FMO DATABASE

FMODB ID: G6R41

Calculation Name: 2YWX-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2YWX

Chain ID: A

ChEMBL ID:

UniProt ID: Q58033

Base Structure: X-ray

Registration Date: 2023-06-22

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	157
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1382362.147849
FMO2-HF: Nuclear repulsion	1322990.430723
FMO2-HF: Total energy	-59371.717126
FMO2-MP2: Total energy	-59544.35283

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:1:MET)

Summations of interaction energy for fragment #1(A: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.
-14.775	-7.682	17.015	-6.415	-17.692	-0.057

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.036 / q_NPA : 0.046

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	3	CYS	0	-0.004	-0.001	3.819	0.512	3.635	0.294	-1.416	-2.001	0.000
4	A	4	ILE	0	-0.013	-0.004	5.377	-1.078	-1.039	-0.001	-0.011	-0.027	0.000
5	A	5	ILE	0	0.001	-0.003	8.598	-0.005	-0.005	0.000	0.000	0.000	0.000
6	A	6	MET	0	-0.012	0.009	11.473	-0.108	-0.108	0.000	0.000	0.000	0.000
7	A	7	GLY	0	0.049	0.026	14.896	-0.005	-0.005	0.000	0.000	0.000	0.000
8	A	8	SER	0	-0.080	-0.066	18.169	-0.028	-0.028	0.000	0.000	0.000	0.000
9	A	9	GLU	-1	-0.857	-0.923	18.388	0.100	0.100	0.000	0.000	0.000	0.000
10	A	10	SER	0	-0.022	-0.017	19.431	-0.002	-0.002	0.000	0.000	0.000	0.000
11	A	11	ASP	-1	-0.830	-0.923	17.588	0.153	0.153	0.000	0.000	0.000	0.000
12	A	12	LEU	0	0.071	0.031	15.566	0.021	0.021	0.000	0.000	0.000	0.000
13	A	13	LYS	1	0.857	0.937	17.410	-0.076	-0.076	0.000	0.000	0.000	0.000
14	A	14	ILE	0	-0.067	-0.028	16.725	-0.013	-0.013	0.000	0.000	0.000	0.000
15	A	15	ALA	0	0.050	0.005	13.016	0.010	0.010	0.000	0.000	0.000	0.000
16	A	16	GLU	-1	-0.858	-0.933	13.307	0.147	0.147	0.000	0.000	0.000	0.000
17	A	17	LYS	1	0.845	0.939	15.026	-0.104	-0.104	0.000	0.000	0.000	0.000
18	A	18	ALA	0	0.001	0.008	11.164	-0.019	-0.019	0.000	0.000	0.000	0.000
19	A	19	VAL	0	0.046	0.015	9.606	0.012	0.012	0.000	0.000	0.000	0.000
20	A	20	ASN	0	-0.035	-0.021	11.225	-0.054	-0.054	0.000	0.000	0.000	0.000
21	A	21	ILE	0	0.026	0.029	11.330	-0.018	-0.018	0.000	0.000	0.000	0.000
22	A	22	LEU	0	-0.017	-0.014	6.047	-0.028	-0.028	0.000	0.000	0.000	0.000
23	A	23	LYS	1	0.877	0.932	9.079	-0.054	-0.054	0.000	0.000	0.000	0.000
24	A	24	GLU	-1	-0.963	-0.978	11.291	0.065	0.065	0.000	0.000	0.000	0.000
25	A	25	PHE	0	-0.061	-0.046	9.159	-0.022	-0.022	0.000	0.000	0.000	0.000
26	A	26	GLY	0	-0.021	0.004	9.741	0.028	0.028	0.000	0.000	0.000	0.000
27	A	27	VAL	0	-0.040	-0.021	4.264	-0.035	0.055	-0.001	-0.006	-0.083	0.000
28	A	28	GLU	-1	-0.880	-0.944	2.168	-8.505	-5.715	3.910	-2.724	-3.976	-0.017
29	A	29	PHE	0	-0.076	-0.058	2.409	-1.288	-0.142	7.530	-4.425	-4.250	-0.023
30	A	30	GLU	-1	-0.776	-0.874	2.886	-2.787	-4.243	2.051	2.400	-2.994	-0.013
31	A	31	VAL	0	-0.050	-0.030	4.566	-0.045	0.012	0.005	0.046	-0.108	0.000
32	A	32	ARG	1	0.885	0.935	7.705	-0.652	-0.652	0.000	0.000	0.000	0.000
33	A	33	VAL	0	-0.002	0.002	10.917	0.001	0.001	0.000	0.000	0.000	0.000
34	A	34	ALA	0	0.011	0.006	14.164	-0.025	-0.025	0.000	0.000	0.000	0.000
35	A	35	SER	0	0.023	0.022	15.863	0.004	0.004	0.000	0.000	0.000	0.000
36	A	36	ALA	0	0.031	0.007	18.354	-0.016	-0.016	0.000	0.000	0.000	0.000
37	A	37	HIS	0	0.034	0.020	19.660	-0.007	-0.007	0.000	0.000	0.000	0.000
38	A	38	ARG	1	0.821	0.891	21.441	-0.108	-0.108	0.000	0.000	0.000	0.000
39	A	39	THR	0	0.016	0.012	18.526	-0.005	-0.005	0.000	0.000	0.000	0.000
40	A	40	PRO	0	0.024	0.028	18.626	0.023	0.023	0.000	0.000	0.000	0.000
41	A	41	GLU	-1	-0.791	-0.903	17.999	0.100	0.100	0.000	0.000	0.000	0.000
42	A	42	LEU	0	0.025	0.015	14.376	0.008	0.008	0.000	0.000	0.000	0.000
43	A	43	VAL	0	-0.029	-0.020	13.891	0.052	0.052	0.000	0.000	0.000	0.000
44	A	44	GLU	-1	-0.812	-0.906	13.118	0.102	0.102	0.000	0.000	0.000	0.000
45	A	45	GLU	-1	-0.977	-0.984	13.231	0.078	0.078	0.000	0.000	0.000	0.000
46	A	46	ILE	0	-0.002	-0.009	8.583	0.022	0.022	0.000	0.000	0.000	0.000
47	A	47	VAL	0	-0.042	-0.028	8.777	0.107	0.107	0.000	0.000	0.000	0.000
48	A	48	LYS	1	0.827	0.911	9.502	-0.090	-0.090	0.000	0.000	0.000	0.000
49	A	49	ASN	0	-0.051	-0.021	9.986	-0.083	-0.083	0.000	0.000	0.000	0.000
50	A	50	SER	0	-0.014	0.007	4.709	-0.038	0.046	-0.001	-0.004	-0.079	0.000
51	A	51	LYS	1	0.853	0.914	3.316	-0.525	-0.041	0.014	-0.089	-0.409	0.000
52	A	52	ALA	0	-0.019	0.012	2.184	-2.753	-0.948	3.010	-2.314	-2.501	-0.003
53	A	53	ASP	-1	-0.808	-0.888	2.804	1.336	-0.214	0.159	2.294	-0.904	-0.001
54	A	54	VAL	0	-0.038	-0.014	5.188	0.495	0.495	0.000	0.000	0.000	0.000
55	A	55	PHE	0	0.048	0.018	5.688	0.371	0.371	0.000	0.000	0.000	0.000
56	A	56	ILE	0	-0.007	-0.008	8.123	-0.180	-0.180	0.000	0.000	0.000	0.000
57	A	57	ALA	0	0.029	0.033	10.719	0.107	0.107	0.000	0.000	0.000	0.000
58	A	58	ILE	0	-0.042	-0.024	13.025	-0.065	-0.065	0.000	0.000	0.000	0.000
59	A	59	ALA	0	0.051	0.016	16.057	0.007	0.007	0.000	0.000	0.000	0.000
60	A	60	GLY	0	0.038	0.026	19.524	-0.012	-0.012	0.000	0.000	0.000	0.000
61	A	61	LEU	0	-0.032	-0.024	23.260	0.000	0.000	0.000	0.000	0.000	0.000
62	A	62	ALA	0	0.065	0.034	25.656	0.001	0.001	0.000	0.000	0.000	0.000
63	A	63	ALA	0	-0.006	0.010	20.856	0.004	0.004	0.000	0.000	0.000	0.000
64	A	64	HIS	0	0.015	-0.022	21.253	-0.002	-0.002	0.000	0.000	0.000	0.000
65	A	65	LEU	0	-0.040	0.002	14.958	-0.010	-0.010	0.000	0.000	0.000	0.000
66	A	66	PRO	0	0.024	-0.005	15.348	0.013	0.013	0.000	0.000	0.000	0.000
67	A	67	GLY	0	0.082	0.033	16.135	-0.008	-0.008	0.000	0.000	0.000	0.000
68	A	68	VAL	0	-0.013	-0.005	17.149	-0.009	-0.009	0.000	0.000	0.000	0.000
69	A	69	VAL	0	0.006	0.005	11.456	-0.002	-0.002	0.000	0.000	0.000	0.000
70	A	70	ALA	0	0.034	0.009	13.738	-0.010	-0.010	0.000	0.000	0.000	0.000
71	A	71	SER	0	-0.087	-0.053	15.385	-0.021	-0.021	0.000	0.000	0.000	0.000
72	A	72	LEU	0	-0.033	-0.010	14.132	-0.010	-0.010	0.000	0.000	0.000	0.000
73	A	73	THR	0	-0.036	-0.021	10.010	-0.026	-0.026	0.000	0.000	0.000	0.000
74	A	74	THR	0	0.012	0.012	12.966	-0.006	-0.006	0.000	0.000	0.000	0.000
75	A	75	LYS	1	0.824	0.917	7.020	0.436	0.436	0.000	0.000	0.000	0.000
76	A	76	PRO	0	0.017	0.003	9.587	0.068	0.068	0.000	0.000	0.000	0.000
77	A	77	VAL	0	0.022	0.022	10.135	0.000	0.000	0.000	0.000	0.000	0.000
78	A	78	ILE	0	-0.010	0.002	10.756	-0.017	-0.017	0.000	0.000	0.000	0.000
79	A	79	ALA	0	0.005	0.005	13.487	0.063	0.063	0.000	0.000	0.000	0.000
80	A	80	VAL	0	-0.028	-0.027	15.040	-0.025	-0.025	0.000	0.000	0.000	0.000
81	A	81	PRO	0	0.019	0.018	17.842	0.013	0.013	0.000	0.000	0.000	0.000
82	A	82	VAL	0	0.019	-0.001	19.872	-0.002	-0.002	0.000	0.000	0.000	0.000
83	A	83	ASP	-1	-0.779	-0.873	22.606	0.072	0.072	0.000	0.000	0.000	0.000
84	A	84	ALA	0	-0.057	-0.022	25.211	-0.005	-0.005	0.000	0.000	0.000	0.000
85	A	85	LYS	1	0.927	0.950	27.088	-0.048	-0.048	0.000	0.000	0.000	0.000
86	A	86	LEU	0	0.013	0.016	29.597	0.002	0.002	0.000	0.000	0.000	0.000
87	A	87	ASP	-1	-0.877	-0.935	30.472	0.041	0.041	0.000	0.000	0.000	0.000
88	A	88	GLY	0	-0.001	0.001	26.868	0.002	0.002	0.000	0.000	0.000	0.000
89	A	89	LEU	0	-0.018	-0.010	26.620	0.004	0.004	0.000	0.000	0.000	0.000
90	A	90	ASP	-1	-0.854	-0.938	28.133	0.050	0.050	0.000	0.000	0.000	0.000
91	A	91	ALA	0	-0.020	-0.004	22.951	0.001	0.001	0.000	0.000	0.000	0.000
92	A	92	LEU	0	-0.008	0.002	23.241	0.005	0.005	0.000	0.000	0.000	0.000
93	A	93	LEU	0	0.040	0.013	24.403	-0.001	-0.001	0.000	0.000	0.000	0.000
94	A	94	SER	0	-0.038	-0.027	23.669	-0.002	-0.002	0.000	0.000	0.000	0.000
95	A	95	SER	0	-0.055	-0.022	19.852	0.005	0.005	0.000	0.000	0.000	0.000
96	A	96	VAL	0	0.015	0.006	21.168	-0.003	-0.003	0.000	0.000	0.000	0.000
97	A	97	GLN	0	-0.063	-0.021	23.288	-0.007	-0.007	0.000	0.000	0.000	0.000
98	A	98	MET	0	-0.014	0.022	19.669	0.003	0.003	0.000	0.000	0.000	0.000
99	A	99	PRO	0	0.000	0.007	23.428	-0.005	-0.005	0.000	0.000	0.000	0.000
100	A	100	PRO	0	-0.006	-0.027	24.110	-0.001	-0.001	0.000	0.000	0.000	0.000
101	A	101	GLY	0	0.004	0.009	23.421	0.001	0.001	0.000	0.000	0.000	0.000
102	A	102	ILE	0	-0.041	-0.013	18.544	-0.004	-0.004	0.000	0.000	0.000	0.000
103	A	103	PRO	0	0.002	0.008	18.085	0.008	0.008	0.000	0.000	0.000	0.000
104	A	104	VAL	0	0.042	0.008	16.684	0.004	0.004	0.000	0.000	0.000	0.000
105	A	105	ALA	0	-0.017	-0.003	15.305	-0.007	-0.007	0.000	0.000	0.000	0.000
106	A	106	THR	0	0.006	0.000	16.886	0.014	0.014	0.000	0.000	0.000	0.000
107	A	107	VAL	0	-0.038	-0.005	16.485	-0.014	-0.014	0.000	0.000	0.000	0.000
108	A	108	GLY	0	0.008	-0.007	19.531	0.003	0.003	0.000	0.000	0.000	0.000
109	A	109	ILE	0	0.046	0.021	21.271	0.012	0.012	0.000	0.000	0.000	0.000
110	A	110	ASH	0	-0.066	-0.079	20.847	-0.004	-0.004	0.000	0.000	0.000	0.000
111	A	111	ARG	1	0.851	0.936	19.354	-0.063	-0.063	0.000	0.000	0.000	0.000
112	A	112	GLY	0	0.090	0.035	15.446	-0.004	-0.004	0.000	0.000	0.000	0.000
113	A	113	GLU	-1	-0.912	-0.956	14.132	0.098	0.098	0.000	0.000	0.000	0.000
114	A	114	ASN	0	0.023	-0.009	14.464	0.001	0.001	0.000	0.000	0.000	0.000
115	A	115	ALA	0	0.021	0.023	13.495	-0.026	-0.026	0.000	0.000	0.000	0.000
116	A	116	ALA	0	0.032	0.026	10.069	-0.030	-0.030	0.000	0.000	0.000	0.000
117	A	117	ILE	0	-0.010	-0.001	9.891	-0.078	-0.078	0.000	0.000	0.000	0.000
118	A	118	LEU	0	0.017	0.011	11.732	-0.037	-0.037	0.000	0.000	0.000	0.000
119	A	119	ALA	0	0.024	-0.001	7.313	-0.041	-0.041	0.000	0.000	0.000	0.000
120	A	120	LEU	0	-0.001	0.002	6.742	-0.236	-0.236	0.000	0.000	0.000	0.000
121	A	121	GLU	-1	-0.831	-0.914	8.395	-0.020	-0.020	0.000	0.000	0.000	0.000
122	A	122	ILE	0	-0.031	-0.008	8.400	0.024	0.024	0.000	0.000	0.000	0.000
123	A	123	LEU	0	0.003	-0.004	3.098	-0.504	-0.023	0.045	-0.166	-0.360	0.000
124	A	124	ALA	0	-0.010	-0.005	7.241	0.182	0.182	0.000	0.000	0.000	0.000
125	A	125	LEU	0	-0.058	-0.021	10.356	0.062	0.062	0.000	0.000	0.000	0.000
126	A	126	LYS	1	0.827	0.903	5.687	0.182	0.182	0.000	0.000	0.000	0.000
127	A	127	ASP	-1	-0.798	-0.875	7.314	0.679	0.679	0.000	0.000	0.000	0.000
128	A	128	GLU	-1	-0.857	-0.943	9.511	0.053	0.053	0.000	0.000	0.000	0.000
129	A	129	ASN	0	-0.038	-0.030	8.786	-0.113	-0.113	0.000	0.000	0.000	0.000
130	A	130	ILE	0	-0.015	-0.002	5.451	-0.048	-0.048	0.000	0.000	0.000	0.000
131	A	131	ALA	0	0.031	0.015	9.995	-0.033	-0.033	0.000	0.000	0.000	0.000
132	A	132	LYS	1	0.863	0.922	13.017	-0.097	-0.097	0.000	0.000	0.000	0.000
133	A	133	LYS	1	0.886	0.944	10.784	-0.236	-0.236	0.000	0.000	0.000	0.000
134	A	134	LEU	0	0.010	0.016	11.014	-0.004	-0.004	0.000	0.000	0.000	0.000
135	A	135	ILE	0	-0.013	0.000	14.596	-0.002	-0.002	0.000	0.000	0.000	0.000
136	A	136	GLU	-1	-0.836	-0.918	17.431	0.077	0.077	0.000	0.000	0.000	0.000
137	A	137	TYR	0	-0.031	-0.006	15.771	-0.005	-0.005	0.000	0.000	0.000	0.000
138	A	138	ARG	1	0.882	0.910	16.950	-0.005	-0.005	0.000	0.000	0.000	0.000
139	A	139	GLU	-1	-0.811	-0.882	20.094	0.026	0.026	0.000	0.000	0.000	0.000
140	A	140	LYS	1	0.892	0.933	17.618	-0.065	-0.065	0.000	0.000	0.000	0.000
141	A	141	MET	0	-0.036	-0.016	19.541	-0.003	-0.003	0.000	0.000	0.000	0.000
142	A	142	LYS	1	0.881	0.931	22.998	-0.025	-0.025	0.000	0.000	0.000	0.000
143	A	143	LYS	1	0.863	0.928	25.503	-0.030	-0.030	0.000	0.000	0.000	0.000
144	A	144	LYS	1	0.968	0.996	22.029	-0.045	-0.045	0.000	0.000	0.000	0.000
145	A	145	VAL	0	0.012	0.025	27.025	-0.001	-0.001	0.000	0.000	0.000	0.000
146	A	146	TYR	0	0.032	0.002	29.502	-0.001	-0.001	0.000	0.000	0.000	0.000
147	A	147	ALA	0	0.018	0.011	30.689	-0.001	-0.001	0.000	0.000	0.000	0.000
148	A	148	SER	0	-0.072	-0.048	30.602	-0.001	-0.001	0.000	0.000	0.000	0.000
149	A	149	ASP	-1	-0.845	-0.920	33.266	0.017	0.017	0.000	0.000	0.000	0.000
150	A	150	GLU	-1	-0.841	-0.917	35.609	0.016	0.016	0.000	0.000	0.000	0.000
151	A	151	LYS	1	0.918	0.967	34.629	-0.023	-0.023	0.000	0.000	0.000	0.000
152	A	152	VAL	0	-0.009	-0.018	36.936	-0.001	-0.001	0.000	0.000	0.000	0.000
153	A	153	LYS	1	0.792	0.883	37.744	-0.018	-0.018	0.000	0.000	0.000	0.000
154	A	154	GLU	-1	-0.822	-0.883	41.391	0.013	0.013	0.000	0.000	0.000	0.000
155	A	155	MET	0	-0.089	-0.029	38.549	0.000	0.000	0.000	0.000	0.000	0.000
156	A	156	PHE	0	-0.005	-0.003	41.717	0.000	0.000	0.000	0.000	0.000	0.000
157	A	157	LYS	1	0.788	0.887	44.990	-0.013	-0.013	0.000	0.000	0.000	0.000

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