FMO DATABASE

FMODB ID: NNYLQ

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	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	149
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1122858.368739
FMO2-HF: Nuclear repulsion	1066976.799646
FMO2-HF: Total energy	-55881.569093
FMO2-MP2: Total energy	-56048.803891

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.
-41.13	-39.46	35.586	-15.58	-21.678	-0.07

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 : 0.023 / q_NPA : 0.020

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	-0.006	0.000	2.800	-3.666	-0.577	0.853	-1.516	-2.426	-0.002
4	A	4	ILE	0	0.020	0.005	4.216	-0.053	0.045	0.000	-0.027	-0.072	0.000
5	A	5	PHE	0	0.031	0.001	7.342	0.191	0.191	0.000	0.000	0.000	0.000
6	A	6	LEU	0	-0.009	-0.008	9.898	-0.058	-0.058	0.000	0.000	0.000	0.000
7	A	7	LYS	1	0.770	0.862	12.939	-0.357	-0.357	0.000	0.000	0.000	0.000
8	A	8	ASP	-1	-0.870	-0.933	13.472	0.162	0.162	0.000	0.000	0.000	0.000
9	A	9	VAL	0	0.041	0.023	12.616	0.004	0.004	0.000	0.000	0.000	0.000
10	A	10	LYS	1	0.851	0.922	15.046	-0.163	-0.163	0.000	0.000	0.000	0.000
11	A	11	GLY	0	0.021	0.021	18.845	-0.003	-0.003	0.000	0.000	0.000	0.000
12	A	12	LYS	1	0.899	0.929	17.466	-0.133	-0.133	0.000	0.000	0.000	0.000
13	A	13	GLY	0	0.005	0.001	13.793	-0.008	-0.008	0.000	0.000	0.000	0.000
14	A	14	LYS	1	0.907	0.949	14.428	-0.128	-0.128	0.000	0.000	0.000	0.000
15	A	15	LYS	1	0.938	0.973	15.566	-0.151	-0.151	0.000	0.000	0.000	0.000
16	A	16	GLY	0	0.015	0.005	13.087	-0.007	-0.007	0.000	0.000	0.000	0.000
17	A	17	GLU	-1	-0.845	-0.912	11.761	0.165	0.165	0.000	0.000	0.000	0.000
18	A	18	ILE	0	-0.004	0.006	7.820	-0.010	-0.010	0.000	0.000	0.000	0.000
19	A	19	LYS	1	0.909	0.951	7.296	0.101	0.101	0.000	0.000	0.000	0.000
20	A	20	ASN	0	0.019	0.012	2.068	-8.117	-11.112	9.208	-3.394	-2.818	0.029
21	A	21	VAL	0	-0.037	-0.020	2.773	-0.340	1.296	0.181	-0.547	-1.270	0.001
22	A	22	ALA	0	0.075	0.041	1.914	-6.830	-9.200	8.503	-3.348	-2.786	-0.039
23	A	23	ASP	-1	-0.785	-0.910	1.881	-17.709	-16.809	12.859	-6.313	-7.446	-0.057
24	A	24	GLY	0	0.034	0.031	3.226	1.268	0.252	0.128	1.315	-0.427	-0.001
25	A	25	TYR	0	-0.013	-0.024	5.712	0.579	0.579	0.000	0.000	0.000	0.000
26	A	26	ALA	0	0.030	0.010	2.917	-0.480	-0.589	2.056	-0.625	-1.323	0.005
27	A	27	ASN	0	0.038	0.017	2.938	-3.024	-1.369	0.217	-0.676	-1.196	-0.005
28	A	28	ASN	0	-0.010	-0.013	4.915	-0.773	-0.754	0.000	-0.020	0.001	0.000
29	A	29	PHE	0	0.017	0.026	8.126	-0.181	-0.181	0.000	0.000	0.000	0.000
30	A	30	LEU	0	0.004	0.006	6.518	-0.032	-0.032	0.000	0.000	0.000	0.000
31	A	31	PHE	0	0.007	-0.005	3.312	-0.797	-0.213	1.582	-0.416	-1.750	-0.001
32	A	32	LYS	1	0.872	0.953	8.198	-0.444	-0.444	0.000	0.000	0.000	0.000
33	A	33	GLN	0	0.051	0.032	11.380	-0.082	-0.082	0.000	0.000	0.000	0.000
34	A	34	GLY	0	0.027	0.010	11.409	-0.059	-0.059	0.000	0.000	0.000	0.000
35	A	35	LEU	0	-0.022	-0.011	10.634	-0.085	-0.085	0.000	0.000	0.000	0.000
36	A	36	ALA	0	-0.030	-0.015	7.035	-0.149	-0.149	0.000	0.000	0.000	0.000
37	A	37	ILE	0	0.033	0.038	7.524	0.173	0.173	0.000	0.000	0.000	0.000
38	A	38	GLU	-1	-0.799	-0.915	4.588	0.406	0.585	-0.001	-0.013	-0.165	0.000
39	A	39	ALA	0	-0.033	-0.009	4.832	-0.208	-0.208	0.000	0.000	0.000	0.000
40	A	40	THR	0	0.039	0.022	6.641	-0.044	-0.044	0.000	0.000	0.000	0.000
41	A	41	PRO	0	0.040	0.004	8.748	0.081	0.081	0.000	0.000	0.000	0.000
42	A	42	ALA	0	0.023	0.016	12.064	0.030	0.030	0.000	0.000	0.000	0.000
43	A	43	ASN	0	0.017	-0.004	9.181	-0.024	-0.024	0.000	0.000	0.000	0.000
44	A	44	LEU	0	-0.022	-0.009	9.272	0.027	0.027	0.000	0.000	0.000	0.000
45	A	45	LYS	1	0.967	0.987	12.661	-0.089	-0.089	0.000	0.000	0.000	0.000
46	A	46	ALA	0	0.028	0.025	15.392	0.002	0.002	0.000	0.000	0.000	0.000
47	A	47	LEU	0	-0.018	-0.001	11.852	0.005	0.005	0.000	0.000	0.000	0.000
48	A	48	GLU	-1	-0.852	-0.917	15.556	0.149	0.149	0.000	0.000	0.000	0.000
49	A	49	ALA	0	0.036	0.026	17.875	-0.003	-0.003	0.000	0.000	0.000	0.000
50	A	50	GLN	0	-0.060	-0.034	17.095	-0.007	-0.007	0.000	0.000	0.000	0.000
51	A	51	LYS	1	0.845	0.904	15.593	-0.159	-0.159	0.000	0.000	0.000	0.000
52	A	52	GLN	0	0.021	-0.002	20.370	-0.004	-0.004	0.000	0.000	0.000	0.000
53	A	53	LYS	1	0.822	0.929	23.014	-0.092	-0.092	0.000	0.000	0.000	0.000
54	A	54	GLU	-1	-0.826	-0.909	21.806	0.106	0.106	0.000	0.000	0.000	0.000
55	A	55	GLN	0	0.011	0.007	24.303	-0.002	-0.002	0.000	0.000	0.000	0.000
56	A	56	ARG	1	0.837	0.896	26.026	-0.057	-0.057	0.000	0.000	0.000	0.000
57	A	57	GLN	0	-0.008	-0.006	27.215	0.000	0.000	0.000	0.000	0.000	0.000
58	A	58	ALA	0	0.052	0.034	28.483	-0.004	-0.004	0.000	0.000	0.000	0.000
59	A	59	ALA	0	-0.012	-0.003	30.329	-0.003	-0.003	0.000	0.000	0.000	0.000
60	A	60	GLU	-1	-0.786	-0.874	32.645	0.045	0.045	0.000	0.000	0.000	0.000
61	A	61	GLU	-1	-0.916	-0.961	31.223	0.061	0.061	0.000	0.000	0.000	0.000
62	A	62	LEU	0	-0.024	0.002	34.321	-0.003	-0.003	0.000	0.000	0.000	0.000
63	A	63	ALA	0	0.037	0.006	36.068	-0.003	-0.003	0.000	0.000	0.000	0.000
64	A	64	ASN	0	-0.012	-0.012	37.801	-0.005	-0.005	0.000	0.000	0.000	0.000
65	A	65	ALA	0	0.025	0.016	38.855	-0.002	-0.002	0.000	0.000	0.000	0.000
66	A	66	LYS	1	0.853	0.913	38.581	-0.051	-0.051	0.000	0.000	0.000	0.000
67	A	67	LYS	1	0.901	0.956	42.158	-0.039	-0.039	0.000	0.000	0.000	0.000
68	A	68	LEU	0	-0.041	-0.018	42.997	-0.002	-0.002	0.000	0.000	0.000	0.000
69	A	69	LYS	1	0.863	0.905	44.941	-0.036	-0.036	0.000	0.000	0.000	0.000
70	A	70	GLU	-1	-0.887	-0.940	46.735	0.033	0.033	0.000	0.000	0.000	0.000
71	A	71	GLN	0	-0.072	-0.039	46.642	0.000	0.000	0.000	0.000	0.000	0.000
72	A	72	LEU	0	0.021	0.000	47.086	-0.001	-0.001	0.000	0.000	0.000	0.000
73	A	73	GLU	-1	-0.761	-0.851	49.881	0.032	0.032	0.000	0.000	0.000	0.000
74	A	74	LYS	1	0.899	0.968	52.523	-0.027	-0.027	0.000	0.000	0.000	0.000
75	A	75	LEU	0	-0.055	-0.003	52.677	-0.001	-0.001	0.000	0.000	0.000	0.000
76	A	76	THR	0	-0.018	-0.033	56.396	0.000	0.000	0.000	0.000	0.000	0.000
77	A	77	VAL	0	-0.042	0.004	54.424	-0.001	-0.001	0.000	0.000	0.000	0.000
78	A	78	THR	0	0.019	-0.006	57.796	0.000	0.000	0.000	0.000	0.000	0.000
79	A	79	ILE	0	-0.022	-0.008	57.389	0.000	0.000	0.000	0.000	0.000	0.000
80	A	80	PRO	0	0.024	0.031	61.544	0.000	0.000	0.000	0.000	0.000	0.000
81	A	81	ALA	0	-0.006	-0.017	63.969	0.000	0.000	0.000	0.000	0.000	0.000
82	A	82	LYS	1	0.844	0.891	65.952	-0.015	-0.015	0.000	0.000	0.000	0.000
83	A	83	ALA	0	0.007	-0.005	67.995	0.000	0.000	0.000	0.000	0.000	0.000
84	A	84	GLY	0	0.057	0.034	70.193	0.000	0.000	0.000	0.000	0.000	0.000
85	A	85	GLU	-1	-0.880	-0.938	70.144	0.015	0.015	0.000	0.000	0.000	0.000
86	A	86	GLY	0	-0.008	-0.010	72.421	0.000	0.000	0.000	0.000	0.000	0.000
87	A	87	GLY	0	0.033	0.015	70.600	0.000	0.000	0.000	0.000	0.000	0.000
88	A	88	ARG	1	0.884	0.949	64.810	-0.017	-0.017	0.000	0.000	0.000	0.000
89	A	89	LEU	0	-0.023	0.001	63.009	0.000	0.000	0.000	0.000	0.000	0.000
90	A	90	PHE	0	0.057	0.030	66.825	0.000	0.000	0.000	0.000	0.000	0.000
91	A	91	GLY	0	0.006	0.018	63.820	0.000	0.000	0.000	0.000	0.000	0.000
92	A	92	SER	0	-0.018	-0.022	59.040	0.000	0.000	0.000	0.000	0.000	0.000
93	A	93	ILE	0	-0.015	0.009	57.078	0.000	0.000	0.000	0.000	0.000	0.000
94	A	94	THR	0	0.023	-0.011	53.402	0.001	0.001	0.000	0.000	0.000	0.000
95	A	95	SER	0	0.070	0.020	49.280	-0.001	-0.001	0.000	0.000	0.000	0.000
96	A	96	LYS	1	0.893	0.959	50.795	-0.024	-0.024	0.000	0.000	0.000	0.000
97	A	97	GLN	0	0.103	0.062	51.753	0.001	0.001	0.000	0.000	0.000	0.000
98	A	98	ILE	0	0.007	0.021	52.676	0.000	0.000	0.000	0.000	0.000	0.000
99	A	99	ALA	0	0.025	0.007	49.408	0.000	0.000	0.000	0.000	0.000	0.000
100	A	100	GLU	-1	-0.933	-0.978	51.298	0.023	0.023	0.000	0.000	0.000	0.000
101	A	101	SER	0	-0.007	-0.016	53.762	-0.001	-0.001	0.000	0.000	0.000	0.000
102	A	102	LEU	0	-0.020	-0.009	49.780	0.000	0.000	0.000	0.000	0.000	0.000
103	A	103	GLN	0	0.010	0.010	49.883	0.001	0.001	0.000	0.000	0.000	0.000
104	A	104	ALA	0	-0.045	-0.027	52.722	0.000	0.000	0.000	0.000	0.000	0.000
105	A	105	GLN	0	-0.020	-0.010	56.378	0.000	0.000	0.000	0.000	0.000	0.000
106	A	106	HIS	0	0.020	0.002	53.984	0.000	0.000	0.000	0.000	0.000	0.000
107	A	107	GLY	0	0.015	0.022	52.811	0.001	0.001	0.000	0.000	0.000	0.000
108	A	108	LEU	0	-0.046	-0.024	48.047	0.001	0.001	0.000	0.000	0.000	0.000
109	A	109	LYS	1	0.908	0.946	45.061	-0.028	-0.028	0.000	0.000	0.000	0.000
110	A	110	LEU	0	-0.001	0.000	44.295	0.002	0.002	0.000	0.000	0.000	0.000
111	A	111	ASP	-1	-0.808	-0.895	41.532	0.036	0.036	0.000	0.000	0.000	0.000
112	A	112	LYN	0	0.076	0.041	44.542	0.001	0.001	0.000	0.000	0.000	0.000
113	A	113	ARG	1	0.836	0.883	41.083	-0.036	-0.036	0.000	0.000	0.000	0.000
114	A	114	LYS	1	0.818	0.911	39.138	-0.043	-0.043	0.000	0.000	0.000	0.000
115	A	115	ILE	0	-0.019	-0.006	43.643	0.000	0.000	0.000	0.000	0.000	0.000
116	A	116	GLU	-1	-0.842	-0.930	44.131	0.038	0.038	0.000	0.000	0.000	0.000
117	A	117	LEU	0	-0.046	-0.027	47.372	-0.001	-0.001	0.000	0.000	0.000	0.000
118	A	118	ALA	0	0.018	0.011	49.817	0.001	0.001	0.000	0.000	0.000	0.000
119	A	119	ASP	-1	-0.915	-0.949	51.752	0.024	0.024	0.000	0.000	0.000	0.000
120	A	120	ALA	0	-0.048	-0.028	55.275	0.000	0.000	0.000	0.000	0.000	0.000
121	A	121	ILE	0	0.038	0.021	56.554	-0.001	-0.001	0.000	0.000	0.000	0.000
122	A	122	ARG	1	0.870	0.902	59.349	-0.019	-0.019	0.000	0.000	0.000	0.000
123	A	123	ALA	0	-0.007	-0.001	62.852	-0.001	-0.001	0.000	0.000	0.000	0.000
124	A	124	LEU	0	0.031	0.019	64.046	0.001	0.001	0.000	0.000	0.000	0.000
125	A	125	GLY	0	0.007	0.013	65.178	0.000	0.000	0.000	0.000	0.000	0.000
126	A	126	TYR	0	-0.032	-0.019	61.272	0.000	0.000	0.000	0.000	0.000	0.000
127	A	127	THR	0	-0.027	-0.018	56.249	0.000	0.000	0.000	0.000	0.000	0.000
128	A	128	ASN	0	0.015	0.014	54.875	-0.001	-0.001	0.000	0.000	0.000	0.000
129	A	129	VAL	0	0.015	0.008	50.878	0.000	0.000	0.000	0.000	0.000	0.000
130	A	130	PRO	0	0.014	0.018	47.674	0.000	0.000	0.000	0.000	0.000	0.000
131	A	131	VAL	0	0.012	0.000	45.141	0.000	0.000	0.000	0.000	0.000	0.000
132	A	132	LYS	1	0.904	0.967	39.522	-0.045	-0.045	0.000	0.000	0.000	0.000
133	A	133	LEU	0	-0.047	-0.020	41.160	0.001	0.001	0.000	0.000	0.000	0.000
134	A	134	HIS	0	0.053	0.029	33.422	0.000	0.000	0.000	0.000	0.000	0.000
135	A	135	PRO	0	0.019	0.006	33.607	-0.002	-0.002	0.000	0.000	0.000	0.000
136	A	136	GLU	-1	-0.847	-0.913	35.845	0.054	0.054	0.000	0.000	0.000	0.000
137	A	137	VAL	0	-0.037	-0.019	38.390	-0.001	-0.001	0.000	0.000	0.000	0.000
138	A	138	THR	0	-0.012	-0.005	41.218	0.001	0.001	0.000	0.000	0.000	0.000
139	A	139	ALA	0	-0.049	-0.019	44.268	0.000	0.000	0.000	0.000	0.000	0.000
140	A	140	THR	0	-0.017	-0.040	47.454	0.000	0.000	0.000	0.000	0.000	0.000
141	A	141	LEU	0	0.014	0.014	50.730	-0.001	-0.001	0.000	0.000	0.000	0.000
142	A	142	LYS	1	0.921	0.971	52.449	-0.023	-0.023	0.000	0.000	0.000	0.000
143	A	143	VAL	0	0.004	0.006	55.143	0.000	0.000	0.000	0.000	0.000	0.000
144	A	144	HIS	0	-0.010	-0.017	57.866	-0.001	-0.001	0.000	0.000	0.000	0.000
145	A	145	VAL	0	0.007	0.011	61.018	0.000	0.000	0.000	0.000	0.000	0.000
146	A	146	THR	0	0.028	0.016	63.502	0.000	0.000	0.000	0.000	0.000	0.000
147	A	147	GLU	-1	-0.846	-0.925	67.087	0.015	0.015	0.000	0.000	0.000	0.000
148	A	148	GLN	0	-0.032	-0.006	66.343	0.000	0.000	0.000	0.000	0.000	0.000
149	A	149	LYN	0	0.025	0.037	70.473	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)