FMO DATABASE

FMODB ID: LN449

Calculation Name: 4B9G-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4B9G

Chain ID: A

ChEMBL ID:

UniProt ID: P53508

Base Structure: X-ray

Registration Date: 2023-09-23

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	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	146
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1275000.545562
FMO2-HF: Nuclear repulsion	1219548.227734
FMO2-HF: Total energy	-55452.317828
FMO2-MP2: Total energy	-55614.646809

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:16:ASP)

Summations of interaction energy for fragment #1(A:16:ASP)

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.
-73.688	-68.771	16.464	-11.114	-10.267	0.113

Interaction energy analysis for fragmet #1(A:16:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.856 / q_NPA : -0.929

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	18	ASP	-1	-0.886	-0.949	2.767	42.718	47.402	0.600	-2.432	-2.852	0.020
4	A	19	SER	0	-0.089	-0.056	1.898	-45.545	-46.015	15.825	-8.508	-6.847	0.090
5	A	20	ALA	0	-0.023	0.003	3.672	-12.669	-12.263	0.035	-0.101	-0.341	0.003
6	A	21	VAL	0	-0.039	-0.031	5.950	-7.130	-7.130	0.000	0.000	0.000	0.000
7	A	22	ARG	1	0.984	1.003	8.381	-19.145	-19.145	0.000	0.000	0.000	0.000
8	A	23	ILE	0	-0.021	-0.016	11.126	-1.500	-1.500	0.000	0.000	0.000	0.000
9	A	24	ILE	0	-0.043	-0.024	14.306	0.068	0.068	0.000	0.000	0.000	0.000
10	A	25	PRO	0	0.010	0.000	17.485	-0.596	-0.596	0.000	0.000	0.000	0.000
11	A	26	VAL	0	-0.014	0.014	20.505	-0.137	-0.137	0.000	0.000	0.000	0.000
12	A	27	ASN	0	-0.029	-0.028	23.516	0.054	0.054	0.000	0.000	0.000	0.000
13	A	28	TYR	0	-0.048	-0.042	26.718	-0.360	-0.360	0.000	0.000	0.000	0.000
14	A	29	ASP	-1	-0.807	-0.887	30.255	9.658	9.658	0.000	0.000	0.000	0.000
15	A	30	SER	0	-0.107	-0.046	33.468	-0.360	-0.360	0.000	0.000	0.000	0.000
16	A	31	ASP	-1	-0.789	-0.907	33.269	9.315	9.315	0.000	0.000	0.000	0.000
17	A	32	PRO	0	-0.026	-0.007	29.915	-0.100	-0.100	0.000	0.000	0.000	0.000
18	A	33	LYS	1	0.976	0.987	32.269	-8.984	-8.984	0.000	0.000	0.000	0.000
19	A	34	LEU	0	0.046	0.018	32.471	0.334	0.334	0.000	0.000	0.000	0.000
20	A	35	ASN	0	-0.049	-0.031	30.826	0.081	0.081	0.000	0.000	0.000	0.000
21	A	36	SER	0	-0.044	-0.020	29.805	0.141	0.141	0.000	0.000	0.000	0.000
22	A	37	GLN	0	0.011	0.010	24.368	0.625	0.625	0.000	0.000	0.000	0.000
23	A	38	LEU	0	0.034	0.025	23.978	-0.162	-0.162	0.000	0.000	0.000	0.000
24	A	39	TYR	0	0.030	-0.010	17.534	0.526	0.526	0.000	0.000	0.000	0.000
25	A	40	THR	0	0.005	0.006	18.175	-0.529	-0.529	0.000	0.000	0.000	0.000
26	A	41	VAL	0	-0.020	-0.005	13.400	0.825	0.825	0.000	0.000	0.000	0.000
27	A	42	GLU	-1	-0.940	-0.971	13.724	17.118	17.118	0.000	0.000	0.000	0.000
28	A	43	MET	0	0.005	0.006	9.441	2.048	2.048	0.000	0.000	0.000	0.000
29	A	44	THR	0	-0.023	-0.016	9.140	-2.624	-2.624	0.000	0.000	0.000	0.000
30	A	45	ILE	0	-0.049	-0.012	7.681	2.750	2.750	0.000	0.000	0.000	0.000
31	A	46	PRO	0	0.039	0.024	3.576	-2.157	-1.960	0.005	-0.054	-0.148	0.000
32	A	47	ALA	0	0.046	0.014	5.940	-1.610	-1.610	0.000	0.000	0.000	0.000
33	A	48	GLY	0	0.003	0.006	6.824	2.279	2.279	0.000	0.000	0.000	0.000
34	A	49	VAL	0	-0.062	-0.005	6.000	-0.252	-0.252	0.000	0.000	0.000	0.000
35	A	50	SER	0	-0.014	-0.017	8.872	-1.486	-1.486	0.000	0.000	0.000	0.000
36	A	51	ALA	0	-0.047	-0.037	11.789	-1.517	-1.517	0.000	0.000	0.000	0.000
37	A	52	VAL	0	0.054	0.040	10.371	1.740	1.740	0.000	0.000	0.000	0.000
38	A	53	LYS	1	0.881	0.947	12.765	-19.345	-19.345	0.000	0.000	0.000	0.000
39	A	54	ILE	0	0.019	0.020	13.560	1.546	1.546	0.000	0.000	0.000	0.000
40	A	55	VAL	0	-0.058	-0.035	15.720	-1.342	-1.342	0.000	0.000	0.000	0.000
41	A	56	PRO	0	0.026	0.032	17.566	0.891	0.891	0.000	0.000	0.000	0.000
42	A	57	THR	0	-0.023	-0.034	17.145	-0.062	-0.062	0.000	0.000	0.000	0.000
43	A	58	ASP	-1	-0.895	-0.939	19.595	14.048	14.048	0.000	0.000	0.000	0.000
44	A	59	SER	0	-0.068	0.001	22.393	-0.704	-0.704	0.000	0.000	0.000	0.000
45	A	60	LEU	0	-0.004	-0.015	24.306	-0.238	-0.238	0.000	0.000	0.000	0.000
46	A	61	THR	0	-0.046	-0.019	27.628	0.111	0.111	0.000	0.000	0.000	0.000
47	A	62	SER	0	-0.001	0.002	29.193	-0.470	-0.470	0.000	0.000	0.000	0.000
48	A	63	SER	0	0.023	0.006	30.977	0.133	0.133	0.000	0.000	0.000	0.000
49	A	64	GLY	0	-0.008	0.001	30.589	0.061	0.061	0.000	0.000	0.000	0.000
50	A	65	GLN	0	-0.067	-0.021	26.968	0.275	0.275	0.000	0.000	0.000	0.000
51	A	66	GLN	0	-0.047	-0.046	22.854	-0.668	-0.668	0.000	0.000	0.000	0.000
52	A	67	ILE	0	-0.007	-0.004	24.612	0.385	0.385	0.000	0.000	0.000	0.000
53	A	68	GLY	0	0.026	0.000	23.659	0.129	0.129	0.000	0.000	0.000	0.000
54	A	69	LYS	1	0.947	0.971	24.478	-11.330	-11.330	0.000	0.000	0.000	0.000
55	A	70	LEU	0	-0.069	-0.018	21.579	0.669	0.669	0.000	0.000	0.000	0.000
56	A	71	VAL	0	0.039	0.004	24.998	-0.599	-0.599	0.000	0.000	0.000	0.000
57	A	72	ASN	0	-0.002	0.013	26.373	0.536	0.536	0.000	0.000	0.000	0.000
58	A	73	VAL	0	-0.018	-0.031	24.342	-0.080	-0.080	0.000	0.000	0.000	0.000
59	A	74	ASN	0	-0.046	-0.020	27.514	0.043	0.043	0.000	0.000	0.000	0.000
60	A	75	ASN	0	-0.014	-0.001	31.134	-0.306	-0.306	0.000	0.000	0.000	0.000
61	A	76	PRO	0	0.044	0.014	30.865	0.158	0.158	0.000	0.000	0.000	0.000
62	A	77	ASP	-1	-0.912	-0.943	31.920	9.106	9.106	0.000	0.000	0.000	0.000
63	A	78	GLN	0	-0.042	-0.014	32.847	-0.022	-0.022	0.000	0.000	0.000	0.000
64	A	79	ASN	0	-0.044	-0.035	29.153	0.451	0.451	0.000	0.000	0.000	0.000
65	A	80	MET	0	-0.002	0.018	27.637	-0.206	-0.206	0.000	0.000	0.000	0.000
66	A	81	ASN	0	0.031	0.009	27.544	0.724	0.724	0.000	0.000	0.000	0.000
67	A	82	TYR	0	0.016	0.018	20.770	0.237	0.237	0.000	0.000	0.000	0.000
68	A	83	TYR	0	0.036	0.026	24.484	0.266	0.266	0.000	0.000	0.000	0.000
69	A	84	ILE	0	0.018	0.014	18.711	-0.020	-0.020	0.000	0.000	0.000	0.000
70	A	85	ARG	1	0.868	0.909	22.076	-12.483	-12.483	0.000	0.000	0.000	0.000
71	A	86	LYS	1	0.854	0.928	18.582	-13.716	-13.716	0.000	0.000	0.000	0.000
72	A	87	ASP	-1	-0.756	-0.866	20.407	12.459	12.459	0.000	0.000	0.000	0.000
73	A	88	SER	0	-0.022	0.009	19.122	-0.255	-0.255	0.000	0.000	0.000	0.000
74	A	89	GLY	0	0.127	0.071	17.347	0.774	0.774	0.000	0.000	0.000	0.000
75	A	90	ALA	0	-0.046	-0.025	18.310	-0.522	-0.522	0.000	0.000	0.000	0.000
76	A	91	GLY	0	0.080	0.036	18.188	0.726	0.726	0.000	0.000	0.000	0.000
77	A	92	LYS	1	0.907	0.948	20.211	-11.724	-11.724	0.000	0.000	0.000	0.000
78	A	93	PHE	0	0.013	0.017	18.863	0.108	0.108	0.000	0.000	0.000	0.000
79	A	94	MET	0	0.005	0.000	21.655	-0.376	-0.376	0.000	0.000	0.000	0.000
80	A	95	ALA	0	0.011	-0.005	23.699	0.441	0.441	0.000	0.000	0.000	0.000
81	A	96	GLY	0	0.043	0.023	23.485	-0.423	-0.423	0.000	0.000	0.000	0.000
82	A	97	GLN	0	0.014	0.029	20.132	-0.603	-0.603	0.000	0.000	0.000	0.000
83	A	98	LYS	1	1.014	0.994	20.968	-12.722	-12.722	0.000	0.000	0.000	0.000
84	A	99	GLY	0	-0.022	-0.004	19.708	0.599	0.599	0.000	0.000	0.000	0.000
85	A	100	SER	0	0.009	0.008	15.575	0.291	0.291	0.000	0.000	0.000	0.000
86	A	101	PHE	0	-0.050	-0.022	15.916	-1.121	-1.121	0.000	0.000	0.000	0.000
87	A	102	SER	0	0.012	-0.004	15.677	0.736	0.736	0.000	0.000	0.000	0.000
88	A	103	VAL	0	-0.046	-0.005	11.609	-0.756	-0.756	0.000	0.000	0.000	0.000
89	A	104	LYS	1	0.927	0.949	14.680	-14.334	-14.334	0.000	0.000	0.000	0.000
90	A	105	GLU	-1	-0.818	-0.898	10.396	20.933	20.933	0.000	0.000	0.000	0.000
91	A	106	ASN	0	-0.013	-0.010	10.150	-0.021	-0.021	0.000	0.000	0.000	0.000
92	A	107	THR	0	-0.069	-0.045	11.536	-1.428	-1.428	0.000	0.000	0.000	0.000
93	A	108	SER	0	0.064	0.022	12.240	1.713	1.713	0.000	0.000	0.000	0.000
94	A	109	TYR	0	-0.092	-0.042	13.070	-1.510	-1.510	0.000	0.000	0.000	0.000
95	A	110	THR	0	0.015	-0.003	14.760	0.756	0.756	0.000	0.000	0.000	0.000
96	A	111	PHE	0	0.002	-0.011	14.331	-0.786	-0.786	0.000	0.000	0.000	0.000
97	A	112	SER	0	0.032	0.010	18.977	0.303	0.303	0.000	0.000	0.000	0.000
98	A	113	ALA	0	-0.012	0.013	21.158	-0.128	-0.128	0.000	0.000	0.000	0.000
99	A	114	ILE	0	-0.037	-0.012	22.732	-0.379	-0.379	0.000	0.000	0.000	0.000
100	A	115	TYR	0	0.043	-0.006	26.503	-0.066	-0.066	0.000	0.000	0.000	0.000
101	A	116	THR	0	-0.045	-0.042	29.022	-0.273	-0.273	0.000	0.000	0.000	0.000
102	A	117	GLY	0	0.041	0.022	31.620	-0.366	-0.366	0.000	0.000	0.000	0.000
103	A	118	GLY	0	-0.043	-0.031	31.788	0.447	0.447	0.000	0.000	0.000	0.000
104	A	119	GLU	-1	-0.930	-0.930	33.319	8.678	8.678	0.000	0.000	0.000	0.000
105	A	120	TYR	0	0.017	-0.007	34.489	0.193	0.193	0.000	0.000	0.000	0.000
106	A	121	PRO	0	0.021	0.023	37.000	-0.206	-0.206	0.000	0.000	0.000	0.000
107	A	122	ASN	0	0.033	-0.008	40.453	0.140	0.140	0.000	0.000	0.000	0.000
108	A	123	SER	0	-0.060	-0.020	40.745	-0.104	-0.104	0.000	0.000	0.000	0.000
109	A	124	GLY	0	0.007	0.020	38.610	0.017	0.017	0.000	0.000	0.000	0.000
110	A	125	TYR	0	-0.047	-0.021	32.543	0.069	0.069	0.000	0.000	0.000	0.000
111	A	126	SER	0	-0.012	-0.003	34.438	-0.164	-0.164	0.000	0.000	0.000	0.000
112	A	127	SER	0	0.004	-0.009	33.054	0.209	0.209	0.000	0.000	0.000	0.000
113	A	128	GLY	0	-0.016	-0.004	30.040	-0.086	-0.086	0.000	0.000	0.000	0.000
114	A	129	THR	0	-0.007	-0.001	23.353	0.043	0.043	0.000	0.000	0.000	0.000
115	A	130	TYR	0	-0.022	-0.016	25.497	-0.223	-0.223	0.000	0.000	0.000	0.000
116	A	131	ALA	0	0.015	-0.011	21.138	0.505	0.505	0.000	0.000	0.000	0.000
117	A	132	GLY	0	0.045	0.024	20.365	-0.731	-0.731	0.000	0.000	0.000	0.000
118	A	133	HIS	0	-0.014	-0.009	15.288	0.331	0.331	0.000	0.000	0.000	0.000
119	A	134	LEU	0	-0.003	0.013	14.407	-1.018	-1.018	0.000	0.000	0.000	0.000
120	A	135	THR	0	-0.021	-0.015	13.376	1.131	1.131	0.000	0.000	0.000	0.000
121	A	136	VAL	0	-0.022	-0.010	9.849	-1.394	-1.394	0.000	0.000	0.000	0.000
122	A	137	SER	0	-0.024	-0.029	9.821	1.143	1.143	0.000	0.000	0.000	0.000
123	A	138	PHE	0	0.023	0.001	4.649	-2.061	-1.961	-0.001	-0.019	-0.079	0.000
124	A	139	TYR	0	-0.011	-0.026	9.045	-0.367	-0.367	0.000	0.000	0.000	0.000
125	A	140	SER	0	0.090	0.053	10.837	0.747	0.747	0.000	0.000	0.000	0.000
126	A	141	ASN	0	-0.090	-0.073	12.236	-1.225	-1.225	0.000	0.000	0.000	0.000
127	A	142	ASP	-1	-0.795	-0.879	14.668	17.715	17.715	0.000	0.000	0.000	0.000
128	A	143	ASN	0	-0.008	-0.015	17.588	-0.576	-0.576	0.000	0.000	0.000	0.000
129	A	144	LYS	1	0.934	0.956	20.916	-11.067	-11.067	0.000	0.000	0.000	0.000
130	A	145	GLN	0	0.024	0.027	19.080	0.027	0.027	0.000	0.000	0.000	0.000
131	A	146	ARG	1	0.884	0.952	15.571	-16.093	-16.093	0.000	0.000	0.000	0.000
132	A	147	THR	0	0.027	0.018	12.941	-0.889	-0.889	0.000	0.000	0.000	0.000
133	A	148	GLU	-1	-0.997	-1.008	10.842	23.269	23.269	0.000	0.000	0.000	0.000
134	A	149	ILE	0	0.008	-0.006	7.002	-0.384	-0.384	0.000	0.000	0.000	0.000
135	A	150	ALA	0	0.024	0.017	5.008	3.536	3.536	0.000	0.000	0.000	0.000
136	A	151	THR	0	0.012	0.016	6.908	-2.961	-2.961	0.000	0.000	0.000	0.000
137	A	152	LYS	1	0.929	0.983	7.697	-32.396	-32.396	0.000	0.000	0.000	0.000
138	A	153	ASN	0	0.049	0.040	9.616	-1.272	-1.272	0.000	0.000	0.000	0.000
139	A	154	PHE	0	0.019	-0.012	7.101	-0.557	-0.557	0.000	0.000	0.000	0.000
140	A	155	PRO	0	-0.002	-0.003	12.447	-1.515	-1.515	0.000	0.000	0.000	0.000
141	A	156	VAL	0	-0.019	0.006	14.872	0.757	0.757	0.000	0.000	0.000	0.000
142	A	157	SER	0	-0.025	-0.027	17.493	-0.839	-0.839	0.000	0.000	0.000	0.000
143	A	158	THR	0	0.002	0.003	20.880	0.105	0.105	0.000	0.000	0.000	0.000
144	A	159	THR	0	-0.007	0.001	23.911	-0.022	-0.022	0.000	0.000	0.000	0.000
145	A	160	ILE	0	0.013	0.024	26.763	-0.075	-0.075	0.000	0.000	0.000	0.000
146	A	161	SER	0	0.004	-0.009	30.524	-0.166	-0.166	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:16:ASP)