FMO DATABASE

FMODB ID: JQ6K9

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	OptH
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	-1211756.238415
FMO2-HF: Nuclear repulsion	1159184.147649
FMO2-HF: Total energy	-52572.090766
FMO2-MP2: Total energy	-52727.930892

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.
109.849	104.54	23.186	-8.093	-9.784	-0.043

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 : 0.910 / q_NPA : 0.958

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	0.098	0.042	3.872	-3.278	-2.050	-0.016	-0.659	-0.553	0.002
4	A	6	ARG	1	0.928	1.017	6.117	28.535	28.535	0.000	0.000	0.000	0.000
5	A	7	THR	0	-0.046	-0.079	7.481	-3.293	-3.293	0.000	0.000	0.000	0.000
6	A	8	VAL	0	0.041	0.048	9.898	-0.010	-0.010	0.000	0.000	0.000	0.000
7	A	9	GLU	-1	-0.840	-0.915	13.709	-16.499	-16.499	0.000	0.000	0.000	0.000
8	A	10	LYS	1	0.865	0.918	9.697	26.569	26.569	0.000	0.000	0.000	0.000
9	A	11	HIS	0	0.073	0.046	13.163	1.629	1.629	0.000	0.000	0.000	0.000
10	A	12	ILE	0	-0.008	-0.027	7.843	1.053	1.053	0.000	0.000	0.000	0.000
11	A	13	LYS	1	0.901	0.959	11.562	20.389	20.389	0.000	0.000	0.000	0.000
12	A	14	THR	0	0.025	0.026	13.566	0.623	0.623	0.000	0.000	0.000	0.000
13	A	15	LYS	1	1.022	1.015	15.323	15.266	15.266	0.000	0.000	0.000	0.000
14	A	16	TYR	0	0.034	0.007	15.559	0.968	0.968	0.000	0.000	0.000	0.000
15	A	17	ASN	0	0.051	0.010	17.975	-0.702	-0.702	0.000	0.000	0.000	0.000
16	A	18	LEU	0	0.024	0.008	16.662	-0.384	-0.384	0.000	0.000	0.000	0.000
17	A	19	GLY	0	-0.013	-0.001	19.389	0.086	0.086	0.000	0.000	0.000	0.000
18	A	20	ASN	0	-0.002	0.004	20.907	0.608	0.608	0.000	0.000	0.000	0.000
19	A	21	ALA	0	0.096	0.040	20.034	-0.763	-0.763	0.000	0.000	0.000	0.000
20	A	22	ASN	0	0.066	0.034	18.745	-0.681	-0.681	0.000	0.000	0.000	0.000
21	A	23	TYR	0	0.002	0.032	14.628	-1.494	-1.494	0.000	0.000	0.000	0.000
22	A	24	ARG	1	0.815	0.885	14.783	16.405	16.405	0.000	0.000	0.000	0.000
23	A	25	ILE	0	0.047	0.029	14.862	-1.203	-1.203	0.000	0.000	0.000	0.000
24	A	26	GLN	0	-0.041	-0.032	11.647	-1.377	-1.377	0.000	0.000	0.000	0.000
25	A	27	LYS	1	0.888	0.938	10.457	21.078	21.078	0.000	0.000	0.000	0.000
26	A	28	GLU	-1	-0.789	-0.891	10.191	-24.043	-24.043	0.000	0.000	0.000	0.000
27	A	29	LEU	0	0.016	0.027	10.214	-1.226	-1.226	0.000	0.000	0.000	0.000
28	A	30	ASN	0	-0.014	-0.022	6.197	-3.125	-3.125	0.000	0.000	0.000	0.000
29	A	31	ASN	0	-0.008	0.002	5.751	-7.628	-7.628	0.000	0.000	0.000	0.000
30	A	32	PHE	0	0.018	0.009	6.527	-1.290	-1.290	0.000	0.000	0.000	0.000
31	A	33	LEU	0	-0.035	-0.019	5.331	0.117	0.117	0.000	0.000	0.000	0.000
32	A	34	LYS	1	0.921	0.953	1.887	55.848	51.325	14.623	-4.531	-5.569	0.001
33	A	35	ASN	0	-0.055	-0.030	2.044	-4.905	-7.095	8.576	-2.830	-3.556	-0.046
34	A	36	PRO	0	0.008	0.008	3.557	2.879	3.055	0.003	-0.073	-0.106	0.000
35	A	37	PRO	0	-0.012	0.001	6.862	0.550	0.550	0.000	0.000	0.000	0.000
36	A	38	ILE	0	0.049	0.014	10.193	-0.105	-0.105	0.000	0.000	0.000	0.000
37	A	39	ASN	0	0.003	0.000	11.289	-0.044	-0.044	0.000	0.000	0.000	0.000
38	A	40	CYS	0	-0.026	0.018	11.200	1.277	1.277	0.000	0.000	0.000	0.000
39	A	41	THR	0	-0.030	-0.007	10.513	-1.211	-1.211	0.000	0.000	0.000	0.000
40	A	42	ILE	0	-0.054	-0.054	10.451	0.377	0.377	0.000	0.000	0.000	0.000
41	A	43	ASP	-1	-0.879	-0.945	13.145	-17.488	-17.488	0.000	0.000	0.000	0.000
42	A	44	VAL	0	-0.083	-0.024	14.168	0.485	0.485	0.000	0.000	0.000	0.000
43	A	45	HIS	0	0.041	0.012	16.877	0.681	0.681	0.000	0.000	0.000	0.000
44	A	46	PRO	0	0.070	0.049	19.874	-0.452	-0.452	0.000	0.000	0.000	0.000
45	A	47	SER	0	-0.103	-0.055	20.779	0.946	0.946	0.000	0.000	0.000	0.000
46	A	48	ASN	0	0.045	0.010	21.211	0.135	0.135	0.000	0.000	0.000	0.000
47	A	49	ILE	0	0.036	0.020	14.891	-0.281	-0.281	0.000	0.000	0.000	0.000
48	A	50	ARG	1	0.848	0.917	18.216	12.886	12.886	0.000	0.000	0.000	0.000
49	A	51	ILE	0	-0.003	0.016	20.657	0.246	0.246	0.000	0.000	0.000	0.000
50	A	52	TRP	0	-0.005	-0.009	13.044	-1.154	-1.154	0.000	0.000	0.000	0.000
51	A	53	ILE	0	0.012	-0.005	17.354	0.995	0.995	0.000	0.000	0.000	0.000
52	A	54	VAL	0	0.005	0.018	13.499	-0.720	-0.720	0.000	0.000	0.000	0.000
53	A	55	GLN	0	-0.027	-0.011	15.238	1.287	1.287	0.000	0.000	0.000	0.000
54	A	56	TYR	0	0.043	0.005	15.254	-0.673	-0.673	0.000	0.000	0.000	0.000
55	A	57	VAL	0	0.003	-0.001	16.210	0.753	0.753	0.000	0.000	0.000	0.000
56	A	58	GLY	0	0.032	0.021	17.585	-0.443	-0.443	0.000	0.000	0.000	0.000
57	A	59	LEU	0	0.002	-0.003	15.472	-0.119	-0.119	0.000	0.000	0.000	0.000
58	A	60	GLU	-1	-0.863	-0.938	19.157	-11.672	-11.672	0.000	0.000	0.000	0.000
59	A	61	ASN	0	-0.072	-0.027	19.333	0.402	0.402	0.000	0.000	0.000	0.000
60	A	62	THR	0	0.004	-0.012	21.407	0.146	0.146	0.000	0.000	0.000	0.000
61	A	63	ILE	0	-0.021	-0.010	24.168	0.076	0.076	0.000	0.000	0.000	0.000
62	A	64	TYR	0	-0.017	-0.014	23.006	0.108	0.108	0.000	0.000	0.000	0.000
63	A	65	ALA	0	-0.033	0.001	22.445	-0.380	-0.380	0.000	0.000	0.000	0.000
64	A	66	ASN	0	-0.046	-0.038	21.495	0.401	0.401	0.000	0.000	0.000	0.000
65	A	67	GLU	-1	-0.845	-0.886	22.509	-10.151	-10.151	0.000	0.000	0.000	0.000
66	A	68	VAL	0	-0.086	-0.040	20.254	-0.395	-0.395	0.000	0.000	0.000	0.000
67	A	69	TYR	0	-0.013	-0.026	20.487	0.472	0.472	0.000	0.000	0.000	0.000
68	A	70	LYS	1	0.921	0.950	19.731	11.861	11.861	0.000	0.000	0.000	0.000
69	A	71	ILE	0	0.033	0.021	17.764	0.569	0.569	0.000	0.000	0.000	0.000
70	A	72	LYS	1	0.914	0.972	19.005	11.412	11.412	0.000	0.000	0.000	0.000
71	A	73	ILE	0	-0.004	-0.003	16.398	0.131	0.131	0.000	0.000	0.000	0.000
72	A	74	ILE	0	0.010	0.004	20.480	-0.234	-0.234	0.000	0.000	0.000	0.000
73	A	75	PHE	0	-0.006	-0.009	16.341	0.314	0.314	0.000	0.000	0.000	0.000
74	A	76	PRO	0	0.001	-0.011	22.279	0.218	0.218	0.000	0.000	0.000	0.000
75	A	77	ASP	-1	-0.920	-0.961	24.872	-11.330	-11.330	0.000	0.000	0.000	0.000
76	A	78	ASN	0	-0.039	-0.016	26.155	-0.334	-0.334	0.000	0.000	0.000	0.000
77	A	79	TYR	0	0.071	0.080	17.843	-0.289	-0.289	0.000	0.000	0.000	0.000
78	A	80	PRO	0	-0.046	-0.050	20.144	-0.147	-0.147	0.000	0.000	0.000	0.000
79	A	81	LEU	0	0.045	0.016	22.272	0.060	0.060	0.000	0.000	0.000	0.000
80	A	82	LYS	1	0.947	0.976	25.920	10.951	10.951	0.000	0.000	0.000	0.000
81	A	83	PRO	0	0.062	0.015	23.655	-0.531	-0.531	0.000	0.000	0.000	0.000
82	A	84	PRO	0	-0.059	-0.032	19.764	0.228	0.228	0.000	0.000	0.000	0.000
83	A	85	ILE	0	0.019	0.002	22.640	0.261	0.261	0.000	0.000	0.000	0.000
84	A	86	VAL	0	-0.024	-0.013	19.835	-0.444	-0.444	0.000	0.000	0.000	0.000
85	A	87	TYR	0	0.024	0.012	22.694	0.365	0.365	0.000	0.000	0.000	0.000
86	A	88	PHE	0	0.029	0.014	21.299	-0.531	-0.531	0.000	0.000	0.000	0.000
87	A	89	LEU	0	-0.041	-0.030	22.916	0.334	0.334	0.000	0.000	0.000	0.000
88	A	90	GLN	0	0.001	-0.013	25.566	0.090	0.090	0.000	0.000	0.000	0.000
89	A	91	LYS	1	0.902	0.960	27.223	8.996	8.996	0.000	0.000	0.000	0.000
90	A	92	PRO	0	0.051	0.023	26.373	-0.269	-0.269	0.000	0.000	0.000	0.000
91	A	93	PRO	0	0.010	0.033	24.113	0.281	0.281	0.000	0.000	0.000	0.000
92	A	94	LYS	1	0.973	0.971	26.970	8.792	8.792	0.000	0.000	0.000	0.000
93	A	95	HIS	0	0.108	0.068	26.805	0.099	0.099	0.000	0.000	0.000	0.000
94	A	96	THR	0	0.004	0.013	29.325	0.168	0.168	0.000	0.000	0.000	0.000
95	A	97	HIS	0	-0.011	-0.019	27.674	0.006	0.006	0.000	0.000	0.000	0.000
96	A	98	VAL	0	-0.042	-0.013	26.017	-0.257	-0.257	0.000	0.000	0.000	0.000
97	A	99	TYR	0	0.024	0.020	28.970	0.296	0.296	0.000	0.000	0.000	0.000
98	A	100	SER	0	0.005	-0.017	30.669	-0.244	-0.244	0.000	0.000	0.000	0.000
99	A	101	ASN	0	-0.024	-0.007	31.826	-0.164	-0.164	0.000	0.000	0.000	0.000
100	A	102	GLY	0	0.025	0.015	28.000	-0.213	-0.213	0.000	0.000	0.000	0.000
101	A	103	ASP	-1	-0.911	-0.955	26.891	-10.114	-10.114	0.000	0.000	0.000	0.000
102	A	104	ILE	0	-0.007	-0.017	22.849	-0.016	-0.016	0.000	0.000	0.000	0.000
103	A	105	CYS	0	-0.048	-0.011	26.913	-0.018	-0.018	0.000	0.000	0.000	0.000
104	A	106	LEU	0	0.028	-0.009	22.045	-0.106	-0.106	0.000	0.000	0.000	0.000
105	A	107	SER	0	0.036	0.033	26.438	-0.225	-0.225	0.000	0.000	0.000	0.000
106	A	108	VAL	0	0.027	0.005	20.723	-0.081	-0.081	0.000	0.000	0.000	0.000
107	A	109	LEU	0	-0.047	-0.037	21.273	-0.450	-0.450	0.000	0.000	0.000	0.000
108	A	110	GLY	0	-0.037	-0.029	24.569	0.089	0.089	0.000	0.000	0.000	0.000
109	A	111	ASP	-1	-0.924	-0.957	28.000	-9.520	-9.520	0.000	0.000	0.000	0.000
110	A	112	ASP	-1	-0.837	-0.912	26.240	-10.344	-10.344	0.000	0.000	0.000	0.000
111	A	113	TYR	0	-0.126	-0.055	20.891	-0.882	-0.882	0.000	0.000	0.000	0.000
112	A	114	ASN	0	0.060	0.042	22.503	-0.041	-0.041	0.000	0.000	0.000	0.000
113	A	115	PRO	0	0.014	-0.003	22.245	-0.622	-0.622	0.000	0.000	0.000	0.000
114	A	116	SER	0	-0.087	-0.055	19.310	-0.954	-0.954	0.000	0.000	0.000	0.000
115	A	117	LEU	0	0.000	0.025	18.021	-0.880	-0.880	0.000	0.000	0.000	0.000
116	A	118	SER	0	0.020	0.019	12.595	0.046	0.046	0.000	0.000	0.000	0.000
117	A	119	ILE	0	0.016	0.012	13.690	0.642	0.642	0.000	0.000	0.000	0.000
118	A	120	SER	0	0.014	-0.010	9.847	0.290	0.290	0.000	0.000	0.000	0.000
119	A	121	GLY	0	0.024	0.017	11.812	0.412	0.412	0.000	0.000	0.000	0.000
120	A	122	LEU	0	-0.004	0.010	14.229	0.869	0.869	0.000	0.000	0.000	0.000
121	A	123	ILE	0	0.019	-0.003	13.855	0.628	0.628	0.000	0.000	0.000	0.000
122	A	124	LEU	0	0.017	0.005	12.283	0.377	0.377	0.000	0.000	0.000	0.000
123	A	125	SER	0	-0.030	-0.020	14.772	0.736	0.736	0.000	0.000	0.000	0.000
124	A	126	ILE	0	-0.006	-0.005	18.265	0.589	0.589	0.000	0.000	0.000	0.000
125	A	127	ILE	0	-0.027	-0.013	14.773	0.443	0.443	0.000	0.000	0.000	0.000
126	A	128	SER	0	-0.056	-0.028	18.138	0.493	0.493	0.000	0.000	0.000	0.000
127	A	129	MET	0	0.013	0.019	19.781	0.462	0.462	0.000	0.000	0.000	0.000
128	A	130	LEU	0	-0.057	-0.023	20.436	0.447	0.447	0.000	0.000	0.000	0.000
129	A	131	SER	0	-0.027	-0.002	20.485	0.281	0.281	0.000	0.000	0.000	0.000
130	A	132	SER	0	-0.027	-0.034	23.023	0.164	0.164	0.000	0.000	0.000	0.000
131	A	133	ALA	0	-0.032	-0.003	26.594	0.141	0.141	0.000	0.000	0.000	0.000
132	A	134	LYS	1	0.977	0.989	29.275	7.873	7.873	0.000	0.000	0.000	0.000
133	A	135	GLU	-1	-0.935	-0.961	29.936	-8.412	-8.412	0.000	0.000	0.000	0.000

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