FMO DATABASE

FMODB ID: RY8K8

Calculation Name: 2H09-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2H09

Chain ID: A

ChEMBL ID:

UniProt ID: P0A9F1

Base Structure: X-ray

Registration Date: 2023-09-27

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	127
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1071637.081155
FMO2-HF: Nuclear repulsion	1020239.797778
FMO2-HF: Total energy	-51397.283377
FMO2-MP2: Total energy	-51546.43569

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:24:GLU)

Summations of interaction energy for fragment #1(A:24:GLU)

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.
-54.071	-50.114	1.466	-2.681	-2.743	0.011

Interaction energy analysis for fragmet #1(A:24:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.944 / q_NPA : -0.976

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	26	PHE	0	0.012	0.010	3.792	-0.618	2.410	-0.044	-1.848	-1.137	0.006
4	A	27	ARG	1	0.860	0.914	6.466	-21.176	-21.176	0.000	0.000	0.000	0.000
5	A	28	GLN	0	0.051	0.028	7.833	0.884	0.884	0.000	0.000	0.000	0.000
6	A	29	VAL	0	0.057	0.028	7.358	-0.673	-0.673	0.000	0.000	0.000	0.000
7	A	30	ARG	1	0.915	0.949	2.095	-53.396	-52.467	1.510	-0.833	-1.606	0.005
8	A	31	GLU	-1	-0.876	-0.938	6.480	23.420	23.420	0.000	0.000	0.000	0.000
9	A	32	ALA	0	-0.009	-0.005	9.905	-1.564	-1.564	0.000	0.000	0.000	0.000
10	A	33	HIS	0	0.047	0.033	7.676	3.273	3.273	0.000	0.000	0.000	0.000
11	A	34	ARG	1	0.829	0.901	6.380	-37.114	-37.114	0.000	0.000	0.000	0.000
12	A	35	ARG	1	0.989	0.980	10.238	-22.206	-22.206	0.000	0.000	0.000	0.000
13	A	36	GLU	-1	-0.765	-0.875	12.942	22.046	22.046	0.000	0.000	0.000	0.000
14	A	37	LEU	0	-0.018	-0.010	9.217	-0.295	-0.295	0.000	0.000	0.000	0.000
15	A	38	ILE	0	-0.087	-0.051	13.307	-0.882	-0.882	0.000	0.000	0.000	0.000
16	A	39	ASP	-1	-0.812	-0.891	15.634	15.820	15.820	0.000	0.000	0.000	0.000
17	A	40	ASP	-1	-0.796	-0.899	16.235	17.624	17.624	0.000	0.000	0.000	0.000
18	A	41	TYR	0	-0.069	-0.056	14.051	-0.622	-0.622	0.000	0.000	0.000	0.000
19	A	42	VAL	0	-0.025	-0.015	18.328	-0.768	-0.768	0.000	0.000	0.000	0.000
20	A	43	GLU	-1	-0.745	-0.892	21.123	12.702	12.702	0.000	0.000	0.000	0.000
21	A	44	LEU	0	0.005	0.026	19.642	-0.670	-0.670	0.000	0.000	0.000	0.000
22	A	45	ILE	0	-0.065	-0.046	21.107	-0.635	-0.635	0.000	0.000	0.000	0.000
23	A	46	SER	0	-0.007	0.002	24.222	-0.542	-0.542	0.000	0.000	0.000	0.000
24	A	47	ASP	-1	-0.817	-0.901	26.012	11.475	11.475	0.000	0.000	0.000	0.000
25	A	48	LEU	0	-0.056	-0.026	24.341	-0.390	-0.390	0.000	0.000	0.000	0.000
26	A	49	ILE	0	-0.084	-0.042	27.759	-0.433	-0.433	0.000	0.000	0.000	0.000
27	A	50	ARG	1	0.775	0.853	29.981	-10.927	-10.927	0.000	0.000	0.000	0.000
28	A	51	GLU	-1	-0.941	-0.950	30.756	9.468	9.468	0.000	0.000	0.000	0.000
29	A	52	VAL	0	-0.078	-0.051	30.267	-0.285	-0.285	0.000	0.000	0.000	0.000
30	A	53	GLY	0	-0.006	0.014	32.930	-0.172	-0.172	0.000	0.000	0.000	0.000
31	A	54	GLU	-1	-0.842	-0.900	30.541	10.097	10.097	0.000	0.000	0.000	0.000
32	A	55	ALA	0	0.086	0.058	25.030	0.199	0.199	0.000	0.000	0.000	0.000
33	A	56	ARG	1	0.769	0.849	26.013	-10.199	-10.199	0.000	0.000	0.000	0.000
34	A	57	GLN	0	0.027	-0.016	21.048	0.731	0.731	0.000	0.000	0.000	0.000
35	A	58	VAL	0	-0.021	-0.020	21.552	0.623	0.623	0.000	0.000	0.000	0.000
36	A	59	ASP	-1	-0.775	-0.871	23.438	12.258	12.258	0.000	0.000	0.000	0.000
37	A	60	MET	0	0.004	0.023	20.009	0.509	0.509	0.000	0.000	0.000	0.000
38	A	61	ALA	0	-0.024	-0.021	18.515	0.519	0.519	0.000	0.000	0.000	0.000
39	A	62	ALA	0	-0.001	-0.003	19.358	0.553	0.553	0.000	0.000	0.000	0.000
40	A	63	ARG	1	0.868	0.918	22.013	-12.010	-12.010	0.000	0.000	0.000	0.000
41	A	64	LEU	0	-0.029	0.006	16.139	0.291	0.291	0.000	0.000	0.000	0.000
42	A	65	GLY	0	0.018	0.025	17.243	0.644	0.644	0.000	0.000	0.000	0.000
43	A	66	VAL	0	-0.061	-0.022	13.121	1.208	1.208	0.000	0.000	0.000	0.000
44	A	67	SER	0	0.016	0.001	15.133	-1.107	-1.107	0.000	0.000	0.000	0.000
45	A	68	GLN	0	0.088	0.025	16.569	0.961	0.961	0.000	0.000	0.000	0.000
46	A	69	PRO	0	0.028	-0.003	15.241	0.307	0.307	0.000	0.000	0.000	0.000
47	A	70	THR	0	-0.058	-0.030	11.532	0.865	0.865	0.000	0.000	0.000	0.000
48	A	71	VAL	0	0.099	0.074	13.398	0.712	0.712	0.000	0.000	0.000	0.000
49	A	72	ALA	0	0.027	0.009	16.063	-0.257	-0.257	0.000	0.000	0.000	0.000
50	A	73	LYS	1	0.847	0.921	10.161	-28.250	-28.250	0.000	0.000	0.000	0.000
51	A	74	MET	0	0.048	0.028	11.661	1.530	1.530	0.000	0.000	0.000	0.000
52	A	75	LEU	0	0.069	0.040	13.944	-0.576	-0.576	0.000	0.000	0.000	0.000
53	A	76	LYS	1	0.918	0.969	16.335	-17.660	-17.660	0.000	0.000	0.000	0.000
54	A	77	ARG	1	0.918	0.971	8.451	-29.679	-29.679	0.000	0.000	0.000	0.000
55	A	78	LEU	0	0.080	0.032	15.357	-0.199	-0.199	0.000	0.000	0.000	0.000
56	A	79	ALA	0	-0.011	0.010	17.921	-0.700	-0.700	0.000	0.000	0.000	0.000
57	A	80	THR	0	-0.080	-0.051	17.440	-0.583	-0.583	0.000	0.000	0.000	0.000
58	A	81	MET	0	-0.064	-0.025	14.517	0.196	0.196	0.000	0.000	0.000	0.000
59	A	82	GLY	0	0.028	0.025	19.690	-0.419	-0.419	0.000	0.000	0.000	0.000
60	A	83	LEU	0	0.004	0.011	18.813	-0.351	-0.351	0.000	0.000	0.000	0.000
61	A	84	ILE	0	-0.038	-0.025	20.583	-0.223	-0.223	0.000	0.000	0.000	0.000
62	A	85	GLU	-1	-0.895	-0.935	23.470	10.894	10.894	0.000	0.000	0.000	0.000
63	A	86	MET	0	-0.085	-0.048	21.637	0.297	0.297	0.000	0.000	0.000	0.000
64	A	87	ILE	0	0.052	0.025	26.292	-0.289	-0.289	0.000	0.000	0.000	0.000
65	A	88	PRO	0	0.028	0.009	29.861	0.071	0.071	0.000	0.000	0.000	0.000
66	A	89	TRP	0	-0.041	-0.033	31.045	-0.178	-0.178	0.000	0.000	0.000	0.000
67	A	90	ARG	1	0.921	0.946	31.143	-9.290	-9.290	0.000	0.000	0.000	0.000
68	A	91	GLY	0	-0.027	0.023	27.404	0.029	0.029	0.000	0.000	0.000	0.000
69	A	92	VAL	0	-0.048	-0.037	22.570	0.036	0.036	0.000	0.000	0.000	0.000
70	A	93	PHE	0	0.049	0.023	25.887	-0.325	-0.325	0.000	0.000	0.000	0.000
71	A	94	LEU	0	-0.002	0.009	23.501	0.493	0.493	0.000	0.000	0.000	0.000
72	A	95	THR	0	0.017	0.011	25.430	-0.400	-0.400	0.000	0.000	0.000	0.000
73	A	96	ALA	0	0.026	0.002	27.628	0.022	0.022	0.000	0.000	0.000	0.000
74	A	97	GLU	-1	-0.906	-0.966	25.058	11.253	11.253	0.000	0.000	0.000	0.000
75	A	98	GLY	0	0.004	-0.009	23.446	0.376	0.376	0.000	0.000	0.000	0.000
76	A	99	GLU	-1	-0.817	-0.885	24.376	11.099	11.099	0.000	0.000	0.000	0.000
77	A	100	LYS	1	0.772	0.873	25.945	-12.120	-12.120	0.000	0.000	0.000	0.000
78	A	101	LEU	0	-0.022	-0.007	19.950	0.066	0.066	0.000	0.000	0.000	0.000
79	A	102	ALA	0	0.031	0.013	23.463	0.224	0.224	0.000	0.000	0.000	0.000
80	A	103	GLN	0	-0.012	-0.002	24.401	-0.013	-0.013	0.000	0.000	0.000	0.000
81	A	104	GLU	-1	-0.765	-0.878	24.989	12.042	12.042	0.000	0.000	0.000	0.000
82	A	105	SER	0	-0.008	0.002	21.056	-0.073	-0.073	0.000	0.000	0.000	0.000
83	A	106	ARG	1	0.881	0.941	23.609	-11.866	-11.866	0.000	0.000	0.000	0.000
84	A	107	GLU	-1	-0.985	-1.005	26.374	10.984	10.984	0.000	0.000	0.000	0.000
85	A	108	ARG	1	0.836	0.906	20.232	-14.963	-14.963	0.000	0.000	0.000	0.000
86	A	109	HIS	0	-0.029	-0.015	21.397	0.228	0.228	0.000	0.000	0.000	0.000
87	A	110	GLN	0	-0.053	-0.028	26.018	-0.622	-0.622	0.000	0.000	0.000	0.000
88	A	111	ILE	0	-0.021	0.009	29.144	-0.430	-0.430	0.000	0.000	0.000	0.000
89	A	112	VAL	0	0.015	0.008	25.400	-0.284	-0.284	0.000	0.000	0.000	0.000
90	A	113	GLU	-1	-0.780	-0.872	28.788	10.290	10.290	0.000	0.000	0.000	0.000
91	A	114	ASN	0	-0.062	-0.063	30.422	-0.565	-0.565	0.000	0.000	0.000	0.000
92	A	115	PHE	0	0.009	0.019	30.788	-0.303	-0.303	0.000	0.000	0.000	0.000
93	A	116	LEU	0	0.013	-0.003	28.082	-0.253	-0.253	0.000	0.000	0.000	0.000
94	A	117	LEU	0	-0.020	-0.004	32.756	-0.245	-0.245	0.000	0.000	0.000	0.000
95	A	118	VAL	0	-0.055	-0.018	35.803	-0.273	-0.273	0.000	0.000	0.000	0.000
96	A	119	LEU	0	-0.057	-0.029	32.865	-0.219	-0.219	0.000	0.000	0.000	0.000
97	A	120	GLY	0	-0.031	0.002	36.661	-0.177	-0.177	0.000	0.000	0.000	0.000
98	A	121	VAL	0	-0.066	-0.024	31.513	-0.088	-0.088	0.000	0.000	0.000	0.000
99	A	122	SER	0	0.007	-0.003	34.639	0.003	0.003	0.000	0.000	0.000	0.000
100	A	123	PRO	0	0.069	0.000	33.783	0.270	0.270	0.000	0.000	0.000	0.000
101	A	124	GLU	-1	-0.984	-0.977	31.089	10.097	10.097	0.000	0.000	0.000	0.000
102	A	125	ILE	0	-0.011	-0.015	29.117	0.369	0.369	0.000	0.000	0.000	0.000
103	A	126	ALA	0	0.004	0.018	28.954	0.393	0.393	0.000	0.000	0.000	0.000
104	A	127	ARG	1	0.881	0.914	28.168	-9.946	-9.946	0.000	0.000	0.000	0.000
105	A	128	ARG	1	0.908	0.963	23.868	-12.192	-12.192	0.000	0.000	0.000	0.000
106	A	129	ASP	-1	-0.876	-0.954	24.399	12.767	12.767	0.000	0.000	0.000	0.000
107	A	130	ALA	0	0.005	-0.001	24.084	0.523	0.523	0.000	0.000	0.000	0.000
108	A	131	GLU	-1	-0.983	-0.980	20.977	15.478	15.478	0.000	0.000	0.000	0.000
109	A	132	GLY	0	0.015	0.012	19.625	0.786	0.786	0.000	0.000	0.000	0.000
110	A	133	MET	0	-0.066	-0.041	19.457	0.636	0.636	0.000	0.000	0.000	0.000
111	A	134	GLU	-1	-0.791	-0.894	20.233	15.731	15.731	0.000	0.000	0.000	0.000
112	A	135	HIS	1	0.871	0.952	16.659	-17.845	-17.845	0.000	0.000	0.000	0.000
113	A	136	HIS	0	-0.155	-0.081	14.002	0.944	0.944	0.000	0.000	0.000	0.000
114	A	137	VAL	0	-0.067	-0.015	18.569	-0.562	-0.562	0.000	0.000	0.000	0.000
115	A	138	SER	0	-0.044	-0.024	21.666	0.054	0.054	0.000	0.000	0.000	0.000
116	A	139	GLU	-1	-0.878	-0.961	22.506	11.689	11.689	0.000	0.000	0.000	0.000
117	A	140	GLU	-1	-0.927	-0.963	25.281	10.450	10.450	0.000	0.000	0.000	0.000
118	A	141	THR	0	-0.038	-0.018	25.421	-0.201	-0.201	0.000	0.000	0.000	0.000
119	A	142	LEU	0	0.059	0.038	25.871	-0.350	-0.350	0.000	0.000	0.000	0.000
120	A	143	ASP	-1	-0.822	-0.888	27.847	10.071	10.071	0.000	0.000	0.000	0.000
121	A	144	ALA	0	-0.040	-0.016	30.556	-0.403	-0.403	0.000	0.000	0.000	0.000
122	A	145	PHE	0	-0.037	-0.028	26.285	-0.231	-0.231	0.000	0.000	0.000	0.000
123	A	146	ARG	1	0.859	0.907	29.860	-10.525	-10.525	0.000	0.000	0.000	0.000
124	A	147	LEU	0	-0.088	-0.042	33.644	-0.334	-0.334	0.000	0.000	0.000	0.000
125	A	148	PHE	0	-0.053	-0.028	35.406	-0.364	-0.364	0.000	0.000	0.000	0.000
126	A	149	THR	0	0.010	0.035	37.242	-0.028	-0.028	0.000	0.000	0.000	0.000
127	A	150	GLN	0	-0.029	-0.022	40.123	-0.113	-0.113	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:24:GLU)