FMO DATABASE

FMODB ID: VV461

Calculation Name: 2JM5-A-Other547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2JM5

Chain ID: A

ChEMBL ID:

UniProt ID: Q9NS28

Base Structure: SolutionNMR

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	134
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1233049.702949
FMO2-HF: Nuclear repulsion	1178220.729606
FMO2-HF: Total energy	-54828.973343
FMO2-MP2: Total energy	-54989.637955

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:1:SER)

Summations of interaction energy for fragment #1(A:1: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.
-192.677	-191.698	16.141	-9.047	-8.074	-0.082

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.814 / q_NPA : 0.877

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	3	VAL	0	0.015	0.018	3.837	4.478	5.902	-0.019	-0.567	-0.838	-0.002
23	A	23	ASP	-1	-0.804	-0.897	2.011	-107.738	-109.640	14.774	-7.648	-5.225	-0.080
24	A	24	GLY	0	0.042	0.022	3.633	-0.930	-0.740	0.000	-0.015	-0.175	0.000
26	A	26	GLU	-1	-0.967	-0.984	2.455	-44.289	-43.470	1.387	-0.736	-1.470	0.000
27	A	27	ALA	0	-0.011	-0.017	4.752	1.518	1.617	-0.001	-0.007	-0.091	0.000
30	A	30	ARG	1	0.931	0.967	3.438	44.871	45.170	0.001	-0.067	-0.233	0.000
129	A	129	LEU	0	-0.009	-0.015	4.499	-1.382	-1.332	-0.001	-0.007	-0.042	0.000
4	A	4	SER	0	0.032	0.022	5.651	1.266	1.266	0.000	0.000	0.000	0.000
5	A	5	PRO	0	0.121	0.047	9.414	-0.091	-0.091	0.000	0.000	0.000	0.000
6	A	6	GLU	-1	-0.974	-0.974	11.267	-18.317	-18.317	0.000	0.000	0.000	0.000
7	A	7	GLU	-1	-0.775	-0.875	8.618	-25.187	-25.187	0.000	0.000	0.000	0.000
8	A	8	ALA	0	0.050	0.029	8.460	0.189	0.189	0.000	0.000	0.000	0.000
9	A	9	VAL	0	0.013	0.012	10.060	1.409	1.409	0.000	0.000	0.000	0.000
10	A	10	LYS	1	0.797	0.897	12.972	18.317	18.317	0.000	0.000	0.000	0.000
11	A	11	TRP	0	-0.021	-0.022	4.866	-0.115	-0.115	0.000	0.000	0.000	0.000
12	A	12	GLY	0	0.040	0.042	12.752	0.528	0.528	0.000	0.000	0.000	0.000
13	A	13	GLU	-1	-0.868	-0.914	15.588	-15.286	-15.286	0.000	0.000	0.000	0.000
14	A	14	SER	0	-0.071	-0.052	16.274	0.929	0.929	0.000	0.000	0.000	0.000
15	A	15	PHE	0	0.024	0.034	14.084	-1.254	-1.254	0.000	0.000	0.000	0.000
16	A	16	ASP	-1	-0.866	-0.929	14.667	-18.685	-18.685	0.000	0.000	0.000	0.000
17	A	17	LYS	1	0.814	0.888	12.048	22.134	22.134	0.000	0.000	0.000	0.000
18	A	18	LEU	0	-0.031	0.008	9.221	-1.861	-1.861	0.000	0.000	0.000	0.000
19	A	19	LEU	0	-0.010	-0.008	9.864	-2.452	-2.452	0.000	0.000	0.000	0.000
20	A	20	SER	0	-0.047	-0.022	11.831	-0.658	-0.658	0.000	0.000	0.000	0.000
21	A	21	HIS	0	-0.003	0.013	5.726	-2.070	-2.070	0.000	0.000	0.000	0.000
22	A	22	ARG	1	0.890	0.934	6.117	26.817	26.817	0.000	0.000	0.000	0.000
25	A	25	LEU	0	-0.003	-0.005	6.865	1.819	1.819	0.000	0.000	0.000	0.000
28	A	28	PHE	0	0.013	-0.008	5.431	3.532	3.532	0.000	0.000	0.000	0.000
29	A	29	THR	0	0.025	0.008	6.742	3.058	3.058	0.000	0.000	0.000	0.000
31	A	31	PHE	0	0.014	0.005	7.628	1.990	1.990	0.000	0.000	0.000	0.000
32	A	32	LEU	0	0.004	0.008	10.529	1.605	1.605	0.000	0.000	0.000	0.000
33	A	33	LYS	1	0.781	0.868	9.087	24.745	24.745	0.000	0.000	0.000	0.000
34	A	34	THR	0	-0.048	-0.010	11.724	1.231	1.231	0.000	0.000	0.000	0.000
35	A	35	GLU	-1	-0.852	-0.886	13.364	-15.063	-15.063	0.000	0.000	0.000	0.000
36	A	36	PHE	0	-0.079	-0.040	15.807	0.824	0.824	0.000	0.000	0.000	0.000
37	A	37	SER	0	0.074	0.051	16.155	1.077	1.077	0.000	0.000	0.000	0.000
38	A	38	GLU	-1	-0.818	-0.908	13.276	-19.743	-19.743	0.000	0.000	0.000	0.000
39	A	39	GLU	-1	-0.863	-0.931	14.722	-15.692	-15.692	0.000	0.000	0.000	0.000
40	A	40	ASN	0	-0.009	-0.014	17.252	1.183	1.183	0.000	0.000	0.000	0.000
41	A	41	ILE	0	0.033	0.005	11.161	0.239	0.239	0.000	0.000	0.000	0.000
42	A	42	GLU	-1	-0.904	-0.967	12.782	-20.850	-20.850	0.000	0.000	0.000	0.000
43	A	43	PHE	0	0.002	0.020	16.113	0.745	0.745	0.000	0.000	0.000	0.000
44	A	44	TRP	0	0.039	0.011	14.094	0.511	0.511	0.000	0.000	0.000	0.000
45	A	45	ILE	0	0.025	0.020	12.776	0.261	0.261	0.000	0.000	0.000	0.000
46	A	46	ALA	0	0.007	0.008	17.197	0.392	0.392	0.000	0.000	0.000	0.000
47	A	47	CYS	0	-0.041	-0.025	20.224	0.854	0.854	0.000	0.000	0.000	0.000
48	A	48	GLU	-1	-0.780	-0.882	18.523	-13.703	-13.703	0.000	0.000	0.000	0.000
49	A	49	ASP	-1	-0.834	-0.904	18.873	-14.962	-14.962	0.000	0.000	0.000	0.000
50	A	50	PHE	0	-0.065	-0.025	20.649	0.575	0.575	0.000	0.000	0.000	0.000
51	A	51	LYS	1	0.877	0.937	21.050	14.853	14.853	0.000	0.000	0.000	0.000
52	A	52	LYS	1	0.865	0.933	17.757	16.545	16.545	0.000	0.000	0.000	0.000
53	A	53	SER	0	-0.046	-0.002	23.463	0.282	0.282	0.000	0.000	0.000	0.000
54	A	54	LYS	1	1.026	0.996	26.808	9.890	9.890	0.000	0.000	0.000	0.000
55	A	55	GLY	0	-0.024	-0.015	29.865	0.393	0.393	0.000	0.000	0.000	0.000
56	A	56	PRO	0	0.053	0.011	32.263	-0.127	-0.127	0.000	0.000	0.000	0.000
57	A	57	GLN	0	0.052	0.032	33.376	-0.013	-0.013	0.000	0.000	0.000	0.000
58	A	58	GLN	0	0.037	0.012	28.692	-0.142	-0.142	0.000	0.000	0.000	0.000
59	A	59	ILE	0	-0.049	-0.011	29.094	-0.314	-0.314	0.000	0.000	0.000	0.000
60	A	60	HIS	0	0.036	-0.007	31.085	0.040	0.040	0.000	0.000	0.000	0.000
61	A	61	LEU	0	-0.045	-0.009	30.913	-0.026	-0.026	0.000	0.000	0.000	0.000
62	A	62	LYS	1	0.867	0.929	22.988	13.011	13.011	0.000	0.000	0.000	0.000
63	A	63	ALA	0	0.019	0.027	27.756	-0.227	-0.227	0.000	0.000	0.000	0.000
64	A	64	LYS	1	0.959	0.974	29.639	8.679	8.679	0.000	0.000	0.000	0.000
65	A	65	ALA	0	0.041	0.025	27.607	-0.025	-0.025	0.000	0.000	0.000	0.000
66	A	66	ILE	0	-0.029	-0.018	23.929	-0.203	-0.203	0.000	0.000	0.000	0.000
67	A	67	TYR	0	0.029	-0.010	26.419	-0.076	-0.076	0.000	0.000	0.000	0.000
68	A	68	GLU	-1	-0.934	-0.987	29.423	-9.111	-9.111	0.000	0.000	0.000	0.000
69	A	69	LYS	1	0.914	0.977	20.849	13.729	13.729	0.000	0.000	0.000	0.000
70	A	70	PHE	0	0.001	-0.017	20.329	-0.254	-0.254	0.000	0.000	0.000	0.000
71	A	71	ILE	0	-0.008	0.001	26.127	0.045	0.045	0.000	0.000	0.000	0.000
72	A	72	GLN	0	-0.009	-0.009	28.831	0.333	0.333	0.000	0.000	0.000	0.000
73	A	73	THR	0	-0.022	-0.001	30.069	-0.279	-0.279	0.000	0.000	0.000	0.000
74	A	74	ASP	-1	-0.940	-0.949	31.889	-8.795	-8.795	0.000	0.000	0.000	0.000
75	A	75	ALA	0	0.015	0.005	28.496	-0.042	-0.042	0.000	0.000	0.000	0.000
76	A	76	PRO	0	-0.078	-0.032	26.727	-0.052	-0.052	0.000	0.000	0.000	0.000
77	A	77	LYS	1	0.769	0.868	20.530	13.320	13.320	0.000	0.000	0.000	0.000
78	A	78	GLU	-1	-0.838	-0.902	25.145	-10.040	-10.040	0.000	0.000	0.000	0.000
79	A	79	VAL	0	0.004	0.005	23.077	-0.529	-0.529	0.000	0.000	0.000	0.000
80	A	80	ASN	0	0.018	0.026	23.823	0.699	0.699	0.000	0.000	0.000	0.000
81	A	81	LEU	0	-0.058	-0.040	26.076	-0.026	-0.026	0.000	0.000	0.000	0.000
82	A	82	ASP	-1	-0.784	-0.880	27.502	-9.370	-9.370	0.000	0.000	0.000	0.000
83	A	83	PHE	0	0.030	0.019	30.279	-0.024	-0.024	0.000	0.000	0.000	0.000
84	A	84	HIS	0	-0.015	-0.013	33.629	0.018	0.018	0.000	0.000	0.000	0.000
85	A	85	THR	0	-0.016	-0.040	28.824	-0.031	-0.031	0.000	0.000	0.000	0.000
86	A	86	LYS	1	0.920	0.952	30.667	9.713	9.713	0.000	0.000	0.000	0.000
87	A	87	GLU	-1	-0.870	-0.908	32.293	-7.957	-7.957	0.000	0.000	0.000	0.000
88	A	88	VAL	0	0.015	0.016	34.534	0.160	0.160	0.000	0.000	0.000	0.000
89	A	89	ILE	0	-0.016	-0.008	29.373	0.048	0.048	0.000	0.000	0.000	0.000
90	A	90	THR	0	-0.067	-0.049	33.644	0.158	0.158	0.000	0.000	0.000	0.000
91	A	91	ASN	0	-0.047	-0.021	36.019	0.342	0.342	0.000	0.000	0.000	0.000
92	A	92	SER	0	0.019	0.003	35.397	0.165	0.165	0.000	0.000	0.000	0.000
93	A	93	ILE	0	-0.073	-0.022	31.311	-0.054	-0.054	0.000	0.000	0.000	0.000
94	A	94	THR	0	-0.041	-0.036	35.154	0.003	0.003	0.000	0.000	0.000	0.000
95	A	95	GLN	0	-0.071	-0.026	37.635	0.292	0.292	0.000	0.000	0.000	0.000
96	A	96	PRO	0	-0.012	0.022	32.590	-0.132	-0.132	0.000	0.000	0.000	0.000
97	A	97	THR	0	0.040	0.008	32.333	-0.021	-0.021	0.000	0.000	0.000	0.000
98	A	98	LEU	0	-0.036	-0.030	27.321	-0.186	-0.186	0.000	0.000	0.000	0.000
99	A	99	HIS	1	0.878	0.912	23.779	12.157	12.157	0.000	0.000	0.000	0.000
100	A	100	SER	0	0.021	0.019	27.550	-0.048	-0.048	0.000	0.000	0.000	0.000
101	A	101	PHE	0	0.032	0.007	25.398	0.181	0.181	0.000	0.000	0.000	0.000
102	A	102	ASP	-1	-0.917	-0.946	25.618	-11.235	-11.235	0.000	0.000	0.000	0.000
103	A	103	ALA	0	0.071	0.027	25.846	-0.385	-0.385	0.000	0.000	0.000	0.000
104	A	104	ALA	0	0.025	0.002	26.045	-0.146	-0.146	0.000	0.000	0.000	0.000
105	A	105	GLN	0	-0.011	-0.002	20.447	-0.576	-0.576	0.000	0.000	0.000	0.000
106	A	106	SER	0	0.011	0.010	21.859	-0.478	-0.478	0.000	0.000	0.000	0.000
107	A	107	ARG	1	0.862	0.926	23.747	10.417	10.417	0.000	0.000	0.000	0.000
108	A	108	VAL	0	0.066	0.020	19.299	-0.030	-0.030	0.000	0.000	0.000	0.000
109	A	109	TYR	0	-0.002	0.008	17.530	-0.676	-0.676	0.000	0.000	0.000	0.000
110	A	110	GLN	0	-0.006	-0.019	19.730	0.073	0.073	0.000	0.000	0.000	0.000
111	A	111	LEU	0	-0.033	-0.007	21.737	0.075	0.075	0.000	0.000	0.000	0.000
112	A	112	MET	0	-0.020	-0.001	16.041	-0.382	-0.382	0.000	0.000	0.000	0.000
113	A	113	GLU	-1	-0.900	-0.952	17.483	-14.894	-14.894	0.000	0.000	0.000	0.000
114	A	114	GLN	0	0.020	-0.001	19.309	-0.149	-0.149	0.000	0.000	0.000	0.000
115	A	115	ASP	-1	-0.867	-0.894	19.728	-14.135	-14.135	0.000	0.000	0.000	0.000
116	A	116	SER	0	-0.005	-0.021	15.620	-0.333	-0.333	0.000	0.000	0.000	0.000
117	A	117	TYR	0	-0.107	-0.068	14.216	-0.658	-0.658	0.000	0.000	0.000	0.000
118	A	118	THR	0	-0.015	-0.009	16.183	-0.687	-0.687	0.000	0.000	0.000	0.000
119	A	119	ARG	1	0.744	0.823	17.228	15.316	15.316	0.000	0.000	0.000	0.000
120	A	120	PHE	0	0.031	0.028	8.677	-0.431	-0.431	0.000	0.000	0.000	0.000
121	A	121	LEU	0	-0.002	0.014	13.121	-1.062	-1.062	0.000	0.000	0.000	0.000
122	A	122	LYS	1	0.828	0.916	14.785	16.218	16.218	0.000	0.000	0.000	0.000
123	A	123	SER	0	0.007	-0.004	12.001	0.019	0.019	0.000	0.000	0.000	0.000
124	A	124	ASP	-1	-0.863	-0.951	11.846	-23.123	-23.123	0.000	0.000	0.000	0.000
125	A	125	ILE	0	-0.033	-0.005	5.206	-2.033	-2.033	0.000	0.000	0.000	0.000
126	A	126	TYR	0	-0.011	-0.029	7.565	-2.792	-2.792	0.000	0.000	0.000	0.000
127	A	127	LEU	0	-0.036	-0.031	9.678	-0.099	-0.099	0.000	0.000	0.000	0.000
128	A	128	ASP	-1	-0.970	-0.972	7.181	-31.428	-31.428	0.000	0.000	0.000	0.000
130	A	130	MET	0	-0.104	-0.043	8.189	1.614	1.614	0.000	0.000	0.000	0.000
131	A	131	GLU	-1	-0.979	-0.974	10.541	-24.160	-24.160	0.000	0.000	0.000	0.000
132	A	132	GLY	0	-0.018	-0.004	12.803	1.491	1.491	0.000	0.000	0.000	0.000
133	A	133	ARG	1	0.842	0.913	16.008	14.425	14.425	0.000	0.000	0.000	0.000
134	A	134	PRO	-1	-0.868	-0.926	14.294	-16.154	-16.154	0.000	0.000	0.000	0.000

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