FMO DATABASE

FMODB ID: ZVVGN

Calculation Name: 5EXV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5EXV

Chain ID: A

ChEMBL ID:

UniProt ID: Q9KL40

Base Structure: X-ray

Registration Date: 2023-09-21

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	163
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1598505.304435
FMO2-HF: Nuclear repulsion	1534432.094055
FMO2-HF: Total energy	-64073.210381
FMO2-MP2: Total energy	-64259.766822

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:3:SER)

Summations of interaction energy for fragment #1(A:3: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.
-9.683	-5.247	6.805	-4.526	-6.715	-0.034

Interaction energy analysis for fragmet #1(A:3:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.013 / q_NPA : 0.010

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	5	GLN	0	0.091	0.041	2.171	-11.779	-9.601	5.307	-3.245	-4.240	-0.032
4	A	6	GLN	0	-0.040	-0.013	2.377	-0.485	1.340	1.498	-1.182	-2.141	-0.002
5	A	7	GLN	0	-0.072	-0.031	3.988	1.470	1.903	0.000	-0.099	-0.334	0.000
6	A	8	VAL	0	0.002	-0.003	5.453	0.835	0.835	0.000	0.000	0.000	0.000
7	A	9	ALA	0	0.071	0.038	8.067	0.277	0.277	0.000	0.000	0.000	0.000
8	A	10	GLN	0	-0.073	-0.036	9.737	0.223	0.223	0.000	0.000	0.000	0.000
9	A	11	LEU	0	0.026	0.011	12.150	0.109	0.109	0.000	0.000	0.000	0.000
10	A	12	LEU	0	-0.032	0.012	11.353	0.097	0.097	0.000	0.000	0.000	0.000
11	A	13	GLU	-1	-0.789	-0.908	14.426	-0.421	-0.421	0.000	0.000	0.000	0.000
12	A	14	GLN	0	0.003	-0.008	16.853	0.028	0.028	0.000	0.000	0.000	0.000
13	A	15	GLN	0	-0.068	-0.020	17.919	0.056	0.056	0.000	0.000	0.000	0.000
14	A	16	PRO	0	0.039	0.027	19.171	-0.001	-0.001	0.000	0.000	0.000	0.000
15	A	17	THR	0	-0.024	-0.030	20.989	0.024	0.024	0.000	0.000	0.000	0.000
16	A	18	LEU	0	0.006	0.006	17.729	0.027	0.027	0.000	0.000	0.000	0.000
17	A	19	LEU	0	0.016	0.008	17.895	-0.034	-0.034	0.000	0.000	0.000	0.000
18	A	20	PRO	0	0.030	-0.002	14.346	0.014	0.014	0.000	0.000	0.000	0.000
19	A	21	ALA	0	-0.007	-0.002	15.437	0.029	0.029	0.000	0.000	0.000	0.000
20	A	22	ALA	0	-0.028	0.002	17.821	0.022	0.022	0.000	0.000	0.000	0.000
21	A	23	MET	0	0.004	-0.002	11.958	0.009	0.009	0.000	0.000	0.000	0.000
22	A	24	ALA	0	0.017	0.012	13.237	0.007	0.007	0.000	0.000	0.000	0.000
23	A	25	GLU	-1	-0.893	-0.946	14.239	0.158	0.158	0.000	0.000	0.000	0.000
24	A	26	GLN	0	-0.091	-0.054	14.988	0.013	0.013	0.000	0.000	0.000	0.000
25	A	27	LEU	0	-0.042	-0.017	10.232	-0.048	-0.048	0.000	0.000	0.000	0.000
26	A	28	ASN	0	-0.079	-0.028	11.301	0.103	0.103	0.000	0.000	0.000	0.000
27	A	29	VAL	0	-0.016	0.007	8.306	0.133	0.133	0.000	0.000	0.000	0.000
28	A	30	THR	0	-0.006	-0.016	11.581	-0.149	-0.149	0.000	0.000	0.000	0.000
29	A	31	GLU	-1	-0.792	-0.902	11.921	-0.016	-0.016	0.000	0.000	0.000	0.000
30	A	32	PHE	0	-0.004	0.006	10.522	-0.043	-0.043	0.000	0.000	0.000	0.000
31	A	33	ASP	-1	-0.816	-0.894	7.787	0.621	0.621	0.000	0.000	0.000	0.000
32	A	34	ILE	0	-0.037	-0.010	7.742	0.067	0.067	0.000	0.000	0.000	0.000
33	A	35	VAL	0	-0.024	-0.020	9.929	-0.169	-0.169	0.000	0.000	0.000	0.000
34	A	36	HIS	0	-0.008	-0.010	5.728	-0.077	-0.077	0.000	0.000	0.000	0.000
35	A	37	ALA	0	-0.055	-0.022	5.824	-0.219	-0.219	0.000	0.000	0.000	0.000
36	A	38	LEU	0	-0.016	-0.003	6.914	-0.378	-0.378	0.000	0.000	0.000	0.000
37	A	39	PRO	0	0.009	-0.005	9.289	-0.129	-0.129	0.000	0.000	0.000	0.000
38	A	40	GLU	-1	-0.834	-0.917	10.864	-0.372	-0.372	0.000	0.000	0.000	0.000
39	A	41	GLU	-1	-0.936	-0.957	12.155	-0.458	-0.458	0.000	0.000	0.000	0.000
40	A	42	MET	0	-0.092	-0.053	13.901	0.076	0.076	0.000	0.000	0.000	0.000
41	A	43	VAL	0	-0.060	-0.036	11.466	0.068	0.068	0.000	0.000	0.000	0.000
42	A	44	ALA	0	0.062	0.035	14.873	-0.020	-0.020	0.000	0.000	0.000	0.000
43	A	45	VAL	0	-0.028	-0.010	11.157	0.053	0.053	0.000	0.000	0.000	0.000
44	A	46	VAL	0	-0.009	-0.004	14.437	-0.013	-0.013	0.000	0.000	0.000	0.000
45	A	47	ASP	-1	-0.866	-0.936	16.853	-0.090	-0.090	0.000	0.000	0.000	0.000
46	A	48	GLY	0	-0.007	-0.002	18.214	0.001	0.001	0.000	0.000	0.000	0.000
47	A	49	SER	0	-0.046	-0.024	20.056	0.007	0.007	0.000	0.000	0.000	0.000
48	A	50	HIS	0	-0.010	-0.019	22.765	-0.008	-0.008	0.000	0.000	0.000	0.000
49	A	51	ALA	0	0.060	0.038	23.036	-0.006	-0.006	0.000	0.000	0.000	0.000
50	A	52	GLN	0	-0.084	-0.067	25.025	0.001	0.001	0.000	0.000	0.000	0.000
51	A	53	THR	0	0.011	0.007	27.519	-0.003	-0.003	0.000	0.000	0.000	0.000
52	A	54	ILE	0	0.018	0.027	23.866	-0.002	-0.002	0.000	0.000	0.000	0.000
53	A	55	LEU	0	-0.006	-0.003	26.842	-0.002	-0.002	0.000	0.000	0.000	0.000
54	A	56	GLU	-1	-0.870	-0.933	29.185	-0.032	-0.032	0.000	0.000	0.000	0.000
55	A	57	SER	0	-0.049	-0.022	29.300	-0.002	-0.002	0.000	0.000	0.000	0.000
56	A	58	LEU	0	0.020	0.010	27.089	-0.002	-0.002	0.000	0.000	0.000	0.000
57	A	59	PRO	0	-0.054	-0.031	31.064	-0.002	-0.002	0.000	0.000	0.000	0.000
58	A	60	GLU	-1	-0.889	-0.906	33.659	-0.073	-0.073	0.000	0.000	0.000	0.000
59	A	61	TRP	0	-0.001	-0.004	27.644	-0.001	-0.001	0.000	0.000	0.000	0.000
60	A	62	GLY	0	0.044	0.044	33.508	-0.002	-0.002	0.000	0.000	0.000	0.000
61	A	63	PRO	0	-0.028	-0.028	34.917	0.001	0.001	0.000	0.000	0.000	0.000
62	A	64	VAL	0	0.017	0.016	30.334	-0.007	-0.007	0.000	0.000	0.000	0.000
63	A	65	THR	0	-0.068	-0.047	30.054	0.004	0.004	0.000	0.000	0.000	0.000
64	A	66	THR	0	0.018	0.024	28.657	-0.005	-0.005	0.000	0.000	0.000	0.000
65	A	67	ILE	0	-0.026	-0.017	26.305	0.002	0.002	0.000	0.000	0.000	0.000
66	A	68	MET	0	0.022	0.013	26.129	-0.001	-0.001	0.000	0.000	0.000	0.000
67	A	69	THR	0	-0.045	-0.038	24.040	-0.002	-0.002	0.000	0.000	0.000	0.000
68	A	70	ILE	0	0.051	0.017	26.398	0.008	0.008	0.000	0.000	0.000	0.000
69	A	71	ALA	0	0.000	-0.007	28.083	-0.005	-0.005	0.000	0.000	0.000	0.000
70	A	72	GLY	0	0.031	0.028	27.012	-0.002	-0.002	0.000	0.000	0.000	0.000
71	A	73	SER	0	-0.026	0.004	28.033	-0.009	-0.009	0.000	0.000	0.000	0.000
72	A	74	ILE	0	-0.004	0.001	26.875	0.003	0.003	0.000	0.000	0.000	0.000
73	A	75	PHE	0	-0.023	-0.007	29.831	-0.001	-0.001	0.000	0.000	0.000	0.000
74	A	76	GLU	-1	-0.814	-0.913	30.384	-0.058	-0.058	0.000	0.000	0.000	0.000
75	A	77	VAL	0	-0.030	-0.011	32.157	0.002	0.002	0.000	0.000	0.000	0.000
76	A	78	LYS	1	0.843	0.904	33.448	0.048	0.048	0.000	0.000	0.000	0.000
77	A	79	ALA	0	0.052	0.033	35.261	0.002	0.002	0.000	0.000	0.000	0.000
78	A	80	PRO	0	0.020	0.007	35.032	-0.004	-0.004	0.000	0.000	0.000	0.000
79	A	81	PHE	0	0.023	0.021	29.988	0.003	0.003	0.000	0.000	0.000	0.000
80	A	82	PRO	0	-0.024	0.009	33.430	0.000	0.000	0.000	0.000	0.000	0.000
81	A	83	LYS	1	0.983	0.973	34.618	0.028	0.028	0.000	0.000	0.000	0.000
82	A	84	GLY	0	0.039	0.012	34.977	0.002	0.002	0.000	0.000	0.000	0.000
83	A	85	LYS	1	0.913	0.963	36.019	0.010	0.010	0.000	0.000	0.000	0.000
84	A	86	VAL	0	0.055	0.037	33.192	0.001	0.001	0.000	0.000	0.000	0.000
85	A	87	ALA	0	-0.008	-0.008	36.170	0.001	0.001	0.000	0.000	0.000	0.000
86	A	88	ARG	1	0.856	0.903	37.391	-0.006	-0.006	0.000	0.000	0.000	0.000
87	A	89	GLY	0	0.045	0.043	35.004	0.003	0.003	0.000	0.000	0.000	0.000
88	A	90	TYR	0	-0.040	-0.016	32.458	0.004	0.004	0.000	0.000	0.000	0.000
89	A	91	TYR	0	0.082	0.046	31.227	-0.001	-0.001	0.000	0.000	0.000	0.000
90	A	92	ASN	0	-0.061	-0.059	33.179	0.001	0.001	0.000	0.000	0.000	0.000
91	A	93	LEU	0	0.029	0.005	36.188	-0.003	-0.003	0.000	0.000	0.000	0.000
92	A	94	MET	0	-0.068	-0.025	37.955	0.001	0.001	0.000	0.000	0.000	0.000
93	A	95	GLY	0	0.048	0.050	39.810	-0.002	-0.002	0.000	0.000	0.000	0.000
94	A	96	ARG	1	0.740	0.845	40.472	0.027	0.027	0.000	0.000	0.000	0.000
95	A	97	ASP	-1	-0.845	-0.933	42.826	-0.023	-0.023	0.000	0.000	0.000	0.000
96	A	98	GLY	0	0.034	0.046	41.548	-0.002	-0.002	0.000	0.000	0.000	0.000
97	A	99	GLU	-1	-0.825	-0.920	37.938	-0.032	-0.032	0.000	0.000	0.000	0.000
98	A	100	LEU	0	0.004	0.010	31.388	0.003	0.003	0.000	0.000	0.000	0.000
99	A	101	HIS	0	-0.030	-0.023	35.883	0.002	0.002	0.000	0.000	0.000	0.000
100	A	102	GLY	0	0.062	0.000	35.489	0.001	0.001	0.000	0.000	0.000	0.000
101	A	103	HIS	0	-0.059	-0.011	34.386	0.001	0.001	0.000	0.000	0.000	0.000
102	A	104	LEU	0	0.053	0.041	28.563	0.001	0.001	0.000	0.000	0.000	0.000
103	A	105	LYS	1	0.820	0.899	27.999	-0.024	-0.024	0.000	0.000	0.000	0.000
104	A	106	LEU	0	0.033	0.012	25.836	0.005	0.005	0.000	0.000	0.000	0.000
105	A	107	GLU	-1	-0.802	-0.888	24.380	0.012	0.012	0.000	0.000	0.000	0.000
106	A	108	ASN	0	-0.054	-0.026	23.453	0.001	0.001	0.000	0.000	0.000	0.000
107	A	109	ILE	0	-0.066	-0.026	20.200	0.013	0.013	0.000	0.000	0.000	0.000
108	A	110	SER	0	-0.029	-0.031	16.186	-0.011	-0.011	0.000	0.000	0.000	0.000
109	A	111	HIS	0	0.003	-0.003	13.457	-0.041	-0.041	0.000	0.000	0.000	0.000
110	A	112	VAL	0	-0.027	-0.013	16.908	0.017	0.017	0.000	0.000	0.000	0.000
111	A	113	ALA	0	0.004	0.008	14.717	-0.021	-0.021	0.000	0.000	0.000	0.000
112	A	114	LEU	0	-0.015	0.003	16.629	0.022	0.022	0.000	0.000	0.000	0.000
113	A	115	VAL	0	0.013	0.008	15.936	-0.038	-0.038	0.000	0.000	0.000	0.000
114	A	116	SER	0	-0.010	-0.021	17.539	0.033	0.033	0.000	0.000	0.000	0.000
115	A	117	LYS	1	0.858	0.941	16.594	0.273	0.273	0.000	0.000	0.000	0.000
116	A	118	PRO	0	-0.013	0.010	18.864	0.033	0.033	0.000	0.000	0.000	0.000
117	A	119	PHE	0	0.015	-0.004	21.089	-0.010	-0.010	0.000	0.000	0.000	0.000
118	A	120	MET	0	-0.051	-0.025	23.747	0.012	0.012	0.000	0.000	0.000	0.000
119	A	121	GLY	0	0.025	0.027	25.456	0.008	0.008	0.000	0.000	0.000	0.000
120	A	122	ARG	1	0.773	0.877	26.171	0.145	0.145	0.000	0.000	0.000	0.000
121	A	123	GLU	-1	-0.822	-0.913	23.996	-0.166	-0.166	0.000	0.000	0.000	0.000
122	A	124	SER	0	-0.082	-0.051	22.120	0.024	0.024	0.000	0.000	0.000	0.000
123	A	125	HIS	0	0.051	0.015	22.035	-0.026	-0.026	0.000	0.000	0.000	0.000
124	A	126	TYR	0	-0.004	-0.011	18.112	0.026	0.026	0.000	0.000	0.000	0.000
125	A	127	PHE	0	0.078	0.045	21.036	-0.018	-0.018	0.000	0.000	0.000	0.000
126	A	128	GLY	0	0.010	-0.002	19.129	0.014	0.014	0.000	0.000	0.000	0.000
127	A	129	PHE	0	0.000	-0.002	19.076	-0.007	-0.007	0.000	0.000	0.000	0.000
128	A	130	PHE	0	0.031	0.000	15.931	0.010	0.010	0.000	0.000	0.000	0.000
129	A	131	THR	0	0.047	0.021	17.970	-0.001	-0.001	0.000	0.000	0.000	0.000
130	A	132	ALA	0	-0.013	0.011	16.717	0.006	0.006	0.000	0.000	0.000	0.000
131	A	133	GLN	0	-0.031	-0.022	15.913	0.024	0.024	0.000	0.000	0.000	0.000
132	A	134	GLY	0	0.069	0.043	13.744	0.037	0.037	0.000	0.000	0.000	0.000
133	A	135	GLU	-1	-0.888	-0.952	14.607	0.091	0.091	0.000	0.000	0.000	0.000
134	A	136	ASN	0	-0.019	-0.005	17.774	-0.024	-0.024	0.000	0.000	0.000	0.000
135	A	137	ALA	0	0.003	0.012	19.483	-0.002	-0.002	0.000	0.000	0.000	0.000
136	A	138	PHE	0	-0.042	-0.029	22.405	-0.002	-0.002	0.000	0.000	0.000	0.000
137	A	139	LYS	1	0.812	0.895	19.589	0.040	0.040	0.000	0.000	0.000	0.000
138	A	140	ILE	0	-0.013	-0.003	23.751	0.007	0.007	0.000	0.000	0.000	0.000
139	A	141	TYR	0	0.023	0.000	22.874	-0.009	-0.009	0.000	0.000	0.000	0.000
140	A	142	LEU	0	0.015	0.007	25.550	0.008	0.008	0.000	0.000	0.000	0.000
141	A	143	GLY	0	-0.035	-0.004	28.574	0.002	0.002	0.000	0.000	0.000	0.000
142	A	144	ARG	1	0.857	0.919	29.437	0.077	0.077	0.000	0.000	0.000	0.000
143	A	145	ASP	-1	-0.846	-0.906	34.186	-0.066	-0.066	0.000	0.000	0.000	0.000
144	A	146	GLU	-1	-0.961	-0.977	37.600	-0.054	-0.054	0.000	0.000	0.000	0.000
145	A	147	LYS	1	0.792	0.903	34.160	0.096	0.096	0.000	0.000	0.000	0.000
146	A	148	ARG	1	0.897	0.910	31.653	0.095	0.095	0.000	0.000	0.000	0.000
147	A	149	GLU	-1	-0.783	-0.876	30.703	-0.106	-0.106	0.000	0.000	0.000	0.000
148	A	150	LEU	0	-0.007	0.000	27.987	0.005	0.005	0.000	0.000	0.000	0.000
149	A	151	ILE	0	0.066	0.045	31.739	-0.001	-0.001	0.000	0.000	0.000	0.000
150	A	152	PRO	0	0.002	-0.014	32.106	-0.006	-0.006	0.000	0.000	0.000	0.000
151	A	153	GLU	-1	-0.907	-0.952	31.787	-0.083	-0.083	0.000	0.000	0.000	0.000
152	A	154	GLN	0	0.002	-0.021	29.866	-0.009	-0.009	0.000	0.000	0.000	0.000
153	A	155	VAL	0	0.001	-0.004	25.794	-0.006	-0.006	0.000	0.000	0.000	0.000
154	A	156	ALA	0	-0.010	0.007	26.680	-0.012	-0.012	0.000	0.000	0.000	0.000
155	A	157	ARG	1	0.845	0.891	27.653	0.081	0.081	0.000	0.000	0.000	0.000
156	A	158	PHE	0	-0.050	-0.024	21.069	-0.004	-0.004	0.000	0.000	0.000	0.000
157	A	159	LYS	1	0.907	0.939	19.258	0.275	0.275	0.000	0.000	0.000	0.000
158	A	160	ALA	0	0.001	0.010	22.959	-0.012	-0.012	0.000	0.000	0.000	0.000
159	A	161	MET	0	-0.080	-0.030	22.103	0.010	0.010	0.000	0.000	0.000	0.000
160	A	162	GLN	0	-0.063	-0.012	15.713	0.035	0.035	0.000	0.000	0.000	0.000
161	A	163	GLN	0	-0.022	-0.016	18.982	0.027	0.027	0.000	0.000	0.000	0.000
162	A	164	GLN	0	0.015	-0.004	20.394	0.009	0.009	0.000	0.000	0.000	0.000
163	A	165	HIS	0	-0.032	0.004	23.258	0.015	0.015	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:SER)