FMO DATABASE

FMODB ID: MNYYZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1276666.294066
FMO2-HF: Nuclear repulsion	1221213.004224
FMO2-HF: Total energy	-55453.289842
FMO2-MP2: Total energy	-55615.763342

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.
-104.383	-117.766	44.437	-19.178	-11.878	0.161

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 : -0.771 / q_NPA : -0.865

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	-0.809	-0.886	2.147	28.559	34.529	3.984	-5.029	-4.925	0.050
4	A	19	SER	0	-0.098	-0.076	1.544	-45.952	-65.860	40.429	-14.260	-6.262	0.107
5	A	20	ALA	0	-0.027	0.000	3.556	-13.881	-13.685	0.025	0.171	-0.393	0.004
6	A	21	VAL	0	-0.018	-0.024	5.695	-8.328	-8.266	-0.001	-0.003	-0.058	0.000
7	A	22	ARG	1	0.858	0.908	8.128	-19.837	-19.837	0.000	0.000	0.000	0.000
8	A	23	ILE	0	0.000	0.001	10.910	-2.003	-2.003	0.000	0.000	0.000	0.000
9	A	24	ILE	0	-0.022	-0.012	13.783	-0.040	-0.040	0.000	0.000	0.000	0.000
10	A	25	PRO	0	0.019	0.008	16.983	-0.704	-0.704	0.000	0.000	0.000	0.000
11	A	26	VAL	0	-0.025	0.007	20.050	-0.192	-0.192	0.000	0.000	0.000	0.000
12	A	27	ASN	0	-0.029	-0.018	23.265	0.111	0.111	0.000	0.000	0.000	0.000
13	A	28	TYR	0	-0.030	-0.027	26.518	-0.345	-0.345	0.000	0.000	0.000	0.000
14	A	29	ASP	-1	-0.810	-0.874	30.252	9.932	9.932	0.000	0.000	0.000	0.000
15	A	30	SER	0	-0.047	-0.022	33.386	-0.387	-0.387	0.000	0.000	0.000	0.000
16	A	31	ASP	-1	-0.800	-0.898	33.074	9.359	9.359	0.000	0.000	0.000	0.000
17	A	32	PRO	0	0.007	0.012	29.545	-0.157	-0.157	0.000	0.000	0.000	0.000
18	A	33	LYS	1	0.869	0.933	31.825	-9.461	-9.461	0.000	0.000	0.000	0.000
19	A	34	LEU	0	0.025	0.013	32.162	0.354	0.354	0.000	0.000	0.000	0.000
20	A	35	ASN	0	-0.039	-0.030	30.221	0.150	0.150	0.000	0.000	0.000	0.000
21	A	36	SER	0	-0.001	-0.001	29.187	0.148	0.148	0.000	0.000	0.000	0.000
22	A	37	GLN	0	0.014	0.010	23.374	0.752	0.752	0.000	0.000	0.000	0.000
23	A	38	LEU	0	0.034	0.027	23.740	-0.163	-0.163	0.000	0.000	0.000	0.000
24	A	39	TYR	0	0.041	-0.002	17.390	0.525	0.525	0.000	0.000	0.000	0.000
25	A	40	THR	0	-0.009	-0.005	18.378	-0.473	-0.473	0.000	0.000	0.000	0.000
26	A	41	VAL	0	-0.029	-0.017	13.031	0.818	0.818	0.000	0.000	0.000	0.000
27	A	42	GLU	-1	-0.821	-0.883	13.063	19.410	19.410	0.000	0.000	0.000	0.000
28	A	43	MET	0	0.005	0.006	9.873	2.084	2.084	0.000	0.000	0.000	0.000
29	A	44	THR	0	-0.020	-0.015	9.394	-2.963	-2.963	0.000	0.000	0.000	0.000
30	A	45	ILE	0	-0.034	-0.002	7.766	3.191	3.191	0.000	0.000	0.000	0.000
31	A	46	PRO	0	0.049	0.024	3.797	-2.350	-2.161	0.001	-0.042	-0.148	0.000
32	A	47	ALA	0	0.039	0.012	5.877	-1.799	-1.799	0.000	0.000	0.000	0.000
33	A	48	GLY	0	-0.012	-0.004	6.761	2.221	2.221	0.000	0.000	0.000	0.000
34	A	49	VAL	0	-0.082	-0.025	6.101	-0.557	-0.557	0.000	0.000	0.000	0.000
35	A	50	SER	0	0.004	-0.004	8.987	-1.389	-1.389	0.000	0.000	0.000	0.000
36	A	51	ALA	0	-0.048	-0.038	11.976	-1.496	-1.496	0.000	0.000	0.000	0.000
37	A	52	VAL	0	0.041	0.027	10.537	1.856	1.856	0.000	0.000	0.000	0.000
38	A	53	LYS	1	0.819	0.914	12.686	-23.408	-23.408	0.000	0.000	0.000	0.000
39	A	54	ILE	0	0.006	0.004	13.151	1.808	1.808	0.000	0.000	0.000	0.000
40	A	55	VAL	0	-0.026	-0.003	15.471	-1.443	-1.443	0.000	0.000	0.000	0.000
41	A	56	PRO	0	0.028	0.019	17.115	0.980	0.980	0.000	0.000	0.000	0.000
42	A	57	THR	0	-0.017	-0.012	16.409	-0.066	-0.066	0.000	0.000	0.000	0.000
43	A	58	ASP	-1	-0.908	-0.952	18.840	14.547	14.547	0.000	0.000	0.000	0.000
44	A	59	SER	0	-0.035	-0.017	21.310	-0.794	-0.794	0.000	0.000	0.000	0.000
45	A	60	LEU	0	-0.012	-0.010	23.832	-0.141	-0.141	0.000	0.000	0.000	0.000
46	A	61	THR	0	-0.054	-0.039	27.094	0.052	0.052	0.000	0.000	0.000	0.000
47	A	62	SER	0	0.009	0.005	28.893	-0.503	-0.503	0.000	0.000	0.000	0.000
48	A	63	SER	0	0.017	0.003	30.794	0.180	0.180	0.000	0.000	0.000	0.000
49	A	64	GLY	0	-0.004	0.007	30.612	-0.006	-0.006	0.000	0.000	0.000	0.000
50	A	65	GLN	0	-0.088	-0.045	26.961	0.169	0.169	0.000	0.000	0.000	0.000
51	A	66	GLN	0	-0.049	-0.035	22.716	-0.786	-0.786	0.000	0.000	0.000	0.000
52	A	67	ILE	0	-0.003	0.008	24.231	0.474	0.474	0.000	0.000	0.000	0.000
53	A	68	GLY	0	0.032	0.004	23.090	0.131	0.131	0.000	0.000	0.000	0.000
54	A	69	LYS	1	0.784	0.866	23.724	-11.433	-11.433	0.000	0.000	0.000	0.000
55	A	70	LEU	0	-0.057	-0.013	21.154	0.754	0.754	0.000	0.000	0.000	0.000
56	A	71	VAL	0	0.030	0.003	24.644	-0.627	-0.627	0.000	0.000	0.000	0.000
57	A	72	ASN	0	0.015	0.021	26.129	0.582	0.582	0.000	0.000	0.000	0.000
58	A	73	VAL	0	-0.018	-0.019	24.222	-0.109	-0.109	0.000	0.000	0.000	0.000
59	A	74	ASN	0	-0.069	-0.029	27.210	-0.092	-0.092	0.000	0.000	0.000	0.000
60	A	75	ASN	0	-0.051	-0.045	30.643	-0.403	-0.403	0.000	0.000	0.000	0.000
61	A	76	PRO	0	0.037	0.021	30.097	0.179	0.179	0.000	0.000	0.000	0.000
62	A	77	ASP	-1	-0.852	-0.915	31.135	9.331	9.331	0.000	0.000	0.000	0.000
63	A	78	GLN	0	-0.023	0.012	32.901	-0.080	-0.080	0.000	0.000	0.000	0.000
64	A	79	ASN	0	-0.041	-0.021	28.529	0.631	0.631	0.000	0.000	0.000	0.000
65	A	80	MET	0	0.000	0.022	27.417	-0.170	-0.170	0.000	0.000	0.000	0.000
66	A	81	ASN	0	-0.001	0.001	27.128	0.815	0.815	0.000	0.000	0.000	0.000
67	A	82	TYR	0	0.018	0.016	20.451	0.236	0.236	0.000	0.000	0.000	0.000
68	A	83	TYR	0	0.036	0.022	24.279	0.251	0.251	0.000	0.000	0.000	0.000
69	A	84	ILE	0	0.022	0.011	18.737	0.094	0.094	0.000	0.000	0.000	0.000
70	A	85	ARG	1	0.849	0.892	21.984	-12.921	-12.921	0.000	0.000	0.000	0.000
71	A	86	LYS	1	0.872	0.931	18.524	-14.153	-14.153	0.000	0.000	0.000	0.000
72	A	87	ASP	-1	-0.756	-0.815	21.143	13.026	13.026	0.000	0.000	0.000	0.000
73	A	88	SER	0	-0.011	0.016	19.365	-0.245	-0.245	0.000	0.000	0.000	0.000
74	A	89	GLY	0	0.113	0.064	17.477	0.801	0.801	0.000	0.000	0.000	0.000
75	A	90	ALA	0	-0.032	-0.015	18.300	-0.638	-0.638	0.000	0.000	0.000	0.000
76	A	91	GLY	0	0.067	0.030	18.331	0.647	0.647	0.000	0.000	0.000	0.000
77	A	92	LYS	1	0.916	0.953	19.895	-11.960	-11.960	0.000	0.000	0.000	0.000
78	A	93	PHE	0	0.018	0.017	18.829	0.091	0.091	0.000	0.000	0.000	0.000
79	A	94	MET	0	0.005	-0.002	21.535	-0.366	-0.366	0.000	0.000	0.000	0.000
80	A	95	ALA	0	0.005	-0.004	23.634	0.510	0.510	0.000	0.000	0.000	0.000
81	A	96	GLY	0	0.068	0.053	23.244	-0.486	-0.486	0.000	0.000	0.000	0.000
82	A	97	GLN	0	-0.004	0.009	20.150	-0.806	-0.806	0.000	0.000	0.000	0.000
83	A	98	LYS	1	0.951	0.963	21.112	-12.615	-12.615	0.000	0.000	0.000	0.000
84	A	99	GLY	0	-0.022	0.002	19.660	0.559	0.559	0.000	0.000	0.000	0.000
85	A	100	SER	0	-0.013	0.008	15.934	0.202	0.202	0.000	0.000	0.000	0.000
86	A	101	PHE	0	-0.037	-0.016	15.952	-1.185	-1.185	0.000	0.000	0.000	0.000
87	A	102	SER	0	0.013	-0.009	15.776	1.080	1.080	0.000	0.000	0.000	0.000
88	A	103	VAL	0	-0.048	-0.002	11.769	-0.682	-0.682	0.000	0.000	0.000	0.000
89	A	104	LYS	1	0.930	0.960	14.448	-15.307	-15.307	0.000	0.000	0.000	0.000
90	A	105	GLU	-1	-0.769	-0.871	10.022	21.605	21.605	0.000	0.000	0.000	0.000
91	A	106	ASN	0	-0.051	-0.037	10.008	-0.346	-0.346	0.000	0.000	0.000	0.000
92	A	107	THR	0	-0.064	-0.025	11.507	-1.453	-1.453	0.000	0.000	0.000	0.000
93	A	108	SER	0	0.042	0.011	12.188	2.063	2.063	0.000	0.000	0.000	0.000
94	A	109	TYR	0	-0.080	-0.056	13.421	-1.591	-1.591	0.000	0.000	0.000	0.000
95	A	110	THR	0	-0.025	-0.023	15.107	0.845	0.845	0.000	0.000	0.000	0.000
96	A	111	PHE	0	-0.022	-0.030	14.497	-0.835	-0.835	0.000	0.000	0.000	0.000
97	A	112	SER	0	0.005	-0.019	18.797	0.243	0.243	0.000	0.000	0.000	0.000
98	A	113	ALA	0	-0.005	0.013	20.794	-0.237	-0.237	0.000	0.000	0.000	0.000
99	A	114	ILE	0	-0.065	-0.018	22.458	-0.476	-0.476	0.000	0.000	0.000	0.000
100	A	115	TYR	0	0.084	0.040	26.184	-0.045	-0.045	0.000	0.000	0.000	0.000
101	A	116	THR	0	-0.049	-0.045	28.710	-0.279	-0.279	0.000	0.000	0.000	0.000
102	A	117	GLY	0	0.033	0.016	31.281	-0.419	-0.419	0.000	0.000	0.000	0.000
103	A	118	GLY	0	-0.003	-0.004	31.391	0.457	0.457	0.000	0.000	0.000	0.000
104	A	119	GLU	-1	-0.825	-0.887	32.496	9.520	9.520	0.000	0.000	0.000	0.000
105	A	120	TYR	0	-0.017	-0.010	34.031	0.297	0.297	0.000	0.000	0.000	0.000
106	A	121	PRO	0	0.031	0.025	36.552	-0.200	-0.200	0.000	0.000	0.000	0.000
107	A	122	ASN	0	-0.001	-0.026	40.092	0.163	0.163	0.000	0.000	0.000	0.000
108	A	123	SER	0	-0.040	-0.009	40.126	-0.144	-0.144	0.000	0.000	0.000	0.000
109	A	124	GLY	0	0.007	0.026	38.547	-0.014	-0.014	0.000	0.000	0.000	0.000
110	A	125	TYR	0	-0.025	-0.053	32.242	0.097	0.097	0.000	0.000	0.000	0.000
111	A	126	SER	0	0.002	-0.007	34.383	-0.195	-0.195	0.000	0.000	0.000	0.000
112	A	127	SER	0	0.015	-0.001	33.103	0.230	0.230	0.000	0.000	0.000	0.000
113	A	128	GLY	0	-0.001	0.003	29.994	-0.045	-0.045	0.000	0.000	0.000	0.000
114	A	129	THR	0	-0.025	-0.023	23.185	0.060	0.060	0.000	0.000	0.000	0.000
115	A	130	TYR	0	-0.032	-0.028	25.553	-0.275	-0.275	0.000	0.000	0.000	0.000
116	A	131	ALA	0	0.013	-0.016	20.881	0.538	0.538	0.000	0.000	0.000	0.000
117	A	132	GLY	0	0.045	0.028	20.117	-0.819	-0.819	0.000	0.000	0.000	0.000
118	A	133	HIS	0	-0.001	-0.004	14.607	0.179	0.179	0.000	0.000	0.000	0.000
119	A	134	LEU	0	-0.013	0.009	13.787	-1.092	-1.092	0.000	0.000	0.000	0.000
120	A	135	THR	0	-0.009	-0.008	13.218	1.451	1.451	0.000	0.000	0.000	0.000
121	A	136	VAL	0	-0.018	-0.004	9.989	-1.541	-1.541	0.000	0.000	0.000	0.000
122	A	137	SER	0	-0.004	-0.016	9.175	1.282	1.282	0.000	0.000	0.000	0.000
123	A	138	PHE	0	0.006	0.002	4.873	-2.369	-2.369	0.000	0.000	0.000	0.000
124	A	139	TYR	0	-0.070	-0.080	9.083	-0.184	-0.184	0.000	0.000	0.000	0.000
125	A	140	SER	0	0.059	0.015	11.006	0.542	0.542	0.000	0.000	0.000	0.000
126	A	141	ASN	0	-0.046	-0.063	12.402	-1.066	-1.066	0.000	0.000	0.000	0.000
127	A	142	ASP	-1	-0.793	-0.855	14.582	17.681	17.681	0.000	0.000	0.000	0.000
128	A	143	ASN	0	-0.045	-0.033	17.471	-0.692	-0.692	0.000	0.000	0.000	0.000
129	A	144	LYS	1	0.946	0.970	20.375	-11.539	-11.539	0.000	0.000	0.000	0.000
130	A	145	GLN	0	0.021	0.025	18.900	0.146	0.146	0.000	0.000	0.000	0.000
131	A	146	ARG	1	0.880	0.934	15.571	-16.602	-16.602	0.000	0.000	0.000	0.000
132	A	147	THR	0	0.043	0.034	12.740	-0.511	-0.511	0.000	0.000	0.000	0.000
133	A	148	GLU	-1	-0.791	-0.867	10.812	23.374	23.374	0.000	0.000	0.000	0.000
134	A	149	ILE	0	-0.014	-0.015	7.272	-0.547	-0.547	0.000	0.000	0.000	0.000
135	A	150	ALA	0	0.018	0.018	4.441	3.561	3.669	-0.001	-0.015	-0.092	0.000
136	A	151	THR	0	-0.025	-0.028	6.317	-3.595	-3.595	0.000	0.000	0.000	0.000
137	A	152	LYS	1	0.830	0.894	6.648	-41.494	-41.494	0.000	0.000	0.000	0.000
138	A	153	ASN	0	0.054	0.052	9.043	-0.987	-0.987	0.000	0.000	0.000	0.000
139	A	154	PHE	0	0.044	0.014	6.608	-0.990	-0.990	0.000	0.000	0.000	0.000
140	A	155	PRO	0	0.003	-0.003	11.875	-1.903	-1.903	0.000	0.000	0.000	0.000
141	A	156	VAL	0	-0.035	-0.005	14.766	0.874	0.874	0.000	0.000	0.000	0.000
142	A	157	SER	0	-0.015	-0.023	17.375	-0.601	-0.601	0.000	0.000	0.000	0.000
143	A	158	THR	0	0.007	0.010	20.874	0.053	0.053	0.000	0.000	0.000	0.000
144	A	159	THR	0	-0.010	-0.007	23.876	0.001	0.001	0.000	0.000	0.000	0.000
145	A	160	ILE	0	-0.006	0.018	26.867	-0.061	-0.061	0.000	0.000	0.000	0.000
146	A	161	SER	0	-0.001	-0.023	30.646	-0.196	-0.196	0.000	0.000	0.000	0.000

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