FMODB

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

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

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FMODB ID: RMJL8

Calculation Name: 7LXT-a-Other547

Preferred Name:

Target Type:

Ligand Name: n-[(1r)-1-(dihydroxyboryl)-3-methylbutyl]-n-(pyrazin-2-ylcarbonyl)-l-phenylalaninamide

Ligand 3-letter code: BO2

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 7LXT

Chain ID: a

ChEMBL ID:

UniProt ID:

Base Structure: ElectronMicroscopy

Registration Date: 2025-10-05

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Homology Modeling
Water No
Procedure Manual calculation
Remarks
ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 213
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2541066.880452
FMO2-HF: Nuclear repulsion 2456757.605246
FMO2-HF: Total energy -84309.275206
FMO2-MP2: Total energy -84555.451895


3D Structure Molmil
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:28:LYS)


Summations of interaction energy for fragment #1(A:28: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.
17.71222.628-0.02-2.259-2.635-0.01
Interaction energy analysis for fragmet #1(A:28:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 2 / q_Mulliken : 1.870 / q_NPA : 1.918
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].
3A30TRP00.0230.0373.3203.5288.298-0.019-2.249-2.501-0.010
4A31TYR00.0600.0365.1565.0775.223-0.001-0.010-0.1340.000
5A32PRO0-0.027-0.0077.4330.3510.3510.0000.0000.0000.000
6A33TYR0-0.025-0.03210.4983.0283.0280.0000.0000.0000.000
7A34ILE0-0.025-0.02710.949-2.847-2.8470.0000.0000.0000.000
8A35ASP-1-0.799-0.88413.236-27.454-27.4540.0000.0000.0000.000
9A36ASN0-0.063-0.04216.617-0.666-0.6660.0000.0000.0000.000
10A37GLY00.0500.03118.7470.7980.7980.0000.0000.0000.000
11A38GLY00.0630.04121.5140.3050.3050.0000.0000.0000.000
12A39THR0-0.057-0.01825.296-0.460-0.4600.0000.0000.0000.000
13A40VAL00.016-0.00128.1110.3730.3730.0000.0000.0000.000
14A41ILE00.004-0.00830.757-0.101-0.1010.0000.0000.0000.000
15A42GLY00.0060.00434.0490.2130.2130.0000.0000.0000.000
16A43LEU00.000-0.00236.574-0.032-0.0320.0000.0000.0000.000
17A44THR0-0.032-0.02240.2630.1070.1070.0000.0000.0000.000
18A45GLY00.0890.04643.2320.1390.1390.0000.0000.0000.000
19A46LYS10.8620.90947.03411.73611.7360.0000.0000.0000.000
20A47ASP-1-0.841-0.91149.584-11.663-11.6630.0000.0000.0000.000
21A48TYR00.026-0.00645.3040.1490.1490.0000.0000.0000.000
22A49VAL0-0.0250.00240.965-0.100-0.1000.0000.0000.0000.000
23A50ILE0-0.021-0.00739.6720.0920.0920.0000.0000.0000.000
24A51LEU0-0.010-0.01433.934-0.261-0.2610.0000.0000.0000.000
25A52ALA00.0250.01935.6380.0830.0830.0000.0000.0000.000
26A53ALA00.0100.02130.375-0.409-0.4090.0000.0000.0000.000
27A54ASP-1-0.759-0.85327.581-20.811-20.8110.0000.0000.0000.000
28A55THR0-0.073-0.04928.760-0.121-0.1210.0000.0000.0000.000
29A56ARG10.8600.96124.05621.62521.6250.0000.0000.0000.000
30A57LEU0-0.028-0.01520.417-0.535-0.5350.0000.0000.0000.000
31A58SER00.0440.02919.7720.5130.5130.0000.0000.0000.000
32A59LEU0-0.040-0.00312.379-1.109-1.1090.0000.0000.0000.000
33A60SER00.010-0.01013.0971.5621.5620.0000.0000.0000.000
34A61TYR00.0830.03915.2141.3791.3790.0000.0000.0000.000
35A62SER0-0.0110.02017.4561.6721.6720.0000.0000.0000.000
36A63ILE00.0320.00419.169-0.735-0.7350.0000.0000.0000.000
37A64TYR0-0.028-0.02015.157-0.489-0.4890.0000.0000.0000.000
38A65THR0-0.016-0.01821.7980.8550.8550.0000.0000.0000.000
39A66ARG10.8850.93825.46120.12320.1230.0000.0000.0000.000
40A67PHE00.0100.00628.2110.6260.6260.0000.0000.0000.000
41A68CYS0-0.019-0.01525.915-0.582-0.5820.0000.0000.0000.000
42A69PRO0-0.0250.00627.843-0.021-0.0210.0000.0000.0000.000
43A70LYS10.8740.94423.93422.93722.9370.0000.0000.0000.000
44A71ILE0-0.024-0.01128.733-0.149-0.1490.0000.0000.0000.000
45A72SER0-0.024-0.01730.7330.1490.1490.0000.0000.0000.000
46A73LYS10.9140.95933.52615.08415.0840.0000.0000.0000.000
47A74LEU0-0.066-0.03533.758-0.269-0.2690.0000.0000.0000.000
48A75THR00.0120.00537.7620.0930.0930.0000.0000.0000.000
49A76ASP-1-0.907-0.96541.599-13.642-13.6420.0000.0000.0000.000
50A77LYS10.9600.99044.07912.75412.7540.0000.0000.0000.000
51A78CYS0-0.043-0.01238.998-0.183-0.1830.0000.0000.0000.000
52A79ILE00.0060.00636.405-0.141-0.1410.0000.0000.0000.000
53A80ILE00.0050.00230.1440.0170.0170.0000.0000.0000.000
54A81GLY00.0400.01930.9410.0060.0060.0000.0000.0000.000
55A82SER0-0.055-0.05326.0600.2470.2470.0000.0000.0000.000
56A83SER0-0.039-0.02524.331-0.405-0.4050.0000.0000.0000.000
57A84GLY00.0670.01320.713-0.006-0.0060.0000.0000.0000.000
58A85MET0-0.0180.02914.964-1.061-1.0610.0000.0000.0000.000
59A86GLN00.026-0.00618.5141.7851.7850.0000.0000.0000.000
60A87SER0-0.021-0.02317.9570.7420.7420.0000.0000.0000.000
61A88ASP-1-0.824-0.90918.656-29.952-29.9520.0000.0000.0000.000
62A89ILE00.0240.01421.1581.1681.1680.0000.0000.0000.000
63A90LYS10.9760.99223.61423.29723.2970.0000.0000.0000.000
64A91THR0-0.050-0.02722.1970.8320.8320.0000.0000.0000.000
65A92LEU0-0.0180.00325.0230.6340.6340.0000.0000.0000.000
66A93HIS00.0130.01426.6501.0611.0610.0000.0000.0000.000
67A94SER00.010-0.00128.5050.4770.4770.0000.0000.0000.000
68A95LEU0-0.031-0.00327.4270.6540.6540.0000.0000.0000.000
69A96LEU00.0340.00730.1430.5880.5880.0000.0000.0000.000
70A97GLN00.0170.00032.4610.2030.2030.0000.0000.0000.000
71A98LYS10.8740.92931.97519.08119.0810.0000.0000.0000.000
72A99LYS00.0170.02532.6150.4020.4020.0000.0000.0000.000
73A100ILE00.0250.01836.2360.4760.4760.0000.0000.0000.000
74A101GLN00.0120.00037.7940.7510.7510.0000.0000.0000.000
75A102LEU00.0000.01038.4980.3040.3040.0000.0000.0000.000
76A103PHE0-0.011-0.01140.3740.3220.3220.0000.0000.0000.000
77A104VAL00.016-0.00442.3270.3560.3560.0000.0000.0000.000
78A105LEU0-0.040-0.01542.4610.3560.3560.0000.0000.0000.000
79A106GLU-1-0.927-0.96443.719-13.705-13.7050.0000.0000.0000.000
80A107HIS10.8510.93045.09813.89113.8910.0000.0000.0000.000
81A108SER0-0.0390.00248.2990.3970.3970.0000.0000.0000.000
82A109HIS0-0.023-0.01547.4980.1120.1120.0000.0000.0000.000
83A110TYR00.0560.00343.160-0.398-0.3980.0000.0000.0000.000
84A111PRO0-0.061-0.00640.9800.2120.2120.0000.0000.0000.000
85A112ASP-1-0.743-0.89143.229-13.739-13.7390.0000.0000.0000.000
86A113ILE00.0330.01439.112-0.395-0.3950.0000.0000.0000.000
87A114HIS10.8250.89440.10113.49913.4990.0000.0000.0000.000
88A115VAL0-0.031-0.00440.691-0.249-0.2490.0000.0000.0000.000
89A116ILE00.007-0.00436.223-0.482-0.4820.0000.0000.0000.000
90A117ALA00.0440.02236.048-0.582-0.5820.0000.0000.0000.000
91A118ARG10.9100.96635.39415.33715.3370.0000.0000.0000.000
92A119LEU00.0120.00434.751-0.450-0.4500.0000.0000.0000.000
93A120LEU00.0170.01029.296-0.605-0.6050.0000.0000.0000.000
94A121CYS0-0.083-0.03130.722-0.651-0.6510.0000.0000.0000.000
95A122VAL00.022-0.00230.979-0.626-0.6260.0000.0000.0000.000
96A123ILE0-0.013-0.00528.090-0.625-0.6250.0000.0000.0000.000
97A124LEU0-0.035-0.01625.437-0.895-0.8950.0000.0000.0000.000
98A125TYR00.0200.00226.121-1.069-1.0690.0000.0000.0000.000
99A126SER0-0.025-0.01227.659-0.200-0.2000.0000.0000.0000.000
100A127ARG10.8700.93818.40429.15329.1530.0000.0000.0000.000
101A128ARG10.9370.96922.18423.53523.5350.0000.0000.0000.000
102A129PHE0-0.020-0.01921.517-0.456-0.4560.0000.0000.0000.000
103A130PHE0-0.0170.00313.999-1.751-1.7510.0000.0000.0000.000
104A131PRO00.0440.05118.5650.1590.1590.0000.0000.0000.000
105A132TYR00.0270.01718.906-1.625-1.6250.0000.0000.0000.000
106A133TYR0-0.072-0.05416.4780.7680.7680.0000.0000.0000.000
107A134ALA00.000-0.01519.239-0.009-0.0090.0000.0000.0000.000
108A135PHE0-0.0040.01421.0650.7740.7740.0000.0000.0000.000
109A136ASN00.0120.01525.307-0.166-0.1660.0000.0000.0000.000
110A137ILE00.0390.02628.6490.1980.1980.0000.0000.0000.000
111A138LEU0-0.042-0.01132.293-0.145-0.1450.0000.0000.0000.000
112A139ALA00.0470.01535.0160.2430.2430.0000.0000.0000.000
113A140GLY00.0410.00038.375-0.123-0.1230.0000.0000.0000.000
114A141VAL0-0.0240.00341.8920.0850.0850.0000.0000.0000.000
115A142ASP-1-0.802-0.86545.372-13.236-13.2360.0000.0000.0000.000
116A143GLU-1-0.969-0.99146.983-11.579-11.5790.0000.0000.0000.000
117A144ASN0-0.070-0.04750.514-0.093-0.0930.0000.0000.0000.000
118A145ASN0-0.005-0.02349.525-0.125-0.1250.0000.0000.0000.000
119A146LYS10.8940.95348.27411.76211.7620.0000.0000.0000.000
120A147GLY00.0840.06245.113-0.181-0.1810.0000.0000.0000.000
121A148VAL0-0.0090.02042.325-0.066-0.0660.0000.0000.0000.000
122A149LEU00.006-0.00536.142-0.294-0.2940.0000.0000.0000.000
123A150TYR0-0.025-0.03735.6450.0100.0100.0000.0000.0000.000
124A151ASN00.0320.01531.589-0.048-0.0480.0000.0000.0000.000
125A152TYR0-0.012-0.02228.8520.1680.1680.0000.0000.0000.000
126A153ASP00.004-0.01625.785-0.426-0.4260.0000.0000.0000.000
127A154SER0-0.0080.01521.976-0.978-0.9780.0000.0000.0000.000
128A155VAL0-0.016-0.03023.205-0.206-0.2060.0000.0000.0000.000
129A156GLY00.0080.01125.8910.5200.5200.0000.0000.0000.000
130A157SER0-0.0100.01229.3950.4810.4810.0000.0000.0000.000
131A158TYR00.0160.00731.165-0.332-0.3320.0000.0000.0000.000
132A159CYS0-0.024-0.00833.9200.2290.2290.0000.0000.0000.000
133A160GLU-1-0.854-0.90936.620-14.516-14.5160.0000.0000.0000.000
134A161ALA0-0.015-0.00437.5720.1170.1170.0000.0000.0000.000
135A162THR0-0.004-0.00139.5430.0090.0090.0000.0000.0000.000
136A163HIS00.007-0.02537.8940.2850.2850.0000.0000.0000.000
137A164SER0-0.020-0.00833.657-0.376-0.3760.0000.0000.0000.000
138A165CYS0-0.0090.01631.6040.0800.0800.0000.0000.0000.000
139A166VAL0-0.0090.01727.120-0.345-0.3450.0000.0000.0000.000
140A167GLY00.0510.01424.2510.1670.1670.0000.0000.0000.000
141A168SER0-0.051-0.05322.8390.2000.2000.0000.0000.0000.000
142A169GLY00.0640.02224.4730.2460.2460.0000.0000.0000.000
143A170SER0-0.102-0.06427.3200.6810.6810.0000.0000.0000.000
144A171GLN00.015-0.01825.9250.8960.8960.0000.0000.0000.000
145A172LEU00.0020.01028.0930.4420.4420.0000.0000.0000.000
146A173ILE00.0050.00031.7410.6040.6040.0000.0000.0000.000
147A174LEU00.0050.00731.6250.5180.5180.0000.0000.0000.000
148A175PRO00.0250.00633.5260.5040.5040.0000.0000.0000.000
149A176ILE0-0.0070.00736.4330.4690.4690.0000.0000.0000.000
150A177LEU0-0.025-0.01636.8120.4410.4410.0000.0000.0000.000
151A178ASP-1-0.862-0.92938.108-15.261-15.2610.0000.0000.0000.000
152A179ASN0-0.059-0.02640.5880.5620.5620.0000.0000.0000.000
153A180ARG10.7580.87540.87614.62214.6220.0000.0000.0000.000
154A181VAL00.0550.02942.0390.0850.0850.0000.0000.0000.000
155A182GLU-1-0.884-0.93142.924-13.080-13.0800.0000.0000.0000.000
156A183GLN0-0.0080.00945.022-0.256-0.2560.0000.0000.0000.000
157A184LYS10.8900.93844.26113.83313.8330.0000.0000.0000.000
158A185ASN0-0.066-0.03846.8240.0740.0740.0000.0000.0000.000
159A186GLN00.000-0.00649.7830.0820.0820.0000.0000.0000.000
160A187LEU00.0060.00253.2160.2290.2290.0000.0000.0000.000
161A188ILE00.0260.02451.617-0.152-0.1520.0000.0000.0000.000
162A189LYS10.9490.97350.11712.23012.2300.0000.0000.0000.000
163A190ASN00.013-0.01750.033-0.192-0.1920.0000.0000.0000.000
164A191THR00.0350.02250.996-0.178-0.1780.0000.0000.0000.000
165A192ASN0-0.095-0.03952.592-0.123-0.1230.0000.0000.0000.000
166A193PHE00.0420.03947.3040.0140.0140.0000.0000.0000.000
167A194ASN0-0.013-0.01849.8590.1790.1790.0000.0000.0000.000
168A195LEU00.0530.03245.947-0.161-0.1610.0000.0000.0000.000
169A196GLY00.0000.00147.457-0.220-0.2200.0000.0000.0000.000
170A197ASP-1-0.929-0.96348.351-12.632-12.6320.0000.0000.0000.000
171A198ASP-1-0.779-0.87944.687-13.411-13.4110.0000.0000.0000.000
172A199ILE0-0.009-0.01343.120-0.442-0.4420.0000.0000.0000.000
173A200ASN0-0.006-0.01142.607-0.501-0.5010.0000.0000.0000.000
174A201PHE00.0240.01042.781-0.311-0.3110.0000.0000.0000.000
175A202VAL00.0120.00837.758-0.388-0.3880.0000.0000.0000.000
176A203LYS10.9370.97438.19113.47813.4780.0000.0000.0000.000
177A204ASP-1-0.844-0.88938.764-15.023-15.0230.0000.0000.0000.000
178A205ALA0-0.0080.01036.408-0.335-0.3350.0000.0000.0000.000
179A206ILE00.000-0.00831.825-0.461-0.4610.0000.0000.0000.000
180A207THR00.003-0.00333.746-0.516-0.5160.0000.0000.0000.000
181A208SER0-0.015-0.01434.970-0.402-0.4020.0000.0000.0000.000
182A209ALA0-0.021-0.01630.613-0.341-0.3410.0000.0000.0000.000
183A210THR0-0.024-0.04430.529-0.571-0.5710.0000.0000.0000.000
184A211GLU-1-0.985-0.98730.822-16.739-16.7390.0000.0000.0000.000
185A212ARG10.8720.94730.70817.53117.5310.0000.0000.0000.000
186A213ASP-1-0.768-0.84824.933-23.419-23.4190.0000.0000.0000.000
187A214ILE00.0020.01421.8740.2320.2320.0000.0000.0000.000
188A215TYR0-0.103-0.07517.663-0.204-0.2040.0000.0000.0000.000
189A216THR0-0.032-0.02123.8150.1590.1590.0000.0000.0000.000
190A217GLY0-0.044-0.05127.418-0.077-0.0770.0000.0000.0000.000
191A218ASP-1-0.804-0.89628.628-19.655-19.6550.0000.0000.0000.000
192A219LYS10.9450.98231.29117.69817.6980.0000.0000.0000.000
193A220THR0-0.043-0.03031.958-0.499-0.4990.0000.0000.0000.000
194A221LEU0-0.014-0.00833.2740.4620.4620.0000.0000.0000.000
195A222ILE00.005-0.00635.627-0.264-0.2640.0000.0000.0000.000
196A223TYR00.0160.00135.6300.4310.4310.0000.0000.0000.000
197A224VAL0-0.003-0.00339.363-0.038-0.0380.0000.0000.0000.000
198A225ILE0-0.046-0.01640.4220.0370.0370.0000.0000.0000.000
199A226ASP-1-0.776-0.89444.332-12.133-12.1330.0000.0000.0000.000
200A227LYS10.8250.89048.12211.53911.5390.0000.0000.0000.000
201A228MET0-0.072-0.02150.5100.0220.0220.0000.0000.0000.000
202A229GLY0-0.0080.00047.0860.0040.0040.0000.0000.0000.000
203A230ILE0-0.040-0.02240.317-0.146-0.1460.0000.0000.0000.000
204A231ASN00.0070.01043.8820.1310.1310.0000.0000.0000.000
205A232VAL00.006-0.00938.449-0.256-0.2560.0000.0000.0000.000
206A233ASN0-0.052-0.01440.9310.2180.2180.0000.0000.0000.000
207A234THR00.005-0.01237.153-0.422-0.4220.0000.0000.0000.000
208A235LEU0-0.011-0.00737.8560.4660.4660.0000.0000.0000.000
209A236ASP-1-0.892-0.94436.347-16.326-16.3260.0000.0000.0000.000
210A237LEU0-0.035-0.01832.8600.3440.3440.0000.0000.0000.000
211A238LYS10.8630.92031.71318.31118.3110.0000.0000.0000.000
212A239GLN0-0.039-0.03831.274-0.735-0.7350.0000.0000.0000.000
213A240ASP-2-1.672-1.79527.729-39.742-39.7420.0000.0000.0000.000