FMO DATABASE

FMODB ID: 6N9QZ

Calculation Name: 2O4D-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2O4D

Chain ID: A

ChEMBL ID:

UniProt ID: Q9I6M1

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	OptAll
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	144
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1316299.836765
FMO2-HF: Nuclear repulsion	1259237.108251
FMO2-HF: Total energy	-57062.728515
FMO2-MP2: Total energy	-57226.938196

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:2:THR)

Summations of interaction energy for fragment #1(A:2:THR)

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.
-13.196	-11.106	10.901	-6.496	-6.495	-0.035

Interaction energy analysis for fragmet #1(A:2:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.021 / q_NPA : 0.000

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	4	ARG	1	0.953	0.990	3.878	0.930	3.005	-0.017	-1.148	-0.910	0.003
4	A	5	LEU	0	0.020	0.005	6.449	0.128	0.128	0.000	0.000	0.000	0.000
5	A	6	GLU	-1	-0.834	-0.912	5.930	1.651	1.651	0.000	0.000	0.000	0.000
6	A	7	TRP	0	0.043	-0.013	8.072	-0.061	-0.061	0.000	0.000	0.000	0.000
7	A	8	ALA	0	-0.007	-0.001	10.349	-0.058	-0.058	0.000	0.000	0.000	0.000
8	A	9	LYS	1	0.833	0.918	8.686	-1.320	-1.320	0.000	0.000	0.000	0.000
9	A	10	ALA	0	-0.031	-0.007	13.098	-0.057	-0.057	0.000	0.000	0.000	0.000
10	A	11	SER	0	-0.014	-0.015	14.976	-0.061	-0.061	0.000	0.000	0.000	0.000
11	A	12	PRO	0	0.028	0.011	16.119	0.000	0.000	0.000	0.000	0.000	0.000
12	A	13	ASP	-1	-0.845	-0.908	17.085	0.208	0.208	0.000	0.000	0.000	0.000
13	A	14	ALA	0	0.012	0.009	16.709	-0.022	-0.022	0.000	0.000	0.000	0.000
14	A	15	TYR	0	-0.013	-0.006	11.831	-0.007	-0.007	0.000	0.000	0.000	0.000
15	A	16	ALA	0	0.003	-0.001	15.793	-0.013	-0.013	0.000	0.000	0.000	0.000
16	A	17	ALA	0	-0.010	-0.006	19.045	-0.021	-0.021	0.000	0.000	0.000	0.000
17	A	18	MET	0	-0.027	-0.004	15.740	-0.031	-0.031	0.000	0.000	0.000	0.000
18	A	19	LEU	0	-0.005	-0.008	15.342	-0.021	-0.021	0.000	0.000	0.000	0.000
19	A	20	GLY	0	-0.014	-0.001	18.705	-0.012	-0.012	0.000	0.000	0.000	0.000
20	A	21	LEU	0	0.011	0.006	19.469	-0.016	-0.016	0.000	0.000	0.000	0.000
21	A	22	GLU	-1	-0.747	-0.848	17.189	0.011	0.011	0.000	0.000	0.000	0.000
22	A	23	LYS	1	0.903	0.952	20.594	-0.137	-0.137	0.000	0.000	0.000	0.000
23	A	24	ALA	0	-0.039	-0.024	23.544	-0.005	-0.005	0.000	0.000	0.000	0.000
24	A	25	LEU	0	0.033	0.011	21.221	-0.005	-0.005	0.000	0.000	0.000	0.000
25	A	26	ALA	0	-0.029	-0.001	22.901	-0.007	-0.007	0.000	0.000	0.000	0.000
26	A	27	LYS	1	0.843	0.921	24.636	-0.059	-0.059	0.000	0.000	0.000	0.000
27	A	28	ALA	0	-0.019	0.011	26.888	-0.003	-0.003	0.000	0.000	0.000	0.000
28	A	29	GLY	0	-0.052	-0.028	28.766	0.004	0.004	0.000	0.000	0.000	0.000
29	A	30	LEU	0	-0.011	0.002	26.212	-0.003	-0.003	0.000	0.000	0.000	0.000
30	A	31	GLU	-1	-0.775	-0.855	27.417	-0.038	-0.038	0.000	0.000	0.000	0.000
31	A	32	ARG	1	0.847	0.908	19.047	-0.019	-0.019	0.000	0.000	0.000	0.000
32	A	33	PRO	0	0.047	0.006	22.718	-0.011	-0.011	0.000	0.000	0.000	0.000
33	A	34	LEU	0	0.028	0.033	23.005	-0.020	-0.020	0.000	0.000	0.000	0.000
34	A	35	ILE	0	0.006	0.008	20.432	-0.019	-0.019	0.000	0.000	0.000	0.000
35	A	36	GLU	-1	-0.798	-0.886	17.162	-0.081	-0.081	0.000	0.000	0.000	0.000
36	A	37	LEU	0	-0.009	0.005	18.709	-0.044	-0.044	0.000	0.000	0.000	0.000
37	A	38	VAL	0	0.035	0.018	20.471	-0.034	-0.034	0.000	0.000	0.000	0.000
38	A	39	TYR	0	-0.051	-0.056	15.754	-0.043	-0.043	0.000	0.000	0.000	0.000
39	A	40	LEU	0	0.002	0.019	14.709	-0.068	-0.068	0.000	0.000	0.000	0.000
40	A	41	ARG	1	0.801	0.901	16.582	0.215	0.215	0.000	0.000	0.000	0.000
41	A	42	THR	0	0.006	-0.028	17.922	-0.023	-0.023	0.000	0.000	0.000	0.000
42	A	43	SER	0	-0.011	-0.024	12.822	-0.040	-0.040	0.000	0.000	0.000	0.000
43	A	44	GLN	0	-0.023	-0.012	14.269	-0.079	-0.079	0.000	0.000	0.000	0.000
44	A	45	ILE	0	-0.034	0.001	16.370	-0.034	-0.034	0.000	0.000	0.000	0.000
45	A	46	ASN	0	-0.066	-0.045	15.567	0.021	0.021	0.000	0.000	0.000	0.000
46	A	47	GLY	0	0.034	0.023	14.211	-0.049	-0.049	0.000	0.000	0.000	0.000
47	A	48	CYS	0	-0.071	0.001	10.310	-0.227	-0.227	0.000	0.000	0.000	0.000
48	A	49	ALA	0	0.053	0.009	7.926	0.028	0.028	0.000	0.000	0.000	0.000
49	A	50	TYR	0	0.007	0.000	3.292	-0.142	0.348	0.007	-0.134	-0.362	0.001
50	A	51	CYS	0	-0.004	0.005	6.519	0.499	0.499	0.000	0.000	0.000	0.000
51	A	52	VAL	0	0.018	0.013	9.934	0.171	0.171	0.000	0.000	0.000	0.000
52	A	53	ASN	0	0.003	-0.002	7.374	0.263	0.263	0.000	0.000	0.000	0.000
53	A	54	MET	0	-0.038	0.007	8.692	0.191	0.191	0.000	0.000	0.000	0.000
54	A	55	HIS	1	0.855	0.894	10.215	0.214	0.214	0.000	0.000	0.000	0.000
55	A	56	ALA	0	0.041	0.034	13.246	0.045	0.045	0.000	0.000	0.000	0.000
56	A	57	ASN	0	-0.003	-0.002	11.322	0.077	0.077	0.000	0.000	0.000	0.000
57	A	58	ASP	-1	-0.845	-0.937	13.907	0.116	0.116	0.000	0.000	0.000	0.000
58	A	59	ALA	0	0.029	0.013	16.044	0.021	0.021	0.000	0.000	0.000	0.000
59	A	60	ARG	1	0.793	0.859	15.134	0.260	0.260	0.000	0.000	0.000	0.000
60	A	61	LYS	1	0.825	0.918	14.796	-0.113	-0.113	0.000	0.000	0.000	0.000
61	A	62	ALA	0	-0.050	-0.016	19.919	0.014	0.014	0.000	0.000	0.000	0.000
62	A	63	GLY	0	0.001	0.004	22.205	-0.001	-0.001	0.000	0.000	0.000	0.000
63	A	64	GLU	-1	-0.835	-0.896	21.213	-0.123	-0.123	0.000	0.000	0.000	0.000
64	A	65	THR	0	-0.012	-0.010	23.193	0.001	0.001	0.000	0.000	0.000	0.000
65	A	66	GLU	-1	-0.764	-0.868	20.115	-0.223	-0.223	0.000	0.000	0.000	0.000
66	A	67	GLN	0	-0.009	0.015	22.986	-0.028	-0.028	0.000	0.000	0.000	0.000
67	A	68	ARG	1	0.792	0.850	24.914	0.102	0.102	0.000	0.000	0.000	0.000
68	A	69	LEU	0	-0.005	-0.006	18.634	-0.016	-0.016	0.000	0.000	0.000	0.000
69	A	70	GLN	0	-0.047	-0.029	20.686	-0.041	-0.041	0.000	0.000	0.000	0.000
70	A	71	ALA	0	0.020	0.012	22.198	-0.013	-0.013	0.000	0.000	0.000	0.000
71	A	72	LEU	0	-0.013	0.001	19.646	-0.001	-0.001	0.000	0.000	0.000	0.000
72	A	73	CYS	0	-0.105	-0.053	20.587	-0.002	-0.002	0.000	0.000	0.000	0.000
73	A	74	VAL	0	0.002	-0.017	22.285	-0.005	-0.005	0.000	0.000	0.000	0.000
74	A	75	TRP	0	0.003	0.005	24.866	0.027	0.027	0.000	0.000	0.000	0.000
75	A	76	GLN	0	0.003	0.008	26.910	0.009	0.009	0.000	0.000	0.000	0.000
76	A	77	GLU	-1	-0.890	-0.934	30.476	-0.120	-0.120	0.000	0.000	0.000	0.000
77	A	78	THR	0	-0.081	-0.042	28.575	0.000	0.000	0.000	0.000	0.000	0.000
78	A	79	PRO	0	0.020	-0.002	31.675	0.004	0.004	0.000	0.000	0.000	0.000
79	A	80	TYR	0	-0.049	-0.025	28.622	0.012	0.012	0.000	0.000	0.000	0.000
80	A	81	PHE	0	-0.003	0.007	25.109	-0.001	-0.001	0.000	0.000	0.000	0.000
81	A	82	THR	0	0.005	-0.027	30.635	0.003	0.003	0.000	0.000	0.000	0.000
82	A	83	PRO	0	0.027	0.002	32.549	-0.006	-0.006	0.000	0.000	0.000	0.000
83	A	84	ARG	1	0.784	0.841	31.866	0.039	0.039	0.000	0.000	0.000	0.000
84	A	85	GLU	-1	-0.737	-0.833	28.201	-0.100	-0.100	0.000	0.000	0.000	0.000
85	A	86	ARG	1	0.841	0.915	28.857	0.107	0.107	0.000	0.000	0.000	0.000
86	A	87	ALA	0	0.080	0.052	30.491	-0.008	-0.008	0.000	0.000	0.000	0.000
87	A	88	ALA	0	0.035	0.013	27.593	-0.003	-0.003	0.000	0.000	0.000	0.000
88	A	89	LEU	0	-0.026	-0.001	23.852	-0.011	-0.011	0.000	0.000	0.000	0.000
89	A	90	ALA	0	0.011	0.007	26.723	-0.015	-0.015	0.000	0.000	0.000	0.000
90	A	91	TRP	0	0.001	-0.018	27.880	-0.008	-0.008	0.000	0.000	0.000	0.000
91	A	92	THR	0	-0.010	-0.026	22.348	-0.003	-0.003	0.000	0.000	0.000	0.000
92	A	93	GLU	-1	-0.766	-0.845	24.415	-0.249	-0.249	0.000	0.000	0.000	0.000
93	A	94	GLN	0	0.005	0.008	25.597	-0.009	-0.009	0.000	0.000	0.000	0.000
94	A	95	LEU	0	0.036	0.017	25.654	-0.005	-0.005	0.000	0.000	0.000	0.000
95	A	96	ALA	0	-0.056	-0.027	21.362	-0.003	-0.003	0.000	0.000	0.000	0.000
96	A	97	ARG	1	0.789	0.871	22.716	0.218	0.218	0.000	0.000	0.000	0.000
97	A	98	LEU	0	0.051	0.032	25.462	0.009	0.009	0.000	0.000	0.000	0.000
98	A	99	SER	0	-0.064	-0.046	25.091	0.008	0.008	0.000	0.000	0.000	0.000
99	A	100	GLN	0	-0.048	-0.012	25.818	-0.006	-0.006	0.000	0.000	0.000	0.000
100	A	101	GLY	0	-0.001	-0.001	29.138	0.005	0.005	0.000	0.000	0.000	0.000
101	A	102	ALA	0	-0.032	-0.005	31.932	0.000	0.000	0.000	0.000	0.000	0.000
102	A	103	LEU	0	0.038	0.019	30.009	-0.004	-0.004	0.000	0.000	0.000	0.000
103	A	104	PRO	0	-0.023	-0.001	33.655	0.007	0.007	0.000	0.000	0.000	0.000
104	A	105	HIS	0	0.020	-0.013	36.805	0.000	0.000	0.000	0.000	0.000	0.000
105	A	106	GLY	0	0.046	0.032	39.562	0.003	0.003	0.000	0.000	0.000	0.000
106	A	107	LEU	0	-0.017	0.004	31.532	0.001	0.001	0.000	0.000	0.000	0.000
107	A	108	LEU	0	0.012	-0.001	34.958	-0.001	-0.001	0.000	0.000	0.000	0.000
108	A	109	ASP	-1	-0.882	-0.946	36.333	-0.046	-0.046	0.000	0.000	0.000	0.000
109	A	110	GLU	-1	-0.912	-0.952	36.050	-0.084	-0.084	0.000	0.000	0.000	0.000
110	A	111	LEU	0	-0.033	-0.016	31.531	0.000	0.000	0.000	0.000	0.000	0.000
111	A	112	ARG	1	0.793	0.843	35.494	0.042	0.042	0.000	0.000	0.000	0.000
112	A	113	GLU	-1	-1.006	-0.973	38.357	-0.050	-0.050	0.000	0.000	0.000	0.000
113	A	114	HIS	0	-0.116	-0.064	34.930	0.000	0.000	0.000	0.000	0.000	0.000
114	A	115	PHE	0	-0.038	-0.025	30.475	-0.001	-0.001	0.000	0.000	0.000	0.000
115	A	116	ASP	-1	-0.804	-0.883	35.643	-0.019	-0.019	0.000	0.000	0.000	0.000
116	A	117	ASP	-1	-0.737	-0.869	35.413	-0.035	-0.035	0.000	0.000	0.000	0.000
117	A	118	LYS	1	0.816	0.901	32.757	0.001	0.001	0.000	0.000	0.000	0.000
118	A	119	GLU	-1	-0.789	-0.871	31.860	-0.031	-0.031	0.000	0.000	0.000	0.000
119	A	120	ILE	0	0.042	0.027	30.642	-0.006	-0.006	0.000	0.000	0.000	0.000
120	A	121	ALA	0	-0.018	0.011	30.456	-0.007	-0.007	0.000	0.000	0.000	0.000
121	A	122	GLU	-1	-0.797	-0.890	28.174	-0.005	-0.005	0.000	0.000	0.000	0.000
122	A	123	LEU	0	0.033	0.024	25.771	-0.003	-0.003	0.000	0.000	0.000	0.000
123	A	124	THR	0	0.003	-0.016	25.622	-0.015	-0.015	0.000	0.000	0.000	0.000
124	A	125	LEU	0	-0.032	0.007	24.327	-0.007	-0.007	0.000	0.000	0.000	0.000
125	A	126	ALA	0	0.029	0.008	22.116	-0.003	-0.003	0.000	0.000	0.000	0.000
126	A	127	VAL	0	0.032	0.012	20.932	-0.016	-0.016	0.000	0.000	0.000	0.000
127	A	128	SER	0	-0.040	-0.030	21.169	-0.026	-0.026	0.000	0.000	0.000	0.000
128	A	129	ALA	0	0.000	0.000	19.419	-0.011	-0.011	0.000	0.000	0.000	0.000
129	A	130	ILE	0	-0.034	0.003	14.113	-0.008	-0.008	0.000	0.000	0.000	0.000
130	A	131	ASN	0	0.045	0.022	16.016	-0.087	-0.087	0.000	0.000	0.000	0.000
131	A	132	ALA	0	0.012	0.020	17.278	-0.037	-0.037	0.000	0.000	0.000	0.000
132	A	133	TRP	0	-0.041	-0.040	12.739	0.003	0.003	0.000	0.000	0.000	0.000
133	A	134	ASN	0	0.016	-0.039	12.200	-0.057	-0.057	0.000	0.000	0.000	0.000
134	A	135	ARG	1	0.860	0.926	12.575	0.151	0.151	0.000	0.000	0.000	0.000
135	A	136	PHE	0	0.008	0.006	12.076	-0.020	-0.020	0.000	0.000	0.000	0.000
136	A	137	GLY	0	0.028	0.000	8.767	-0.017	-0.017	0.000	0.000	0.000	0.000
137	A	138	VAL	0	0.002	-0.003	8.672	-0.325	-0.325	0.000	0.000	0.000	0.000
138	A	139	GLY	0	-0.009	0.009	10.633	-0.058	-0.058	0.000	0.000	0.000	0.000
139	A	140	MET	0	-0.054	-0.021	8.892	0.093	0.093	0.000	0.000	0.000	0.000
140	A	141	GLY	0	-0.017	-0.015	7.135	0.078	0.078	0.000	0.000	0.000	0.000
141	A	142	MET	0	-0.058	-0.019	4.373	-1.107	-0.821	-0.001	-0.094	-0.191	0.000
142	A	143	GLN	0	-0.039	-0.023	2.338	-0.159	1.439	1.058	-1.069	-1.586	0.002
143	A	144	PRO	0	-0.007	0.012	1.803	-12.241	-15.063	9.852	-3.996	-3.035	-0.041
144	A	145	GLU	-1	-0.951	-0.971	3.997	-0.697	-0.234	0.002	-0.055	-0.411	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:THR)