FMO DATABASE

FMODB ID: 5255Z

Calculation Name: 5C8O-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5C8O

Chain ID: A

ChEMBL ID:

UniProt ID: G4N991

Base Structure: X-ray

Registration Date: 2023-06-22

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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	151
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1392776.931378
FMO2-HF: Nuclear repulsion	1332732.641306
FMO2-HF: Total energy	-60044.290072
FMO2-MP2: Total energy	-60219.530608

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:1:GLY)

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

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.
0.662	1.503	-0.008	-0.446	-0.387	0.001

Interaction energy analysis for fragmet #1(A:1:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.003 / q_NPA : -0.014

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	3	TYR	0	0.033	0.017	3.807	0.383	1.224	-0.008	-0.446	-0.387	0.001
4	A	4	ALA	0	-0.008	-0.010	6.613	0.385	0.385	0.000	0.000	0.000	0.000
5	A	5	GLY	0	-0.014	0.002	8.875	0.163	0.163	0.000	0.000	0.000	0.000
6	A	6	ASN	0	-0.055	-0.042	10.023	0.030	0.030	0.000	0.000	0.000	0.000
7	A	7	PHE	0	0.041	0.017	11.988	0.092	0.092	0.000	0.000	0.000	0.000
8	A	8	SER	0	-0.057	-0.057	14.759	0.059	0.059	0.000	0.000	0.000	0.000
9	A	9	GLY	0	0.008	0.015	14.436	0.030	0.030	0.000	0.000	0.000	0.000
10	A	10	SER	0	-0.069	-0.018	15.415	0.064	0.064	0.000	0.000	0.000	0.000
11	A	11	SER	0	-0.015	-0.025	18.219	0.047	0.047	0.000	0.000	0.000	0.000
12	A	12	ARG	1	0.935	0.977	20.749	0.094	0.094	0.000	0.000	0.000	0.000
13	A	13	ASP	-1	-0.886	-0.948	23.513	-0.129	-0.129	0.000	0.000	0.000	0.000
14	A	14	ILE	0	-0.052	-0.009	19.981	0.008	0.008	0.000	0.000	0.000	0.000
15	A	15	CYS	0	-0.022	-0.010	24.233	0.002	0.002	0.000	0.000	0.000	0.000
16	A	16	LEU	0	0.020	-0.008	24.508	-0.007	-0.007	0.000	0.000	0.000	0.000
17	A	17	ASP	-1	-0.897	-0.935	27.375	-0.094	-0.094	0.000	0.000	0.000	0.000
18	A	18	GLY	0	0.020	0.013	30.183	0.005	0.005	0.000	0.000	0.000	0.000
19	A	19	ALA	0	0.020	0.009	26.324	-0.011	-0.011	0.000	0.000	0.000	0.000
20	A	20	ARG	1	0.911	0.952	25.613	0.082	0.082	0.000	0.000	0.000	0.000
21	A	21	LEU	0	0.019	0.020	20.154	-0.001	-0.001	0.000	0.000	0.000	0.000
22	A	22	ARG	1	0.892	0.925	24.612	0.116	0.116	0.000	0.000	0.000	0.000
23	A	23	ALA	0	0.014	0.009	23.024	-0.017	-0.017	0.000	0.000	0.000	0.000
24	A	24	GLU	-1	-0.837	-0.897	24.935	-0.084	-0.084	0.000	0.000	0.000	0.000
25	A	25	CYS	0	-0.051	-0.027	21.317	-0.015	-0.015	0.000	0.000	0.000	0.000
26	A	26	ARG	1	0.936	0.969	20.738	0.095	0.095	0.000	0.000	0.000	0.000
27	A	27	ARG	1	0.856	0.927	21.862	0.032	0.032	0.000	0.000	0.000	0.000
28	A	28	GLY	0	-0.005	-0.018	22.555	-0.002	-0.002	0.000	0.000	0.000	0.000
29	A	29	ASP	-1	-0.844	-0.907	23.445	-0.020	-0.020	0.000	0.000	0.000	0.000
30	A	30	GLY	0	-0.035	-0.012	25.227	0.001	0.001	0.000	0.000	0.000	0.000
31	A	31	GLY	0	0.004	0.013	26.234	-0.007	-0.007	0.000	0.000	0.000	0.000
32	A	32	TYR	0	-0.022	-0.037	23.635	-0.002	-0.002	0.000	0.000	0.000	0.000
33	A	33	SER	0	-0.015	-0.004	26.315	0.013	0.013	0.000	0.000	0.000	0.000
34	A	34	THR	0	0.005	0.010	26.811	-0.008	-0.008	0.000	0.000	0.000	0.000
35	A	35	SER	0	0.015	0.018	24.589	0.014	0.014	0.000	0.000	0.000	0.000
36	A	36	VAL	0	-0.068	-0.051	26.057	-0.010	-0.010	0.000	0.000	0.000	0.000
37	A	37	ILE	0	-0.009	0.011	20.335	0.011	0.011	0.000	0.000	0.000	0.000
38	A	38	ASP	-1	-0.890	-0.952	24.402	-0.125	-0.125	0.000	0.000	0.000	0.000
39	A	39	LEU	0	0.038	0.013	20.071	0.001	0.001	0.000	0.000	0.000	0.000
40	A	40	ASN	0	0.040	0.025	22.862	-0.017	-0.017	0.000	0.000	0.000	0.000
41	A	41	ARG	1	0.936	0.991	23.798	0.079	0.079	0.000	0.000	0.000	0.000
42	A	42	TYR	0	-0.019	-0.024	18.910	0.019	0.019	0.000	0.000	0.000	0.000
43	A	43	LEU	0	0.008	0.019	17.664	-0.017	-0.017	0.000	0.000	0.000	0.000
44	A	44	SER	0	-0.017	0.002	21.023	0.025	0.025	0.000	0.000	0.000	0.000
45	A	45	ASN	0	0.023	-0.025	22.225	-0.033	-0.033	0.000	0.000	0.000	0.000
46	A	46	ASP	-1	-0.807	-0.885	22.089	-0.143	-0.143	0.000	0.000	0.000	0.000
47	A	47	ASN	0	0.028	-0.004	24.103	-0.003	-0.003	0.000	0.000	0.000	0.000
48	A	48	GLY	0	0.013	0.002	26.262	0.000	0.000	0.000	0.000	0.000	0.000
49	A	49	HIS	0	-0.039	-0.009	20.693	-0.025	-0.025	0.000	0.000	0.000	0.000
50	A	50	PHE	0	0.014	0.010	19.080	0.012	0.012	0.000	0.000	0.000	0.000
51	A	51	ARG	1	0.881	0.921	17.183	0.214	0.214	0.000	0.000	0.000	0.000
52	A	52	TRP	0	-0.062	-0.032	13.390	0.063	0.063	0.000	0.000	0.000	0.000
53	A	53	VAL	0	0.024	0.028	17.021	0.019	0.019	0.000	0.000	0.000	0.000
54	A	54	SER	0	0.004	-0.008	19.589	-0.011	-0.011	0.000	0.000	0.000	0.000
55	A	55	THR	0	-0.040	-0.015	21.533	0.008	0.008	0.000	0.000	0.000	0.000
56	A	56	ALA	0	-0.017	-0.001	24.234	0.009	0.009	0.000	0.000	0.000	0.000
57	A	57	THR	0	-0.023	-0.012	26.321	-0.004	-0.004	0.000	0.000	0.000	0.000
58	A	58	VAL	0	-0.015	0.003	26.383	0.008	0.008	0.000	0.000	0.000	0.000
59	A	59	THR	0	0.003	-0.003	29.265	-0.001	-0.001	0.000	0.000	0.000	0.000
60	A	60	VAL	0	-0.022	-0.001	31.376	0.002	0.002	0.000	0.000	0.000	0.000
61	A	61	GLN	0	-0.027	-0.021	30.657	0.008	0.008	0.000	0.000	0.000	0.000
62	A	62	GLN	0	0.028	-0.004	33.628	-0.004	-0.004	0.000	0.000	0.000	0.000
63	A	63	GLY	0	-0.031	-0.020	35.049	0.002	0.002	0.000	0.000	0.000	0.000
64	A	64	ASP	-1	-0.750	-0.816	31.539	-0.010	-0.010	0.000	0.000	0.000	0.000
65	A	65	THR	0	-0.001	-0.006	33.272	-0.003	-0.003	0.000	0.000	0.000	0.000
66	A	66	LEU	0	0.075	0.014	32.305	-0.001	-0.001	0.000	0.000	0.000	0.000
67	A	67	ARG	1	0.824	0.887	30.079	0.049	0.049	0.000	0.000	0.000	0.000
68	A	68	ASP	-1	-0.817	-0.891	28.461	-0.033	-0.033	0.000	0.000	0.000	0.000
69	A	69	ILE	0	-0.032	-0.010	27.543	0.001	0.001	0.000	0.000	0.000	0.000
70	A	70	GLY	0	0.002	-0.002	26.296	-0.002	-0.002	0.000	0.000	0.000	0.000
71	A	71	ARG	1	0.904	0.950	23.948	0.040	0.040	0.000	0.000	0.000	0.000
72	A	72	ARG	1	0.755	0.859	22.649	0.004	0.004	0.000	0.000	0.000	0.000
73	A	73	PHE	0	-0.021	-0.029	21.757	0.010	0.010	0.000	0.000	0.000	0.000
74	A	74	ASP	-1	-0.897	-0.930	18.037	-0.196	-0.196	0.000	0.000	0.000	0.000
75	A	75	CYS	0	-0.070	-0.040	21.273	-0.016	-0.016	0.000	0.000	0.000	0.000
76	A	76	ASP	-1	-0.732	-0.857	24.211	-0.093	-0.093	0.000	0.000	0.000	0.000
77	A	77	PHE	0	-0.005	-0.024	27.122	0.005	0.005	0.000	0.000	0.000	0.000
78	A	78	HIS	1	0.816	0.892	30.319	0.091	0.091	0.000	0.000	0.000	0.000
79	A	79	GLU	-1	-0.809	-0.878	27.815	-0.092	-0.092	0.000	0.000	0.000	0.000
80	A	80	ILE	0	-0.024	-0.006	27.563	0.005	0.005	0.000	0.000	0.000	0.000
81	A	81	ALA	0	0.029	0.024	31.124	0.006	0.006	0.000	0.000	0.000	0.000
82	A	82	ARG	1	0.857	0.919	31.450	0.088	0.088	0.000	0.000	0.000	0.000
83	A	83	ARG	1	0.856	0.935	28.299	0.075	0.075	0.000	0.000	0.000	0.000
84	A	84	ASN	0	-0.042	-0.035	31.881	0.008	0.008	0.000	0.000	0.000	0.000
85	A	85	ASN	0	-0.069	-0.025	35.768	0.005	0.005	0.000	0.000	0.000	0.000
86	A	86	ILE	0	0.005	0.021	35.848	0.004	0.004	0.000	0.000	0.000	0.000
87	A	87	GLN	0	-0.037	-0.028	38.672	-0.006	-0.006	0.000	0.000	0.000	0.000
88	A	88	ASN	0	-0.014	-0.028	35.926	-0.001	-0.001	0.000	0.000	0.000	0.000
89	A	89	GLU	-1	-0.837	-0.917	36.597	-0.050	-0.050	0.000	0.000	0.000	0.000
90	A	90	ASP	-1	-0.845	-0.894	38.995	-0.032	-0.032	0.000	0.000	0.000	0.000
91	A	91	LEU	0	-0.053	-0.029	38.221	-0.001	-0.001	0.000	0.000	0.000	0.000
92	A	92	ILE	0	-0.015	0.001	33.856	-0.001	-0.001	0.000	0.000	0.000	0.000
93	A	93	TYR	0	0.006	-0.009	38.199	0.002	0.002	0.000	0.000	0.000	0.000
94	A	94	PRO	0	0.011	0.003	36.747	0.000	0.000	0.000	0.000	0.000	0.000
95	A	95	GLY	0	-0.017	-0.006	36.309	0.001	0.001	0.000	0.000	0.000	0.000
96	A	96	GLN	0	0.018	0.014	36.379	0.001	0.001	0.000	0.000	0.000	0.000
97	A	97	VAL	0	-0.005	-0.002	33.010	0.001	0.001	0.000	0.000	0.000	0.000
98	A	98	LEU	0	-0.016	-0.010	31.495	-0.003	-0.003	0.000	0.000	0.000	0.000
99	A	99	GLN	0	-0.024	-0.014	30.311	-0.001	-0.001	0.000	0.000	0.000	0.000
100	A	100	VAL	0	0.018	0.008	25.133	-0.004	-0.004	0.000	0.000	0.000	0.000
101	A	101	GLY	0	0.067	0.017	23.913	0.003	0.003	0.000	0.000	0.000	0.000
102	A	102	GLY	0	-0.063	-0.028	23.121	0.009	0.009	0.000	0.000	0.000	0.000
103	A	103	ASN	0	-0.028	-0.051	24.506	0.002	0.002	0.000	0.000	0.000	0.000
104	A	104	PHE	0	0.043	0.019	24.147	0.001	0.001	0.000	0.000	0.000	0.000
105	A	105	TRP	0	-0.033	-0.019	26.315	-0.002	-0.002	0.000	0.000	0.000	0.000
106	A	106	ASP	-1	-0.875	-0.932	28.927	-0.086	-0.086	0.000	0.000	0.000	0.000
107	A	107	SER	0	-0.093	-0.029	29.447	0.002	0.002	0.000	0.000	0.000	0.000
108	A	108	ALA	0	0.009	0.003	27.873	-0.008	-0.008	0.000	0.000	0.000	0.000
109	A	109	ARG	1	0.852	0.912	29.783	0.132	0.132	0.000	0.000	0.000	0.000
110	A	110	ASP	-1	-0.893	-0.941	29.743	-0.144	-0.144	0.000	0.000	0.000	0.000
111	A	111	VAL	0	-0.047	-0.022	25.857	-0.014	-0.014	0.000	0.000	0.000	0.000
112	A	112	ARG	1	0.889	0.933	26.033	0.200	0.200	0.000	0.000	0.000	0.000
113	A	113	LEU	0	0.004	0.014	21.477	-0.020	-0.020	0.000	0.000	0.000	0.000
114	A	114	VAL	0	0.002	0.002	21.168	0.020	0.020	0.000	0.000	0.000	0.000
115	A	115	ASP	-1	-0.904	-0.969	19.018	-0.397	-0.397	0.000	0.000	0.000	0.000
116	A	116	GLY	0	-0.006	-0.016	19.508	-0.032	-0.032	0.000	0.000	0.000	0.000
117	A	117	GLY	0	0.017	0.008	21.012	0.003	0.003	0.000	0.000	0.000	0.000
118	A	118	LYS	1	0.945	0.980	14.910	0.491	0.491	0.000	0.000	0.000	0.000
119	A	119	VAL	0	-0.054	-0.017	16.501	-0.062	-0.062	0.000	0.000	0.000	0.000
120	A	120	LEU	0	-0.001	0.016	18.498	0.046	0.046	0.000	0.000	0.000	0.000
121	A	121	GLU	-1	-0.808	-0.917	20.547	-0.260	-0.260	0.000	0.000	0.000	0.000
122	A	122	ALA	0	0.005	0.005	23.190	0.017	0.017	0.000	0.000	0.000	0.000
123	A	123	GLU	-1	-0.835	-0.887	25.766	-0.154	-0.154	0.000	0.000	0.000	0.000
124	A	124	LEU	0	-0.026	-0.018	23.454	0.010	0.010	0.000	0.000	0.000	0.000
125	A	125	ARG	1	0.949	0.978	27.994	0.097	0.097	0.000	0.000	0.000	0.000
126	A	126	TYR	0	0.031	0.017	28.779	-0.005	-0.005	0.000	0.000	0.000	0.000
127	A	127	SER	0	-0.038	-0.037	30.567	0.008	0.008	0.000	0.000	0.000	0.000
128	A	128	GLY	0	-0.033	-0.010	33.251	0.006	0.006	0.000	0.000	0.000	0.000
129	A	129	GLY	0	-0.015	0.006	33.933	0.002	0.002	0.000	0.000	0.000	0.000
130	A	130	TRP	0	-0.023	-0.010	30.751	0.000	0.000	0.000	0.000	0.000	0.000
131	A	131	ASN	0	-0.001	-0.009	24.513	0.005	0.005	0.000	0.000	0.000	0.000
132	A	132	ARG	1	0.893	0.959	21.854	0.261	0.261	0.000	0.000	0.000	0.000
133	A	133	SER	0	0.026	0.019	20.979	-0.017	-0.017	0.000	0.000	0.000	0.000
134	A	134	ARG	1	0.897	0.932	16.328	0.482	0.482	0.000	0.000	0.000	0.000
135	A	135	ILE	0	0.015	0.010	15.135	-0.024	-0.024	0.000	0.000	0.000	0.000
136	A	136	TYR	0	0.056	0.030	12.343	0.051	0.051	0.000	0.000	0.000	0.000
137	A	137	LEU	0	0.070	0.028	13.401	-0.043	-0.043	0.000	0.000	0.000	0.000
138	A	138	ASP	-1	-0.792	-0.866	11.485	-0.588	-0.588	0.000	0.000	0.000	0.000
139	A	139	GLU	-1	-0.912	-0.938	9.300	-1.006	-1.006	0.000	0.000	0.000	0.000
140	A	140	HIS	1	0.822	0.881	10.279	0.431	0.431	0.000	0.000	0.000	0.000
141	A	141	ILE	0	0.017	0.042	13.058	0.094	0.094	0.000	0.000	0.000	0.000
142	A	142	GLY	0	0.061	0.023	14.594	-0.075	-0.075	0.000	0.000	0.000	0.000
143	A	143	ASN	0	-0.041	-0.043	15.621	0.044	0.044	0.000	0.000	0.000	0.000
144	A	144	ARG	1	0.929	0.972	17.464	0.018	0.018	0.000	0.000	0.000	0.000
145	A	145	ASN	0	-0.015	-0.021	19.378	0.002	0.002	0.000	0.000	0.000	0.000
146	A	146	GLY	0	0.054	0.029	21.671	0.010	0.010	0.000	0.000	0.000	0.000
147	A	147	GLU	-1	-0.920	-0.956	22.444	-0.045	-0.045	0.000	0.000	0.000	0.000
148	A	148	LEU	0	-0.029	-0.024	20.044	-0.006	-0.006	0.000	0.000	0.000	0.000
149	A	149	ILE	0	-0.032	-0.013	16.924	0.024	0.024	0.000	0.000	0.000	0.000
150	A	150	HIS	0	0.053	0.020	15.945	-0.067	-0.067	0.000	0.000	0.000	0.000
151	A	151	CYS	0	0.006	0.022	11.801	-0.010	-0.010	0.000	0.000	0.000	0.000

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