FMO DATABASE

FMODB ID: R4J58

Calculation Name: 1YB3-A-Xray549

Preferred Name:

Target Type:

Ligand Name: unknown atom or ion

Ligand 3-letter code: UNX

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1YB3

Chain ID: A

ChEMBL ID:

UniProt ID: Q8U4C0

Base Structure: X-ray

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	166
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1857933.601792
FMO2-HF: Nuclear repulsion	1789427.708842
FMO2-HF: Total energy	-68505.89295
FMO2-MP2: Total energy	-68709.366504

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:MET)

Summations of interaction energy for fragment #1(A:2: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.
-247.207	-243.152	21.231	-13.713	-11.574	-0.161

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.764 / q_NPA : 0.864

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	LYS	1	0.928	0.979	3.577	41.536	43.382	-0.004	-0.753	-1.089	-0.001
4	A	5	GLU	-1	-0.688	-0.837	1.748	-134.888	-133.848	20.323	-12.496	-8.868	-0.157
5	A	6	VAL	0	0.009	0.008	2.396	6.440	7.609	0.912	-0.464	-1.617	-0.003
6	A	7	HIS	0	0.018	0.009	5.643	5.877	5.877	0.000	0.000	0.000	0.000
7	A	8	GLU	-1	-0.916	-0.969	7.749	-32.074	-32.074	0.000	0.000	0.000	0.000
8	A	9	LEU	0	-0.011	-0.013	6.843	3.072	3.072	0.000	0.000	0.000	0.000
9	A	10	LEU	0	-0.007	0.006	7.866	2.379	2.379	0.000	0.000	0.000	0.000
10	A	11	ASN	0	-0.033	-0.029	10.700	3.523	3.523	0.000	0.000	0.000	0.000
11	A	12	ARG	1	0.864	0.963	11.712	24.448	24.448	0.000	0.000	0.000	0.000
12	A	13	ILE	0	-0.019	-0.003	10.384	1.012	1.012	0.000	0.000	0.000	0.000
13	A	14	TRP	0	-0.034	-0.028	12.028	0.232	0.232	0.000	0.000	0.000	0.000
14	A	15	GLY	0	-0.028	-0.006	16.707	1.010	1.010	0.000	0.000	0.000	0.000
15	A	16	ASP	-1	-0.829	-0.934	17.896	-16.529	-16.529	0.000	0.000	0.000	0.000
16	A	17	ILE	0	-0.007	0.008	18.993	0.785	0.785	0.000	0.000	0.000	0.000
17	A	18	PHE	0	-0.037	-0.033	19.507	0.633	0.633	0.000	0.000	0.000	0.000
18	A	19	GLU	-1	-0.871	-0.903	22.440	-13.500	-13.500	0.000	0.000	0.000	0.000
19	A	20	LEU	0	0.034	0.014	23.191	0.616	0.616	0.000	0.000	0.000	0.000
20	A	21	ARG	1	0.739	0.847	24.895	10.879	10.879	0.000	0.000	0.000	0.000
21	A	22	GLU	-1	-0.855	-0.929	26.748	-9.977	-9.977	0.000	0.000	0.000	0.000
22	A	23	GLU	-1	-0.856	-0.925	26.710	-11.408	-11.408	0.000	0.000	0.000	0.000
23	A	24	LEU	0	0.027	0.003	27.202	0.467	0.467	0.000	0.000	0.000	0.000
24	A	25	LYS	1	0.901	0.973	30.543	9.374	9.374	0.000	0.000	0.000	0.000
25	A	26	GLU	-1	-0.981	-0.980	32.612	-9.140	-9.140	0.000	0.000	0.000	0.000
26	A	27	GLU	-1	-0.882	-0.933	31.376	-9.834	-9.834	0.000	0.000	0.000	0.000
27	A	28	LEU	0	-0.020	0.005	31.046	0.313	0.313	0.000	0.000	0.000	0.000
28	A	29	LYS	1	0.849	0.893	35.244	8.454	8.454	0.000	0.000	0.000	0.000
29	A	30	GLY	0	-0.041	-0.021	38.749	0.102	0.102	0.000	0.000	0.000	0.000
30	A	31	PHE	0	0.004	0.015	35.478	0.115	0.115	0.000	0.000	0.000	0.000
31	A	32	THR	0	-0.080	-0.035	35.549	0.031	0.031	0.000	0.000	0.000	0.000
32	A	33	VAL	0	-0.011	0.013	30.178	-0.066	-0.066	0.000	0.000	0.000	0.000
33	A	34	GLU	-1	-0.847	-0.920	30.431	-8.681	-8.681	0.000	0.000	0.000	0.000
34	A	35	GLU	-1	-0.870	-0.930	28.659	-10.248	-10.248	0.000	0.000	0.000	0.000
35	A	36	VAL	0	-0.024	-0.005	22.048	-0.047	-0.047	0.000	0.000	0.000	0.000
36	A	37	SER	0	-0.089	-0.032	23.920	0.254	0.254	0.000	0.000	0.000	0.000
37	A	38	GLU	-1	-0.809	-0.913	18.266	-15.543	-15.543	0.000	0.000	0.000	0.000
38	A	39	VAL	0	0.024	0.010	19.963	0.486	0.486	0.000	0.000	0.000	0.000
39	A	40	PHE	0	-0.034	-0.029	18.111	-0.797	-0.797	0.000	0.000	0.000	0.000
40	A	41	ASN	0	-0.048	-0.034	18.264	0.074	0.074	0.000	0.000	0.000	0.000
41	A	42	ALA	0	0.067	0.056	19.252	0.382	0.382	0.000	0.000	0.000	0.000
42	A	43	TYR	0	-0.005	-0.017	17.825	-0.771	-0.771	0.000	0.000	0.000	0.000
43	A	44	LEU	0	0.004	0.006	12.567	0.110	0.110	0.000	0.000	0.000	0.000
44	A	45	TYR	0	0.003	0.002	16.682	0.064	0.064	0.000	0.000	0.000	0.000
45	A	46	ILE	0	-0.015	-0.012	10.878	-0.738	-0.738	0.000	0.000	0.000	0.000
46	A	47	ASP	-1	-0.925	-0.961	12.243	-18.149	-18.149	0.000	0.000	0.000	0.000
47	A	48	GLY	0	0.017	0.017	15.613	0.410	0.410	0.000	0.000	0.000	0.000
48	A	49	LYS	1	0.749	0.857	16.389	15.277	15.277	0.000	0.000	0.000	0.000
49	A	50	TRP	0	0.042	0.043	17.342	-0.729	-0.729	0.000	0.000	0.000	0.000
50	A	51	GLU	-1	-0.844	-0.905	13.586	-15.397	-15.397	0.000	0.000	0.000	0.000
51	A	52	GLU	-1	-0.789	-0.877	16.160	-13.056	-13.056	0.000	0.000	0.000	0.000
52	A	53	MET	0	-0.036	-0.008	13.598	-1.407	-1.407	0.000	0.000	0.000	0.000
53	A	54	LYS	1	0.806	0.884	14.458	14.093	14.093	0.000	0.000	0.000	0.000
54	A	55	TYR	0	-0.061	-0.022	10.699	-0.258	-0.258	0.000	0.000	0.000	0.000
55	A	56	PRO	0	-0.026	-0.005	14.149	0.323	0.323	0.000	0.000	0.000	0.000
56	A	57	HIS	0	-0.003	0.001	14.582	-1.023	-1.023	0.000	0.000	0.000	0.000
57	A	58	PRO	0	0.024	0.038	16.249	0.804	0.804	0.000	0.000	0.000	0.000
58	A	59	ALA	0	0.045	0.001	19.227	-0.215	-0.215	0.000	0.000	0.000	0.000
59	A	60	PHE	0	0.009	-0.004	22.467	0.179	0.179	0.000	0.000	0.000	0.000
60	A	61	ALA	0	0.068	0.056	26.155	0.067	0.067	0.000	0.000	0.000	0.000
61	A	62	VAL	0	-0.031	-0.030	29.277	0.119	0.119	0.000	0.000	0.000	0.000
62	A	63	LYS	1	0.822	0.923	31.820	8.603	8.603	0.000	0.000	0.000	0.000
63	A	64	PRO	0	0.004	-0.021	35.123	0.071	0.071	0.000	0.000	0.000	0.000
64	A	65	GLY	0	0.069	0.006	33.829	-0.050	-0.050	0.000	0.000	0.000	0.000
65	A	66	GLY	0	0.038	0.038	30.564	-0.121	-0.121	0.000	0.000	0.000	0.000
66	A	67	GLU	-1	-0.900	-0.963	25.670	-10.697	-10.697	0.000	0.000	0.000	0.000
67	A	68	VAL	0	-0.011	-0.007	23.859	-0.065	-0.065	0.000	0.000	0.000	0.000
68	A	69	GLY	0	0.055	0.033	21.032	0.041	0.041	0.000	0.000	0.000	0.000
69	A	70	ALA	0	-0.026	-0.007	16.334	-0.096	-0.096	0.000	0.000	0.000	0.000
70	A	71	THR	0	0.049	0.028	14.026	-0.641	-0.641	0.000	0.000	0.000	0.000
71	A	72	PRO	0	-0.029	-0.042	8.628	-0.469	-0.469	0.000	0.000	0.000	0.000
72	A	73	GLN	0	-0.035	-0.022	10.572	-0.870	-0.870	0.000	0.000	0.000	0.000
73	A	74	GLY	0	-0.030	-0.024	12.760	0.140	0.140	0.000	0.000	0.000	0.000
74	A	75	PHE	0	0.001	-0.008	15.329	0.132	0.132	0.000	0.000	0.000	0.000
75	A	76	TYR	0	-0.025	-0.018	18.738	0.107	0.107	0.000	0.000	0.000	0.000
76	A	77	PHE	0	-0.009	-0.003	21.335	0.080	0.080	0.000	0.000	0.000	0.000
77	A	78	VAL	0	0.028	0.012	24.974	-0.020	-0.020	0.000	0.000	0.000	0.000
78	A	79	PHE	0	-0.005	0.004	27.079	0.086	0.086	0.000	0.000	0.000	0.000
79	A	80	ALA	0	0.007	0.014	30.834	0.028	0.028	0.000	0.000	0.000	0.000
80	A	81	PHE	0	-0.014	-0.022	32.780	0.120	0.120	0.000	0.000	0.000	0.000
81	A	82	PRO	0	0.041	0.015	36.451	-0.092	-0.092	0.000	0.000	0.000	0.000
82	A	83	LYS	1	0.871	0.949	39.231	7.293	7.293	0.000	0.000	0.000	0.000
83	A	84	GLU	-1	-0.891	-0.925	40.142	-6.906	-6.906	0.000	0.000	0.000	0.000
84	A	85	GLU	-1	-0.958	-0.980	41.065	-7.049	-7.049	0.000	0.000	0.000	0.000
85	A	86	LEU	0	-0.028	0.008	36.865	-0.045	-0.045	0.000	0.000	0.000	0.000
86	A	87	SER	0	-0.009	-0.017	40.747	0.174	0.174	0.000	0.000	0.000	0.000
87	A	88	LYS	1	0.888	0.936	40.524	6.609	6.609	0.000	0.000	0.000	0.000
88	A	89	GLU	-1	-0.943	-0.968	40.410	-6.896	-6.896	0.000	0.000	0.000	0.000
89	A	90	PHE	0	0.030	0.023	35.125	-0.125	-0.125	0.000	0.000	0.000	0.000
90	A	91	ILE	0	0.017	0.009	35.406	-0.242	-0.242	0.000	0.000	0.000	0.000
91	A	92	GLU	-1	-0.880	-0.955	35.656	-7.351	-7.351	0.000	0.000	0.000	0.000
92	A	93	ASP	-1	-0.793	-0.874	36.605	-7.600	-7.600	0.000	0.000	0.000	0.000
93	A	94	VAL	0	0.007	-0.001	31.622	-0.193	-0.193	0.000	0.000	0.000	0.000
94	A	95	ILE	0	-0.020	-0.010	31.906	-0.252	-0.252	0.000	0.000	0.000	0.000
95	A	96	ARG	1	0.733	0.856	32.441	7.407	7.407	0.000	0.000	0.000	0.000
96	A	97	ALA	0	-0.046	0.008	33.319	-0.023	-0.023	0.000	0.000	0.000	0.000
97	A	98	PHE	0	0.012	-0.006	28.008	-0.115	-0.115	0.000	0.000	0.000	0.000
98	A	99	GLU	-1	-0.894	-0.942	23.241	-12.170	-12.170	0.000	0.000	0.000	0.000
99	A	100	LYS	1	0.906	0.964	18.555	14.319	14.319	0.000	0.000	0.000	0.000
100	A	101	LEU	0	-0.024	-0.002	23.639	-0.196	-0.196	0.000	0.000	0.000	0.000
101	A	102	PHE	0	-0.012	-0.018	20.398	-0.077	-0.077	0.000	0.000	0.000	0.000
102	A	103	ILE	0	-0.014	-0.008	26.165	0.179	0.179	0.000	0.000	0.000	0.000
103	A	104	TYR	0	-0.059	-0.051	24.263	0.061	0.061	0.000	0.000	0.000	0.000
104	A	105	GLY	0	0.055	0.027	29.419	0.185	0.185	0.000	0.000	0.000	0.000
105	A	106	ALA	0	-0.016	0.000	29.995	-0.218	-0.218	0.000	0.000	0.000	0.000
106	A	107	GLU	-1	-0.918	-0.961	26.079	-10.680	-10.680	0.000	0.000	0.000	0.000
107	A	108	ASN	0	-0.027	-0.027	20.911	0.160	0.160	0.000	0.000	0.000	0.000
108	A	109	PHE	0	-0.047	-0.036	21.964	-0.009	-0.009	0.000	0.000	0.000	0.000
109	A	110	LEU	0	-0.088	-0.029	23.709	0.047	0.047	0.000	0.000	0.000	0.000
110	A	111	GLU	-1	-0.849	-0.923	27.429	-9.089	-9.089	0.000	0.000	0.000	0.000
111	A	112	ASP	-1	-0.843	-0.934	26.194	-10.392	-10.392	0.000	0.000	0.000	0.000
112	A	113	PHE	0	0.007	-0.008	28.362	0.237	0.237	0.000	0.000	0.000	0.000
113	A	114	TYR	0	-0.015	-0.034	28.151	0.161	0.161	0.000	0.000	0.000	0.000
114	A	115	ASN	0	0.052	0.032	22.333	-0.289	-0.289	0.000	0.000	0.000	0.000
115	A	116	PHE	0	0.033	0.015	20.247	0.161	0.161	0.000	0.000	0.000	0.000
116	A	117	GLU	-1	-0.933	-0.957	19.321	-13.575	-13.575	0.000	0.000	0.000	0.000
117	A	118	HIS	1	0.762	0.886	24.053	10.896	10.896	0.000	0.000	0.000	0.000
118	A	119	PRO	0	-0.012	0.024	27.089	0.240	0.240	0.000	0.000	0.000	0.000
119	A	120	ILE	0	-0.006	0.005	29.780	0.169	0.169	0.000	0.000	0.000	0.000
120	A	121	SER	0	-0.026	-0.020	33.286	0.036	0.036	0.000	0.000	0.000	0.000
121	A	122	GLY	0	0.078	0.017	36.302	-0.023	-0.023	0.000	0.000	0.000	0.000
122	A	123	ASP	-1	-0.883	-0.927	37.216	-6.805	-6.805	0.000	0.000	0.000	0.000
123	A	124	GLU	-1	-0.851	-0.931	35.878	-7.953	-7.953	0.000	0.000	0.000	0.000
124	A	125	VAL	0	-0.014	-0.008	33.337	-0.034	-0.034	0.000	0.000	0.000	0.000
125	A	126	TRP	0	0.002	0.001	35.964	-0.023	-0.023	0.000	0.000	0.000	0.000
126	A	127	ASP	-1	-0.892	-0.946	39.037	-6.836	-6.836	0.000	0.000	0.000	0.000
127	A	128	ARG	1	0.775	0.882	31.086	8.759	8.759	0.000	0.000	0.000	0.000
128	A	129	ILE	0	0.037	0.036	34.759	-0.013	-0.013	0.000	0.000	0.000	0.000
129	A	130	VAL	0	-0.027	-0.004	37.710	0.091	0.091	0.000	0.000	0.000	0.000
130	A	131	ASN	0	-0.109	-0.057	40.604	0.230	0.230	0.000	0.000	0.000	0.000
131	A	132	SER	0	-0.052	-0.025	36.838	-0.061	-0.061	0.000	0.000	0.000	0.000
132	A	133	ASP	-1	-0.967	-0.997	37.232	-7.564	-7.564	0.000	0.000	0.000	0.000
133	A	134	GLU	-1	-0.835	-0.911	33.718	-8.457	-8.457	0.000	0.000	0.000	0.000
134	A	135	GLU	0	-0.103	-0.088	36.820	0.188	0.188	0.000	0.000	0.000	0.000
135	A	136	MET	0	-0.050	-0.017	34.419	0.173	0.173	0.000	0.000	0.000	0.000
136	A	137	ILE	0	-0.002	0.001	33.125	-0.143	-0.143	0.000	0.000	0.000	0.000
137	A	138	ASN	0	-0.012	-0.013	28.403	0.002	0.002	0.000	0.000	0.000	0.000
138	A	139	PHE	0	-0.011	-0.015	29.534	0.056	0.056	0.000	0.000	0.000	0.000
139	A	140	GLU	-1	-0.792	-0.846	21.542	-12.460	-12.460	0.000	0.000	0.000	0.000
140	A	141	VAL	0	-0.009	-0.005	24.521	0.080	0.080	0.000	0.000	0.000	0.000
141	A	142	ASP	0	-0.056	-0.065	18.953	-0.329	-0.329	0.000	0.000	0.000	0.000
142	A	143	LEU	0	0.014	-0.012	20.110	0.147	0.147	0.000	0.000	0.000	0.000
143	A	144	GLY	0	-0.009	0.021	16.350	-0.206	-0.206	0.000	0.000	0.000	0.000
144	A	145	PHE	0	-0.018	-0.027	12.356	-0.380	-0.380	0.000	0.000	0.000	0.000
145	A	146	ASP	-1	-0.853	-0.923	17.516	-13.454	-13.454	0.000	0.000	0.000	0.000
146	A	147	LYS	1	0.823	0.873	20.053	15.584	15.584	0.000	0.000	0.000	0.000
147	A	148	GLU	-1	-0.892	-0.909	23.687	-10.302	-10.302	0.000	0.000	0.000	0.000
148	A	149	GLU	-1	-0.839	-0.909	24.016	-11.648	-11.648	0.000	0.000	0.000	0.000
149	A	150	VAL	0	0.022	0.011	22.363	0.446	0.446	0.000	0.000	0.000	0.000
150	A	151	LYS	1	0.787	0.888	25.511	11.440	11.440	0.000	0.000	0.000	0.000
151	A	152	ARG	1	0.669	0.798	27.696	11.283	11.283	0.000	0.000	0.000	0.000
152	A	153	GLU	-1	-0.786	-0.892	26.908	-9.764	-9.764	0.000	0.000	0.000	0.000
153	A	154	ILE	0	0.037	0.029	26.593	0.309	0.309	0.000	0.000	0.000	0.000
154	A	155	LYS	1	0.891	0.961	30.205	9.138	9.138	0.000	0.000	0.000	0.000
155	A	156	ARG	1	0.797	0.866	31.029	9.711	9.711	0.000	0.000	0.000	0.000
156	A	157	PHE	0	0.003	0.015	31.245	0.265	0.265	0.000	0.000	0.000	0.000
157	A	158	ILE	0	0.023	0.014	33.370	0.274	0.274	0.000	0.000	0.000	0.000
158	A	159	GLU	-1	-0.991	-1.014	35.973	-8.056	-8.056	0.000	0.000	0.000	0.000
159	A	160	LEU	0	-0.039	-0.021	35.106	0.262	0.262	0.000	0.000	0.000	0.000
160	A	161	ALA	0	0.062	0.021	36.446	0.213	0.213	0.000	0.000	0.000	0.000
161	A	162	ARG	1	0.896	0.963	38.402	7.936	7.936	0.000	0.000	0.000	0.000
162	A	163	ARG	1	0.760	0.881	40.763	7.433	7.433	0.000	0.000	0.000	0.000
163	A	164	TYR	0	-0.043	-0.038	40.357	0.211	0.211	0.000	0.000	0.000	0.000
164	A	165	ASN	0	-0.096	-0.043	43.009	0.129	0.129	0.000	0.000	0.000	0.000
165	A	166	LEU	0	0.009	0.015	37.996	0.048	0.048	0.000	0.000	0.000	0.000
166	A	167	LEU	-1	-0.912	-0.957	34.753	-7.698	-7.698	0.000	0.000	0.000	0.000

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