FMO DATABASE

FMODB ID: VVGY1

Calculation Name: 1RIL-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1RIL

Chain ID: A

ChEMBL ID:

UniProt ID: P29253

Base Structure: X-ray

Registration Date: 2025-10-03

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	147
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1404169.353469
FMO2-HF: Nuclear repulsion	1345830.970675
FMO2-HF: Total energy	-58338.382794
FMO2-MP2: Total energy	-58508.975472

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:ARG)

Summations of interaction energy for fragment #1(A:2:ARG)

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.
30.449	22.942	36.839	-11.031	-18.305	-0.017

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.898 / q_NPA : 0.950

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	ARG	1	0.862	0.921	1.932	19.096	11.437	17.022	-1.114	-8.250	0.039
4	A	5	VAL	0	0.023	0.030	3.100	2.237	2.208	0.173	0.308	-0.453	0.004
60	A	61	GLU	-1	-0.895	-0.946	3.853	-44.605	-44.471	0.000	-0.037	-0.098	0.000
61	A	62	PRO	0	0.014	0.022	4.221	-3.168	-2.886	-0.001	-0.098	-0.183	0.000
62	A	63	CYS	0	-0.081	-0.031	1.794	-33.828	-31.979	11.470	-9.464	-3.855	-0.039
63	A	64	GLU	-1	-0.829	-0.894	1.975	-41.519	-44.090	8.172	-0.579	-5.023	-0.021
64	A	65	VAL	0	0.028	0.007	3.869	2.560	2.754	0.003	-0.001	-0.195	0.000
115	A	115	ARG	1	0.885	0.935	3.665	46.348	46.641	0.000	-0.046	-0.248	0.000
5	A	6	ALA	0	-0.045	-0.017	6.624	0.144	0.144	0.000	0.000	0.000	0.000
6	A	7	LEU	0	0.002	0.008	9.280	0.719	0.719	0.000	0.000	0.000	0.000
7	A	8	PHE	0	0.012	0.002	11.981	0.554	0.554	0.000	0.000	0.000	0.000
8	A	9	THR	0	-0.036	-0.027	15.240	-0.142	-0.142	0.000	0.000	0.000	0.000
9	A	10	ASP	-1	-0.835	-0.919	18.114	-11.609	-11.609	0.000	0.000	0.000	0.000
10	A	11	GLY	0	-0.041	-0.035	21.876	-0.227	-0.227	0.000	0.000	0.000	0.000
11	A	12	ALA	0	-0.012	0.015	25.239	0.269	0.269	0.000	0.000	0.000	0.000
12	A	13	CYS	0	-0.082	-0.049	28.834	-0.112	-0.112	0.000	0.000	0.000	0.000
13	A	14	LEU	0	-0.004	0.003	32.055	0.090	0.090	0.000	0.000	0.000	0.000
14	A	15	GLY	0	0.022	0.013	35.552	0.293	0.293	0.000	0.000	0.000	0.000
15	A	16	ASN	0	-0.069	-0.016	35.696	-0.477	-0.477	0.000	0.000	0.000	0.000
16	A	17	PRO	0	0.020	0.004	36.552	0.138	0.138	0.000	0.000	0.000	0.000
17	A	18	GLY	0	0.048	0.012	36.081	0.254	0.254	0.000	0.000	0.000	0.000
18	A	19	PRO	0	0.033	0.040	35.038	-0.262	-0.262	0.000	0.000	0.000	0.000
19	A	20	GLY	0	0.032	0.006	31.188	-0.001	-0.001	0.000	0.000	0.000	0.000
20	A	21	GLY	0	-0.007	-0.020	28.552	0.038	0.038	0.000	0.000	0.000	0.000
21	A	22	TRP	0	0.006	-0.002	20.255	-0.214	-0.214	0.000	0.000	0.000	0.000
22	A	23	ALA	0	-0.006	-0.011	21.757	0.081	0.081	0.000	0.000	0.000	0.000
23	A	24	ALA	0	0.021	0.008	16.814	-0.250	-0.250	0.000	0.000	0.000	0.000
24	A	25	LEU	0	-0.032	-0.011	15.121	-0.015	-0.015	0.000	0.000	0.000	0.000
25	A	26	LEU	0	-0.013	-0.003	10.888	-0.587	-0.587	0.000	0.000	0.000	0.000
26	A	27	ARG	1	0.890	0.925	9.932	18.246	18.246	0.000	0.000	0.000	0.000
27	A	28	PHE	0	-0.016	-0.018	8.165	-1.242	-1.242	0.000	0.000	0.000	0.000
28	A	29	HIS	0	0.008	-0.013	6.527	3.814	3.814	0.000	0.000	0.000	0.000
29	A	30	ALA	0	0.031	0.025	9.256	0.922	0.922	0.000	0.000	0.000	0.000
30	A	31	HIS	0	0.021	0.025	12.301	1.578	1.578	0.000	0.000	0.000	0.000
31	A	32	GLU	-1	-0.818	-0.891	13.795	-15.777	-15.777	0.000	0.000	0.000	0.000
32	A	33	LYS	1	0.943	0.980	13.731	19.502	19.502	0.000	0.000	0.000	0.000
33	A	34	LEU	0	-0.012	-0.005	16.284	-0.558	-0.558	0.000	0.000	0.000	0.000
34	A	35	LEU	0	-0.020	-0.004	16.279	0.250	0.250	0.000	0.000	0.000	0.000
35	A	36	SER	0	-0.032	-0.055	20.019	-0.067	-0.067	0.000	0.000	0.000	0.000
36	A	37	GLY	0	0.026	0.018	23.388	0.028	0.028	0.000	0.000	0.000	0.000
37	A	38	GLY	0	0.016	0.001	26.153	-0.029	-0.029	0.000	0.000	0.000	0.000
38	A	39	GLU	-1	-0.897	-0.943	28.591	-10.709	-10.709	0.000	0.000	0.000	0.000
39	A	40	ALA	0	0.038	0.010	31.202	0.097	0.097	0.000	0.000	0.000	0.000
40	A	41	CYS	0	0.013	0.009	34.708	0.169	0.169	0.000	0.000	0.000	0.000
41	A	42	THR	0	-0.089	-0.025	30.604	-0.257	-0.257	0.000	0.000	0.000	0.000
42	A	43	THR	0	0.086	0.008	31.587	0.110	0.110	0.000	0.000	0.000	0.000
43	A	44	ASN	0	0.073	0.033	28.710	-0.094	-0.094	0.000	0.000	0.000	0.000
44	A	45	ASN	0	0.004	0.001	27.184	-0.462	-0.462	0.000	0.000	0.000	0.000
45	A	46	ARG	1	0.830	0.894	26.333	10.065	10.065	0.000	0.000	0.000	0.000
46	A	47	MET	0	-0.022	0.017	25.621	-0.523	-0.523	0.000	0.000	0.000	0.000
47	A	48	GLU	-1	-0.765	-0.889	23.121	-11.795	-11.795	0.000	0.000	0.000	0.000
48	A	49	LEU	0	-0.032	-0.013	20.955	-0.650	-0.650	0.000	0.000	0.000	0.000
49	A	50	LYS	1	0.889	0.929	20.815	11.135	11.135	0.000	0.000	0.000	0.000
50	A	51	ALA	0	0.030	0.022	20.213	-0.510	-0.510	0.000	0.000	0.000	0.000
51	A	52	ALA	0	0.006	0.013	17.076	-0.803	-0.803	0.000	0.000	0.000	0.000
52	A	53	ILE	0	-0.023	-0.005	15.874	-1.256	-1.256	0.000	0.000	0.000	0.000
53	A	54	GLU	-1	-0.850	-0.921	16.276	-15.563	-15.563	0.000	0.000	0.000	0.000
54	A	55	GLY	0	0.024	0.010	15.126	-0.584	-0.584	0.000	0.000	0.000	0.000
55	A	56	LEU	0	-0.022	-0.023	10.336	-1.377	-1.377	0.000	0.000	0.000	0.000
56	A	57	LYS	1	0.841	0.908	11.670	13.857	13.857	0.000	0.000	0.000	0.000
57	A	58	ALA	0	-0.097	-0.030	13.481	-0.162	-0.162	0.000	0.000	0.000	0.000
58	A	59	LEU	0	-0.008	-0.002	7.251	-0.521	-0.521	0.000	0.000	0.000	0.000
59	A	60	LYS	1	0.958	0.966	9.631	21.269	21.269	0.000	0.000	0.000	0.000
65	A	66	ASP	-1	-0.777	-0.841	6.314	-23.591	-23.591	0.000	0.000	0.000	0.000
66	A	67	LEU	0	0.020	0.012	8.428	0.546	0.546	0.000	0.000	0.000	0.000
67	A	68	TYR	0	-0.038	-0.034	10.524	0.408	0.408	0.000	0.000	0.000	0.000
68	A	69	THR	0	0.034	0.007	14.920	0.217	0.217	0.000	0.000	0.000	0.000
69	A	70	ASP	-1	-0.877	-0.933	18.588	-11.454	-11.454	0.000	0.000	0.000	0.000
70	A	71	SER	0	-0.078	-0.036	21.685	0.394	0.394	0.000	0.000	0.000	0.000
71	A	72	HIS	0	0.035	0.002	23.340	-0.043	-0.043	0.000	0.000	0.000	0.000
72	A	73	TYR	0	0.010	0.022	25.409	-0.031	-0.031	0.000	0.000	0.000	0.000
73	A	74	LEU	0	0.025	-0.007	19.231	-0.090	-0.090	0.000	0.000	0.000	0.000
74	A	75	LYS	1	0.975	1.001	21.345	11.330	11.330	0.000	0.000	0.000	0.000
75	A	76	LYS	1	0.943	1.020	22.340	10.291	10.291	0.000	0.000	0.000	0.000
76	A	77	ALA	0	-0.060	-0.027	23.506	0.009	0.009	0.000	0.000	0.000	0.000
77	A	78	PHE	0	-0.004	-0.016	18.120	-0.147	-0.147	0.000	0.000	0.000	0.000
78	A	79	THR	0	-0.058	-0.038	20.458	-0.045	-0.045	0.000	0.000	0.000	0.000
79	A	80	GLU	-1	-0.877	-0.940	22.603	-10.248	-10.248	0.000	0.000	0.000	0.000
80	A	80	GLY	0	0.017	0.009	24.676	0.317	0.317	0.000	0.000	0.000	0.000
81	A	81	TRP	0	-0.005	-0.017	25.728	-0.036	-0.036	0.000	0.000	0.000	0.000
82	A	82	LEU	0	0.005	0.003	20.241	0.198	0.198	0.000	0.000	0.000	0.000
83	A	83	GLU	-1	-0.827	-0.926	20.709	-14.517	-14.517	0.000	0.000	0.000	0.000
84	A	84	GLY	0	0.028	0.010	23.966	0.145	0.145	0.000	0.000	0.000	0.000
85	A	85	TRP	0	-0.049	-0.023	25.715	0.228	0.228	0.000	0.000	0.000	0.000
86	A	86	ARG	1	0.914	0.963	17.648	15.671	15.671	0.000	0.000	0.000	0.000
87	A	87	LYS	1	0.886	0.934	22.875	13.232	13.232	0.000	0.000	0.000	0.000
88	A	88	ARG	1	0.920	0.984	27.679	10.064	10.064	0.000	0.000	0.000	0.000
89	A	89	GLY	0	0.077	0.054	28.715	0.277	0.277	0.000	0.000	0.000	0.000
90	A	90	TRP	0	-0.003	-0.004	22.656	0.380	0.380	0.000	0.000	0.000	0.000
91	A	91	ARG	1	0.897	0.943	29.385	9.766	9.766	0.000	0.000	0.000	0.000
92	A	92	THR	0	-0.027	-0.022	32.008	-0.294	-0.294	0.000	0.000	0.000	0.000
93	A	93	ALA	0	0.000	-0.010	34.133	0.071	0.071	0.000	0.000	0.000	0.000
94	A	94	GLU	-1	-0.872	-0.939	35.892	-7.649	-7.649	0.000	0.000	0.000	0.000
95	A	95	GLY	0	0.042	0.025	37.349	0.179	0.179	0.000	0.000	0.000	0.000
96	A	96	LYS	1	0.940	0.976	37.547	7.526	7.526	0.000	0.000	0.000	0.000
97	A	97	PRO	0	-0.007	0.011	34.078	-0.285	-0.285	0.000	0.000	0.000	0.000
98	A	98	VAL	0	0.034	0.018	28.898	0.098	0.098	0.000	0.000	0.000	0.000
99	A	99	LYS	1	0.984	0.983	31.947	8.740	8.740	0.000	0.000	0.000	0.000
100	A	100	ASN	0	0.008	0.001	27.865	0.005	0.005	0.000	0.000	0.000	0.000
101	A	101	ARG	1	0.922	0.957	27.059	9.319	9.319	0.000	0.000	0.000	0.000
102	A	102	ASP	-1	-0.766	-0.863	26.005	-11.291	-11.291	0.000	0.000	0.000	0.000
103	A	103	LEU	0	0.001	0.000	23.758	-0.473	-0.473	0.000	0.000	0.000	0.000
104	A	104	TRP	0	-0.012	-0.016	21.107	-0.895	-0.895	0.000	0.000	0.000	0.000
105	A	105	GLU	-1	-0.923	-0.964	21.418	-12.852	-12.852	0.000	0.000	0.000	0.000
106	A	106	ALA	0	0.003	0.012	20.304	-0.789	-0.789	0.000	0.000	0.000	0.000
107	A	107	LEU	0	0.013	-0.004	16.673	-0.948	-0.948	0.000	0.000	0.000	0.000
108	A	108	LEU	0	-0.045	-0.028	16.445	-1.168	-1.168	0.000	0.000	0.000	0.000
109	A	109	LEU	0	0.017	0.001	15.960	-1.126	-1.126	0.000	0.000	0.000	0.000
110	A	110	ALA	0	-0.020	0.001	14.385	-1.162	-1.162	0.000	0.000	0.000	0.000
111	A	111	MET	0	-0.055	-0.047	12.009	-1.581	-1.581	0.000	0.000	0.000	0.000
112	A	112	ALA	0	-0.004	0.021	10.962	-2.161	-2.161	0.000	0.000	0.000	0.000
113	A	113	PRO	0	-0.011	0.000	8.499	-0.884	-0.884	0.000	0.000	0.000	0.000
114	A	114	HIS	0	0.024	0.013	6.335	-9.608	-9.608	0.000	0.000	0.000	0.000
116	A	116	VAL	0	0.017	0.000	6.928	-1.391	-1.391	0.000	0.000	0.000	0.000
117	A	117	ARG	1	0.797	0.897	5.189	30.425	30.425	0.000	0.000	0.000	0.000
118	A	118	PHE	0	0.045	0.013	10.668	-0.098	-0.098	0.000	0.000	0.000	0.000
119	A	119	HIS	1	0.799	0.886	9.794	19.197	19.197	0.000	0.000	0.000	0.000
120	A	120	PHE	0	0.051	0.025	14.982	0.235	0.235	0.000	0.000	0.000	0.000
121	A	121	VAL	0	0.001	-0.003	17.643	0.631	0.631	0.000	0.000	0.000	0.000
122	A	122	LYS	1	0.894	0.943	19.574	10.466	10.466	0.000	0.000	0.000	0.000
123	A	123	GLY	0	0.114	0.050	22.645	0.308	0.308	0.000	0.000	0.000	0.000
124	A	124	HIS	1	0.782	0.880	21.480	10.996	10.996	0.000	0.000	0.000	0.000
125	A	125	THR	0	-0.010	-0.008	20.734	0.277	0.277	0.000	0.000	0.000	0.000
126	A	126	GLY	0	-0.025	-0.006	17.908	-0.331	-0.331	0.000	0.000	0.000	0.000
127	A	127	HIS	0	0.028	0.007	14.330	0.146	0.146	0.000	0.000	0.000	0.000
128	A	128	PRO	0	0.077	0.034	17.985	0.034	0.034	0.000	0.000	0.000	0.000
129	A	129	GLU	-1	-0.798	-0.886	14.710	-15.015	-15.015	0.000	0.000	0.000	0.000
130	A	130	ASN	0	-0.044	-0.030	17.707	0.176	0.176	0.000	0.000	0.000	0.000
131	A	131	GLU	-1	-0.756	-0.860	20.209	-10.830	-10.830	0.000	0.000	0.000	0.000
132	A	132	ARG	1	0.790	0.873	19.458	13.707	13.707	0.000	0.000	0.000	0.000
133	A	133	VAL	0	-0.001	0.002	18.125	0.099	0.099	0.000	0.000	0.000	0.000
134	A	134	ASP	-1	-0.793	-0.893	21.484	-10.287	-10.287	0.000	0.000	0.000	0.000
135	A	135	ARG	1	0.926	0.960	24.393	10.148	10.148	0.000	0.000	0.000	0.000
136	A	136	GLU	-1	-0.768	-0.845	23.945	-10.738	-10.738	0.000	0.000	0.000	0.000
137	A	137	ALA	0	0.010	0.006	24.283	0.212	0.212	0.000	0.000	0.000	0.000
138	A	138	ARG	1	0.872	0.929	26.147	10.146	10.146	0.000	0.000	0.000	0.000
139	A	139	ARG	1	0.868	0.926	28.472	10.460	10.460	0.000	0.000	0.000	0.000
140	A	140	GLN	0	-0.062	-0.015	27.297	0.582	0.582	0.000	0.000	0.000	0.000
141	A	141	ALA	0	0.045	0.026	30.165	0.235	0.235	0.000	0.000	0.000	0.000
142	A	142	GLN	0	-0.035	-0.027	31.937	0.083	0.083	0.000	0.000	0.000	0.000
143	A	143	SER	0	-0.085	-0.031	33.313	0.334	0.334	0.000	0.000	0.000	0.000
144	A	144	GLN	0	-0.019	-0.002	31.592	-0.058	-0.058	0.000	0.000	0.000	0.000
145	A	145	ALA	0	-0.012	-0.011	35.802	0.259	0.259	0.000	0.000	0.000	0.000
146	A	146	LYS	1	0.880	0.916	38.196	7.547	7.547	0.000	0.000	0.000	0.000
147	A	147	THR	-1	-0.866	-0.907	40.429	-7.457	-7.457	0.000	0.000	0.000	0.000

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