FMO DATABASE

FMODB ID: 7KM1K

Calculation Name: 2CY9-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2CY9

Chain ID: A

ChEMBL ID:

UniProt ID: Q9CQR4

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	127
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1016935.812911
FMO2-HF: Nuclear repulsion	968042.051983
FMO2-HF: Total energy	-48893.760928
FMO2-MP2: Total energy	-49032.422128

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:13:LYS)

Summations of interaction energy for fragment #1(A:13: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.
-43.123	-35.641	13.016	-9.449	-11.049	-0.111

Interaction energy analysis for fragmet #1(A:13:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 2 / q_Mulliken : 1.799 / q_NPA : 1.901

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	15	MET	0	-0.018	-0.020	1.944	-38.894	-37.396	9.819	-4.909	-6.407	-0.058
4	A	16	PHE	0	0.031	-0.003	4.640	9.140	9.437	-0.001	-0.052	-0.244	0.000
19	A	31	VAL	0	-0.024	-0.038	4.698	-2.869	-2.813	-0.001	-0.008	-0.046	0.000
20	A	32	SER	0	-0.035	-0.006	4.077	-8.789	-8.669	-0.001	-0.033	-0.087	0.000
21	A	33	ALA	0	0.003	0.005	2.472	6.934	8.245	0.303	-0.567	-1.047	-0.004
22	A	34	ALA	0	-0.021	-0.015	2.296	-43.180	-38.989	2.898	-3.876	-3.214	-0.049
23	A	35	PRO	0	0.043	0.018	5.261	2.486	2.495	-0.001	-0.004	-0.004	0.000
5	A	17	LYS	1	0.870	0.936	7.552	55.657	55.657	0.000	0.000	0.000	0.000
6	A	18	VAL	0	0.086	0.041	9.180	3.572	3.572	0.000	0.000	0.000	0.000
7	A	19	PRO	0	-0.015	0.006	11.424	2.575	2.575	0.000	0.000	0.000	0.000
8	A	20	GLY	0	0.061	0.009	14.562	-1.098	-1.098	0.000	0.000	0.000	0.000
9	A	21	PHE	0	-0.019	0.006	17.111	0.854	0.854	0.000	0.000	0.000	0.000
10	A	22	ASP	-1	-0.849	-0.913	19.020	-31.090	-31.090	0.000	0.000	0.000	0.000
11	A	23	ARG	1	0.818	0.892	21.901	25.631	25.631	0.000	0.000	0.000	0.000
12	A	24	VAL	0	0.012	0.021	22.892	0.086	0.086	0.000	0.000	0.000	0.000
13	A	25	LEU	0	0.001	-0.003	20.557	-0.987	-0.987	0.000	0.000	0.000	0.000
14	A	26	GLU	-1	-0.828	-0.900	20.234	-28.126	-28.126	0.000	0.000	0.000	0.000
15	A	27	LYS	1	0.835	0.906	13.206	41.112	41.112	0.000	0.000	0.000	0.000
16	A	28	VAL	0	0.017	0.023	17.085	-0.924	-0.924	0.000	0.000	0.000	0.000
17	A	29	THR	0	-0.021	0.002	12.925	-0.798	-0.798	0.000	0.000	0.000	0.000
18	A	30	LEU	0	0.013	0.006	10.618	-1.901	-1.901	0.000	0.000	0.000	0.000
24	A	36	GLU	-1	-0.870	-0.943	8.128	-36.100	-36.100	0.000	0.000	0.000	0.000
25	A	37	LYS	1	0.874	0.956	8.394	49.049	49.049	0.000	0.000	0.000	0.000
26	A	38	LEU	0	-0.058	-0.036	6.526	-9.752	-9.752	0.000	0.000	0.000	0.000
27	A	39	ILE	0	0.046	0.035	7.032	5.697	5.697	0.000	0.000	0.000	0.000
28	A	40	CYS	0	-0.061	-0.025	7.744	-6.819	-6.819	0.000	0.000	0.000	0.000
29	A	41	GLU	-1	-0.793	-0.886	10.361	-40.432	-40.432	0.000	0.000	0.000	0.000
30	A	42	MET	0	-0.057	-0.030	13.315	-1.225	-1.225	0.000	0.000	0.000	0.000
31	A	43	LYS	1	0.940	0.989	15.194	36.271	36.271	0.000	0.000	0.000	0.000
32	A	44	VAL	0	-0.037	-0.011	19.982	-0.061	-0.061	0.000	0.000	0.000	0.000
33	A	45	GLU	-1	-0.788	-0.912	21.278	-26.995	-26.995	0.000	0.000	0.000	0.000
34	A	46	GLU	-1	-0.903	-0.957	25.021	-20.525	-20.525	0.000	0.000	0.000	0.000
35	A	47	GLN	0	0.003	-0.002	23.501	1.169	1.169	0.000	0.000	0.000	0.000
36	A	48	HIS	0	-0.003	0.007	21.131	0.505	0.505	0.000	0.000	0.000	0.000
37	A	49	THR	0	-0.111	-0.053	25.378	0.334	0.334	0.000	0.000	0.000	0.000
38	A	50	ASN	0	-0.006	-0.013	28.342	0.491	0.491	0.000	0.000	0.000	0.000
39	A	51	LYS	1	0.932	0.945	31.299	18.491	18.491	0.000	0.000	0.000	0.000
40	A	52	LEU	0	-0.004	0.010	33.412	0.476	0.476	0.000	0.000	0.000	0.000
41	A	53	GLY	0	0.057	0.049	31.184	-0.064	-0.064	0.000	0.000	0.000	0.000
42	A	54	THR	0	-0.020	-0.015	28.292	-0.458	-0.458	0.000	0.000	0.000	0.000
43	A	55	LEU	0	0.036	0.034	21.784	0.318	0.318	0.000	0.000	0.000	0.000
44	A	56	HIS	0	0.013	-0.007	26.352	0.903	0.903	0.000	0.000	0.000	0.000
45	A	57	GLY	0	0.073	0.009	26.059	-0.819	-0.819	0.000	0.000	0.000	0.000
46	A	58	GLY	0	-0.024	0.007	25.919	-0.457	-0.457	0.000	0.000	0.000	0.000
47	A	59	LEU	0	0.026	0.008	21.457	-0.532	-0.532	0.000	0.000	0.000	0.000
48	A	60	THR	0	-0.005	-0.012	21.605	-1.217	-1.217	0.000	0.000	0.000	0.000
49	A	61	ALA	0	0.026	0.020	21.242	-1.067	-1.067	0.000	0.000	0.000	0.000
50	A	62	THR	0	-0.001	0.009	21.529	-1.414	-1.414	0.000	0.000	0.000	0.000
51	A	63	LEU	0	-0.034	-0.027	16.778	-1.635	-1.635	0.000	0.000	0.000	0.000
52	A	64	VAL	0	0.006	0.009	16.821	-1.825	-1.825	0.000	0.000	0.000	0.000
53	A	65	ASP	-1	-0.759	-0.877	18.351	-29.994	-29.994	0.000	0.000	0.000	0.000
54	A	66	SER	0	0.072	0.008	15.605	-2.973	-2.973	0.000	0.000	0.000	0.000
55	A	67	ILE	0	-0.042	-0.029	11.492	0.048	0.048	0.000	0.000	0.000	0.000
56	A	68	SER	0	0.017	0.013	12.549	-2.701	-2.701	0.000	0.000	0.000	0.000
57	A	69	THR	0	0.010	-0.015	13.662	-1.504	-1.504	0.000	0.000	0.000	0.000
58	A	70	MET	0	-0.085	-0.023	9.945	0.001	0.001	0.000	0.000	0.000	0.000
59	A	71	ALA	0	-0.025	-0.020	8.965	-4.216	-4.216	0.000	0.000	0.000	0.000
60	A	72	LEU	0	0.019	0.026	10.034	-1.196	-1.196	0.000	0.000	0.000	0.000
61	A	73	MET	0	0.017	0.011	10.367	1.782	1.782	0.000	0.000	0.000	0.000
62	A	74	CYS	0	-0.132	-0.061	6.195	-1.667	-1.667	0.000	0.000	0.000	0.000
63	A	75	THR	0	-0.005	-0.002	7.262	-4.615	-4.615	0.000	0.000	0.000	0.000
64	A	76	GLU	-1	-0.749	-0.873	9.985	-35.660	-35.660	0.000	0.000	0.000	0.000
65	A	77	ARG	1	0.900	0.949	13.077	35.906	35.906	0.000	0.000	0.000	0.000
66	A	78	GLY	0	0.006	-0.003	14.694	1.171	1.171	0.000	0.000	0.000	0.000
67	A	79	ALA	0	0.008	0.006	14.694	1.606	1.606	0.000	0.000	0.000	0.000
68	A	80	PRO	0	-0.079	-0.034	14.820	0.466	0.466	0.000	0.000	0.000	0.000
69	A	81	GLY	0	0.035	0.017	17.032	1.032	1.032	0.000	0.000	0.000	0.000
70	A	82	VAL	0	0.006	0.005	20.764	-0.478	-0.478	0.000	0.000	0.000	0.000
71	A	83	SER	0	-0.012	-0.038	22.561	-0.668	-0.668	0.000	0.000	0.000	0.000
72	A	84	VAL	0	-0.072	-0.021	23.683	0.840	0.840	0.000	0.000	0.000	0.000
73	A	85	ASP	-1	-0.900	-0.951	25.378	-20.361	-20.361	0.000	0.000	0.000	0.000
74	A	86	MET	0	-0.003	-0.009	22.667	-1.675	-1.675	0.000	0.000	0.000	0.000
75	A	87	ASN	0	-0.042	-0.008	24.948	0.879	0.879	0.000	0.000	0.000	0.000
76	A	88	ILE	0	0.036	-0.001	23.412	-1.072	-1.072	0.000	0.000	0.000	0.000
77	A	89	THR	0	-0.024	0.001	25.239	1.237	1.237	0.000	0.000	0.000	0.000
78	A	90	TYR	0	0.021	-0.006	25.499	-1.130	-1.130	0.000	0.000	0.000	0.000
79	A	91	MET	0	-0.059	-0.024	24.924	0.751	0.751	0.000	0.000	0.000	0.000
80	A	92	SER	0	0.013	0.018	25.823	0.624	0.624	0.000	0.000	0.000	0.000
81	A	93	PRO	0	-0.024	-0.002	26.601	-0.545	-0.545	0.000	0.000	0.000	0.000
82	A	94	ALA	0	0.053	0.013	23.649	-0.333	-0.333	0.000	0.000	0.000	0.000
83	A	95	LYS	1	0.977	0.976	25.625	19.397	19.397	0.000	0.000	0.000	0.000
84	A	96	ILE	0	0.043	0.011	25.951	-0.846	-0.846	0.000	0.000	0.000	0.000
85	A	97	GLY	0	-0.025	-0.009	25.223	0.671	0.671	0.000	0.000	0.000	0.000
86	A	98	GLU	-1	-0.920	-0.932	23.119	-23.529	-23.529	0.000	0.000	0.000	0.000
87	A	99	GLU	-1	-0.904	-0.961	16.679	-34.402	-34.402	0.000	0.000	0.000	0.000
88	A	100	ILE	0	-0.053	-0.016	16.757	0.554	0.554	0.000	0.000	0.000	0.000
89	A	101	VAL	0	0.024	-0.006	13.257	-2.152	-2.152	0.000	0.000	0.000	0.000
90	A	102	ILE	0	-0.001	-0.004	13.204	2.004	2.004	0.000	0.000	0.000	0.000
91	A	103	THR	0	-0.030	-0.028	11.059	-4.889	-4.889	0.000	0.000	0.000	0.000
92	A	104	ALA	0	0.030	0.029	11.327	3.108	3.108	0.000	0.000	0.000	0.000
93	A	105	HIS	0	0.034	0.008	11.384	-4.679	-4.679	0.000	0.000	0.000	0.000
94	A	106	ILE	0	-0.036	-0.016	12.009	2.320	2.320	0.000	0.000	0.000	0.000
95	A	107	LEU	0	-0.011	-0.003	14.736	0.340	0.340	0.000	0.000	0.000	0.000
96	A	108	LYS	1	0.967	0.976	17.950	27.268	27.268	0.000	0.000	0.000	0.000
97	A	109	GLN	0	0.032	0.015	13.531	-1.586	-1.586	0.000	0.000	0.000	0.000
98	A	110	GLY	0	-0.058	-0.031	18.242	0.502	0.502	0.000	0.000	0.000	0.000
99	A	111	LYS	0	0.069	0.036	21.680	-0.494	-0.494	0.000	0.000	0.000	0.000
100	A	112	THR	0	0.041	0.021	23.612	0.295	0.295	0.000	0.000	0.000	0.000
101	A	113	LEU	0	-0.014	0.004	23.276	0.326	0.326	0.000	0.000	0.000	0.000
102	A	114	ALA	0	-0.008	0.013	17.844	-0.375	-0.375	0.000	0.000	0.000	0.000
103	A	115	PHE	0	-0.002	-0.004	19.292	0.818	0.818	0.000	0.000	0.000	0.000
104	A	116	ALA	0	0.035	0.018	16.059	-1.595	-1.595	0.000	0.000	0.000	0.000
105	A	117	SER	0	0.014	-0.006	16.855	2.517	2.517	0.000	0.000	0.000	0.000
106	A	118	VAL	0	-0.043	-0.023	15.219	-2.446	-2.446	0.000	0.000	0.000	0.000
107	A	119	ASP	-1	-0.880	-0.931	15.957	-27.702	-27.702	0.000	0.000	0.000	0.000
108	A	120	LEU	0	0.008	0.002	16.179	-2.113	-2.113	0.000	0.000	0.000	0.000
109	A	121	THR	0	0.058	0.027	17.350	1.350	1.350	0.000	0.000	0.000	0.000
110	A	122	ASN	0	-0.013	-0.017	18.456	-1.728	-1.728	0.000	0.000	0.000	0.000
111	A	123	LYS	1	0.844	0.913	13.433	38.080	38.080	0.000	0.000	0.000	0.000
112	A	124	THR	0	-0.015	0.004	18.397	0.038	0.038	0.000	0.000	0.000	0.000
113	A	125	THR	0	-0.013	-0.021	21.512	0.732	0.732	0.000	0.000	0.000	0.000
114	A	126	GLY	0	0.028	0.017	20.303	0.675	0.675	0.000	0.000	0.000	0.000
115	A	127	LYS	1	0.913	0.946	21.390	21.443	21.443	0.000	0.000	0.000	0.000
116	A	128	LEU	0	-0.004	0.003	20.857	-0.622	-0.622	0.000	0.000	0.000	0.000
117	A	129	ILE	0	-0.054	-0.010	21.774	1.066	1.066	0.000	0.000	0.000	0.000
118	A	130	ALA	0	0.013	-0.017	22.022	1.227	1.227	0.000	0.000	0.000	0.000
119	A	131	GLN	0	-0.005	0.007	20.542	-1.886	-1.886	0.000	0.000	0.000	0.000
120	A	132	GLY	0	0.026	0.013	20.633	1.315	1.315	0.000	0.000	0.000	0.000
121	A	133	ARG	1	0.924	0.972	20.302	22.636	22.636	0.000	0.000	0.000	0.000
122	A	134	HIS	0	-0.067	-0.027	19.272	1.633	1.633	0.000	0.000	0.000	0.000
123	A	135	THR	0	-0.005	0.006	20.641	-1.114	-1.114	0.000	0.000	0.000	0.000
124	A	136	LYS	1	0.874	0.938	18.431	31.010	31.010	0.000	0.000	0.000	0.000
125	A	137	HIS	1	0.785	0.873	21.839	23.313	23.313	0.000	0.000	0.000	0.000
126	A	138	LEU	0	-0.054	-0.012	19.277	-0.503	-0.503	0.000	0.000	0.000	0.000
127	A	139	GLY	-1	-0.833	-0.899	22.604	-22.353	-22.353	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:13:LYS)