FMO DATABASE

FMODB ID: MNY9Z

Calculation Name: 3IV4-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3IV4

Chain ID: A

ChEMBL ID:

UniProt ID: A0A0H3

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	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	112
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-987269.340472
FMO2-HF: Nuclear repulsion	941262.818512
FMO2-HF: Total energy	-46006.52196
FMO2-MP2: Total energy	-46141.461996

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:-5:ASN)

Summations of interaction energy for fragment #1(A:-5:ASN)

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.
-4.21	-0.158	1.183	-1.89	-3.345	0.01

Interaction energy analysis for fragmet #1(A:-5:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.021 / q_NPA : -0.032

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	-3	TYR	0	0.000	-0.012	3.894	-1.245	0.078	-0.008	-0.655	-0.661	0.002
4	A	-2	PHE	0	-0.002	-0.005	2.421	-1.340	0.444	1.181	-0.886	-2.078	0.010
5	A	-1	GLN	0	0.047	0.014	7.734	-0.285	-0.285	0.000	0.000	0.000	0.000
6	A	0	GLY	0	-0.018	0.005	10.248	-0.158	-0.158	0.000	0.000	0.000	0.000
7	A	1	VAL	0	0.009	0.022	10.090	-0.118	-0.118	0.000	0.000	0.000	0.000
8	A	2	ALA	0	-0.001	0.009	10.247	-0.003	-0.003	0.000	0.000	0.000	0.000
9	A	3	ILE	0	0.034	0.012	12.163	-0.200	-0.200	0.000	0.000	0.000	0.000
10	A	4	LYS	1	0.772	0.872	14.995	0.435	0.435	0.000	0.000	0.000	0.000
11	A	5	LEU	0	0.023	0.010	16.612	0.013	0.013	0.000	0.000	0.000	0.000
12	A	6	SER	0	-0.056	-0.047	20.021	-0.044	-0.044	0.000	0.000	0.000	0.000
13	A	7	SER	0	-0.055	-0.059	22.507	0.001	0.001	0.000	0.000	0.000	0.000
14	A	8	ILE	0	0.039	0.015	25.602	0.009	0.009	0.000	0.000	0.000	0.000
15	A	9	ASP	-1	-0.830	-0.883	28.054	-0.098	-0.098	0.000	0.000	0.000	0.000
16	A	10	GLN	0	-0.001	0.003	22.946	0.006	0.006	0.000	0.000	0.000	0.000
17	A	11	PHE	0	0.006	0.003	23.134	0.015	0.015	0.000	0.000	0.000	0.000
18	A	12	GLU	-1	-0.739	-0.848	24.969	0.008	0.008	0.000	0.000	0.000	0.000
19	A	13	GLN	0	-0.073	-0.039	27.332	0.010	0.010	0.000	0.000	0.000	0.000
20	A	14	VAL	0	0.014	0.012	21.524	0.016	0.016	0.000	0.000	0.000	0.000
21	A	15	ILE	0	-0.059	-0.034	23.868	0.027	0.027	0.000	0.000	0.000	0.000
22	A	16	GLU	-1	-0.965	-0.961	26.042	0.056	0.056	0.000	0.000	0.000	0.000
23	A	17	GLU	-1	-0.931	-0.957	26.604	0.018	0.018	0.000	0.000	0.000	0.000
24	A	18	ASN	0	-0.084	-0.034	23.375	0.035	0.035	0.000	0.000	0.000	0.000
25	A	19	LYS	1	0.865	0.935	25.541	-0.160	-0.160	0.000	0.000	0.000	0.000
26	A	20	TYR	0	0.022	-0.002	22.501	-0.008	-0.008	0.000	0.000	0.000	0.000
27	A	21	VAL	0	0.050	0.035	20.214	0.008	0.008	0.000	0.000	0.000	0.000
28	A	22	PHE	0	0.032	0.030	16.314	-0.021	-0.021	0.000	0.000	0.000	0.000
29	A	23	VAL	0	-0.011	-0.009	17.587	-0.031	-0.031	0.000	0.000	0.000	0.000
30	A	24	LEU	0	-0.018	-0.009	12.069	0.011	0.011	0.000	0.000	0.000	0.000
31	A	25	LYS	1	0.838	0.923	16.250	0.033	0.033	0.000	0.000	0.000	0.000
32	A	26	HIS	0	0.103	0.056	10.850	0.123	0.123	0.000	0.000	0.000	0.000
33	A	27	SER	0	-0.024	-0.030	15.052	0.012	0.012	0.000	0.000	0.000	0.000
34	A	28	GLU	-1	-0.847	-0.928	13.574	-0.701	-0.701	0.000	0.000	0.000	0.000
35	A	29	THR	0	-0.008	0.000	13.684	-0.103	-0.103	0.000	0.000	0.000	0.000
36	A	30	CYS	0	-0.050	-0.007	14.449	0.066	0.066	0.000	0.000	0.000	0.000
37	A	31	PRO	0	0.052	0.020	11.642	-0.038	-0.038	0.000	0.000	0.000	0.000
38	A	32	ILE	0	0.037	0.012	11.473	0.001	0.001	0.000	0.000	0.000	0.000
39	A	33	SER	0	0.044	0.002	12.504	0.115	0.115	0.000	0.000	0.000	0.000
40	A	34	ALA	0	-0.006	0.002	8.051	0.009	0.009	0.000	0.000	0.000	0.000
41	A	35	ASN	0	-0.022	-0.012	7.581	-0.203	-0.203	0.000	0.000	0.000	0.000
42	A	36	ALA	0	0.057	0.027	8.544	0.167	0.167	0.000	0.000	0.000	0.000
43	A	37	TYR	0	-0.006	-0.002	6.927	0.136	0.136	0.000	0.000	0.000	0.000
44	A	38	ASP	-1	-0.826	-0.888	3.370	-0.204	0.442	0.010	-0.309	-0.347	-0.002
45	A	39	GLN	0	-0.036	-0.015	5.520	0.720	0.720	0.000	0.000	0.000	0.000
46	A	40	PHE	0	0.013	0.006	8.469	0.208	0.208	0.000	0.000	0.000	0.000
47	A	41	ASN	0	-0.017	-0.022	5.931	0.139	0.139	0.000	0.000	0.000	0.000
48	A	42	LYS	1	0.821	0.893	3.661	-4.232	-3.933	0.000	-0.040	-0.259	0.000
49	A	43	PHE	0	-0.018	-0.003	7.691	0.040	0.040	0.000	0.000	0.000	0.000
50	A	44	LEU	0	0.021	0.018	11.056	-0.020	-0.020	0.000	0.000	0.000	0.000
51	A	45	TYR	0	-0.008	-0.001	9.023	0.128	0.128	0.000	0.000	0.000	0.000
52	A	46	GLU	-1	-0.991	-0.992	10.974	1.980	1.980	0.000	0.000	0.000	0.000
53	A	47	ARG	1	0.731	0.827	12.791	-0.967	-0.967	0.000	0.000	0.000	0.000
54	A	48	ASP	-1	-0.982	-0.971	14.475	0.597	0.597	0.000	0.000	0.000	0.000
55	A	49	MET	0	-0.036	-0.007	15.032	-0.131	-0.131	0.000	0.000	0.000	0.000
56	A	50	ASP	-1	-0.888	-0.945	14.921	0.262	0.262	0.000	0.000	0.000	0.000
57	A	51	GLY	0	-0.023	-0.020	14.971	0.009	0.009	0.000	0.000	0.000	0.000
58	A	52	TYR	0	0.020	0.007	15.247	-0.076	-0.076	0.000	0.000	0.000	0.000
59	A	53	TYR	0	-0.042	-0.028	12.103	-0.017	-0.017	0.000	0.000	0.000	0.000
60	A	54	LEU	0	0.018	0.025	15.923	-0.013	-0.013	0.000	0.000	0.000	0.000
61	A	55	ILE	0	0.032	0.020	14.738	-0.011	-0.011	0.000	0.000	0.000	0.000
62	A	56	VAL	0	-0.016	-0.011	17.731	0.034	0.034	0.000	0.000	0.000	0.000
63	A	57	GLN	0	-0.025	-0.033	18.540	0.011	0.011	0.000	0.000	0.000	0.000
64	A	58	GLN	0	-0.041	-0.032	19.152	0.052	0.052	0.000	0.000	0.000	0.000
65	A	59	GLU	-1	-0.801	-0.886	20.246	-0.320	-0.320	0.000	0.000	0.000	0.000
66	A	60	ARG	1	0.873	0.937	23.072	0.264	0.264	0.000	0.000	0.000	0.000
67	A	61	ASP	-1	-0.835	-0.922	25.638	-0.154	-0.154	0.000	0.000	0.000	0.000
68	A	62	LEU	0	-0.006	0.006	22.377	0.019	0.019	0.000	0.000	0.000	0.000
69	A	63	SER	0	0.000	-0.012	23.070	0.014	0.014	0.000	0.000	0.000	0.000
70	A	64	ASP	-1	-0.839	-0.900	24.275	-0.076	-0.076	0.000	0.000	0.000	0.000
71	A	65	TYR	0	-0.031	-0.040	27.838	0.014	0.014	0.000	0.000	0.000	0.000
72	A	66	ILE	0	0.029	0.016	22.087	0.016	0.016	0.000	0.000	0.000	0.000
73	A	67	ALA	0	-0.029	-0.005	26.228	0.017	0.017	0.000	0.000	0.000	0.000
74	A	68	LYS	1	0.732	0.844	27.874	0.090	0.090	0.000	0.000	0.000	0.000
75	A	69	LYS	1	0.807	0.899	27.942	0.006	0.006	0.000	0.000	0.000	0.000
76	A	70	THR	0	0.048	0.007	25.892	0.013	0.013	0.000	0.000	0.000	0.000
77	A	71	ASN	0	-0.023	0.000	29.242	0.001	0.001	0.000	0.000	0.000	0.000
78	A	72	VAL	0	0.011	0.021	24.992	-0.002	-0.002	0.000	0.000	0.000	0.000
79	A	73	LYS	1	0.852	0.915	27.482	0.008	0.008	0.000	0.000	0.000	0.000
80	A	74	HIS	0	0.048	0.030	21.949	0.022	0.022	0.000	0.000	0.000	0.000
81	A	75	GLU	-1	-0.813	-0.905	21.661	-0.103	-0.103	0.000	0.000	0.000	0.000
82	A	76	SER	0	-0.098	-0.015	17.799	-0.038	-0.038	0.000	0.000	0.000	0.000
83	A	77	PRO	0	-0.042	-0.004	14.363	-0.014	-0.014	0.000	0.000	0.000	0.000
84	A	78	GLN	0	0.060	0.004	16.594	0.023	0.023	0.000	0.000	0.000	0.000
85	A	79	ALA	0	-0.001	0.005	15.914	-0.030	-0.030	0.000	0.000	0.000	0.000
86	A	80	PHE	0	0.000	-0.019	17.986	0.006	0.006	0.000	0.000	0.000	0.000
87	A	81	TYR	0	0.032	0.018	19.363	0.015	0.015	0.000	0.000	0.000	0.000
88	A	82	PHE	0	-0.007	-0.017	21.601	-0.020	-0.020	0.000	0.000	0.000	0.000
89	A	83	VAL	0	0.028	0.003	24.201	0.023	0.023	0.000	0.000	0.000	0.000
90	A	84	ASN	0	-0.023	-0.017	26.958	0.001	0.001	0.000	0.000	0.000	0.000
91	A	85	GLY	0	0.105	0.065	27.959	-0.009	-0.009	0.000	0.000	0.000	0.000
92	A	86	GLU	-1	-0.982	-0.984	29.121	0.064	0.064	0.000	0.000	0.000	0.000
93	A	87	MET	0	-0.063	-0.001	24.694	0.009	0.009	0.000	0.000	0.000	0.000
94	A	88	VAL	0	0.027	0.015	25.018	-0.005	-0.005	0.000	0.000	0.000	0.000
95	A	89	TRP	0	-0.008	-0.001	17.275	-0.007	-0.007	0.000	0.000	0.000	0.000
96	A	90	ASN	0	-0.024	-0.045	21.472	-0.020	-0.020	0.000	0.000	0.000	0.000
97	A	91	ARG	1	0.882	0.950	18.691	-0.176	-0.176	0.000	0.000	0.000	0.000
98	A	92	ASP	-1	-0.819	-0.905	18.897	0.000	0.000	0.000	0.000	0.000	0.000
99	A	93	HIS	1	0.771	0.853	17.132	0.084	0.084	0.000	0.000	0.000	0.000
100	A	94	GLY	0	0.030	0.009	15.057	-0.001	-0.001	0.000	0.000	0.000	0.000
101	A	95	ASP	-1	-0.862	-0.919	15.779	0.301	0.301	0.000	0.000	0.000	0.000
102	A	96	ILE	0	-0.049	0.021	13.024	0.024	0.024	0.000	0.000	0.000	0.000
103	A	97	ASN	0	0.015	0.005	12.213	0.041	0.041	0.000	0.000	0.000	0.000
104	A	98	VAL	0	0.039	0.013	9.910	-0.041	-0.041	0.000	0.000	0.000	0.000
105	A	99	SER	0	-0.017	-0.012	12.772	-0.007	-0.007	0.000	0.000	0.000	0.000
106	A	100	SER	0	-0.034	-0.049	16.417	-0.024	-0.024	0.000	0.000	0.000	0.000
107	A	101	LEU	0	-0.031	-0.015	12.619	-0.066	-0.066	0.000	0.000	0.000	0.000
108	A	102	ALA	0	0.043	0.016	16.586	-0.034	-0.034	0.000	0.000	0.000	0.000
109	A	103	GLN	0	-0.033	-0.017	18.212	-0.053	-0.053	0.000	0.000	0.000	0.000
110	A	104	ALA	0	-0.065	-0.020	20.173	-0.043	-0.043	0.000	0.000	0.000	0.000
111	A	105	GLU	-1	-0.829	-0.907	19.186	0.537	0.537	0.000	0.000	0.000	0.000
112	A	106	GLU	-1	-1.009	-0.989	22.686	0.338	0.338	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:-5:ASN)