FMO DATABASE

FMODB ID: 72LQK

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	OptH
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	-1279401.17088
FMO2-HF: Nuclear repulsion	1219652.846412
FMO2-HF: Total energy	-59748.324468
FMO2-MP2: Total energy	-59922.227308

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.
-0.298	1.571	-0.008	-0.983	-0.878	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 : 0.012 / 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	0.000	0.005	3.847	1.118	2.940	-0.007	-0.980	-0.835	0.004
4	A	10	GLU	-1	-0.941	-0.965	6.550	-0.645	-0.645	0.000	0.000	0.000	0.000
5	A	11	HIS	0	-0.038	-0.023	7.552	0.485	0.485	0.000	0.000	0.000	0.000
6	A	12	SER	0	-0.007	0.004	12.510	-0.011	-0.011	0.000	0.000	0.000	0.000
7	A	13	ALA	0	0.028	0.003	16.211	0.006	0.006	0.000	0.000	0.000	0.000
8	A	14	ILE	0	-0.014	0.003	19.356	0.003	0.003	0.000	0.000	0.000	0.000
9	A	15	VAL	0	0.015	0.012	22.928	0.007	0.007	0.000	0.000	0.000	0.000
10	A	16	THR	0	-0.028	-0.016	25.453	0.015	0.015	0.000	0.000	0.000	0.000
11	A	17	TRP	0	0.011	0.001	29.090	0.002	0.002	0.000	0.000	0.000	0.000
12	A	18	LYS	1	0.900	0.942	32.439	0.091	0.091	0.000	0.000	0.000	0.000
13	A	19	ARG	1	0.926	0.984	35.820	0.071	0.071	0.000	0.000	0.000	0.000
14	A	20	LYS	1	0.957	0.971	37.835	0.084	0.084	0.000	0.000	0.000	0.000
15	A	21	ASP	-1	-0.872	-0.931	41.400	-0.058	-0.058	0.000	0.000	0.000	0.000
16	A	22	SER	0	-0.056	-0.034	44.778	0.000	0.000	0.000	0.000	0.000	0.000
17	A	23	GLU	-1	-0.837	-0.918	40.638	-0.091	-0.091	0.000	0.000	0.000	0.000
18	A	24	ALA	0	0.032	0.018	44.846	0.000	0.000	0.000	0.000	0.000	0.000
19	A	25	PHE	0	-0.017	-0.003	38.281	0.000	0.000	0.000	0.000	0.000	0.000
20	A	26	THR	0	0.006	-0.016	43.272	-0.004	-0.004	0.000	0.000	0.000	0.000
21	A	27	ASP	-1	-0.866	-0.931	45.274	-0.078	-0.078	0.000	0.000	0.000	0.000
22	A	28	ASN	0	-0.045	-0.034	40.981	-0.004	-0.004	0.000	0.000	0.000	0.000
23	A	29	GLN	0	0.013	0.016	42.463	-0.007	-0.007	0.000	0.000	0.000	0.000
24	A	30	TYR	0	-0.028	0.007	36.599	0.000	0.000	0.000	0.000	0.000	0.000
25	A	31	SER	0	0.061	0.044	37.787	-0.007	-0.007	0.000	0.000	0.000	0.000
26	A	32	ARG	1	0.832	0.874	34.384	0.116	0.116	0.000	0.000	0.000	0.000
27	A	33	ALA	0	-0.001	0.028	33.145	-0.012	-0.012	0.000	0.000	0.000	0.000
28	A	34	HIS	0	-0.106	-0.065	28.068	-0.008	-0.008	0.000	0.000	0.000	0.000
29	A	35	THR	0	-0.006	0.004	27.822	0.005	0.005	0.000	0.000	0.000	0.000
30	A	36	TRP	0	-0.032	-0.017	22.544	-0.016	-0.016	0.000	0.000	0.000	0.000
31	A	37	GLU	-1	-0.948	-0.977	22.884	-0.096	-0.096	0.000	0.000	0.000	0.000
32	A	38	PHE	0	0.001	0.001	17.893	-0.027	-0.027	0.000	0.000	0.000	0.000
33	A	39	ASP	-1	-0.853	-0.932	16.194	-0.066	-0.066	0.000	0.000	0.000	0.000
34	A	40	GLY	0	-0.047	-0.016	17.554	0.035	0.035	0.000	0.000	0.000	0.000
35	A	41	GLY	0	0.005	0.005	18.805	0.019	0.019	0.000	0.000	0.000	0.000
36	A	42	SER	0	-0.078	-0.031	21.323	0.004	0.004	0.000	0.000	0.000	0.000
37	A	43	LYS	1	0.996	0.986	22.866	0.078	0.078	0.000	0.000	0.000	0.000
38	A	44	ILE	0	-0.004	-0.002	22.302	0.008	0.008	0.000	0.000	0.000	0.000
39	A	45	LEU	0	-0.035	-0.017	26.123	-0.001	-0.001	0.000	0.000	0.000	0.000
40	A	46	ALA	0	0.058	0.031	26.952	-0.005	-0.005	0.000	0.000	0.000	0.000
41	A	47	SER	0	-0.006	-0.022	28.946	0.022	0.022	0.000	0.000	0.000	0.000
42	A	48	ALA	0	0.008	0.006	29.993	-0.016	-0.016	0.000	0.000	0.000	0.000
43	A	49	SER	0	0.092	0.055	30.678	0.013	0.013	0.000	0.000	0.000	0.000
44	A	50	PRO	0	0.058	0.012	32.347	0.005	0.005	0.000	0.000	0.000	0.000
45	A	51	HIS	0	-0.050	-0.021	32.934	0.011	0.011	0.000	0.000	0.000	0.000
46	A	52	VAL	0	-0.075	-0.034	33.037	0.003	0.003	0.000	0.000	0.000	0.000
47	A	53	VAL	0	-0.020	-0.007	35.511	0.005	0.005	0.000	0.000	0.000	0.000
48	A	54	PRO	0	0.007	0.027	37.702	-0.002	-0.002	0.000	0.000	0.000	0.000
49	A	55	VAL	0	0.053	0.057	38.504	0.000	0.000	0.000	0.000	0.000	0.000
50	A	56	PRO	0	-0.051	-0.040	40.679	0.004	0.004	0.000	0.000	0.000	0.000
51	A	57	LEU	0	-0.039	-0.017	39.937	0.000	0.000	0.000	0.000	0.000	0.000
52	A	58	SER	0	-0.056	-0.038	35.453	-0.002	-0.002	0.000	0.000	0.000	0.000
53	A	59	VAL	0	0.001	-0.017	34.808	0.008	0.008	0.000	0.000	0.000	0.000
54	A	60	GLU	-1	-0.869	-0.962	34.175	-0.111	-0.111	0.000	0.000	0.000	0.000
55	A	61	ALA	0	-0.062	-0.024	33.611	-0.006	-0.006	0.000	0.000	0.000	0.000
56	A	62	ASN	0	-0.060	-0.019	30.919	0.005	0.005	0.000	0.000	0.000	0.000
57	A	63	VAL	0	0.018	0.025	24.614	-0.003	-0.003	0.000	0.000	0.000	0.000
58	A	64	ASP	-1	-0.790	-0.896	27.990	-0.209	-0.209	0.000	0.000	0.000	0.000
59	A	65	PRO	0	-0.016	-0.037	24.655	-0.021	-0.021	0.000	0.000	0.000	0.000
60	A	66	GLU	-1	-0.916	-0.956	24.048	-0.263	-0.263	0.000	0.000	0.000	0.000
61	A	67	GLU	-1	-0.881	-0.948	24.719	-0.218	-0.218	0.000	0.000	0.000	0.000
62	A	68	ALA	0	-0.023	-0.014	21.525	-0.016	-0.016	0.000	0.000	0.000	0.000
63	A	69	PHE	0	-0.031	-0.006	19.593	-0.045	-0.045	0.000	0.000	0.000	0.000
64	A	70	VAL	0	0.000	-0.004	19.997	-0.037	-0.037	0.000	0.000	0.000	0.000
65	A	71	ALA	0	0.011	0.008	20.932	-0.018	-0.018	0.000	0.000	0.000	0.000
66	A	72	ALA	0	-0.013	-0.007	16.107	-0.019	-0.019	0.000	0.000	0.000	0.000
67	A	73	LEU	0	0.022	0.003	16.106	-0.065	-0.065	0.000	0.000	0.000	0.000
68	A	74	SER	0	-0.066	-0.043	17.035	-0.013	-0.013	0.000	0.000	0.000	0.000
69	A	75	SER	0	-0.010	-0.013	16.563	0.001	0.001	0.000	0.000	0.000	0.000
70	A	76	CYS	0	-0.035	0.003	11.108	-0.051	-0.051	0.000	0.000	0.000	0.000
71	A	77	HIS	0	0.091	0.044	13.265	0.010	0.010	0.000	0.000	0.000	0.000
72	A	78	MET	0	-0.012	0.000	15.596	0.048	0.048	0.000	0.000	0.000	0.000
73	A	79	LEU	0	-0.001	-0.007	12.384	0.052	0.052	0.000	0.000	0.000	0.000
74	A	80	VAL	0	0.008	0.020	10.352	0.070	0.070	0.000	0.000	0.000	0.000
75	A	81	PHE	0	0.047	0.017	12.869	0.102	0.102	0.000	0.000	0.000	0.000
76	A	82	LEU	0	0.012	0.007	16.386	0.056	0.056	0.000	0.000	0.000	0.000
77	A	83	SER	0	-0.073	-0.039	12.707	0.062	0.062	0.000	0.000	0.000	0.000
78	A	84	ILE	0	-0.001	-0.007	14.110	0.079	0.079	0.000	0.000	0.000	0.000
79	A	85	ALA	0	0.008	-0.008	16.105	0.041	0.041	0.000	0.000	0.000	0.000
80	A	86	ALA	0	0.011	0.011	17.162	0.026	0.026	0.000	0.000	0.000	0.000
81	A	87	LYS	1	0.931	0.964	11.346	-0.124	-0.124	0.000	0.000	0.000	0.000
82	A	88	GLN	0	-0.063	-0.016	18.086	0.025	0.025	0.000	0.000	0.000	0.000
83	A	89	ARG	1	0.919	0.962	21.117	-0.046	-0.046	0.000	0.000	0.000	0.000
84	A	90	TYR	0	-0.040	-0.021	22.553	-0.003	-0.003	0.000	0.000	0.000	0.000
85	A	91	LEU	0	0.011	0.013	23.175	-0.003	-0.003	0.000	0.000	0.000	0.000
86	A	92	VAL	0	-0.044	-0.026	21.715	-0.007	-0.007	0.000	0.000	0.000	0.000
87	A	93	GLU	-1	-0.826	-0.877	24.653	-0.029	-0.029	0.000	0.000	0.000	0.000
88	A	94	SER	0	-0.018	-0.012	25.335	-0.004	-0.004	0.000	0.000	0.000	0.000
89	A	95	TYR	0	0.043	-0.002	20.461	-0.003	-0.003	0.000	0.000	0.000	0.000
90	A	96	THR	0	0.005	0.008	24.151	-0.004	-0.004	0.000	0.000	0.000	0.000
91	A	97	ASP	-1	-0.762	-0.871	22.464	-0.261	-0.261	0.000	0.000	0.000	0.000
92	A	98	ASN	0	-0.051	-0.002	25.013	0.004	0.004	0.000	0.000	0.000	0.000
93	A	99	ALA	0	0.038	0.019	23.734	0.004	0.004	0.000	0.000	0.000	0.000
94	A	100	VAL	0	-0.028	-0.013	25.792	0.012	0.012	0.000	0.000	0.000	0.000
95	A	101	GLY	0	0.033	0.018	26.473	-0.015	-0.015	0.000	0.000	0.000	0.000
96	A	102	ILE	0	-0.043	-0.013	27.088	0.020	0.020	0.000	0.000	0.000	0.000
97	A	103	LEU	0	0.045	0.011	28.793	-0.015	-0.015	0.000	0.000	0.000	0.000
98	A	104	GLY	0	0.015	0.003	30.810	0.016	0.016	0.000	0.000	0.000	0.000
99	A	105	LYS	1	0.883	0.950	31.445	0.141	0.141	0.000	0.000	0.000	0.000
100	A	106	ASN	0	0.120	0.058	27.502	0.018	0.018	0.000	0.000	0.000	0.000
101	A	107	SER	0	0.037	0.005	29.214	0.010	0.010	0.000	0.000	0.000	0.000
102	A	108	LYS	1	0.939	0.970	27.363	0.263	0.263	0.000	0.000	0.000	0.000
103	A	109	GLY	0	0.008	0.016	32.142	0.008	0.008	0.000	0.000	0.000	0.000
104	A	110	LYS	1	0.925	0.954	29.074	0.235	0.235	0.000	0.000	0.000	0.000
105	A	111	THR	0	-0.003	-0.010	31.170	-0.003	-0.003	0.000	0.000	0.000	0.000
106	A	112	SER	0	-0.019	-0.001	26.364	-0.014	-0.014	0.000	0.000	0.000	0.000
107	A	113	VAL	0	0.111	0.055	24.340	0.020	0.020	0.000	0.000	0.000	0.000
108	A	114	THR	0	-0.047	0.004	25.148	-0.024	-0.024	0.000	0.000	0.000	0.000
109	A	115	LYS	1	0.958	0.977	25.908	0.192	0.192	0.000	0.000	0.000	0.000
110	A	116	VAL	0	0.033	0.011	22.206	0.006	0.006	0.000	0.000	0.000	0.000
111	A	117	VAL	0	-0.032	-0.007	24.382	-0.006	-0.006	0.000	0.000	0.000	0.000
112	A	118	LEU	0	0.001	0.006	19.623	0.001	0.001	0.000	0.000	0.000	0.000
113	A	119	ARG	1	0.910	0.961	24.125	0.184	0.184	0.000	0.000	0.000	0.000
114	A	120	PRO	0	-0.020	-0.005	22.580	0.011	0.011	0.000	0.000	0.000	0.000
115	A	121	GLN	0	-0.001	-0.006	24.987	0.020	0.020	0.000	0.000	0.000	0.000
116	A	122	VAL	0	-0.036	-0.018	23.161	-0.004	-0.004	0.000	0.000	0.000	0.000
117	A	123	VAL	0	-0.005	0.021	26.255	0.010	0.010	0.000	0.000	0.000	0.000
118	A	124	PHE	0	0.035	0.002	23.741	0.000	0.000	0.000	0.000	0.000	0.000
119	A	125	SER	0	-0.094	-0.101	28.337	0.004	0.004	0.000	0.000	0.000	0.000
120	A	126	GLY	0	0.019	0.008	29.573	0.003	0.003	0.000	0.000	0.000	0.000
121	A	127	THR	0	-0.021	-0.033	31.537	-0.005	-0.005	0.000	0.000	0.000	0.000
122	A	128	SER	0	-0.001	0.006	27.471	0.002	0.002	0.000	0.000	0.000	0.000
123	A	129	LYS	1	0.929	0.979	28.184	0.030	0.030	0.000	0.000	0.000	0.000
124	A	130	PRO	0	0.023	0.032	25.386	0.005	0.005	0.000	0.000	0.000	0.000
125	A	131	THR	0	-0.015	-0.020	27.944	-0.004	-0.004	0.000	0.000	0.000	0.000
126	A	132	LEU	0	0.064	0.017	28.277	-0.007	-0.007	0.000	0.000	0.000	0.000
127	A	133	GLN	0	0.064	0.025	28.013	-0.010	-0.010	0.000	0.000	0.000	0.000
128	A	134	GLN	0	-0.023	0.004	25.169	-0.008	-0.008	0.000	0.000	0.000	0.000
129	A	135	LEU	0	0.048	0.019	23.655	-0.012	-0.012	0.000	0.000	0.000	0.000
130	A	136	GLU	-1	-0.912	-0.969	23.120	-0.146	-0.146	0.000	0.000	0.000	0.000
131	A	137	LYS	1	0.976	0.990	20.748	0.065	0.065	0.000	0.000	0.000	0.000
132	A	138	MET	0	-0.064	-0.016	19.199	-0.010	-0.010	0.000	0.000	0.000	0.000
133	A	139	HIS	1	0.858	0.923	18.235	0.193	0.193	0.000	0.000	0.000	0.000
134	A	140	HIS	0	0.026	0.025	18.770	-0.039	-0.039	0.000	0.000	0.000	0.000
135	A	141	LEU	0	0.025	0.010	15.082	-0.028	-0.028	0.000	0.000	0.000	0.000
136	A	142	ALA	0	-0.034	-0.022	14.274	-0.063	-0.063	0.000	0.000	0.000	0.000
137	A	143	HIS	0	-0.003	-0.013	14.071	-0.102	-0.102	0.000	0.000	0.000	0.000
138	A	144	GLU	-1	-0.913	-0.953	14.295	-0.362	-0.362	0.000	0.000	0.000	0.000
139	A	145	ASN	0	-0.076	-0.038	9.841	-0.122	-0.122	0.000	0.000	0.000	0.000
140	A	146	CYS	0	-0.024	0.042	9.684	-0.236	-0.236	0.000	0.000	0.000	0.000
141	A	147	PHE	0	0.021	-0.005	4.777	-0.218	-0.171	-0.001	-0.003	-0.043	0.000
142	A	148	ILE	0	0.050	0.016	9.804	0.063	0.063	0.000	0.000	0.000	0.000
143	A	149	ALA	0	0.035	-0.010	13.235	0.074	0.074	0.000	0.000	0.000	0.000
144	A	150	ASN	0	-0.049	-0.019	10.374	0.177	0.177	0.000	0.000	0.000	0.000
145	A	151	SER	0	-0.073	-0.044	12.505	-0.059	-0.059	0.000	0.000	0.000	0.000
146	A	152	VAL	0	-0.084	-0.032	14.561	0.070	0.070	0.000	0.000	0.000	0.000
147	A	153	GLU	-1	-0.967	-0.988	18.201	-0.341	-0.341	0.000	0.000	0.000	0.000
148	A	154	THR	0	-0.104	-0.060	21.354	0.022	0.022	0.000	0.000	0.000	0.000
149	A	155	GLU	-1	-0.872	-0.932	21.565	-0.254	-0.254	0.000	0.000	0.000	0.000
150	A	156	VAL	0	-0.026	-0.019	19.219	0.011	0.011	0.000	0.000	0.000	0.000
151	A	157	VAL	0	0.002	0.011	22.111	0.005	0.005	0.000	0.000	0.000	0.000
152	A	158	THR	0	-0.010	-0.015	21.679	-0.012	-0.012	0.000	0.000	0.000	0.000
153	A	159	GLU	-1	-0.944	-0.974	24.055	-0.150	-0.150	0.000	0.000	0.000	0.000
154	A	160	ILE	0	-0.027	-0.025	24.564	-0.002	-0.002	0.000	0.000	0.000	0.000
155	A	161	ILE	0	-0.008	0.006	27.191	0.014	0.014	0.000	0.000	0.000	0.000

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