FMO DATABASE

FMODB ID: 8K1NY

Calculation Name: 2DM9-A-Xray549

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2DM9

Chain ID: A

ChEMBL ID:

UniProt ID: O57724

Base Structure: X-ray

Registration Date: 2025-10-11

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	OptH
Protonation	MOE:Protonate 3D
Complement	ac.sh, 23 2024 Oct
Water	No
Procedure	Manual calculation
Remarks

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	-944732.833392
FMO2-HF: Nuclear repulsion	897506.22895
FMO2-HF: Total energy	-47226.604443
FMO2-MP2: Total energy	-47363.57418

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:81:GLU)

Summations of interaction energy for fragment #1(A:81:GLU)

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.
-22.876	-14.767	5.93	-5.064	-8.976	-0.008

Interaction energy analysis for fragmet #1(A:81:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.030 / q_NPA : -0.017

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	83	ILE	0	0.113	0.054	2.276	-14.947	-10.030	3.022	-2.957	-4.983	0.009
4	A	84	SER	0	0.019	0.000	1.963	-13.342	-11.209	2.904	-1.781	-3.257	-0.018
5	A	85	SER	0	-0.015	-0.009	3.934	2.802	3.335	0.004	-0.143	-0.394	0.000
105	A	185	GLU	-1	-0.827	-0.885	5.165	16.940	17.043	-0.001	-0.001	-0.100	0.000
109	A	189	ARG	1	0.821	0.888	3.694	-21.031	-20.608	0.001	-0.182	-0.242	0.001
6	A	86	VAL	0	0.023	0.000	5.589	1.973	1.973	0.000	0.000	0.000	0.000
7	A	87	LEU	0	0.040	0.016	6.005	0.486	0.486	0.000	0.000	0.000	0.000
8	A	88	GLU	-1	-0.976	-0.998	5.991	-13.046	-13.046	0.000	0.000	0.000	0.000
9	A	89	GLU	-1	-0.846	-0.893	9.753	-2.241	-2.241	0.000	0.000	0.000	0.000
10	A	90	VAL	0	-0.022	-0.009	11.299	0.387	0.387	0.000	0.000	0.000	0.000
11	A	91	LYS	1	0.930	0.955	9.488	4.361	4.361	0.000	0.000	0.000	0.000
12	A	92	ARG	1	0.857	0.915	10.269	4.717	4.717	0.000	0.000	0.000	0.000
13	A	93	ARG	1	0.877	0.930	15.760	0.724	0.724	0.000	0.000	0.000	0.000
14	A	94	LEU	0	-0.019	-0.029	15.153	0.164	0.164	0.000	0.000	0.000	0.000
15	A	95	GLU	-1	-0.991	-0.979	18.252	-1.896	-1.896	0.000	0.000	0.000	0.000
16	A	96	THR	0	-0.070	-0.039	19.999	0.100	0.100	0.000	0.000	0.000	0.000
17	A	97	MET	0	-0.058	0.016	19.363	0.135	0.135	0.000	0.000	0.000	0.000
18	A	98	SER	0	0.013	0.010	22.902	0.024	0.024	0.000	0.000	0.000	0.000
19	A	99	GLU	-1	-0.817	-0.928	25.298	-0.232	-0.232	0.000	0.000	0.000	0.000
20	A	100	ASP	-1	-0.814	-0.895	26.878	-0.099	-0.099	0.000	0.000	0.000	0.000
21	A	101	GLU	-1	-0.868	-0.922	22.885	-0.341	-0.341	0.000	0.000	0.000	0.000
22	A	102	TYR	0	0.009	-0.028	19.003	0.068	0.068	0.000	0.000	0.000	0.000
23	A	103	PHE	0	-0.003	-0.003	23.267	0.097	0.097	0.000	0.000	0.000	0.000
24	A	104	GLU	-1	-0.818	-0.898	25.423	0.215	0.215	0.000	0.000	0.000	0.000
25	A	105	SER	0	-0.049	-0.014	19.085	0.152	0.152	0.000	0.000	0.000	0.000
26	A	106	VAL	0	0.017	0.000	21.926	0.126	0.126	0.000	0.000	0.000	0.000
27	A	107	LYS	1	0.745	0.859	23.381	-0.067	-0.067	0.000	0.000	0.000	0.000
28	A	108	ALA	0	-0.017	-0.011	22.638	0.067	0.067	0.000	0.000	0.000	0.000
29	A	109	LEU	0	-0.031	-0.013	17.736	0.111	0.111	0.000	0.000	0.000	0.000
30	A	110	LEU	0	0.035	0.019	21.688	0.109	0.109	0.000	0.000	0.000	0.000
31	A	111	LYS	1	0.777	0.894	24.714	-0.343	-0.343	0.000	0.000	0.000	0.000
32	A	112	GLU	-1	-0.829	-0.879	20.149	1.391	1.391	0.000	0.000	0.000	0.000
33	A	113	ALA	0	0.054	0.027	22.104	0.033	0.033	0.000	0.000	0.000	0.000
34	A	114	ILE	0	0.017	-0.002	23.959	0.001	0.001	0.000	0.000	0.000	0.000
35	A	115	LYS	1	0.890	0.945	27.407	-0.646	-0.646	0.000	0.000	0.000	0.000
36	A	116	GLU	-1	-0.959	-0.967	22.843	1.510	1.510	0.000	0.000	0.000	0.000
37	A	117	LEU	0	-0.026	-0.013	25.316	0.004	0.004	0.000	0.000	0.000	0.000
38	A	118	ASN	0	-0.065	-0.029	28.158	-0.073	-0.073	0.000	0.000	0.000	0.000
39	A	119	GLU	-1	-0.843	-0.906	31.217	0.701	0.701	0.000	0.000	0.000	0.000
40	A	120	LYS	1	0.885	0.936	32.736	-0.525	-0.525	0.000	0.000	0.000	0.000
41	A	121	LYS	1	0.805	0.892	33.955	-0.483	-0.483	0.000	0.000	0.000	0.000
42	A	122	VAL	0	0.003	0.011	28.364	0.041	0.041	0.000	0.000	0.000	0.000
43	A	123	ARG	1	0.768	0.889	27.275	-0.607	-0.607	0.000	0.000	0.000	0.000
44	A	124	VAL	0	-0.007	-0.008	23.904	0.080	0.080	0.000	0.000	0.000	0.000
45	A	125	MET	0	0.003	0.021	21.828	-0.087	-0.087	0.000	0.000	0.000	0.000
46	A	126	SER	0	-0.001	-0.037	19.754	0.055	0.055	0.000	0.000	0.000	0.000
47	A	127	ASN	0	0.048	0.048	18.163	0.001	0.001	0.000	0.000	0.000	0.000
48	A	128	GLU	-1	-0.901	-0.972	20.958	-0.206	-0.206	0.000	0.000	0.000	0.000
49	A	129	LYS	1	0.873	0.934	23.096	0.393	0.393	0.000	0.000	0.000	0.000
50	A	130	THR	0	0.014	0.008	21.646	0.015	0.015	0.000	0.000	0.000	0.000
51	A	131	LEU	0	0.002	0.007	24.248	0.033	0.033	0.000	0.000	0.000	0.000
52	A	132	GLY	0	0.030	0.015	26.654	0.013	0.013	0.000	0.000	0.000	0.000
53	A	133	LEU	0	-0.033	-0.006	25.559	-0.002	-0.002	0.000	0.000	0.000	0.000
54	A	134	ILE	0	0.002	-0.004	25.227	0.019	0.019	0.000	0.000	0.000	0.000
55	A	135	ALA	0	-0.022	-0.007	29.409	0.014	0.014	0.000	0.000	0.000	0.000
56	A	136	SER	0	-0.073	-0.049	32.128	-0.007	-0.007	0.000	0.000	0.000	0.000
57	A	137	ARG	1	0.811	0.907	30.549	0.054	0.054	0.000	0.000	0.000	0.000
58	A	138	ILE	0	0.042	0.032	32.601	0.028	0.028	0.000	0.000	0.000	0.000
59	A	139	GLU	-1	-0.815	-0.911	34.106	0.196	0.196	0.000	0.000	0.000	0.000
60	A	140	GLU	-1	-0.836	-0.897	31.810	0.091	0.091	0.000	0.000	0.000	0.000
61	A	141	ILE	0	-0.007	-0.007	29.328	0.030	0.030	0.000	0.000	0.000	0.000
62	A	142	LYS	1	0.847	0.904	32.196	-0.174	-0.174	0.000	0.000	0.000	0.000
63	A	143	SER	0	-0.036	-0.033	35.371	0.011	0.011	0.000	0.000	0.000	0.000
64	A	144	GLU	-1	-0.857	-0.927	31.146	0.258	0.258	0.000	0.000	0.000	0.000
65	A	145	LEU	0	-0.097	-0.058	30.208	0.051	0.051	0.000	0.000	0.000	0.000
66	A	146	GLY	0	0.036	0.027	33.966	-0.001	-0.001	0.000	0.000	0.000	0.000
67	A	147	ASP	-1	-0.911	-0.965	36.262	0.412	0.412	0.000	0.000	0.000	0.000
68	A	148	VAL	0	-0.051	-0.012	31.150	0.015	0.015	0.000	0.000	0.000	0.000
69	A	149	SER	0	-0.044	-0.017	34.564	-0.048	-0.048	0.000	0.000	0.000	0.000
70	A	150	ILE	0	-0.003	-0.013	29.428	0.039	0.039	0.000	0.000	0.000	0.000
71	A	151	GLU	-1	-0.870	-0.924	31.320	0.334	0.334	0.000	0.000	0.000	0.000
72	A	152	LEU	0	-0.037	-0.027	28.169	0.036	0.036	0.000	0.000	0.000	0.000
73	A	153	GLY	0	0.046	0.007	26.705	-0.006	-0.006	0.000	0.000	0.000	0.000
74	A	154	GLU	-1	-0.937	-0.965	23.474	0.474	0.474	0.000	0.000	0.000	0.000
75	A	155	THR	0	-0.027	-0.022	23.195	0.043	0.043	0.000	0.000	0.000	0.000
76	A	156	VAL	0	-0.049	-0.026	18.252	0.026	0.026	0.000	0.000	0.000	0.000
77	A	157	ASP	-1	-0.957	-0.979	14.373	-0.570	-0.570	0.000	0.000	0.000	0.000
78	A	158	THR	0	-0.027	-0.035	14.005	0.210	0.210	0.000	0.000	0.000	0.000
79	A	159	MET	0	-0.057	-0.025	10.219	-0.260	-0.260	0.000	0.000	0.000	0.000
80	A	160	GLY	0	-0.003	-0.016	14.837	-0.143	-0.143	0.000	0.000	0.000	0.000
81	A	161	GLY	0	0.031	0.038	16.074	0.216	0.216	0.000	0.000	0.000	0.000
82	A	162	VAL	0	-0.046	-0.027	18.391	-0.129	-0.129	0.000	0.000	0.000	0.000
83	A	163	ILE	0	-0.012	0.013	17.022	0.185	0.185	0.000	0.000	0.000	0.000
84	A	164	VAL	0	0.002	-0.005	20.150	-0.157	-0.157	0.000	0.000	0.000	0.000
85	A	165	GLU	-1	-0.854	-0.927	23.341	0.958	0.958	0.000	0.000	0.000	0.000
86	A	166	THR	0	0.006	-0.014	25.647	-0.059	-0.059	0.000	0.000	0.000	0.000
87	A	167	GLU	-1	-0.807	-0.888	29.148	0.454	0.454	0.000	0.000	0.000	0.000
88	A	168	ASP	-1	-0.813	-0.878	30.991	0.729	0.729	0.000	0.000	0.000	0.000
89	A	169	GLY	0	0.039	0.028	27.347	0.001	0.001	0.000	0.000	0.000	0.000
90	A	170	ARG	1	0.688	0.829	26.621	-0.743	-0.743	0.000	0.000	0.000	0.000
91	A	171	ILE	0	-0.020	-0.017	25.143	0.097	0.097	0.000	0.000	0.000	0.000
92	A	172	ARG	1	0.980	0.990	17.557	-1.480	-1.480	0.000	0.000	0.000	0.000
93	A	173	ILE	0	-0.009	0.008	20.018	0.171	0.171	0.000	0.000	0.000	0.000
94	A	174	ASP	-1	-0.827	-0.903	15.225	1.778	1.778	0.000	0.000	0.000	0.000
95	A	175	ASN	0	-0.003	-0.025	16.413	0.501	0.501	0.000	0.000	0.000	0.000
96	A	176	THR	0	0.009	0.003	13.628	-0.149	-0.149	0.000	0.000	0.000	0.000
97	A	177	PHE	0	-0.014	-0.019	12.318	0.292	0.292	0.000	0.000	0.000	0.000
98	A	178	GLU	-1	-0.763	-0.864	9.088	0.577	0.577	0.000	0.000	0.000	0.000
99	A	179	ALA	0	0.064	0.035	9.133	1.006	1.006	0.000	0.000	0.000	0.000
100	A	180	ARG	1	0.775	0.857	11.380	-1.050	-1.050	0.000	0.000	0.000	0.000
101	A	181	MET	0	-0.026	-0.001	6.594	0.260	0.260	0.000	0.000	0.000	0.000
102	A	182	GLU	-1	-0.965	-0.990	6.585	9.848	9.848	0.000	0.000	0.000	0.000
103	A	183	ARG	1	0.828	0.908	8.345	-2.295	-2.295	0.000	0.000	0.000	0.000
104	A	184	PHE	0	0.010	0.016	10.736	-0.321	-0.321	0.000	0.000	0.000	0.000
106	A	186	GLY	0	0.074	0.021	8.248	-0.337	-0.337	0.000	0.000	0.000	0.000
107	A	187	GLU	-1	-0.912	-0.940	10.854	1.596	1.596	0.000	0.000	0.000	0.000
108	A	188	ILE	0	0.002	0.008	8.182	-0.745	-0.745	0.000	0.000	0.000	0.000
110	A	190	SER	0	-0.012	-0.015	10.069	-0.803	-0.803	0.000	0.000	0.000	0.000
111	A	191	THR	0	-0.055	-0.033	12.748	-0.593	-0.593	0.000	0.000	0.000	0.000
112	A	192	ILE	0	-0.024	-0.020	8.394	-0.416	-0.416	0.000	0.000	0.000	0.000
113	A	193	ALA	0	-0.002	-0.007	12.584	-0.358	-0.358	0.000	0.000	0.000	0.000
114	A	194	LYS	1	0.830	0.918	14.901	-1.279	-1.279	0.000	0.000	0.000	0.000
115	A	195	VAL	0	-0.042	-0.023	15.442	-0.210	-0.210	0.000	0.000	0.000	0.000
116	A	196	LEU	0	-0.070	-0.024	13.661	-0.186	-0.186	0.000	0.000	0.000	0.000
117	A	197	PHE	0	-0.071	-0.043	15.998	-0.059	-0.059	0.000	0.000	0.000	0.000
118	A	198	GLY	-1	-0.832	-0.888	20.230	0.877	0.877	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:81:GLU)