FMO DATABASE

FMODB ID: LG189

Calculation Name: 6SPD-U-Other547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 6SPD

Chain ID: U

ChEMBL ID:

UniProt ID: A0A2V3

Base Structure: ElectronMicroscopy

Registration Date: 2025-10-04

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	103
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-682908.63578
FMO2-HF: Nuclear repulsion	643508.099762
FMO2-HF: Total energy	-39400.536018
FMO2-MP2: Total energy	-39516.855137

3D Structure Molmil

Snapshot

Ligand structure

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/A	N/A	N/A	N/A	N/A	N/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.
174.967	184.295	9.747	-6.933	-12.144	-0.068

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 : 0.795 / q_NPA : 0.907

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 ES EX CT+mix DI(MP2)

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].
3	A	3	LYS	1	0.889	0.935	3.701	38.229	41.500	0.366	-1.554	-2.083	-0.009
5	A	5	ARG	1	0.929	0.961	3.789	32.250	32.642	0.056	-0.089	-0.360	0.001
84	A	84	PHE	0	-0.026	-0.018	2.535	-18.335	-15.965	6.840	-3.281	-5.930	-0.040
90	A	90	LYS	1	0.858	0.932	2.482	44.470	44.716	0.881	-0.212	-0.915	0.001
91	A	91	LYS	1	0.951	0.980	2.708	42.574	43.171	0.902	-0.302	-1.196	-0.002
92	A	92	ILE	0	0.049	0.025	2.647	-10.847	-8.757	0.700	-1.446	-1.344	-0.019
93	A	93	ARG	1	0.733	0.846	4.447	27.859	28.221	0.002	-0.049	-0.316	0.000
4	A	4	ILE	0	0.045	0.037	5.911	1.819	1.819	0.000	0.000	0.000	0.000
6	A	6	ARG	1	0.963	0.971	7.913	21.834	21.834	0.000	0.000	0.000	0.000
7	A	7	ASP	-1	-0.907	-0.950	10.989	-18.480	-18.480	0.000	0.000	0.000	0.000
8	A	8	ASP	-1	-0.716	-0.818	9.690	-28.732	-28.732	0.000	0.000	0.000	0.000
9	A	9	GLU	-1	-0.888	-0.948	12.802	-15.284	-15.284	0.000	0.000	0.000	0.000
10	A	10	VAL	0	-0.021	-0.013	13.965	-0.779	-0.779	0.000	0.000	0.000	0.000
11	A	11	ILE	0	0.007	0.001	16.559	1.127	1.127	0.000	0.000	0.000	0.000
12	A	12	VAL	0	0.001	0.008	18.469	-0.933	-0.933	0.000	0.000	0.000	0.000
13	A	13	ILE	0	-0.020	-0.020	18.998	0.935	0.935	0.000	0.000	0.000	0.000
14	A	14	ALA	0	-0.009	-0.006	21.151	-0.079	-0.079	0.000	0.000	0.000	0.000
15	A	15	GLY	0	0.069	0.032	22.987	-0.213	-0.213	0.000	0.000	0.000	0.000
16	A	16	LYS	1	0.934	0.963	24.781	10.496	10.496	0.000	0.000	0.000	0.000
17	A	17	ASP	-1	-0.836	-0.910	25.645	-10.865	-10.865	0.000	0.000	0.000	0.000
18	A	18	LYS	1	0.934	0.964	24.318	10.887	10.887	0.000	0.000	0.000	0.000
19	A	19	GLY	0	0.007	-0.001	24.025	0.500	0.500	0.000	0.000	0.000	0.000
20	A	20	LYS	1	0.876	0.944	24.042	11.265	11.265	0.000	0.000	0.000	0.000
21	A	21	ARG	1	0.902	0.946	18.946	14.078	14.078	0.000	0.000	0.000	0.000
22	A	22	GLY	0	0.045	0.017	20.100	0.620	0.620	0.000	0.000	0.000	0.000
23	A	23	LYS	1	0.960	0.982	16.910	15.038	15.038	0.000	0.000	0.000	0.000
24	A	24	VAL	0	-0.047	-0.003	12.207	0.709	0.709	0.000	0.000	0.000	0.000
25	A	25	LEU	0	0.009	0.012	15.265	0.473	0.473	0.000	0.000	0.000	0.000
26	A	26	LYS	1	0.922	0.952	14.362	16.584	16.584	0.000	0.000	0.000	0.000
27	A	27	VAL	0	0.008	0.011	9.328	0.045	0.045	0.000	0.000	0.000	0.000
28	A	28	LEU	0	-0.037	-0.010	12.381	0.469	0.469	0.000	0.000	0.000	0.000
29	A	29	ALA	0	0.012	-0.008	12.205	-1.599	-1.599	0.000	0.000	0.000	0.000
30	A	30	ASP	-1	-0.876	-0.943	13.295	-18.429	-18.429	0.000	0.000	0.000	0.000
31	A	31	ASP	-1	-0.850	-0.920	12.412	-19.991	-19.991	0.000	0.000	0.000	0.000
32	A	32	ARG	1	0.929	0.982	13.478	15.868	15.868	0.000	0.000	0.000	0.000
33	A	33	LEU	0	0.007	-0.010	11.385	-0.716	-0.716	0.000	0.000	0.000	0.000
34	A	34	VAL	0	-0.015	-0.009	15.216	1.068	1.068	0.000	0.000	0.000	0.000
35	A	35	VAL	0	0.006	-0.005	16.433	-0.707	-0.707	0.000	0.000	0.000	0.000
36	A	36	GLY	0	0.014	-0.003	18.483	0.634	0.634	0.000	0.000	0.000	0.000
37	A	37	GLY	0	0.008	0.004	21.255	-0.044	-0.044	0.000	0.000	0.000	0.000
38	A	38	VAL	0	-0.043	-0.027	21.508	0.339	0.339	0.000	0.000	0.000	0.000
39	A	39	ASN	0	-0.054	-0.039	23.010	0.176	0.176	0.000	0.000	0.000	0.000
40	A	40	LEU	0	0.016	0.021	25.352	-0.197	-0.197	0.000	0.000	0.000	0.000
41	A	41	ILE	0	-0.068	-0.026	27.461	0.206	0.206	0.000	0.000	0.000	0.000
42	A	42	LYS	1	0.927	0.973	29.524	9.100	9.100	0.000	0.000	0.000	0.000
43	A	43	ARG	1	0.920	0.954	31.206	9.340	9.340	0.000	0.000	0.000	0.000
44	A	44	HIS	0	0.055	0.025	33.588	-0.024	-0.024	0.000	0.000	0.000	0.000
45	A	45	THR	0	-0.071	-0.033	34.658	-0.213	-0.213	0.000	0.000	0.000	0.000
46	A	46	LYS	1	0.987	0.997	37.128	7.537	7.537	0.000	0.000	0.000	0.000
47	A	47	PRO	0	0.002	0.002	38.667	-0.179	-0.179	0.000	0.000	0.000	0.000
48	A	48	ASN	0	-0.027	-0.010	35.225	0.002	0.002	0.000	0.000	0.000	0.000
49	A	49	PRO	0	0.042	0.023	38.370	0.165	0.165	0.000	0.000	0.000	0.000
50	A	50	MET	0	-0.032	-0.028	38.573	-0.077	-0.077	0.000	0.000	0.000	0.000
51	A	51	LEU	0	0.038	0.023	41.096	-0.083	-0.083	0.000	0.000	0.000	0.000
52	A	52	GLY	0	0.022	0.031	39.165	-0.112	-0.112	0.000	0.000	0.000	0.000
53	A	53	GLN	0	0.029	-0.003	38.725	0.251	0.251	0.000	0.000	0.000	0.000
54	A	54	GLN	0	-0.059	-0.054	35.075	-0.099	-0.099	0.000	0.000	0.000	0.000
55	A	55	GLY	0	0.037	0.026	38.202	-0.043	-0.043	0.000	0.000	0.000	0.000
56	A	56	GLY	0	0.071	0.022	39.118	0.168	0.168	0.000	0.000	0.000	0.000
57	A	57	ILE	0	-0.052	-0.007	36.224	-0.247	-0.247	0.000	0.000	0.000	0.000
58	A	58	VAL	0	0.015	0.014	31.700	0.041	0.041	0.000	0.000	0.000	0.000
59	A	59	GLU	-1	-0.842	-0.937	30.621	-9.634	-9.634	0.000	0.000	0.000	0.000
60	A	60	LYS	1	0.936	0.971	24.986	11.625	11.625	0.000	0.000	0.000	0.000
61	A	61	GLU	-1	-0.792	-0.891	22.550	-12.193	-12.193	0.000	0.000	0.000	0.000
62	A	62	ALA	0	-0.060	-0.027	23.514	0.009	0.009	0.000	0.000	0.000	0.000
63	A	63	PRO	0	-0.029	-0.005	18.420	-0.151	-0.151	0.000	0.000	0.000	0.000
64	A	64	LEU	0	-0.027	-0.014	17.762	0.649	0.649	0.000	0.000	0.000	0.000
65	A	65	HIS	0	0.039	0.022	14.566	-0.751	-0.751	0.000	0.000	0.000	0.000
66	A	66	VAL	0	0.015	0.005	10.397	0.036	0.036	0.000	0.000	0.000	0.000
67	A	67	SER	0	-0.033	-0.038	13.545	-1.015	-1.015	0.000	0.000	0.000	0.000
68	A	68	ASN	0	-0.023	0.000	14.829	0.515	0.515	0.000	0.000	0.000	0.000
69	A	69	VAL	0	-0.030	-0.007	14.127	0.936	0.936	0.000	0.000	0.000	0.000
70	A	70	ALA	0	0.000	-0.002	13.672	-1.502	-1.502	0.000	0.000	0.000	0.000
71	A	71	ILE	0	0.008	-0.001	9.921	0.852	0.852	0.000	0.000	0.000	0.000
72	A	72	PHE	0	0.003	-0.004	13.569	0.641	0.641	0.000	0.000	0.000	0.000
73	A	73	ASN	0	0.025	-0.006	16.083	-0.440	-0.440	0.000	0.000	0.000	0.000
74	A	74	THR	0	-0.075	-0.035	17.135	0.247	0.247	0.000	0.000	0.000	0.000
75	A	75	GLU	-1	-0.772	-0.868	17.616	-15.750	-15.750	0.000	0.000	0.000	0.000
76	A	76	THR	0	-0.022	-0.018	20.345	0.336	0.336	0.000	0.000	0.000	0.000
77	A	77	SER	0	-0.027	-0.013	22.230	0.048	0.048	0.000	0.000	0.000	0.000
78	A	78	LYS	1	0.960	0.992	19.621	15.629	15.629	0.000	0.000	0.000	0.000
79	A	79	ALA	0	0.032	0.017	17.249	-0.674	-0.674	0.000	0.000	0.000	0.000
80	A	80	ASP	-1	-0.792	-0.869	15.383	-18.619	-18.619	0.000	0.000	0.000	0.000
81	A	81	ARG	1	0.916	0.961	12.251	17.516	17.516	0.000	0.000	0.000	0.000
82	A	82	VAL	0	0.075	0.045	7.761	-0.021	-0.021	0.000	0.000	0.000	0.000
83	A	83	GLY	0	-0.080	-0.052	7.002	-1.263	-1.263	0.000	0.000	0.000	0.000
85	A	85	LYS	1	0.931	0.955	6.255	31.376	31.376	0.000	0.000	0.000	0.000
86	A	86	VAL	0	0.126	0.096	7.930	1.886	1.886	0.000	0.000	0.000	0.000
87	A	87	GLU	-1	-0.974	-1.026	6.938	-37.256	-37.256	0.000	0.000	0.000	0.000
88	A	88	ASP	-1	-0.834	-0.903	8.309	-20.824	-20.824	0.000	0.000	0.000	0.000
89	A	89	GLY	0	0.026	0.019	9.581	1.524	1.524	0.000	0.000	0.000	0.000
94	A	94	VAL	0	0.048	0.031	5.747	3.065	3.065	0.000	0.000	0.000	0.000
95	A	95	PHE	0	0.052	0.028	9.178	-1.907	-1.907	0.000	0.000	0.000	0.000
96	A	96	LYS	1	0.907	0.937	10.926	24.648	24.648	0.000	0.000	0.000	0.000
97	A	97	SER	0	-0.069	-0.064	14.205	1.137	1.137	0.000	0.000	0.000	0.000
98	A	98	THR	0	-0.033	-0.043	16.171	0.389	0.389	0.000	0.000	0.000	0.000
99	A	99	GLN	0	-0.028	-0.007	13.577	-0.550	-0.550	0.000	0.000	0.000	0.000
100	A	100	LYS	1	0.955	1.018	13.855	17.409	17.409	0.000	0.000	0.000	0.000
101	A	101	PRO	0	-0.010	-0.023	9.988	-1.444	-1.444	0.000	0.000	0.000	0.000
102	A	102	VAL	0	-0.081	-0.051	8.495	0.963	0.963	0.000	0.000	0.000	0.000
103	A	103	GLN	-1	-0.893	-0.945	10.132	-22.324	-22.324	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:1:MET)