FMO DATABASE

FMODB ID: YZR12

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1393812.100528
FMO2-HF: Nuclear repulsion	1333767.320066
FMO2-HF: Total energy	-60044.780462
FMO2-MP2: Total energy	-60220.040435

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.
-1.203	0.411	-0.011	-0.975	-0.628	0.005

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 : 0.027 / q_NPA : 0.013

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	-0.012	-0.008	3.807	-1.618	-0.004	-0.011	-0.975	-0.628	0.005
4	A	4	ALA	0	-0.002	-0.005	6.721	0.297	0.297	0.000	0.000	0.000	0.000
5	A	5	GLY	0	-0.007	0.000	8.525	0.329	0.329	0.000	0.000	0.000	0.000
6	A	6	ASN	0	-0.069	-0.046	9.941	0.101	0.101	0.000	0.000	0.000	0.000
7	A	7	PHE	0	0.051	0.022	11.988	0.150	0.150	0.000	0.000	0.000	0.000
8	A	8	SER	0	-0.044	-0.043	14.763	0.105	0.105	0.000	0.000	0.000	0.000
9	A	9	GLY	0	0.007	0.014	14.432	0.067	0.067	0.000	0.000	0.000	0.000
10	A	10	SER	0	-0.068	-0.024	15.415	0.086	0.086	0.000	0.000	0.000	0.000
11	A	11	SER	0	-0.010	-0.021	18.214	0.056	0.056	0.000	0.000	0.000	0.000
12	A	12	ARG	1	0.842	0.925	20.749	0.208	0.208	0.000	0.000	0.000	0.000
13	A	13	ASP	-1	-0.849	-0.936	23.513	-0.232	-0.232	0.000	0.000	0.000	0.000
14	A	14	ILE	0	-0.037	-0.001	19.884	0.006	0.006	0.000	0.000	0.000	0.000
15	A	15	CYS	0	-0.039	-0.019	24.233	0.016	0.016	0.000	0.000	0.000	0.000
16	A	16	LEU	0	0.018	-0.002	25.097	-0.021	-0.021	0.000	0.000	0.000	0.000
17	A	17	ASP	-1	-0.859	-0.900	27.606	-0.181	-0.181	0.000	0.000	0.000	0.000
18	A	18	GLY	0	0.031	0.019	30.487	0.001	0.001	0.000	0.000	0.000	0.000
19	A	19	ALA	0	0.023	0.009	26.724	-0.012	-0.012	0.000	0.000	0.000	0.000
20	A	20	ARG	1	0.910	0.954	25.929	0.192	0.192	0.000	0.000	0.000	0.000
21	A	21	LEU	0	0.010	0.016	20.288	0.010	0.010	0.000	0.000	0.000	0.000
22	A	22	ARG	1	0.845	0.887	24.848	0.221	0.221	0.000	0.000	0.000	0.000
23	A	23	ALA	0	0.018	0.009	23.029	-0.016	-0.016	0.000	0.000	0.000	0.000
24	A	24	GLU	-1	-0.812	-0.873	24.935	-0.196	-0.196	0.000	0.000	0.000	0.000
25	A	25	CYS	0	-0.063	-0.034	21.144	-0.022	-0.022	0.000	0.000	0.000	0.000
26	A	26	ARG	1	0.925	0.966	20.713	0.244	0.244	0.000	0.000	0.000	0.000
27	A	27	ARG	1	0.858	0.917	21.856	0.156	0.156	0.000	0.000	0.000	0.000
28	A	28	GLY	0	0.000	-0.014	22.549	0.000	0.000	0.000	0.000	0.000	0.000
29	A	29	ASP	-1	-0.845	-0.899	23.440	-0.153	-0.153	0.000	0.000	0.000	0.000
30	A	30	GLY	0	-0.041	-0.018	25.222	0.013	0.013	0.000	0.000	0.000	0.000
31	A	31	GLY	0	0.011	0.014	26.229	0.002	0.002	0.000	0.000	0.000	0.000
32	A	32	TYR	0	-0.002	-0.027	23.734	-0.009	-0.009	0.000	0.000	0.000	0.000
33	A	33	SER	0	-0.022	-0.008	26.340	0.020	0.020	0.000	0.000	0.000	0.000
34	A	34	THR	0	0.027	0.015	26.805	-0.013	-0.013	0.000	0.000	0.000	0.000
35	A	35	SER	0	-0.010	0.007	24.539	0.002	0.002	0.000	0.000	0.000	0.000
36	A	36	VAL	0	-0.039	-0.040	26.104	-0.001	-0.001	0.000	0.000	0.000	0.000
37	A	37	ILE	0	-0.004	0.015	20.262	0.004	0.004	0.000	0.000	0.000	0.000
38	A	38	ASP	-1	-0.877	-0.946	24.429	-0.273	-0.273	0.000	0.000	0.000	0.000
39	A	39	LEU	0	0.037	0.013	20.444	-0.014	-0.014	0.000	0.000	0.000	0.000
40	A	40	ASN	0	0.025	0.013	23.181	-0.021	-0.021	0.000	0.000	0.000	0.000
41	A	41	ARG	1	0.951	1.001	23.889	0.287	0.287	0.000	0.000	0.000	0.000
42	A	42	TYR	0	-0.045	-0.035	19.073	0.010	0.010	0.000	0.000	0.000	0.000
43	A	43	LEU	0	0.013	0.022	17.879	-0.033	-0.033	0.000	0.000	0.000	0.000
44	A	44	SER	0	-0.001	0.006	21.323	0.028	0.028	0.000	0.000	0.000	0.000
45	A	45	ASN	0	0.023	-0.024	22.455	-0.034	-0.034	0.000	0.000	0.000	0.000
46	A	46	ASP	-1	-0.800	-0.887	22.236	-0.223	-0.223	0.000	0.000	0.000	0.000
47	A	47	ASN	0	0.012	-0.013	24.277	0.009	0.009	0.000	0.000	0.000	0.000
48	A	48	GLY	0	0.028	0.014	26.377	0.010	0.010	0.000	0.000	0.000	0.000
49	A	49	HIS	0	-0.067	-0.024	20.849	-0.008	-0.008	0.000	0.000	0.000	0.000
50	A	50	PHE	0	0.027	0.014	19.311	0.006	0.006	0.000	0.000	0.000	0.000
51	A	51	ARG	1	0.848	0.911	17.619	0.311	0.311	0.000	0.000	0.000	0.000
52	A	52	TRP	0	-0.046	-0.027	13.540	0.046	0.046	0.000	0.000	0.000	0.000
53	A	53	VAL	0	0.020	0.023	17.314	0.000	0.000	0.000	0.000	0.000	0.000
54	A	54	SER	0	-0.005	-0.011	19.627	0.005	0.005	0.000	0.000	0.000	0.000
55	A	55	THR	0	-0.041	-0.018	21.606	0.016	0.016	0.000	0.000	0.000	0.000
56	A	56	ALA	0	-0.010	0.002	24.137	-0.004	-0.004	0.000	0.000	0.000	0.000
57	A	57	THR	0	-0.017	-0.004	26.256	0.008	0.008	0.000	0.000	0.000	0.000
58	A	58	VAL	0	-0.016	-0.004	26.287	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	59	THR	0	0.008	0.003	29.188	0.004	0.004	0.000	0.000	0.000	0.000
60	A	60	VAL	0	-0.024	0.003	31.292	0.000	0.000	0.000	0.000	0.000	0.000
61	A	61	GLN	0	-0.028	-0.028	30.461	0.013	0.013	0.000	0.000	0.000	0.000
62	A	62	GLN	0	0.036	-0.001	33.575	-0.003	-0.003	0.000	0.000	0.000	0.000
63	A	63	GLY	0	-0.024	-0.014	35.063	0.002	0.002	0.000	0.000	0.000	0.000
64	A	64	ASP	-1	-0.763	-0.821	31.530	-0.085	-0.085	0.000	0.000	0.000	0.000
65	A	65	THR	0	-0.004	-0.033	33.383	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	66	LEU	0	0.076	0.015	32.503	-0.006	-0.006	0.000	0.000	0.000	0.000
67	A	67	ARG	1	0.838	0.873	30.245	0.076	0.076	0.000	0.000	0.000	0.000
68	A	68	ASP	-1	-0.790	-0.836	28.623	-0.084	-0.084	0.000	0.000	0.000	0.000
69	A	69	ILE	0	-0.017	0.001	27.734	-0.007	-0.007	0.000	0.000	0.000	0.000
70	A	70	GLY	0	0.001	-0.001	26.523	-0.014	-0.014	0.000	0.000	0.000	0.000
71	A	71	ARG	1	0.848	0.900	24.007	0.074	0.074	0.000	0.000	0.000	0.000
72	A	72	ARG	1	0.753	0.854	22.822	0.089	0.089	0.000	0.000	0.000	0.000
73	A	73	PHE	0	-0.015	-0.026	21.930	-0.005	-0.005	0.000	0.000	0.000	0.000
74	A	74	ASP	-1	-0.892	-0.932	17.976	-0.368	-0.368	0.000	0.000	0.000	0.000
75	A	75	CYS	0	-0.069	-0.041	21.477	-0.027	-0.027	0.000	0.000	0.000	0.000
76	A	76	ASP	-1	-0.745	-0.859	24.428	-0.140	-0.140	0.000	0.000	0.000	0.000
77	A	77	PHE	0	-0.010	-0.020	27.307	0.002	0.002	0.000	0.000	0.000	0.000
78	A	78	HIS	1	0.855	0.908	30.512	0.138	0.138	0.000	0.000	0.000	0.000
79	A	79	GLU	-1	-0.806	-0.865	28.116	-0.176	-0.176	0.000	0.000	0.000	0.000
80	A	80	ILE	0	-0.006	-0.001	27.638	0.003	0.003	0.000	0.000	0.000	0.000
81	A	81	ALA	0	0.031	0.022	31.377	0.005	0.005	0.000	0.000	0.000	0.000
82	A	82	ARG	1	0.757	0.844	31.456	0.169	0.169	0.000	0.000	0.000	0.000
83	A	83	ARG	1	0.829	0.925	28.403	0.195	0.195	0.000	0.000	0.000	0.000
84	A	84	ASN	0	-0.060	-0.047	32.085	0.003	0.003	0.000	0.000	0.000	0.000
85	A	85	ASN	0	-0.069	-0.026	36.024	0.005	0.005	0.000	0.000	0.000	0.000
86	A	86	ILE	0	0.008	0.022	36.173	0.007	0.007	0.000	0.000	0.000	0.000
87	A	87	GLN	0	-0.080	-0.055	38.910	-0.004	-0.004	0.000	0.000	0.000	0.000
88	A	88	ASN	0	-0.025	-0.033	36.003	-0.007	-0.007	0.000	0.000	0.000	0.000
89	A	89	GLU	-1	-0.828	-0.891	36.775	-0.084	-0.084	0.000	0.000	0.000	0.000
90	A	90	ASP	-1	-0.801	-0.871	39.194	-0.072	-0.072	0.000	0.000	0.000	0.000
91	A	91	LEU	0	-0.040	-0.020	38.423	-0.003	-0.003	0.000	0.000	0.000	0.000
92	A	92	ILE	0	-0.029	-0.008	33.958	-0.004	-0.004	0.000	0.000	0.000	0.000
93	A	93	TYR	0	0.013	-0.006	38.399	0.006	0.006	0.000	0.000	0.000	0.000
94	A	94	PRO	0	0.007	0.003	36.723	-0.005	-0.005	0.000	0.000	0.000	0.000
95	A	95	GLY	0	-0.014	-0.008	36.220	0.003	0.003	0.000	0.000	0.000	0.000
96	A	96	GLN	0	0.020	0.016	36.555	0.001	0.001	0.000	0.000	0.000	0.000
97	A	97	VAL	0	-0.007	-0.003	32.902	-0.004	-0.004	0.000	0.000	0.000	0.000
98	A	98	LEU	0	-0.015	-0.007	31.598	0.002	0.002	0.000	0.000	0.000	0.000
99	A	99	GLN	0	0.006	0.002	30.375	-0.017	-0.017	0.000	0.000	0.000	0.000
100	A	100	VAL	0	0.009	0.003	25.368	0.004	0.004	0.000	0.000	0.000	0.000
101	A	101	GLY	0	0.075	0.026	24.163	-0.008	-0.008	0.000	0.000	0.000	0.000
102	A	102	GLY	0	-0.060	-0.024	23.394	0.020	0.020	0.000	0.000	0.000	0.000
103	A	103	ASN	0	-0.050	-0.071	24.792	0.007	0.007	0.000	0.000	0.000	0.000
104	A	104	PHE	0	0.020	0.010	24.410	0.013	0.013	0.000	0.000	0.000	0.000
105	A	105	TRP	0	-0.013	-0.006	26.575	0.008	0.008	0.000	0.000	0.000	0.000
106	A	106	ASP	-1	-0.811	-0.877	29.194	-0.172	-0.172	0.000	0.000	0.000	0.000
107	A	107	SER	0	-0.069	-0.024	29.747	0.011	0.011	0.000	0.000	0.000	0.000
108	A	108	ALA	0	0.003	0.008	28.071	-0.004	-0.004	0.000	0.000	0.000	0.000
109	A	109	ARG	1	0.839	0.905	29.966	0.169	0.169	0.000	0.000	0.000	0.000
110	A	110	ASP	-1	-0.902	-0.954	29.901	-0.185	-0.185	0.000	0.000	0.000	0.000
111	A	111	VAL	0	-0.036	-0.010	26.121	-0.015	-0.015	0.000	0.000	0.000	0.000
112	A	112	ARG	1	0.862	0.912	26.195	0.248	0.248	0.000	0.000	0.000	0.000
113	A	113	LEU	0	0.018	0.017	21.797	-0.026	-0.026	0.000	0.000	0.000	0.000
114	A	114	VAL	0	-0.001	-0.002	21.235	0.033	0.033	0.000	0.000	0.000	0.000
115	A	115	ASP	-1	-0.871	-0.955	19.051	-0.456	-0.456	0.000	0.000	0.000	0.000
116	A	116	GLY	0	-0.001	-0.003	19.521	-0.049	-0.049	0.000	0.000	0.000	0.000
117	A	117	GLY	0	0.018	0.009	21.012	-0.009	-0.009	0.000	0.000	0.000	0.000
118	A	118	LYS	1	0.912	0.951	14.883	0.562	0.562	0.000	0.000	0.000	0.000
119	A	119	VAL	0	-0.054	-0.016	16.592	-0.085	-0.085	0.000	0.000	0.000	0.000
120	A	120	LEU	0	-0.008	0.015	18.644	0.057	0.057	0.000	0.000	0.000	0.000
121	A	121	GLU	-1	-0.792	-0.882	20.699	-0.296	-0.296	0.000	0.000	0.000	0.000
122	A	122	ALA	0	0.018	0.009	23.324	0.014	0.014	0.000	0.000	0.000	0.000
123	A	123	GLU	-1	-0.836	-0.886	25.881	-0.178	-0.178	0.000	0.000	0.000	0.000
124	A	124	LEU	0	-0.032	-0.015	23.588	0.004	0.004	0.000	0.000	0.000	0.000
125	A	125	ARG	1	0.944	0.973	28.141	0.151	0.151	0.000	0.000	0.000	0.000
126	A	126	TYR	0	0.025	0.016	28.938	-0.010	-0.010	0.000	0.000	0.000	0.000
127	A	127	SER	0	-0.024	-0.027	30.686	0.010	0.010	0.000	0.000	0.000	0.000
128	A	128	GLY	0	-0.027	-0.009	33.337	0.007	0.007	0.000	0.000	0.000	0.000
129	A	129	GLY	0	-0.017	0.001	34.025	0.006	0.006	0.000	0.000	0.000	0.000
130	A	130	TRP	0	-0.011	-0.007	31.066	-0.006	-0.006	0.000	0.000	0.000	0.000
131	A	131	ASN	0	0.008	0.000	24.622	0.018	0.018	0.000	0.000	0.000	0.000
132	A	132	ARG	1	0.887	0.941	22.561	0.264	0.264	0.000	0.000	0.000	0.000
133	A	133	SER	0	0.007	0.011	21.587	-0.021	-0.021	0.000	0.000	0.000	0.000
134	A	134	ARG	1	0.915	0.935	16.637	0.496	0.496	0.000	0.000	0.000	0.000
135	A	135	ILE	0	0.010	0.013	15.309	-0.021	-0.021	0.000	0.000	0.000	0.000
136	A	136	TYR	0	0.051	0.034	12.524	0.093	0.093	0.000	0.000	0.000	0.000
137	A	137	LEU	0	0.058	0.025	13.635	-0.105	-0.105	0.000	0.000	0.000	0.000
138	A	138	ASP	-1	-0.799	-0.881	11.561	-0.956	-0.956	0.000	0.000	0.000	0.000
139	A	139	GLU	-1	-0.854	-0.911	9.519	-1.483	-1.483	0.000	0.000	0.000	0.000
140	A	140	HIS	1	0.846	0.904	10.423	0.914	0.914	0.000	0.000	0.000	0.000
141	A	141	ILE	0	0.008	0.037	13.158	0.117	0.117	0.000	0.000	0.000	0.000
142	A	142	GLY	0	0.063	0.027	14.601	-0.115	-0.115	0.000	0.000	0.000	0.000
143	A	143	ASN	0	-0.042	-0.038	15.572	0.108	0.108	0.000	0.000	0.000	0.000
144	A	144	ARG	1	0.857	0.924	17.456	0.313	0.313	0.000	0.000	0.000	0.000
145	A	145	ASN	0	-0.006	-0.019	19.370	0.037	0.037	0.000	0.000	0.000	0.000
146	A	146	GLY	0	0.057	0.033	21.661	0.031	0.031	0.000	0.000	0.000	0.000
147	A	147	GLU	-1	-0.891	-0.932	22.417	-0.272	-0.272	0.000	0.000	0.000	0.000
148	A	148	LEU	0	0.001	-0.005	20.017	-0.041	-0.041	0.000	0.000	0.000	0.000
149	A	149	ILE	0	-0.034	-0.014	16.815	0.039	0.039	0.000	0.000	0.000	0.000
150	A	150	HIS	0	0.050	0.018	16.366	-0.090	-0.090	0.000	0.000	0.000	0.000
151	A	151	CYS	0	-0.008	0.008	11.476	0.028	0.028	0.000	0.000	0.000	0.000

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