GLU-1-0.800-0.87041.957-6.648-6.6480.0000.0000.0000.000
119A134LEU0-0.014-0.00442.7770.2020.2020.0000.0000.0000.000
120A135LEU0-0.005-0.01445.0740.1820.1820.0000.0000.0000.000
121A136ALA0-0.028-0.00446.4400.1650.1650.0000.0000.0000.000
122A137ARG10.7270.83446.1326.4936.4930.0000.0000.0000.000
123A138SER0-0.074-0.03750.5420.1550.1550.0000.0000.0000.000
124A139GLY0-0.0070.00052.3230.1240.1240.0000.0000.0000.000
125A140ALA0-0.027-0.00951.6250.0680.0680.0000.0000.0000.000
126A141PRO00.013-0.00151.593-0.107-0.1070.0000.0000.0000.000
127A142GLY00.0500.01648.442-0.070-0.0700.0000.0000.0000.000
128A143ALA00.001-0.00247.139-0.126-0.1260.0000.0000.0000.000
129A144GLN00.007-0.00347.429-0.045-0.0450.0000.0000.0000.000
130A145VAL00.0350.02245.957-0.070-0.0700.0000.0000.0000.000
131A146ALA00.0110.01043.308-0.126-0.1260.0000.0000.0000.000
132A147TRP0-0.021-0.02942.899-0.097-0.0970.0000.0000.0000.000
133A148GLY00.0350.00344.636-0.038-0.0380.0000.0000.0000.000
134A149VAL00.0270.00940.640-0.009-0.0090.0000.0000.0000.000
135A150ASP-1-0.813-0.86239.058-7.698-7.6980.0000.0000.0000.000
136A151LYS10.8680.91740.8616.9526.9520.0000.0000.0000.000
137A152LEU0-0.0050.00443.4690.0210.0210.0000.0000.0000.000
138A153LEU00.0290.02237.029-0.033-0.0330.0000.0000.0000.000
139A154GLN0-0.0170.01139.203-0.049-0.0490.0000.0000.0000.000
140A155ASP-1-0.838-0.90040.477-6.553-6.5530.0000.0000.0000.000
141A156ALA00.0400.03340.2090.0100.0100.0000.0000.0000.000
142A157THR0-0.024-0.03435.611-0.145-0.1450.0000.0000.0000.000
143A158ALA0-0.020-0.01338.356-0.091-0.0910.0000.0000.0000.000
144A159THR00.0220.00540.7870.0340.0340.0000.0000.0000.000
145A160ALA00.007-0.00437.6340.0390.0390.0000.0000.0000.000
146A161ALA0-0.037-0.00837.312-0.099-0.0990.0000.0000.0000.000
147A162GLU-1-0.950-0.97538.273-6.637-6.6370.0000.0000.0000.000
148A163GLN0-0.093-0.03339.0830.1530.1530.0000.0000.0000.000
149A164ALA0-0.023-0.02438.989-0.139-0.1390.0000.0000.0000.000
150A165THR0-0.0050.00933.201-0.084-0.0840.0000.0000.0000.000
151A177SER00.0520.02548.8610.0530.0530.0000.0000.0000.000
152A178ALA00.0360.00450.2200.0990.0990.0000.0000.0000.000
153A179THR00.0590.02750.5860.0920.0920.0000.0000.0000.000
154A180VAL00.0370.01952.0330.1020.1020.0000.0000.0000.000
155A181ARG10.8710.94851.3635.7695.7690.0000.0000.0000.000
156A182ALA00.0890.03556.0730.0870.0870.0000.0000.0000.000
157A183LEU0-0.004-0.01455.5040.0630.0630.0000.0000.0000.000
158A184ARG10.8410.91556.9855.2605.2600.0000.0000.0000.000
159A185ASP-1-0.903-0.95159.565-5.036-5.0360.0000.0000.0000.000
160A186ALA0-0.068-0.02561.3360.0440.0440.0000.0000.0000.000
161A187ASP-1-0.863-0.92563.127-4.432-4.4320.0000.0000.0000.000
162A188GLU-1-0.861-0.94966.925-4.443-4.4430.0000.0000.0000.000
163A189ALA0-0.052-0.02269.1510.0220.0220.0000.0000.0000.000
164A190THR0-0.047-0.04166.0880.0320.0320.0000.0000.0000.000
165A191HIS0-0.048-0.01562.628-0.034-0.0340.0000.0000.0000.000
166A192PRO00.1010.06465.405-0.055-0.0550.0000.0000.0000.000
167A193ALA0-0.030-0.01964.287-0.007-0.0070.0000.0000.0000.000
168A194ILE0-0.021-0.00259.817-0.060-0.0600.0000.0000.0000.000
169A195ALA00.0520.02962.842-0.033-0.0330.0000.0000.0000.000
170A196SER0-0.010-0.01265.5080.0200.0200.0000.0000.0000.000
171A197HIS0-0.066-0.03461.5090.0130.0130.0000.0000.0000.000
172A198MET0-0.0570.01159.314-0.136-0.1360.0000.0000.0000.000
173A199PRO00.007-0.01460.5670.0680.0680.0000.0000.0000.000
174A200LEU00.025-0.00459.116-0.102-0.1020.0000.0000.0000.000
175A201LEU00.0430.02356.652-0.105-0.1050.0000.0000.0000.000
176A202VAL0-0.066-0.02954.770-0.123-0.1230.0000.0000.0000.000
177A203ALA0-0.0230.00555.250-0.029-0.0290.0000.0000.0000.000
178A204GLY00.0330.01954.257-0.029-0.0290.0000.0000.0000.000
179A205SER0-0.034-0.04949.685-0.110-0.1100.0000.0000.0000.000
180A206ALA00.0740.01845.3800.0220.0220.0000.0000.0000.000
181A207HIS00.0190.00547.251-0.068-0.0680.0000.0000.0000.000
182A208ASP-1-0.815-0.87648.120-5.703-5.7030.0000.0000.0000.000
183A209ARG10.8160.89549.0555.7465.7460.0000.0000.0000.000
184A210LEU00.0660.04343.6430.0200.0200.0000.0000.0000.000
185A211ARG10.8860.95047.6645.7655.7650.0000.0000.0000.000
186A212TRP0-0.0060.00050.2710.0220.0220.0000.0000.0000.000
187A213SER0-0.011-0.03646.9110.0830.0830.0000.0000.0000.000
188A214PHE00.0500.02946.3940.0190.0190.0000.0000.0000.000
189A215ASP-1-0.767-0.85248.864-5.691-5.6910.0000.0000.0000.000
190A216VAL0-0.024-0.01252.5140.0820.0820.0000.0000.0000.000
191A217LEU00.0060.01246.6240.0520.0520.0000.0000.0000.000
192A218VAL00.0350.02148.8590.0220.0220.0000.0000.0000.000
193A219ASN0-0.0370.00151.0920.0640.0640.0000.0000.0000.000
194A220GLY00.0230.02253.5200.0700.0700.0000.0000.0000.000
195A221ILE00.0140.02347.5350.0480.0480.0000.0000.0000.000
196A222THR0-0.012-0.02551.6390.0670.0670.0000.0000.0000.000
197A223ARG10.8240.91054.1355.3775.3770.0000.0000.0000.000
198A224THR0-0.034-0.01753.6450.1180.1180.0000.0000.0000.000
199A225PRO0-0.010-0.00553.545-0.116-0.1160.0000.0000.0000.000
200A226VAL0-0.0080.00649.1700.0190.0190.0000.0000.0000.000
201A227PRO0-0.016-0.00952.2940.0590.0590.0000.0000.0000.000
202A228GLY00.0190.02052.215-0.105-0.1050.0000.0000.0000.000
203A229PRO00.0020.00049.940-0.026-0.0260.0000.0000.0000.000
204A230ALA0-0.029-0.01451.3090.1440.1440.0000.0000.0000.000