FMO DATABASE

FMODB ID: 5G7RZ

Calculation Name: 1RYL-A-Xray549

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1RYL

Chain ID: A

ChEMBL ID:

UniProt ID: P76483

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	164
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1715250.874162
FMO2-HF: Nuclear repulsion	1649160.238986
FMO2-HF: Total energy	-66090.635176
FMO2-MP2: Total energy	-66282.863814

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:MET)

Summations of interaction energy for fragment #1(A:3: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.
-321.445	-309.348	26.471	-17.383	-21.185	-0.163

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.807 / q_NPA : 0.896

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	5	GLY	0	0.058	0.021	3.265	-5.343	-3.369	0.052	-0.945	-1.081	0.000
42	A	44	LYS	1	0.867	0.909	4.290	43.076	43.290	-0.001	-0.069	-0.144	0.000
44	A	46	TRP	0	0.020	0.003	2.127	5.204	6.411	2.474	-1.036	-2.645	-0.002
57	A	59	PHE	0	-0.019	-0.026	2.485	-1.777	-0.974	1.140	-0.395	-1.548	-0.001
81	A	83	GLY	0	-0.005	-0.015	3.372	-12.007	-11.123	0.087	-0.318	-0.654	-0.002
82	A	84	PHE	0	-0.057	-0.026	3.747	4.692	5.319	0.077	-0.141	-0.562	0.000
121	A	123	TYR	0	0.010	0.017	2.448	-4.515	-2.444	2.569	-1.241	-3.399	-0.013
163	A	165	ILE	0	-0.014	-0.017	2.885	-2.151	-1.333	0.130	-0.229	-0.719	-0.001
164	A	166	VAL	-1	-0.763	-0.854	2.040	-139.128	-135.629	19.943	-13.009	-10.433	-0.144
4	A	6	TYR	0	-0.062	-0.049	5.981	6.020	6.020	0.000	0.000	0.000	0.000
5	A	7	PHE	0	0.019	0.013	9.304	-0.014	-0.014	0.000	0.000	0.000	0.000
6	A	8	ALA	0	0.006	-0.009	12.578	1.201	1.201	0.000	0.000	0.000	0.000
7	A	9	GLU	-1	-0.808	-0.895	14.208	-13.438	-13.438	0.000	0.000	0.000	0.000
8	A	10	ILE	0	0.023	0.013	17.363	-0.013	-0.013	0.000	0.000	0.000	0.000
9	A	11	ASP	-1	-0.781	-0.888	19.522	-12.474	-12.474	0.000	0.000	0.000	0.000
10	A	12	SER	0	0.037	-0.009	22.804	-0.447	-0.447	0.000	0.000	0.000	0.000
11	A	13	GLU	-1	-0.881	-0.913	25.410	-11.681	-11.681	0.000	0.000	0.000	0.000
12	A	14	LYS	1	0.832	0.909	20.750	12.977	12.977	0.000	0.000	0.000	0.000
13	A	15	ILE	0	0.006	0.005	18.337	-0.489	-0.489	0.000	0.000	0.000	0.000
14	A	16	ASN	0	-0.066	-0.029	21.169	-0.105	-0.105	0.000	0.000	0.000	0.000
15	A	17	GLN	0	0.074	0.040	22.103	-0.510	-0.510	0.000	0.000	0.000	0.000
16	A	18	LEU	0	-0.008	-0.001	15.922	-0.006	-0.006	0.000	0.000	0.000	0.000
17	A	19	LEU	0	-0.008	-0.021	18.681	-0.270	-0.270	0.000	0.000	0.000	0.000
18	A	20	GLU	-1	-0.967	-0.976	21.150	-11.187	-11.187	0.000	0.000	0.000	0.000
19	A	21	SER	0	-0.109	-0.059	22.740	0.359	0.359	0.000	0.000	0.000	0.000
20	A	22	THR	0	-0.032	-0.030	18.524	-0.302	-0.302	0.000	0.000	0.000	0.000
21	A	23	GLU	-1	-0.807	-0.864	17.766	-15.202	-15.202	0.000	0.000	0.000	0.000
22	A	24	LYS	1	0.857	0.888	17.506	13.173	13.173	0.000	0.000	0.000	0.000
23	A	25	PRO	0	-0.034	-0.022	15.991	-0.331	-0.331	0.000	0.000	0.000	0.000
24	A	26	LEU	0	0.006	0.031	13.677	-1.243	-1.243	0.000	0.000	0.000	0.000
25	A	27	MET	0	-0.010	-0.014	6.942	-2.334	-2.334	0.000	0.000	0.000	0.000
26	A	28	ASP	-1	-0.862	-0.914	10.077	-24.903	-24.903	0.000	0.000	0.000	0.000
27	A	29	ASN	0	-0.090	-0.068	11.093	0.099	0.099	0.000	0.000	0.000	0.000
28	A	30	ILE	0	0.013	0.026	8.737	0.270	0.270	0.000	0.000	0.000	0.000
29	A	31	HIS	0	-0.033	-0.010	6.287	0.550	0.550	0.000	0.000	0.000	0.000
30	A	32	ASP	-1	-0.924	-0.967	10.876	-17.949	-17.949	0.000	0.000	0.000	0.000
31	A	33	THR	0	0.034	0.008	14.671	0.611	0.611	0.000	0.000	0.000	0.000
32	A	34	LEU	0	0.018	0.012	11.285	1.192	1.192	0.000	0.000	0.000	0.000
33	A	35	SER	0	-0.043	-0.005	13.914	-0.345	-0.345	0.000	0.000	0.000	0.000
34	A	36	GLY	0	-0.018	-0.013	14.853	0.239	0.239	0.000	0.000	0.000	0.000
35	A	37	LEU	0	-0.017	0.014	15.466	1.142	1.142	0.000	0.000	0.000	0.000
36	A	38	ARG	1	0.936	0.967	16.067	14.052	14.052	0.000	0.000	0.000	0.000
37	A	39	ARG	1	0.880	0.944	11.100	24.392	24.392	0.000	0.000	0.000	0.000
38	A	40	LEU	0	-0.098	-0.022	13.839	1.092	1.092	0.000	0.000	0.000	0.000
39	A	41	ASP	-1	-0.838	-0.935	9.443	-34.635	-34.635	0.000	0.000	0.000	0.000
40	A	42	ILE	0	-0.042	-0.016	8.995	2.711	2.711	0.000	0.000	0.000	0.000
41	A	43	ASP	-1	-0.829	-0.909	7.567	-39.532	-39.532	0.000	0.000	0.000	0.000
43	A	45	ARG	1	0.846	0.909	6.312	25.828	25.828	0.000	0.000	0.000	0.000
45	A	47	ASP	-1	-0.716	-0.820	6.802	-23.270	-23.270	0.000	0.000	0.000	0.000
46	A	48	PHE	0	0.019	0.003	8.555	2.276	2.276	0.000	0.000	0.000	0.000
47	A	49	LEU	0	-0.013	-0.007	11.000	1.839	1.839	0.000	0.000	0.000	0.000
48	A	50	HIS	0	0.050	0.036	10.836	1.514	1.514	0.000	0.000	0.000	0.000
49	A	51	PHE	0	0.010	0.017	12.500	1.697	1.697	0.000	0.000	0.000	0.000
50	A	52	GLY	0	-0.055	-0.038	14.450	1.187	1.187	0.000	0.000	0.000	0.000
51	A	53	LEU	0	-0.041	-0.024	15.953	1.004	1.004	0.000	0.000	0.000	0.000
52	A	54	THR	0	-0.024	-0.007	15.441	0.654	0.654	0.000	0.000	0.000	0.000
53	A	55	GLY	0	-0.018	0.008	17.707	0.599	0.599	0.000	0.000	0.000	0.000
54	A	56	THR	0	0.003	-0.014	15.030	0.189	0.189	0.000	0.000	0.000	0.000
55	A	57	SER	0	0.056	0.007	8.954	-0.700	-0.700	0.000	0.000	0.000	0.000
56	A	58	ALA	0	-0.010	-0.019	7.952	0.990	0.990	0.000	0.000	0.000	0.000
58	A	60	ASP	-1	-0.989	-0.980	8.563	-15.726	-15.726	0.000	0.000	0.000	0.000
59	A	61	PRO	0	0.011	0.028	11.700	0.945	0.945	0.000	0.000	0.000	0.000
60	A	62	ALA	0	0.023	0.009	14.491	0.771	0.771	0.000	0.000	0.000	0.000
61	A	63	LYS	1	0.950	0.948	18.296	13.213	13.213	0.000	0.000	0.000	0.000
62	A	64	ASN	0	-0.056	-0.032	20.148	0.183	0.183	0.000	0.000	0.000	0.000
63	A	65	ASP	-1	-0.728	-0.847	18.039	-14.308	-14.308	0.000	0.000	0.000	0.000
64	A	66	PRO	0	-0.031	-0.027	18.947	-0.567	-0.567	0.000	0.000	0.000	0.000
65	A	67	LEU	0	-0.002	-0.013	19.053	-0.095	-0.095	0.000	0.000	0.000	0.000
66	A	68	SER	0	-0.021	-0.025	13.942	-0.696	-0.696	0.000	0.000	0.000	0.000
67	A	69	ARG	1	0.867	0.921	14.942	12.863	12.863	0.000	0.000	0.000	0.000
68	A	70	ALA	0	-0.018	0.006	16.876	-0.199	-0.199	0.000	0.000	0.000	0.000
69	A	71	VAL	0	-0.019	0.003	11.296	-0.219	-0.219	0.000	0.000	0.000	0.000
70	A	72	LEU	0	0.031	0.004	9.595	-1.329	-1.329	0.000	0.000	0.000	0.000
71	A	73	GLY	0	0.029	0.029	12.563	-0.542	-0.542	0.000	0.000	0.000	0.000
72	A	74	GLU	-1	-0.891	-0.960	15.610	-13.402	-13.402	0.000	0.000	0.000	0.000
73	A	75	HIS	1	0.730	0.842	17.290	14.909	14.909	0.000	0.000	0.000	0.000
74	A	76	SER	0	-0.029	-0.036	12.839	-0.357	-0.357	0.000	0.000	0.000	0.000
75	A	77	LEU	0	-0.049	-0.040	13.204	1.330	1.330	0.000	0.000	0.000	0.000
76	A	78	GLU	-1	-0.829	-0.935	10.862	-22.001	-22.001	0.000	0.000	0.000	0.000
77	A	79	ASP	-1	-0.795	-0.860	8.748	-26.097	-26.097	0.000	0.000	0.000	0.000
78	A	80	GLY	0	-0.019	0.000	9.290	0.519	0.519	0.000	0.000	0.000	0.000
79	A	81	ILE	0	-0.072	-0.032	9.283	-0.363	-0.363	0.000	0.000	0.000	0.000
80	A	82	ASP	-1	-0.962	-0.983	5.430	-34.342	-34.342	0.000	0.000	0.000	0.000
83	A	85	LEU	0	-0.022	-0.002	6.665	-2.553	-2.553	0.000	0.000	0.000	0.000
84	A	86	GLY	0	0.071	0.046	9.704	2.011	2.011	0.000	0.000	0.000	0.000
85	A	87	LEU	0	-0.063	-0.028	12.909	-0.228	-0.228	0.000	0.000	0.000	0.000
86	A	88	THR	0	-0.026	-0.010	16.325	0.407	0.407	0.000	0.000	0.000	0.000
87	A	89	TRP	0	0.030	0.010	19.239	-0.119	-0.119	0.000	0.000	0.000	0.000
88	A	90	ASN	0	-0.056	-0.032	22.442	0.554	0.554	0.000	0.000	0.000	0.000
89	A	91	GLN	0	-0.037	-0.035	24.879	0.368	0.368	0.000	0.000	0.000	0.000
90	A	92	GLU	-1	-0.786	-0.862	22.059	-13.051	-13.051	0.000	0.000	0.000	0.000
91	A	93	LEU	0	-0.003	0.010	19.939	-0.103	-0.103	0.000	0.000	0.000	0.000
92	A	94	ALA	0	-0.007	0.000	23.543	-0.029	-0.029	0.000	0.000	0.000	0.000
93	A	95	ALA	0	0.022	0.006	25.937	0.112	0.112	0.000	0.000	0.000	0.000
94	A	96	THR	0	-0.033	-0.018	19.693	-0.155	-0.155	0.000	0.000	0.000	0.000
95	A	97	ILE	0	-0.046	-0.025	22.582	-0.260	-0.260	0.000	0.000	0.000	0.000
96	A	98	ASP	-1	-0.875	-0.933	24.207	-10.504	-10.504	0.000	0.000	0.000	0.000
97	A	99	ARG	1	0.877	0.953	21.889	12.911	12.911	0.000	0.000	0.000	0.000
98	A	100	LEU	0	0.027	0.009	18.700	-0.073	-0.073	0.000	0.000	0.000	0.000
99	A	101	GLU	-1	-0.877	-0.935	22.844	-11.184	-11.184	0.000	0.000	0.000	0.000
100	A	102	SER	0	-0.020	-0.016	26.117	0.341	0.341	0.000	0.000	0.000	0.000
101	A	103	LEU	0	-0.042	0.005	21.717	0.201	0.201	0.000	0.000	0.000	0.000
102	A	104	ASP	-1	-0.816	-0.906	26.117	-10.000	-10.000	0.000	0.000	0.000	0.000
103	A	105	ARG	1	0.814	0.867	24.290	11.656	11.656	0.000	0.000	0.000	0.000
104	A	106	ASN	0	-0.050	-0.027	25.793	-0.346	-0.346	0.000	0.000	0.000	0.000
105	A	107	GLU	-1	-0.947	-0.963	26.691	-10.713	-10.713	0.000	0.000	0.000	0.000
106	A	108	LEU	0	0.033	0.011	21.097	-0.179	-0.179	0.000	0.000	0.000	0.000
107	A	109	ARG	1	0.785	0.876	22.827	11.606	11.606	0.000	0.000	0.000	0.000
108	A	110	LYS	1	0.882	0.942	24.566	9.689	9.689	0.000	0.000	0.000	0.000
109	A	111	GLN	0	0.023	0.012	23.101	0.103	0.103	0.000	0.000	0.000	0.000
110	A	112	PHE	0	-0.036	-0.004	16.558	-0.302	-0.302	0.000	0.000	0.000	0.000
111	A	113	SER	0	-0.022	-0.019	20.391	0.497	0.497	0.000	0.000	0.000	0.000
112	A	114	ILE	0	0.013	-0.006	17.802	-0.593	-0.593	0.000	0.000	0.000	0.000
113	A	115	LYS	1	0.881	0.956	18.891	10.705	10.705	0.000	0.000	0.000	0.000
114	A	116	ARG	1	0.898	0.941	18.522	13.905	13.905	0.000	0.000	0.000	0.000
115	A	117	LEU	0	-0.019	0.011	13.600	-0.354	-0.354	0.000	0.000	0.000	0.000
116	A	118	ASN	0	-0.013	-0.027	14.384	-1.599	-1.599	0.000	0.000	0.000	0.000
117	A	119	GLU	-1	-0.995	-0.983	15.768	-14.521	-14.521	0.000	0.000	0.000	0.000
118	A	120	MET	0	-0.023	-0.013	13.850	0.031	0.031	0.000	0.000	0.000	0.000
119	A	121	GLU	-1	-0.953	-0.970	10.497	-19.974	-19.974	0.000	0.000	0.000	0.000
120	A	122	ILE	0	-0.018	0.008	9.345	-1.667	-1.667	0.000	0.000	0.000	0.000
122	A	124	PRO	0	-0.097	-0.070	5.915	0.494	0.494	0.000	0.000	0.000	0.000
123	A	125	GLY	0	0.044	0.011	6.928	0.303	0.303	0.000	0.000	0.000	0.000
124	A	126	VAL	0	-0.087	-0.029	9.601	1.507	1.507	0.000	0.000	0.000	0.000
125	A	127	THR	0	0.000	0.004	12.363	0.464	0.464	0.000	0.000	0.000	0.000
126	A	128	PHE	0	-0.026	-0.019	13.428	0.183	0.183	0.000	0.000	0.000	0.000
127	A	129	SER	0	0.025	0.006	18.274	0.309	0.309	0.000	0.000	0.000	0.000
128	A	130	GLU	-1	-0.853	-0.945	21.950	-11.949	-11.949	0.000	0.000	0.000	0.000
129	A	131	GLU	-1	-0.912	-0.971	23.727	-11.600	-11.600	0.000	0.000	0.000	0.000
130	A	132	LEU	0	-0.029	-0.012	19.910	0.074	0.074	0.000	0.000	0.000	0.000
131	A	133	GLU	-1	-0.773	-0.849	21.008	-12.723	-12.723	0.000	0.000	0.000	0.000
132	A	134	GLY	0	-0.004	-0.009	21.413	-0.262	-0.262	0.000	0.000	0.000	0.000
133	A	135	GLN	0	-0.016	-0.016	21.473	0.143	0.143	0.000	0.000	0.000	0.000
134	A	136	LEU	0	0.017	0.017	14.303	-0.264	-0.264	0.000	0.000	0.000	0.000
135	A	137	PHE	0	0.049	0.025	17.607	-0.532	-0.532	0.000	0.000	0.000	0.000
136	A	138	ALA	0	0.009	-0.002	19.692	-0.153	-0.153	0.000	0.000	0.000	0.000
137	A	139	SER	0	-0.041	-0.019	16.259	-0.225	-0.225	0.000	0.000	0.000	0.000
138	A	140	ILE	0	0.032	0.020	14.275	-0.506	-0.506	0.000	0.000	0.000	0.000
139	A	141	MET	0	-0.005	0.005	16.417	0.090	0.090	0.000	0.000	0.000	0.000
140	A	142	LEU	0	-0.029	-0.008	18.884	0.125	0.125	0.000	0.000	0.000	0.000
141	A	143	ASP	-1	-0.775	-0.874	13.689	-21.086	-21.086	0.000	0.000	0.000	0.000
142	A	144	MET	0	0.034	0.028	16.410	-0.257	-0.257	0.000	0.000	0.000	0.000
143	A	145	GLU	-1	-0.816	-0.898	18.054	-12.498	-12.498	0.000	0.000	0.000	0.000
144	A	146	LYS	1	0.822	0.926	16.673	18.453	18.453	0.000	0.000	0.000	0.000
145	A	147	LEU	0	0.011	0.011	14.736	0.204	0.204	0.000	0.000	0.000	0.000
146	A	148	ILE	0	0.035	0.026	17.841	0.329	0.329	0.000	0.000	0.000	0.000
147	A	149	SER	0	-0.064	-0.054	21.471	0.636	0.636	0.000	0.000	0.000	0.000
148	A	150	ALA	0	-0.084	-0.037	17.991	0.384	0.384	0.000	0.000	0.000	0.000
149	A	151	TYR	0	0.053	-0.006	16.423	0.382	0.382	0.000	0.000	0.000	0.000
150	A	152	ARG	1	0.863	0.919	21.103	11.739	11.739	0.000	0.000	0.000	0.000
151	A	153	ARG	1	0.733	0.855	18.779	15.655	15.655	0.000	0.000	0.000	0.000
152	A	154	MET	0	-0.034	0.014	17.620	0.297	0.297	0.000	0.000	0.000	0.000
153	A	155	LEU	0	0.030	0.019	23.019	0.331	0.331	0.000	0.000	0.000	0.000
154	A	156	ARG	1	0.917	0.963	25.720	11.597	11.597	0.000	0.000	0.000	0.000
155	A	157	GLN	0	-0.063	-0.033	25.173	0.508	0.508	0.000	0.000	0.000	0.000
156	A	158	GLY	0	0.009	0.014	27.268	0.112	0.112	0.000	0.000	0.000	0.000
157	A	159	ASN	0	-0.084	-0.047	22.224	0.215	0.215	0.000	0.000	0.000	0.000
158	A	160	HIS	0	0.060	0.014	20.489	0.157	0.157	0.000	0.000	0.000	0.000
159	A	161	ALA	0	0.001	-0.023	16.421	-0.346	-0.346	0.000	0.000	0.000	0.000
160	A	162	LEU	0	0.030	0.014	13.068	0.519	0.519	0.000	0.000	0.000	0.000
161	A	163	THR	0	-0.035	-0.018	9.327	-0.380	-0.380	0.000	0.000	0.000	0.000
162	A	164	VAL	0	-0.004	-0.005	7.009	0.518	0.518	0.000	0.000	0.000	0.000

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