FMO DATABASE

FMODB ID: Q5M9Y

Calculation Name: 6V3A-U-Other547

Preferred Name:

Target Type:

Ligand 3-letter code: 7MG | 2MG | MA6 | 2MA | 4OC | 6MZ | PSU | 3TD | 5MC | 5MU | OMG | UR3 | 4SU | H2U | OMU

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 6V3A

Chain ID: U

ChEMBL ID:

UniProt ID: B7I9B0

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	97
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-689384.840396
FMO2-HF: Nuclear repulsion	652199.092986
FMO2-HF: Total energy	-37185.74741
FMO2-MP2: Total energy	-37296.363547

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:2:ALA)

Summations of interaction energy for fragment #1(A:2: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.
-42.545	-41.057	-0.006	-0.684	-0.798	-0.002

Interaction energy analysis for fragmet #1(A:2:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.819 / q_NPA : 0.893

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	4	PHE	0	-0.007	0.006	3.593	-6.823	-5.488	-0.005	-0.649	-0.682	-0.002
62	A	63	GLU	-1	-0.848	-0.945	4.436	-57.302	-57.149	-0.001	-0.035	-0.116	0.000
4	A	5	VAL	0	0.041	0.020	5.915	6.381	6.381	0.000	0.000	0.000	0.000
5	A	6	LEU	0	-0.017	-0.013	8.276	0.709	0.709	0.000	0.000	0.000	0.000
6	A	7	ASN	0	-0.063	-0.022	11.500	0.710	0.710	0.000	0.000	0.000	0.000
7	A	8	ALA	0	0.007	-0.001	14.479	0.074	0.074	0.000	0.000	0.000	0.000
8	A	9	GLN	0	0.033	0.012	17.773	0.287	0.287	0.000	0.000	0.000	0.000
9	A	10	ALA	0	0.050	0.016	21.521	0.065	0.065	0.000	0.000	0.000	0.000
10	A	11	ARG	1	0.794	0.915	24.140	12.565	12.565	0.000	0.000	0.000	0.000
11	A	12	ALA	0	0.084	0.038	26.878	0.168	0.168	0.000	0.000	0.000	0.000
12	A	13	GLU	-1	-0.919	-0.967	30.399	-9.073	-9.073	0.000	0.000	0.000	0.000
13	A	14	ASP	-1	-0.862	-0.921	33.129	-9.179	-9.179	0.000	0.000	0.000	0.000
14	A	15	LYS	1	0.901	0.943	28.491	10.925	10.925	0.000	0.000	0.000	0.000
15	A	16	GLN	0	-0.052	-0.029	29.290	-0.274	-0.274	0.000	0.000	0.000	0.000
16	A	17	GLY	0	0.115	0.062	31.550	0.316	0.316	0.000	0.000	0.000	0.000
17	A	18	LYS	1	0.933	0.962	32.508	8.242	8.242	0.000	0.000	0.000	0.000
18	A	19	GLY	0	0.017	-0.001	33.278	-0.171	-0.171	0.000	0.000	0.000	0.000
19	A	20	ALA	0	0.057	0.041	31.577	-0.102	-0.102	0.000	0.000	0.000	0.000
20	A	21	SER	0	0.031	-0.001	28.789	-0.423	-0.423	0.000	0.000	0.000	0.000
21	A	22	ARG	1	0.864	0.930	28.734	8.853	8.853	0.000	0.000	0.000	0.000
22	A	23	ARG	1	1.005	1.006	30.431	9.151	9.151	0.000	0.000	0.000	0.000
23	A	24	LEU	0	0.084	0.052	25.460	-0.061	-0.061	0.000	0.000	0.000	0.000
24	A	25	ARG	1	0.851	0.911	25.063	11.809	11.809	0.000	0.000	0.000	0.000
25	A	26	ARG	1	0.822	0.911	26.414	10.141	10.141	0.000	0.000	0.000	0.000
26	A	27	GLU	-1	-0.903	-0.938	26.020	-11.389	-11.389	0.000	0.000	0.000	0.000
27	A	28	SER	0	-0.058	-0.021	21.968	-0.722	-0.722	0.000	0.000	0.000	0.000
28	A	29	LEU	0	0.021	0.013	21.159	-0.880	-0.880	0.000	0.000	0.000	0.000
29	A	30	VAL	0	-0.024	-0.027	19.665	0.745	0.745	0.000	0.000	0.000	0.000
30	A	31	PRO	0	-0.069	-0.037	21.353	-0.340	-0.340	0.000	0.000	0.000	0.000
31	A	32	ALA	0	0.038	0.023	19.964	-0.223	-0.223	0.000	0.000	0.000	0.000
32	A	33	ILE	0	-0.060	-0.036	21.724	0.668	0.668	0.000	0.000	0.000	0.000
33	A	34	ILE	0	0.048	0.037	18.387	-0.612	-0.612	0.000	0.000	0.000	0.000
34	A	35	TYR	0	-0.006	-0.019	21.772	0.854	0.854	0.000	0.000	0.000	0.000
35	A	36	GLY	0	0.029	0.004	22.500	-0.740	-0.740	0.000	0.000	0.000	0.000
36	A	37	GLY	0	0.006	0.010	24.179	0.559	0.559	0.000	0.000	0.000	0.000
37	A	38	ASN	0	-0.043	-0.036	23.729	-0.410	-0.410	0.000	0.000	0.000	0.000
38	A	39	ALA	0	0.039	0.040	25.045	0.235	0.235	0.000	0.000	0.000	0.000
39	A	40	GLU	-1	-0.918	-0.952	27.206	-11.752	-11.752	0.000	0.000	0.000	0.000
40	A	41	PRO	0	-0.017	-0.021	26.094	-0.558	-0.558	0.000	0.000	0.000	0.000
41	A	42	VAL	0	0.074	0.060	22.921	0.311	0.311	0.000	0.000	0.000	0.000
42	A	43	ALA	0	-0.012	-0.007	23.484	-0.523	-0.523	0.000	0.000	0.000	0.000
43	A	44	VAL	0	0.001	-0.001	19.163	0.126	0.126	0.000	0.000	0.000	0.000
44	A	45	THR	0	-0.034	-0.027	21.321	0.562	0.562	0.000	0.000	0.000	0.000
45	A	46	LEU	0	0.039	0.025	15.287	-0.618	-0.618	0.000	0.000	0.000	0.000
46	A	47	GLU	-1	-0.784	-0.884	16.364	-16.942	-16.942	0.000	0.000	0.000	0.000
47	A	48	LEU	0	-0.013	-0.009	16.393	-1.096	-1.096	0.000	0.000	0.000	0.000
48	A	49	ARG	1	0.822	0.888	14.277	19.098	19.098	0.000	0.000	0.000	0.000
49	A	50	GLU	-1	-0.835	-0.914	12.100	-24.293	-24.293	0.000	0.000	0.000	0.000
50	A	51	LEU	0	0.001	0.005	11.824	-1.658	-1.658	0.000	0.000	0.000	0.000
51	A	52	VAL	0	-0.042	-0.042	13.388	-0.515	-0.515	0.000	0.000	0.000	0.000
52	A	53	LYS	1	0.847	0.920	9.322	26.130	26.130	0.000	0.000	0.000	0.000
53	A	54	ALA	0	0.004	0.004	8.612	-2.538	-2.538	0.000	0.000	0.000	0.000
54	A	55	LEU	0	-0.039	-0.032	9.681	-0.384	-0.384	0.000	0.000	0.000	0.000
55	A	56	GLU	-1	-0.874	-0.911	10.918	-23.166	-23.166	0.000	0.000	0.000	0.000
56	A	57	SER	0	-0.040	0.000	6.802	1.519	1.519	0.000	0.000	0.000	0.000
57	A	58	ASN	0	0.023	-0.009	9.786	-1.032	-1.032	0.000	0.000	0.000	0.000
58	A	59	VAL	0	0.050	0.026	5.787	1.194	1.194	0.000	0.000	0.000	0.000
59	A	60	PHE	0	0.005	0.017	8.230	-0.341	-0.341	0.000	0.000	0.000	0.000
60	A	61	PHE	0	-0.044	-0.023	8.956	2.030	2.030	0.000	0.000	0.000	0.000
61	A	62	GLU	-1	-1.021	-1.000	8.454	-29.574	-29.574	0.000	0.000	0.000	0.000
63	A	64	VAL	0	-0.035	-0.005	8.494	3.299	3.299	0.000	0.000	0.000	0.000
64	A	65	VAL	0	-0.021	-0.006	8.635	-3.484	-3.484	0.000	0.000	0.000	0.000
65	A	66	GLU	-1	-0.897	-0.961	9.788	-23.854	-23.854	0.000	0.000	0.000	0.000
66	A	67	ILE	0	-0.031	-0.019	11.362	-0.981	-0.981	0.000	0.000	0.000	0.000
67	A	68	LYS	1	0.926	0.966	10.126	28.281	28.281	0.000	0.000	0.000	0.000
68	A	69	VAL	0	-0.005	-0.015	15.709	0.181	0.181	0.000	0.000	0.000	0.000
69	A	70	GLY	0	-0.027	-0.016	19.397	0.521	0.521	0.000	0.000	0.000	0.000
70	A	71	ASP	-1	-0.913	-0.956	19.086	-14.650	-14.650	0.000	0.000	0.000	0.000
71	A	72	LYS	1	0.854	0.947	20.107	15.148	15.148	0.000	0.000	0.000	0.000
72	A	73	VAL	0	0.033	0.012	14.794	-0.454	-0.454	0.000	0.000	0.000	0.000
73	A	74	GLU	-1	-0.826	-0.916	15.958	-13.982	-13.982	0.000	0.000	0.000	0.000
74	A	75	ASN	0	-0.015	0.005	11.541	0.147	0.147	0.000	0.000	0.000	0.000
75	A	76	VAL	0	-0.020	-0.014	13.721	1.773	1.773	0.000	0.000	0.000	0.000
76	A	77	LYS	1	0.924	0.961	12.717	20.387	20.387	0.000	0.000	0.000	0.000
77	A	78	ILE	0	-0.009	0.000	13.726	1.496	1.496	0.000	0.000	0.000	0.000
78	A	79	GLN	0	-0.017	0.007	15.979	0.000	0.000	0.000	0.000	0.000	0.000
79	A	80	ALA	0	-0.014	-0.008	19.486	0.323	0.323	0.000	0.000	0.000	0.000
80	A	81	LEU	0	0.001	-0.011	17.646	-0.579	-0.579	0.000	0.000	0.000	0.000
81	A	82	GLN	0	-0.029	-0.002	20.728	0.748	0.748	0.000	0.000	0.000	0.000
82	A	83	ARG	1	0.966	0.966	17.828	15.484	15.484	0.000	0.000	0.000	0.000
83	A	84	HIS	0	0.002	-0.010	24.248	0.457	0.457	0.000	0.000	0.000	0.000
84	A	85	PRO	0	-0.001	-0.011	27.122	-0.183	-0.183	0.000	0.000	0.000	0.000
85	A	86	ALA	0	0.013	0.015	29.401	0.080	0.080	0.000	0.000	0.000	0.000
86	A	87	LYS	1	0.943	0.968	26.579	10.539	10.539	0.000	0.000	0.000	0.000
87	A	88	ASN	0	0.045	0.030	21.848	-0.237	-0.237	0.000	0.000	0.000	0.000
88	A	89	THR	0	0.032	0.024	21.747	-0.568	-0.568	0.000	0.000	0.000	0.000
89	A	90	PRO	0	0.017	0.003	18.000	0.712	0.712	0.000	0.000	0.000	0.000
90	A	91	MET	0	-0.071	-0.025	21.129	0.531	0.531	0.000	0.000	0.000	0.000
91	A	92	HIS	0	0.051	0.024	22.646	0.558	0.558	0.000	0.000	0.000	0.000
92	A	93	ALA	0	0.024	0.026	17.957	-0.155	-0.155	0.000	0.000	0.000	0.000
93	A	94	ASP	-1	-0.876	-0.935	20.067	-14.066	-14.066	0.000	0.000	0.000	0.000
94	A	95	PHE	0	0.024	0.009	13.958	-0.801	-0.801	0.000	0.000	0.000	0.000
95	A	96	LYS	1	0.971	0.992	18.661	14.939	14.939	0.000	0.000	0.000	0.000
96	A	97	ARG	1	0.795	0.872	18.079	13.148	13.148	0.000	0.000	0.000	0.000
97	A	98	ALA	-1	-0.945	-0.954	15.769	-18.016	-18.016	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:ALA)