FMO DATABASE

FMODB ID: MV37Z

Calculation Name: 3W1Y-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3W1Y

Chain ID: A

ChEMBL ID:

UniProt ID: P0A7R5

Base Structure: X-ray

Registration Date: 2023-06-21

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	120
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1024610.226633
FMO2-HF: Nuclear repulsion	975090.187304
FMO2-HF: Total energy	-49520.039329
FMO2-MP2: Total energy	-49662.529743

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:4:HIS)

Summations of interaction energy for fragment #1(A:4:HIS)

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.
-74.67	-72.004	28.219	-11.605	-19.282	-0.047

Interaction energy analysis for fragmet #1(A:4:HIS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.897 / q_NPA : 0.970

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	6	ARG	1	0.842	0.879	2.536	14.602	17.477	0.758	-1.611	-2.022	-0.020
4	A	7	TYR	0	-0.005	-0.024	5.129	1.040	1.120	-0.001	-0.002	-0.077	0.000
5	A	8	GLN	0	-0.032	-0.029	2.295	-12.392	-10.451	6.350	-2.467	-5.825	-0.021
6	A	9	TYR	0	-0.085	-0.062	1.897	-30.332	-32.704	21.113	-7.498	-11.243	-0.006
7	A	10	THR	0	-0.067	-0.040	4.102	7.303	7.445	-0.001	-0.027	-0.115	0.000
8	A	11	ARG	1	0.833	0.900	6.801	29.153	29.153	0.000	0.000	0.000	0.000
9	A	12	SER	0	-0.035	-0.047	6.720	-5.030	-5.030	0.000	0.000	0.000	0.000
10	A	13	PHE	0	0.027	-0.008	6.941	-0.608	-0.608	0.000	0.000	0.000	0.000
11	A	14	ALA	0	0.024	0.018	8.936	1.377	1.377	0.000	0.000	0.000	0.000
12	A	15	GLU	-1	-0.814	-0.874	11.012	-23.097	-23.097	0.000	0.000	0.000	0.000
13	A	16	ARG	1	0.813	0.896	5.023	43.346	43.346	0.000	0.000	0.000	0.000
14	A	17	ALA	0	0.051	0.031	11.424	1.060	1.060	0.000	0.000	0.000	0.000
15	A	18	LYS	1	0.852	0.918	13.508	16.672	16.672	0.000	0.000	0.000	0.000
16	A	19	GLU	-1	-0.771	-0.829	13.508	-20.576	-20.576	0.000	0.000	0.000	0.000
17	A	20	THR	0	-0.037	-0.041	12.818	1.796	1.796	0.000	0.000	0.000	0.000
18	A	21	GLU	-1	-0.857	-0.901	16.201	-14.439	-14.439	0.000	0.000	0.000	0.000
19	A	22	SER	0	-0.031	-0.051	18.910	1.272	1.272	0.000	0.000	0.000	0.000
20	A	23	ALA	0	-0.036	-0.010	18.364	0.844	0.844	0.000	0.000	0.000	0.000
21	A	24	ARG	1	0.854	0.913	18.666	15.486	15.486	0.000	0.000	0.000	0.000
22	A	25	LEU	0	-0.014	0.006	21.286	0.650	0.650	0.000	0.000	0.000	0.000
23	A	26	ARG	1	0.915	0.964	24.123	12.285	12.285	0.000	0.000	0.000	0.000
24	A	27	TYR	0	-0.010	-0.012	22.819	0.575	0.575	0.000	0.000	0.000	0.000
25	A	28	PRO	0	0.036	0.023	22.923	-0.545	-0.545	0.000	0.000	0.000	0.000
26	A	29	LYS	1	0.844	0.914	24.161	11.368	11.368	0.000	0.000	0.000	0.000
27	A	30	HIS	0	0.009	0.012	21.306	0.107	0.107	0.000	0.000	0.000	0.000
28	A	31	ILE	0	0.004	0.010	15.557	-0.347	-0.347	0.000	0.000	0.000	0.000
29	A	32	PRO	0	-0.001	0.013	14.559	0.351	0.351	0.000	0.000	0.000	0.000
30	A	33	ILE	0	0.007	-0.007	12.727	-1.119	-1.119	0.000	0.000	0.000	0.000
31	A	34	LEU	0	-0.034	-0.012	8.123	0.787	0.787	0.000	0.000	0.000	0.000
32	A	35	CYS	0	-0.008	0.011	9.573	-1.354	-1.354	0.000	0.000	0.000	0.000
33	A	36	GLU	-1	-0.740	-0.868	6.618	-39.662	-39.662	0.000	0.000	0.000	0.000
34	A	37	PRO	0	0.032	0.017	9.989	-0.082	-0.082	0.000	0.000	0.000	0.000
35	A	38	THR	0	-0.020	-0.025	8.779	-2.340	-2.340	0.000	0.000	0.000	0.000
36	A	39	SER	0	-0.043	0.001	9.014	-0.471	-0.471	0.000	0.000	0.000	0.000
37	A	49	VAL	0	0.021	-0.003	12.768	0.316	0.316	0.000	0.000	0.000	0.000
38	A	50	ARG	1	0.996	0.994	16.167	11.843	11.843	0.000	0.000	0.000	0.000
39	A	51	LEU	0	0.010	0.022	15.686	0.546	0.546	0.000	0.000	0.000	0.000
40	A	52	PHE	0	0.040	0.021	16.474	-0.979	-0.979	0.000	0.000	0.000	0.000
41	A	53	SER	0	0.020	-0.002	18.430	0.659	0.659	0.000	0.000	0.000	0.000
42	A	54	THR	0	0.029	0.007	19.463	-0.737	-0.737	0.000	0.000	0.000	0.000
43	A	55	ARG	1	0.997	1.003	20.613	11.798	11.798	0.000	0.000	0.000	0.000
44	A	56	GLN	0	-0.034	-0.011	14.616	-1.412	-1.412	0.000	0.000	0.000	0.000
45	A	57	GLN	0	0.047	0.024	12.878	-2.258	-2.258	0.000	0.000	0.000	0.000
46	A	58	VAL	0	0.040	0.016	14.712	-0.823	-0.823	0.000	0.000	0.000	0.000
47	A	59	GLN	0	0.004	-0.008	17.007	0.319	0.319	0.000	0.000	0.000	0.000
48	A	60	ARG	1	0.984	0.987	10.859	21.908	21.908	0.000	0.000	0.000	0.000
49	A	61	GLU	-1	-0.817	-0.843	12.053	-24.962	-24.962	0.000	0.000	0.000	0.000
50	A	62	LEU	0	-0.009	-0.003	13.965	-0.171	-0.171	0.000	0.000	0.000	0.000
51	A	63	ASP	-1	-0.855	-0.921	13.229	-19.036	-19.036	0.000	0.000	0.000	0.000
52	A	64	CYS	0	-0.103	-0.030	9.275	-0.723	-0.723	0.000	0.000	0.000	0.000
53	A	65	ASN	0	-0.023	-0.021	12.373	2.065	2.065	0.000	0.000	0.000	0.000
54	A	66	LYS	1	0.847	0.898	12.588	21.224	21.224	0.000	0.000	0.000	0.000
55	A	67	PHE	0	-0.028	-0.021	15.145	1.498	1.498	0.000	0.000	0.000	0.000
56	A	68	LEU	0	0.011	0.007	16.681	-0.819	-0.819	0.000	0.000	0.000	0.000
57	A	69	LEU	0	0.011	0.018	19.125	0.829	0.829	0.000	0.000	0.000	0.000
58	A	70	PRO	0	0.028	0.013	20.933	-0.435	-0.435	0.000	0.000	0.000	0.000
59	A	71	GLU	-1	-0.811	-0.913	21.290	-13.000	-13.000	0.000	0.000	0.000	0.000
60	A	72	THR	0	0.007	-0.009	22.323	-0.213	-0.213	0.000	0.000	0.000	0.000
61	A	73	ALA	0	0.012	0.033	22.930	0.303	0.303	0.000	0.000	0.000	0.000
62	A	74	THR	0	-0.026	-0.053	22.630	-0.559	-0.559	0.000	0.000	0.000	0.000
63	A	75	VAL	0	-0.016	-0.010	18.324	-0.375	-0.375	0.000	0.000	0.000	0.000
64	A	76	MET	0	0.022	0.020	20.638	-0.292	-0.292	0.000	0.000	0.000	0.000
65	A	77	GLU	-1	-0.807	-0.872	23.496	-11.505	-11.505	0.000	0.000	0.000	0.000
66	A	78	PHE	0	-0.009	-0.010	14.488	-0.145	-0.145	0.000	0.000	0.000	0.000
67	A	79	MET	0	-0.003	-0.001	18.926	-0.395	-0.395	0.000	0.000	0.000	0.000
68	A	80	MET	0	-0.025	-0.002	20.693	0.125	0.125	0.000	0.000	0.000	0.000
69	A	81	ALA	0	0.031	0.013	21.282	0.078	0.078	0.000	0.000	0.000	0.000
70	A	82	LEU	0	-0.022	-0.014	16.099	-0.121	-0.121	0.000	0.000	0.000	0.000
71	A	83	ARG	1	0.832	0.881	19.945	11.316	11.316	0.000	0.000	0.000	0.000
72	A	84	GLN	0	-0.049	-0.027	22.625	0.249	0.249	0.000	0.000	0.000	0.000
73	A	85	ARG	1	0.836	0.922	18.864	15.532	15.532	0.000	0.000	0.000	0.000
74	A	86	LEU	0	-0.022	-0.018	17.554	-0.074	-0.074	0.000	0.000	0.000	0.000
75	A	87	LEU	0	-0.061	-0.022	21.734	0.264	0.264	0.000	0.000	0.000	0.000
76	A	88	LEU	0	0.002	0.022	20.909	0.247	0.247	0.000	0.000	0.000	0.000
77	A	89	GLU	-1	-0.876	-0.929	25.272	-9.774	-9.774	0.000	0.000	0.000	0.000
78	A	90	GLU	-1	-0.940	-0.974	27.999	-9.014	-9.014	0.000	0.000	0.000	0.000
79	A	91	GLY	0	-0.004	0.007	29.402	-0.007	-0.007	0.000	0.000	0.000	0.000
80	A	92	GLN	0	-0.033	-0.006	24.049	-0.184	-0.184	0.000	0.000	0.000	0.000
81	A	93	ALA	0	0.001	0.009	23.385	0.212	0.212	0.000	0.000	0.000	0.000
82	A	94	VAL	0	0.003	-0.009	17.869	-0.407	-0.407	0.000	0.000	0.000	0.000
83	A	95	PHE	0	-0.005	0.005	15.508	0.389	0.389	0.000	0.000	0.000	0.000
84	A	96	VAL	0	0.000	-0.012	13.893	-0.821	-0.821	0.000	0.000	0.000	0.000
85	A	97	PHE	0	0.030	0.001	10.553	0.795	0.795	0.000	0.000	0.000	0.000
86	A	98	ILE	0	-0.004	-0.004	9.864	-1.711	-1.711	0.000	0.000	0.000	0.000
87	A	99	GLY	0	0.005	0.001	7.792	1.005	1.005	0.000	0.000	0.000	0.000
88	A	100	ASN	0	-0.027	-0.019	8.790	0.094	0.094	0.000	0.000	0.000	0.000
89	A	101	GLU	-1	-0.919	-0.946	10.659	-16.501	-16.501	0.000	0.000	0.000	0.000
90	A	102	LEU	0	0.019	0.013	13.836	-0.658	-0.658	0.000	0.000	0.000	0.000
91	A	103	PRO	0	-0.058	-0.009	15.104	0.670	0.670	0.000	0.000	0.000	0.000
92	A	104	PRO	0	0.058	0.004	17.834	0.485	0.485	0.000	0.000	0.000	0.000
93	A	105	ASN	0	0.053	0.007	21.673	-0.416	-0.416	0.000	0.000	0.000	0.000
94	A	106	SER	0	-0.011	-0.003	23.144	-0.094	-0.094	0.000	0.000	0.000	0.000
95	A	107	ALA	0	-0.002	0.012	20.735	0.255	0.255	0.000	0.000	0.000	0.000
96	A	108	CYS	0	0.010	0.001	21.937	-0.064	-0.064	0.000	0.000	0.000	0.000
97	A	109	LEU	0	0.004	-0.007	17.308	-0.705	-0.705	0.000	0.000	0.000	0.000
98	A	110	GLY	0	0.005	-0.006	17.908	-0.907	-0.907	0.000	0.000	0.000	0.000
99	A	111	ASP	-1	-0.883	-0.940	19.068	-13.648	-13.648	0.000	0.000	0.000	0.000
100	A	112	ILE	0	-0.057	-0.026	14.045	-0.539	-0.539	0.000	0.000	0.000	0.000
101	A	113	TYR	0	-0.065	-0.055	13.738	-0.565	-0.565	0.000	0.000	0.000	0.000
102	A	114	ALA	0	-0.051	-0.033	15.174	-0.790	-0.790	0.000	0.000	0.000	0.000
103	A	115	ARG	1	0.921	0.960	14.981	17.783	17.783	0.000	0.000	0.000	0.000
104	A	116	ALA	0	-0.015	-0.003	11.164	-0.580	-0.580	0.000	0.000	0.000	0.000
105	A	117	LYS	1	0.912	0.983	9.993	17.324	17.324	0.000	0.000	0.000	0.000
106	A	118	ASP	-1	-0.826	-0.915	5.795	-46.324	-46.324	0.000	0.000	0.000	0.000
107	A	119	PRO	0	-0.008	-0.019	7.386	2.832	2.832	0.000	0.000	0.000	0.000
108	A	120	ASP	-1	-0.766	-0.846	8.297	-33.286	-33.286	0.000	0.000	0.000	0.000
109	A	121	GLY	0	0.042	0.042	10.305	2.240	2.240	0.000	0.000	0.000	0.000
110	A	122	PHE	0	0.007	0.005	9.517	2.372	2.372	0.000	0.000	0.000	0.000
111	A	123	LEU	0	-0.005	-0.003	10.113	-1.203	-1.203	0.000	0.000	0.000	0.000
112	A	124	TYR	0	-0.060	-0.063	6.090	-1.098	-1.098	0.000	0.000	0.000	0.000
113	A	125	VAL	0	-0.026	-0.013	8.063	1.301	1.301	0.000	0.000	0.000	0.000
114	A	126	SER	0	0.005	0.017	7.558	-2.616	-2.616	0.000	0.000	0.000	0.000
115	A	127	TYR	0	-0.049	-0.041	9.290	2.163	2.163	0.000	0.000	0.000	0.000
116	A	128	GLY	0	0.012	0.012	12.715	-0.826	-0.826	0.000	0.000	0.000	0.000
117	A	129	VAL	0	0.010	-0.005	15.220	0.418	0.418	0.000	0.000	0.000	0.000
118	A	130	GLU	-1	-0.860	-0.908	18.816	-13.083	-13.083	0.000	0.000	0.000	0.000
119	A	131	ASN	0	-0.041	-0.029	21.602	0.383	0.383	0.000	0.000	0.000	0.000
120	A	132	THR	0	-0.048	-0.023	25.181	0.665	0.665	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:4:HIS)