FMO DATABASE

FMODB ID: 5Q2NZ

Calculation Name: 3D9R-A-Xray549

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3D9R

Chain ID: A

ChEMBL ID:

UniProt ID: Q6D750

Base Structure: X-ray

Registration Date: 2025-10-12

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	132
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1082675.693799
FMO2-HF: Nuclear repulsion	1032928.652566
FMO2-HF: Total energy	-49747.041233
FMO2-MP2: Total energy	-49893.13427

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:3:LYS)

Summations of interaction energy for fragment #1(A:3:LYS)

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.
-119.344	-116.429	15.185	-6.99	-11.11	-0.074

Interaction energy analysis for fragmet #1(A:3:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.791 / q_NPA : 0.884

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	5	PHE	0	0.096	0.039	2.907	2.657	5.447	0.051	-1.173	-1.668	-0.004
4	A	6	ASN	0	-0.013	-0.020	1.953	-12.498	-13.969	11.397	-4.926	-5.000	-0.039
5	A	7	GLU	-1	-0.910	-0.939	2.988	-23.034	-23.988	0.049	1.570	-0.665	-0.002
6	A	8	GLU	-1	-0.771	-0.885	2.196	-47.701	-45.533	2.263	-1.915	-2.516	-0.031
7	A	9	LEU	0	0.010	0.009	4.114	1.629	1.678	-0.001	-0.012	-0.036	0.000
9	A	11	VAL	0	-0.060	-0.028	2.252	-0.277	0.056	1.426	-0.534	-1.225	0.002
8	A	10	ALA	0	0.081	0.044	5.702	1.559	1.559	0.000	0.000	0.000	0.000
10	A	12	ILE	0	-0.017	-0.008	5.665	2.052	2.052	0.000	0.000	0.000	0.000
11	A	13	GLU	-1	-0.872	-0.946	8.400	-17.713	-17.713	0.000	0.000	0.000	0.000
12	A	14	ALA	0	-0.030	-0.012	8.415	1.170	1.170	0.000	0.000	0.000	0.000
13	A	15	ALA	0	-0.006	0.003	9.745	0.978	0.978	0.000	0.000	0.000	0.000
14	A	16	ALA	0	0.028	0.018	11.396	1.253	1.253	0.000	0.000	0.000	0.000
15	A	17	ILE	0	0.020	0.006	13.247	1.075	1.075	0.000	0.000	0.000	0.000
16	A	18	ALA	0	-0.034	0.000	13.548	0.838	0.838	0.000	0.000	0.000	0.000
17	A	19	TYR	0	0.021	0.020	15.378	0.897	0.897	0.000	0.000	0.000	0.000
18	A	20	LEU	0	0.000	-0.002	17.518	0.761	0.761	0.000	0.000	0.000	0.000
19	A	21	THR	0	-0.041	-0.040	17.637	0.620	0.620	0.000	0.000	0.000	0.000
20	A	22	ALA	0	-0.042	-0.015	19.385	0.487	0.487	0.000	0.000	0.000	0.000
21	A	23	PHE	0	0.008	0.001	21.195	0.589	0.589	0.000	0.000	0.000	0.000
22	A	24	ASN	0	0.038	0.019	23.282	0.786	0.786	0.000	0.000	0.000	0.000
23	A	25	ARG	1	0.794	0.899	18.818	15.310	15.310	0.000	0.000	0.000	0.000
24	A	26	ALA	0	-0.013	0.006	25.198	0.312	0.312	0.000	0.000	0.000	0.000
25	A	27	ASP	-1	-0.830	-0.900	21.532	-14.006	-14.006	0.000	0.000	0.000	0.000
26	A	28	ILE	0	0.050	0.019	23.099	-0.523	-0.523	0.000	0.000	0.000	0.000
27	A	29	PRO	0	-0.014	-0.011	22.460	-0.284	-0.284	0.000	0.000	0.000	0.000
28	A	30	ALA	0	-0.003	0.001	18.562	-0.547	-0.547	0.000	0.000	0.000	0.000
29	A	31	VAL	0	0.016	0.008	18.945	-0.685	-0.685	0.000	0.000	0.000	0.000
30	A	32	ILE	0	-0.006	0.009	19.943	-0.392	-0.392	0.000	0.000	0.000	0.000
31	A	33	ALA	0	-0.038	-0.018	17.137	-0.240	-0.240	0.000	0.000	0.000	0.000
32	A	34	THR	0	-0.069	-0.038	15.384	-0.754	-0.754	0.000	0.000	0.000	0.000
33	A	35	TYR	0	0.002	0.001	15.526	-0.579	-0.579	0.000	0.000	0.000	0.000
34	A	36	THR	0	-0.046	-0.053	16.019	-0.508	-0.508	0.000	0.000	0.000	0.000
35	A	37	ASP	-1	-0.848	-0.933	18.210	-14.066	-14.066	0.000	0.000	0.000	0.000
36	A	38	ASP	-1	-0.848	-0.897	20.749	-12.602	-12.602	0.000	0.000	0.000	0.000
37	A	39	GLY	0	-0.011	0.007	20.953	0.242	0.242	0.000	0.000	0.000	0.000
38	A	40	VAL	0	-0.029	-0.018	21.582	0.415	0.415	0.000	0.000	0.000	0.000
39	A	41	LEU	0	0.020	0.021	22.891	-0.395	-0.395	0.000	0.000	0.000	0.000
40	A	42	MET	0	-0.022	-0.024	25.208	0.548	0.548	0.000	0.000	0.000	0.000
41	A	43	GLY	0	0.069	0.024	26.885	-0.339	-0.339	0.000	0.000	0.000	0.000
42	A	44	PRO	0	-0.009	-0.009	29.455	0.267	0.267	0.000	0.000	0.000	0.000
43	A	45	GLY	0	-0.021	-0.004	32.976	-0.013	-0.013	0.000	0.000	0.000	0.000
44	A	46	ARG	1	0.889	0.944	32.029	9.015	9.015	0.000	0.000	0.000	0.000
45	A	47	PRO	0	-0.005	-0.005	33.572	-0.036	-0.036	0.000	0.000	0.000	0.000
46	A	48	ALA	0	-0.032	-0.011	28.970	-0.174	-0.174	0.000	0.000	0.000	0.000
47	A	49	ALA	0	0.009	0.022	28.220	0.225	0.225	0.000	0.000	0.000	0.000
48	A	50	VAL	0	-0.047	-0.048	26.549	-0.466	-0.466	0.000	0.000	0.000	0.000
49	A	51	GLY	0	0.058	0.029	24.587	0.192	0.192	0.000	0.000	0.000	0.000
50	A	52	LYS	1	0.773	0.872	18.798	15.102	15.102	0.000	0.000	0.000	0.000
51	A	53	ASP	-1	-0.897	-0.932	25.259	-10.511	-10.511	0.000	0.000	0.000	0.000
52	A	54	GLU	-1	-0.804	-0.903	29.060	-9.389	-9.389	0.000	0.000	0.000	0.000
53	A	55	LEU	0	-0.060	-0.026	22.852	0.060	0.060	0.000	0.000	0.000	0.000
54	A	56	ALA	0	0.001	-0.004	26.976	0.026	0.026	0.000	0.000	0.000	0.000
55	A	57	GLU	-1	-0.930	-0.957	28.339	-8.889	-8.889	0.000	0.000	0.000	0.000
56	A	58	VAL	0	-0.032	-0.018	29.212	0.278	0.278	0.000	0.000	0.000	0.000
57	A	59	TYR	0	0.011	-0.017	23.640	0.015	0.015	0.000	0.000	0.000	0.000
58	A	60	LEU	0	-0.006	0.003	28.952	0.036	0.036	0.000	0.000	0.000	0.000
59	A	61	SER	0	0.065	0.058	31.935	0.167	0.167	0.000	0.000	0.000	0.000
60	A	62	VAL	0	-0.041	-0.015	29.623	0.272	0.272	0.000	0.000	0.000	0.000
61	A	63	PHE	0	0.034	0.012	26.409	0.153	0.153	0.000	0.000	0.000	0.000
62	A	64	GLU	-1	-0.947	-0.963	32.343	-8.542	-8.542	0.000	0.000	0.000	0.000
63	A	65	THR	0	-0.068	-0.042	35.721	0.303	0.303	0.000	0.000	0.000	0.000
64	A	66	VAL	0	-0.018	-0.011	33.296	0.264	0.264	0.000	0.000	0.000	0.000
65	A	67	GLY	0	-0.061	-0.017	33.193	-0.229	-0.229	0.000	0.000	0.000	0.000
66	A	68	PHE	0	0.007	-0.016	29.460	0.197	0.197	0.000	0.000	0.000	0.000
67	A	69	ASP	-1	-0.941	-0.958	29.738	-10.242	-10.242	0.000	0.000	0.000	0.000
68	A	70	MET	0	-0.054	-0.014	26.692	0.379	0.379	0.000	0.000	0.000	0.000
69	A	71	ALA	0	0.012	0.016	25.062	-0.471	-0.471	0.000	0.000	0.000	0.000
70	A	72	TYR	0	0.005	-0.021	17.161	0.140	0.140	0.000	0.000	0.000	0.000
71	A	73	GLU	-1	-0.831	-0.899	20.814	-11.907	-11.907	0.000	0.000	0.000	0.000
72	A	74	ILE	0	-0.008	-0.011	15.186	0.318	0.318	0.000	0.000	0.000	0.000
73	A	75	LYS	1	0.780	0.876	18.534	11.672	11.672	0.000	0.000	0.000	0.000
74	A	76	GLU	-1	-0.859	-0.915	17.383	-12.358	-12.358	0.000	0.000	0.000	0.000
75	A	77	VAL	0	0.022	0.007	10.817	-0.117	-0.117	0.000	0.000	0.000	0.000
76	A	78	VAL	0	-0.008	0.005	13.422	-0.159	-0.159	0.000	0.000	0.000	0.000
77	A	79	GLN	0	-0.011	-0.008	7.366	-0.908	-0.908	0.000	0.000	0.000	0.000
78	A	80	THR	0	-0.039	-0.029	11.537	0.484	0.484	0.000	0.000	0.000	0.000
79	A	81	SER	0	-0.024	-0.017	12.680	0.643	0.643	0.000	0.000	0.000	0.000
80	A	82	ALA	0	0.010	-0.001	9.821	-0.955	-0.955	0.000	0.000	0.000	0.000
81	A	83	ASP	-1	-0.879	-0.946	8.919	-22.115	-22.115	0.000	0.000	0.000	0.000
82	A	84	TRP	0	-0.004	-0.009	11.189	0.563	0.563	0.000	0.000	0.000	0.000
83	A	85	ALA	0	0.035	0.019	10.519	-0.426	-0.426	0.000	0.000	0.000	0.000
84	A	86	PHE	0	-0.031	-0.005	12.666	0.633	0.633	0.000	0.000	0.000	0.000
85	A	87	VAL	0	0.031	0.020	13.030	-0.666	-0.666	0.000	0.000	0.000	0.000
86	A	88	ARG	1	0.836	0.915	15.721	12.284	12.284	0.000	0.000	0.000	0.000
87	A	89	SER	0	-0.053	-0.059	18.911	-0.615	-0.615	0.000	0.000	0.000	0.000
88	A	90	ALA	0	0.016	0.008	20.743	0.515	0.515	0.000	0.000	0.000	0.000
89	A	91	THR	0	-0.020	-0.021	23.255	-0.369	-0.369	0.000	0.000	0.000	0.000
90	A	92	GLU	-1	-0.961	-0.979	25.587	-9.366	-9.366	0.000	0.000	0.000	0.000
91	A	93	GLY	0	0.047	0.027	28.721	-0.299	-0.299	0.000	0.000	0.000	0.000
92	A	94	THR	0	-0.075	-0.038	31.414	0.407	0.407	0.000	0.000	0.000	0.000
93	A	95	GLU	-1	-0.791	-0.883	32.668	-9.049	-9.049	0.000	0.000	0.000	0.000
94	A	96	THR	0	0.001	-0.001	34.761	0.344	0.344	0.000	0.000	0.000	0.000
95	A	97	ASN	0	0.047	0.033	37.085	-0.009	-0.009	0.000	0.000	0.000	0.000
96	A	98	LYS	1	0.872	0.907	33.847	9.263	9.263	0.000	0.000	0.000	0.000
97	A	99	ALA	0	-0.041	-0.002	39.981	0.104	0.104	0.000	0.000	0.000	0.000
98	A	100	THR	0	-0.049	-0.050	43.200	0.154	0.154	0.000	0.000	0.000	0.000
99	A	101	GLY	0	-0.002	0.010	42.331	0.131	0.131	0.000	0.000	0.000	0.000
100	A	102	VAL	0	-0.037	-0.016	42.454	-0.024	-0.024	0.000	0.000	0.000	0.000
101	A	103	VAL	0	0.012	0.010	37.832	-0.151	-0.151	0.000	0.000	0.000	0.000
102	A	104	THR	0	-0.063	-0.032	38.049	0.209	0.209	0.000	0.000	0.000	0.000
103	A	105	PRO	0	0.018	0.004	36.031	-0.201	-0.201	0.000	0.000	0.000	0.000
104	A	106	ALA	0	0.002	-0.004	32.780	0.137	0.137	0.000	0.000	0.000	0.000
105	A	107	ALA	0	0.042	0.024	30.318	-0.227	-0.227	0.000	0.000	0.000	0.000
106	A	108	TYR	0	-0.063	-0.056	27.413	0.329	0.329	0.000	0.000	0.000	0.000
107	A	109	GLN	0	0.009	0.008	25.234	-0.328	-0.328	0.000	0.000	0.000	0.000
108	A	110	GLU	-1	-0.834	-0.883	21.334	-11.794	-11.794	0.000	0.000	0.000	0.000
109	A	111	LEU	0	-0.027	-0.012	19.657	-0.221	-0.221	0.000	0.000	0.000	0.000
110	A	112	PHE	0	0.019	0.007	16.149	0.127	0.127	0.000	0.000	0.000	0.000
111	A	113	LEU	0	0.004	-0.004	16.509	-0.208	-0.208	0.000	0.000	0.000	0.000
112	A	114	LEU	0	-0.006	-0.008	11.135	0.064	0.064	0.000	0.000	0.000	0.000
113	A	115	ARG	1	0.936	0.967	12.851	16.654	16.654	0.000	0.000	0.000	0.000
114	A	116	LYS	1	0.857	0.944	5.041	30.169	30.169	0.000	0.000	0.000	0.000
115	A	117	SER	0	-0.007	-0.009	10.423	0.941	0.941	0.000	0.000	0.000	0.000
116	A	118	ALA	0	0.028	0.002	10.761	-1.035	-1.035	0.000	0.000	0.000	0.000
117	A	119	THR	0	-0.033	-0.013	10.662	-0.222	-0.222	0.000	0.000	0.000	0.000
118	A	120	GLY	0	-0.011	-0.005	6.837	-2.799	-2.799	0.000	0.000	0.000	0.000
119	A	121	SER	0	-0.029	-0.011	6.512	-2.065	-2.065	0.000	0.000	0.000	0.000
120	A	122	TRP	0	-0.023	-0.021	4.945	3.486	3.486	0.000	0.000	0.000	0.000
121	A	123	GLN	0	-0.003	-0.001	9.141	-0.084	-0.084	0.000	0.000	0.000	0.000
122	A	124	THR	0	0.027	0.012	12.957	0.018	0.018	0.000	0.000	0.000	0.000
123	A	125	ALA	0	0.006	0.011	15.910	0.404	0.404	0.000	0.000	0.000	0.000
124	A	126	ARG	1	0.802	0.880	17.831	13.102	13.102	0.000	0.000	0.000	0.000
125	A	127	TYR	0	0.034	0.023	19.401	-0.337	-0.337	0.000	0.000	0.000	0.000
126	A	128	CYS	0	-0.041	-0.012	21.403	0.612	0.612	0.000	0.000	0.000	0.000
127	A	129	THR	0	0.017	0.019	23.735	-0.175	-0.175	0.000	0.000	0.000	0.000
128	A	130	SER	0	-0.001	-0.014	26.173	0.412	0.412	0.000	0.000	0.000	0.000
129	A	131	LYS	1	0.858	0.929	29.055	8.106	8.106	0.000	0.000	0.000	0.000
130	A	132	ILE	0	-0.060	-0.031	28.380	0.186	0.186	0.000	0.000	0.000	0.000
131	A	133	SER	0	-0.013	-0.014	32.570	0.294	0.294	0.000	0.000	0.000	0.000
132	A	134	PRO	-1	-0.857	-0.906	34.643	-8.084	-8.084	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:LYS)