FMO DATABASE

FMODB ID: LVVG9

Calculation Name: 2P9M-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2P9M

Chain ID: A

ChEMBL ID:

UniProt ID: Q58332

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	133
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1145258.089468
FMO2-HF: Nuclear repulsion	1093269.549859
FMO2-HF: Total energy	-51988.539609
FMO2-MP2: Total energy	-52140.4876

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:5:LEU)

Summations of interaction energy for fragment #1(A:5:LEU)

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.
-44.756	-34.5	4.445	-4.061	-10.635	-0.035

Interaction energy analysis for fragmet #1(A:5:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.899 / q_NPA : 0.945

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	7	ASN	0	0.001	-0.001	3.504	5.810	7.839	-0.012	-0.905	-1.113	-0.001
4	A	8	ILE	0	-0.026	0.009	2.648	3.250	4.895	0.419	-0.594	-1.469	-0.003
5	A	9	LYS	1	0.957	0.976	4.958	28.664	28.688	-0.001	-0.006	-0.016	0.000
88	A	92	ILE	0	0.014	-0.009	2.574	-0.082	1.010	0.841	-0.321	-1.611	-0.001
89	A	93	LEU	0	-0.038	-0.016	3.279	-0.103	0.972	0.041	-0.261	-0.854	-0.001
90	A	94	GLU	-1	-0.814	-0.891	4.548	-23.843	-23.742	0.000	-0.021	-0.080	0.000
92	A	96	ILE	0	-0.001	-0.001	2.859	0.810	1.351	0.213	-0.133	-0.621	-0.002
126	A	130	ILE	0	0.010	0.017	4.639	-3.529	-3.426	-0.001	-0.004	-0.097	0.000
127	A	131	ILE	0	0.018	0.013	5.145	-4.280	-4.182	-0.001	-0.001	-0.095	0.000
129	A	133	THR	0	-0.073	-0.058	3.123	-0.564	-0.228	0.055	-0.078	-0.313	0.000
130	A	134	ILE	0	-0.019	-0.027	2.319	-7.020	-5.929	1.270	-0.467	-1.894	-0.006
131	A	135	SER	0	-0.015	-0.004	3.974	0.369	0.458	0.002	-0.040	-0.051	0.000
133	A	137	ILE	-1	-0.951	-0.953	2.365	-47.769	-45.737	1.619	-1.230	-2.421	-0.021
6	A	10	VAL	0	0.046	0.023	7.862	0.004	0.004	0.000	0.000	0.000	0.000
7	A	11	LYS	1	0.860	0.905	9.327	20.371	20.371	0.000	0.000	0.000	0.000
8	A	12	ASP	-1	-0.911	-0.949	8.338	-29.125	-29.125	0.000	0.000	0.000	0.000
9	A	13	VAL	0	-0.084	-0.047	6.201	0.542	0.542	0.000	0.000	0.000	0.000
10	A	14	MET	0	-0.050	0.007	9.611	1.108	1.108	0.000	0.000	0.000	0.000
11	A	15	THR	0	0.012	0.009	12.232	0.794	0.794	0.000	0.000	0.000	0.000
12	A	16	LYS	1	0.923	0.953	14.109	19.984	19.984	0.000	0.000	0.000	0.000
13	A	17	ASN	0	0.005	0.007	18.074	0.270	0.270	0.000	0.000	0.000	0.000
14	A	18	VAL	0	-0.005	0.000	18.539	0.357	0.357	0.000	0.000	0.000	0.000
15	A	19	ILE	0	0.002	0.000	21.663	0.444	0.444	0.000	0.000	0.000	0.000
16	A	20	THR	0	-0.006	-0.009	23.959	-0.173	-0.173	0.000	0.000	0.000	0.000
17	A	21	ALA	0	-0.015	-0.002	26.066	0.300	0.300	0.000	0.000	0.000	0.000
18	A	22	LYS	1	0.830	0.902	28.879	9.212	9.212	0.000	0.000	0.000	0.000
19	A	23	ARG	1	0.964	0.959	31.669	8.990	8.990	0.000	0.000	0.000	0.000
20	A	24	HIS	0	0.018	0.002	32.970	0.021	0.021	0.000	0.000	0.000	0.000
21	A	25	GLU	-1	-0.836	-0.903	32.125	-8.987	-8.987	0.000	0.000	0.000	0.000
22	A	26	GLY	0	0.094	0.052	35.270	-0.124	-0.124	0.000	0.000	0.000	0.000
23	A	27	VAL	0	-0.055	-0.041	32.125	-0.236	-0.236	0.000	0.000	0.000	0.000
24	A	28	VAL	0	0.014	0.006	33.249	-0.248	-0.248	0.000	0.000	0.000	0.000
25	A	29	GLU	-1	-0.851	-0.926	34.739	-8.049	-8.049	0.000	0.000	0.000	0.000
26	A	30	ALA	0	-0.032	-0.017	30.520	-0.206	-0.206	0.000	0.000	0.000	0.000
27	A	31	PHE	0	0.003	-0.003	29.482	-0.380	-0.380	0.000	0.000	0.000	0.000
28	A	32	GLU	-1	-0.897	-0.950	30.878	-8.243	-8.243	0.000	0.000	0.000	0.000
29	A	33	LYS	1	0.899	0.951	29.573	9.539	9.539	0.000	0.000	0.000	0.000
30	A	34	MET	0	-0.039	-0.019	26.295	-0.370	-0.370	0.000	0.000	0.000	0.000
31	A	35	LEU	0	0.010	0.012	27.459	-0.299	-0.299	0.000	0.000	0.000	0.000
32	A	36	LYS	1	0.895	0.958	29.367	8.569	8.569	0.000	0.000	0.000	0.000
33	A	37	TYR	0	-0.031	-0.024	27.431	0.187	0.187	0.000	0.000	0.000	0.000
34	A	38	LYS	1	0.911	0.961	24.634	10.701	10.701	0.000	0.000	0.000	0.000
35	A	39	ILE	0	-0.004	0.017	22.733	-0.552	-0.552	0.000	0.000	0.000	0.000
36	A	40	SER	0	0.023	0.004	19.473	0.162	0.162	0.000	0.000	0.000	0.000
37	A	41	SER	0	-0.006	-0.014	19.463	0.122	0.122	0.000	0.000	0.000	0.000
38	A	42	LEU	0	0.026	0.016	22.350	-0.048	-0.048	0.000	0.000	0.000	0.000
39	A	43	PRO	0	-0.005	-0.001	20.624	0.182	0.182	0.000	0.000	0.000	0.000
40	A	44	VAL	0	-0.018	-0.005	23.380	0.342	0.342	0.000	0.000	0.000	0.000
41	A	45	ILE	0	0.001	-0.001	25.411	-0.215	-0.215	0.000	0.000	0.000	0.000
42	A	46	ASP	-1	-0.782	-0.899	27.956	-9.773	-9.773	0.000	0.000	0.000	0.000
43	A	47	ASP	-1	-0.862	-0.932	30.609	-8.913	-8.913	0.000	0.000	0.000	0.000
44	A	48	GLU	-1	-0.862	-0.907	30.135	-9.849	-9.849	0.000	0.000	0.000	0.000
45	A	49	ASN	0	-0.024	-0.014	24.192	-0.242	-0.242	0.000	0.000	0.000	0.000
46	A	50	LYS	1	0.888	0.942	25.311	9.777	9.777	0.000	0.000	0.000	0.000
47	A	51	VAL	0	-0.004	-0.007	21.040	0.213	0.213	0.000	0.000	0.000	0.000
48	A	52	ILE	0	-0.061	-0.030	24.381	0.056	0.056	0.000	0.000	0.000	0.000
49	A	53	GLY	0	0.043	0.014	25.496	0.210	0.210	0.000	0.000	0.000	0.000
50	A	54	ILE	0	-0.040	-0.019	19.958	-0.334	-0.334	0.000	0.000	0.000	0.000
51	A	55	VAL	0	0.008	0.020	24.075	0.303	0.303	0.000	0.000	0.000	0.000
52	A	56	THR	0	0.054	0.012	21.797	-0.194	-0.194	0.000	0.000	0.000	0.000
53	A	57	THR	0	0.033	0.002	24.375	0.334	0.334	0.000	0.000	0.000	0.000
54	A	58	THR	0	0.018	0.010	22.863	0.462	0.462	0.000	0.000	0.000	0.000
55	A	59	ASP	-1	-0.801	-0.899	24.583	-10.995	-10.995	0.000	0.000	0.000	0.000
56	A	60	ILE	0	-0.016	0.008	27.616	0.370	0.370	0.000	0.000	0.000	0.000
57	A	61	GLY	0	0.068	0.027	29.329	0.345	0.345	0.000	0.000	0.000	0.000
58	A	62	TYR	0	-0.023	-0.019	29.392	0.328	0.328	0.000	0.000	0.000	0.000
59	A	63	ASN	0	-0.036	-0.036	31.021	0.450	0.450	0.000	0.000	0.000	0.000
60	A	64	LEU	0	0.029	0.023	33.668	0.259	0.259	0.000	0.000	0.000	0.000
61	A	65	ILE	0	-0.033	-0.011	34.226	0.226	0.226	0.000	0.000	0.000	0.000
62	A	66	ARG	1	0.822	0.910	32.859	8.705	8.705	0.000	0.000	0.000	0.000
63	A	67	ASP	-1	-0.880	-0.928	38.176	-7.117	-7.117	0.000	0.000	0.000	0.000
64	A	68	LYS	1	0.861	0.931	36.219	8.064	8.064	0.000	0.000	0.000	0.000
65	A	69	TYR	0	-0.044	-0.019	32.432	-0.213	-0.213	0.000	0.000	0.000	0.000
66	A	70	THR	0	0.041	0.010	38.603	0.097	0.097	0.000	0.000	0.000	0.000
67	A	71	LEU	0	-0.008	-0.019	39.691	-0.166	-0.166	0.000	0.000	0.000	0.000
68	A	72	GLU	-1	-0.892	-0.936	40.681	-6.886	-6.886	0.000	0.000	0.000	0.000
69	A	73	THR	0	-0.069	-0.006	37.658	-0.080	-0.080	0.000	0.000	0.000	0.000
70	A	74	THR	0	0.031	-0.003	36.208	-0.224	-0.224	0.000	0.000	0.000	0.000
71	A	75	ILE	0	-0.007	-0.017	29.779	-0.182	-0.182	0.000	0.000	0.000	0.000
72	A	76	GLY	0	-0.011	-0.021	31.860	-0.235	-0.235	0.000	0.000	0.000	0.000
73	A	77	ASP	-1	-0.906	-0.919	33.612	-7.975	-7.975	0.000	0.000	0.000	0.000
74	A	78	VAL	0	-0.052	-0.029	31.118	-0.050	-0.050	0.000	0.000	0.000	0.000
75	A	79	MET	0	-0.053	0.008	27.867	-0.313	-0.313	0.000	0.000	0.000	0.000
76	A	80	THR	0	-0.031	-0.031	25.370	0.296	0.296	0.000	0.000	0.000	0.000
77	A	81	LYS	1	0.978	0.975	26.581	8.875	8.875	0.000	0.000	0.000	0.000
78	A	82	ASP	-1	-0.911	-0.931	24.597	-10.830	-10.830	0.000	0.000	0.000	0.000
79	A	83	VAL	0	-0.044	-0.022	21.323	-0.479	-0.479	0.000	0.000	0.000	0.000
80	A	84	ILE	0	0.014	0.012	16.368	-0.301	-0.301	0.000	0.000	0.000	0.000
81	A	85	THR	0	0.021	0.019	17.238	-0.492	-0.492	0.000	0.000	0.000	0.000
82	A	86	ILE	0	-0.050	-0.021	10.487	-0.464	-0.464	0.000	0.000	0.000	0.000
83	A	87	HIS	0	0.032	0.027	14.204	-0.366	-0.366	0.000	0.000	0.000	0.000
84	A	88	GLU	-1	-0.799	-0.912	12.865	-18.975	-18.975	0.000	0.000	0.000	0.000
85	A	89	ASP	-1	-0.889	-0.957	12.129	-21.749	-21.749	0.000	0.000	0.000	0.000
86	A	90	ALA	0	0.005	0.020	10.357	-1.559	-1.559	0.000	0.000	0.000	0.000
87	A	91	SER	0	-0.042	-0.049	4.981	-3.018	-3.018	0.000	0.000	0.000	0.000
91	A	95	ALA	0	0.004	-0.008	6.674	2.548	2.548	0.000	0.000	0.000	0.000
93	A	97	LYS	1	0.951	0.966	6.935	27.347	27.347	0.000	0.000	0.000	0.000
94	A	98	LYS	1	0.874	0.942	9.450	19.992	19.992	0.000	0.000	0.000	0.000
95	A	99	MET	0	-0.021	-0.011	10.352	0.831	0.831	0.000	0.000	0.000	0.000
96	A	100	ASP	-1	-0.972	-0.978	10.848	-19.405	-19.405	0.000	0.000	0.000	0.000
97	A	101	ILE	0	-0.033	-0.002	12.471	0.965	0.965	0.000	0.000	0.000	0.000
98	A	102	SER	0	0.001	-0.010	16.101	0.015	0.015	0.000	0.000	0.000	0.000
99	A	103	GLY	0	-0.022	0.002	19.234	0.108	0.108	0.000	0.000	0.000	0.000
100	A	104	LYS	1	0.883	0.933	20.915	10.915	10.915	0.000	0.000	0.000	0.000
101	A	105	LYS	1	0.781	0.869	24.700	11.328	11.328	0.000	0.000	0.000	0.000
102	A	106	GLU	-1	-0.804	-0.895	21.392	-11.488	-11.488	0.000	0.000	0.000	0.000
103	A	107	GLU	-1	-0.890	-0.937	19.215	-12.848	-12.848	0.000	0.000	0.000	0.000
104	A	108	ILE	0	0.003	0.023	13.432	-0.250	-0.250	0.000	0.000	0.000	0.000
105	A	109	ILE	0	-0.042	-0.017	15.146	0.644	0.644	0.000	0.000	0.000	0.000
106	A	110	ASN	0	-0.001	-0.006	14.610	-1.152	-1.152	0.000	0.000	0.000	0.000
107	A	111	GLN	0	-0.049	-0.039	14.443	-0.424	-0.424	0.000	0.000	0.000	0.000
108	A	112	LEU	0	0.008	0.015	11.659	0.519	0.519	0.000	0.000	0.000	0.000
109	A	113	PRO	0	-0.002	-0.003	14.942	-0.516	-0.516	0.000	0.000	0.000	0.000
110	A	114	VAL	0	-0.028	-0.010	13.327	-0.570	-0.570	0.000	0.000	0.000	0.000
111	A	115	VAL	0	0.000	-0.003	15.984	0.941	0.941	0.000	0.000	0.000	0.000
112	A	116	ASP	-1	-0.745	-0.869	17.326	-14.415	-14.415	0.000	0.000	0.000	0.000
113	A	117	LYS	1	0.906	0.934	19.547	13.715	13.715	0.000	0.000	0.000	0.000
114	A	118	ASN	0	-0.079	-0.035	21.096	0.556	0.556	0.000	0.000	0.000	0.000
115	A	119	ASN	0	-0.027	-0.020	21.803	0.749	0.749	0.000	0.000	0.000	0.000
116	A	120	LYS	1	0.844	0.927	22.827	11.175	11.175	0.000	0.000	0.000	0.000
117	A	121	LEU	0	-0.006	0.000	19.699	-0.717	-0.717	0.000	0.000	0.000	0.000
118	A	122	VAL	0	-0.026	-0.019	16.953	0.379	0.379	0.000	0.000	0.000	0.000
119	A	123	GLY	0	0.039	0.010	16.569	-0.340	-0.340	0.000	0.000	0.000	0.000
120	A	124	ILE	0	-0.053	-0.018	15.263	0.382	0.382	0.000	0.000	0.000	0.000
121	A	125	ILE	0	-0.025	-0.002	7.471	-0.877	-0.877	0.000	0.000	0.000	0.000
122	A	126	SER	0	0.001	-0.037	11.535	0.921	0.921	0.000	0.000	0.000	0.000
123	A	127	ASP	-1	-0.780	-0.898	10.298	-20.908	-20.908	0.000	0.000	0.000	0.000
124	A	128	GLY	0	0.000	-0.003	9.862	-1.627	-1.627	0.000	0.000	0.000	0.000
125	A	129	ASP	-1	-0.796	-0.861	9.473	-22.092	-22.092	0.000	0.000	0.000	0.000
128	A	132	ARG	1	0.835	0.910	7.280	22.275	22.275	0.000	0.000	0.000	0.000
132	A	136	LYS	1	0.869	0.941	6.572	32.513	32.513	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:5:LEU)