FMO DATABASE

FMODB ID: QV2NY

Calculation Name: 4YTW-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4YTW

Chain ID: B

ChEMBL ID:

UniProt ID: O60200

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	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	168
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1477356.79245
FMO2-HF: Nuclear repulsion	1409759.898029
FMO2-HF: Total energy	-67596.894421
FMO2-MP2: Total energy	-67793.752764

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(B:1:MET)

Summations of interaction energy for fragment #1(B:1: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.
-8.675	-5.693	9.631	-5.224	-7.387	-0.035

Interaction energy analysis for fragmet #1(B:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.029 / q_NPA : -0.017

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	B	3	LEU	0	0.002	0.012	2.598	-2.166	0.865	0.742	-1.027	-2.745	0.002
4	B	4	LEU	0	-0.024	-0.018	4.899	0.039	0.095	-0.001	-0.003	-0.052	0.000
5	B	5	HIS	0	0.023	0.018	7.620	-0.054	-0.054	0.000	0.000	0.000	0.000
6	B	6	LYS	1	0.941	0.954	11.597	-0.154	-0.154	0.000	0.000	0.000	0.000
7	B	7	SER	0	0.016	0.017	15.248	0.008	0.008	0.000	0.000	0.000	0.000
8	B	8	THR	0	-0.003	-0.014	18.592	0.001	0.001	0.000	0.000	0.000	0.000
9	B	9	HIS	0	-0.043	-0.013	22.199	-0.002	-0.002	0.000	0.000	0.000	0.000
10	B	10	ILE	0	0.044	0.022	25.247	0.001	0.001	0.000	0.000	0.000	0.000
11	B	11	PHE	0	-0.005	0.005	26.132	-0.001	-0.001	0.000	0.000	0.000	0.000
12	B	12	PRO	0	0.040	0.042	31.083	0.000	0.000	0.000	0.000	0.000	0.000
13	B	13	THR	0	-0.036	-0.039	34.184	-0.002	-0.002	0.000	0.000	0.000	0.000
14	B	14	ASP	-1	-0.726	-0.837	34.819	0.041	0.041	0.000	0.000	0.000	0.000
15	B	15	PHE	0	0.065	0.020	30.875	0.001	0.001	0.000	0.000	0.000	0.000
16	B	16	ALA	0	0.010	0.030	34.270	0.001	0.001	0.000	0.000	0.000	0.000
17	B	17	SER	0	-0.071	-0.070	36.023	-0.001	-0.001	0.000	0.000	0.000	0.000
18	B	18	VAL	0	0.010	0.013	29.679	0.001	0.001	0.000	0.000	0.000	0.000
19	B	19	SER	0	-0.002	-0.022	30.870	0.001	0.001	0.000	0.000	0.000	0.000
20	B	20	ARG	1	0.947	0.976	31.891	-0.034	-0.034	0.000	0.000	0.000	0.000
21	B	21	ALA	0	0.026	0.014	31.655	-0.001	-0.001	0.000	0.000	0.000	0.000
22	B	22	PHE	0	-0.007	0.001	23.921	0.001	0.001	0.000	0.000	0.000	0.000
23	B	23	PHE	0	-0.013	-0.034	28.945	0.000	0.000	0.000	0.000	0.000	0.000
24	B	24	ASN	0	-0.053	-0.022	31.174	-0.003	-0.003	0.000	0.000	0.000	0.000
25	B	25	ARG	1	0.947	1.008	22.648	-0.070	-0.070	0.000	0.000	0.000	0.000
26	B	26	TYR	0	-0.028	0.022	23.858	0.002	0.002	0.000	0.000	0.000	0.000
27	B	27	PRO	0	0.064	0.018	30.370	-0.001	-0.001	0.000	0.000	0.000	0.000
28	B	28	ASN	0	0.024	-0.028	27.304	0.001	0.001	0.000	0.000	0.000	0.000
29	B	29	PRO	0	0.039	0.002	29.745	0.001	0.001	0.000	0.000	0.000	0.000
30	B	30	TYR	0	0.024	0.021	26.353	0.000	0.000	0.000	0.000	0.000	0.000
31	B	31	SER	0	-0.077	-0.031	24.922	0.009	0.009	0.000	0.000	0.000	0.000
32	B	32	PRO	0	0.039	0.020	25.781	-0.002	-0.002	0.000	0.000	0.000	0.000
33	B	33	HIS	0	-0.070	-0.036	22.813	-0.004	-0.004	0.000	0.000	0.000	0.000
34	B	34	VAL	0	-0.029	-0.005	23.896	0.000	0.000	0.000	0.000	0.000	0.000
35	B	35	LEU	0	-0.020	-0.011	25.773	-0.003	-0.003	0.000	0.000	0.000	0.000
36	B	36	SER	0	0.024	0.014	27.441	-0.003	-0.003	0.000	0.000	0.000	0.000
37	B	37	ILE	0	-0.022	-0.025	26.968	0.004	0.004	0.000	0.000	0.000	0.000
38	B	38	ASP	-1	-0.887	-0.916	28.557	0.026	0.026	0.000	0.000	0.000	0.000
39	B	39	THR	0	-0.034	-0.037	29.089	0.004	0.004	0.000	0.000	0.000	0.000
40	B	40	ILE	0	-0.027	-0.011	26.984	-0.002	-0.002	0.000	0.000	0.000	0.000
41	B	41	SER	0	0.014	0.000	28.982	-0.001	-0.001	0.000	0.000	0.000	0.000
42	B	42	ARG	1	0.923	0.942	30.856	-0.040	-0.040	0.000	0.000	0.000	0.000
43	B	43	ASN	0	-0.036	0.002	32.089	-0.001	-0.001	0.000	0.000	0.000	0.000
44	B	44	VAL	0	0.035	0.025	34.272	0.002	0.002	0.000	0.000	0.000	0.000
45	B	45	ASP	-1	-0.749	-0.863	32.522	0.057	0.057	0.000	0.000	0.000	0.000
46	B	46	GLN	0	0.024	-0.008	35.437	-0.002	-0.002	0.000	0.000	0.000	0.000
47	B	47	GLU	-1	-0.997	-0.991	32.806	0.064	0.064	0.000	0.000	0.000	0.000
48	B	48	GLY	0	-0.013	0.006	36.937	-0.001	-0.001	0.000	0.000	0.000	0.000
49	B	49	ASN	0	-0.036	-0.020	32.583	-0.002	-0.002	0.000	0.000	0.000	0.000
50	B	50	LEU	0	-0.040	-0.014	33.282	-0.001	-0.001	0.000	0.000	0.000	0.000
51	B	51	ARG	1	0.868	0.922	27.211	-0.065	-0.065	0.000	0.000	0.000	0.000
52	B	52	THR	0	0.000	-0.003	29.019	-0.005	-0.005	0.000	0.000	0.000	0.000
53	B	53	THR	0	-0.006	0.008	24.551	0.006	0.006	0.000	0.000	0.000	0.000
54	B	54	ARG	1	0.741	0.819	25.739	-0.054	-0.054	0.000	0.000	0.000	0.000
55	B	55	LEU	0	-0.003	0.000	23.295	0.003	0.003	0.000	0.000	0.000	0.000
56	B	56	LEU	0	0.022	0.012	22.992	-0.002	-0.002	0.000	0.000	0.000	0.000
57	B	57	LYS	1	0.872	0.948	23.085	-0.013	-0.013	0.000	0.000	0.000	0.000
58	B	58	LYS	1	0.881	0.937	18.954	-0.076	-0.076	0.000	0.000	0.000	0.000
59	B	59	SER	0	0.073	0.038	21.503	0.000	0.000	0.000	0.000	0.000	0.000
60	B	60	GLY	0	-0.017	-0.034	19.344	0.013	0.013	0.000	0.000	0.000	0.000
61	B	61	LYS	1	0.961	0.974	18.951	-0.031	-0.031	0.000	0.000	0.000	0.000
62	B	62	LEU	0	0.021	0.028	13.785	0.021	0.021	0.000	0.000	0.000	0.000
63	B	63	PRO	0	0.045	0.020	12.082	-0.018	-0.018	0.000	0.000	0.000	0.000
64	B	64	THR	0	0.029	-0.005	15.143	-0.022	-0.022	0.000	0.000	0.000	0.000
65	B	65	TRP	0	0.045	0.018	7.508	-0.030	-0.030	0.000	0.000	0.000	0.000
66	B	66	VAL	0	-0.003	-0.001	10.369	-0.040	-0.040	0.000	0.000	0.000	0.000
67	B	67	LYS	1	0.944	0.963	12.905	0.004	0.004	0.000	0.000	0.000	0.000
68	B	68	PRO	0	0.028	0.032	14.958	-0.002	-0.002	0.000	0.000	0.000	0.000
69	B	69	PHE	0	-0.050	-0.024	11.616	-0.026	-0.026	0.000	0.000	0.000	0.000
70	B	70	LEU	0	-0.047	-0.018	11.104	-0.016	-0.016	0.000	0.000	0.000	0.000
71	B	71	ARG	1	0.951	0.979	14.783	0.089	0.089	0.000	0.000	0.000	0.000
72	B	72	GLY	0	0.023	-0.001	17.718	0.009	0.009	0.000	0.000	0.000	0.000
73	B	73	ILE	0	-0.041	-0.022	15.205	-0.001	-0.001	0.000	0.000	0.000	0.000
74	B	74	THR	0	0.029	0.006	19.250	0.007	0.007	0.000	0.000	0.000	0.000
75	B	75	GLU	-1	-0.845	-0.900	20.923	0.017	0.017	0.000	0.000	0.000	0.000
76	B	76	THR	0	-0.093	-0.040	16.248	-0.002	-0.002	0.000	0.000	0.000	0.000
77	B	77	TRP	0	0.065	0.038	19.395	0.008	0.008	0.000	0.000	0.000	0.000
78	B	78	ILE	0	-0.027	-0.025	17.860	0.000	0.000	0.000	0.000	0.000	0.000
79	B	79	ILE	0	0.006	0.022	18.693	-0.002	-0.002	0.000	0.000	0.000	0.000
80	B	80	GLU	-1	-0.801	-0.880	20.298	0.064	0.064	0.000	0.000	0.000	0.000
81	B	81	VAL	0	0.003	-0.002	21.732	-0.004	-0.004	0.000	0.000	0.000	0.000
82	B	82	SER	0	-0.002	-0.013	23.589	0.003	0.003	0.000	0.000	0.000	0.000
83	B	83	VAL	0	-0.017	-0.010	26.163	-0.002	-0.002	0.000	0.000	0.000	0.000
84	B	84	VAL	0	-0.013	-0.009	28.671	0.002	0.002	0.000	0.000	0.000	0.000
85	B	85	ASN	0	0.065	0.042	31.409	-0.004	-0.004	0.000	0.000	0.000	0.000
86	B	86	PRO	0	0.015	-0.011	33.432	0.000	0.000	0.000	0.000	0.000	0.000
87	B	87	ALA	0	0.003	0.017	36.609	-0.002	-0.002	0.000	0.000	0.000	0.000
88	B	88	ASN	0	0.012	-0.013	31.289	-0.001	-0.001	0.000	0.000	0.000	0.000
89	B	89	SER	0	-0.005	0.014	33.955	0.000	0.000	0.000	0.000	0.000	0.000
90	B	90	THR	0	0.009	0.005	28.162	0.003	0.003	0.000	0.000	0.000	0.000
91	B	91	MET	0	-0.037	-0.009	27.340	-0.002	-0.002	0.000	0.000	0.000	0.000
92	B	92	LYS	1	0.960	0.992	23.925	-0.084	-0.084	0.000	0.000	0.000	0.000
93	B	93	THR	0	-0.025	-0.034	22.624	-0.003	-0.003	0.000	0.000	0.000	0.000
94	B	94	TYR	0	-0.026	-0.037	14.354	0.004	0.004	0.000	0.000	0.000	0.000
95	B	95	THR	0	-0.002	0.012	17.814	-0.007	-0.007	0.000	0.000	0.000	0.000
96	B	96	ARG	1	0.959	0.983	13.994	-0.051	-0.051	0.000	0.000	0.000	0.000
97	B	97	ASN	0	-0.013	-0.001	12.026	0.008	0.008	0.000	0.000	0.000	0.000
98	B	98	LEU	0	-0.021	-0.026	15.070	-0.007	-0.007	0.000	0.000	0.000	0.000
99	B	99	ASP	-1	-0.777	-0.886	16.470	-0.004	-0.004	0.000	0.000	0.000	0.000
100	B	100	HIS	0	0.048	0.013	13.752	-0.012	-0.012	0.000	0.000	0.000	0.000
101	B	101	THR	0	0.007	0.006	10.966	-0.028	-0.028	0.000	0.000	0.000	0.000
102	B	102	GLY	0	0.001	0.018	9.138	-0.076	-0.076	0.000	0.000	0.000	0.000
103	B	103	ILE	0	-0.058	-0.024	8.685	-0.164	-0.164	0.000	0.000	0.000	0.000
104	B	104	MET	0	0.004	0.014	4.557	-0.502	-0.290	0.003	-0.041	-0.173	0.000
105	B	105	LYS	1	0.893	0.961	7.557	-0.035	-0.035	0.000	0.000	0.000	0.000
106	B	106	VAL	0	0.004	-0.005	8.637	-0.047	-0.047	0.000	0.000	0.000	0.000
107	B	107	GLU	-1	-0.809	-0.875	10.834	0.139	0.139	0.000	0.000	0.000	0.000
108	B	108	GLU	-1	-0.844	-0.891	12.578	0.110	0.110	0.000	0.000	0.000	0.000
109	B	109	TYR	0	-0.014	-0.019	14.464	-0.001	-0.001	0.000	0.000	0.000	0.000
110	B	110	THR	0	0.012	-0.012	17.752	0.007	0.007	0.000	0.000	0.000	0.000
111	B	111	THR	0	-0.062	-0.015	20.549	-0.004	-0.004	0.000	0.000	0.000	0.000
112	B	112	TYR	0	0.010	0.009	23.571	0.000	0.000	0.000	0.000	0.000	0.000
113	B	113	GLN	0	0.002	-0.012	26.994	0.002	0.002	0.000	0.000	0.000	0.000
114	B	114	PHE	0	0.004	0.007	29.526	-0.001	-0.001	0.000	0.000	0.000	0.000
115	B	115	ASP	-1	-0.784	-0.874	32.486	0.049	0.049	0.000	0.000	0.000	0.000
116	B	116	SER	0	0.001	-0.022	34.246	-0.002	-0.002	0.000	0.000	0.000	0.000
117	B	117	ALA	0	-0.039	-0.003	36.791	-0.002	-0.002	0.000	0.000	0.000	0.000
118	B	118	THR	0	-0.041	-0.049	34.605	-0.001	-0.001	0.000	0.000	0.000	0.000
119	B	119	SER	0	-0.058	-0.015	37.075	-0.001	-0.001	0.000	0.000	0.000	0.000
120	B	120	SER	0	-0.022	-0.005	33.021	-0.001	-0.001	0.000	0.000	0.000	0.000
121	B	121	THR	0	-0.041	-0.027	29.496	0.001	0.001	0.000	0.000	0.000	0.000
122	B	122	ILE	0	-0.001	0.005	26.064	0.001	0.001	0.000	0.000	0.000	0.000
123	B	123	ALA	0	-0.003	-0.006	24.178	0.001	0.001	0.000	0.000	0.000	0.000
124	B	124	ASP	-1	-0.842	-0.896	21.122	0.088	0.088	0.000	0.000	0.000	0.000
125	B	125	SER	0	-0.012	-0.034	17.533	0.000	0.000	0.000	0.000	0.000	0.000
126	B	126	ARG	1	0.847	0.929	14.387	-0.128	-0.128	0.000	0.000	0.000	0.000
127	B	127	VAL	0	0.025	0.010	10.965	-0.005	-0.005	0.000	0.000	0.000	0.000
128	B	128	LYS	1	0.860	0.922	7.476	-0.172	-0.172	0.000	0.000	0.000	0.000
129	B	129	PHE	0	0.017	0.009	5.679	0.067	0.067	0.000	0.000	0.000	0.000
130	B	130	SER	0	-0.025	-0.029	4.530	-0.748	-0.569	-0.001	-0.075	-0.103	0.000
131	B	131	SER	0	0.010	-0.033	2.891	0.609	1.801	0.034	-0.395	-0.831	0.000
132	B	132	GLY	0	0.068	0.038	1.949	-6.868	-9.085	8.848	-3.552	-3.079	-0.037
133	B	133	PHE	0	0.026	0.033	3.888	0.421	0.578	0.002	-0.041	-0.119	0.000
134	B	134	ASN	0	-0.058	-0.032	3.790	-0.945	-0.573	0.004	-0.090	-0.285	0.000
135	B	135	MET	0	0.014	0.002	5.597	0.243	0.243	0.000	0.000	0.000	0.000
136	B	136	GLY	0	0.033	0.016	8.608	0.099	0.099	0.000	0.000	0.000	0.000
137	B	137	ILE	0	-0.010	-0.011	8.085	0.105	0.105	0.000	0.000	0.000	0.000
138	B	138	LYS	1	0.972	0.981	7.797	1.079	1.079	0.000	0.000	0.000	0.000
139	B	139	SER	0	0.079	0.040	11.811	0.071	0.071	0.000	0.000	0.000	0.000
140	B	140	LYS	1	0.951	0.989	13.150	0.358	0.358	0.000	0.000	0.000	0.000
141	B	141	VAL	0	-0.008	-0.002	12.601	0.035	0.035	0.000	0.000	0.000	0.000
142	B	142	GLU	-1	-0.871	-0.918	15.406	-0.172	-0.172	0.000	0.000	0.000	0.000
143	B	143	ASP	-1	-0.805	-0.896	17.846	-0.197	-0.197	0.000	0.000	0.000	0.000
144	B	144	TRP	0	-0.017	0.000	18.557	0.024	0.024	0.000	0.000	0.000	0.000
145	B	145	SER	0	-0.013	-0.026	18.621	0.020	0.020	0.000	0.000	0.000	0.000
146	B	146	ARG	1	0.809	0.889	20.627	0.201	0.201	0.000	0.000	0.000	0.000
147	B	147	THR	0	-0.015	-0.014	23.369	0.019	0.019	0.000	0.000	0.000	0.000
148	B	148	LYS	1	0.838	0.913	23.891	0.157	0.157	0.000	0.000	0.000	0.000
149	B	149	PHE	0	0.021	0.008	25.348	0.012	0.012	0.000	0.000	0.000	0.000
150	B	150	ASP	-1	-0.793	-0.883	27.184	-0.084	-0.084	0.000	0.000	0.000	0.000
151	B	151	GLU	-1	-0.838	-0.905	28.174	-0.112	-0.112	0.000	0.000	0.000	0.000
152	B	152	ASN	0	-0.008	-0.029	27.945	0.010	0.010	0.000	0.000	0.000	0.000
153	B	153	VAL	0	-0.004	0.013	31.086	0.008	0.008	0.000	0.000	0.000	0.000
154	B	154	LYS	1	0.811	0.887	32.621	0.093	0.093	0.000	0.000	0.000	0.000
155	B	155	LYS	1	0.944	0.978	31.967	0.095	0.095	0.000	0.000	0.000	0.000
156	B	156	SER	0	-0.018	0.006	34.781	0.006	0.006	0.000	0.000	0.000	0.000
157	B	157	ARG	1	0.997	0.996	36.643	0.068	0.068	0.000	0.000	0.000	0.000
158	B	158	MET	0	-0.024	-0.024	39.019	0.003	0.003	0.000	0.000	0.000	0.000
159	B	159	GLY	0	0.032	0.030	39.608	0.003	0.003	0.000	0.000	0.000	0.000
160	B	160	MET	0	0.004	-0.004	40.201	0.003	0.003	0.000	0.000	0.000	0.000
161	B	161	ALA	0	-0.001	0.003	42.565	0.003	0.003	0.000	0.000	0.000	0.000
162	B	162	PHE	0	-0.021	-0.007	44.259	0.002	0.002	0.000	0.000	0.000	0.000
163	B	163	VAL	0	-0.022	-0.025	44.127	0.002	0.002	0.000	0.000	0.000	0.000
164	B	164	ILE	0	0.026	0.010	45.522	0.002	0.002	0.000	0.000	0.000	0.000
165	B	165	GLN	0	0.028	0.023	48.535	0.001	0.001	0.000	0.000	0.000	0.000
166	B	166	LYS	1	0.897	0.967	47.626	0.045	0.045	0.000	0.000	0.000	0.000
167	B	167	LEU	0	-0.076	-0.048	49.264	0.001	0.001	0.000	0.000	0.000	0.000
168	B	168	GLU	-1	-1.009	-0.987	52.504	-0.029	-0.029	0.000	0.000	0.000	0.000

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