FMO DATABASE

FMODB ID: ZV53N

Calculation Name: 3A7L-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3A7L

Chain ID: A

ChEMBL ID:

UniProt ID: P0A6T9

Base Structure: X-ray

Registration Date: 2023-09-23

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	128
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1037346.511417
FMO2-HF: Nuclear repulsion	989387.892728
FMO2-HF: Total energy	-47958.618689
FMO2-MP2: Total energy	-48099.563715

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:SER)

Summations of interaction energy for fragment #1(A:1: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.
-12.257	-5.292	3.998	-4.2	-6.762	0.003

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.026 / q_NPA : 0.016

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

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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	0.065	0.056	3.820	0.074	2.537	-0.006	-1.221	-1.236	0.006
4	A	4	PRO	0	-0.008	0.011	6.082	-0.291	-0.291	0.000	0.000	0.000	0.000
5	A	5	ALA	0	0.030	0.006	9.576	0.066	0.066	0.000	0.000	0.000	0.000
6	A	6	GLU	-1	-1.013	-1.008	12.199	-0.048	-0.048	0.000	0.000	0.000	0.000
7	A	7	LEU	0	-0.060	-0.004	10.185	0.011	0.011	0.000	0.000	0.000	0.000
8	A	8	LYS	1	0.912	0.964	13.131	0.031	0.031	0.000	0.000	0.000	0.000
9	A	9	TYR	0	0.055	0.000	7.811	0.120	0.120	0.000	0.000	0.000	0.000
10	A	10	SER	0	0.014	0.005	11.782	-0.059	-0.059	0.000	0.000	0.000	0.000
11	A	11	LYS	1	0.930	0.945	11.215	0.107	0.107	0.000	0.000	0.000	0.000
12	A	12	GLU	-1	-0.890	-0.927	11.803	-0.072	-0.072	0.000	0.000	0.000	0.000
13	A	13	HIS	0	0.017	0.050	7.155	0.193	0.193	0.000	0.000	0.000	0.000
14	A	14	GLH	0	-0.019	-0.031	9.460	0.108	0.108	0.000	0.000	0.000	0.000
15	A	15	TRP	0	-0.031	-0.015	9.428	-0.058	-0.058	0.000	0.000	0.000	0.000
16	A	16	LEU	0	0.004	-0.010	11.790	-0.032	-0.032	0.000	0.000	0.000	0.000
17	A	17	ARG	1	0.862	0.908	15.166	-0.085	-0.085	0.000	0.000	0.000	0.000
18	A	18	LYS	1	0.819	0.932	17.000	0.006	0.006	0.000	0.000	0.000	0.000
19	A	19	GLU	-1	-0.750	-0.839	20.434	0.045	0.045	0.000	0.000	0.000	0.000
20	A	20	ALA	0	-0.026	-0.028	22.843	-0.006	-0.006	0.000	0.000	0.000	0.000
21	A	21	ASP	-1	-0.891	-0.929	26.148	0.014	0.014	0.000	0.000	0.000	0.000
22	A	22	GLY	0	-0.058	-0.030	25.759	-0.002	-0.002	0.000	0.000	0.000	0.000
23	A	23	THR	0	-0.071	-0.048	24.579	0.002	0.002	0.000	0.000	0.000	0.000
24	A	24	TYR	0	0.033	0.007	19.221	-0.005	-0.005	0.000	0.000	0.000	0.000
25	A	25	THR	0	-0.030	-0.011	16.662	0.000	0.000	0.000	0.000	0.000	0.000
26	A	26	VAL	0	0.023	0.011	15.516	0.003	0.003	0.000	0.000	0.000	0.000
27	A	27	GLY	0	0.067	0.030	13.031	-0.018	-0.018	0.000	0.000	0.000	0.000
28	A	28	ILE	0	0.022	0.027	9.610	-0.006	-0.006	0.000	0.000	0.000	0.000
29	A	29	THR	0	-0.017	-0.034	5.270	-0.017	-0.017	0.000	0.000	0.000	0.000
30	A	30	GLU	-1	-0.896	-0.953	2.455	-0.669	-0.244	1.526	-0.628	-1.323	-0.002
31	A	31	HIS	0	-0.050	-0.039	2.349	-6.898	-4.180	1.864	-1.753	-2.828	-0.001
32	A	32	ALA	0	0.032	0.019	3.766	-1.056	-0.694	0.058	-0.134	-0.286	0.001
33	A	33	GLN	0	-0.020	-0.006	5.750	-0.232	-0.232	0.000	0.000	0.000	0.000
34	A	34	GLU	-1	-0.924	-0.948	4.919	0.501	0.501	0.000	0.000	0.000	0.000
35	A	35	LEU	0	-0.060	-0.024	6.735	0.028	0.028	0.000	0.000	0.000	0.000
36	A	36	LEU	0	0.021	0.009	8.786	0.006	0.006	0.000	0.000	0.000	0.000
37	A	37	GLY	0	-0.060	-0.009	10.591	-0.019	-0.019	0.000	0.000	0.000	0.000
38	A	38	ASP	-1	-0.950	-0.972	12.205	0.174	0.174	0.000	0.000	0.000	0.000
39	A	39	MET	0	0.026	0.013	12.143	-0.027	-0.027	0.000	0.000	0.000	0.000
40	A	40	VAL	0	-0.067	-0.048	15.798	-0.005	-0.005	0.000	0.000	0.000	0.000
41	A	41	PHE	0	-0.034	-0.012	18.896	-0.008	-0.008	0.000	0.000	0.000	0.000
42	A	42	VAL	0	-0.004	-0.006	16.874	0.010	0.010	0.000	0.000	0.000	0.000
43	A	43	ASP	-1	-0.921	-0.944	19.659	0.049	0.049	0.000	0.000	0.000	0.000
44	A	44	LEU	0	-0.028	-0.021	20.472	0.004	0.004	0.000	0.000	0.000	0.000
45	A	45	PRO	0	0.032	0.020	21.977	-0.006	-0.006	0.000	0.000	0.000	0.000
46	A	46	GLU	-1	-0.952	-0.977	25.054	0.031	0.031	0.000	0.000	0.000	0.000
47	A	47	VAL	0	-0.021	-0.025	27.233	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	48	GLY	0	-0.040	-0.019	29.009	-0.002	-0.002	0.000	0.000	0.000	0.000
49	A	49	ALA	0	-0.026	-0.001	28.094	-0.004	-0.004	0.000	0.000	0.000	0.000
50	A	50	THR	0	-0.075	-0.045	28.882	0.000	0.000	0.000	0.000	0.000	0.000
51	A	51	VAL	0	-0.006	0.002	24.158	0.000	0.000	0.000	0.000	0.000	0.000
52	A	52	SER	0	-0.042	-0.041	26.685	-0.003	-0.003	0.000	0.000	0.000	0.000
53	A	53	ALA	0	-0.037	-0.019	22.409	0.004	0.004	0.000	0.000	0.000	0.000
54	A	54	GLY	0	-0.042	-0.030	20.843	-0.006	-0.006	0.000	0.000	0.000	0.000
55	A	55	ASP	-1	-0.816	-0.889	21.910	0.010	0.010	0.000	0.000	0.000	0.000
56	A	56	ASP	-1	-0.944	-0.967	21.312	0.031	0.031	0.000	0.000	0.000	0.000
57	A	57	CYS	0	-0.090	-0.046	20.958	0.000	0.000	0.000	0.000	0.000	0.000
58	A	58	ALA	0	0.017	0.008	18.966	0.003	0.003	0.000	0.000	0.000	0.000
59	A	59	VAL	0	0.005	0.016	19.099	-0.003	-0.003	0.000	0.000	0.000	0.000
60	A	60	ALA	0	-0.005	0.005	14.861	0.007	0.007	0.000	0.000	0.000	0.000
61	A	61	GLU	-1	-0.908	-0.966	16.880	0.060	0.060	0.000	0.000	0.000	0.000
62	A	62	SER	0	0.008	-0.029	14.846	0.004	0.004	0.000	0.000	0.000	0.000
63	A	63	VAL	0	-0.044	-0.023	16.882	-0.013	-0.013	0.000	0.000	0.000	0.000
64	A	64	LYS	1	0.773	0.891	11.632	-0.131	-0.131	0.000	0.000	0.000	0.000
65	A	65	ALA	0	-0.041	-0.015	15.315	-0.014	-0.014	0.000	0.000	0.000	0.000
66	A	66	ALA	0	0.034	0.023	17.482	0.011	0.011	0.000	0.000	0.000	0.000
67	A	67	SER	0	-0.036	-0.018	14.849	-0.021	-0.021	0.000	0.000	0.000	0.000
68	A	68	ASP	-1	-0.848	-0.897	16.811	0.045	0.045	0.000	0.000	0.000	0.000
69	A	69	ILE	0	-0.055	-0.024	14.788	0.011	0.011	0.000	0.000	0.000	0.000
70	A	70	TYR	0	0.024	-0.014	16.545	-0.012	-0.012	0.000	0.000	0.000	0.000
71	A	71	ALA	0	0.014	0.031	17.933	0.017	0.017	0.000	0.000	0.000	0.000
72	A	72	PRO	0	-0.049	-0.018	16.572	-0.011	-0.011	0.000	0.000	0.000	0.000
73	A	73	VAL	0	-0.030	-0.026	18.671	-0.013	-0.013	0.000	0.000	0.000	0.000
74	A	74	SER	0	-0.019	-0.051	22.085	0.006	0.006	0.000	0.000	0.000	0.000
75	A	75	GLY	0	-0.020	-0.023	25.628	-0.001	-0.001	0.000	0.000	0.000	0.000
76	A	76	GLU	-1	-0.982	-0.971	27.229	0.019	0.019	0.000	0.000	0.000	0.000
77	A	77	ILE	0	0.043	0.020	23.412	0.002	0.002	0.000	0.000	0.000	0.000
78	A	78	VAL	0	-0.027	-0.022	25.731	-0.003	-0.003	0.000	0.000	0.000	0.000
79	A	79	ALA	0	-0.052	-0.036	24.282	-0.002	-0.002	0.000	0.000	0.000	0.000
80	A	80	VAL	0	0.049	0.024	22.439	0.004	0.004	0.000	0.000	0.000	0.000
81	A	81	ASN	0	-0.028	-0.022	17.759	-0.017	-0.017	0.000	0.000	0.000	0.000
82	A	82	ASP	-1	-0.871	-0.940	21.497	0.061	0.061	0.000	0.000	0.000	0.000
83	A	83	ALA	0	-0.039	-0.019	20.922	-0.001	-0.001	0.000	0.000	0.000	0.000
84	A	84	LEU	0	-0.023	-0.010	16.651	0.004	0.004	0.000	0.000	0.000	0.000
85	A	85	SER	0	-0.041	-0.020	20.236	0.001	0.001	0.000	0.000	0.000	0.000
86	A	86	ASP	-1	-1.005	-0.998	23.411	0.062	0.062	0.000	0.000	0.000	0.000
87	A	87	SER	0	-0.088	-0.057	19.601	-0.003	-0.003	0.000	0.000	0.000	0.000
88	A	88	PRO	0	0.016	0.023	17.809	0.011	0.011	0.000	0.000	0.000	0.000
89	A	89	GLU	-1	-0.800	-0.894	15.111	0.142	0.142	0.000	0.000	0.000	0.000
90	A	90	LEU	0	-0.037	-0.026	13.903	0.023	0.023	0.000	0.000	0.000	0.000
91	A	91	VAL	0	-0.029	-0.016	11.073	0.024	0.024	0.000	0.000	0.000	0.000
92	A	92	ASN	0	-0.014	-0.037	9.726	0.028	0.028	0.000	0.000	0.000	0.000
93	A	93	SER	0	-0.030	-0.006	9.165	0.038	0.038	0.000	0.000	0.000	0.000
94	A	94	GLU	-1	-0.932	-0.972	10.547	0.120	0.120	0.000	0.000	0.000	0.000
95	A	95	PRO	0	0.074	0.064	6.771	-0.040	-0.040	0.000	0.000	0.000	0.000
96	A	96	TYR	0	-0.059	-0.053	4.856	0.006	0.006	0.000	0.000	0.000	0.000
97	A	97	ALA	0	-0.072	-0.049	10.760	-0.053	-0.053	0.000	0.000	0.000	0.000
98	A	98	GLY	0	-0.021	-0.015	13.955	-0.005	-0.005	0.000	0.000	0.000	0.000
99	A	99	GLY	0	0.027	0.016	13.235	-0.012	-0.012	0.000	0.000	0.000	0.000
100	A	100	TRP	0	-0.113	-0.039	14.151	0.009	0.009	0.000	0.000	0.000	0.000
101	A	101	ILE	0	0.060	0.034	13.972	-0.011	-0.011	0.000	0.000	0.000	0.000
102	A	102	PHE	0	0.017	0.000	17.487	-0.017	-0.017	0.000	0.000	0.000	0.000
103	A	103	LYS	1	0.835	0.917	19.355	-0.052	-0.052	0.000	0.000	0.000	0.000
104	A	104	ILE	0	0.022	0.017	21.167	-0.004	-0.004	0.000	0.000	0.000	0.000
105	A	105	LYS	1	0.934	0.969	23.781	-0.011	-0.011	0.000	0.000	0.000	0.000
106	A	106	ALA	0	0.017	0.014	24.259	-0.001	-0.001	0.000	0.000	0.000	0.000
107	A	107	SER	0	-0.014	-0.021	26.130	-0.001	-0.001	0.000	0.000	0.000	0.000
108	A	108	ASP	-1	-0.888	-0.923	27.530	-0.018	-0.018	0.000	0.000	0.000	0.000
109	A	109	GLU	-1	-0.857	-0.942	26.345	-0.009	-0.009	0.000	0.000	0.000	0.000
110	A	110	SER	0	-0.074	-0.057	25.687	-0.004	-0.004	0.000	0.000	0.000	0.000
111	A	111	GLU	-1	-0.724	-0.829	23.419	-0.007	-0.007	0.000	0.000	0.000	0.000
112	A	112	LEU	0	-0.041	-0.024	21.141	0.000	0.000	0.000	0.000	0.000	0.000
113	A	113	GLU	-1	-1.001	-0.993	20.445	-0.053	-0.053	0.000	0.000	0.000	0.000
114	A	114	SER	0	-0.068	-0.023	20.208	-0.012	-0.012	0.000	0.000	0.000	0.000
115	A	115	LEU	0	-0.070	-0.028	16.345	-0.002	-0.002	0.000	0.000	0.000	0.000
116	A	116	LEU	0	-0.039	-0.010	11.739	-0.022	-0.022	0.000	0.000	0.000	0.000
117	A	117	ASP	-1	-0.913	-0.974	13.695	-0.171	-0.171	0.000	0.000	0.000	0.000
118	A	118	ALA	0	0.064	0.017	10.026	0.002	0.002	0.000	0.000	0.000	0.000
119	A	119	THR	0	0.014	0.022	9.574	-0.059	-0.059	0.000	0.000	0.000	0.000
120	A	120	ALA	0	-0.027	-0.016	10.881	-0.071	-0.071	0.000	0.000	0.000	0.000
121	A	121	TYR	0	-0.006	-0.027	4.525	-0.007	0.104	-0.001	-0.013	-0.097	0.000
122	A	122	GLU	-1	-0.897	-0.961	5.765	-1.307	-1.307	0.000	0.000	0.000	0.000
123	A	123	ALA	0	-0.021	-0.010	7.188	-0.194	-0.194	0.000	0.000	0.000	0.000
124	A	124	LEU	0	-0.026	-0.016	8.992	0.035	0.035	0.000	0.000	0.000	0.000
125	A	125	LEU	0	-0.011	-0.003	2.399	-0.926	-0.040	0.557	-0.451	-0.992	-0.001
126	A	126	GLU	-1	-1.049	-1.018	6.445	-0.815	-0.815	0.000	0.000	0.000	0.000
127	A	127	ASP	-1	-1.023	-1.004	8.413	-0.127	-0.127	0.000	0.000	0.000	0.000
128	A	128	GLU	-1	-0.981	-0.968	7.386	-0.749	-0.749	0.000	0.000	0.000	0.000

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