FMO DATABASE

FMODB ID: LVM19

Calculation Name: 1JA3-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1JA3

Chain ID: A

ChEMBL ID:

UniProt ID: Q9JHN9

Base Structure: X-ray

Registration Date: 2025-10-05

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	118
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1148551.176701
FMO2-HF: Nuclear repulsion	1095785.601706
FMO2-HF: Total energy	-52765.574994
FMO2-MP2: Total energy	-52913.650751

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:140:VAL)

Summations of interaction energy for fragment #1(A:140:VAL)

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.
-6.902	-1.111	11.605	-7.72	-9.674	-0.078

Interaction energy analysis for fragmet #1(A:140:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.840 / q_NPA : 0.912

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

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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	142	TYR	0	0.009	0.030	2.595	1.018	3.809	0.330	-1.102	-2.020	-0.005
4	A	143	TRP	0	0.026	0.009	4.728	0.638	0.654	-0.001	-0.006	-0.009	0.000
14	A	154	ILE	0	-0.024	-0.020	3.841	-9.732	-9.390	0.003	-0.133	-0.211	-0.001
15	A	155	MET	0	0.003	0.022	2.039	7.051	6.350	6.764	-1.919	-4.143	-0.006
16	A	156	ASN	0	-0.001	-0.021	2.007	-37.530	-34.250	4.510	-4.548	-3.242	-0.066
17	A	157	LYS	1	0.832	0.926	4.772	33.600	33.663	-0.001	-0.012	-0.049	0.000
5	A	144	PHE	0	0.033	0.012	8.401	0.348	0.348	0.000	0.000	0.000	0.000
6	A	145	CYS	0	-0.024	0.006	11.114	-0.118	-0.118	0.000	0.000	0.000	0.000
7	A	146	TYR	0	0.016	0.013	14.807	0.232	0.232	0.000	0.000	0.000	0.000
8	A	147	GLY	0	0.040	0.028	17.500	0.123	0.123	0.000	0.000	0.000	0.000
9	A	148	THR	0	0.003	0.000	20.915	-0.166	-0.166	0.000	0.000	0.000	0.000
10	A	149	LYS	1	0.794	0.880	17.196	15.223	15.223	0.000	0.000	0.000	0.000
11	A	151	TYR	0	-0.052	-0.072	11.208	0.004	0.004	0.000	0.000	0.000	0.000
12	A	152	TYR	0	0.023	-0.004	7.485	-0.518	-0.518	0.000	0.000	0.000	0.000
13	A	153	PHE	0	0.023	0.014	5.213	1.237	1.237	0.000	0.000	0.000	0.000
18	A	158	THR	0	-0.023	-0.021	8.041	1.770	1.770	0.000	0.000	0.000	0.000
19	A	159	THR	0	0.065	0.045	10.745	0.107	0.107	0.000	0.000	0.000	0.000
20	A	160	TRP	0	0.030	0.019	13.214	-1.226	-1.226	0.000	0.000	0.000	0.000
21	A	161	SER	0	-0.017	-0.046	15.147	-0.111	-0.111	0.000	0.000	0.000	0.000
22	A	162	GLY	0	0.016	0.015	12.248	0.326	0.326	0.000	0.000	0.000	0.000
23	A	163	CYS	0	-0.035	-0.011	7.793	2.024	2.024	0.000	0.000	0.000	0.000
24	A	164	LYS	1	0.931	0.993	12.749	15.648	15.648	0.000	0.000	0.000	0.000
25	A	165	ALA	0	0.049	0.033	13.396	0.112	0.112	0.000	0.000	0.000	0.000
26	A	166	ASN	0	0.012	-0.016	8.305	-1.517	-1.517	0.000	0.000	0.000	0.000
27	A	167	CYS	0	-0.086	-0.024	10.156	0.538	0.538	0.000	0.000	0.000	0.000
28	A	168	GLN	0	0.023	0.011	13.461	0.414	0.414	0.000	0.000	0.000	0.000
29	A	169	HIS	0	-0.022	-0.003	10.850	-0.626	-0.626	0.000	0.000	0.000	0.000
30	A	170	TYR	0	-0.028	-0.022	7.800	-2.085	-2.085	0.000	0.000	0.000	0.000
31	A	171	SER	0	-0.012	0.003	13.330	0.826	0.826	0.000	0.000	0.000	0.000
32	A	172	VAL	0	-0.038	-0.010	13.848	0.954	0.954	0.000	0.000	0.000	0.000
33	A	173	PRO	0	0.019	0.022	15.730	-0.633	-0.633	0.000	0.000	0.000	0.000
34	A	174	ILE	0	0.016	-0.016	13.477	-1.202	-1.202	0.000	0.000	0.000	0.000
35	A	175	VAL	0	-0.026	-0.010	13.950	1.248	1.248	0.000	0.000	0.000	0.000
36	A	176	LYS	1	0.888	0.954	15.820	12.878	12.878	0.000	0.000	0.000	0.000
37	A	177	ILE	0	-0.029	-0.025	16.691	-0.169	-0.169	0.000	0.000	0.000	0.000
38	A	178	GLU	-1	-0.850	-0.928	19.978	-12.728	-12.728	0.000	0.000	0.000	0.000
39	A	179	ASP	-1	-0.823	-0.910	22.453	-12.025	-12.025	0.000	0.000	0.000	0.000
40	A	180	GLU	-1	-0.872	-0.960	22.175	-11.849	-11.849	0.000	0.000	0.000	0.000
41	A	181	ASP	-1	-0.894	-0.929	22.149	-11.941	-11.941	0.000	0.000	0.000	0.000
42	A	182	GLU	-1	-0.782	-0.844	17.846	-16.111	-16.111	0.000	0.000	0.000	0.000
43	A	183	LEU	0	-0.025	-0.010	17.981	-0.912	-0.912	0.000	0.000	0.000	0.000
44	A	184	LYS	1	0.903	0.941	17.735	11.858	11.858	0.000	0.000	0.000	0.000
45	A	185	PHE	0	0.008	0.016	13.360	-0.555	-0.555	0.000	0.000	0.000	0.000
46	A	186	LEU	0	0.025	0.003	13.314	-1.035	-1.035	0.000	0.000	0.000	0.000
47	A	187	GLN	0	-0.049	-0.031	13.378	-0.767	-0.767	0.000	0.000	0.000	0.000
48	A	188	ARG	1	0.887	0.934	15.056	14.219	14.219	0.000	0.000	0.000	0.000
49	A	189	HIS	0	0.004	0.021	8.465	-0.651	-0.651	0.000	0.000	0.000	0.000
50	A	190	VAL	0	-0.071	-0.018	8.731	-1.684	-1.684	0.000	0.000	0.000	0.000
51	A	191	ILE	0	0.041	0.026	7.212	1.644	1.644	0.000	0.000	0.000	0.000
52	A	192	PRO	0	-0.029	-0.041	9.678	0.387	0.387	0.000	0.000	0.000	0.000
53	A	193	GLU	-1	-0.794	-0.882	8.576	-29.051	-29.051	0.000	0.000	0.000	0.000
54	A	194	GLY	0	-0.020	0.004	11.897	1.311	1.311	0.000	0.000	0.000	0.000
55	A	195	TYR	0	-0.009	-0.033	6.054	-2.284	-2.284	0.000	0.000	0.000	0.000
56	A	196	TRP	0	0.007	-0.022	11.774	2.729	2.729	0.000	0.000	0.000	0.000
57	A	197	ILE	0	-0.019	-0.008	13.310	-0.718	-0.718	0.000	0.000	0.000	0.000
58	A	198	GLY	0	0.026	0.002	16.074	0.190	0.190	0.000	0.000	0.000	0.000
59	A	199	LEU	0	-0.059	-0.010	18.544	0.616	0.616	0.000	0.000	0.000	0.000
60	A	200	SER	0	-0.011	-0.016	20.989	-0.411	-0.411	0.000	0.000	0.000	0.000
61	A	201	TYR	-1	-0.855	-0.942	22.949	-9.939	-9.939	0.000	0.000	0.000	0.000
62	A	202	ASP	-1	-0.872	-0.937	26.171	-11.246	-11.246	0.000	0.000	0.000	0.000
63	A	203	LYS	1	0.890	0.931	28.259	11.303	11.303	0.000	0.000	0.000	0.000
64	A	204	LYS	1	0.890	0.954	31.351	9.986	9.986	0.000	0.000	0.000	0.000
65	A	205	LYS	1	0.830	0.902	30.467	10.365	10.365	0.000	0.000	0.000	0.000
66	A	206	LYS	1	1.003	1.023	33.488	9.315	9.315	0.000	0.000	0.000	0.000
67	A	207	GLU	-1	-0.885	-0.949	30.858	-9.518	-9.518	0.000	0.000	0.000	0.000
68	A	208	TRP	0	-0.006	0.008	22.752	-0.434	-0.434	0.000	0.000	0.000	0.000
69	A	209	ALA	0	-0.016	-0.013	25.912	0.373	0.373	0.000	0.000	0.000	0.000
70	A	210	TRP	0	0.000	0.001	19.325	-0.732	-0.732	0.000	0.000	0.000	0.000
71	A	211	ILE	0	0.019	-0.003	20.812	-0.660	-0.660	0.000	0.000	0.000	0.000
72	A	212	ASP	-1	-0.847	-0.895	23.917	-11.501	-11.501	0.000	0.000	0.000	0.000
73	A	213	ASN	0	-0.021	-0.045	26.214	-0.496	-0.496	0.000	0.000	0.000	0.000
74	A	214	GLY	0	0.000	-0.005	27.009	-0.078	-0.078	0.000	0.000	0.000	0.000
75	A	215	PRO	0	0.014	0.004	26.360	0.178	0.178	0.000	0.000	0.000	0.000
76	A	216	SER	0	-0.025	0.003	24.921	-0.033	-0.033	0.000	0.000	0.000	0.000
77	A	217	LYS	0	0.056	0.027	24.990	0.252	0.252	0.000	0.000	0.000	0.000
78	A	218	PHE	0	0.013	0.001	27.642	0.262	0.262	0.000	0.000	0.000	0.000
79	A	219	ASP	-1	-0.786	-0.871	28.411	-9.723	-9.723	0.000	0.000	0.000	0.000
80	A	220	MET	0	-0.021	-0.002	24.865	-0.007	-0.007	0.000	0.000	0.000	0.000
81	A	221	LYS	1	0.895	0.920	29.540	8.972	8.972	0.000	0.000	0.000	0.000
82	A	222	ILE	0	0.019	0.020	26.859	0.054	0.054	0.000	0.000	0.000	0.000
83	A	223	ARG	1	0.797	0.917	25.410	11.032	11.032	0.000	0.000	0.000	0.000
84	A	224	LYS	1	0.912	0.940	25.598	12.230	12.230	0.000	0.000	0.000	0.000
85	A	225	MET	0	0.077	0.066	31.049	0.259	0.259	0.000	0.000	0.000	0.000
86	A	226	ASN	0	-0.051	-0.039	27.983	0.570	0.570	0.000	0.000	0.000	0.000
87	A	227	PHE	0	0.021	0.011	29.921	-0.244	-0.244	0.000	0.000	0.000	0.000
88	A	228	LYS	1	0.825	0.893	31.839	9.089	9.089	0.000	0.000	0.000	0.000
89	A	229	SER	0	-0.035	0.000	27.675	0.178	0.178	0.000	0.000	0.000	0.000
90	A	230	ARG	0	0.051	0.032	27.397	-0.209	-0.209	0.000	0.000	0.000	0.000
91	A	231	GLY	0	0.020	0.014	23.836	0.046	0.046	0.000	0.000	0.000	0.000
92	A	232	CYS	0	-0.090	-0.052	18.579	-0.563	-0.563	0.000	0.000	0.000	0.000
93	A	233	VAL	0	0.018	0.006	19.661	0.184	0.184	0.000	0.000	0.000	0.000
94	A	234	PHE	0	-0.031	-0.009	15.641	-0.948	-0.948	0.000	0.000	0.000	0.000
95	A	235	LEU	0	0.002	-0.002	13.325	1.264	1.264	0.000	0.000	0.000	0.000
96	A	236	SER	0	0.028	0.003	14.452	-1.042	-1.042	0.000	0.000	0.000	0.000
97	A	237	LYS	1	0.967	0.983	14.869	16.205	16.205	0.000	0.000	0.000	0.000
98	A	238	ALA	0	-0.062	-0.029	16.354	0.851	0.851	0.000	0.000	0.000	0.000
99	A	239	ARG	1	0.882	0.933	19.346	14.118	14.118	0.000	0.000	0.000	0.000
100	A	240	ILE	0	0.063	0.039	18.473	-0.874	-0.874	0.000	0.000	0.000	0.000
101	A	241	GLU	-1	-0.878	-0.927	20.228	-12.471	-12.471	0.000	0.000	0.000	0.000
102	A	242	ASP	-1	-0.788	-0.905	20.897	-12.823	-12.823	0.000	0.000	0.000	0.000
103	A	243	THR	0	-0.006	-0.003	19.558	0.204	0.204	0.000	0.000	0.000	0.000
104	A	244	ASP	-1	-0.769	-0.871	20.563	-13.685	-13.685	0.000	0.000	0.000	0.000
105	A	246	ASN	0	-0.063	-0.052	17.250	-1.427	-1.427	0.000	0.000	0.000	0.000
106	A	247	ILE	0	0.061	0.036	14.871	-0.446	-0.446	0.000	0.000	0.000	0.000
107	A	248	PRO	0	-0.014	-0.012	11.668	-0.959	-0.959	0.000	0.000	0.000	0.000
108	A	249	TYR	0	-0.003	-0.014	10.821	-0.093	-0.093	0.000	0.000	0.000	0.000
109	A	250	TYR	0	0.016	0.025	5.642	-4.762	-4.762	0.000	0.000	0.000	0.000
110	A	252	ILE	0	0.048	0.031	8.093	-3.118	-3.118	0.000	0.000	0.000	0.000
111	A	254	GLY	0	0.018	-0.007	12.002	-0.682	-0.682	0.000	0.000	0.000	0.000
112	A	255	LYS	1	0.927	0.983	14.664	15.612	15.612	0.000	0.000	0.000	0.000
113	A	256	LYS	1	0.924	0.961	17.472	12.706	12.706	0.000	0.000	0.000	0.000
114	A	257	LEU	0	0.012	-0.005	18.153	-0.263	-0.263	0.000	0.000	0.000	0.000
115	A	258	ASP	-1	-0.870	-0.926	21.938	-11.867	-11.867	0.000	0.000	0.000	0.000
116	A	259	LYS	1	0.805	0.871	24.418	11.204	11.204	0.000	0.000	0.000	0.000
117	A	260	PHE	0	-0.016	-0.001	23.328	0.147	0.147	0.000	0.000	0.000	0.000
118	A	261	PRO	-1	-0.900	-0.926	21.600	-13.936	-13.936	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:140:VAL)