FMO DATABASE

FMODB ID: 879RY

Calculation Name: 3JS5-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3JS5

Chain ID: A

ChEMBL ID:

UniProt ID: C4LSE7

Base Structure: X-ray

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	156
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1645861.342172
FMO2-HF: Nuclear repulsion	1580959.542068
FMO2-HF: Total energy	-64901.800104
FMO2-MP2: Total energy	-65084.212638

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:0:SER)

Summations of interaction energy for fragment #1(A:0:SER)

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.
-152.388	-143.437	8.876	-9.684	-8.142	-0.113

Interaction energy analysis for fragmet #1(A:0:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.752 / q_NPA : 0.872

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	2	LYS	1	0.806	0.903	3.415	42.666	44.326	0.011	-0.779	-0.892	-0.002
34	A	33	LYS	1	0.775	0.884	2.740	9.682	13.456	0.539	-2.090	-2.223	-0.019
35	A	34	TYR	0	0.004	-0.043	1.883	-45.953	-43.122	8.274	-6.635	-4.470	-0.090
36	A	35	ILE	0	0.002	0.009	2.966	4.268	4.981	0.053	-0.179	-0.586	-0.002
37	A	36	CYS	0	-0.059	-0.018	5.223	2.797	2.770	-0.001	-0.001	0.029	0.000
4	A	3	LEU	0	0.014	0.006	5.778	5.141	5.141	0.000	0.000	0.000	0.000
5	A	4	LEU	0	-0.008	0.010	9.175	-0.073	-0.073	0.000	0.000	0.000	0.000
6	A	5	PHE	0	0.007	-0.010	11.337	1.433	1.433	0.000	0.000	0.000	0.000
7	A	6	VAL	0	0.053	0.005	15.428	0.329	0.329	0.000	0.000	0.000	0.000
8	A	7	CYS	-1	-0.838	-0.779	18.737	-13.788	-13.788	0.000	0.000	0.000	0.000
9	A	8	LEU	0	0.068	0.038	22.322	-0.097	-0.097	0.000	0.000	0.000	0.000
10	A	9	GLY	0	0.030	0.000	24.867	0.068	0.068	0.000	0.000	0.000	0.000
11	A	10	ASN	0	0.028	-0.023	17.965	0.103	0.103	0.000	0.000	0.000	0.000
12	A	11	ILE	0	0.059	0.037	21.496	-0.329	-0.329	0.000	0.000	0.000	0.000
13	A	12	CYS	0	-0.070	-0.038	23.650	0.525	0.525	0.000	0.000	0.000	0.000
14	A	13	ARG	1	0.806	0.871	22.708	11.784	11.784	0.000	0.000	0.000	0.000
15	A	14	SER	0	0.026	-0.079	17.896	-0.511	-0.511	0.000	0.000	0.000	0.000
16	A	15	PRO	0	0.012	0.010	17.430	-0.943	-0.943	0.000	0.000	0.000	0.000
17	A	16	ALA	0	-0.017	-0.006	18.041	-0.544	-0.544	0.000	0.000	0.000	0.000
18	A	17	ALA	0	0.026	-0.001	16.904	-0.379	-0.379	0.000	0.000	0.000	0.000
19	A	18	GLU	-1	-0.789	-0.852	12.755	-22.912	-22.912	0.000	0.000	0.000	0.000
20	A	19	ALA	0	-0.018	-0.007	13.608	-1.374	-1.374	0.000	0.000	0.000	0.000
21	A	20	VAL	0	0.002	-0.007	15.729	-0.371	-0.371	0.000	0.000	0.000	0.000
22	A	21	MET	0	0.032	0.026	10.818	0.203	0.203	0.000	0.000	0.000	0.000
23	A	22	LYS	1	0.859	0.922	10.652	23.618	23.618	0.000	0.000	0.000	0.000
24	A	23	LYS	1	0.898	0.965	11.984	16.595	16.595	0.000	0.000	0.000	0.000
25	A	24	VAL	0	0.003	0.007	13.308	0.250	0.250	0.000	0.000	0.000	0.000
26	A	25	ILE	0	0.017	-0.001	7.542	-0.065	-0.065	0.000	0.000	0.000	0.000
27	A	26	GLN	0	-0.014	-0.009	10.746	0.201	0.201	0.000	0.000	0.000	0.000
28	A	27	ASN	0	-0.043	-0.028	12.696	0.764	0.764	0.000	0.000	0.000	0.000
29	A	28	HIS	1	0.799	0.885	12.431	21.386	21.386	0.000	0.000	0.000	0.000
30	A	29	HIS	0	-0.017	0.003	12.172	-0.810	-0.810	0.000	0.000	0.000	0.000
31	A	30	LEU	0	-0.005	0.002	7.744	-1.344	-1.344	0.000	0.000	0.000	0.000
32	A	31	THR	0	-0.009	-0.047	6.244	-5.476	-5.476	0.000	0.000	0.000	0.000
33	A	32	GLU	-1	-0.869	-0.904	4.998	-43.469	-43.469	0.000	0.000	0.000	0.000
38	A	37	ASP	-1	-0.784	-0.886	8.871	-23.278	-23.278	0.000	0.000	0.000	0.000
39	A	38	SER	0	-0.060	-0.061	11.383	0.849	0.849	0.000	0.000	0.000	0.000
40	A	39	ALA	0	0.054	0.032	15.021	-0.031	-0.031	0.000	0.000	0.000	0.000
41	A	40	GLY	0	-0.009	-0.003	17.767	0.232	0.232	0.000	0.000	0.000	0.000
42	A	41	THR	0	-0.005	-0.007	21.487	-0.083	-0.083	0.000	0.000	0.000	0.000
43	A	42	CYS	0	-0.019	0.008	23.596	0.399	0.399	0.000	0.000	0.000	0.000
44	A	43	SER	0	0.061	0.026	24.922	-0.233	-0.233	0.000	0.000	0.000	0.000
45	A	44	TYR	0	-0.025	-0.021	25.902	0.171	0.171	0.000	0.000	0.000	0.000
46	A	45	HIS	0	-0.063	-0.040	25.970	0.364	0.364	0.000	0.000	0.000	0.000
47	A	46	GLU	-1	-0.867	-0.944	22.704	-13.746	-13.746	0.000	0.000	0.000	0.000
48	A	47	GLY	0	-0.019	-0.008	23.142	0.453	0.453	0.000	0.000	0.000	0.000
49	A	48	GLN	0	-0.038	0.000	24.337	0.377	0.377	0.000	0.000	0.000	0.000
50	A	49	GLN	0	-0.008	-0.011	23.711	-0.548	-0.548	0.000	0.000	0.000	0.000
51	A	50	ALA	0	0.066	0.037	21.917	0.414	0.414	0.000	0.000	0.000	0.000
52	A	51	ASP	-1	-0.782	-0.870	24.035	-10.245	-10.245	0.000	0.000	0.000	0.000
53	A	52	SER	0	0.024	-0.003	27.009	-0.240	-0.240	0.000	0.000	0.000	0.000
54	A	53	ARG	1	0.737	0.855	29.205	10.009	10.009	0.000	0.000	0.000	0.000
55	A	54	MET	0	0.020	0.025	23.797	0.058	0.058	0.000	0.000	0.000	0.000
56	A	55	ARG	1	0.898	0.954	24.062	11.830	11.830	0.000	0.000	0.000	0.000
57	A	56	LYS	1	0.809	0.889	25.716	9.519	9.519	0.000	0.000	0.000	0.000
58	A	57	VAL	0	-0.021	-0.012	26.868	0.038	0.038	0.000	0.000	0.000	0.000
59	A	58	GLY	0	0.082	0.047	23.633	-0.043	-0.043	0.000	0.000	0.000	0.000
60	A	59	LYS	1	0.988	1.003	24.093	11.195	11.195	0.000	0.000	0.000	0.000
61	A	60	SER	0	-0.146	-0.093	25.561	0.172	0.172	0.000	0.000	0.000	0.000
62	A	61	ARG	1	0.755	0.833	24.608	12.317	12.317	0.000	0.000	0.000	0.000
63	A	62	GLY	0	0.003	0.021	23.244	-0.259	-0.259	0.000	0.000	0.000	0.000
64	A	63	TYR	0	-0.084	-0.074	18.237	-1.098	-1.098	0.000	0.000	0.000	0.000
65	A	64	GLN	0	-0.016	-0.010	18.567	1.123	1.123	0.000	0.000	0.000	0.000
66	A	65	VAL	0	-0.022	-0.021	18.586	-0.866	-0.866	0.000	0.000	0.000	0.000
67	A	66	ASP	-1	-0.999	-1.002	18.746	-14.681	-14.681	0.000	0.000	0.000	0.000
68	A	67	SER	0	0.030	0.014	16.517	-0.780	-0.780	0.000	0.000	0.000	0.000
69	A	68	ILE	0	-0.068	-0.035	18.502	1.076	1.076	0.000	0.000	0.000	0.000
70	A	69	SER	0	-0.035	-0.009	19.096	-0.847	-0.847	0.000	0.000	0.000	0.000
71	A	70	ARG	1	0.805	0.864	13.177	21.054	21.054	0.000	0.000	0.000	0.000
72	A	71	PRO	0	0.029	0.024	20.097	-0.158	-0.158	0.000	0.000	0.000	0.000
73	A	72	VAL	0	-0.015	-0.002	17.777	-0.888	-0.888	0.000	0.000	0.000	0.000
74	A	73	VAL	0	-0.017	-0.014	17.095	1.087	1.087	0.000	0.000	0.000	0.000
75	A	74	SER	0	0.029	0.003	18.222	-0.836	-0.836	0.000	0.000	0.000	0.000
76	A	75	SER	0	-0.015	-0.013	15.540	-0.310	-0.310	0.000	0.000	0.000	0.000
77	A	76	ASP	-1	-0.714	-0.828	13.668	-21.911	-21.911	0.000	0.000	0.000	0.000
78	A	77	PHE	0	0.045	0.017	13.434	-1.733	-1.733	0.000	0.000	0.000	0.000
79	A	78	LYS	1	0.939	0.985	13.058	18.960	18.960	0.000	0.000	0.000	0.000
80	A	79	ASN	0	-0.038	-0.035	10.523	-0.961	-0.961	0.000	0.000	0.000	0.000
81	A	80	PHE	0	0.006	0.009	8.804	-4.474	-4.474	0.000	0.000	0.000	0.000
82	A	81	ASP	-1	-0.847	-0.907	5.940	-43.793	-43.793	0.000	0.000	0.000	0.000
83	A	82	TYR	0	-0.047	-0.055	9.247	1.303	1.303	0.000	0.000	0.000	0.000
84	A	83	ILE	0	-0.011	-0.009	11.757	-1.288	-1.288	0.000	0.000	0.000	0.000
85	A	84	PHE	0	0.002	0.001	11.670	1.127	1.127	0.000	0.000	0.000	0.000
86	A	85	ALA	0	0.022	0.026	16.787	0.068	0.068	0.000	0.000	0.000	0.000
87	A	86	MET	0	-0.051	-0.014	18.354	0.156	0.156	0.000	0.000	0.000	0.000
88	A	87	ASP	-1	-0.742	-0.857	22.354	-11.696	-11.696	0.000	0.000	0.000	0.000
89	A	88	ASN	0	0.061	0.013	24.879	-0.677	-0.677	0.000	0.000	0.000	0.000
90	A	89	ASP	-1	-0.864	-0.908	27.223	-10.575	-10.575	0.000	0.000	0.000	0.000
91	A	90	ASN	0	-0.040	-0.049	22.499	-0.555	-0.555	0.000	0.000	0.000	0.000
92	A	91	TYR	0	-0.001	0.001	21.764	-0.147	-0.147	0.000	0.000	0.000	0.000
93	A	92	TYR	0	-0.002	-0.017	23.746	-0.195	-0.195	0.000	0.000	0.000	0.000
94	A	93	GLU	-1	-0.839	-0.909	24.894	-11.689	-11.689	0.000	0.000	0.000	0.000
95	A	94	LEU	0	-0.030	-0.019	18.747	-0.262	-0.262	0.000	0.000	0.000	0.000
96	A	95	LEU	0	-0.026	-0.027	22.178	-0.193	-0.193	0.000	0.000	0.000	0.000
97	A	96	ASP	-1	-0.970	-0.968	24.007	-10.981	-10.981	0.000	0.000	0.000	0.000
98	A	97	ARG	1	0.801	0.882	22.833	12.964	12.964	0.000	0.000	0.000	0.000
99	A	98	CYS	0	-0.050	0.004	19.870	-0.797	-0.797	0.000	0.000	0.000	0.000
100	A	99	PRO	0	-0.025	-0.021	19.941	0.521	0.521	0.000	0.000	0.000	0.000
101	A	100	GLU	-1	-0.797	-0.897	21.017	-13.005	-13.005	0.000	0.000	0.000	0.000
102	A	101	GLN	0	-0.030	-0.018	18.523	-0.708	-0.708	0.000	0.000	0.000	0.000
103	A	102	TYR	0	-0.006	-0.007	15.474	-1.122	-1.122	0.000	0.000	0.000	0.000
104	A	103	LYS	1	0.906	0.951	17.355	11.817	11.817	0.000	0.000	0.000	0.000
105	A	104	GLN	0	-0.020	-0.014	15.421	0.617	0.617	0.000	0.000	0.000	0.000
106	A	105	LYS	1	0.795	0.899	11.804	23.835	23.835	0.000	0.000	0.000	0.000
107	A	106	ILE	0	-0.034	-0.005	15.435	-0.959	-0.959	0.000	0.000	0.000	0.000
108	A	107	PHE	0	0.027	0.012	15.775	0.875	0.875	0.000	0.000	0.000	0.000
109	A	108	LYS	1	0.894	0.956	19.088	12.093	12.093	0.000	0.000	0.000	0.000
110	A	109	MET	0	-0.023	-0.015	16.087	-0.584	-0.584	0.000	0.000	0.000	0.000
111	A	110	VAL	0	0.024	-0.014	19.699	-0.148	-0.148	0.000	0.000	0.000	0.000
112	A	111	ASP	-1	-0.906	-0.937	21.455	-12.974	-12.974	0.000	0.000	0.000	0.000
113	A	112	PHE	0	-0.006	-0.002	16.396	-0.309	-0.309	0.000	0.000	0.000	0.000
114	A	113	CYS	0	-0.072	-0.009	20.451	-0.251	-0.251	0.000	0.000	0.000	0.000
115	A	114	THR	0	-0.064	-0.047	22.525	0.300	0.300	0.000	0.000	0.000	0.000
116	A	115	THR	0	-0.078	-0.040	25.284	0.653	0.653	0.000	0.000	0.000	0.000
117	A	116	ILE	0	-0.071	-0.049	26.570	0.635	0.635	0.000	0.000	0.000	0.000
118	A	117	LYS	1	0.961	0.979	27.670	9.344	9.344	0.000	0.000	0.000	0.000
119	A	118	THR	0	-0.038	-0.050	26.798	0.471	0.471	0.000	0.000	0.000	0.000
120	A	119	THR	0	0.029	0.014	28.550	-0.120	-0.120	0.000	0.000	0.000	0.000
121	A	120	GLU	-1	-0.904	-0.949	26.135	-10.974	-10.974	0.000	0.000	0.000	0.000
122	A	121	VAL	0	0.020	0.014	22.049	0.205	0.205	0.000	0.000	0.000	0.000
123	A	122	PRO	0	0.008	0.001	25.520	-0.067	-0.067	0.000	0.000	0.000	0.000
124	A	123	ASP	-1	-0.823	-0.913	28.194	-11.454	-11.454	0.000	0.000	0.000	0.000
125	A	124	PRO	0	-0.032	-0.011	27.243	0.390	0.390	0.000	0.000	0.000	0.000
126	A	125	TYR	0	0.008	0.011	29.663	0.377	0.377	0.000	0.000	0.000	0.000
127	A	126	TYR	0	0.037	0.011	31.280	0.311	0.311	0.000	0.000	0.000	0.000
128	A	127	GLY	0	0.011	0.020	33.849	0.318	0.318	0.000	0.000	0.000	0.000
129	A	128	GLY	0	0.031	0.003	34.793	-0.034	-0.034	0.000	0.000	0.000	0.000
130	A	129	GLU	-1	-0.803	-0.898	32.364	-9.790	-9.790	0.000	0.000	0.000	0.000
131	A	130	LYS	1	0.859	0.933	30.971	9.917	9.917	0.000	0.000	0.000	0.000
132	A	131	GLY	0	0.028	0.016	31.628	-0.176	-0.176	0.000	0.000	0.000	0.000
133	A	132	PHE	0	0.058	0.006	27.483	-0.356	-0.356	0.000	0.000	0.000	0.000
134	A	133	HIS	0	0.037	0.014	27.008	-0.650	-0.650	0.000	0.000	0.000	0.000
135	A	134	ARG	1	0.890	0.970	27.475	10.395	10.395	0.000	0.000	0.000	0.000
136	A	135	VAL	0	0.026	0.013	23.282	-0.240	-0.240	0.000	0.000	0.000	0.000
137	A	136	ILE	0	-0.001	0.001	22.321	-0.518	-0.518	0.000	0.000	0.000	0.000
138	A	137	ASP	-1	-0.803	-0.892	23.265	-11.431	-11.431	0.000	0.000	0.000	0.000
139	A	138	ILE	0	-0.058	-0.024	23.084	-0.065	-0.065	0.000	0.000	0.000	0.000
140	A	139	LEU	0	0.036	0.024	18.537	-0.433	-0.433	0.000	0.000	0.000	0.000
141	A	140	GLU	-1	-0.786	-0.858	19.315	-14.159	-14.159	0.000	0.000	0.000	0.000
142	A	141	ASP	-1	-0.768	-0.840	20.643	-13.431	-13.431	0.000	0.000	0.000	0.000
143	A	142	ALA	0	0.015	0.005	19.621	-0.517	-0.517	0.000	0.000	0.000	0.000
144	A	143	CYS	0	-0.008	-0.022	15.241	-0.686	-0.686	0.000	0.000	0.000	0.000
145	A	144	GLU	-1	-0.807	-0.879	15.119	-19.400	-19.400	0.000	0.000	0.000	0.000
146	A	145	ASN	0	-0.026	-0.033	16.865	-0.722	-0.722	0.000	0.000	0.000	0.000
147	A	146	LEU	0	0.000	0.008	12.655	-0.569	-0.569	0.000	0.000	0.000	0.000
148	A	147	ILE	0	-0.016	-0.015	9.329	-1.379	-1.379	0.000	0.000	0.000	0.000
149	A	148	ILE	0	-0.004	0.006	12.165	-1.054	-1.054	0.000	0.000	0.000	0.000
150	A	149	LYS	1	0.910	0.955	14.210	15.707	15.707	0.000	0.000	0.000	0.000
151	A	150	LEU	0	0.009	0.017	9.088	-0.233	-0.233	0.000	0.000	0.000	0.000
152	A	151	GLU	-1	-0.815	-0.870	8.311	-34.726	-34.726	0.000	0.000	0.000	0.000
153	A	152	GLU	-1	-0.943	-0.960	10.995	-15.884	-15.884	0.000	0.000	0.000	0.000
154	A	153	GLY	0	-0.025	-0.003	12.065	1.035	1.035	0.000	0.000	0.000	0.000
155	A	154	LYS	1	0.752	0.854	12.959	17.670	17.670	0.000	0.000	0.000	0.000
156	A	155	LEU	-1	-0.870	-0.893	12.780	-20.339	-20.339	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:0:SER)