FMO DATABASE

FMODB ID: 2J61R

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1310901.952417
FMO2-HF: Nuclear repulsion	1253839.44286
FMO2-HF: Total energy	-57062.509556
FMO2-MP2: Total energy	-57226.753841

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.
-12.796	-8.643	7.017	-5.249	-5.921	-0.029

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 : 0.015 / q_NPA : -0.002

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	0.948	0.989	3.829	0.543	2.818	-0.024	-1.230	-1.020	0.002
4	A	5	LEU	0	0.005	0.001	6.260	0.090	0.090	0.000	0.000	0.000	0.000
5	A	6	GLU	-1	-0.889	-0.949	6.240	1.587	1.587	0.000	0.000	0.000	0.000
6	A	7	TRP	0	0.053	-0.005	8.276	-0.094	-0.094	0.000	0.000	0.000	0.000
7	A	8	ALA	0	-0.004	0.004	10.443	-0.074	-0.074	0.000	0.000	0.000	0.000
8	A	9	LYS	1	0.910	0.966	9.444	-1.176	-1.176	0.000	0.000	0.000	0.000
9	A	10	ALA	0	-0.016	-0.001	12.666	-0.067	-0.067	0.000	0.000	0.000	0.000
10	A	11	SER	0	-0.007	-0.003	14.635	-0.065	-0.065	0.000	0.000	0.000	0.000
11	A	12	PRO	0	0.054	0.017	16.275	-0.005	-0.005	0.000	0.000	0.000	0.000
12	A	13	ASP	-1	-0.902	-0.944	17.351	0.203	0.203	0.000	0.000	0.000	0.000
13	A	14	ALA	0	0.004	0.004	16.744	-0.024	-0.024	0.000	0.000	0.000	0.000
14	A	15	TYR	0	-0.017	-0.011	12.573	-0.007	-0.007	0.000	0.000	0.000	0.000
15	A	16	ALA	0	0.011	0.002	16.201	-0.018	-0.018	0.000	0.000	0.000	0.000
16	A	17	ALA	0	-0.007	0.000	19.508	-0.023	-0.023	0.000	0.000	0.000	0.000
17	A	18	MET	0	-0.023	-0.005	15.867	-0.033	-0.033	0.000	0.000	0.000	0.000
18	A	19	LEU	0	-0.010	-0.010	15.847	-0.025	-0.025	0.000	0.000	0.000	0.000
19	A	20	GLY	0	-0.015	-0.002	19.148	-0.016	-0.016	0.000	0.000	0.000	0.000
20	A	21	LEU	0	0.014	0.004	19.744	-0.016	-0.016	0.000	0.000	0.000	0.000
21	A	22	GLU	-1	-0.776	-0.858	17.367	-0.001	-0.001	0.000	0.000	0.000	0.000
22	A	23	LYS	1	0.900	0.957	20.819	-0.120	-0.120	0.000	0.000	0.000	0.000
23	A	24	ALA	0	-0.042	-0.030	23.792	-0.007	-0.007	0.000	0.000	0.000	0.000
24	A	25	LEU	0	0.039	0.017	21.467	-0.007	-0.007	0.000	0.000	0.000	0.000
25	A	26	ALA	0	-0.057	-0.023	23.181	-0.007	-0.007	0.000	0.000	0.000	0.000
26	A	27	LYS	1	0.867	0.933	24.912	-0.055	-0.055	0.000	0.000	0.000	0.000
27	A	28	ALA	0	-0.032	0.014	27.530	-0.002	-0.002	0.000	0.000	0.000	0.000
28	A	29	GLY	0	-0.042	-0.017	29.345	0.002	0.002	0.000	0.000	0.000	0.000
29	A	30	LEU	0	-0.022	-0.002	26.580	-0.004	-0.004	0.000	0.000	0.000	0.000
30	A	31	GLU	-1	-0.779	-0.856	27.829	-0.046	-0.046	0.000	0.000	0.000	0.000
31	A	32	ARG	1	0.920	0.934	19.572	0.005	0.005	0.000	0.000	0.000	0.000
32	A	33	PRO	0	0.049	0.009	23.188	-0.011	-0.011	0.000	0.000	0.000	0.000
33	A	34	LEU	0	0.030	0.031	23.647	-0.020	-0.020	0.000	0.000	0.000	0.000
34	A	35	ILE	0	0.011	0.006	20.785	-0.017	-0.017	0.000	0.000	0.000	0.000
35	A	36	GLU	-1	-0.805	-0.886	17.625	-0.108	-0.108	0.000	0.000	0.000	0.000
36	A	37	LEU	0	0.001	0.013	19.182	-0.043	-0.043	0.000	0.000	0.000	0.000
37	A	38	VAL	0	0.038	0.027	20.907	-0.031	-0.031	0.000	0.000	0.000	0.000
38	A	39	TYR	0	-0.050	-0.062	16.024	-0.038	-0.038	0.000	0.000	0.000	0.000
39	A	40	LEU	0	0.002	0.012	15.205	-0.062	-0.062	0.000	0.000	0.000	0.000
40	A	41	ARG	1	0.842	0.915	17.032	0.221	0.221	0.000	0.000	0.000	0.000
41	A	42	THR	0	-0.002	-0.025	18.184	-0.020	-0.020	0.000	0.000	0.000	0.000
42	A	43	SER	0	-0.008	-0.019	13.182	-0.033	-0.033	0.000	0.000	0.000	0.000
43	A	44	GLN	0	-0.010	-0.010	14.629	-0.068	-0.068	0.000	0.000	0.000	0.000
44	A	45	ILE	0	-0.067	-0.013	16.528	-0.031	-0.031	0.000	0.000	0.000	0.000
45	A	46	ASN	0	-0.073	-0.051	15.883	0.013	0.013	0.000	0.000	0.000	0.000
46	A	47	GLY	0	0.026	0.037	14.217	-0.031	-0.031	0.000	0.000	0.000	0.000
47	A	48	CYS	0	-0.071	-0.008	10.244	-0.211	-0.211	0.000	0.000	0.000	0.000
48	A	49	ALA	0	0.048	0.013	7.850	0.060	0.060	0.000	0.000	0.000	0.000
49	A	50	TYR	0	0.018	0.007	3.728	0.062	0.293	-0.001	-0.030	-0.200	0.000
50	A	51	CYS	0	0.001	-0.005	6.826	0.409	0.409	0.000	0.000	0.000	0.000
51	A	52	VAL	0	0.026	0.013	10.345	0.139	0.139	0.000	0.000	0.000	0.000
52	A	53	ASN	0	0.012	0.006	7.599	0.179	0.179	0.000	0.000	0.000	0.000
53	A	54	MET	0	-0.031	0.004	9.279	0.161	0.161	0.000	0.000	0.000	0.000
54	A	55	HIS	1	0.869	0.898	10.762	0.227	0.227	0.000	0.000	0.000	0.000
55	A	56	ALA	0	0.047	0.044	13.703	0.049	0.049	0.000	0.000	0.000	0.000
56	A	57	ASN	0	-0.016	-0.015	11.170	0.068	0.068	0.000	0.000	0.000	0.000
57	A	58	ASP	-1	-0.842	-0.947	14.545	0.044	0.044	0.000	0.000	0.000	0.000
58	A	59	ALA	0	0.008	0.005	16.543	0.026	0.026	0.000	0.000	0.000	0.000
59	A	60	ARG	1	0.823	0.882	15.658	0.290	0.290	0.000	0.000	0.000	0.000
60	A	61	LYS	1	0.818	0.920	15.679	-0.040	-0.040	0.000	0.000	0.000	0.000
61	A	62	ALA	0	-0.061	-0.022	20.369	0.017	0.017	0.000	0.000	0.000	0.000
62	A	63	GLY	0	0.004	0.002	22.801	0.001	0.001	0.000	0.000	0.000	0.000
63	A	64	GLU	-1	-0.839	-0.888	21.759	-0.131	-0.131	0.000	0.000	0.000	0.000
64	A	65	THR	0	-0.003	0.000	23.392	-0.004	-0.004	0.000	0.000	0.000	0.000
65	A	66	GLU	-1	-0.756	-0.867	20.669	-0.242	-0.242	0.000	0.000	0.000	0.000
66	A	67	GLN	0	-0.018	0.011	23.539	-0.027	-0.027	0.000	0.000	0.000	0.000
67	A	68	ARG	1	0.790	0.837	25.108	0.111	0.111	0.000	0.000	0.000	0.000
68	A	69	LEU	0	-0.009	-0.005	18.868	-0.015	-0.015	0.000	0.000	0.000	0.000
69	A	70	GLN	0	-0.059	-0.037	20.811	-0.041	-0.041	0.000	0.000	0.000	0.000
70	A	71	ALA	0	0.011	0.008	22.402	-0.010	-0.010	0.000	0.000	0.000	0.000
71	A	72	LEU	0	-0.006	0.010	20.012	0.003	0.003	0.000	0.000	0.000	0.000
72	A	73	CYS	0	-0.077	-0.047	20.718	0.005	0.005	0.000	0.000	0.000	0.000
73	A	74	VAL	0	-0.008	-0.010	22.669	0.000	0.000	0.000	0.000	0.000	0.000
74	A	75	TRP	0	0.009	0.007	25.261	0.026	0.026	0.000	0.000	0.000	0.000
75	A	76	GLN	0	-0.008	-0.007	27.148	0.009	0.009	0.000	0.000	0.000	0.000
76	A	77	GLU	-1	-0.901	-0.937	30.664	-0.118	-0.118	0.000	0.000	0.000	0.000
77	A	78	THR	0	-0.078	-0.032	29.044	0.001	0.001	0.000	0.000	0.000	0.000
78	A	79	PRO	0	-0.003	-0.012	32.123	0.004	0.004	0.000	0.000	0.000	0.000
79	A	80	TYR	0	-0.027	-0.021	28.717	0.011	0.011	0.000	0.000	0.000	0.000
80	A	81	PHE	0	-0.009	0.008	25.359	0.001	0.001	0.000	0.000	0.000	0.000
81	A	82	THR	0	0.008	-0.028	30.777	0.005	0.005	0.000	0.000	0.000	0.000
82	A	83	PRO	0	0.039	0.011	32.861	-0.006	-0.006	0.000	0.000	0.000	0.000
83	A	84	ARG	1	0.811	0.857	31.994	0.045	0.045	0.000	0.000	0.000	0.000
84	A	85	GLU	-1	-0.759	-0.845	28.198	-0.109	-0.109	0.000	0.000	0.000	0.000
85	A	86	ARG	1	0.851	0.920	29.242	0.110	0.110	0.000	0.000	0.000	0.000
86	A	87	ALA	0	0.063	0.051	30.954	-0.007	-0.007	0.000	0.000	0.000	0.000
87	A	88	ALA	0	0.025	0.005	27.769	-0.003	-0.003	0.000	0.000	0.000	0.000
88	A	89	LEU	0	-0.013	0.003	24.307	-0.010	-0.010	0.000	0.000	0.000	0.000
89	A	90	ALA	0	0.017	0.013	27.038	-0.014	-0.014	0.000	0.000	0.000	0.000
90	A	91	TRP	0	0.005	-0.006	28.137	-0.008	-0.008	0.000	0.000	0.000	0.000
91	A	92	THR	0	-0.013	-0.033	22.654	-0.003	-0.003	0.000	0.000	0.000	0.000
92	A	93	GLU	-1	-0.759	-0.837	24.528	-0.242	-0.242	0.000	0.000	0.000	0.000
93	A	94	GLN	0	-0.016	-0.018	25.699	-0.009	-0.009	0.000	0.000	0.000	0.000
94	A	95	LEU	0	0.012	0.006	25.934	0.000	0.000	0.000	0.000	0.000	0.000
95	A	96	ALA	0	-0.048	-0.017	21.622	-0.003	-0.003	0.000	0.000	0.000	0.000
96	A	97	ARG	1	0.778	0.874	23.081	0.220	0.220	0.000	0.000	0.000	0.000
97	A	98	LEU	0	0.068	0.043	25.461	0.009	0.009	0.000	0.000	0.000	0.000
98	A	99	SER	0	-0.061	-0.046	25.216	0.007	0.007	0.000	0.000	0.000	0.000
99	A	100	GLN	0	-0.056	-0.019	26.115	-0.001	-0.001	0.000	0.000	0.000	0.000
100	A	101	GLY	0	0.010	0.010	29.060	0.004	0.004	0.000	0.000	0.000	0.000
101	A	102	ALA	0	-0.047	-0.015	32.017	-0.001	-0.001	0.000	0.000	0.000	0.000
102	A	103	LEU	0	0.039	0.020	30.317	-0.005	-0.005	0.000	0.000	0.000	0.000
103	A	104	PRO	0	-0.013	-0.003	33.783	0.006	0.006	0.000	0.000	0.000	0.000
104	A	105	HIS	0	0.021	-0.006	36.994	-0.001	-0.001	0.000	0.000	0.000	0.000
105	A	106	GLY	0	0.031	0.021	39.831	0.003	0.003	0.000	0.000	0.000	0.000
106	A	107	LEU	0	-0.005	0.014	31.877	0.000	0.000	0.000	0.000	0.000	0.000
107	A	108	LEU	0	0.009	-0.006	35.139	0.000	0.000	0.000	0.000	0.000	0.000
108	A	109	ASP	-1	-0.918	-0.970	36.671	-0.046	-0.046	0.000	0.000	0.000	0.000
109	A	110	GLU	-1	-0.912	-0.948	36.872	-0.081	-0.081	0.000	0.000	0.000	0.000
110	A	111	LEU	0	-0.040	-0.027	31.807	0.000	0.000	0.000	0.000	0.000	0.000
111	A	112	ARG	1	0.824	0.861	35.747	0.040	0.040	0.000	0.000	0.000	0.000
112	A	113	GLU	-1	-0.997	-0.965	38.607	-0.052	-0.052	0.000	0.000	0.000	0.000
113	A	114	HIS	0	-0.110	-0.057	35.529	0.000	0.000	0.000	0.000	0.000	0.000
114	A	115	PHE	0	-0.053	-0.027	30.812	-0.001	-0.001	0.000	0.000	0.000	0.000
115	A	116	ASP	-1	-0.815	-0.896	36.014	-0.021	-0.021	0.000	0.000	0.000	0.000
116	A	117	ASP	-1	-0.736	-0.876	35.921	-0.033	-0.033	0.000	0.000	0.000	0.000
117	A	118	LYS	1	0.803	0.891	33.220	0.003	0.003	0.000	0.000	0.000	0.000
118	A	119	GLU	-1	-0.770	-0.861	32.269	-0.036	-0.036	0.000	0.000	0.000	0.000
119	A	120	ILE	0	0.032	0.031	31.097	-0.006	-0.006	0.000	0.000	0.000	0.000
120	A	121	ALA	0	-0.020	0.003	30.782	-0.006	-0.006	0.000	0.000	0.000	0.000
121	A	122	GLU	-1	-0.788	-0.891	28.567	-0.008	-0.008	0.000	0.000	0.000	0.000
122	A	123	LEU	0	0.029	0.018	26.281	-0.004	-0.004	0.000	0.000	0.000	0.000
123	A	124	THR	0	0.000	-0.018	25.989	-0.015	-0.015	0.000	0.000	0.000	0.000
124	A	125	LEU	0	-0.021	0.012	24.471	-0.006	-0.006	0.000	0.000	0.000	0.000
125	A	126	ALA	0	0.032	0.011	22.432	-0.002	-0.002	0.000	0.000	0.000	0.000
126	A	127	VAL	0	0.025	0.010	21.250	-0.016	-0.016	0.000	0.000	0.000	0.000
127	A	128	SER	0	-0.042	-0.036	21.330	-0.021	-0.021	0.000	0.000	0.000	0.000
128	A	129	ALA	0	0.003	0.005	19.542	-0.006	-0.006	0.000	0.000	0.000	0.000
129	A	130	ILE	0	-0.040	0.004	14.484	-0.007	-0.007	0.000	0.000	0.000	0.000
130	A	131	ASN	0	0.037	0.015	16.298	-0.076	-0.076	0.000	0.000	0.000	0.000
131	A	132	ALA	0	0.012	0.015	17.366	-0.032	-0.032	0.000	0.000	0.000	0.000
132	A	133	TRP	0	-0.025	-0.039	12.780	0.017	0.017	0.000	0.000	0.000	0.000
133	A	134	ASN	0	0.003	-0.035	12.416	-0.059	-0.059	0.000	0.000	0.000	0.000
134	A	135	ARG	1	0.886	0.942	12.913	0.132	0.132	0.000	0.000	0.000	0.000
135	A	136	PHE	0	0.001	0.006	11.939	-0.022	-0.022	0.000	0.000	0.000	0.000
136	A	137	GLY	0	0.007	-0.010	8.780	-0.005	-0.005	0.000	0.000	0.000	0.000
137	A	138	VAL	0	0.019	0.002	8.429	-0.328	-0.328	0.000	0.000	0.000	0.000
138	A	139	GLY	0	-0.001	0.012	10.291	-0.064	-0.064	0.000	0.000	0.000	0.000
139	A	140	MET	0	-0.068	-0.027	8.838	0.062	0.062	0.000	0.000	0.000	0.000
140	A	141	GLY	0	-0.012	-0.012	6.779	0.148	0.148	0.000	0.000	0.000	0.000
141	A	142	MET	0	-0.058	-0.024	4.168	-1.225	-0.863	0.000	-0.141	-0.221	0.000
142	A	143	GLN	0	-0.049	-0.027	2.286	-0.104	1.321	1.435	-1.182	-1.678	0.001
143	A	144	PRO	0	-0.003	0.005	1.910	-11.021	-11.561	5.607	-2.621	-2.447	-0.032
144	A	145	GLU	-1	-0.993	-0.988	4.075	-1.205	-0.805	0.000	-0.045	-0.355	0.000

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