FMO DATABASE

FMODB ID: K3YV3

Calculation Name: 5C9B-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5C9B

Chain ID: A

ChEMBL ID:

UniProt ID: Q92FY8

Base Structure: X-ray

Registration Date: 2023-06-20

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	131
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1080481.927893
FMO2-HF: Nuclear repulsion	1029787.280074
FMO2-HF: Total energy	-50694.647819
FMO2-MP2: Total energy	-50844.130992

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:104:MET)

Summations of interaction energy for fragment #1(A:104:MET)

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.
-8.516	-4.58	2.234	-2.101	-4.068	0.011

Interaction energy analysis for fragmet #1(A:104:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.032 / q_NPA : 0.016

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	106	LYS	1	0.945	0.973	2.424	-8.286	-4.534	2.232	-2.051	-3.932	0.011
4	A	107	TRP	0	0.045	0.015	4.237	-0.668	-0.484	0.002	-0.050	-0.136	0.000
5	A	108	SER	0	-0.042	-0.027	7.942	0.558	0.558	0.000	0.000	0.000	0.000
6	A	109	THR	0	-0.045	-0.015	10.583	-0.153	-0.153	0.000	0.000	0.000	0.000
7	A	110	GLU	-1	-0.867	-0.900	14.376	0.284	0.284	0.000	0.000	0.000	0.000
8	A	111	VAL	0	0.006	-0.025	17.000	-0.053	-0.053	0.000	0.000	0.000	0.000
9	A	112	GLY	0	0.067	0.032	19.406	0.018	0.018	0.000	0.000	0.000	0.000
10	A	113	GLU	-1	-0.873	-0.947	22.977	0.121	0.121	0.000	0.000	0.000	0.000
11	A	114	ILE	0	-0.031	-0.001	26.202	0.003	0.003	0.000	0.000	0.000	0.000
12	A	115	ILE	0	0.012	0.006	29.722	-0.007	-0.007	0.000	0.000	0.000	0.000
13	A	116	ILE	0	-0.023	-0.016	32.575	0.000	0.000	0.000	0.000	0.000	0.000
14	A	117	ALA	0	0.032	0.019	35.998	-0.003	-0.003	0.000	0.000	0.000	0.000
15	A	118	ARG	1	0.797	0.890	39.266	-0.043	-0.043	0.000	0.000	0.000	0.000
16	A	119	ASN	0	-0.005	-0.005	42.281	0.003	0.003	0.000	0.000	0.000	0.000
17	A	120	ARG	1	0.964	0.967	45.048	-0.045	-0.045	0.000	0.000	0.000	0.000
18	A	121	ASP	-1	-0.756	-0.840	47.700	0.034	0.034	0.000	0.000	0.000	0.000
19	A	122	GLY	0	0.020	0.004	47.367	-0.002	-0.002	0.000	0.000	0.000	0.000
20	A	123	HIS	1	0.887	0.947	45.009	-0.029	-0.029	0.000	0.000	0.000	0.000
21	A	124	PHE	0	0.032	0.017	39.416	0.002	0.002	0.000	0.000	0.000	0.000
22	A	125	TYR	0	-0.040	-0.048	40.920	-0.003	-0.003	0.000	0.000	0.000	0.000
23	A	126	ILE	0	-0.004	0.008	35.065	0.005	0.005	0.000	0.000	0.000	0.000
24	A	127	ASN	0	-0.034	-0.010	37.215	-0.008	-0.008	0.000	0.000	0.000	0.000
25	A	128	ALA	0	0.040	0.017	35.018	0.006	0.006	0.000	0.000	0.000	0.000
26	A	129	PHE	0	0.037	0.016	33.493	-0.002	-0.002	0.000	0.000	0.000	0.000
27	A	130	VAL	0	0.037	0.011	34.553	0.000	0.000	0.000	0.000	0.000	0.000
28	A	131	ASN	0	0.049	0.018	35.515	-0.001	-0.001	0.000	0.000	0.000	0.000
29	A	132	ASN	0	-0.027	-0.018	33.911	0.004	0.004	0.000	0.000	0.000	0.000
30	A	133	VAL	0	0.052	0.036	36.386	0.002	0.002	0.000	0.000	0.000	0.000
31	A	134	LYS	1	0.795	0.923	36.288	-0.061	-0.061	0.000	0.000	0.000	0.000
32	A	135	ILE	0	0.041	0.014	39.268	-0.003	-0.003	0.000	0.000	0.000	0.000
33	A	136	LYS	1	0.909	0.956	39.709	-0.043	-0.043	0.000	0.000	0.000	0.000
34	A	137	PHE	0	0.036	0.014	38.584	-0.003	-0.003	0.000	0.000	0.000	0.000
35	A	138	MET	0	-0.002	0.002	41.490	0.004	0.004	0.000	0.000	0.000	0.000
36	A	139	VAL	0	-0.046	-0.033	38.430	-0.002	-0.002	0.000	0.000	0.000	0.000
37	A	140	ASP	-1	-0.845	-0.937	41.148	0.017	0.017	0.000	0.000	0.000	0.000
38	A	141	THR	0	-0.014	-0.025	39.845	0.000	0.000	0.000	0.000	0.000	0.000
39	A	142	GLY	0	0.016	0.012	41.083	-0.002	-0.002	0.000	0.000	0.000	0.000
40	A	143	ALA	0	0.008	0.031	42.612	-0.003	-0.003	0.000	0.000	0.000	0.000
41	A	144	SER	0	0.049	0.023	40.283	0.001	0.001	0.000	0.000	0.000	0.000
42	A	145	ASP	-1	-0.856	-0.905	39.413	0.000	0.000	0.000	0.000	0.000	0.000
43	A	146	ILE	0	-0.028	-0.012	37.142	0.002	0.002	0.000	0.000	0.000	0.000
44	A	147	ALA	0	0.019	0.026	41.215	-0.003	-0.003	0.000	0.000	0.000	0.000
45	A	148	LEU	0	0.014	-0.004	41.732	0.003	0.003	0.000	0.000	0.000	0.000
46	A	149	THR	0	0.051	0.026	45.540	-0.003	-0.003	0.000	0.000	0.000	0.000
47	A	150	LYS	1	0.987	0.987	48.164	-0.011	-0.011	0.000	0.000	0.000	0.000
48	A	151	GLU	-1	-0.792	-0.889	49.685	0.023	0.023	0.000	0.000	0.000	0.000
49	A	152	ASP	-1	-0.785	-0.872	44.649	0.026	0.026	0.000	0.000	0.000	0.000
50	A	153	ALA	0	0.010	-0.010	45.513	0.000	0.000	0.000	0.000	0.000	0.000
51	A	154	GLN	0	-0.030	-0.026	46.632	-0.001	-0.001	0.000	0.000	0.000	0.000
52	A	155	LYS	1	0.807	0.901	45.045	-0.028	-0.028	0.000	0.000	0.000	0.000
53	A	156	LEU	0	-0.091	-0.043	40.412	0.001	0.001	0.000	0.000	0.000	0.000
54	A	157	GLY	0	-0.009	0.011	43.603	-0.002	-0.002	0.000	0.000	0.000	0.000
55	A	158	PHE	0	-0.038	-0.015	41.634	-0.003	-0.003	0.000	0.000	0.000	0.000
56	A	159	ASP	-1	-0.805	-0.905	47.174	0.002	0.002	0.000	0.000	0.000	0.000
57	A	160	LEU	0	0.024	0.000	50.165	-0.002	-0.002	0.000	0.000	0.000	0.000
58	A	161	THR	0	-0.049	-0.013	52.398	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	162	LYS	1	0.922	0.958	52.353	0.003	0.003	0.000	0.000	0.000	0.000
60	A	163	LEU	0	-0.043	0.006	47.772	-0.002	-0.002	0.000	0.000	0.000	0.000
61	A	164	LYS	1	0.944	0.960	50.038	0.011	0.011	0.000	0.000	0.000	0.000
62	A	165	TYR	0	0.019	-0.006	50.378	0.000	0.000	0.000	0.000	0.000	0.000
63	A	166	THR	0	-0.006	-0.012	49.017	0.000	0.000	0.000	0.000	0.000	0.000
64	A	167	ARG	1	0.839	0.899	43.573	0.004	0.004	0.000	0.000	0.000	0.000
65	A	168	THR	0	-0.084	-0.066	50.580	0.001	0.001	0.000	0.000	0.000	0.000
66	A	169	TYR	0	-0.008	-0.006	47.222	-0.001	-0.001	0.000	0.000	0.000	0.000
67	A	170	LEU	0	0.034	0.056	53.365	0.000	0.000	0.000	0.000	0.000	0.000
68	A	171	THR	0	0.014	-0.008	53.568	0.001	0.001	0.000	0.000	0.000	0.000
69	A	172	ALA	0	0.000	0.000	55.261	-0.001	-0.001	0.000	0.000	0.000	0.000
70	A	173	ASN	0	-0.029	-0.015	57.634	0.000	0.000	0.000	0.000	0.000	0.000
71	A	174	GLY	0	0.036	0.036	58.961	-0.001	-0.001	0.000	0.000	0.000	0.000
72	A	175	GLU	-1	-0.888	-0.972	57.137	-0.005	-0.005	0.000	0.000	0.000	0.000
73	A	176	ASN	0	0.020	0.024	53.044	0.000	0.000	0.000	0.000	0.000	0.000
74	A	177	LYS	1	0.899	0.931	53.910	0.007	0.007	0.000	0.000	0.000	0.000
75	A	178	ALA	0	0.005	0.013	49.776	0.001	0.001	0.000	0.000	0.000	0.000
76	A	179	ALA	0	0.009	-0.005	49.255	-0.002	-0.002	0.000	0.000	0.000	0.000
77	A	180	PRO	0	-0.074	-0.021	44.578	0.002	0.002	0.000	0.000	0.000	0.000
78	A	181	ILE	0	0.017	0.021	42.462	-0.001	-0.001	0.000	0.000	0.000	0.000
79	A	182	THR	0	-0.058	-0.036	36.943	-0.002	-0.002	0.000	0.000	0.000	0.000
80	A	183	LEU	0	0.014	0.015	36.899	0.001	0.001	0.000	0.000	0.000	0.000
81	A	184	ASN	0	0.008	-0.002	34.321	-0.004	-0.004	0.000	0.000	0.000	0.000
82	A	185	SER	0	0.006	-0.003	31.492	-0.003	-0.003	0.000	0.000	0.000	0.000
83	A	186	VAL	0	0.029	0.019	31.909	0.001	0.001	0.000	0.000	0.000	0.000
84	A	187	VAL	0	-0.001	0.005	28.890	0.001	0.001	0.000	0.000	0.000	0.000
85	A	188	ILE	0	0.018	0.006	30.158	0.000	0.000	0.000	0.000	0.000	0.000
86	A	189	GLY	0	0.038	0.022	27.522	-0.001	-0.001	0.000	0.000	0.000	0.000
87	A	190	LYS	1	0.880	0.945	22.581	-0.051	-0.051	0.000	0.000	0.000	0.000
88	A	191	GLU	-1	-0.840	-0.918	25.790	0.028	0.028	0.000	0.000	0.000	0.000
89	A	192	PHE	0	-0.072	-0.030	26.633	-0.008	-0.008	0.000	0.000	0.000	0.000
90	A	193	LYS	1	0.904	0.923	26.976	-0.017	-0.017	0.000	0.000	0.000	0.000
91	A	194	ASN	0	-0.034	-0.016	30.407	-0.001	-0.001	0.000	0.000	0.000	0.000
92	A	195	ILE	0	-0.028	-0.003	31.830	-0.004	-0.004	0.000	0.000	0.000	0.000
93	A	196	LYS	1	0.972	0.987	35.125	0.024	0.024	0.000	0.000	0.000	0.000
94	A	197	GLY	0	0.079	0.026	38.408	0.004	0.004	0.000	0.000	0.000	0.000
95	A	198	HIS	0	-0.051	-0.023	41.568	-0.003	-0.003	0.000	0.000	0.000	0.000
96	A	199	VAL	0	-0.009	0.005	45.271	0.003	0.003	0.000	0.000	0.000	0.000
97	A	200	GLY	0	0.022	0.010	47.926	-0.002	-0.002	0.000	0.000	0.000	0.000
98	A	201	LEU	0	-0.010	-0.012	49.947	-0.001	-0.001	0.000	0.000	0.000	0.000
99	A	202	GLY	0	-0.045	-0.041	52.902	0.001	0.001	0.000	0.000	0.000	0.000
100	A	203	ASP	-1	-0.885	-0.945	55.491	0.010	0.010	0.000	0.000	0.000	0.000
101	A	204	LEU	0	-0.090	-0.024	47.665	0.001	0.001	0.000	0.000	0.000	0.000
102	A	205	ASP	-1	-0.871	-0.937	51.086	0.022	0.022	0.000	0.000	0.000	0.000
103	A	206	ILE	0	-0.050	-0.034	45.423	0.002	0.002	0.000	0.000	0.000	0.000
104	A	207	SER	0	-0.025	-0.018	43.644	-0.003	-0.003	0.000	0.000	0.000	0.000
105	A	208	LEU	0	-0.020	-0.010	43.470	0.003	0.003	0.000	0.000	0.000	0.000
106	A	209	LEU	0	-0.025	-0.012	35.789	-0.002	-0.002	0.000	0.000	0.000	0.000
107	A	210	GLY	0	0.071	0.036	39.316	0.002	0.002	0.000	0.000	0.000	0.000
108	A	211	MET	0	0.006	-0.003	36.568	0.003	0.003	0.000	0.000	0.000	0.000
109	A	212	SER	0	-0.024	-0.005	35.188	0.000	0.000	0.000	0.000	0.000	0.000
110	A	213	LEU	0	-0.067	-0.035	32.059	-0.002	-0.002	0.000	0.000	0.000	0.000
111	A	214	LEU	0	0.014	-0.008	32.184	0.004	0.004	0.000	0.000	0.000	0.000
112	A	215	GLU	-1	-0.924	-0.949	31.529	0.002	0.002	0.000	0.000	0.000	0.000
113	A	216	ARG	1	0.822	0.910	28.652	0.000	0.000	0.000	0.000	0.000	0.000
114	A	217	PHE	0	-0.069	-0.025	27.082	0.006	0.006	0.000	0.000	0.000	0.000
115	A	218	LYS	1	0.950	0.979	19.131	-0.170	-0.170	0.000	0.000	0.000	0.000
116	A	219	GLY	0	0.003	-0.004	24.973	-0.002	-0.002	0.000	0.000	0.000	0.000
117	A	220	PHE	0	0.055	0.014	27.391	0.005	0.005	0.000	0.000	0.000	0.000
118	A	221	ARG	1	0.885	0.960	28.363	-0.097	-0.097	0.000	0.000	0.000	0.000
119	A	222	ILE	0	0.027	0.012	33.680	0.004	0.004	0.000	0.000	0.000	0.000
120	A	223	ASP	-1	-0.829	-0.892	36.407	0.055	0.055	0.000	0.000	0.000	0.000
121	A	224	LYS	1	0.848	0.908	38.120	-0.054	-0.054	0.000	0.000	0.000	0.000
122	A	225	ASP	-1	-0.896	-0.942	41.060	0.057	0.057	0.000	0.000	0.000	0.000
123	A	226	LEU	0	0.044	0.034	35.211	0.002	0.002	0.000	0.000	0.000	0.000
124	A	227	LEU	0	-0.006	0.007	34.072	-0.004	-0.004	0.000	0.000	0.000	0.000
125	A	228	ILE	0	-0.054	-0.034	29.526	0.005	0.005	0.000	0.000	0.000	0.000
126	A	229	LEU	0	0.012	0.009	29.640	-0.007	-0.007	0.000	0.000	0.000	0.000
127	A	230	ASN	0	-0.049	-0.041	24.401	0.001	0.001	0.000	0.000	0.000	0.000
128	A	231	TYR	0	-0.062	-0.033	23.174	-0.029	-0.029	0.000	0.000	0.000	0.000
129	A	232	ALA	0	0.020	0.002	18.681	0.023	0.023	0.000	0.000	0.000	0.000
130	A	233	ALA	0	0.028	0.018	19.345	-0.046	-0.046	0.000	0.000	0.000	0.000
131	A	234	ALA	0	0.036	0.018	15.857	0.065	0.065	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:104:MET)