FMO DATABASE

FMODB ID: LV679

Calculation Name: 3DKU-F-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3DKU

Chain ID: F

ChEMBL ID:

UniProt ID: A1AA28

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	149
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1448361.008956
FMO2-HF: Nuclear repulsion	1387809.448026
FMO2-HF: Total energy	-60551.56093
FMO2-MP2: Total energy	-60725.393105

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:MET)

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

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.
-82.448	-79.647	0.063	-1.003	-1.861	-0.003

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.864 / q_NPA : 0.912

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	LYS	1	0.986	0.981	3.379	41.276	44.077	0.063	-1.003	-1.861	-0.003
4	A	4	PRO	0	-0.008	0.018	5.843	0.216	0.216	0.000	0.000	0.000	0.000
5	A	5	HIS	0	0.031	0.008	9.692	-1.574	-1.574	0.000	0.000	0.000	0.000
6	A	6	VAL	0	-0.003	0.000	11.294	0.852	0.852	0.000	0.000	0.000	0.000
7	A	7	THR	0	0.004	-0.002	13.828	0.607	0.607	0.000	0.000	0.000	0.000
8	A	8	VAL	0	0.021	0.012	17.551	-0.099	-0.099	0.000	0.000	0.000	0.000
9	A	9	ALA	0	-0.010	-0.008	20.910	0.174	0.174	0.000	0.000	0.000	0.000
10	A	10	CYS	0	0.007	0.016	24.529	-0.088	-0.088	0.000	0.000	0.000	0.000
11	A	11	VAL	0	-0.025	-0.022	28.028	0.188	0.188	0.000	0.000	0.000	0.000
12	A	12	VAL	0	0.021	0.015	31.024	0.086	0.086	0.000	0.000	0.000	0.000
13	A	13	HIS	0	-0.068	-0.054	33.685	0.216	0.216	0.000	0.000	0.000	0.000
14	A	14	ALA	0	0.081	0.040	37.163	0.035	0.035	0.000	0.000	0.000	0.000
15	A	15	GLU	-1	-0.889	-0.940	40.801	-6.760	-6.760	0.000	0.000	0.000	0.000
16	A	16	GLY	0	-0.021	0.004	42.496	0.118	0.118	0.000	0.000	0.000	0.000
17	A	17	LYS	1	0.836	0.918	40.601	7.169	7.169	0.000	0.000	0.000	0.000
18	A	18	PHE	0	0.008	-0.009	35.093	-0.075	-0.075	0.000	0.000	0.000	0.000
19	A	19	LEU	0	-0.009	0.016	34.131	0.097	0.097	0.000	0.000	0.000	0.000
20	A	20	VAL	0	-0.078	-0.034	32.425	-0.312	-0.312	0.000	0.000	0.000	0.000
21	A	21	VAL	0	0.063	0.012	29.317	0.327	0.327	0.000	0.000	0.000	0.000
22	A	22	GLU	-1	-0.850	-0.927	31.930	-8.639	-8.639	0.000	0.000	0.000	0.000
23	A	23	GLU	-1	-0.680	-0.803	26.421	-11.822	-11.822	0.000	0.000	0.000	0.000
24	A	24	THR	0	-0.060	-0.051	30.766	0.105	0.105	0.000	0.000	0.000	0.000
25	A	25	ILE	0	-0.022	0.010	24.879	-0.149	-0.149	0.000	0.000	0.000	0.000
26	A	26	ASN	0	-0.021	-0.045	28.529	-0.017	-0.017	0.000	0.000	0.000	0.000
27	A	27	GLY	0	0.001	0.024	31.093	0.161	0.161	0.000	0.000	0.000	0.000
28	A	28	LYS	1	0.846	0.911	33.278	8.923	8.923	0.000	0.000	0.000	0.000
29	A	29	ALA	0	0.082	0.051	32.722	-0.286	-0.286	0.000	0.000	0.000	0.000
30	A	30	LEU	0	-0.084	-0.057	28.703	0.117	0.117	0.000	0.000	0.000	0.000
31	A	31	TRP	0	-0.049	-0.017	31.205	-0.075	-0.075	0.000	0.000	0.000	0.000
32	A	32	ASN	0	0.007	-0.017	25.095	-0.342	-0.342	0.000	0.000	0.000	0.000
33	A	33	GLN	0	0.005	0.004	27.470	-0.028	-0.028	0.000	0.000	0.000	0.000
34	A	34	PRO	0	0.045	0.030	27.659	-0.262	-0.262	0.000	0.000	0.000	0.000
35	A	35	ALA	0	-0.107	-0.062	23.468	-0.164	-0.164	0.000	0.000	0.000	0.000
36	A	36	GLY	0	0.088	0.060	21.357	0.163	0.163	0.000	0.000	0.000	0.000
37	A	37	HIS	0	-0.058	-0.043	16.285	-1.345	-1.345	0.000	0.000	0.000	0.000
38	A	38	LEU	0	-0.051	-0.010	13.941	0.432	0.432	0.000	0.000	0.000	0.000
39	A	39	GLU	-1	-0.921	-0.963	14.993	-15.086	-15.086	0.000	0.000	0.000	0.000
40	A	40	ALA	0	-0.098	-0.068	14.158	-0.881	-0.881	0.000	0.000	0.000	0.000
41	A	41	ASP	-1	-0.964	-0.992	14.830	-15.514	-15.514	0.000	0.000	0.000	0.000
42	A	42	GLU	-1	-0.678	-0.784	16.741	-13.537	-13.537	0.000	0.000	0.000	0.000
43	A	43	THR	0	-0.018	-0.020	17.367	-1.121	-1.121	0.000	0.000	0.000	0.000
44	A	44	LEU	0	-0.021	-0.032	16.174	0.272	0.272	0.000	0.000	0.000	0.000
45	A	45	VAL	0	-0.021	-0.024	19.651	0.264	0.264	0.000	0.000	0.000	0.000
46	A	46	GLU	-1	-0.838	-0.908	22.051	-12.386	-12.386	0.000	0.000	0.000	0.000
47	A	47	ALA	0	0.031	0.034	19.831	0.318	0.318	0.000	0.000	0.000	0.000
48	A	48	ALA	0	-0.041	-0.029	21.922	0.339	0.339	0.000	0.000	0.000	0.000
49	A	49	ALA	0	-0.017	-0.014	24.508	0.389	0.389	0.000	0.000	0.000	0.000
50	A	50	ARG	1	0.799	0.866	20.066	14.029	14.029	0.000	0.000	0.000	0.000
51	A	51	GLU	-1	-0.787	-0.887	21.601	-12.922	-12.922	0.000	0.000	0.000	0.000
52	A	52	LEU	0	-0.037	-0.011	25.678	0.384	0.384	0.000	0.000	0.000	0.000
53	A	53	TRP	0	-0.034	0.001	29.050	0.427	0.427	0.000	0.000	0.000	0.000
54	A	54	GLU	-1	-0.868	-0.950	26.509	-10.032	-10.032	0.000	0.000	0.000	0.000
55	A	55	GLU	-1	-0.786	-0.896	26.275	-10.963	-10.963	0.000	0.000	0.000	0.000
56	A	56	THR	0	-0.042	-0.070	30.146	0.404	0.404	0.000	0.000	0.000	0.000
57	A	57	GLY	0	-0.001	0.014	33.041	0.343	0.343	0.000	0.000	0.000	0.000
58	A	58	ILE	0	-0.046	-0.030	34.352	0.179	0.179	0.000	0.000	0.000	0.000
59	A	59	SER	0	-0.034	-0.016	33.336	-0.362	-0.362	0.000	0.000	0.000	0.000
60	A	60	ALA	0	0.008	-0.005	32.565	0.264	0.264	0.000	0.000	0.000	0.000
61	A	61	GLN	0	0.036	0.018	28.046	-0.572	-0.572	0.000	0.000	0.000	0.000
62	A	62	PRO	0	0.003	-0.006	25.976	0.269	0.269	0.000	0.000	0.000	0.000
63	A	63	GLN	0	-0.022	0.008	28.937	0.097	0.097	0.000	0.000	0.000	0.000
64	A	64	HIS	0	-0.013	-0.014	28.674	-0.001	-0.001	0.000	0.000	0.000	0.000
65	A	65	PHE	0	0.027	0.017	20.321	-0.240	-0.240	0.000	0.000	0.000	0.000
66	A	66	ILE	0	-0.026	-0.017	25.864	0.324	0.324	0.000	0.000	0.000	0.000
67	A	67	ARG	1	0.912	0.921	21.985	12.791	12.791	0.000	0.000	0.000	0.000
68	A	68	MET	0	0.029	0.052	15.488	-0.439	-0.439	0.000	0.000	0.000	0.000
69	A	69	HIS	0	-0.024	-0.020	20.099	0.157	0.157	0.000	0.000	0.000	0.000
70	A	70	GLN	0	0.009	0.016	13.230	0.045	0.045	0.000	0.000	0.000	0.000
71	A	71	TRP	0	-0.004	-0.016	17.233	1.018	1.018	0.000	0.000	0.000	0.000
72	A	72	ILE	0	-0.016	-0.010	15.129	-1.308	-1.308	0.000	0.000	0.000	0.000
73	A	73	ALA	0	0.033	0.045	17.804	1.028	1.028	0.000	0.000	0.000	0.000
74	A	74	PRO	0	0.013	-0.016	19.756	-0.439	-0.439	0.000	0.000	0.000	0.000
75	A	75	ASP	-1	-0.849	-0.901	18.859	-16.651	-16.651	0.000	0.000	0.000	0.000
76	A	76	LYS	1	0.857	0.920	15.918	16.221	16.221	0.000	0.000	0.000	0.000
77	A	77	THR	0	0.019	0.007	14.058	-2.004	-2.004	0.000	0.000	0.000	0.000
78	A	78	PRO	0	-0.062	-0.022	10.993	0.984	0.984	0.000	0.000	0.000	0.000
79	A	79	PHE	0	0.040	0.007	12.778	-1.217	-1.217	0.000	0.000	0.000	0.000
80	A	80	LEU	0	-0.023	-0.026	12.019	0.088	0.088	0.000	0.000	0.000	0.000
81	A	81	ARG	1	0.881	0.947	15.583	12.632	12.632	0.000	0.000	0.000	0.000
82	A	82	PHE	0	0.008	-0.008	15.034	0.302	0.302	0.000	0.000	0.000	0.000
83	A	83	LEU	0	-0.035	-0.003	20.399	0.243	0.243	0.000	0.000	0.000	0.000
84	A	84	PHE	0	0.060	0.014	21.732	0.127	0.127	0.000	0.000	0.000	0.000
85	A	85	ALA	0	0.002	-0.004	26.740	0.152	0.152	0.000	0.000	0.000	0.000
86	A	86	ILE	0	-0.007	-0.004	29.908	-0.090	-0.090	0.000	0.000	0.000	0.000
87	A	87	GLU	-1	-0.780	-0.848	33.115	-8.260	-8.260	0.000	0.000	0.000	0.000
88	A	88	LEU	0	-0.011	-0.012	36.493	-0.056	-0.056	0.000	0.000	0.000	0.000
89	A	89	GLU	-1	-0.932	-0.968	39.376	-7.215	-7.215	0.000	0.000	0.000	0.000
90	A	90	GLN	0	-0.051	-0.030	42.743	0.132	0.132	0.000	0.000	0.000	0.000
91	A	91	ILE	0	-0.032	-0.008	41.692	-0.198	-0.198	0.000	0.000	0.000	0.000
92	A	92	CYS	0	-0.051	-0.007	39.276	0.108	0.108	0.000	0.000	0.000	0.000
93	A	93	PRO	0	-0.035	-0.024	40.769	-0.089	-0.089	0.000	0.000	0.000	0.000
94	A	94	THR	0	0.025	0.010	36.822	-0.098	-0.098	0.000	0.000	0.000	0.000
95	A	95	GLN	0	-0.076	-0.052	37.182	0.178	0.178	0.000	0.000	0.000	0.000
96	A	96	PRO	0	0.028	0.024	33.174	-0.053	-0.053	0.000	0.000	0.000	0.000
97	A	97	HIS	1	0.760	0.886	31.537	9.215	9.215	0.000	0.000	0.000	0.000
98	A	98	ASP	-1	-0.780	-0.885	26.677	-11.022	-11.022	0.000	0.000	0.000	0.000
99	A	99	SER	0	-0.078	-0.041	30.091	0.319	0.319	0.000	0.000	0.000	0.000
100	A	100	ASP	-1	-0.954	-0.970	26.278	-11.037	-11.037	0.000	0.000	0.000	0.000
101	A	101	ILE	0	-0.089	-0.041	28.520	0.067	0.067	0.000	0.000	0.000	0.000
102	A	102	ASP	-1	-0.847	-0.897	31.764	-8.874	-8.874	0.000	0.000	0.000	0.000
103	A	103	CYS	0	-0.116	-0.072	34.953	0.387	0.387	0.000	0.000	0.000	0.000
104	A	104	CYS	0	0.025	0.027	33.983	-0.284	-0.284	0.000	0.000	0.000	0.000
105	A	105	ARG	1	0.875	0.939	36.331	8.162	8.162	0.000	0.000	0.000	0.000
106	A	106	TRP	0	0.069	0.030	37.448	-0.205	-0.205	0.000	0.000	0.000	0.000
107	A	107	VAL	0	-0.020	-0.003	37.762	0.237	0.237	0.000	0.000	0.000	0.000
108	A	108	SER	0	-0.003	-0.017	39.267	-0.107	-0.107	0.000	0.000	0.000	0.000
109	A	109	ALA	0	0.028	0.006	37.848	-0.181	-0.181	0.000	0.000	0.000	0.000
110	A	110	GLU	-1	-0.851	-0.931	38.065	-7.588	-7.588	0.000	0.000	0.000	0.000
111	A	111	GLU	-1	-0.930	-0.964	40.206	-7.600	-7.600	0.000	0.000	0.000	0.000
112	A	112	ILE	0	0.024	0.002	33.454	-0.151	-0.151	0.000	0.000	0.000	0.000
113	A	113	LEU	0	-0.092	-0.051	34.502	-0.230	-0.230	0.000	0.000	0.000	0.000
114	A	114	GLN	0	-0.068	-0.028	36.578	0.004	0.004	0.000	0.000	0.000	0.000
115	A	115	ALA	0	0.023	0.037	35.844	0.133	0.133	0.000	0.000	0.000	0.000
116	A	116	SER	0	-0.033	-0.028	35.459	-0.220	-0.220	0.000	0.000	0.000	0.000
117	A	117	ASN	0	-0.054	-0.017	33.966	-0.173	-0.173	0.000	0.000	0.000	0.000
118	A	118	LEU	0	0.037	0.025	30.511	-0.083	-0.083	0.000	0.000	0.000	0.000
119	A	119	ARG	1	0.796	0.872	23.733	11.928	11.928	0.000	0.000	0.000	0.000
120	A	120	SER	0	0.003	-0.010	24.475	-0.532	-0.532	0.000	0.000	0.000	0.000
121	A	121	PRO	0	0.035	0.006	25.467	0.304	0.304	0.000	0.000	0.000	0.000
122	A	122	LEU	0	0.011	0.005	21.993	0.309	0.309	0.000	0.000	0.000	0.000
123	A	123	VAL	0	-0.028	0.037	26.180	0.100	0.100	0.000	0.000	0.000	0.000
124	A	124	ALA	0	0.077	0.038	28.753	0.283	0.283	0.000	0.000	0.000	0.000
125	A	125	GLU	-1	-0.866	-0.920	27.081	-10.294	-10.294	0.000	0.000	0.000	0.000
126	A	126	SER	0	0.002	-0.014	27.354	-0.089	-0.089	0.000	0.000	0.000	0.000
127	A	127	ILE	0	0.026	0.028	29.103	0.138	0.138	0.000	0.000	0.000	0.000
128	A	128	ARG	1	0.889	0.930	30.693	10.080	10.080	0.000	0.000	0.000	0.000
129	A	129	CYS	0	-0.077	-0.029	28.036	-0.016	-0.016	0.000	0.000	0.000	0.000
130	A	130	TYR	0	-0.018	-0.031	30.418	0.104	0.104	0.000	0.000	0.000	0.000
131	A	131	GLN	0	0.039	0.003	32.634	0.079	0.079	0.000	0.000	0.000	0.000
132	A	132	SER	0	-0.090	-0.045	32.063	0.136	0.136	0.000	0.000	0.000	0.000
133	A	133	GLY	0	0.013	0.010	34.507	0.064	0.064	0.000	0.000	0.000	0.000
134	A	134	GLN	0	-0.073	-0.022	27.811	-0.254	-0.254	0.000	0.000	0.000	0.000
135	A	135	ARG	1	0.856	0.918	29.755	9.032	9.032	0.000	0.000	0.000	0.000
136	A	136	TYR	0	-0.049	-0.015	25.878	0.229	0.229	0.000	0.000	0.000	0.000
137	A	137	PRO	0	0.024	0.017	26.513	-0.012	-0.012	0.000	0.000	0.000	0.000
138	A	138	LEU	0	0.031	0.004	24.900	-0.394	-0.394	0.000	0.000	0.000	0.000
139	A	139	GLU	-1	-0.886	-0.949	23.088	-10.813	-10.813	0.000	0.000	0.000	0.000
140	A	140	MET	0	-0.096	-0.039	21.706	-0.429	-0.429	0.000	0.000	0.000	0.000
141	A	141	ILE	0	-0.091	-0.050	18.204	-0.542	-0.542	0.000	0.000	0.000	0.000
142	A	142	GLY	0	0.027	0.027	18.789	-0.315	-0.315	0.000	0.000	0.000	0.000
143	A	143	ASP	-1	-0.889	-0.925	17.536	-13.723	-13.723	0.000	0.000	0.000	0.000
144	A	144	PHE	0	-0.014	-0.036	16.633	0.542	0.542	0.000	0.000	0.000	0.000
145	A	145	ASN	0	-0.099	-0.054	17.480	-0.201	-0.201	0.000	0.000	0.000	0.000
146	A	146	TRP	0	0.064	0.047	15.576	-0.870	-0.870	0.000	0.000	0.000	0.000
147	A	147	PRO	0	-0.073	-0.031	17.294	0.554	0.554	0.000	0.000	0.000	0.000
148	A	148	PHE	0	-0.046	-0.025	17.360	0.120	0.120	0.000	0.000	0.000	0.000
149	A	149	THR	-1	-0.926	-0.951	22.632	-10.734	-10.734	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

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