FMO DATABASE

FMODB ID: 2J69R

Calculation Name: 2D7V-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2D7V

Chain ID: A

ChEMBL ID:

UniProt ID: Q9KMK9

Base Structure: X-ray

Registration Date: 2023-09-20

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	155
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1281223.856374
FMO2-HF: Nuclear repulsion	1221474.685748
FMO2-HF: Total energy	-59749.170626
FMO2-MP2: Total energy	-59923.050127

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:7:SER)

Summations of interaction energy for fragment #1(A:7:SER)

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.
0.29	2.142	-0.008	-0.993	-0.852	0.004

Interaction energy analysis for fragmet #1(A:7:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.008 / q_NPA : 0.005

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	9	SER	0	-0.004	-0.001	3.875	1.376	3.228	-0.008	-0.993	-0.852	0.004
4	A	10	GLU	-1	-0.960	-0.967	6.551	-0.515	-0.515	0.000	0.000	0.000	0.000
5	A	11	HIS	0	-0.028	-0.023	7.504	0.373	0.373	0.000	0.000	0.000	0.000
6	A	12	SER	0	-0.049	-0.024	12.566	0.000	0.000	0.000	0.000	0.000	0.000
7	A	13	ALA	0	0.027	-0.002	16.265	-0.003	-0.003	0.000	0.000	0.000	0.000
8	A	14	ILE	0	-0.019	0.001	19.414	0.008	0.008	0.000	0.000	0.000	0.000
9	A	15	VAL	0	0.026	0.016	23.003	0.003	0.003	0.000	0.000	0.000	0.000
10	A	16	THR	0	-0.055	-0.032	25.516	0.015	0.015	0.000	0.000	0.000	0.000
11	A	17	TRP	0	0.028	0.016	29.150	0.001	0.001	0.000	0.000	0.000	0.000
12	A	18	LYS	1	0.898	0.940	32.502	0.079	0.079	0.000	0.000	0.000	0.000
13	A	19	ARG	1	0.889	0.956	35.880	0.059	0.059	0.000	0.000	0.000	0.000
14	A	20	LYS	1	0.953	0.971	37.772	0.077	0.077	0.000	0.000	0.000	0.000
15	A	21	ASP	-1	-0.853	-0.933	41.460	-0.051	-0.051	0.000	0.000	0.000	0.000
16	A	22	SER	0	-0.036	-0.027	44.835	0.000	0.000	0.000	0.000	0.000	0.000
17	A	23	GLU	-1	-0.839	-0.902	40.669	-0.079	-0.079	0.000	0.000	0.000	0.000
18	A	24	ALA	0	0.038	0.025	44.912	0.001	0.001	0.000	0.000	0.000	0.000
19	A	25	PHE	0	-0.012	0.000	38.202	0.001	0.001	0.000	0.000	0.000	0.000
20	A	26	THR	0	0.005	-0.015	43.346	-0.003	-0.003	0.000	0.000	0.000	0.000
21	A	27	ASP	-1	-0.856	-0.926	45.334	-0.067	-0.067	0.000	0.000	0.000	0.000
22	A	28	ASN	0	-0.043	-0.025	40.816	-0.004	-0.004	0.000	0.000	0.000	0.000
23	A	29	GLN	0	0.023	0.021	42.452	-0.006	-0.006	0.000	0.000	0.000	0.000
24	A	30	TYR	0	-0.033	0.003	36.624	0.000	0.000	0.000	0.000	0.000	0.000
25	A	31	SER	0	0.060	0.027	38.067	-0.006	-0.006	0.000	0.000	0.000	0.000
26	A	32	ARG	1	0.815	0.866	34.295	0.100	0.100	0.000	0.000	0.000	0.000
27	A	33	ALA	0	-0.003	0.025	33.216	-0.010	-0.010	0.000	0.000	0.000	0.000
28	A	34	HIS	0	-0.090	-0.046	28.088	-0.007	-0.007	0.000	0.000	0.000	0.000
29	A	35	THR	0	-0.007	0.006	27.991	0.003	0.003	0.000	0.000	0.000	0.000
30	A	36	TRP	0	-0.039	-0.027	22.774	-0.013	-0.013	0.000	0.000	0.000	0.000
31	A	37	GLU	-1	-0.813	-0.885	23.199	-0.088	-0.088	0.000	0.000	0.000	0.000
32	A	38	PHE	0	0.028	0.011	17.690	-0.019	-0.019	0.000	0.000	0.000	0.000
33	A	39	ASP	-1	-0.798	-0.887	16.047	-0.126	-0.126	0.000	0.000	0.000	0.000
34	A	40	GLY	0	-0.064	-0.027	17.601	0.031	0.031	0.000	0.000	0.000	0.000
35	A	41	GLY	0	0.002	0.003	18.825	0.015	0.015	0.000	0.000	0.000	0.000
36	A	42	SER	0	-0.064	-0.026	21.439	0.008	0.008	0.000	0.000	0.000	0.000
37	A	43	LYS	1	0.826	0.880	22.906	0.082	0.082	0.000	0.000	0.000	0.000
38	A	44	ILE	0	-0.001	-0.002	22.009	0.005	0.005	0.000	0.000	0.000	0.000
39	A	45	LEU	0	-0.023	-0.009	26.175	0.000	0.000	0.000	0.000	0.000	0.000
40	A	46	ALA	0	0.056	0.028	26.944	-0.005	-0.005	0.000	0.000	0.000	0.000
41	A	47	SER	0	-0.006	-0.016	29.012	0.020	0.020	0.000	0.000	0.000	0.000
42	A	48	ALA	0	0.004	0.003	30.046	-0.014	-0.014	0.000	0.000	0.000	0.000
43	A	49	SER	0	0.038	0.002	30.547	0.009	0.009	0.000	0.000	0.000	0.000
44	A	50	PRO	0	0.031	0.008	32.280	0.005	0.005	0.000	0.000	0.000	0.000
45	A	51	HIS	0	-0.045	-0.016	32.692	0.011	0.011	0.000	0.000	0.000	0.000
46	A	52	VAL	0	-0.082	-0.037	32.615	0.002	0.002	0.000	0.000	0.000	0.000
47	A	53	VAL	0	-0.007	-0.003	35.664	0.005	0.005	0.000	0.000	0.000	0.000
48	A	54	PRO	0	0.004	0.030	37.636	-0.002	-0.002	0.000	0.000	0.000	0.000
49	A	55	VAL	0	0.065	0.059	38.497	0.000	0.000	0.000	0.000	0.000	0.000
50	A	56	PRO	0	-0.057	-0.042	40.674	0.003	0.003	0.000	0.000	0.000	0.000
51	A	57	LEU	0	-0.031	-0.009	39.931	0.000	0.000	0.000	0.000	0.000	0.000
52	A	58	SER	0	-0.061	-0.041	35.422	-0.002	-0.002	0.000	0.000	0.000	0.000
53	A	59	VAL	0	-0.006	-0.025	34.940	0.007	0.007	0.000	0.000	0.000	0.000
54	A	60	GLU	-1	-0.871	-0.956	34.244	-0.100	-0.100	0.000	0.000	0.000	0.000
55	A	61	ALA	0	-0.061	-0.027	33.677	-0.006	-0.006	0.000	0.000	0.000	0.000
56	A	62	ASN	0	-0.072	-0.029	30.963	0.003	0.003	0.000	0.000	0.000	0.000
57	A	63	VAL	0	0.020	0.025	24.723	-0.003	-0.003	0.000	0.000	0.000	0.000
58	A	64	ASP	-1	-0.730	-0.846	27.980	-0.182	-0.182	0.000	0.000	0.000	0.000
59	A	65	PRO	0	-0.003	-0.031	24.585	-0.019	-0.019	0.000	0.000	0.000	0.000
60	A	66	GLU	-1	-0.905	-0.955	23.983	-0.233	-0.233	0.000	0.000	0.000	0.000
61	A	67	GLU	-1	-0.892	-0.953	24.660	-0.196	-0.196	0.000	0.000	0.000	0.000
62	A	68	ALA	0	-0.019	-0.016	21.605	-0.015	-0.015	0.000	0.000	0.000	0.000
63	A	69	PHE	0	-0.017	-0.001	19.641	-0.042	-0.042	0.000	0.000	0.000	0.000
64	A	70	VAL	0	-0.001	-0.004	19.943	-0.032	-0.032	0.000	0.000	0.000	0.000
65	A	71	ALA	0	0.009	0.008	20.883	-0.017	-0.017	0.000	0.000	0.000	0.000
66	A	72	ALA	0	-0.016	-0.010	16.183	-0.021	-0.021	0.000	0.000	0.000	0.000
67	A	73	LEU	0	0.021	0.008	16.054	-0.061	-0.061	0.000	0.000	0.000	0.000
68	A	74	SER	0	-0.057	-0.044	16.997	-0.013	-0.013	0.000	0.000	0.000	0.000
69	A	75	SER	0	-0.006	-0.012	16.777	0.001	0.001	0.000	0.000	0.000	0.000
70	A	76	CYS	0	-0.026	0.001	11.647	-0.072	-0.072	0.000	0.000	0.000	0.000
71	A	77	HIS	0	0.084	0.056	13.234	0.006	0.006	0.000	0.000	0.000	0.000
72	A	78	MET	0	-0.012	0.001	15.571	0.043	0.043	0.000	0.000	0.000	0.000
73	A	79	LEU	0	-0.004	-0.007	12.337	0.042	0.042	0.000	0.000	0.000	0.000
74	A	80	VAL	0	-0.003	0.013	10.304	0.055	0.055	0.000	0.000	0.000	0.000
75	A	81	PHE	0	0.054	0.010	12.858	0.090	0.090	0.000	0.000	0.000	0.000
76	A	82	LEU	0	0.015	0.010	16.403	0.050	0.050	0.000	0.000	0.000	0.000
77	A	83	SER	0	-0.067	-0.031	12.530	0.059	0.059	0.000	0.000	0.000	0.000
78	A	84	ILE	0	-0.003	-0.006	14.092	0.067	0.067	0.000	0.000	0.000	0.000
79	A	85	ALA	0	0.010	-0.007	16.122	0.037	0.037	0.000	0.000	0.000	0.000
80	A	86	ALA	0	0.006	0.007	17.101	0.023	0.023	0.000	0.000	0.000	0.000
81	A	87	LYS	1	0.937	0.968	11.111	-0.058	-0.058	0.000	0.000	0.000	0.000
82	A	88	GLN	0	-0.073	-0.023	18.111	0.019	0.019	0.000	0.000	0.000	0.000
83	A	89	ARG	1	0.920	0.964	21.139	-0.021	-0.021	0.000	0.000	0.000	0.000
84	A	90	TYR	0	-0.028	-0.015	22.488	-0.001	-0.001	0.000	0.000	0.000	0.000
85	A	91	LEU	0	0.012	0.012	23.179	-0.005	-0.005	0.000	0.000	0.000	0.000
86	A	92	VAL	0	-0.041	-0.025	21.753	-0.003	-0.003	0.000	0.000	0.000	0.000
87	A	93	GLU	-1	-0.857	-0.895	24.661	-0.046	-0.046	0.000	0.000	0.000	0.000
88	A	94	SER	0	-0.010	-0.009	25.372	-0.004	-0.004	0.000	0.000	0.000	0.000
89	A	95	TYR	0	0.049	0.005	20.299	0.001	0.001	0.000	0.000	0.000	0.000
90	A	96	THR	0	-0.012	0.000	24.124	-0.004	-0.004	0.000	0.000	0.000	0.000
91	A	97	ASP	-1	-0.761	-0.868	22.278	-0.235	-0.235	0.000	0.000	0.000	0.000
92	A	98	ASN	0	-0.023	0.012	24.978	0.003	0.003	0.000	0.000	0.000	0.000
93	A	99	ALA	0	0.046	0.031	23.714	0.006	0.006	0.000	0.000	0.000	0.000
94	A	100	VAL	0	-0.018	-0.010	25.753	0.010	0.010	0.000	0.000	0.000	0.000
95	A	101	GLY	0	0.029	0.016	26.426	-0.012	-0.012	0.000	0.000	0.000	0.000
96	A	102	ILE	0	-0.043	-0.017	27.045	0.016	0.016	0.000	0.000	0.000	0.000
97	A	103	LEU	0	0.043	0.018	28.709	-0.012	-0.012	0.000	0.000	0.000	0.000
98	A	104	GLY	0	0.027	0.007	30.765	0.013	0.013	0.000	0.000	0.000	0.000
99	A	105	LYS	1	0.832	0.920	31.407	0.122	0.122	0.000	0.000	0.000	0.000
100	A	106	ASN	0	0.101	0.045	27.170	0.016	0.016	0.000	0.000	0.000	0.000
101	A	107	SER	0	0.033	0.005	29.066	0.009	0.009	0.000	0.000	0.000	0.000
102	A	108	LYS	1	0.839	0.919	25.588	0.243	0.243	0.000	0.000	0.000	0.000
103	A	109	GLY	0	0.030	0.028	32.118	0.007	0.007	0.000	0.000	0.000	0.000
104	A	110	LYS	1	0.937	0.962	29.024	0.192	0.192	0.000	0.000	0.000	0.000
105	A	111	THR	0	0.012	-0.005	31.133	-0.002	-0.002	0.000	0.000	0.000	0.000
106	A	112	SER	0	-0.024	0.001	26.364	-0.011	-0.011	0.000	0.000	0.000	0.000
107	A	113	VAL	0	0.119	0.057	24.298	0.016	0.016	0.000	0.000	0.000	0.000
108	A	114	THR	0	-0.060	-0.007	25.112	-0.019	-0.019	0.000	0.000	0.000	0.000
109	A	115	LYS	1	0.833	0.888	25.874	0.173	0.173	0.000	0.000	0.000	0.000
110	A	116	VAL	0	0.028	0.010	22.132	0.004	0.004	0.000	0.000	0.000	0.000
111	A	117	VAL	0	-0.022	0.003	24.356	-0.005	-0.005	0.000	0.000	0.000	0.000
112	A	118	LEU	0	-0.007	0.003	19.498	-0.001	-0.001	0.000	0.000	0.000	0.000
113	A	119	ARG	1	0.874	0.932	24.099	0.167	0.167	0.000	0.000	0.000	0.000
114	A	120	PRO	0	-0.028	-0.009	22.634	0.008	0.008	0.000	0.000	0.000	0.000
115	A	121	GLN	0	0.021	0.003	24.965	0.017	0.017	0.000	0.000	0.000	0.000
116	A	122	VAL	0	-0.033	-0.017	23.249	-0.005	-0.005	0.000	0.000	0.000	0.000
117	A	123	VAL	0	0.006	0.024	26.240	0.010	0.010	0.000	0.000	0.000	0.000
118	A	124	PHE	0	0.053	0.013	23.646	-0.002	-0.002	0.000	0.000	0.000	0.000
119	A	125	SER	0	-0.066	-0.085	28.332	0.006	0.006	0.000	0.000	0.000	0.000
120	A	126	GLY	0	0.043	0.023	29.576	0.002	0.002	0.000	0.000	0.000	0.000
121	A	127	THR	0	-0.019	-0.027	31.529	-0.003	-0.003	0.000	0.000	0.000	0.000
122	A	128	SER	0	-0.009	0.001	27.544	0.004	0.004	0.000	0.000	0.000	0.000
123	A	129	LYS	1	0.875	0.949	28.198	0.039	0.039	0.000	0.000	0.000	0.000
124	A	130	PRO	0	0.009	0.025	25.304	0.005	0.005	0.000	0.000	0.000	0.000
125	A	131	THR	0	-0.019	-0.018	27.962	-0.004	-0.004	0.000	0.000	0.000	0.000
126	A	132	LEU	0	0.063	0.021	28.295	-0.006	-0.006	0.000	0.000	0.000	0.000
127	A	133	GLN	0	0.078	0.024	28.030	-0.009	-0.009	0.000	0.000	0.000	0.000
128	A	134	GLN	0	-0.025	0.002	25.252	-0.007	-0.007	0.000	0.000	0.000	0.000
129	A	135	LEU	0	0.043	0.017	23.662	-0.010	-0.010	0.000	0.000	0.000	0.000
130	A	136	GLU	-1	-0.903	-0.966	23.132	-0.117	-0.117	0.000	0.000	0.000	0.000
131	A	137	LYS	1	0.972	0.985	21.018	0.049	0.049	0.000	0.000	0.000	0.000
132	A	138	MET	0	-0.054	-0.007	19.212	-0.006	-0.006	0.000	0.000	0.000	0.000
133	A	139	HIS	1	0.849	0.909	18.227	0.175	0.175	0.000	0.000	0.000	0.000
134	A	140	HIS	0	-0.046	-0.011	18.777	-0.031	-0.031	0.000	0.000	0.000	0.000
135	A	141	LEU	0	0.012	0.004	15.410	-0.022	-0.022	0.000	0.000	0.000	0.000
136	A	142	ALA	0	-0.020	-0.014	14.284	-0.051	-0.051	0.000	0.000	0.000	0.000
137	A	143	HIS	0	0.000	-0.008	14.070	-0.095	-0.095	0.000	0.000	0.000	0.000
138	A	144	GLU	-1	-0.847	-0.915	14.438	-0.275	-0.275	0.000	0.000	0.000	0.000
139	A	145	ASN	0	-0.079	-0.044	9.916	-0.049	-0.049	0.000	0.000	0.000	0.000
140	A	146	CYS	0	-0.049	0.013	9.682	-0.202	-0.202	0.000	0.000	0.000	0.000
141	A	147	PHE	0	0.042	0.005	5.223	-0.150	-0.150	0.000	0.000	0.000	0.000
142	A	148	ILE	0	0.044	0.015	9.774	0.058	0.058	0.000	0.000	0.000	0.000
143	A	149	ALA	0	0.050	0.006	13.194	0.066	0.066	0.000	0.000	0.000	0.000
144	A	150	ASN	0	-0.076	-0.044	11.445	0.118	0.118	0.000	0.000	0.000	0.000
145	A	151	SER	0	-0.060	-0.022	12.189	-0.037	-0.037	0.000	0.000	0.000	0.000
146	A	152	VAL	0	-0.082	-0.033	14.531	0.063	0.063	0.000	0.000	0.000	0.000
147	A	153	GLU	-1	-0.867	-0.932	18.171	-0.256	-0.256	0.000	0.000	0.000	0.000
148	A	154	THR	0	-0.082	-0.049	21.216	0.018	0.018	0.000	0.000	0.000	0.000
149	A	155	GLU	-1	-0.790	-0.865	21.545	-0.209	-0.209	0.000	0.000	0.000	0.000
150	A	156	VAL	0	-0.003	-0.008	19.133	0.007	0.007	0.000	0.000	0.000	0.000
151	A	157	VAL	0	0.010	0.016	22.093	0.005	0.005	0.000	0.000	0.000	0.000
152	A	158	THR	0	-0.024	-0.021	21.692	-0.012	-0.012	0.000	0.000	0.000	0.000
153	A	159	GLU	-1	-0.917	-0.969	24.044	-0.132	-0.132	0.000	0.000	0.000	0.000
154	A	160	ILE	0	-0.021	-0.020	24.427	-0.003	-0.003	0.000	0.000	0.000	0.000
155	A	161	ILE	0	-0.030	-0.001	27.184	0.012	0.012	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:7:SER)