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: RLNM8

Calculation Name: 1GV1-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1GV1

Chain ID: A

ChEMBL ID:

UniProt ID: P0C890

Base Structure: X-ray

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 305
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -4194048.924572
FMO2-HF: Nuclear repulsion 4077742.404309
FMO2-HF: Total energy -116306.520263
FMO2-MP2: Total energy -116640.144158


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:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-183.444-175.45423.456-12.827-18.616-0.133
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.763 / q_NPA : 0.869
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].
3A3ILE0-0.016-0.0122.9040.4032.8660.353-0.607-2.209-0.001
24A24LEU0-0.032-0.0104.649-2.280-2.108-0.001-0.019-0.1510.000
25A25ALA0-0.001-0.0062.460-12.445-10.6391.804-1.317-2.293-0.013
26A26ARG10.9310.9683.03262.66864.0400.082-0.218-1.236-0.002
27A27GLU-1-0.880-0.9324.857-32.320-32.074-0.001-0.030-0.2150.000
71A71ASP-1-0.839-0.9011.910-117.865-117.40117.170-9.640-7.994-0.113
72A72ILE0-0.031-0.0223.6605.1876.0860.231-0.167-0.9620.000
73A73VAL00.0180.0046.081-1.081-1.078-0.001-0.0030.0020.000
236A236VAL00.0110.0085.745-1.128-1.055-0.001-0.004-0.0680.000
239A239ILE0-0.0170.0113.997-0.0330.081-0.001-0.015-0.0980.000
240A240VAL0-0.024-0.0322.387-3.377-3.1613.822-0.878-3.160-0.003
241A241LEU0-0.048-0.0283.489-2.180-2.018-0.0010.071-0.232-0.001
4A4THR00.0490.0195.5603.0773.0770.0000.0000.0000.000
5A5VAL0-0.055-0.0259.3960.7200.7200.0000.0000.0000.000
6A6ILE00.0300.02011.7790.7610.7610.0000.0000.0000.000
7A7GLY00.0290.02215.4300.5760.5760.0000.0000.0000.000
8A8ALA00.0110.00117.219-0.545-0.5450.0000.0000.0000.000
9A9GLY00.0160.00919.1440.6560.6560.0000.0000.0000.000
10A10ASN0-0.017-0.01919.211-0.755-0.7550.0000.0000.0000.000
11A11VAL00.0290.02417.118-0.353-0.3530.0000.0000.0000.000
12A12GLY00.0810.06014.977-0.709-0.7090.0000.0000.0000.000
13A13ALA00.0160.00314.237-1.086-1.0860.0000.0000.0000.000
14A14THR0-0.010-0.02215.150-0.330-0.3300.0000.0000.0000.000
15A15THR0-0.044-0.04310.831-0.388-0.3880.0000.0000.0000.000
16A16ALA0-0.004-0.00110.269-1.445-1.4450.0000.0000.0000.000
17A17PHE00.0740.02510.407-1.475-1.4750.0000.0000.0000.000
18A18ARG10.9430.97412.05616.78216.7820.0000.0000.0000.000
19A19ILE0-0.004-0.0055.584-0.476-0.4760.0000.0000.0000.000
20A20ALA0-0.0060.0057.618-2.334-2.3340.0000.0000.0000.000
21A21ASP-1-0.900-0.9419.208-18.524-18.5240.0000.0000.0000.000
22A22LYS10.8590.9069.35720.66920.6690.0000.0000.0000.000
23A23LYS10.8370.9278.12720.47820.4780.0000.0000.0000.000
28A28LEU0-0.014-0.0085.524-5.879-5.8790.0000.0000.0000.000
29A29VAL00.0260.0237.9272.6872.6870.0000.0000.0000.000
30A30LEU0-0.036-0.01410.9620.0340.0340.0000.0000.0000.000
31A31LEU00.0120.01613.6900.7440.7440.0000.0000.0000.000
32A32ASP-1-0.825-0.91916.397-13.667-13.6670.0000.0000.0000.000
33A33VAL00.0310.01619.959-0.077-0.0770.0000.0000.0000.000
34A34VAL0-0.078-0.03623.1350.5180.5180.0000.0000.0000.000
35A35GLU-1-0.878-0.94823.803-12.129-12.1290.0000.0000.0000.000
36A36GLY00.0650.03924.027-0.456-0.4560.0000.0000.0000.000
37A37ILE0-0.047-0.02321.887-0.132-0.1320.0000.0000.0000.000
38A38PRO0-0.0020.00018.094-0.274-0.2740.0000.0000.0000.000
39A39GLN00.0240.01518.355-0.801-0.8010.0000.0000.0000.000
40A40GLY00.0180.01319.832-0.286-0.2860.0000.0000.0000.000
41A41LYS10.8790.92618.48213.58213.5820.0000.0000.0000.000
42A42GLY00.0250.01115.704-0.420-0.4200.0000.0000.0000.000
43A43LEU0-0.018-0.00216.336-0.750-0.7500.0000.0000.0000.000
44A44ASP-1-0.899-0.94218.993-13.943-13.9430.0000.0000.0000.000
45A45MET0-0.049-0.02314.504-0.703-0.7030.0000.0000.0000.000
46A46TYR0-0.031-0.01513.576-0.951-0.9510.0000.0000.0000.000
47A47GLU-1-0.923-0.96816.236-13.252-13.2520.0000.0000.0000.000
48A48THR0-0.031-0.01717.2290.6800.6800.0000.0000.0000.000
49A49GLY00.0180.01715.5910.0860.0860.0000.0000.0000.000
50A50PRO0-0.029-0.03416.392-0.024-0.0240.0000.0000.0000.000
51A51VAL0-0.040-0.01319.3490.5270.5270.0000.0000.0000.000
52A52GLY00.0240.01316.5270.3140.3140.0000.0000.0000.000
53A53LEU0-0.058-0.02116.029-0.646-0.6460.0000.0000.0000.000
54A54PHE0-0.057-0.01911.291-1.214-1.2140.0000.0000.0000.000
55A55ASP-1-0.869-0.92811.145-20.464-20.4640.0000.0000.0000.000
56A56THR0-0.089-0.0497.170-0.434-0.4340.0000.0000.0000.000
57A57LYS10.9520.9678.84130.17930.1790.0000.0000.0000.000
58A58ILE0-0.0020.0079.953-2.482-2.4820.0000.0000.0000.000
59A59THR00.0050.00811.9011.8841.8840.0000.0000.0000.000
60A60GLY00.0030.00513.719-0.836-0.8360.0000.0000.0000.000
61A61SER0-0.030-0.05616.4291.0441.0440.0000.0000.0000.000
62A62ASN0-0.023-0.03818.2550.2030.2030.0000.0000.0000.000
63A63ASP-1-0.879-0.92318.513-15.628-15.6280.0000.0000.0000.000
64A64TYR00.040-0.01016.323-1.092-1.0920.0000.0000.0000.000
65A65ALA00.0120.02914.969-1.406-1.4060.0000.0000.0000.000
66A66ASP-1-0.818-0.87513.508-21.069-21.0690.0000.0000.0000.000
67A67THR0-0.125-0.08711.068-2.484-2.4840.0000.0000.0000.000
68A68ALA00.0090.01710.432-1.711-1.7110.0000.0000.0000.000
69A69ASP-1-0.943-0.9767.088-32.354-32.3540.0000.0000.0000.000
70A70SER0-0.032-0.0145.640-7.896-7.8960.0000.0000.0000.000
74A74ILE0-0.014-0.0028.4021.5371.5370.0000.0000.0000.000
75A75ILE00.0340.01611.6450.3890.3890.0000.0000.0000.000
76A76THR0-0.056-0.05315.1150.8360.8360.0000.0000.0000.000
77A77ALA00.0240.02117.8250.8160.8160.0000.0000.0000.000
78A78GLY00.0350.02720.692-0.023-0.0230.0000.0000.0000.000
79A79LEU0-0.020-0.01123.4610.5160.5160.0000.0000.0000.000
80A80PRO0-0.006-0.00824.8590.2180.2180.0000.0000.0000.000
81A81ARG10.9470.94126.9469.0519.0510.0000.0000.0000.000
82A82LYS10.8650.96330.7748.4078.4070.0000.0000.0000.000
83A83PRO00.0540.01232.8740.1730.1730.0000.0000.0000.000
84A84GLY00.0460.03436.0980.0820.0820.0000.0000.0000.000
85A85MET0-0.044-0.01131.9380.0060.0060.0000.0000.0000.000
86A86THR00.0540.02536.906-0.018-0.0180.0000.0000.0000.000
87A87ARG10.9700.98333.8148.2428.2420.0000.0000.0000.000
88A88GLU-1-0.785-0.91733.476-8.940-8.9400.0000.0000.0000.000
89A89ASP-1-0.925-0.96134.278-8.742-8.7420.0000.0000.0000.000
90A90LEU0-0.020-0.01728.089-0.113-0.1130.0000.0000.0000.000
91A91LEU00.0110.01729.273-0.389-0.3890.0000.0000.0000.000
92A92MET00.0250.01629.979-0.256-0.2560.0000.0000.0000.000
93A93LYS10.8970.95629.3519.1099.1090.0000.0000.0000.000
94A94ASN0-0.018-0.01825.357-0.310-0.3100.0000.0000.0000.000
95A95ALA00.0840.04525.155-0.494-0.4940.0000.0000.0000.000
96A96GLY0-0.0170.01326.529-0.141-0.1410.0000.0000.0000.000
97A97ILE00.0320.00422.389-0.323-0.3230.0000.0000.0000.000
98A98VAL0-0.002-0.00320.140-0.569-0.5690.0000.0000.0000.000
99A99LYS10.8880.93921.02010.48310.4830.0000.0000.0000.000
100A100GLU-1-0.935-0.95022.613-12.491-12.4910.0000.0000.0000.000
101A101VAL00.000-0.01017.213-0.502-0.5020.0000.0000.0000.000
102A102THR0-0.035-0.02717.455-1.181-1.1810.0000.0000.0000.000
103A103ASP-1-0.805-0.87618.351-13.587-13.5870.0000.0000.0000.000
104A104ASN0-0.045-0.01419.2000.2290.2290.0000.0000.0000.000
105A105ILE00.0290.01113.094-0.508-0.5080.0000.0000.0000.000
106A106MET0-0.0080.00714.520-1.689-1.6890.0000.0000.0000.000
107A107LYS10.7950.90216.30414.66414.6640.0000.0000.0000.000
108A108HIS00.0180.01613.504-0.151-0.1510.0000.0000.0000.000
109A109SER00.0170.01710.158-3.106-3.1060.0000.0000.0000.000
110A110LYS10.9770.98011.59819.08819.0880.0000.0000.0000.000
111A111ASN0-0.004-0.01411.2311.8001.8000.0000.0000.0000.000
112A112PRO00.0490.0538.442-2.270-2.2700.0000.0000.0000.000
113A113ILE0-0.040-0.0196.1162.2552.2550.0000.0000.0000.000
114A114ILE0-0.008-0.0058.834-1.238-1.2380.0000.0000.0000.000
115A115ILE00.0040.0018.8451.0211.0210.0000.0000.0000.000
116A116VAL0-0.003-0.00612.474-0.018-0.0180.0000.0000.0000.000
117A117VAL0-0.001-0.02015.4050.2500.2500.0000.0000.0000.000
118A118SER0-0.016-0.00318.1000.3870.3870.0000.0000.0000.000
119A119ASN00.0010.00021.011-0.059-0.0590.0000.0000.0000.000
120A120PRO00.016-0.00324.3880.1200.1200.0000.0000.0000.000
121A121LEU00.0730.03418.987-0.012-0.0120.0000.0000.0000.000
122A122ASP-1-0.869-0.91922.351-12.164-12.1640.0000.0000.0000.000
123A123ILE00.009-0.00123.769-0.156-0.1560.0000.0000.0000.000
124A124MET0-0.052-0.01921.912-0.152-0.1520.0000.0000.0000.000
125A125THR0-0.012-0.02317.777-0.698-0.6980.0000.0000.0000.000
126A126HIS00.0510.03819.959-0.661-0.6610.0000.0000.0000.000
127A127VAL0-0.023-0.01822.506-0.100-0.1000.0000.0000.0000.000
128A128ALA00.0160.00017.731-0.119-0.1190.0000.0000.0000.000
129A129TRP0-0.024-0.01017.757-0.107-0.1070.0000.0000.0000.000
130A130VAL00.000-0.00119.255-0.228-0.2280.0000.0000.0000.000
131A131ARG10.7870.86421.31112.59712.5970.0000.0000.0000.000
132A132SER0-0.026-0.02216.363-0.430-0.4300.0000.0000.0000.000
133A133GLY0-0.0020.00418.349-0.336-0.3360.0000.0000.0000.000
134A134LEU0-0.033-0.00612.943-0.106-0.1060.0000.0000.0000.000
135A135PRO00.014-0.00314.8740.7520.7520.0000.0000.0000.000
136A136LYS10.8500.91815.57712.27212.2720.0000.0000.0000.000
137A137GLU-1-0.835-0.91114.280-15.280-15.2800.0000.0000.0000.000
138A138ARG10.8600.9297.44225.73525.7350.0000.0000.0000.000
139A139VAL0-0.0020.00111.839-1.163-1.1630.0000.0000.0000.000
140A140ILE00.0070.01511.3480.9040.9040.0000.0000.0000.000
141A141GLY00.0410.02515.089-0.574-0.5740.0000.0000.0000.000
142A142MET0-0.094-0.03215.5240.4290.4290.0000.0000.0000.000
143A143ALA00.0640.01217.4930.3830.3830.0000.0000.0000.000
144A144GLY00.0630.03121.1890.1880.1880.0000.0000.0000.000
145A145VAL00.0120.00516.8510.3460.3460.0000.0000.0000.000
146A146LEU00.0020.00220.2660.2620.2620.0000.0000.0000.000
147A147ASP-1-0.813-0.91521.993-10.756-10.7560.0000.0000.0000.000
148A148ALA00.0450.01723.1280.4280.4280.0000.0000.0000.000
149A149ALA0-0.036-0.01322.1030.2550.2550.0000.0000.0000.000
150A150ARG10.8810.95324.25111.22111.2210.0000.0000.0000.000
151A151PHE00.0810.05227.4180.2690.2690.0000.0000.0000.000
152A152ARG10.8990.93321.47512.17812.1780.0000.0000.0000.000
153A153SER0-0.059-0.04227.3300.2460.2460.0000.0000.0000.000
154A154PHE0-0.009-0.02529.1140.2430.2430.0000.0000.0000.000
155A155ILE00.0400.02130.6920.2640.2640.0000.0000.0000.000
156A156ALA0-0.006-0.00430.3880.2000.2000.0000.0000.0000.000
157A157MET0-0.107-0.05232.4440.1180.1180.0000.0000.0000.000
158A158GLU-1-0.943-0.96534.886-7.383-7.3830.0000.0000.0000.000
159A159LEU0-0.008-0.01235.1250.1810.1810.0000.0000.0000.000
160A160GLY0-0.0150.01635.8050.1000.1000.0000.0000.0000.000
161A161VAL0-0.039-0.01932.221-0.021-0.0210.0000.0000.0000.000
162A162SER0-0.008-0.00728.076-0.301-0.3010.0000.0000.0000.000
163A163MET00.0500.00925.903-0.076-0.0760.0000.0000.0000.000
164A164GLN0-0.080-0.02422.946-0.654-0.6540.0000.0000.0000.000
165A165ASP-1-0.870-0.93325.041-10.335-10.3350.0000.0000.0000.000
166A166ILE0-0.0180.00627.2510.2900.2900.0000.0000.0000.000
167A167ASN0-0.046-0.01224.776-0.870-0.8700.0000.0000.0000.000
168A168ALA00.016-0.00325.7080.3950.3950.0000.0000.0000.000
169A169CYS0-0.065-0.00925.481-0.448-0.4480.0000.0000.0000.000
170A170VAL00.003-0.01125.4100.3480.3480.0000.0000.0000.000
171A171LEU0-0.013-0.00224.858-0.501-0.5010.0000.0000.0000.000
172A172GLY00.0230.02126.1470.2870.2870.0000.0000.0000.000
173A173GLY00.0430.02025.340-0.478-0.4780.0000.0000.0000.000
174A174HIS0-0.106-0.06723.899-0.174-0.1740.0000.0000.0000.000
175A175GLY00.0260.00728.5510.1760.1760.0000.0000.0000.000
176A176ASP-1-0.914-0.97132.319-8.229-8.2290.0000.0000.0000.000
177A177ALA0-0.022-0.00830.3910.1270.1270.0000.0000.0000.000
178A178MET0-0.0660.00928.235-0.173-0.1730.0000.0000.0000.000
179A179VAL00.0280.00529.5920.3480.3480.0000.0000.0000.000
180A180PRO0-0.007-0.00729.765-0.298-0.2980.0000.0000.0000.000
181A181VAL00.0450.03329.9350.2630.2630.0000.0000.0000.000
182A182VAL00.031-0.00631.488-0.144-0.1440.0000.0000.0000.000
183A183LYS10.8270.91033.8818.1608.1600.0000.0000.0000.000
184A184TYR0-0.014-0.01429.3100.0540.0540.0000.0000.0000.000
185A185THR0-0.033-0.01129.362-0.478-0.4780.0000.0000.0000.000
186A186THR0-0.031-0.01629.8810.2140.2140.0000.0000.0000.000
187A187VAL00.0580.02030.316-0.308-0.3080.0000.0000.0000.000
188A188ALA0-0.003-0.00430.4800.2230.2230.0000.0000.0000.000
189A189GLY0-0.039-0.01530.8110.1150.1150.0000.0000.0000.000
190A190ILE00.0000.00531.8350.1440.1440.0000.0000.0000.000
191A191PRO00.0160.00334.365-0.206-0.2060.0000.0000.0000.000
192A192ILE00.0290.00233.6100.1580.1580.0000.0000.0000.000
193A193SER0-0.025-0.02236.3730.0850.0850.0000.0000.0000.000
194A194ASP-1-0.907-0.94039.095-7.250-7.2500.0000.0000.0000.000
195A195LEU0-0.080-0.03436.5350.0820.0820.0000.0000.0000.000
196A196LEU0-0.017-0.00936.9360.1070.1070.0000.0000.0000.000
197A197PRO00.0230.01640.9850.0340.0340.0000.0000.0000.000
198A198ALA00.0620.03341.956-0.171-0.1710.0000.0000.0000.000
199A199GLU-1-0.858-0.94141.982-6.682-6.6820.0000.0000.0000.000
200A200THR0-0.090-0.05239.8990.0030.0030.0000.0000.0000.000
201A201ILE00.0060.00436.544-0.218-0.2180.0000.0000.0000.000
202A202ASP-1-0.852-0.92437.480-7.447-7.4470.0000.0000.0000.000
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204A204LEU0-0.0110.00134.666-0.186-0.1860.0000.0000.0000.000
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