FMO DATABASE

FMODB ID: Y1ZN2

Calculation Name: 3D9Y-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3D9Y

Chain ID: A

ChEMBL ID:

UniProt ID: P39825

Base Structure: X-ray

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	126
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1015336.353315
FMO2-HF: Nuclear repulsion	969067.456121
FMO2-HF: Total energy	-46268.897194
FMO2-MP2: Total energy	-46404.977617

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.
-30.218	-25.181	0.829	-2.286	-3.58	-0.001

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 : 0.862 / q_NPA : 0.918

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	3	GLN	0	0.018	-0.010	2.962	2.772	4.900	0.109	-0.958	-1.278	-0.002
4	A	4	ALA	0	-0.003	0.007	2.477	1.627	3.939	0.719	-1.169	-1.862	0.002
5	A	5	TYR	0	0.017	0.004	4.039	5.055	5.652	0.001	-0.159	-0.440	-0.001
6	A	6	VAL	0	0.015	0.015	6.393	5.234	5.234	0.000	0.000	0.000	0.000
7	A	7	ASP	-1	-0.804	-0.907	7.220	-28.918	-28.918	0.000	0.000	0.000	0.000
8	A	8	THR	0	-0.053	-0.037	7.064	1.034	1.034	0.000	0.000	0.000	0.000
9	A	9	SER	0	-0.041	-0.022	7.225	2.248	2.248	0.000	0.000	0.000	0.000
10	A	10	LEU	0	-0.005	0.016	9.733	2.262	2.262	0.000	0.000	0.000	0.000
11	A	11	LEU	0	-0.021	0.005	11.592	1.852	1.852	0.000	0.000	0.000	0.000
12	A	12	GLY	0	-0.013	-0.001	11.983	1.665	1.665	0.000	0.000	0.000	0.000
13	A	13	THR	0	-0.052	-0.035	13.340	1.562	1.562	0.000	0.000	0.000	0.000
14	A	14	GLY	0	-0.016	-0.003	15.925	1.135	1.135	0.000	0.000	0.000	0.000
15	A	15	LYS	1	0.781	0.867	17.983	14.563	14.563	0.000	0.000	0.000	0.000
16	A	16	ILE	0	-0.028	-0.008	15.388	0.547	0.547	0.000	0.000	0.000	0.000
17	A	17	ASP	-1	-0.817	-0.903	16.619	-15.995	-15.995	0.000	0.000	0.000	0.000
18	A	18	ARG	1	0.857	0.930	15.555	15.570	15.570	0.000	0.000	0.000	0.000
19	A	19	ALA	0	0.035	0.015	12.430	0.307	0.307	0.000	0.000	0.000	0.000
20	A	20	ALA	0	0.005	-0.004	11.075	-0.488	-0.488	0.000	0.000	0.000	0.000
21	A	21	ILE	0	-0.027	0.001	7.211	-0.222	-0.222	0.000	0.000	0.000	0.000
22	A	22	VAL	0	0.002	0.007	10.554	-0.632	-0.632	0.000	0.000	0.000	0.000
23	A	23	SER	0	0.001	-0.014	12.758	-0.361	-0.361	0.000	0.000	0.000	0.000
24	A	24	ARG	1	0.895	0.942	14.195	16.387	16.387	0.000	0.000	0.000	0.000
25	A	25	ALA	0	-0.017	-0.009	16.934	1.077	1.077	0.000	0.000	0.000	0.000
26	A	26	GLY	0	0.014	0.013	17.773	0.770	0.770	0.000	0.000	0.000	0.000
27	A	27	ASP	-1	-0.831	-0.867	15.637	-18.429	-18.429	0.000	0.000	0.000	0.000
28	A	28	SER	0	-0.020	-0.044	12.699	-0.592	-0.592	0.000	0.000	0.000	0.000
29	A	29	VAL	0	0.000	0.000	10.660	-0.170	-0.170	0.000	0.000	0.000	0.000
30	A	30	TRP	0	-0.061	-0.044	7.253	-1.437	-1.437	0.000	0.000	0.000	0.000
31	A	31	ALA	0	-0.011	-0.014	5.759	-5.311	-5.311	0.000	0.000	0.000	0.000
32	A	32	ALA	0	0.008	0.004	7.584	2.888	2.888	0.000	0.000	0.000	0.000
33	A	33	SER	0	0.041	0.044	10.067	-0.400	-0.400	0.000	0.000	0.000	0.000
34	A	34	ALA	0	0.033	0.004	12.050	0.931	0.931	0.000	0.000	0.000	0.000
35	A	35	GLY	0	0.032	0.017	14.285	0.907	0.907	0.000	0.000	0.000	0.000
36	A	36	PHE	0	-0.052	-0.017	14.656	1.243	1.243	0.000	0.000	0.000	0.000
37	A	37	ASN	0	-0.013	-0.019	15.579	-1.494	-1.494	0.000	0.000	0.000	0.000
38	A	38	LEU	0	0.022	0.018	14.986	0.955	0.955	0.000	0.000	0.000	0.000
39	A	39	SER	0	-0.017	-0.031	17.006	-0.360	-0.360	0.000	0.000	0.000	0.000
40	A	40	PRO	0	0.019	-0.012	18.873	-0.171	-0.171	0.000	0.000	0.000	0.000
41	A	41	GLN	0	0.070	0.026	20.026	-0.391	-0.391	0.000	0.000	0.000	0.000
42	A	42	GLU	-1	-0.765	-0.848	20.812	-13.686	-13.686	0.000	0.000	0.000	0.000
43	A	43	ILE	0	-0.020	-0.004	15.991	-0.004	-0.004	0.000	0.000	0.000	0.000
44	A	44	GLN	0	-0.034	-0.006	19.394	0.478	0.478	0.000	0.000	0.000	0.000
45	A	45	GLY	0	0.005	0.009	22.176	0.316	0.316	0.000	0.000	0.000	0.000
46	A	46	LEU	0	-0.011	-0.010	18.598	0.259	0.259	0.000	0.000	0.000	0.000
47	A	47	ALA	0	0.001	-0.005	19.931	0.074	0.074	0.000	0.000	0.000	0.000
48	A	48	ALA	0	-0.011	-0.002	21.594	0.240	0.240	0.000	0.000	0.000	0.000
49	A	49	GLY	0	0.069	0.013	24.997	0.413	0.413	0.000	0.000	0.000	0.000
50	A	50	PHE	0	-0.072	-0.049	19.671	0.184	0.184	0.000	0.000	0.000	0.000
51	A	51	GLN	0	-0.098	-0.044	23.581	0.455	0.455	0.000	0.000	0.000	0.000
52	A	52	ASP	-1	-0.854	-0.933	26.966	-9.391	-9.391	0.000	0.000	0.000	0.000
53	A	53	PRO	0	0.010	0.029	27.137	0.089	0.089	0.000	0.000	0.000	0.000
54	A	54	PRO	0	-0.006	-0.020	29.202	0.051	0.051	0.000	0.000	0.000	0.000
55	A	55	SER	0	-0.028	-0.008	30.379	0.098	0.098	0.000	0.000	0.000	0.000
56	A	56	MET	0	0.054	0.039	25.485	0.083	0.083	0.000	0.000	0.000	0.000
57	A	57	PHE	0	-0.052	-0.017	29.986	-0.100	-0.100	0.000	0.000	0.000	0.000
58	A	58	GLY	0	-0.023	0.008	32.921	0.231	0.231	0.000	0.000	0.000	0.000
59	A	59	THR	0	-0.032	-0.026	29.380	0.178	0.178	0.000	0.000	0.000	0.000
60	A	60	GLY	0	-0.015	0.011	30.262	0.090	0.090	0.000	0.000	0.000	0.000
61	A	61	ILE	0	0.015	0.014	23.598	-0.161	-0.161	0.000	0.000	0.000	0.000
62	A	62	ILE	0	-0.042	-0.027	25.279	0.243	0.243	0.000	0.000	0.000	0.000
63	A	63	LEU	0	0.019	0.000	18.983	-0.489	-0.489	0.000	0.000	0.000	0.000
64	A	64	ALA	0	0.013	0.017	19.300	0.156	0.156	0.000	0.000	0.000	0.000
65	A	65	GLY	0	-0.036	-0.016	21.152	0.312	0.312	0.000	0.000	0.000	0.000
66	A	66	GLN	0	-0.014	0.008	24.240	0.867	0.867	0.000	0.000	0.000	0.000
67	A	67	LYS	1	0.870	0.922	25.518	9.738	9.738	0.000	0.000	0.000	0.000
68	A	68	TYR	0	-0.020	-0.020	23.337	0.204	0.204	0.000	0.000	0.000	0.000
69	A	69	ILE	0	-0.029	-0.022	28.042	0.155	0.155	0.000	0.000	0.000	0.000
70	A	70	THR	0	-0.004	-0.021	28.297	-0.290	-0.290	0.000	0.000	0.000	0.000
71	A	71	ILE	0	-0.089	-0.050	27.898	0.456	0.456	0.000	0.000	0.000	0.000
72	A	72	ARG	1	0.844	0.913	26.305	11.384	11.384	0.000	0.000	0.000	0.000
73	A	73	ALA	0	0.038	0.026	26.994	-0.396	-0.396	0.000	0.000	0.000	0.000
74	A	74	GLU	-1	-0.852	-0.909	26.235	-11.058	-11.058	0.000	0.000	0.000	0.000
75	A	75	GLY	0	0.025	0.005	25.425	-0.347	-0.347	0.000	0.000	0.000	0.000
76	A	76	ARG	1	0.823	0.917	17.254	16.081	16.081	0.000	0.000	0.000	0.000
77	A	77	SER	0	0.002	-0.029	20.946	-0.769	-0.769	0.000	0.000	0.000	0.000
78	A	78	ILE	0	0.007	0.003	22.347	0.793	0.793	0.000	0.000	0.000	0.000
79	A	79	TYR	0	-0.078	-0.069	21.861	-0.258	-0.258	0.000	0.000	0.000	0.000
80	A	80	GLY	0	0.065	0.012	25.008	0.599	0.599	0.000	0.000	0.000	0.000
81	A	81	LYS	1	0.920	0.978	26.232	9.305	9.305	0.000	0.000	0.000	0.000
82	A	82	LEU	0	0.019	-0.001	27.811	0.243	0.243	0.000	0.000	0.000	0.000
83	A	83	GLN	0	0.041	0.012	29.387	0.053	0.053	0.000	0.000	0.000	0.000
84	A	84	LYS	1	0.869	0.927	30.584	9.715	9.715	0.000	0.000	0.000	0.000
85	A	85	GLU	-1	-0.874	-0.909	25.354	-12.151	-12.151	0.000	0.000	0.000	0.000
86	A	86	GLY	0	-0.032	-0.034	24.628	0.529	0.529	0.000	0.000	0.000	0.000
87	A	87	ILE	0	-0.019	0.008	19.509	-0.609	-0.609	0.000	0.000	0.000	0.000
88	A	88	ILE	0	-0.023	-0.017	19.252	0.715	0.715	0.000	0.000	0.000	0.000
89	A	89	CYS	0	-0.012	0.008	18.349	-1.098	-1.098	0.000	0.000	0.000	0.000
90	A	90	VAL	0	0.010	-0.001	16.756	0.875	0.875	0.000	0.000	0.000	0.000
91	A	91	ALA	0	-0.028	0.003	16.377	-1.349	-1.349	0.000	0.000	0.000	0.000
92	A	92	THR	0	-0.059	-0.057	12.737	0.438	0.438	0.000	0.000	0.000	0.000
93	A	93	LYS	1	0.860	0.925	15.507	20.031	20.031	0.000	0.000	0.000	0.000
94	A	94	LEU	0	-0.054	-0.033	12.314	0.948	0.948	0.000	0.000	0.000	0.000
95	A	95	CYS	0	-0.048	-0.023	10.950	-1.135	-1.135	0.000	0.000	0.000	0.000
96	A	96	ILE	0	-0.009	0.006	13.153	1.426	1.426	0.000	0.000	0.000	0.000
97	A	97	LEU	0	-0.009	0.006	10.549	-1.756	-1.756	0.000	0.000	0.000	0.000
98	A	98	VAL	0	0.003	-0.008	13.800	1.915	1.915	0.000	0.000	0.000	0.000
99	A	99	SER	0	0.038	-0.002	14.978	-1.669	-1.669	0.000	0.000	0.000	0.000
100	A	100	HIS	0	-0.055	-0.025	17.011	1.474	1.474	0.000	0.000	0.000	0.000
101	A	101	TYR	0	0.031	0.010	19.100	-0.594	-0.594	0.000	0.000	0.000	0.000
102	A	102	PRO	0	0.056	0.036	21.457	0.584	0.584	0.000	0.000	0.000	0.000
103	A	103	GLU	-1	-0.940	-0.995	24.474	-10.205	-10.205	0.000	0.000	0.000	0.000
104	A	104	THR	0	-0.043	-0.016	25.214	0.357	0.357	0.000	0.000	0.000	0.000
105	A	105	THR	0	-0.024	0.002	22.343	-0.245	-0.245	0.000	0.000	0.000	0.000
106	A	106	LEU	0	-0.011	-0.001	25.610	0.319	0.319	0.000	0.000	0.000	0.000
107	A	107	PRO	0	0.042	0.014	25.021	-0.504	-0.504	0.000	0.000	0.000	0.000
108	A	108	GLY	0	-0.005	-0.008	24.261	-0.454	-0.454	0.000	0.000	0.000	0.000
109	A	109	GLU	-1	-0.849	-0.914	22.231	-13.036	-13.036	0.000	0.000	0.000	0.000
110	A	110	ALA	0	0.092	0.045	19.696	-0.635	-0.635	0.000	0.000	0.000	0.000
111	A	111	ALA	0	0.018	0.021	19.268	-0.852	-0.852	0.000	0.000	0.000	0.000
112	A	112	LYS	1	0.932	0.972	19.869	11.837	11.837	0.000	0.000	0.000	0.000
113	A	113	ILE	0	0.011	0.012	15.438	-0.403	-0.403	0.000	0.000	0.000	0.000
114	A	114	THR	0	0.007	-0.005	15.131	-1.556	-1.556	0.000	0.000	0.000	0.000
115	A	115	GLU	-1	-0.761	-0.836	15.637	-16.083	-16.083	0.000	0.000	0.000	0.000
116	A	116	ALA	0	0.017	0.017	16.707	-0.506	-0.506	0.000	0.000	0.000	0.000
117	A	117	LEU	0	-0.006	-0.001	9.179	-1.028	-1.028	0.000	0.000	0.000	0.000
118	A	118	ALA	0	0.030	0.009	12.072	-1.776	-1.776	0.000	0.000	0.000	0.000
119	A	119	ASP	-1	-0.873	-0.934	14.240	-16.396	-16.396	0.000	0.000	0.000	0.000
120	A	120	TYR	0	-0.053	-0.023	7.802	1.124	1.124	0.000	0.000	0.000	0.000
121	A	121	LEU	0	-0.011	-0.011	7.569	-0.828	-0.828	0.000	0.000	0.000	0.000
122	A	122	VAL	0	0.001	0.009	11.471	0.045	0.045	0.000	0.000	0.000	0.000
123	A	123	GLY	0	-0.044	-0.013	14.977	0.691	0.691	0.000	0.000	0.000	0.000
124	A	124	VAL	0	-0.057	-0.027	9.143	0.292	0.292	0.000	0.000	0.000	0.000
125	A	125	GLY	0	-0.006	0.010	12.515	-0.290	-0.290	0.000	0.000	0.000	0.000
126	A	126	TYR	-1	-0.755	-0.869	8.171	-22.474	-22.474	0.000	0.000	0.000	0.000

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