FMO DATABASE

FMODB ID: 89YQY

Calculation Name: 1DIV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1DIV

Chain ID: A

ChEMBL ID:

UniProt ID: P02417

Base Structure: X-ray

Registration Date: 2023-09-24

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	149
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1123941.469254
FMO2-HF: Nuclear repulsion	1068060.825599
FMO2-HF: Total energy	-55880.643655
FMO2-MP2: Total energy	-56048.013954

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.
-39.545	-42.232	41.043	-17.009	-21.345	-0.061

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 : 0.017 / q_NPA : 0.019

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	VAL	0	-0.003	-0.006	2.911	-3.467	-0.396	0.524	-1.533	-2.062	0.000
4	A	4	ILE	0	-0.001	0.002	4.498	0.083	0.178	-0.001	-0.018	-0.076	0.000
5	A	5	PHE	0	0.020	-0.008	7.812	0.126	0.126	0.000	0.000	0.000	0.000
6	A	6	LEU	0	0.019	-0.001	10.104	-0.030	-0.030	0.000	0.000	0.000	0.000
7	A	7	LYS	1	0.774	0.864	12.870	-0.203	-0.203	0.000	0.000	0.000	0.000
8	A	8	ASP	-1	-0.892	-0.945	13.876	0.085	0.085	0.000	0.000	0.000	0.000
9	A	9	VAL	0	0.035	0.024	12.989	-0.003	-0.003	0.000	0.000	0.000	0.000
10	A	10	LYS	1	0.875	0.969	15.393	-0.125	-0.125	0.000	0.000	0.000	0.000
11	A	11	GLY	0	0.036	0.018	19.244	-0.002	-0.002	0.000	0.000	0.000	0.000
12	A	12	LYS	1	0.943	0.960	17.613	-0.082	-0.082	0.000	0.000	0.000	0.000
13	A	13	GLY	0	0.010	0.000	14.903	-0.003	-0.003	0.000	0.000	0.000	0.000
14	A	14	LYS	1	0.899	0.948	14.509	-0.079	-0.079	0.000	0.000	0.000	0.000
15	A	15	LYS	1	0.920	0.951	15.501	-0.113	-0.113	0.000	0.000	0.000	0.000
16	A	16	GLY	0	0.023	-0.004	13.271	-0.004	-0.004	0.000	0.000	0.000	0.000
17	A	17	GLU	-1	-0.906	-0.952	12.131	0.156	0.156	0.000	0.000	0.000	0.000
18	A	18	ILE	0	0.029	0.021	7.859	-0.039	-0.039	0.000	0.000	0.000	0.000
19	A	19	LYS	1	0.985	0.995	7.199	-0.009	-0.009	0.000	0.000	0.000	0.000
20	A	20	ASN	0	-0.034	-0.027	2.046	-9.343	-12.373	10.297	-3.831	-3.436	0.034
21	A	21	VAL	0	-0.046	-0.016	3.273	-0.286	1.592	0.033	-0.781	-1.130	0.000
22	A	22	ALA	0	0.060	0.036	1.732	-7.521	-15.301	17.415	-6.267	-3.368	-0.051
23	A	23	ASP	-1	-0.789	-0.918	2.033	-16.415	-13.774	10.457	-5.859	-7.239	-0.045
24	A	24	GLY	0	0.040	0.022	2.993	1.555	-0.505	0.158	2.413	-0.511	0.000
25	A	25	TYR	0	0.011	-0.014	5.914	0.477	0.477	0.000	0.000	0.000	0.000
26	A	26	ALA	0	0.035	0.026	3.126	-0.449	-0.096	1.016	-0.406	-0.963	0.003
27	A	27	ASN	0	0.013	0.004	3.561	-1.836	-0.862	0.034	-0.338	-0.669	-0.001
28	A	28	ASN	0	-0.006	-0.007	5.655	-0.563	-0.563	0.000	0.000	0.000	0.000
29	A	29	PHE	0	0.002	0.015	8.585	-0.147	-0.147	0.000	0.000	0.000	0.000
30	A	30	LEU	0	0.003	0.017	6.892	-0.016	-0.016	0.000	0.000	0.000	0.000
31	A	31	PHE	0	-0.014	-0.019	3.492	-0.687	0.093	1.110	-0.343	-1.547	-0.001
32	A	32	LYS	1	0.898	0.961	8.175	-0.357	-0.357	0.000	0.000	0.000	0.000
33	A	33	GLN	0	0.020	0.015	11.387	-0.071	-0.071	0.000	0.000	0.000	0.000
34	A	34	GLY	0	0.025	-0.002	12.188	-0.049	-0.049	0.000	0.000	0.000	0.000
35	A	35	LEU	0	-0.032	-0.013	10.955	-0.027	-0.027	0.000	0.000	0.000	0.000
36	A	36	ALA	0	-0.031	-0.005	6.920	-0.117	-0.117	0.000	0.000	0.000	0.000
37	A	37	ILE	0	0.031	0.034	7.498	0.109	0.109	0.000	0.000	0.000	0.000
38	A	38	GLU	-1	-0.792	-0.918	4.304	0.266	0.541	0.001	-0.037	-0.238	0.000
39	A	39	ALA	0	-0.048	-0.003	4.416	-0.389	-0.273	-0.001	-0.009	-0.106	0.000
40	A	40	THR	0	0.035	0.008	6.258	-0.037	-0.037	0.000	0.000	0.000	0.000
41	A	41	PRO	0	0.026	-0.011	8.281	0.088	0.088	0.000	0.000	0.000	0.000
42	A	42	ALA	0	0.015	0.020	11.418	0.038	0.038	0.000	0.000	0.000	0.000
43	A	43	ASN	0	0.016	0.002	9.460	0.000	0.000	0.000	0.000	0.000	0.000
44	A	44	LEU	0	0.006	0.012	8.872	0.030	0.030	0.000	0.000	0.000	0.000
45	A	45	LYS	1	0.969	0.978	12.105	-0.041	-0.041	0.000	0.000	0.000	0.000
46	A	46	ALA	0	0.007	0.004	15.115	0.009	0.009	0.000	0.000	0.000	0.000
47	A	47	LEU	0	-0.026	0.015	11.958	0.008	0.008	0.000	0.000	0.000	0.000
48	A	48	GLU	-1	-0.832	-0.908	15.533	0.119	0.119	0.000	0.000	0.000	0.000
49	A	49	ALA	0	0.056	0.032	17.748	0.001	0.001	0.000	0.000	0.000	0.000
50	A	50	GLN	0	-0.043	-0.016	16.971	-0.004	-0.004	0.000	0.000	0.000	0.000
51	A	51	LYS	1	0.851	0.901	15.406	-0.122	-0.122	0.000	0.000	0.000	0.000
52	A	52	GLN	0	-0.006	-0.019	20.474	0.000	0.000	0.000	0.000	0.000	0.000
53	A	53	LYS	1	0.872	0.960	23.048	-0.055	-0.055	0.000	0.000	0.000	0.000
54	A	54	GLU	-1	-0.889	-0.948	21.558	0.071	0.071	0.000	0.000	0.000	0.000
55	A	55	GLN	0	0.016	0.014	24.586	-0.002	-0.002	0.000	0.000	0.000	0.000
56	A	56	ARG	1	0.862	0.923	26.274	-0.039	-0.039	0.000	0.000	0.000	0.000
57	A	57	GLN	0	0.042	0.007	27.078	0.001	0.001	0.000	0.000	0.000	0.000
58	A	58	ALA	0	0.043	0.034	28.378	-0.002	-0.002	0.000	0.000	0.000	0.000
59	A	59	ALA	0	-0.007	-0.008	30.293	-0.001	-0.001	0.000	0.000	0.000	0.000
60	A	60	GLU	-1	-0.835	-0.895	32.589	0.032	0.032	0.000	0.000	0.000	0.000
61	A	61	GLU	-1	-0.940	-0.972	31.641	0.042	0.042	0.000	0.000	0.000	0.000
62	A	62	LEU	0	-0.039	-0.007	34.607	-0.002	-0.002	0.000	0.000	0.000	0.000
63	A	63	ALA	0	0.056	0.018	36.376	-0.002	-0.002	0.000	0.000	0.000	0.000
64	A	64	ASN	0	-0.020	-0.020	37.886	-0.004	-0.004	0.000	0.000	0.000	0.000
65	A	65	ALA	0	-0.016	-0.007	39.133	-0.002	-0.002	0.000	0.000	0.000	0.000
66	A	66	LYS	1	0.867	0.912	38.762	-0.042	-0.042	0.000	0.000	0.000	0.000
67	A	67	LYS	1	0.962	1.018	42.182	-0.028	-0.028	0.000	0.000	0.000	0.000
68	A	68	LEU	0	-0.062	-0.038	43.216	-0.001	-0.001	0.000	0.000	0.000	0.000
69	A	69	LYS	1	0.852	0.900	44.940	-0.030	-0.030	0.000	0.000	0.000	0.000
70	A	70	GLU	-1	-0.896	-0.950	46.594	0.027	0.027	0.000	0.000	0.000	0.000
71	A	71	GLN	0	-0.065	-0.038	47.090	0.000	0.000	0.000	0.000	0.000	0.000
72	A	72	LEU	0	0.020	-0.016	47.444	-0.001	-0.001	0.000	0.000	0.000	0.000
73	A	73	GLU	-1	-0.782	-0.864	49.955	0.026	0.026	0.000	0.000	0.000	0.000
74	A	74	LYS	1	0.926	0.987	52.652	-0.020	-0.020	0.000	0.000	0.000	0.000
75	A	75	LEU	0	-0.121	-0.041	52.599	-0.001	-0.001	0.000	0.000	0.000	0.000
76	A	76	THR	0	0.020	-0.010	56.346	0.000	0.000	0.000	0.000	0.000	0.000
77	A	77	VAL	0	-0.050	-0.005	54.842	-0.001	-0.001	0.000	0.000	0.000	0.000
78	A	78	THR	0	0.018	0.007	58.120	0.000	0.000	0.000	0.000	0.000	0.000
79	A	79	ILE	0	-0.025	-0.014	57.484	0.000	0.000	0.000	0.000	0.000	0.000
80	A	80	PRO	0	0.017	0.016	61.724	0.000	0.000	0.000	0.000	0.000	0.000
81	A	81	ALA	0	-0.037	-0.054	64.256	0.000	0.000	0.000	0.000	0.000	0.000
82	A	82	LYS	1	0.872	0.915	66.309	-0.010	-0.010	0.000	0.000	0.000	0.000
83	A	83	ALA	0	-0.008	-0.004	68.306	0.000	0.000	0.000	0.000	0.000	0.000
84	A	84	GLY	0	0.066	0.031	70.306	0.000	0.000	0.000	0.000	0.000	0.000
85	A	85	GLU	-1	-0.899	-0.961	70.653	0.011	0.011	0.000	0.000	0.000	0.000
86	A	86	GLY	0	0.001	0.013	72.301	0.000	0.000	0.000	0.000	0.000	0.000
87	A	87	GLY	0	0.012	0.006	70.516	0.000	0.000	0.000	0.000	0.000	0.000
88	A	88	ARG	1	0.896	0.940	64.770	-0.013	-0.013	0.000	0.000	0.000	0.000
89	A	89	LEU	0	-0.014	0.009	63.229	0.000	0.000	0.000	0.000	0.000	0.000
90	A	90	PHE	0	0.067	0.042	67.075	0.000	0.000	0.000	0.000	0.000	0.000
91	A	91	GLY	0	0.012	0.012	63.685	0.000	0.000	0.000	0.000	0.000	0.000
92	A	92	SER	0	-0.044	-0.029	58.883	0.000	0.000	0.000	0.000	0.000	0.000
93	A	93	ILE	0	-0.001	0.006	57.449	0.000	0.000	0.000	0.000	0.000	0.000
94	A	94	THR	0	-0.029	-0.045	53.865	0.001	0.001	0.000	0.000	0.000	0.000
95	A	95	SER	0	0.076	0.017	49.669	0.000	0.000	0.000	0.000	0.000	0.000
96	A	96	LYS	1	0.934	0.980	51.306	-0.017	-0.017	0.000	0.000	0.000	0.000
97	A	97	GLN	0	0.100	0.081	52.281	0.000	0.000	0.000	0.000	0.000	0.000
98	A	98	ILE	0	0.014	0.007	52.896	0.000	0.000	0.000	0.000	0.000	0.000
99	A	99	ALA	0	0.012	0.001	49.676	0.000	0.000	0.000	0.000	0.000	0.000
100	A	100	GLU	-1	-0.920	-0.972	51.508	0.015	0.015	0.000	0.000	0.000	0.000
101	A	101	SER	0	-0.022	-0.013	53.975	-0.001	-0.001	0.000	0.000	0.000	0.000
102	A	102	LEU	0	-0.017	0.003	49.988	0.000	0.000	0.000	0.000	0.000	0.000
103	A	103	GLN	0	0.038	0.016	49.980	0.000	0.000	0.000	0.000	0.000	0.000
104	A	104	ALA	0	-0.064	-0.039	52.876	0.000	0.000	0.000	0.000	0.000	0.000
105	A	105	GLN	0	-0.001	-0.011	56.470	0.000	0.000	0.000	0.000	0.000	0.000
106	A	106	HIS	0	0.015	0.001	53.927	0.000	0.000	0.000	0.000	0.000	0.000
107	A	107	GLY	0	-0.001	0.022	52.915	0.000	0.000	0.000	0.000	0.000	0.000
108	A	108	LEU	0	-0.062	-0.025	48.170	0.001	0.001	0.000	0.000	0.000	0.000
109	A	109	LYS	1	0.932	0.962	44.981	-0.018	-0.018	0.000	0.000	0.000	0.000
110	A	110	LEU	0	-0.019	-0.009	44.470	0.001	0.001	0.000	0.000	0.000	0.000
111	A	111	ASP	-1	-0.798	-0.895	41.585	0.024	0.024	0.000	0.000	0.000	0.000
112	A	112	LYN	0	0.095	0.040	44.520	0.001	0.001	0.000	0.000	0.000	0.000
113	A	113	ARG	1	0.812	0.874	41.054	-0.024	-0.024	0.000	0.000	0.000	0.000
114	A	114	LYS	1	0.824	0.933	39.587	-0.030	-0.030	0.000	0.000	0.000	0.000
115	A	115	ILE	0	-0.019	0.002	44.051	0.000	0.000	0.000	0.000	0.000	0.000
116	A	116	GLU	-1	-0.893	-0.954	44.123	0.030	0.030	0.000	0.000	0.000	0.000
117	A	117	LEU	0	-0.045	-0.027	47.723	0.000	0.000	0.000	0.000	0.000	0.000
118	A	118	ALA	0	-0.002	0.006	50.326	0.000	0.000	0.000	0.000	0.000	0.000
119	A	119	ASP	-1	-0.879	-0.929	51.907	0.018	0.018	0.000	0.000	0.000	0.000
120	A	120	ALA	0	-0.080	-0.054	55.271	0.000	0.000	0.000	0.000	0.000	0.000
121	A	121	ILE	0	0.064	0.036	56.789	0.000	0.000	0.000	0.000	0.000	0.000
122	A	122	ARG	1	0.869	0.909	59.407	-0.014	-0.014	0.000	0.000	0.000	0.000
123	A	123	ALA	0	-0.008	-0.014	62.849	0.000	0.000	0.000	0.000	0.000	0.000
124	A	124	LEU	0	0.044	0.040	64.162	0.000	0.000	0.000	0.000	0.000	0.000
125	A	125	GLY	0	0.009	0.015	65.411	0.000	0.000	0.000	0.000	0.000	0.000
126	A	126	TYR	0	-0.030	-0.019	61.732	0.000	0.000	0.000	0.000	0.000	0.000
127	A	127	THR	0	-0.030	-0.020	56.694	0.000	0.000	0.000	0.000	0.000	0.000
128	A	128	ASN	0	0.020	0.020	55.053	-0.001	-0.001	0.000	0.000	0.000	0.000
129	A	129	VAL	0	0.024	0.007	50.853	0.000	0.000	0.000	0.000	0.000	0.000
130	A	130	PRO	0	0.015	0.033	47.786	0.000	0.000	0.000	0.000	0.000	0.000
131	A	131	VAL	0	0.011	-0.003	45.264	0.000	0.000	0.000	0.000	0.000	0.000
132	A	132	LYS	1	0.901	0.969	39.708	-0.036	-0.036	0.000	0.000	0.000	0.000
133	A	133	LEU	0	-0.025	-0.027	41.651	0.000	0.000	0.000	0.000	0.000	0.000
134	A	134	HIS	0	0.071	0.030	33.676	-0.001	-0.001	0.000	0.000	0.000	0.000
135	A	135	PRO	0	0.001	0.005	33.627	-0.001	-0.001	0.000	0.000	0.000	0.000
136	A	136	GLU	-1	-0.852	-0.918	35.888	0.048	0.048	0.000	0.000	0.000	0.000
137	A	137	VAL	0	-0.028	-0.022	38.435	0.000	0.000	0.000	0.000	0.000	0.000
138	A	138	THR	0	0.025	0.004	41.251	0.000	0.000	0.000	0.000	0.000	0.000
139	A	139	ALA	0	-0.030	0.002	44.452	0.000	0.000	0.000	0.000	0.000	0.000
140	A	140	THR	0	-0.011	-0.015	47.743	0.000	0.000	0.000	0.000	0.000	0.000
141	A	141	LEU	0	0.008	0.001	51.123	-0.001	-0.001	0.000	0.000	0.000	0.000
142	A	142	LYS	1	0.923	0.969	52.919	-0.019	-0.019	0.000	0.000	0.000	0.000
143	A	143	VAL	0	0.003	-0.002	55.444	0.000	0.000	0.000	0.000	0.000	0.000
144	A	144	HIS	0	-0.015	-0.016	58.109	0.000	0.000	0.000	0.000	0.000	0.000
145	A	145	VAL	0	0.019	0.007	61.229	0.000	0.000	0.000	0.000	0.000	0.000
146	A	146	THR	0	0.007	0.006	63.596	0.000	0.000	0.000	0.000	0.000	0.000
147	A	147	GLU	-1	-0.858	-0.912	67.103	0.011	0.011	0.000	0.000	0.000	0.000
148	A	148	GLN	0	0.004	0.020	67.279	0.000	0.000	0.000	0.000	0.000	0.000
149	A	149	LYN	0	0.027	0.033	70.526	0.000	0.000	0.000	0.000	0.000	0.000

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