FMO DATABASE

FMODB ID: VV4G1

Calculation Name: 2K56-A-Other547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2K56

Chain ID: A

ChEMBL ID:

UniProt ID: Q8VHV5

Base Structure: SolutionNMR

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	112
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-919021.091189
FMO2-HF: Nuclear repulsion	870742.42068
FMO2-HF: Total energy	-48278.670509
FMO2-MP2: Total energy	-48413.231094

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:119:GLY)

Summations of interaction energy for fragment #1(A:119:GLY)

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.
-14.59	-13.627	-0.018	-0.352	-0.593	-0.001

Interaction energy analysis for fragmet #1(A:119:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.864 / q_NPA : 0.919

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	121	VAL	0	0.034	0.033	3.813	2.373	3.336	-0.018	-0.352	-0.593	-0.001
4	A	122	VAL	0	0.066	0.038	6.522	1.647	1.647	0.000	0.000	0.000	0.000
5	A	123	GLY	0	-0.001	-0.004	10.065	0.201	0.201	0.000	0.000	0.000	0.000
6	A	124	GLY	0	-0.016	-0.007	12.540	1.474	1.474	0.000	0.000	0.000	0.000
7	A	125	LEU	0	-0.017	-0.016	14.120	1.219	1.219	0.000	0.000	0.000	0.000
8	A	126	GLY	0	0.001	0.008	15.784	-0.532	-0.532	0.000	0.000	0.000	0.000
9	A	127	GLY	0	-0.019	-0.007	17.135	0.727	0.727	0.000	0.000	0.000	0.000
10	A	128	TYR	0	-0.082	-0.048	18.598	0.467	0.467	0.000	0.000	0.000	0.000
11	A	129	MET	0	-0.023	-0.009	18.801	-0.867	-0.867	0.000	0.000	0.000	0.000
12	A	130	LEU	0	-0.034	-0.025	19.523	-0.080	-0.080	0.000	0.000	0.000	0.000
13	A	131	GLY	0	0.055	0.044	22.198	0.189	0.189	0.000	0.000	0.000	0.000
14	A	132	SER	0	-0.035	-0.017	25.629	0.000	0.000	0.000	0.000	0.000	0.000
15	A	133	ALA	0	-0.016	0.002	25.899	-0.144	-0.144	0.000	0.000	0.000	0.000
16	A	134	MET	0	-0.026	-0.013	27.580	0.540	0.540	0.000	0.000	0.000	0.000
17	A	135	SER	0	-0.010	-0.006	30.380	-0.297	-0.297	0.000	0.000	0.000	0.000
18	A	136	ARG	1	0.934	0.949	31.900	9.575	9.575	0.000	0.000	0.000	0.000
19	A	137	PRO	0	0.041	0.033	32.234	0.313	0.313	0.000	0.000	0.000	0.000
20	A	138	MET	0	0.002	0.002	35.199	0.010	0.010	0.000	0.000	0.000	0.000
21	A	139	ILE	0	-0.034	-0.016	33.957	0.210	0.210	0.000	0.000	0.000	0.000
22	A	140	HIS	0	-0.021	-0.014	38.311	0.105	0.105	0.000	0.000	0.000	0.000
23	A	141	PHE	0	0.029	-0.002	34.781	0.046	0.046	0.000	0.000	0.000	0.000
24	A	142	GLY	0	-0.026	0.011	41.019	0.089	0.089	0.000	0.000	0.000	0.000
25	A	143	ASN	0	-0.055	-0.042	41.948	0.323	0.323	0.000	0.000	0.000	0.000
26	A	144	ASP	-1	-0.918	-0.959	41.699	-7.639	-7.639	0.000	0.000	0.000	0.000
27	A	145	TRP	0	0.012	-0.009	37.028	-0.259	-0.259	0.000	0.000	0.000	0.000
28	A	146	GLU	-1	-0.855	-0.916	37.523	-8.409	-8.409	0.000	0.000	0.000	0.000
29	A	147	ASP	-1	-0.868	-0.941	36.572	-8.655	-8.655	0.000	0.000	0.000	0.000
30	A	148	ARG	1	0.836	0.888	36.077	8.467	8.467	0.000	0.000	0.000	0.000
31	A	149	TYR	0	-0.056	-0.056	30.203	-0.102	-0.102	0.000	0.000	0.000	0.000
32	A	150	TYR	0	0.037	0.006	31.691	-0.555	-0.555	0.000	0.000	0.000	0.000
33	A	151	ARG	1	0.906	0.947	32.225	8.324	8.324	0.000	0.000	0.000	0.000
34	A	152	GLU	-1	-0.860	-0.904	31.885	-9.345	-9.345	0.000	0.000	0.000	0.000
35	A	153	ASN	0	-0.057	-0.030	28.251	-0.690	-0.690	0.000	0.000	0.000	0.000
36	A	154	MET	0	0.030	0.056	27.775	-0.461	-0.461	0.000	0.000	0.000	0.000
37	A	155	ASN	0	-0.049	-0.027	26.497	0.110	0.110	0.000	0.000	0.000	0.000
38	A	156	ARG	1	0.907	0.965	23.502	11.904	11.904	0.000	0.000	0.000	0.000
39	A	157	TYR	0	0.031	0.008	22.914	-0.494	-0.494	0.000	0.000	0.000	0.000
40	A	158	PRO	0	0.009	0.021	21.708	0.019	0.019	0.000	0.000	0.000	0.000
41	A	159	ASN	0	-0.037	-0.036	23.485	0.695	0.695	0.000	0.000	0.000	0.000
42	A	160	GLN	0	-0.020	-0.022	21.602	0.446	0.446	0.000	0.000	0.000	0.000
43	A	161	VAL	0	0.024	-0.002	24.163	-0.142	-0.142	0.000	0.000	0.000	0.000
44	A	162	TYR	0	0.020	0.002	17.640	-0.077	-0.077	0.000	0.000	0.000	0.000
45	A	163	TYR	0	-0.024	-0.059	22.528	0.212	0.212	0.000	0.000	0.000	0.000
46	A	164	ARG	1	0.868	0.940	23.355	11.359	11.359	0.000	0.000	0.000	0.000
47	A	165	PRO	0	0.042	0.020	24.305	0.296	0.296	0.000	0.000	0.000	0.000
48	A	166	VAL	0	0.063	0.017	27.091	0.124	0.124	0.000	0.000	0.000	0.000
49	A	167	ASP	-1	-0.896	-0.943	30.021	-10.110	-10.110	0.000	0.000	0.000	0.000
50	A	168	GLN	0	-0.059	-0.029	27.082	-0.179	-0.179	0.000	0.000	0.000	0.000
51	A	169	TYR	0	-0.024	-0.016	27.195	-0.429	-0.429	0.000	0.000	0.000	0.000
52	A	170	ASN	0	0.008	0.003	32.252	0.109	0.109	0.000	0.000	0.000	0.000
53	A	171	ASN	0	-0.014	-0.018	34.453	0.264	0.264	0.000	0.000	0.000	0.000
54	A	172	GLN	0	0.049	0.034	33.752	-0.298	-0.298	0.000	0.000	0.000	0.000
55	A	173	ASN	0	0.006	0.003	33.576	-0.304	-0.304	0.000	0.000	0.000	0.000
56	A	174	ASN	0	0.009	-0.004	31.025	-0.014	-0.014	0.000	0.000	0.000	0.000
57	A	175	PHE	0	0.027	0.023	28.585	-0.388	-0.388	0.000	0.000	0.000	0.000
58	A	176	VAL	0	0.021	0.003	28.811	-0.408	-0.408	0.000	0.000	0.000	0.000
59	A	177	HIS	0	0.019	0.024	29.142	-0.564	-0.564	0.000	0.000	0.000	0.000
60	A	178	ASP	-1	-0.855	-0.932	25.117	-12.730	-12.730	0.000	0.000	0.000	0.000
61	A	179	CYS	0	-0.046	-0.002	24.453	-0.644	-0.644	0.000	0.000	0.000	0.000
62	A	180	VAL	0	0.021	0.014	24.791	-0.546	-0.546	0.000	0.000	0.000	0.000
63	A	181	ASN	0	-0.021	-0.010	23.556	-0.496	-0.496	0.000	0.000	0.000	0.000
64	A	182	ILE	0	-0.016	-0.015	18.991	-0.809	-0.809	0.000	0.000	0.000	0.000
65	A	183	THR	0	0.001	-0.006	19.952	-0.963	-0.963	0.000	0.000	0.000	0.000
66	A	184	ILE	0	0.043	0.033	20.828	-0.595	-0.595	0.000	0.000	0.000	0.000
67	A	185	LYS	1	0.922	0.975	17.221	16.436	16.436	0.000	0.000	0.000	0.000
68	A	186	GLN	0	-0.011	-0.032	14.788	-0.121	-0.121	0.000	0.000	0.000	0.000
69	A	187	HIS	0	0.021	0.023	15.587	-1.046	-1.046	0.000	0.000	0.000	0.000
70	A	188	THR	0	0.032	0.006	16.702	-0.690	-0.690	0.000	0.000	0.000	0.000
71	A	189	VAL	0	-0.050	-0.017	15.376	-0.466	-0.466	0.000	0.000	0.000	0.000
72	A	190	THR	0	-0.054	-0.041	12.083	-1.931	-1.931	0.000	0.000	0.000	0.000
73	A	191	THR	0	-0.023	-0.021	12.709	-2.149	-2.149	0.000	0.000	0.000	0.000
74	A	192	THR	0	0.011	0.015	15.105	0.018	0.018	0.000	0.000	0.000	0.000
75	A	193	THR	0	-0.015	-0.026	12.317	0.191	0.191	0.000	0.000	0.000	0.000
76	A	194	LYS	1	0.818	0.900	10.286	25.587	25.587	0.000	0.000	0.000	0.000
77	A	195	GLY	0	-0.014	0.017	14.849	0.539	0.539	0.000	0.000	0.000	0.000
78	A	196	GLU	-1	-0.902	-0.926	18.403	-15.165	-15.165	0.000	0.000	0.000	0.000
79	A	197	ASN	0	-0.041	-0.034	20.258	0.062	0.062	0.000	0.000	0.000	0.000
80	A	198	PHE	0	0.005	0.008	20.921	0.241	0.241	0.000	0.000	0.000	0.000
81	A	199	THR	0	-0.010	-0.028	25.673	0.181	0.181	0.000	0.000	0.000	0.000
82	A	200	GLU	-1	-0.874	-0.953	29.120	-9.727	-9.727	0.000	0.000	0.000	0.000
83	A	201	THR	0	0.021	0.008	31.315	0.099	0.099	0.000	0.000	0.000	0.000
84	A	202	ASP	-1	-0.772	-0.840	27.331	-11.057	-11.057	0.000	0.000	0.000	0.000
85	A	203	VAL	0	-0.006	-0.003	26.139	-0.185	-0.185	0.000	0.000	0.000	0.000
86	A	204	LYS	1	0.881	0.931	28.399	9.701	9.701	0.000	0.000	0.000	0.000
87	A	205	MET	0	-0.023	0.011	30.453	0.147	0.147	0.000	0.000	0.000	0.000
88	A	206	MET	0	-0.019	-0.007	24.209	-0.158	-0.158	0.000	0.000	0.000	0.000
89	A	207	GLU	-1	-0.859	-0.919	28.165	-10.525	-10.525	0.000	0.000	0.000	0.000
90	A	208	ARG	1	0.930	0.983	29.840	8.715	8.715	0.000	0.000	0.000	0.000
91	A	209	VAL	0	0.010	-0.005	28.947	0.200	0.200	0.000	0.000	0.000	0.000
92	A	210	VAL	0	-0.006	-0.007	25.457	0.017	0.017	0.000	0.000	0.000	0.000
93	A	211	GLU	-1	-0.867	-0.943	28.525	-9.345	-9.345	0.000	0.000	0.000	0.000
94	A	212	GLN	0	-0.047	-0.018	31.613	0.266	0.266	0.000	0.000	0.000	0.000
95	A	213	MET	0	-0.052	-0.016	26.004	0.166	0.166	0.000	0.000	0.000	0.000
96	A	215	VAL	0	0.015	0.019	30.200	0.079	0.079	0.000	0.000	0.000	0.000
97	A	216	THR	0	0.021	0.010	33.746	0.198	0.198	0.000	0.000	0.000	0.000
98	A	217	GLN	0	0.022	0.010	28.629	-0.080	-0.080	0.000	0.000	0.000	0.000
99	A	218	TYR	0	0.033	0.021	31.345	0.074	0.074	0.000	0.000	0.000	0.000
100	A	219	GLN	0	-0.031	-0.017	32.732	0.060	0.060	0.000	0.000	0.000	0.000
101	A	220	LYS	1	0.871	0.950	34.096	9.010	9.010	0.000	0.000	0.000	0.000
102	A	221	GLU	-1	-0.825	-0.901	28.469	-10.861	-10.861	0.000	0.000	0.000	0.000
103	A	222	SER	0	-0.039	-0.037	32.657	-0.033	-0.033	0.000	0.000	0.000	0.000
104	A	223	GLN	0	-0.011	-0.008	34.761	0.019	0.019	0.000	0.000	0.000	0.000
105	A	224	ALA	0	0.006	0.014	33.047	0.120	0.120	0.000	0.000	0.000	0.000
106	A	225	TYR	0	-0.023	-0.014	27.893	-0.206	-0.206	0.000	0.000	0.000	0.000
107	A	226	TYR	0	-0.130	-0.068	33.517	0.090	0.090	0.000	0.000	0.000	0.000
108	A	227	GLU	-1	-0.867	-0.924	37.006	-7.626	-7.626	0.000	0.000	0.000	0.000
109	A	228	GLY	0	-0.004	-0.011	40.378	0.204	0.204	0.000	0.000	0.000	0.000
110	A	229	ARG	1	0.851	0.922	33.100	9.320	9.320	0.000	0.000	0.000	0.000
111	A	230	SER	0	-0.025	-0.002	39.213	0.055	0.055	0.000	0.000	0.000	0.000
112	A	231	SER	-1	-0.861	-0.905	35.488	-8.626	-8.626	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:119:GLY)