FMO DATABASE

FMODB ID: 432YN

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:

Apendix: None

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	131
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1079343.240639
FMO2-HF: Nuclear repulsion	1028648.001572
FMO2-HF: Total energy	-50695.239067
FMO2-MP2: Total energy	-50844.807303

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.
-10.809	-6.936	2.588	-2.38	-4.081	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 : 0.028 / 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	0.941	0.966	2.532	-10.836	-7.076	2.589	-2.358	-3.991	0.011
4	A	107	TRP	0	0.033	0.012	4.539	-0.434	-0.321	-0.001	-0.022	-0.090	0.000
5	A	108	SER	0	-0.009	-0.009	8.173	0.586	0.586	0.000	0.000	0.000	0.000
6	A	109	THR	0	-0.060	-0.020	10.823	-0.154	-0.154	0.000	0.000	0.000	0.000
7	A	110	GLU	-1	-0.841	-0.901	14.626	0.292	0.292	0.000	0.000	0.000	0.000
8	A	111	VAL	0	0.004	-0.032	16.902	-0.054	-0.054	0.000	0.000	0.000	0.000
9	A	112	GLY	0	0.053	0.041	19.484	0.024	0.024	0.000	0.000	0.000	0.000
10	A	113	GLU	-1	-0.853	-0.919	22.975	0.107	0.107	0.000	0.000	0.000	0.000
11	A	114	ILE	0	-0.021	0.006	26.357	0.006	0.006	0.000	0.000	0.000	0.000
12	A	115	ILE	0	0.029	0.014	29.891	-0.008	-0.008	0.000	0.000	0.000	0.000
13	A	116	ILE	0	-0.042	-0.019	32.909	0.001	0.001	0.000	0.000	0.000	0.000
14	A	117	ALA	0	0.047	0.022	36.438	-0.003	-0.003	0.000	0.000	0.000	0.000
15	A	118	ARG	1	0.789	0.888	39.744	-0.041	-0.041	0.000	0.000	0.000	0.000
16	A	119	ASN	0	-0.017	-0.017	42.806	0.003	0.003	0.000	0.000	0.000	0.000
17	A	120	ARG	1	0.965	0.959	45.547	-0.045	-0.045	0.000	0.000	0.000	0.000
18	A	121	ASP	-1	-0.759	-0.831	47.869	0.034	0.034	0.000	0.000	0.000	0.000
19	A	122	GLY	0	0.022	0.012	47.686	-0.002	-0.002	0.000	0.000	0.000	0.000
20	A	123	HIS	1	0.876	0.941	45.330	-0.028	-0.028	0.000	0.000	0.000	0.000
21	A	124	PHE	0	0.037	0.025	39.830	0.002	0.002	0.000	0.000	0.000	0.000
22	A	125	TYR	0	-0.048	-0.055	40.793	-0.004	-0.004	0.000	0.000	0.000	0.000
23	A	126	ILE	0	0.016	0.012	35.193	0.005	0.005	0.000	0.000	0.000	0.000
24	A	127	ASN	0	-0.016	0.000	37.462	-0.009	-0.009	0.000	0.000	0.000	0.000
25	A	128	ALA	0	0.046	0.022	35.198	0.006	0.006	0.000	0.000	0.000	0.000
26	A	129	PHE	0	0.024	0.003	33.467	-0.002	-0.002	0.000	0.000	0.000	0.000
27	A	130	VAL	0	0.023	0.002	34.790	0.000	0.000	0.000	0.000	0.000	0.000
28	A	131	ASN	0	0.029	0.006	35.796	-0.001	-0.001	0.000	0.000	0.000	0.000
29	A	132	ASN	0	-0.007	-0.008	33.758	0.003	0.003	0.000	0.000	0.000	0.000
30	A	133	VAL	0	0.048	0.047	36.279	0.004	0.004	0.000	0.000	0.000	0.000
31	A	134	LYS	1	0.791	0.909	36.423	-0.064	-0.064	0.000	0.000	0.000	0.000
32	A	135	ILE	0	0.032	0.023	39.513	-0.003	-0.003	0.000	0.000	0.000	0.000
33	A	136	LYS	1	0.904	0.947	39.983	-0.044	-0.044	0.000	0.000	0.000	0.000
34	A	137	PHE	0	0.033	0.012	38.486	-0.004	-0.004	0.000	0.000	0.000	0.000
35	A	138	MET	0	0.003	0.007	41.803	0.004	0.004	0.000	0.000	0.000	0.000
36	A	139	VAL	0	-0.049	-0.034	38.820	-0.002	-0.002	0.000	0.000	0.000	0.000
37	A	140	ASP	-1	-0.827	-0.921	41.434	0.015	0.015	0.000	0.000	0.000	0.000
38	A	141	THR	0	-0.043	-0.047	40.403	0.000	0.000	0.000	0.000	0.000	0.000
39	A	142	GLY	0	0.003	0.009	41.536	-0.002	-0.002	0.000	0.000	0.000	0.000
40	A	143	ALA	0	-0.008	0.012	42.977	-0.003	-0.003	0.000	0.000	0.000	0.000
41	A	144	SER	0	0.027	0.003	40.912	0.001	0.001	0.000	0.000	0.000	0.000
42	A	145	ASP	-1	-0.838	-0.873	39.528	-0.002	-0.002	0.000	0.000	0.000	0.000
43	A	146	ILE	0	-0.011	-0.003	37.253	0.002	0.002	0.000	0.000	0.000	0.000
44	A	147	ALA	0	0.026	0.035	41.322	-0.003	-0.003	0.000	0.000	0.000	0.000
45	A	148	LEU	0	0.013	-0.005	42.019	0.003	0.003	0.000	0.000	0.000	0.000
46	A	149	THR	0	0.043	0.015	45.741	-0.003	-0.003	0.000	0.000	0.000	0.000
47	A	150	LYS	1	0.922	0.954	48.340	-0.012	-0.012	0.000	0.000	0.000	0.000
48	A	151	GLU	-1	-0.789	-0.883	49.930	0.025	0.025	0.000	0.000	0.000	0.000
49	A	152	ASP	-1	-0.764	-0.849	44.569	0.028	0.028	0.000	0.000	0.000	0.000
50	A	153	ALA	0	0.017	-0.001	45.144	0.000	0.000	0.000	0.000	0.000	0.000
51	A	154	GLN	0	-0.024	-0.023	46.430	-0.001	-0.001	0.000	0.000	0.000	0.000
52	A	155	LYS	1	0.787	0.884	44.745	-0.029	-0.029	0.000	0.000	0.000	0.000
53	A	156	LEU	0	-0.067	-0.030	40.239	0.001	0.001	0.000	0.000	0.000	0.000
54	A	157	GLY	0	-0.001	0.014	43.519	-0.002	-0.002	0.000	0.000	0.000	0.000
55	A	158	PHE	0	-0.039	-0.025	41.627	-0.003	-0.003	0.000	0.000	0.000	0.000
56	A	159	ASP	-1	-0.778	-0.870	47.261	0.003	0.003	0.000	0.000	0.000	0.000
57	A	160	LEU	0	0.030	0.000	50.058	-0.002	-0.002	0.000	0.000	0.000	0.000
58	A	161	THR	0	-0.043	-0.019	52.373	-0.002	-0.002	0.000	0.000	0.000	0.000
59	A	162	LYS	1	0.883	0.939	52.561	0.000	0.000	0.000	0.000	0.000	0.000
60	A	163	LEU	0	0.003	0.026	47.727	-0.002	-0.002	0.000	0.000	0.000	0.000
61	A	164	LYS	1	0.887	0.932	49.880	0.009	0.009	0.000	0.000	0.000	0.000
62	A	165	TYR	0	0.029	0.004	50.356	-0.001	-0.001	0.000	0.000	0.000	0.000
63	A	166	THR	0	0.013	-0.003	48.788	0.000	0.000	0.000	0.000	0.000	0.000
64	A	167	ARG	1	0.838	0.890	43.574	0.005	0.005	0.000	0.000	0.000	0.000
65	A	168	THR	0	-0.089	-0.067	50.693	0.000	0.000	0.000	0.000	0.000	0.000
66	A	169	TYR	0	-0.023	-0.023	47.139	-0.001	-0.001	0.000	0.000	0.000	0.000
67	A	170	LEU	0	0.032	0.039	53.336	-0.001	-0.001	0.000	0.000	0.000	0.000
68	A	171	THR	0	0.003	0.000	54.047	0.001	0.001	0.000	0.000	0.000	0.000
69	A	172	ALA	0	-0.004	-0.004	55.938	-0.001	-0.001	0.000	0.000	0.000	0.000
70	A	173	ASN	0	-0.029	-0.012	58.249	0.000	0.000	0.000	0.000	0.000	0.000
71	A	174	GLY	0	0.033	0.037	59.641	-0.001	-0.001	0.000	0.000	0.000	0.000
72	A	175	GLU	-1	-0.820	-0.921	56.687	-0.006	-0.006	0.000	0.000	0.000	0.000
73	A	176	ASN	0	-0.021	-0.010	53.296	0.001	0.001	0.000	0.000	0.000	0.000
74	A	177	LYS	1	0.872	0.926	54.038	0.008	0.008	0.000	0.000	0.000	0.000
75	A	178	ALA	0	0.025	0.011	49.979	0.002	0.002	0.000	0.000	0.000	0.000
76	A	179	ALA	0	-0.004	0.001	49.405	-0.002	-0.002	0.000	0.000	0.000	0.000
77	A	180	PRO	0	-0.057	-0.022	44.469	0.002	0.002	0.000	0.000	0.000	0.000
78	A	181	ILE	0	0.003	0.020	42.189	0.000	0.000	0.000	0.000	0.000	0.000
79	A	182	THR	0	-0.078	-0.049	36.791	-0.004	-0.004	0.000	0.000	0.000	0.000
80	A	183	LEU	0	0.008	0.017	36.838	0.001	0.001	0.000	0.000	0.000	0.000
81	A	184	ASN	0	0.034	0.013	34.467	-0.002	-0.002	0.000	0.000	0.000	0.000
82	A	185	SER	0	-0.005	-0.001	31.631	-0.002	-0.002	0.000	0.000	0.000	0.000
83	A	186	VAL	0	0.041	0.025	32.002	0.000	0.000	0.000	0.000	0.000	0.000
84	A	187	VAL	0	-0.030	-0.016	29.119	0.002	0.002	0.000	0.000	0.000	0.000
85	A	188	ILE	0	0.017	0.000	30.075	0.000	0.000	0.000	0.000	0.000	0.000
86	A	189	GLY	0	0.046	0.031	27.411	0.000	0.000	0.000	0.000	0.000	0.000
87	A	190	LYS	1	0.874	0.946	22.813	-0.050	-0.050	0.000	0.000	0.000	0.000
88	A	191	GLU	-1	-0.840	-0.913	26.090	0.029	0.029	0.000	0.000	0.000	0.000
89	A	192	PHE	0	-0.063	-0.025	26.480	-0.004	-0.004	0.000	0.000	0.000	0.000
90	A	193	LYS	1	0.898	0.921	26.711	-0.020	-0.020	0.000	0.000	0.000	0.000
91	A	194	ASN	0	-0.009	-0.008	30.258	0.001	0.001	0.000	0.000	0.000	0.000
92	A	195	ILE	0	-0.017	0.008	31.934	-0.005	-0.005	0.000	0.000	0.000	0.000
93	A	196	LYS	1	0.991	0.987	35.209	0.027	0.027	0.000	0.000	0.000	0.000
94	A	197	GLY	0	0.081	0.032	38.375	0.004	0.004	0.000	0.000	0.000	0.000
95	A	198	HIS	0	-0.068	-0.032	41.606	-0.003	-0.003	0.000	0.000	0.000	0.000
96	A	199	VAL	0	0.000	0.013	45.333	0.003	0.003	0.000	0.000	0.000	0.000
97	A	200	GLY	0	0.019	0.004	48.032	-0.002	-0.002	0.000	0.000	0.000	0.000
98	A	201	LEU	0	-0.005	-0.005	50.083	-0.001	-0.001	0.000	0.000	0.000	0.000
99	A	202	GLY	0	-0.035	-0.028	53.399	0.001	0.001	0.000	0.000	0.000	0.000
100	A	203	ASP	-1	-0.854	-0.937	56.024	0.010	0.010	0.000	0.000	0.000	0.000
101	A	204	LEU	0	-0.095	-0.037	47.931	0.001	0.001	0.000	0.000	0.000	0.000
102	A	205	ASP	-1	-0.894	-0.946	51.740	0.023	0.023	0.000	0.000	0.000	0.000
103	A	206	ILE	0	-0.026	-0.020	45.811	0.002	0.002	0.000	0.000	0.000	0.000
104	A	207	SER	0	-0.026	-0.024	43.799	-0.003	-0.003	0.000	0.000	0.000	0.000
105	A	208	LEU	0	-0.010	-0.002	43.854	0.003	0.003	0.000	0.000	0.000	0.000
106	A	209	LEU	0	-0.033	-0.027	36.041	-0.001	-0.001	0.000	0.000	0.000	0.000
107	A	210	GLY	0	0.088	0.043	39.536	0.002	0.002	0.000	0.000	0.000	0.000
108	A	211	MET	0	0.029	0.017	37.022	0.002	0.002	0.000	0.000	0.000	0.000
109	A	212	SER	0	-0.025	-0.022	35.294	0.001	0.001	0.000	0.000	0.000	0.000
110	A	213	LEU	0	-0.133	-0.066	31.874	-0.003	-0.003	0.000	0.000	0.000	0.000
111	A	214	LEU	0	0.012	-0.001	32.228	0.004	0.004	0.000	0.000	0.000	0.000
112	A	215	GLU	-1	-0.867	-0.922	31.716	-0.002	-0.002	0.000	0.000	0.000	0.000
113	A	216	ARG	1	0.801	0.901	28.824	-0.003	-0.003	0.000	0.000	0.000	0.000
114	A	217	PHE	0	-0.051	-0.024	27.267	0.006	0.006	0.000	0.000	0.000	0.000
115	A	218	LYS	1	0.896	0.965	19.012	-0.173	-0.173	0.000	0.000	0.000	0.000
116	A	219	GLY	0	0.022	0.007	24.884	-0.003	-0.003	0.000	0.000	0.000	0.000
117	A	220	PHE	0	0.035	0.014	27.692	0.008	0.008	0.000	0.000	0.000	0.000
118	A	221	ARG	1	0.856	0.923	28.582	-0.095	-0.095	0.000	0.000	0.000	0.000
119	A	222	ILE	0	0.013	-0.004	33.898	0.004	0.004	0.000	0.000	0.000	0.000
120	A	223	ASP	-1	-0.817	-0.883	36.990	0.051	0.051	0.000	0.000	0.000	0.000
121	A	224	LYS	1	0.850	0.913	38.698	-0.051	-0.051	0.000	0.000	0.000	0.000
122	A	225	ASP	-1	-0.879	-0.933	41.162	0.055	0.055	0.000	0.000	0.000	0.000
123	A	226	LEU	0	0.020	0.010	35.712	0.003	0.003	0.000	0.000	0.000	0.000
124	A	227	LEU	0	0.004	0.012	34.617	-0.005	-0.005	0.000	0.000	0.000	0.000
125	A	228	ILE	0	-0.044	-0.031	29.975	0.006	0.006	0.000	0.000	0.000	0.000
126	A	229	LEU	0	-0.002	0.009	30.065	-0.009	-0.009	0.000	0.000	0.000	0.000
127	A	230	ASN	0	-0.037	-0.028	24.695	0.002	0.002	0.000	0.000	0.000	0.000
128	A	231	TYR	0	-0.040	-0.052	23.386	-0.030	-0.030	0.000	0.000	0.000	0.000
129	A	232	ALA	0	0.036	0.007	18.931	0.022	0.022	0.000	0.000	0.000	0.000
130	A	233	ALA	0	0.001	0.015	19.486	-0.048	-0.048	0.000	0.000	0.000	0.000
131	A	234	ALA	0	0.042	0.027	15.692	0.071	0.071	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

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