FMO DATABASE

FMODB ID: 2RY6R

Calculation Name: 6SPC-i-Other547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 6SPC

Chain ID: i

ChEMBL ID:

UniProt ID: E2RXU3

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	126
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-976601.926073
FMO2-HF: Nuclear repulsion	928022.62244
FMO2-HF: Total energy	-48579.303634
FMO2-MP2: Total energy	-48723.801775

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:3:ALA)

Summations of interaction energy for fragment #1(A:3:ALA)

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.
121.495	123.988	0.413	-1.11	-1.795	-0.005

Interaction energy analysis for fragmet #1(A:3:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.848 / q_NPA : 0.910

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

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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	5	GLN	0	-0.034	-0.004	2.505	12.709	15.204	0.413	-1.089	-1.818	-0.005
4	A	6	ASN	0	0.029	0.007	4.116	-3.791	-3.793	0.000	-0.021	0.023	0.000
5	A	7	TYR	0	-0.014	-0.002	7.344	3.104	3.104	0.000	0.000	0.000	0.000
6	A	8	GLY	0	0.128	0.078	11.084	0.971	0.971	0.000	0.000	0.000	0.000
7	A	9	THR	0	-0.060	-0.059	13.327	1.433	1.433	0.000	0.000	0.000	0.000
8	A	10	GLY	0	0.075	0.025	16.897	0.014	0.014	0.000	0.000	0.000	0.000
9	A	11	ARG	1	0.903	0.949	20.019	15.361	15.361	0.000	0.000	0.000	0.000
10	A	12	ARG	1	0.826	0.888	23.540	10.469	10.469	0.000	0.000	0.000	0.000
11	A	13	LYS	1	0.861	0.931	27.141	9.447	9.447	0.000	0.000	0.000	0.000
12	A	14	THR	0	0.021	0.010	28.449	0.055	0.055	0.000	0.000	0.000	0.000
13	A	15	ALA	0	0.075	0.053	23.754	0.080	0.080	0.000	0.000	0.000	0.000
14	A	16	THR	0	-0.032	-0.038	19.962	-0.056	-0.056	0.000	0.000	0.000	0.000
15	A	17	ALA	0	-0.024	0.016	18.419	-0.029	-0.029	0.000	0.000	0.000	0.000
16	A	18	ARG	1	0.954	0.979	14.491	16.638	16.638	0.000	0.000	0.000	0.000
17	A	19	VAL	0	-0.014	0.004	11.488	1.011	1.011	0.000	0.000	0.000	0.000
18	A	20	PHE	0	-0.016	-0.016	9.240	-1.206	-1.206	0.000	0.000	0.000	0.000
19	A	21	LEU	0	-0.007	0.008	9.107	1.115	1.115	0.000	0.000	0.000	0.000
20	A	22	ARG	1	0.914	0.952	5.772	24.462	24.462	0.000	0.000	0.000	0.000
21	A	23	PRO	0	0.066	0.029	5.887	3.362	3.362	0.000	0.000	0.000	0.000
22	A	24	GLY	0	-0.029	-0.038	8.771	-0.347	-0.347	0.000	0.000	0.000	0.000
23	A	25	THR	0	0.005	0.017	11.766	0.370	0.370	0.000	0.000	0.000	0.000
24	A	26	GLY	0	0.075	0.054	15.478	0.900	0.900	0.000	0.000	0.000	0.000
25	A	27	LYS	1	0.812	0.925	13.343	19.960	19.960	0.000	0.000	0.000	0.000
26	A	28	ILE	0	0.039	0.018	15.500	-0.850	-0.850	0.000	0.000	0.000	0.000
27	A	29	SER	0	-0.075	-0.059	16.010	0.674	0.674	0.000	0.000	0.000	0.000
28	A	30	ILE	0	0.028	0.006	17.559	-0.604	-0.604	0.000	0.000	0.000	0.000
29	A	31	ASN	0	0.002	-0.017	19.643	0.060	0.060	0.000	0.000	0.000	0.000
30	A	32	ASN	0	-0.010	-0.008	18.360	-0.115	-0.115	0.000	0.000	0.000	0.000
31	A	33	ARG	1	0.965	1.001	19.849	11.739	11.739	0.000	0.000	0.000	0.000
32	A	34	GLY	0	0.090	0.060	19.943	-0.801	-0.801	0.000	0.000	0.000	0.000
33	A	35	LEU	0	-0.016	-0.016	21.069	0.390	0.390	0.000	0.000	0.000	0.000
34	A	36	ASP	-1	-0.816	-0.875	22.687	-11.131	-11.131	0.000	0.000	0.000	0.000
35	A	37	GLN	0	-0.041	-0.030	23.876	0.143	0.143	0.000	0.000	0.000	0.000
36	A	38	PHE	0	-0.064	-0.020	25.872	0.286	0.286	0.000	0.000	0.000	0.000
37	A	39	PHE	0	0.020	0.020	24.607	0.245	0.245	0.000	0.000	0.000	0.000
38	A	40	GLY	0	0.038	-0.003	27.936	-0.177	-0.177	0.000	0.000	0.000	0.000
39	A	41	ARG	1	0.928	0.964	30.448	8.339	8.339	0.000	0.000	0.000	0.000
40	A	42	GLU	-1	-0.821	-0.893	30.420	-9.756	-9.756	0.000	0.000	0.000	0.000
41	A	43	THR	0	0.044	0.004	32.239	-0.292	-0.292	0.000	0.000	0.000	0.000
42	A	44	ALA	0	0.010	0.003	29.706	-0.142	-0.142	0.000	0.000	0.000	0.000
43	A	45	ARG	1	0.841	0.899	27.037	10.410	10.410	0.000	0.000	0.000	0.000
44	A	46	MET	0	0.053	0.019	26.359	-0.551	-0.551	0.000	0.000	0.000	0.000
45	A	47	VAL	0	0.005	0.020	27.655	-0.174	-0.174	0.000	0.000	0.000	0.000
46	A	48	VAL	0	-0.020	-0.022	22.876	-0.190	-0.190	0.000	0.000	0.000	0.000
47	A	49	ARG	1	0.905	0.943	22.834	11.687	11.687	0.000	0.000	0.000	0.000
48	A	50	GLN	0	0.061	0.046	24.508	-0.256	-0.256	0.000	0.000	0.000	0.000
49	A	51	PRO	0	-0.037	-0.019	21.802	-0.016	-0.016	0.000	0.000	0.000	0.000
50	A	52	LEU	0	-0.023	0.001	18.059	-0.335	-0.335	0.000	0.000	0.000	0.000
51	A	53	GLU	-1	-0.906	-0.953	21.399	-11.432	-11.432	0.000	0.000	0.000	0.000
52	A	54	LEU	0	-0.069	-0.031	24.242	0.062	0.062	0.000	0.000	0.000	0.000
53	A	55	THR	0	-0.059	-0.039	19.588	-0.256	-0.256	0.000	0.000	0.000	0.000
54	A	56	GLU	-1	-0.826	-0.890	19.765	-15.523	-15.523	0.000	0.000	0.000	0.000
55	A	57	THR	0	0.033	-0.008	16.163	-0.748	-0.748	0.000	0.000	0.000	0.000
56	A	58	VAL	0	-0.087	-0.043	16.613	-0.857	-0.857	0.000	0.000	0.000	0.000
57	A	59	GLU	-1	-0.820	-0.930	17.755	-15.461	-15.461	0.000	0.000	0.000	0.000
58	A	60	LYS	1	0.867	0.945	14.069	16.376	16.376	0.000	0.000	0.000	0.000
59	A	61	PHE	0	0.015	0.005	9.885	-2.012	-2.012	0.000	0.000	0.000	0.000
60	A	62	ASP	-1	-0.915	-0.947	10.311	-20.902	-20.902	0.000	0.000	0.000	0.000
61	A	63	ILE	0	0.020	0.011	10.709	-2.061	-2.061	0.000	0.000	0.000	0.000
62	A	64	PHE	0	0.021	0.016	12.452	1.547	1.547	0.000	0.000	0.000	0.000
63	A	65	VAL	0	0.018	-0.008	13.615	-1.148	-1.148	0.000	0.000	0.000	0.000
64	A	66	THR	0	-0.018	-0.003	16.376	1.367	1.367	0.000	0.000	0.000	0.000
65	A	67	VAL	0	-0.048	-0.038	18.616	-0.266	-0.266	0.000	0.000	0.000	0.000
66	A	68	VAL	0	0.059	0.040	21.905	0.371	0.371	0.000	0.000	0.000	0.000
67	A	69	GLY	0	0.080	0.045	25.183	-0.088	-0.088	0.000	0.000	0.000	0.000
68	A	70	GLY	0	-0.040	-0.032	28.601	-0.004	-0.004	0.000	0.000	0.000	0.000
69	A	71	GLY	0	-0.001	-0.012	30.886	0.385	0.385	0.000	0.000	0.000	0.000
70	A	72	VAL	0	0.049	0.039	30.594	-0.255	-0.255	0.000	0.000	0.000	0.000
71	A	73	SER	0	0.029	-0.003	30.051	-0.264	-0.264	0.000	0.000	0.000	0.000
72	A	74	GLY	0	-0.044	-0.014	30.920	-0.117	-0.117	0.000	0.000	0.000	0.000
73	A	75	GLN	0	-0.053	-0.043	26.060	-0.282	-0.282	0.000	0.000	0.000	0.000
74	A	76	ALA	0	0.073	0.039	25.956	-0.506	-0.506	0.000	0.000	0.000	0.000
75	A	77	GLY	0	-0.065	-0.041	26.106	-0.283	-0.283	0.000	0.000	0.000	0.000
76	A	78	ALA	0	-0.034	-0.023	23.019	-0.164	-0.164	0.000	0.000	0.000	0.000
77	A	79	ILE	0	0.034	0.022	20.444	-0.648	-0.648	0.000	0.000	0.000	0.000
78	A	80	ARG	1	0.944	0.984	20.971	10.925	10.925	0.000	0.000	0.000	0.000
79	A	81	HIS	0	-0.034	0.002	22.265	-0.744	-0.744	0.000	0.000	0.000	0.000
80	A	82	GLY	0	0.033	-0.006	18.508	-0.210	-0.210	0.000	0.000	0.000	0.000
81	A	83	ILE	0	-0.041	0.005	16.938	-1.109	-1.109	0.000	0.000	0.000	0.000
82	A	84	THR	0	0.076	0.026	16.146	-0.795	-0.795	0.000	0.000	0.000	0.000
83	A	85	ARG	1	0.840	0.949	15.772	16.645	16.645	0.000	0.000	0.000	0.000
84	A	86	ALA	0	0.023	0.006	11.340	-0.423	-0.423	0.000	0.000	0.000	0.000
85	A	87	LEU	0	-0.020	0.006	11.216	-1.606	-1.606	0.000	0.000	0.000	0.000
86	A	88	ILE	0	-0.023	-0.026	13.184	-0.316	-0.316	0.000	0.000	0.000	0.000
87	A	89	GLU	-1	-0.957	-0.972	10.793	-24.544	-24.544	0.000	0.000	0.000	0.000
88	A	90	TYR	0	-0.094	-0.045	7.620	-2.502	-2.502	0.000	0.000	0.000	0.000
89	A	91	ASP	-1	-0.831	-0.897	10.315	-22.040	-22.040	0.000	0.000	0.000	0.000
90	A	92	GLU	-1	-0.922	-0.970	13.571	-18.809	-18.809	0.000	0.000	0.000	0.000
91	A	93	THR	0	-0.021	-0.027	15.275	1.506	1.506	0.000	0.000	0.000	0.000
92	A	94	LEU	0	0.052	0.013	17.965	1.028	1.028	0.000	0.000	0.000	0.000
93	A	95	ARG	1	0.926	0.985	17.688	17.522	17.522	0.000	0.000	0.000	0.000
94	A	96	SER	0	-0.018	-0.030	21.009	0.179	0.179	0.000	0.000	0.000	0.000
95	A	97	SER	0	0.000	0.008	23.474	0.739	0.739	0.000	0.000	0.000	0.000
96	A	98	LEU	0	0.016	0.012	19.456	0.388	0.388	0.000	0.000	0.000	0.000
97	A	99	ARG	1	0.918	0.963	24.169	11.893	11.893	0.000	0.000	0.000	0.000
98	A	100	LYS	1	0.976	0.976	27.215	10.447	10.447	0.000	0.000	0.000	0.000
99	A	101	ALA	0	0.035	0.034	25.590	0.283	0.283	0.000	0.000	0.000	0.000
100	A	102	GLY	0	0.009	0.012	27.665	0.216	0.216	0.000	0.000	0.000	0.000
101	A	103	TYR	0	-0.013	-0.031	24.290	0.109	0.109	0.000	0.000	0.000	0.000
102	A	104	VAL	0	0.046	0.024	22.298	-0.091	-0.091	0.000	0.000	0.000	0.000
103	A	105	THR	0	-0.012	-0.014	24.815	-0.206	-0.206	0.000	0.000	0.000	0.000
104	A	106	ARG	1	0.933	0.974	26.466	11.398	11.398	0.000	0.000	0.000	0.000
105	A	107	ASP	-1	-0.787	-0.876	28.336	-9.206	-9.206	0.000	0.000	0.000	0.000
106	A	108	ALA	0	0.030	0.010	32.071	-0.136	-0.136	0.000	0.000	0.000	0.000
107	A	109	ARG	1	0.816	0.894	34.854	9.237	9.237	0.000	0.000	0.000	0.000
108	A	110	GLU	-1	-0.768	-0.863	33.792	-9.403	-9.403	0.000	0.000	0.000	0.000
109	A	111	VAL	0	-0.082	-0.045	37.232	0.262	0.262	0.000	0.000	0.000	0.000
110	A	112	GLU	-1	-0.870	-0.933	35.943	-8.968	-8.968	0.000	0.000	0.000	0.000
111	A	113	ARG	1	0.940	0.981	39.358	7.422	7.422	0.000	0.000	0.000	0.000
112	A	114	LYS	1	0.947	0.967	41.973	7.019	7.019	0.000	0.000	0.000	0.000
113	A	115	LYS	1	0.944	0.970	45.071	6.815	6.815	0.000	0.000	0.000	0.000
114	A	116	VAL	0	0.086	0.048	48.384	-0.009	-0.009	0.000	0.000	0.000	0.000
115	A	117	GLY	0	0.057	0.037	51.745	0.011	0.011	0.000	0.000	0.000	0.000
116	A	118	LEU	0	-0.045	-0.026	49.219	0.055	0.055	0.000	0.000	0.000	0.000
117	A	119	ARG	1	0.974	0.993	50.985	5.979	5.979	0.000	0.000	0.000	0.000
118	A	120	LYS	1	0.897	0.924	45.697	6.775	6.775	0.000	0.000	0.000	0.000
119	A	121	ALA	0	0.059	0.032	42.967	0.106	0.106	0.000	0.000	0.000	0.000
120	A	122	ARG	1	1.005	1.002	43.377	7.342	7.342	0.000	0.000	0.000	0.000
121	A	123	LYS	1	0.918	0.975	47.409	6.414	6.414	0.000	0.000	0.000	0.000
122	A	124	ARG	1	0.995	1.004	49.654	5.724	5.724	0.000	0.000	0.000	0.000
123	A	125	PRO	0	-0.017	-0.026	53.338	-0.072	-0.072	0.000	0.000	0.000	0.000
124	A	126	GLN	0	0.013	0.010	55.941	-0.083	-0.083	0.000	0.000	0.000	0.000
125	A	127	TYR	0	-0.004	-0.017	57.961	-0.070	-0.070	0.000	0.000	0.000	0.000
126	A	128	SER	-1	-0.861	-0.914	61.851	-5.048	-5.048	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:ALA)