FMO DATABASE

FMODB ID: YR932

Calculation Name: 2H2Y-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2H2Y

Chain ID: A

ChEMBL ID:

UniProt ID: Q8IDP1

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	133
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1209159.550825
FMO2-HF: Nuclear repulsion	1156586.467737
FMO2-HF: Total energy	-52573.083088
FMO2-MP2: Total energy	-52728.627199

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.
119.103	123.293	11.932	-8.167	-7.954	-0.067

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 : 2 / q_Mulliken : 1.763 / q_NPA : 1.880

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	SER	0	0.109	0.052	3.870	-2.067	-0.974	-0.012	-0.491	-0.589	0.000
32	A	34	LYS	1	0.866	0.929	2.159	71.342	72.579	5.502	-3.168	-3.571	-0.012
33	A	35	ASN	0	-0.040	-0.034	2.109	-36.711	-35.040	6.438	-4.435	-3.674	-0.055
34	A	36	PRO	0	0.015	0.012	3.445	7.725	7.914	0.004	-0.073	-0.120	0.000
4	A	6	ARG	1	0.922	0.995	5.998	61.655	61.655	0.000	0.000	0.000	0.000
5	A	7	THR	0	-0.046	-0.062	6.948	-4.623	-4.623	0.000	0.000	0.000	0.000
6	A	8	VAL	0	0.078	0.062	9.559	0.646	0.646	0.000	0.000	0.000	0.000
7	A	9	GLU	-1	-0.856	-0.927	13.398	-32.604	-32.604	0.000	0.000	0.000	0.000
8	A	10	LYS	1	0.879	0.922	9.383	49.380	49.380	0.000	0.000	0.000	0.000
9	A	11	HIS	0	0.091	0.041	13.201	2.486	2.486	0.000	0.000	0.000	0.000
10	A	12	ILE	0	-0.020	-0.009	7.544	1.091	1.091	0.000	0.000	0.000	0.000
11	A	13	LYS	1	0.931	0.967	11.097	37.121	37.121	0.000	0.000	0.000	0.000
12	A	14	THR	0	0.006	0.023	13.118	1.776	1.776	0.000	0.000	0.000	0.000
13	A	15	LYS	1	1.006	1.006	15.458	27.735	27.735	0.000	0.000	0.000	0.000
14	A	16	TYR	0	0.057	0.022	15.669	1.712	1.712	0.000	0.000	0.000	0.000
15	A	17	ASN	0	0.028	0.004	18.059	-0.968	-0.968	0.000	0.000	0.000	0.000
16	A	18	LEU	0	0.016	-0.003	17.063	-0.540	-0.540	0.000	0.000	0.000	0.000
17	A	19	GLY	0	0.039	0.029	19.824	0.019	0.019	0.000	0.000	0.000	0.000
18	A	20	ASN	0	-0.037	-0.009	21.150	0.845	0.845	0.000	0.000	0.000	0.000
19	A	21	ALA	0	0.083	0.045	20.096	-1.475	-1.475	0.000	0.000	0.000	0.000
20	A	22	ASN	0	0.012	-0.002	18.535	-1.039	-1.039	0.000	0.000	0.000	0.000
21	A	23	TYR	0	0.022	0.026	14.633	-2.373	-2.373	0.000	0.000	0.000	0.000
22	A	24	ARG	1	0.779	0.874	14.750	32.108	32.108	0.000	0.000	0.000	0.000
23	A	25	ILE	0	0.031	0.018	14.751	-2.550	-2.550	0.000	0.000	0.000	0.000
24	A	26	GLN	0	-0.030	-0.032	11.482	-2.256	-2.256	0.000	0.000	0.000	0.000
25	A	27	LYS	1	0.932	0.966	10.490	38.465	38.465	0.000	0.000	0.000	0.000
26	A	28	GLU	-1	-0.802	-0.878	10.153	-47.084	-47.084	0.000	0.000	0.000	0.000
27	A	29	LEU	0	0.016	0.019	10.309	-3.698	-3.698	0.000	0.000	0.000	0.000
28	A	30	ASN	0	-0.005	-0.022	6.525	-6.609	-6.609	0.000	0.000	0.000	0.000
29	A	31	ASN	0	-0.032	-0.012	5.643	-15.514	-15.514	0.000	0.000	0.000	0.000
30	A	32	PHE	0	0.044	0.019	6.411	-6.215	-6.215	0.000	0.000	0.000	0.000
31	A	33	LEU	0	-0.011	-0.002	4.973	-1.890	-1.890	0.000	0.000	0.000	0.000
35	A	37	PRO	0	0.006	0.005	6.709	-0.252	-0.252	0.000	0.000	0.000	0.000
36	A	38	ILE	0	0.038	0.017	10.030	-2.092	-2.092	0.000	0.000	0.000	0.000
37	A	39	ASN	0	0.015	0.001	11.432	0.186	0.186	0.000	0.000	0.000	0.000
38	A	40	CYS	0	-0.054	0.007	10.890	3.418	3.418	0.000	0.000	0.000	0.000
39	A	41	THR	0	-0.066	-0.027	10.245	-3.681	-3.681	0.000	0.000	0.000	0.000
40	A	42	ILE	0	-0.039	-0.035	9.963	1.370	1.370	0.000	0.000	0.000	0.000
41	A	43	ASP	-1	-0.873	-0.929	12.709	-35.784	-35.784	0.000	0.000	0.000	0.000
42	A	44	VAL	0	-0.076	-0.044	14.030	0.363	0.363	0.000	0.000	0.000	0.000
43	A	45	HIS	0	0.012	0.008	16.796	1.184	1.184	0.000	0.000	0.000	0.000
44	A	46	PRO	0	0.076	0.054	20.163	-0.371	-0.371	0.000	0.000	0.000	0.000
45	A	47	SER	0	-0.086	-0.049	20.848	1.822	1.822	0.000	0.000	0.000	0.000
46	A	48	ASN	0	0.023	0.004	21.219	0.213	0.213	0.000	0.000	0.000	0.000
47	A	49	ILE	0	0.029	0.017	14.636	-0.502	-0.502	0.000	0.000	0.000	0.000
48	A	50	ARG	1	0.809	0.902	18.362	25.133	25.133	0.000	0.000	0.000	0.000
49	A	51	ILE	0	0.004	0.013	20.525	0.542	0.542	0.000	0.000	0.000	0.000
50	A	52	TRP	0	-0.017	-0.015	12.718	-2.355	-2.355	0.000	0.000	0.000	0.000
51	A	53	ILE	0	0.006	-0.010	17.216	2.063	2.063	0.000	0.000	0.000	0.000
52	A	54	VAL	0	0.024	0.015	13.199	-2.131	-2.131	0.000	0.000	0.000	0.000
53	A	55	GLN	0	-0.027	-0.016	14.993	3.589	3.589	0.000	0.000	0.000	0.000
54	A	56	TYR	0	0.054	0.017	14.762	-2.088	-2.088	0.000	0.000	0.000	0.000
55	A	57	VAL	0	-0.027	-0.006	15.998	1.779	1.779	0.000	0.000	0.000	0.000
56	A	58	GLY	0	0.059	0.023	17.379	-1.338	-1.338	0.000	0.000	0.000	0.000
57	A	59	LEU	0	0.000	-0.008	15.113	-0.439	-0.439	0.000	0.000	0.000	0.000
58	A	60	GLU	-1	-0.852	-0.907	18.866	-26.755	-26.755	0.000	0.000	0.000	0.000
59	A	61	ASN	0	-0.055	-0.023	18.677	0.789	0.789	0.000	0.000	0.000	0.000
60	A	62	THR	0	-0.041	-0.035	21.087	0.441	0.441	0.000	0.000	0.000	0.000
61	A	63	ILE	0	0.018	0.003	23.637	0.223	0.223	0.000	0.000	0.000	0.000
62	A	64	TYR	0	-0.030	-0.004	22.959	0.058	0.058	0.000	0.000	0.000	0.000
63	A	65	ALA	0	-0.014	0.010	22.302	-0.978	-0.978	0.000	0.000	0.000	0.000
64	A	66	ASN	0	-0.072	-0.065	20.956	1.249	1.249	0.000	0.000	0.000	0.000
65	A	67	GLU	-1	-0.852	-0.884	22.017	-22.124	-22.124	0.000	0.000	0.000	0.000
66	A	68	VAL	0	-0.072	-0.035	19.689	-1.214	-1.214	0.000	0.000	0.000	0.000
67	A	69	TYR	0	-0.019	-0.028	20.378	0.968	0.968	0.000	0.000	0.000	0.000
68	A	70	LYS	1	0.904	0.939	19.441	25.403	25.403	0.000	0.000	0.000	0.000
69	A	71	ILE	0	0.042	0.030	17.628	1.204	1.204	0.000	0.000	0.000	0.000
70	A	72	LYS	1	0.905	0.969	18.782	23.442	23.442	0.000	0.000	0.000	0.000
71	A	73	ILE	0	-0.001	0.003	16.023	0.190	0.190	0.000	0.000	0.000	0.000
72	A	74	ILE	0	0.007	0.005	20.193	-0.237	-0.237	0.000	0.000	0.000	0.000
73	A	75	PHE	0	0.022	0.000	16.237	0.404	0.404	0.000	0.000	0.000	0.000
74	A	76	PRO	0	0.019	0.021	22.326	0.465	0.465	0.000	0.000	0.000	0.000
75	A	77	ASP	-1	-0.904	-0.959	24.956	-22.102	-22.102	0.000	0.000	0.000	0.000
76	A	78	ASN	0	0.007	-0.007	25.888	-0.767	-0.767	0.000	0.000	0.000	0.000
77	A	79	TYR	0	0.044	0.061	18.051	-0.624	-0.624	0.000	0.000	0.000	0.000
78	A	80	PRO	0	-0.052	-0.047	20.314	-0.287	-0.287	0.000	0.000	0.000	0.000
79	A	81	LEU	0	0.046	0.016	22.420	0.050	0.050	0.000	0.000	0.000	0.000
80	A	82	LYS	1	0.949	0.978	26.123	21.620	21.620	0.000	0.000	0.000	0.000
81	A	83	PRO	0	0.083	0.043	23.599	-1.088	-1.088	0.000	0.000	0.000	0.000
82	A	84	PRO	0	-0.072	-0.041	19.461	0.415	0.415	0.000	0.000	0.000	0.000
83	A	85	ILE	0	0.011	-0.002	22.318	0.246	0.246	0.000	0.000	0.000	0.000
84	A	86	VAL	0	-0.015	-0.015	19.646	-0.849	-0.849	0.000	0.000	0.000	0.000
85	A	87	TYR	0	0.039	0.027	22.281	0.720	0.720	0.000	0.000	0.000	0.000
86	A	88	PHE	0	0.030	0.002	21.190	-1.219	-1.219	0.000	0.000	0.000	0.000
87	A	89	LEU	0	-0.054	-0.034	22.324	0.776	0.776	0.000	0.000	0.000	0.000
88	A	90	GLN	0	0.020	-0.010	25.209	0.306	0.306	0.000	0.000	0.000	0.000
89	A	91	LYS	1	0.903	0.956	26.516	18.727	18.727	0.000	0.000	0.000	0.000
90	A	92	PRO	0	0.056	0.033	25.909	-0.759	-0.759	0.000	0.000	0.000	0.000
91	A	93	PRO	0	0.000	0.021	23.809	0.614	0.614	0.000	0.000	0.000	0.000
92	A	94	LYS	1	0.929	0.956	26.790	19.140	19.140	0.000	0.000	0.000	0.000
93	A	95	HIS	0	0.142	0.068	27.090	-0.352	-0.352	0.000	0.000	0.000	0.000
94	A	96	THR	0	-0.018	-0.001	29.177	0.420	0.420	0.000	0.000	0.000	0.000
95	A	97	HIS	0	-0.005	-0.007	27.349	0.139	0.139	0.000	0.000	0.000	0.000
96	A	98	VAL	0	-0.038	-0.014	25.531	-0.636	-0.636	0.000	0.000	0.000	0.000
97	A	99	TYR	0	0.050	0.033	28.641	0.594	0.594	0.000	0.000	0.000	0.000
98	A	100	SER	0	0.005	-0.016	30.388	-0.547	-0.547	0.000	0.000	0.000	0.000
99	A	101	ASN	0	-0.069	-0.046	31.749	-0.184	-0.184	0.000	0.000	0.000	0.000
100	A	102	GLY	0	0.005	0.005	27.644	-0.351	-0.351	0.000	0.000	0.000	0.000
101	A	103	ASP	-1	-0.868	-0.915	26.509	-20.919	-20.919	0.000	0.000	0.000	0.000
102	A	104	ILE	0	-0.023	-0.019	22.396	-0.006	-0.006	0.000	0.000	0.000	0.000
103	A	105	CYS	0	-0.034	-0.008	26.523	-0.050	-0.050	0.000	0.000	0.000	0.000
104	A	106	LEU	0	0.027	-0.002	21.649	-0.126	-0.126	0.000	0.000	0.000	0.000
105	A	107	SER	0	0.007	-0.017	26.021	-0.504	-0.504	0.000	0.000	0.000	0.000
106	A	108	VAL	0	0.016	0.001	20.627	-0.021	-0.021	0.000	0.000	0.000	0.000
107	A	109	LEU	0	-0.064	-0.043	21.025	-1.101	-1.101	0.000	0.000	0.000	0.000
108	A	110	GLY	0	-0.013	-0.013	24.430	0.328	0.328	0.000	0.000	0.000	0.000
109	A	111	ASP	-1	-0.923	-0.955	27.937	-19.547	-19.547	0.000	0.000	0.000	0.000
110	A	112	ASP	-1	-0.840	-0.882	26.021	-21.387	-21.387	0.000	0.000	0.000	0.000
111	A	113	TYR	0	-0.111	-0.067	20.978	-1.834	-1.834	0.000	0.000	0.000	0.000
112	A	114	ASN	0	0.055	0.034	22.956	0.134	0.134	0.000	0.000	0.000	0.000
113	A	115	PRO	0	0.035	0.002	22.241	-1.235	-1.235	0.000	0.000	0.000	0.000
114	A	116	SER	0	-0.067	-0.043	19.667	-1.797	-1.797	0.000	0.000	0.000	0.000
115	A	117	LEU	0	-0.008	0.018	17.882	-2.109	-2.109	0.000	0.000	0.000	0.000
116	A	118	SER	0	-0.009	-0.003	12.549	0.179	0.179	0.000	0.000	0.000	0.000
117	A	119	ILE	0	0.009	-0.007	13.294	0.884	0.884	0.000	0.000	0.000	0.000
118	A	120	SER	0	-0.018	-0.012	9.096	2.121	2.121	0.000	0.000	0.000	0.000
119	A	121	GLY	0	0.053	0.034	11.533	0.689	0.689	0.000	0.000	0.000	0.000
120	A	122	LEU	0	0.001	0.013	14.239	1.677	1.677	0.000	0.000	0.000	0.000
121	A	123	ILE	0	0.010	0.000	13.585	1.063	1.063	0.000	0.000	0.000	0.000
122	A	124	LEU	0	-0.001	-0.004	11.945	0.664	0.664	0.000	0.000	0.000	0.000
123	A	125	SER	0	-0.002	-0.003	14.729	1.554	1.554	0.000	0.000	0.000	0.000
124	A	126	ILE	0	0.034	0.023	18.208	1.260	1.260	0.000	0.000	0.000	0.000
125	A	127	ILE	0	-0.043	-0.020	14.792	0.798	0.798	0.000	0.000	0.000	0.000
126	A	128	SER	0	-0.064	-0.033	17.965	1.200	1.200	0.000	0.000	0.000	0.000
127	A	129	MET	0	-0.005	0.011	19.788	0.998	0.998	0.000	0.000	0.000	0.000
128	A	130	LEU	0	-0.012	0.005	20.587	0.953	0.953	0.000	0.000	0.000	0.000
129	A	131	SER	0	-0.053	-0.025	20.061	0.355	0.355	0.000	0.000	0.000	0.000
130	A	132	SER	0	-0.052	-0.046	22.560	0.538	0.538	0.000	0.000	0.000	0.000
131	A	133	ALA	0	-0.022	-0.009	26.237	0.331	0.331	0.000	0.000	0.000	0.000
132	A	134	LYS	1	0.929	0.955	29.204	16.852	16.852	0.000	0.000	0.000	0.000
133	A	135	GLU	-2	-1.801	-1.889	30.158	-36.888	-36.888	0.000	0.000	0.000	0.000

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