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: 2G2MR

Calculation Name: 6SPD-D-Other547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 6SPD

Chain ID: D

ChEMBL ID:

UniProt ID: A0A2V3

Base Structure: ElectronMicroscopy

Registration Date: 2025-10-06

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 207
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1867246.442126
FMO2-HF: Nuclear repulsion 1789808.172651
FMO2-HF: Total energy -77438.269475
FMO2-MP2: Total energy -77664.556663


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:3:ILE)


Summations of interaction energy for fragment #1(A:3:ILE)
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.
-6.8420.311.344-5.202-13.283-0.038
Interaction energy analysis for fragmet #1(A:3:ILE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.859 / q_NPA : 0.933
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].
3A5VAL00.0320.0282.660-5.035-1.3220.701-2.133-2.281-0.018
33A35VAL00.0160.0154.309-0.916-0.819-0.001-0.008-0.0870.000
47A49VAL00.0450.0442.2691.3190.9691.972-0.347-1.275-0.002
49A51VAL00.0180.0042.787-1.182-0.6950.140-0.121-0.506-0.001
81A83PHE0-0.074-0.0442.412-3.559-2.7453.412-0.945-3.281-0.004
82A84ARG10.9820.9904.35226.54626.728-0.001-0.018-0.1630.000
83A85LEU0-0.053-0.0252.983-12.254-10.9080.161-0.341-1.166-0.003
84A86GLY00.0040.0074.9245.8605.873-0.001-0.004-0.0080.000
86A88GLU-1-0.857-0.9404.174-46.499-46.266-0.001-0.021-0.2120.000
88A90TYR00.0220.0192.129-4.734-4.8622.833-0.789-1.915-0.006
94A96ILE00.0080.0102.332-0.882-1.0311.743-0.253-1.341-0.002
98A100LEU0-0.0240.0012.732-1.745-1.1940.386-0.150-0.787-0.002
203A205PRO00.0710.0343.8035.3155.6480.000-0.072-0.2610.000
4A6VAL0-0.038-0.0155.5161.8921.8920.0000.0000.0000.000
5A7GLY00.0480.0228.4120.6920.6920.0000.0000.0000.000
6A8ARG10.8720.93211.67215.31415.3140.0000.0000.0000.000
7A9LYS10.9250.98315.38214.81214.8120.0000.0000.0000.000
8A10CYS0-0.0160.00217.9760.9610.9610.0000.0000.0000.000
9A11GLY0-0.010-0.01720.7570.7910.7910.0000.0000.0000.000
10A12MET0-0.087-0.03221.939-0.522-0.5220.0000.0000.0000.000
11A13THR00.0050.00423.6820.4320.4320.0000.0000.0000.000
12A14ARG10.9500.97525.5639.6429.6420.0000.0000.0000.000
13A15ILE00.0010.01423.1980.2840.2840.0000.0000.0000.000
14A16PHE0-0.007-0.01627.2050.0750.0750.0000.0000.0000.000
15A17THR00.0100.01628.243-0.427-0.4270.0000.0000.0000.000
16A18GLU-1-0.965-0.99629.495-9.418-9.4180.0000.0000.0000.000
17A19GLU-1-0.864-0.92632.325-9.232-9.2320.0000.0000.0000.000
18A20GLY00.0510.03333.0930.3090.3090.0000.0000.0000.000
19A21VAL0-0.059-0.02029.543-0.060-0.0600.0000.0000.0000.000
20A22SER0-0.062-0.04129.856-0.138-0.1380.0000.0000.0000.000
21A23ILE00.0100.00323.185-0.167-0.1670.0000.0000.0000.000
22A24PRO0-0.048-0.01925.1610.0450.0450.0000.0000.0000.000
23A25VAL00.0500.01019.978-0.549-0.5490.0000.0000.0000.000
24A26THR0-0.052-0.04118.5400.8110.8110.0000.0000.0000.000
25A27VAL0-0.0020.00218.414-0.686-0.6860.0000.0000.0000.000
26A28ILE0-0.047-0.02912.9760.3680.3680.0000.0000.0000.000
27A29GLU-1-0.814-0.90015.315-15.585-15.5850.0000.0000.0000.000
28A30VAL00.002-0.0149.752-0.954-0.9540.0000.0000.0000.000
29A31GLU-1-0.756-0.85512.870-17.151-17.1510.0000.0000.0000.000
30A32PRO00.0260.00610.670-1.824-1.8240.0000.0000.0000.000
31A33ASN0-0.021-0.0016.436-1.610-1.6100.0000.0000.0000.000
32A34ARG10.8700.9327.63417.91417.9140.0000.0000.0000.000
34A36THR0-0.059-0.0306.7941.9011.9010.0000.0000.0000.000
35A37GLN00.024-0.0068.3521.4361.4360.0000.0000.0000.000
36A38PHE00.0210.0186.383-2.343-2.3430.0000.0000.0000.000
37A39LYS10.8180.9128.65723.54423.5440.0000.0000.0000.000
38A40THR00.018-0.02810.348-2.235-2.2350.0000.0000.0000.000
39A41GLU-1-0.986-1.00012.921-17.518-17.5180.0000.0000.0000.000
40A42GLU-1-0.862-0.91214.983-15.160-15.1600.0000.0000.0000.000
41A43THR0-0.039-0.02816.3590.7410.7410.0000.0000.0000.000
42A44ASP-1-0.879-0.92113.962-18.124-18.1240.0000.0000.0000.000
43A45GLY0-0.0120.01115.977-0.200-0.2000.0000.0000.0000.000
44A46TYR0-0.197-0.12610.190-0.452-0.4520.0000.0000.0000.000
45A47ARG11.0071.0188.42626.26226.2620.0000.0000.0000.000
46A48ALA0-0.052-0.0476.351-2.954-2.9540.0000.0000.0000.000
48A50GLN00.0090.0015.580-0.164-0.1640.0000.0000.0000.000
50A52THR0-0.021-0.0176.0301.6151.6150.0000.0000.0000.000
51A53ALA00.0070.0219.501-0.669-0.6690.0000.0000.0000.000
52A54GLY00.017-0.01812.0850.7450.7450.0000.0000.0000.000
53A55GLU-1-0.936-0.96315.478-13.732-13.7320.0000.0000.0000.000
54A56ARG10.9190.97018.93313.53713.5370.0000.0000.0000.000
55A57ARG10.9920.99220.59310.45910.4590.0000.0000.0000.000
56A58ALA00.1150.05623.770-0.088-0.0880.0000.0000.0000.000
57A59SER0-0.065-0.04924.6100.4260.4260.0000.0000.0000.000
58A60ARG10.8840.93923.96310.25710.2570.0000.0000.0000.000
59A61VAL00.0390.04719.805-0.223-0.2230.0000.0000.0000.000
60A62THR00.0470.01322.4790.3310.3310.0000.0000.0000.000
61A63LYS11.0090.98322.9449.1049.1040.0000.0000.0000.000
62A64ALA00.0280.02722.492-0.068-0.0680.0000.0000.0000.000
63A65GLN00.0030.00216.829-0.647-0.6470.0000.0000.0000.000
64A66ALA0-0.011-0.00818.678-0.429-0.4290.0000.0000.0000.000
65A67GLY00.0190.01220.354-0.095-0.0950.0000.0000.0000.000
66A68HIS0-0.022-0.00412.9390.6690.6690.0000.0000.0000.000
67A69PHE0-0.030-0.03813.062-0.407-0.4070.0000.0000.0000.000
68A70ALA00.0230.02216.5520.1240.1240.0000.0000.0000.000
69A71LYS10.8620.94316.09613.31513.3150.0000.0000.0000.000
70A72ALA00.1110.06313.1930.0280.0280.0000.0000.0000.000
71A73ASN0-0.039-0.01315.2780.3230.3230.0000.0000.0000.000
72A74VAL00.000-0.01011.7670.0980.0980.0000.0000.0000.000
73A75ALA0-0.006-0.00814.232-0.126-0.1260.0000.0000.0000.000
74A76ALA00.0010.01514.201-0.160-0.1600.0000.0000.0000.000
75A77GLY0-0.027-0.02814.8601.0401.0400.0000.0000.0000.000
76A78ARG10.7620.88215.10117.33717.3370.0000.0000.0000.000
77A79GLY00.0300.01413.899-0.703-0.7030.0000.0000.0000.000
78A80VAL00.0050.00110.155-0.223-0.2230.0000.0000.0000.000
79A81TRP0-0.022-0.0048.0850.7260.7260.0000.0000.0000.000
80A82GLU-1-0.760-0.8616.903-24.726-24.7260.0000.0000.0000.000
85A87GLU-1-0.957-0.9936.793-24.154-24.1540.0000.0000.0000.000
87A89GLN0-0.104-0.0427.2104.8984.8980.0000.0000.0000.000
89A91ALA00.0060.0077.0651.0771.0770.0000.0000.0000.000
90A92ALA0-0.039-0.03110.3820.8040.8040.0000.0000.0000.000
91A93GLY00.000-0.00810.3270.1970.1970.0000.0000.0000.000
92A94ASP-1-0.858-0.9137.417-23.113-23.1130.0000.0000.0000.000
93A95GLN0-0.033-0.0457.636-0.967-0.9670.0000.0000.0000.000
95A97THR0-0.023-0.0396.1550.9170.9170.0000.0000.0000.000
96A98VAL0-0.009-0.0207.289-3.057-3.0570.0000.0000.0000.000
97A99ASP-1-0.843-0.9089.118-23.329-23.3290.0000.0000.0000.000
99A101PHE0-0.070-0.0326.190-1.777-1.7770.0000.0000.0000.000
100A102GLN00.0180.0019.2742.2232.2230.0000.0000.0000.000
101A103ALA00.0240.01012.964-0.407-0.4070.0000.0000.0000.000
102A104GLY00.0150.00915.635-0.209-0.2090.0000.0000.0000.000
103A105GLN0-0.044-0.0239.441-1.147-1.1470.0000.0000.0000.000
104A106MET00.0630.04012.066-0.274-0.2740.0000.0000.0000.000
105A107VAL00.0000.0008.880-3.156-3.1560.0000.0000.0000.000
106A108ASP-1-0.827-0.9059.222-24.365-24.3650.0000.0000.0000.000
107A109VAL0-0.018-0.0179.958-2.211-2.2110.0000.0000.0000.000
108A110THR0-0.055-0.03910.5321.5491.5490.0000.0000.0000.000
109A111GLY00.0480.02812.922-0.794-0.7940.0000.0000.0000.000
110A112GLU-1-0.866-0.93315.642-16.611-16.6110.0000.0000.0000.000
111A113SER0-0.018-0.03418.9540.1290.1290.0000.0000.0000.000
112A114LYS10.9300.98022.29911.89311.8930.0000.0000.0000.000
113A115GLY00.0600.04225.5420.1620.1620.0000.0000.0000.000
114A116LYS10.8110.88627.62011.52511.5250.0000.0000.0000.000
115A117GLY00.0580.03031.3460.0080.0080.0000.0000.0000.000
116A118PHE00.0690.03233.309-0.194-0.1940.0000.0000.0000.000
117A119ALA0-0.0150.00833.7800.1910.1910.0000.0000.0000.000
118A120GLY00.0920.02735.6650.0040.0040.0000.0000.0000.000
119A121THR00.0320.00237.210-0.183-0.1830.0000.0000.0000.000
120A122ILE00.0040.01337.126-0.245-0.2450.0000.0000.0000.000
121A123LYS10.9690.97233.8628.9378.9370.0000.0000.0000.000
122A124ARG10.8500.94030.6399.5709.5700.0000.0000.0000.000
123A125TRP0-0.020-0.03030.361-0.309-0.3090.0000.0000.0000.000
124A126ASN00.0030.01534.3680.2260.2260.0000.0000.0000.000
125A127PHE0-0.021-0.00936.2690.1190.1190.0000.0000.0000.000
126A128ARG10.9680.97739.3147.5547.5540.0000.0000.0000.000
127A129GLY00.0100.00442.4480.0300.0300.0000.0000.0000.000
128A130GLN0-0.023-0.01145.5290.0100.0100.0000.0000.0000.000
129A131ASP-1-0.832-0.89549.361-6.210-6.2100.0000.0000.0000.000
130A132ASN0-0.042-0.03549.831-0.026-0.0260.0000.0000.0000.000
131A133THR00.0290.01653.6780.0430.0430.0000.0000.0000.000
132A134HIS00.014-0.00756.4240.0240.0240.0000.0000.0000.000
133A135GLY00.0640.04459.2540.0220.0220.0000.0000.0000.000
134A136ASN0-0.057-0.01854.4910.0100.0100.0000.0000.0000.000
135A137SER00.0680.03156.417-0.024-0.0240.0000.0000.0000.000
136A138VAL00.0420.00853.374-0.055-0.0550.0000.0000.0000.000
137A139SER0-0.054-0.02450.899-0.106-0.1060.0000.0000.0000.000
138A140HIS10.8660.93050.3726.0496.0490.0000.0000.0000.000
139A141ARG10.9590.97641.9367.2577.2570.0000.0000.0000.000
140A142VAL00.0090.02244.742-0.173-0.1730.0000.0000.0000.000
141A143PRO0-0.036-0.02742.509-0.045-0.0450.0000.0000.0000.000
142A144GLY00.0500.02944.4130.1400.1400.0000.0000.0000.000
143A145SER00.0300.02347.137-0.010-0.0100.0000.0000.0000.000
144A146ILE0-0.049-0.03943.104-0.204-0.2040.0000.0000.0000.000
145A147GLY00.035-0.00644.100-0.203-0.2030.0000.0000.0000.000
146A148GLN0-0.023-0.01044.8260.0780.0780.0000.0000.0000.000
147A149CYS-1-0.706-0.79749.296-5.906-5.9060.0000.0000.0000.000
148A150GLN0-0.061-0.10351.353-0.119-0.1190.0000.0000.0000.000
149A151THR0-0.042-0.00850.648-0.036-0.0360.0000.0000.0000.000
150A152PRO0-0.062-0.01446.621-0.064-0.0640.0000.0000.0000.000
151A153GLY00.0510.03047.988-0.085-0.0850.0000.0000.0000.000
152A154ARG10.8860.94641.7017.3027.3020.0000.0000.0000.000
153A155VAL0-0.005-0.01041.187-0.038-0.0380.0000.0000.0000.000
154A156PHE00.0540.02439.940-0.153-0.1530.0000.0000.0000.000
155A157LYS10.9640.97834.4538.6458.6450.0000.0000.0000.000
156A158GLY00.0450.02233.490-0.051-0.0510.0000.0000.0000.000
157A159LYS10.9110.98234.3717.6947.6940.0000.0000.0000.000
158A160LYS10.9370.97632.7439.2959.2950.0000.0000.0000.000
159A161MET00.0380.02636.1120.3120.3120.0000.0000.0000.000
160A162SER0-0.015-0.01236.092-0.161-0.1610.0000.0000.0000.000
161A163GLY00.0070.00035.2250.0820.0820.0000.0000.0000.000
162A164HIS0-0.014-0.02328.470-0.516-0.5160.0000.0000.0000.000
163A165LEU0-0.025-0.00929.176-0.135-0.1350.0000.0000.0000.000
164A166GLY00.0740.04325.7320.0670.0670.0000.0000.0000.000
165A167ALA0-0.046-0.01924.031-0.052-0.0520.0000.0000.0000.000
166A168GLU-1-0.929-0.96120.684-14.644-14.6440.0000.0000.0000.000
167A169ARG10.9740.99911.59421.75321.7530.0000.0000.0000.000
168A170VAL0-0.0130.00817.862-0.236-0.2360.0000.0000.0000.000
169A171THR0-0.021-0.03313.341-1.115-1.1150.0000.0000.0000.000
170A172VAL0-0.038-0.01015.2471.1731.1730.0000.0000.0000.000
171A173GLN00.000-0.00912.764-1.300-1.3000.0000.0000.0000.000
172A174SER0-0.013-0.00313.0601.6781.6780.0000.0000.0000.000
173A175LEU0-0.034-0.00814.1211.4941.4940.0000.0000.0000.000
174A176GLU-1-0.809-0.91514.401-17.092-17.0920.0000.0000.0000.000
175A177ILE0-0.029-0.00610.9240.5960.5960.0000.0000.0000.000
176A178VAL00.009-0.00115.5360.4900.4900.0000.0000.0000.000
177A179ARG10.9050.94317.04514.66614.6660.0000.0000.0000.000
178A180VAL00.0280.01712.023-0.720-0.7200.0000.0000.0000.000
179A181ASP-1-0.875-0.93414.780-14.558-14.5580.0000.0000.0000.000
180A182ALA00.0610.01714.751-0.236-0.2360.0000.0000.0000.000
181A183GLU-1-0.940-0.96815.690-13.108-13.1080.0000.0000.0000.000
182A184ARG10.8920.93518.31812.98512.9850.0000.0000.0000.000
183A185ASN0-0.0080.01013.890-0.897-0.8970.0000.0000.0000.000
184A186LEU0-0.025-0.01215.069-0.078-0.0780.0000.0000.0000.000
185A187LEU00.0160.0159.569-0.619-0.6190.0000.0000.0000.000
186A188LEU0-0.048-0.01814.2410.9360.9360.0000.0000.0000.000
187A189VAL00.0460.02013.898-0.332-0.3320.0000.0000.0000.000
188A190LYS10.9040.96116.77015.18715.1870.0000.0000.0000.000
189A191GLY00.0040.00919.525-0.284-0.2840.0000.0000.0000.000
190A192ALA0-0.036-0.01721.0930.1320.1320.0000.0000.0000.000
191A193VAL00.0680.03216.178-0.665-0.6650.0000.0000.0000.000
192A194PRO0-0.027-0.00316.9551.1171.1170.0000.0000.0000.000
193A195GLY00.0300.01818.726-0.446-0.4460.0000.0000.0000.000
194A196ALA0-0.054-0.05421.0840.6020.6020.0000.0000.0000.000
195A197THR00.0030.00321.100-0.531-0.5310.0000.0000.0000.000
196A198GLY0-0.006-0.00820.9310.5240.5240.0000.0000.0000.000
197A199GLY0-0.044-0.01019.0980.0030.0030.0000.0000.0000.000
198A200ASP-1-0.824-0.90514.006-17.540-17.5400.0000.0000.0000.000
199A201VAL0-0.042-0.03111.9910.5330.5330.0000.0000.0000.000
200A202ILE0-0.028-0.0026.913-1.076-1.0760.0000.0000.0000.000
201A203VAL00.0110.0118.1351.8321.8320.0000.0000.0000.000
202A204ARG10.9590.9665.00436.87036.8700.0000.0000.0000.000
204A206ALA0-0.040-0.0176.271-2.053-2.0530.0000.0000.0000.000
205A207ALA0-0.049-0.0288.632-0.658-0.6580.0000.0000.0000.000
206A208LYS10.8100.9219.50319.50219.5020.0000.0000.0000.000
207A209ALA-1-0.857-0.91611.312-19.721-19.7210.0000.0000.0000.000