FMO DATABASE

FMODB ID: 3J3GL

Calculation Name: 2H2Y-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2H2Y

Chain ID: A

ChEMBL ID:

UniProt ID: Q8IDP1

Base Structure: X-ray

Registration Date: 2023-09-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptHSide
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

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. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1210903.023211
FMO2-HF: Nuclear repulsion	1158329.847505
FMO2-HF: Total energy	-52573.175706
FMO2-MP2: Total energy	-52728.869826

3D Structure

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.
99.058	98.075	16.588	-7.325	-8.281	-0.047

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 : 0.949 / q_NPA : 0.982

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	5	SER	0	0.099	0.043	3.872	-3.228	-1.570	-0.016	-0.921	-0.722	0.003
4	A	6	ARG	1	0.917	0.999	6.381	31.891	31.891	0.000	0.000	0.000	0.000
5	A	7	THR	0	-0.041	-0.067	6.965	-3.684	-3.684	0.000	0.000	0.000	0.000
6	A	8	VAL	0	0.037	0.045	9.376	-0.006	-0.006	0.000	0.000	0.000	0.000
7	A	9	GLU	-1	-0.823	-0.913	13.152	-17.328	-17.328	0.000	0.000	0.000	0.000
8	A	10	LYS	1	0.876	0.930	8.517	30.717	30.717	0.000	0.000	0.000	0.000
9	A	11	HIS	0	0.075	0.051	12.278	1.820	1.820	0.000	0.000	0.000	0.000
10	A	12	ILE	0	-0.023	-0.026	6.879	1.181	1.181	0.000	0.000	0.000	0.000
11	A	13	LYS	1	0.927	0.969	10.511	21.462	21.462	0.000	0.000	0.000	0.000
12	A	14	THR	0	0.031	0.028	12.411	0.762	0.762	0.000	0.000	0.000	0.000
13	A	15	LYS	1	1.019	1.018	14.609	15.286	15.286	0.000	0.000	0.000	0.000
14	A	16	TYR	0	0.031	0.006	15.291	1.071	1.071	0.000	0.000	0.000	0.000
15	A	17	ASN	0	0.005	-0.007	17.888	-0.505	-0.505	0.000	0.000	0.000	0.000
16	A	18	LEU	0	0.053	0.016	16.907	-0.339	-0.339	0.000	0.000	0.000	0.000
17	A	19	GLY	0	-0.007	0.003	19.669	0.146	0.146	0.000	0.000	0.000	0.000
18	A	20	ASN	0	-0.014	0.003	21.078	0.521	0.521	0.000	0.000	0.000	0.000
19	A	21	ALA	0	0.108	0.048	20.190	-0.729	-0.729	0.000	0.000	0.000	0.000
20	A	22	ASN	0	0.019	0.007	18.339	-0.246	-0.246	0.000	0.000	0.000	0.000
21	A	23	TYR	0	0.024	0.039	14.757	-1.307	-1.307	0.000	0.000	0.000	0.000
22	A	24	ARG	1	0.849	0.903	14.888	16.071	16.071	0.000	0.000	0.000	0.000
23	A	25	ILE	0	0.026	0.017	15.025	-1.149	-1.149	0.000	0.000	0.000	0.000
24	A	26	GLN	0	-0.034	-0.042	11.332	-1.091	-1.091	0.000	0.000	0.000	0.000
25	A	27	LYS	1	0.853	0.925	10.753	20.271	20.271	0.000	0.000	0.000	0.000
26	A	28	GLU	-1	-0.800	-0.896	10.276	-23.764	-23.764	0.000	0.000	0.000	0.000
27	A	29	LEU	0	0.029	0.029	10.072	-1.233	-1.233	0.000	0.000	0.000	0.000
28	A	30	ASN	0	-0.054	-0.043	6.295	-5.711	-5.711	0.000	0.000	0.000	0.000
29	A	31	ASN	0	-0.029	-0.006	5.651	-6.555	-6.555	0.000	0.000	0.000	0.000
30	A	32	PHE	0	0.044	0.020	6.543	-0.958	-0.958	0.000	0.000	0.000	0.000
31	A	33	LEU	0	-0.041	-0.024	5.464	-0.075	-0.075	0.000	0.000	0.000	0.000
32	A	34	LYS	1	0.909	0.959	2.070	37.477	36.191	8.105	-2.877	-3.942	-0.004
33	A	35	ASN	0	-0.036	-0.036	2.046	-3.906	-5.403	8.498	-3.468	-3.533	-0.046
34	A	36	PRO	0	0.013	0.011	3.688	2.907	3.049	0.001	-0.059	-0.084	0.000
35	A	37	PRO	0	-0.009	0.006	6.881	0.517	0.517	0.000	0.000	0.000	0.000
36	A	38	ILE	0	0.044	0.007	10.203	-0.311	-0.311	0.000	0.000	0.000	0.000
37	A	39	ASN	0	0.001	0.003	11.295	-0.051	-0.051	0.000	0.000	0.000	0.000
38	A	40	CYS	0	-0.029	0.018	11.214	1.431	1.431	0.000	0.000	0.000	0.000
39	A	41	THR	0	-0.037	-0.014	10.540	-1.401	-1.401	0.000	0.000	0.000	0.000
40	A	42	ILE	0	-0.060	-0.055	10.391	0.474	0.474	0.000	0.000	0.000	0.000
41	A	43	ASP	-1	-0.878	-0.941	13.182	-18.430	-18.430	0.000	0.000	0.000	0.000
42	A	44	VAL	0	-0.081	-0.028	14.210	0.612	0.612	0.000	0.000	0.000	0.000
43	A	45	HIS	0	0.026	0.004	16.966	0.636	0.636	0.000	0.000	0.000	0.000
44	A	46	PRO	0	0.064	0.049	19.476	-0.449	-0.449	0.000	0.000	0.000	0.000
45	A	47	SER	0	-0.082	-0.045	20.032	1.052	1.052	0.000	0.000	0.000	0.000
46	A	48	ASN	0	0.038	0.002	20.532	0.257	0.257	0.000	0.000	0.000	0.000
47	A	49	ILE	0	0.030	0.023	14.187	-0.291	-0.291	0.000	0.000	0.000	0.000
48	A	50	ARG	1	0.784	0.882	18.028	13.120	13.120	0.000	0.000	0.000	0.000
49	A	51	ILE	0	-0.002	0.014	20.578	0.275	0.275	0.000	0.000	0.000	0.000
50	A	52	TRP	0	-0.004	-0.008	13.177	-1.281	-1.281	0.000	0.000	0.000	0.000
51	A	53	ILE	0	0.010	-0.002	17.442	1.056	1.056	0.000	0.000	0.000	0.000
52	A	54	VAL	0	0.004	0.018	13.672	-0.845	-0.845	0.000	0.000	0.000	0.000
53	A	55	GLN	0	0.000	0.004	15.268	1.810	1.810	0.000	0.000	0.000	0.000
54	A	56	TYR	0	0.059	0.012	15.282	-1.072	-1.072	0.000	0.000	0.000	0.000
55	A	57	VAL	0	0.008	0.002	16.231	0.783	0.783	0.000	0.000	0.000	0.000
56	A	58	GLY	0	0.031	0.019	17.600	-0.468	-0.468	0.000	0.000	0.000	0.000
57	A	59	LEU	0	0.008	-0.002	15.428	-0.141	-0.141	0.000	0.000	0.000	0.000
58	A	60	GLU	-1	-0.824	-0.900	19.011	-12.177	-12.177	0.000	0.000	0.000	0.000
59	A	61	ASN	0	-0.059	-0.022	19.416	0.268	0.268	0.000	0.000	0.000	0.000
60	A	62	THR	0	-0.012	-0.022	21.303	0.196	0.196	0.000	0.000	0.000	0.000
61	A	63	ILE	0	-0.025	-0.008	24.021	0.069	0.069	0.000	0.000	0.000	0.000
62	A	64	TYR	0	-0.034	-0.039	23.098	0.125	0.125	0.000	0.000	0.000	0.000
63	A	65	ALA	0	-0.032	0.003	22.327	-0.414	-0.414	0.000	0.000	0.000	0.000
64	A	66	ASN	0	-0.082	-0.073	21.360	0.554	0.554	0.000	0.000	0.000	0.000
65	A	67	GLU	-1	-0.848	-0.877	22.456	-10.371	-10.371	0.000	0.000	0.000	0.000
66	A	68	VAL	0	-0.092	-0.046	19.751	-0.403	-0.403	0.000	0.000	0.000	0.000
67	A	69	TYR	0	-0.011	-0.020	20.500	0.451	0.451	0.000	0.000	0.000	0.000
68	A	70	LYS	1	0.891	0.931	19.758	12.487	12.487	0.000	0.000	0.000	0.000
69	A	71	ILE	0	0.029	0.016	17.742	0.605	0.605	0.000	0.000	0.000	0.000
70	A	72	LYS	1	0.921	0.978	19.035	11.536	11.536	0.000	0.000	0.000	0.000
71	A	73	ILE	0	-0.003	-0.005	16.332	0.163	0.163	0.000	0.000	0.000	0.000
72	A	74	ILE	0	0.008	0.000	20.509	-0.285	-0.285	0.000	0.000	0.000	0.000
73	A	75	PHE	0	0.008	0.001	16.361	0.318	0.318	0.000	0.000	0.000	0.000
74	A	76	PRO	0	0.029	0.017	22.375	0.158	0.158	0.000	0.000	0.000	0.000
75	A	77	ASP	-1	-0.784	-0.873	24.690	-11.242	-11.242	0.000	0.000	0.000	0.000
76	A	78	ASN	0	-0.035	-0.033	26.128	-0.305	-0.305	0.000	0.000	0.000	0.000
77	A	79	TYR	0	0.066	0.082	18.092	-0.327	-0.327	0.000	0.000	0.000	0.000
78	A	80	PRO	0	-0.047	-0.048	20.297	-0.196	-0.196	0.000	0.000	0.000	0.000
79	A	81	LEU	0	0.048	0.014	22.397	0.069	0.069	0.000	0.000	0.000	0.000
80	A	82	LYS	1	0.865	0.928	26.097	10.900	10.900	0.000	0.000	0.000	0.000
81	A	83	PRO	0	0.067	0.022	23.676	-0.538	-0.538	0.000	0.000	0.000	0.000
82	A	84	PRO	0	-0.078	-0.035	19.756	0.156	0.156	0.000	0.000	0.000	0.000
83	A	85	ILE	0	0.014	-0.004	22.677	0.253	0.253	0.000	0.000	0.000	0.000
84	A	86	VAL	0	-0.021	-0.012	19.973	-0.497	-0.497	0.000	0.000	0.000	0.000
85	A	87	TYR	0	0.036	0.021	22.717	0.347	0.347	0.000	0.000	0.000	0.000
86	A	88	PHE	0	0.029	0.011	21.467	-0.573	-0.573	0.000	0.000	0.000	0.000
87	A	89	LEU	0	-0.045	-0.033	22.694	0.343	0.343	0.000	0.000	0.000	0.000
88	A	90	GLN	0	-0.022	-0.027	25.596	0.147	0.147	0.000	0.000	0.000	0.000
89	A	91	LYS	1	0.938	0.980	27.252	9.118	9.118	0.000	0.000	0.000	0.000
90	A	92	PRO	0	0.050	0.023	26.389	-0.295	-0.295	0.000	0.000	0.000	0.000
91	A	93	PRO	0	0.023	0.037	24.003	0.258	0.258	0.000	0.000	0.000	0.000
92	A	94	LYS	1	0.841	0.890	26.990	8.878	8.878	0.000	0.000	0.000	0.000
93	A	95	HIS	0	0.112	0.072	26.750	0.050	0.050	0.000	0.000	0.000	0.000
94	A	96	THR	0	-0.003	0.007	29.338	0.168	0.168	0.000	0.000	0.000	0.000
95	A	97	HIS	0	0.009	-0.002	27.680	0.091	0.091	0.000	0.000	0.000	0.000
96	A	98	VAL	0	-0.044	-0.015	25.894	-0.258	-0.258	0.000	0.000	0.000	0.000
97	A	99	TYR	0	0.031	0.021	28.986	0.350	0.350	0.000	0.000	0.000	0.000
98	A	100	SER	0	0.018	-0.008	30.691	-0.260	-0.260	0.000	0.000	0.000	0.000
99	A	101	ASN	0	-0.068	-0.052	32.016	-0.123	-0.123	0.000	0.000	0.000	0.000
100	A	102	GLY	0	0.019	0.009	28.025	-0.225	-0.225	0.000	0.000	0.000	0.000
101	A	103	ASP	-1	-0.880	-0.918	26.913	-10.190	-10.190	0.000	0.000	0.000	0.000
102	A	104	ILE	0	-0.017	-0.021	22.763	-0.022	-0.022	0.000	0.000	0.000	0.000
103	A	105	CYS	0	-0.056	-0.012	26.930	0.018	0.018	0.000	0.000	0.000	0.000
104	A	106	LEU	0	0.032	-0.005	21.836	-0.088	-0.088	0.000	0.000	0.000	0.000
105	A	107	SER	0	0.013	-0.010	26.447	-0.225	-0.225	0.000	0.000	0.000	0.000
106	A	108	VAL	0	0.028	0.007	20.765	-0.077	-0.077	0.000	0.000	0.000	0.000
107	A	109	LEU	0	-0.053	-0.037	21.244	-0.448	-0.448	0.000	0.000	0.000	0.000
108	A	110	GLY	0	-0.025	-0.023	24.582	0.070	0.070	0.000	0.000	0.000	0.000
109	A	111	ASP	-1	-0.933	-0.960	28.012	-9.464	-9.464	0.000	0.000	0.000	0.000
110	A	112	ASP	-1	-0.818	-0.885	26.112	-10.215	-10.215	0.000	0.000	0.000	0.000
111	A	113	TYR	0	-0.125	-0.049	20.984	-0.831	-0.831	0.000	0.000	0.000	0.000
112	A	114	ASN	0	0.067	0.030	22.783	0.025	0.025	0.000	0.000	0.000	0.000
113	A	115	PRO	0	0.029	0.004	22.251	-0.601	-0.601	0.000	0.000	0.000	0.000
114	A	116	SER	0	-0.075	-0.039	19.588	-0.903	-0.903	0.000	0.000	0.000	0.000
115	A	117	LEU	0	0.006	0.026	18.022	-0.861	-0.861	0.000	0.000	0.000	0.000
116	A	118	SER	0	0.005	0.003	12.888	-0.099	-0.099	0.000	0.000	0.000	0.000
117	A	119	ILE	0	0.015	0.010	13.826	0.458	0.458	0.000	0.000	0.000	0.000
118	A	120	SER	0	0.009	0.000	9.512	0.874	0.874	0.000	0.000	0.000	0.000
119	A	121	GLY	0	0.066	0.037	11.825	0.385	0.385	0.000	0.000	0.000	0.000
120	A	122	LEU	0	-0.006	0.010	14.234	0.804	0.804	0.000	0.000	0.000	0.000
121	A	123	ILE	0	0.015	-0.007	13.963	0.556	0.556	0.000	0.000	0.000	0.000
122	A	124	LEU	0	0.011	0.009	11.854	0.302	0.302	0.000	0.000	0.000	0.000
123	A	125	SER	0	-0.021	-0.018	14.779	0.723	0.723	0.000	0.000	0.000	0.000
124	A	126	ILE	0	-0.001	0.000	18.269	0.564	0.564	0.000	0.000	0.000	0.000
125	A	127	ILE	0	-0.027	-0.011	15.109	0.462	0.462	0.000	0.000	0.000	0.000
126	A	128	SER	0	-0.054	-0.030	18.147	0.487	0.487	0.000	0.000	0.000	0.000
127	A	129	MET	0	-0.010	0.007	19.783	0.490	0.490	0.000	0.000	0.000	0.000
128	A	130	LEU	0	-0.042	-0.018	20.623	0.428	0.428	0.000	0.000	0.000	0.000
129	A	131	SER	0	-0.043	-0.013	20.399	0.254	0.254	0.000	0.000	0.000	0.000
130	A	132	SER	0	-0.009	-0.021	23.026	0.191	0.191	0.000	0.000	0.000	0.000
131	A	133	ALA	0	-0.046	-0.014	26.595	0.120	0.120	0.000	0.000	0.000	0.000
132	A	134	LYS	1	0.983	0.989	29.279	7.849	7.849	0.000	0.000	0.000	0.000
133	A	135	GLU	-1	-0.805	-0.878	29.700	-8.599	-8.599	0.000	0.000	0.000	0.000

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