FMO DATABASE

FMODB ID: YZ8Z2

Calculation Name: 4ODD-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4ODD

Chain ID: B

ChEMBL ID:

UniProt ID: J9P950

Base Structure: X-ray

Registration Date: 2023-09-19

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	151
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1469030.831504
FMO2-HF: Nuclear repulsion	1409674.749716
FMO2-HF: Total energy	-59356.081788
FMO2-MP2: Total energy	-59529.178221

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(B:5:PRO)

Summations of interaction energy for fragment #1(B:5:PRO)

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.
-4.182	1.051	2.388	-2.377	-5.245	-0.011

Interaction energy analysis for fragmet #1(B:5:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.030 / q_NPA : -0.009

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	B	7	VAL	0	0.059	0.038	3.913	-1.734	-0.157	-0.008	-0.649	-0.920	0.001
4	B	8	LEU	0	0.019	-0.007	2.564	-0.854	0.752	0.641	-0.532	-1.716	0.000
5	B	9	THR	0	-0.011	0.000	4.268	-0.263	-0.004	-0.001	-0.047	-0.211	0.000
6	B	10	GLN	0	0.001	-0.006	5.960	0.362	0.362	0.000	0.000	0.000	0.000
7	B	11	VAL	0	0.026	0.014	7.630	0.177	0.177	0.000	0.000	0.000	0.000
8	B	12	SER	0	0.010	0.027	9.975	0.112	0.112	0.000	0.000	0.000	0.000
9	B	13	GLY	0	-0.003	0.009	12.064	0.079	0.079	0.000	0.000	0.000	0.000
10	B	14	PRO	0	0.018	0.004	15.814	-0.031	-0.031	0.000	0.000	0.000	0.000
11	B	15	TRP	0	-0.064	-0.051	12.715	0.003	0.003	0.000	0.000	0.000	0.000
12	B	16	LYS	1	0.849	0.935	18.397	0.165	0.165	0.000	0.000	0.000	0.000
13	B	17	THR	0	-0.017	-0.034	20.357	-0.020	-0.020	0.000	0.000	0.000	0.000
14	B	18	LEU	0	-0.032	-0.002	20.501	0.022	0.022	0.000	0.000	0.000	0.000
15	B	19	TYR	0	0.047	0.004	21.946	0.021	0.021	0.000	0.000	0.000	0.000
16	B	20	VAL	0	0.013	0.017	21.241	-0.028	-0.028	0.000	0.000	0.000	0.000
17	B	21	SER	0	0.026	0.004	22.298	0.016	0.016	0.000	0.000	0.000	0.000
18	B	22	SER	0	0.049	0.005	22.723	-0.017	-0.017	0.000	0.000	0.000	0.000
19	B	23	ASN	0	0.017	0.011	24.759	0.002	0.002	0.000	0.000	0.000	0.000
20	B	24	ASN	0	-0.052	-0.026	26.792	0.021	0.021	0.000	0.000	0.000	0.000
21	B	25	LEU	0	0.089	0.037	28.300	-0.008	-0.008	0.000	0.000	0.000	0.000
22	B	26	ASP	-1	-0.838	-0.918	30.272	-0.135	-0.135	0.000	0.000	0.000	0.000
23	B	27	LYS	1	0.811	0.895	25.915	0.180	0.180	0.000	0.000	0.000	0.000
24	B	28	ILE	0	-0.040	-0.007	24.771	-0.011	-0.011	0.000	0.000	0.000	0.000
25	B	29	GLY	0	0.043	0.027	27.838	0.003	0.003	0.000	0.000	0.000	0.000
26	B	30	GLU	-1	-0.812	-0.921	31.003	-0.129	-0.129	0.000	0.000	0.000	0.000
27	B	31	ASN	0	-0.022	-0.018	32.629	0.003	0.003	0.000	0.000	0.000	0.000
28	B	32	GLY	0	-0.003	0.028	29.752	-0.002	-0.002	0.000	0.000	0.000	0.000
29	B	33	PRO	0	-0.011	-0.012	26.221	-0.007	-0.007	0.000	0.000	0.000	0.000
30	B	34	PHE	0	0.022	0.003	20.244	-0.015	-0.015	0.000	0.000	0.000	0.000
31	B	35	ARG	1	0.793	0.913	23.777	0.122	0.122	0.000	0.000	0.000	0.000
32	B	36	ILE	0	-0.024	-0.006	20.092	0.005	0.005	0.000	0.000	0.000	0.000
33	B	37	TYR	0	0.042	0.041	23.389	0.003	0.003	0.000	0.000	0.000	0.000
34	B	38	LEU	0	-0.055	-0.041	17.212	-0.004	-0.004	0.000	0.000	0.000	0.000
35	B	39	ARG	1	0.770	0.868	20.500	0.202	0.202	0.000	0.000	0.000	0.000
36	B	40	GLY	0	0.016	-0.006	17.855	0.015	0.015	0.000	0.000	0.000	0.000
37	B	41	ILE	0	-0.028	0.015	11.708	-0.017	-0.017	0.000	0.000	0.000	0.000
38	B	42	ASN	0	-0.026	-0.013	13.584	0.038	0.038	0.000	0.000	0.000	0.000
39	B	43	VAL	0	0.033	0.010	6.987	-0.034	-0.034	0.000	0.000	0.000	0.000
40	B	44	ASP	-1	-0.818	-0.891	10.352	-0.434	-0.434	0.000	0.000	0.000	0.000
41	B	45	ILE	0	0.038	0.000	5.626	-0.046	-0.046	0.000	0.000	0.000	0.000
42	B	46	PRO	0	-0.022	0.000	8.013	-0.049	-0.049	0.000	0.000	0.000	0.000
43	B	47	ARG	1	0.874	0.927	10.251	0.430	0.430	0.000	0.000	0.000	0.000
44	B	48	LEU	0	-0.008	0.005	6.174	0.011	0.011	0.000	0.000	0.000	0.000
45	B	49	LYS	1	0.868	0.932	9.046	0.603	0.603	0.000	0.000	0.000	0.000
46	B	50	MET	0	-0.009	-0.003	9.057	-0.210	-0.210	0.000	0.000	0.000	0.000
47	B	51	LEU	0	-0.022	-0.003	11.902	0.086	0.086	0.000	0.000	0.000	0.000
48	B	52	PHE	0	0.019	0.000	11.528	-0.056	-0.056	0.000	0.000	0.000	0.000
49	B	53	ASN	0	-0.049	-0.029	16.856	0.038	0.038	0.000	0.000	0.000	0.000
50	B	54	PHE	0	0.035	-0.007	19.613	-0.009	-0.009	0.000	0.000	0.000	0.000
51	B	55	TYR	0	0.034	-0.024	22.359	0.015	0.015	0.000	0.000	0.000	0.000
52	B	56	VAL	0	-0.036	-0.013	25.044	-0.011	-0.011	0.000	0.000	0.000	0.000
53	B	57	LYS	1	0.849	0.937	27.605	0.131	0.131	0.000	0.000	0.000	0.000
54	B	58	VAL	0	-0.027	-0.022	30.834	-0.003	-0.003	0.000	0.000	0.000	0.000
55	B	59	ASP	-1	-0.860	-0.927	33.354	-0.103	-0.103	0.000	0.000	0.000	0.000
56	B	60	GLY	0	-0.036	-0.012	35.748	0.006	0.006	0.000	0.000	0.000	0.000
57	B	61	GLU	-1	-0.930	-0.955	35.343	-0.098	-0.098	0.000	0.000	0.000	0.000
58	B	62	CYS	0	-0.069	-0.023	29.035	-0.002	-0.002	0.000	0.000	0.000	0.000
59	B	63	VAL	0	0.019	0.012	28.882	0.001	0.001	0.000	0.000	0.000	0.000
60	B	64	GLU	-1	-0.822	-0.871	25.361	-0.198	-0.198	0.000	0.000	0.000	0.000
61	B	65	ASN	0	-0.078	-0.048	23.113	-0.005	-0.005	0.000	0.000	0.000	0.000
62	B	66	SER	0	0.054	0.013	20.923	-0.013	-0.013	0.000	0.000	0.000	0.000
63	B	67	VAL	0	0.008	0.033	18.075	0.002	0.002	0.000	0.000	0.000	0.000
64	B	68	GLY	0	0.016	0.013	16.517	-0.041	-0.041	0.000	0.000	0.000	0.000
65	B	69	ALA	0	-0.022	-0.022	13.159	0.024	0.024	0.000	0.000	0.000	0.000
66	B	70	SER	0	-0.045	-0.027	11.576	0.007	0.007	0.000	0.000	0.000	0.000
67	B	71	ILE	0	-0.006	0.009	4.819	0.008	0.008	0.000	0.000	0.000	0.000
68	B	72	GLY	0	0.020	0.011	8.258	0.105	0.105	0.000	0.000	0.000	0.000
69	B	73	ARG	1	0.877	0.900	6.897	0.124	0.124	0.000	0.000	0.000	0.000
70	B	74	ASP	-1	-0.822	-0.895	6.260	-0.382	-0.382	0.000	0.000	0.000	0.000
71	B	75	ASN	0	0.015	0.012	2.438	-2.797	-1.006	1.756	-1.149	-2.398	-0.012
72	B	76	LEU	0	-0.046	0.000	5.701	0.057	0.057	0.000	0.000	0.000	0.000
73	B	77	ILE	0	0.007	0.002	7.505	-0.091	-0.091	0.000	0.000	0.000	0.000
74	B	78	LYS	1	0.918	0.960	10.681	0.446	0.446	0.000	0.000	0.000	0.000
75	B	79	GLY	0	0.019	-0.001	14.197	-0.028	-0.028	0.000	0.000	0.000	0.000
76	B	80	GLU	-1	-0.939	-0.958	16.994	-0.244	-0.244	0.000	0.000	0.000	0.000
77	B	81	TYR	0	-0.043	-0.051	20.810	0.000	0.000	0.000	0.000	0.000	0.000
78	B	82	ASN	0	0.038	0.017	22.636	0.000	0.000	0.000	0.000	0.000	0.000
79	B	83	GLY	0	0.054	0.040	24.505	0.012	0.012	0.000	0.000	0.000	0.000
80	B	84	GLY	0	0.060	0.049	21.025	-0.019	-0.019	0.000	0.000	0.000	0.000
81	B	85	ASN	0	-0.049	-0.034	17.588	0.031	0.031	0.000	0.000	0.000	0.000
82	B	86	TYR	0	-0.057	-0.040	14.819	-0.029	-0.029	0.000	0.000	0.000	0.000
83	B	87	PHE	0	0.074	0.049	11.211	0.000	0.000	0.000	0.000	0.000	0.000
84	B	88	ARG	1	0.840	0.899	7.603	0.629	0.629	0.000	0.000	0.000	0.000
85	B	89	ILE	0	0.033	0.022	7.155	0.083	0.083	0.000	0.000	0.000	0.000
86	B	90	ILE	0	-0.116	-0.057	8.665	-0.004	-0.004	0.000	0.000	0.000	0.000
87	B	91	ASP	-1	-0.793	-0.898	10.518	-0.160	-0.160	0.000	0.000	0.000	0.000
88	B	92	MET	0	-0.061	-0.026	9.819	-0.151	-0.151	0.000	0.000	0.000	0.000
89	B	93	THR	0	-0.001	0.019	11.620	0.055	0.055	0.000	0.000	0.000	0.000
90	B	94	PRO	0	-0.010	-0.031	14.335	-0.043	-0.043	0.000	0.000	0.000	0.000
91	B	95	ASN	0	-0.004	0.009	15.838	-0.021	-0.021	0.000	0.000	0.000	0.000
92	B	96	ALA	0	0.033	0.020	16.535	-0.011	-0.011	0.000	0.000	0.000	0.000
93	B	97	LEU	0	0.000	0.006	10.546	-0.052	-0.052	0.000	0.000	0.000	0.000
94	B	98	ILE	0	0.018	0.009	12.881	0.046	0.046	0.000	0.000	0.000	0.000
95	B	99	GLY	0	0.026	0.005	12.186	-0.101	-0.101	0.000	0.000	0.000	0.000
96	B	100	TYR	0	-0.008	-0.021	13.255	0.086	0.086	0.000	0.000	0.000	0.000
97	B	101	ASP	-1	-0.752	-0.893	14.003	-0.464	-0.464	0.000	0.000	0.000	0.000
98	B	102	VAL	0	-0.064	-0.042	16.555	0.043	0.043	0.000	0.000	0.000	0.000
99	B	103	ASN	0	0.045	0.032	19.117	0.013	0.013	0.000	0.000	0.000	0.000
100	B	104	VAL	0	-0.034	-0.018	21.325	0.021	0.021	0.000	0.000	0.000	0.000
101	B	105	ASP	-1	-0.774	-0.883	24.011	-0.165	-0.165	0.000	0.000	0.000	0.000
102	B	106	SER	0	0.015	-0.007	27.003	0.003	0.003	0.000	0.000	0.000	0.000
103	B	107	LYS	1	0.921	0.963	29.576	0.115	0.115	0.000	0.000	0.000	0.000
104	B	108	GLY	0	0.020	0.017	27.749	0.007	0.007	0.000	0.000	0.000	0.000
105	B	109	LYS	1	0.806	0.912	28.126	0.137	0.137	0.000	0.000	0.000	0.000
106	B	110	ILE	0	-0.008	-0.011	23.117	-0.011	-0.011	0.000	0.000	0.000	0.000
107	B	111	THR	0	-0.026	-0.012	23.723	0.021	0.021	0.000	0.000	0.000	0.000
108	B	112	LYS	1	0.827	0.923	20.833	0.133	0.133	0.000	0.000	0.000	0.000
109	B	113	VAL	0	0.007	0.017	19.536	0.020	0.020	0.000	0.000	0.000	0.000
110	B	114	ALA	0	-0.025	-0.003	17.945	-0.034	-0.034	0.000	0.000	0.000	0.000
111	B	115	LEU	0	0.008	-0.003	16.705	0.019	0.019	0.000	0.000	0.000	0.000
112	B	116	LEU	0	0.006	0.012	16.947	-0.026	-0.026	0.000	0.000	0.000	0.000
113	B	117	MET	0	-0.022	-0.011	14.675	0.008	0.008	0.000	0.000	0.000	0.000
114	B	118	GLY	0	0.059	0.020	17.664	-0.003	-0.003	0.000	0.000	0.000	0.000
115	B	119	ARG	1	0.803	0.896	13.175	0.354	0.354	0.000	0.000	0.000	0.000
116	B	120	GLY	0	0.024	0.007	19.451	0.021	0.021	0.000	0.000	0.000	0.000
117	B	121	ALA	0	0.004	-0.001	23.299	-0.002	-0.002	0.000	0.000	0.000	0.000
118	B	122	HIS	0	-0.055	-0.036	22.769	-0.006	-0.006	0.000	0.000	0.000	0.000
119	B	123	VAL	0	0.013	0.016	22.467	0.007	0.007	0.000	0.000	0.000	0.000
120	B	124	ASN	0	-0.040	-0.022	20.685	0.000	0.000	0.000	0.000	0.000	0.000
121	B	125	GLU	-1	-0.903	-0.947	22.554	-0.080	-0.080	0.000	0.000	0.000	0.000
122	B	126	GLU	-1	-0.792	-0.902	21.406	-0.053	-0.053	0.000	0.000	0.000	0.000
123	B	127	ASP	-1	-0.791	-0.893	18.012	-0.140	-0.140	0.000	0.000	0.000	0.000
124	B	128	ILE	0	0.007	0.004	19.874	-0.024	-0.024	0.000	0.000	0.000	0.000
125	B	129	ALA	0	0.009	0.015	22.623	-0.006	-0.006	0.000	0.000	0.000	0.000
126	B	130	LYS	1	0.738	0.849	15.574	0.119	0.119	0.000	0.000	0.000	0.000
127	B	131	PHE	0	0.000	0.003	18.960	-0.013	-0.013	0.000	0.000	0.000	0.000
128	B	132	LYS	1	0.920	0.942	19.871	0.082	0.082	0.000	0.000	0.000	0.000
129	B	133	LYS	1	0.831	0.904	18.715	0.088	0.088	0.000	0.000	0.000	0.000
130	B	134	LEU	0	-0.026	-0.010	15.588	0.001	0.001	0.000	0.000	0.000	0.000
131	B	135	SER	0	0.031	0.015	19.246	-0.008	-0.008	0.000	0.000	0.000	0.000
132	B	136	ARG	1	0.927	0.947	22.084	0.080	0.080	0.000	0.000	0.000	0.000
133	B	137	GLU	-1	-0.794	-0.861	19.648	-0.082	-0.082	0.000	0.000	0.000	0.000
134	B	138	LYS	1	0.861	0.958	15.240	0.254	0.254	0.000	0.000	0.000	0.000
135	B	139	GLY	0	0.006	0.012	21.319	-0.003	-0.003	0.000	0.000	0.000	0.000
136	B	140	ILE	0	-0.078	-0.040	21.751	-0.004	-0.004	0.000	0.000	0.000	0.000
137	B	141	PRO	0	0.010	0.012	25.703	0.003	0.003	0.000	0.000	0.000	0.000
138	B	142	GLU	-1	-0.835	-0.905	27.660	-0.091	-0.091	0.000	0.000	0.000	0.000
139	B	143	GLU	-1	-0.888	-0.956	28.853	-0.089	-0.089	0.000	0.000	0.000	0.000
140	B	144	ASN	0	-0.069	-0.047	27.993	0.006	0.006	0.000	0.000	0.000	0.000
141	B	145	ILE	0	-0.051	-0.032	25.128	-0.015	-0.015	0.000	0.000	0.000	0.000
142	B	146	ILE	0	-0.021	-0.009	26.421	0.011	0.011	0.000	0.000	0.000	0.000
143	B	147	TYR	0	-0.010	-0.004	26.175	-0.016	-0.016	0.000	0.000	0.000	0.000
144	B	148	LEU	0	-0.028	-0.021	24.557	0.004	0.004	0.000	0.000	0.000	0.000
145	B	149	GLY	0	0.006	0.000	26.219	-0.004	-0.004	0.000	0.000	0.000	0.000
146	B	150	ASP	-1	-0.865	-0.930	27.091	-0.104	-0.104	0.000	0.000	0.000	0.000
147	B	151	THR	0	-0.013	-0.007	30.355	-0.001	-0.001	0.000	0.000	0.000	0.000
148	B	152	ASP	-1	-0.788	-0.856	26.220	-0.167	-0.167	0.000	0.000	0.000	0.000
149	B	153	ASN	0	0.000	-0.010	29.563	0.000	0.000	0.000	0.000	0.000	0.000
150	B	155	PRO	0	0.053	0.031	30.208	0.000	0.000	0.000	0.000	0.000	0.000
151	B	156	ASN	0	0.016	0.021	26.815	-0.008	-0.008	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(B:5:PRO)