FMO DATABASE

FMODB ID: 4G4LN

Calculation Name: 1YS5-A-Other549

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1YS5

Chain ID: A

ChEMBL ID:

UniProt ID: Q6VRZ6

Base Structure: SolutionNMR

Registration Date: 2025-10-11

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	OptH
Protonation	MOE:Protonate 3D
Complement	ac.sh, 23 2024 Oct
Water	No
Procedure	Manual calculation
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	156
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1263375.62238
FMO2-HF: Nuclear repulsion	1205845.666851
FMO2-HF: Total energy	-57529.95553
FMO2-MP2: Total energy	-57699.907254

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.
-27.855	-25.421	7.047	-4.243	-5.238	-0.05

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 : 0.838 / 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	SER	0	0.009	0.001	1.954	-22.497	-20.246	7.046	-4.186	-5.111	-0.050
4	A	4	HIS	0	0.017	0.017	4.150	-2.366	-2.183	0.001	-0.057	-0.127	0.000
5	A	5	SER	0	0.023	-0.007	7.289	2.616	2.616	0.000	0.000	0.000	0.000
6	A	6	ALA	0	-0.007	0.006	10.759	-0.419	-0.419	0.000	0.000	0.000	0.000
7	A	7	LEU	0	0.000	0.001	14.096	0.683	0.683	0.000	0.000	0.000	0.000
8	A	8	THR	0	-0.016	-0.011	17.567	0.054	0.054	0.000	0.000	0.000	0.000
9	A	9	ALA	0	0.005	-0.001	20.896	0.181	0.181	0.000	0.000	0.000	0.000
10	A	10	PHE	0	0.007	0.008	24.650	-0.042	-0.042	0.000	0.000	0.000	0.000
11	A	11	GLN	0	-0.029	-0.012	27.941	-0.029	-0.029	0.000	0.000	0.000	0.000
12	A	12	THR	0	0.017	-0.003	31.686	0.026	0.026	0.000	0.000	0.000	0.000
13	A	13	GLU	-1	-0.758	-0.890	34.982	-7.863	-7.863	0.000	0.000	0.000	0.000
14	A	14	GLN	0	-0.077	-0.028	34.468	-0.029	-0.029	0.000	0.000	0.000	0.000
15	A	15	ILE	0	-0.049	-0.025	32.307	0.018	0.018	0.000	0.000	0.000	0.000
16	A	16	GLN	0	0.024	-0.012	35.555	0.146	0.146	0.000	0.000	0.000	0.000
17	A	17	ASP	-1	-0.874	-0.928	36.730	-8.661	-8.661	0.000	0.000	0.000	0.000
18	A	18	SER	0	-0.024	-0.024	33.723	-0.104	-0.104	0.000	0.000	0.000	0.000
19	A	19	GLU	-1	-0.790	-0.854	35.827	-7.838	-7.838	0.000	0.000	0.000	0.000
20	A	20	HIS	0	-0.074	-0.042	38.702	0.335	0.335	0.000	0.000	0.000	0.000
21	A	21	SER	0	-0.062	-0.031	35.626	0.079	0.079	0.000	0.000	0.000	0.000
22	A	22	GLY	0	-0.012	-0.006	36.976	0.007	0.007	0.000	0.000	0.000	0.000
23	A	23	LYS	1	0.816	0.905	37.814	7.713	7.713	0.000	0.000	0.000	0.000
24	A	24	MET	0	-0.040	0.005	41.542	0.011	0.011	0.000	0.000	0.000	0.000
25	A	25	VAL	0	-0.004	-0.013	43.617	-0.102	-0.102	0.000	0.000	0.000	0.000
26	A	26	ALA	0	0.024	0.016	44.404	0.179	0.179	0.000	0.000	0.000	0.000
27	A	27	LYS	1	0.800	0.888	39.293	7.810	7.810	0.000	0.000	0.000	0.000
28	A	28	ARG	1	0.931	0.971	40.809	7.705	7.705	0.000	0.000	0.000	0.000
29	A	29	GLN	0	0.090	0.049	35.694	0.183	0.183	0.000	0.000	0.000	0.000
30	A	30	PHE	0	-0.031	-0.027	36.327	0.072	0.072	0.000	0.000	0.000	0.000
31	A	31	ARG	1	0.907	0.931	38.990	7.519	7.519	0.000	0.000	0.000	0.000
32	A	32	ILE	0	0.000	0.023	33.540	0.009	0.009	0.000	0.000	0.000	0.000
33	A	33	GLY	0	0.038	0.018	37.618	0.085	0.085	0.000	0.000	0.000	0.000
34	A	34	ASP	-1	-0.756	-0.864	37.109	-8.623	-8.623	0.000	0.000	0.000	0.000
35	A	35	ILE	0	-0.065	-0.032	38.182	-0.043	-0.043	0.000	0.000	0.000	0.000
36	A	36	ALA	0	-0.005	-0.002	38.228	0.085	0.085	0.000	0.000	0.000	0.000
37	A	37	GLY	0	0.113	0.032	40.048	0.149	0.149	0.000	0.000	0.000	0.000
38	A	38	GLU	-1	-0.900	-0.945	41.476	-7.358	-7.358	0.000	0.000	0.000	0.000
39	A	39	HIS	0	-0.030	-0.034	43.696	0.230	0.230	0.000	0.000	0.000	0.000
40	A	40	THR	0	-0.036	-0.017	43.885	0.138	0.138	0.000	0.000	0.000	0.000
41	A	41	SER	0	0.103	0.049	42.549	-0.011	-0.011	0.000	0.000	0.000	0.000
42	A	42	PHE	0	-0.030	-0.009	44.662	0.156	0.156	0.000	0.000	0.000	0.000
43	A	43	ASP	-1	-0.842	-0.918	47.336	-6.354	-6.354	0.000	0.000	0.000	0.000
44	A	44	LYS	1	0.851	0.925	48.396	6.244	6.244	0.000	0.000	0.000	0.000
45	A	45	LEU	0	-0.008	0.010	44.806	0.081	0.081	0.000	0.000	0.000	0.000
46	A	46	PRO	0	-0.001	0.013	42.926	-0.070	-0.070	0.000	0.000	0.000	0.000
47	A	47	GLU	-1	-0.861	-0.945	36.999	-8.603	-8.603	0.000	0.000	0.000	0.000
48	A	48	GLY	0	0.007	0.017	38.040	-0.227	-0.227	0.000	0.000	0.000	0.000
49	A	49	GLY	0	0.027	0.013	39.083	-0.041	-0.041	0.000	0.000	0.000	0.000
50	A	50	ARG	1	0.936	0.962	37.788	8.293	8.293	0.000	0.000	0.000	0.000
51	A	51	ALA	0	0.047	0.043	42.566	0.126	0.126	0.000	0.000	0.000	0.000
52	A	52	THR	0	-0.057	-0.044	46.032	-0.003	-0.003	0.000	0.000	0.000	0.000
53	A	53	TYR	0	0.085	0.034	48.382	0.157	0.157	0.000	0.000	0.000	0.000
54	A	54	ARG	1	0.926	0.970	50.261	5.954	5.954	0.000	0.000	0.000	0.000
55	A	55	GLY	0	0.052	0.011	52.942	0.100	0.100	0.000	0.000	0.000	0.000
56	A	56	THR	0	-0.077	-0.023	54.771	-0.055	-0.055	0.000	0.000	0.000	0.000
57	A	57	ALA	0	0.024	0.009	54.248	0.027	0.027	0.000	0.000	0.000	0.000
58	A	58	PHE	0	0.026	0.035	56.375	-0.027	-0.027	0.000	0.000	0.000	0.000
59	A	59	GLY	0	0.045	0.003	59.324	-0.035	-0.035	0.000	0.000	0.000	0.000
60	A	60	SER	0	-0.052	-0.029	60.099	0.095	0.095	0.000	0.000	0.000	0.000
61	A	61	ASP	-1	-0.968	-0.991	62.139	-5.034	-5.034	0.000	0.000	0.000	0.000
62	A	62	ASP	-1	-0.850	-0.928	61.009	-5.279	-5.279	0.000	0.000	0.000	0.000
63	A	63	ALA	0	-0.028	0.004	59.145	-0.011	-0.011	0.000	0.000	0.000	0.000
64	A	64	GLY	0	0.023	0.003	57.612	-0.093	-0.093	0.000	0.000	0.000	0.000
65	A	65	GLY	0	-0.008	-0.018	54.223	-0.051	-0.051	0.000	0.000	0.000	0.000
66	A	66	LYS	1	0.836	0.918	52.785	6.108	6.108	0.000	0.000	0.000	0.000
67	A	67	LEU	0	0.010	0.011	49.311	-0.092	-0.092	0.000	0.000	0.000	0.000
68	A	68	THR	0	-0.045	-0.034	46.749	0.087	0.087	0.000	0.000	0.000	0.000
69	A	69	TYR	0	-0.029	-0.004	46.605	-0.018	-0.018	0.000	0.000	0.000	0.000
70	A	70	THR	0	-0.076	-0.050	41.441	-0.146	-0.146	0.000	0.000	0.000	0.000
71	A	71	ILE	0	0.025	0.035	42.664	-0.004	-0.004	0.000	0.000	0.000	0.000
72	A	72	ASP	-1	-0.877	-0.933	38.349	-8.321	-8.321	0.000	0.000	0.000	0.000
73	A	73	PHE	0	-0.049	-0.061	40.764	0.120	0.120	0.000	0.000	0.000	0.000
74	A	74	ALA	0	-0.012	-0.002	37.240	0.074	0.074	0.000	0.000	0.000	0.000
75	A	75	ALA	0	0.023	0.023	38.499	-0.106	-0.106	0.000	0.000	0.000	0.000
76	A	76	LYS	1	0.793	0.921	40.473	7.058	7.058	0.000	0.000	0.000	0.000
77	A	77	GLN	0	0.076	0.024	38.437	0.247	0.247	0.000	0.000	0.000	0.000
78	A	78	GLY	0	-0.005	-0.018	42.410	0.000	0.000	0.000	0.000	0.000	0.000
79	A	79	ASN	0	0.010	0.000	42.668	-0.023	-0.023	0.000	0.000	0.000	0.000
80	A	80	GLY	0	0.088	0.013	45.304	0.019	0.019	0.000	0.000	0.000	0.000
81	A	81	LYS	1	0.803	0.911	41.686	7.629	7.629	0.000	0.000	0.000	0.000
82	A	82	ILE	0	-0.015	0.020	46.840	0.124	0.124	0.000	0.000	0.000	0.000
83	A	83	GLU	-1	-0.920	-0.975	46.102	-7.029	-7.029	0.000	0.000	0.000	0.000
84	A	84	HIS	0	-0.022	-0.029	49.993	0.091	0.091	0.000	0.000	0.000	0.000
85	A	85	LEU	0	0.048	0.039	53.347	0.127	0.127	0.000	0.000	0.000	0.000
86	A	86	LYS	1	0.925	0.962	55.108	5.343	5.343	0.000	0.000	0.000	0.000
87	A	87	SER	0	0.008	0.007	55.466	0.095	0.095	0.000	0.000	0.000	0.000
88	A	88	PRO	0	0.044	0.035	49.937	-0.038	-0.038	0.000	0.000	0.000	0.000
89	A	89	GLU	-1	-0.863	-0.951	50.273	-6.102	-6.102	0.000	0.000	0.000	0.000
90	A	90	LEU	0	-0.064	-0.047	51.463	-0.023	-0.023	0.000	0.000	0.000	0.000
91	A	91	ASN	0	0.007	0.013	48.726	0.147	0.147	0.000	0.000	0.000	0.000
92	A	92	VAL	0	-0.008	-0.004	48.661	-0.078	-0.078	0.000	0.000	0.000	0.000
93	A	93	ASP	-1	-0.798	-0.887	42.739	-7.529	-7.529	0.000	0.000	0.000	0.000
94	A	94	LEU	0	-0.062	-0.029	44.561	0.035	0.035	0.000	0.000	0.000	0.000
95	A	95	ALA	0	0.004	0.007	40.471	-0.146	-0.146	0.000	0.000	0.000	0.000
96	A	96	ALA	0	-0.024	-0.014	37.806	0.132	0.132	0.000	0.000	0.000	0.000
97	A	97	ALA	0	-0.045	-0.026	39.300	-0.135	-0.135	0.000	0.000	0.000	0.000
98	A	98	ASP	-1	-0.856	-0.937	38.503	-8.117	-8.117	0.000	0.000	0.000	0.000
99	A	99	ILE	0	-0.111	-0.045	41.054	0.156	0.156	0.000	0.000	0.000	0.000
100	A	100	LYS	1	0.940	0.970	42.040	7.065	7.065	0.000	0.000	0.000	0.000
101	A	101	PRO	0	-0.069	-0.022	43.280	0.196	0.196	0.000	0.000	0.000	0.000
102	A	102	ASP	-1	-0.791	-0.884	46.379	-6.553	-6.553	0.000	0.000	0.000	0.000
103	A	103	GLY	0	-0.002	0.001	49.026	0.085	0.085	0.000	0.000	0.000	0.000
104	A	104	LYS	1	0.852	0.906	50.987	5.845	5.845	0.000	0.000	0.000	0.000
105	A	105	ARG	1	0.855	0.924	49.423	5.912	5.912	0.000	0.000	0.000	0.000
106	A	106	HIS	0	0.035	0.022	46.357	0.036	0.036	0.000	0.000	0.000	0.000
107	A	107	ALA	0	-0.017	-0.015	50.149	-0.036	-0.036	0.000	0.000	0.000	0.000
108	A	108	VAL	0	-0.029	-0.014	50.461	0.109	0.109	0.000	0.000	0.000	0.000
109	A	109	ILE	0	0.019	0.043	45.072	-0.104	-0.104	0.000	0.000	0.000	0.000
110	A	110	SER	0	-0.030	-0.025	45.877	0.119	0.119	0.000	0.000	0.000	0.000
111	A	111	GLY	0	0.026	0.017	44.688	-0.164	-0.164	0.000	0.000	0.000	0.000
112	A	112	SER	0	0.015	0.009	43.244	0.222	0.222	0.000	0.000	0.000	0.000
113	A	113	VAL	0	-0.017	-0.008	44.633	-0.078	-0.078	0.000	0.000	0.000	0.000
114	A	114	LEU	0	-0.014	-0.005	42.412	0.055	0.055	0.000	0.000	0.000	0.000
115	A	115	TYR	0	0.011	0.022	46.321	0.045	0.045	0.000	0.000	0.000	0.000
116	A	116	ASN	0	-0.021	-0.005	46.250	-0.055	-0.055	0.000	0.000	0.000	0.000
117	A	117	GLN	0	0.026	0.013	44.246	-0.206	-0.206	0.000	0.000	0.000	0.000
118	A	118	ALA	0	-0.026	-0.018	44.822	-0.094	-0.094	0.000	0.000	0.000	0.000
119	A	119	GLU	-1	-0.895	-0.943	42.216	-7.537	-7.537	0.000	0.000	0.000	0.000
120	A	120	LYS	1	0.857	0.924	45.965	6.620	6.620	0.000	0.000	0.000	0.000
121	A	121	GLY	0	0.042	0.006	48.551	0.196	0.196	0.000	0.000	0.000	0.000
122	A	122	SER	0	0.008	-0.012	48.369	-0.196	-0.196	0.000	0.000	0.000	0.000
123	A	123	TYR	0	0.005	-0.007	48.898	0.176	0.176	0.000	0.000	0.000	0.000
124	A	124	SER	0	-0.013	-0.008	49.790	-0.065	-0.065	0.000	0.000	0.000	0.000
125	A	125	LEU	0	-0.029	0.005	48.803	0.160	0.160	0.000	0.000	0.000	0.000
126	A	126	GLY	0	0.093	0.036	50.287	-0.107	-0.107	0.000	0.000	0.000	0.000
127	A	127	ILE	0	-0.059	-0.028	49.861	-0.038	-0.038	0.000	0.000	0.000	0.000
128	A	128	PHE	0	0.018	0.003	52.615	0.032	0.032	0.000	0.000	0.000	0.000
129	A	129	GLY	0	0.065	0.021	54.660	-0.062	-0.062	0.000	0.000	0.000	0.000
130	A	130	GLY	0	-0.072	-0.023	52.879	0.013	0.013	0.000	0.000	0.000	0.000
131	A	131	LYS	1	0.880	0.938	50.375	5.920	5.920	0.000	0.000	0.000	0.000
132	A	132	ALA	0	0.026	0.027	50.134	-0.083	-0.083	0.000	0.000	0.000	0.000
133	A	133	GLN	0	-0.108	-0.071	52.071	0.111	0.111	0.000	0.000	0.000	0.000
134	A	134	GLU	-1	-0.824	-0.926	55.597	-5.543	-5.543	0.000	0.000	0.000	0.000
135	A	135	VAL	0	-0.059	-0.020	51.232	-0.026	-0.026	0.000	0.000	0.000	0.000
136	A	136	ALA	0	0.020	0.005	53.965	-0.013	-0.013	0.000	0.000	0.000	0.000
137	A	137	GLY	0	0.030	0.006	54.519	-0.113	-0.113	0.000	0.000	0.000	0.000
138	A	138	SER	0	-0.041	-0.010	54.618	0.154	0.154	0.000	0.000	0.000	0.000
139	A	139	ALA	0	0.009	0.011	52.683	-0.153	-0.153	0.000	0.000	0.000	0.000
140	A	140	GLU	-1	-0.746	-0.830	53.563	-5.853	-5.853	0.000	0.000	0.000	0.000
141	A	141	VAL	0	0.004	0.013	51.589	-0.053	-0.053	0.000	0.000	0.000	0.000
142	A	142	LYS	1	0.831	0.899	52.508	6.205	6.205	0.000	0.000	0.000	0.000
143	A	143	THR	0	-0.017	-0.025	52.657	-0.146	-0.146	0.000	0.000	0.000	0.000
144	A	144	VAL	0	0.026	0.018	55.051	0.083	0.083	0.000	0.000	0.000	0.000
145	A	145	ASN	0	0.001	0.006	53.065	0.098	0.098	0.000	0.000	0.000	0.000
146	A	146	GLY	0	0.026	0.006	55.696	-0.078	-0.078	0.000	0.000	0.000	0.000
147	A	147	ILE	0	-0.016	0.005	56.353	0.077	0.077	0.000	0.000	0.000	0.000
148	A	148	ARG	1	0.787	0.861	56.706	5.639	5.639	0.000	0.000	0.000	0.000
149	A	149	HIS	0	0.015	0.008	57.238	-0.077	-0.077	0.000	0.000	0.000	0.000
150	A	150	ILE	0	0.012	0.022	54.624	0.061	0.061	0.000	0.000	0.000	0.000
151	A	151	GLY	0	0.019	0.011	57.993	-0.035	-0.035	0.000	0.000	0.000	0.000
152	A	152	LEU	0	-0.071	-0.022	53.323	-0.029	-0.029	0.000	0.000	0.000	0.000
153	A	153	ALA	0	0.013	0.007	57.231	0.038	0.038	0.000	0.000	0.000	0.000
154	A	154	ALA	0	0.001	-0.018	54.614	-0.058	-0.058	0.000	0.000	0.000	0.000
155	A	155	LYS	1	0.931	0.967	56.184	5.350	5.350	0.000	0.000	0.000	0.000
156	A	156	GLN	-1	-0.844	-0.896	51.209	-6.005	-6.005	0.000	0.000	0.000	0.000

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