FMO DATABASE

FMODB ID: 668NZ

Calculation Name: 1IM3-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1IM3

Chain ID: D

ChEMBL ID:

UniProt ID: P61769

Base Structure: X-ray

Registration Date: 2023-06-19

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	94
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-703106.537195
FMO2-HF: Nuclear repulsion	664828.83727
FMO2-HF: Total energy	-38277.699924
FMO2-MP2: Total energy	-38388.912487

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(D:43:PRO)

Summations of interaction energy for fragment #1(D:43:PRO)

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.
-9.737	-4.055	1.073	-2.971	-3.782	-0.011

Interaction energy analysis for fragmet #1(D:43:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.073 / q_NPA : -0.031

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	D	45	PHE	0	0.045	-0.012	3.806	-1.355	0.687	-0.028	-0.989	-1.024	0.004
4	D	46	GLN	0	-0.048	-0.011	6.855	0.027	0.027	0.000	0.000	0.000	0.000
5	D	47	ILE	0	-0.004	-0.011	10.565	0.045	0.045	0.000	0.000	0.000	0.000
6	D	48	GLU	-1	-0.902	-0.903	13.615	0.047	0.047	0.000	0.000	0.000	0.000
7	D	49	ASP	-1	-0.788	-0.879	16.218	-0.071	-0.071	0.000	0.000	0.000	0.000
8	D	50	ASN	0	-0.064	-0.064	18.013	-0.035	-0.035	0.000	0.000	0.000	0.000
9	D	51	ARG	1	0.839	0.925	20.319	0.073	0.073	0.000	0.000	0.000	0.000
10	D	52	CYS	0	-0.027	-0.020	20.843	0.004	0.004	0.000	0.000	0.000	0.000
11	D	53	TYR	0	0.020	0.014	26.487	0.004	0.004	0.000	0.000	0.000	0.000
12	D	54	ILE	0	0.008	0.001	30.252	-0.002	-0.002	0.000	0.000	0.000	0.000
13	D	55	ASP	-1	-0.890	-0.938	32.850	-0.045	-0.045	0.000	0.000	0.000	0.000
14	D	56	ASN	0	-0.104	-0.069	35.949	0.001	0.001	0.000	0.000	0.000	0.000
15	D	57	GLY	0	0.014	0.012	36.506	0.001	0.001	0.000	0.000	0.000	0.000
16	D	58	LYS	1	0.887	0.971	33.468	0.054	0.054	0.000	0.000	0.000	0.000
17	D	59	LEU	0	-0.009	-0.008	26.186	0.000	0.000	0.000	0.000	0.000	0.000
18	D	60	PHE	0	-0.016	-0.008	28.434	0.004	0.004	0.000	0.000	0.000	0.000
19	D	61	ALA	0	0.010	-0.007	23.538	-0.004	-0.004	0.000	0.000	0.000	0.000
20	D	62	ARG	1	0.854	0.927	22.164	0.056	0.056	0.000	0.000	0.000	0.000
21	D	63	GLY	0	0.046	0.011	18.899	-0.008	-0.008	0.000	0.000	0.000	0.000
22	D	64	SER	0	-0.096	-0.069	15.893	0.020	0.020	0.000	0.000	0.000	0.000
23	D	65	ILE	0	0.037	0.019	9.797	-0.038	-0.038	0.000	0.000	0.000	0.000
24	D	66	VAL	0	0.020	0.028	10.675	0.034	0.034	0.000	0.000	0.000	0.000
25	D	67	GLY	0	0.045	-0.020	6.561	-0.190	-0.190	0.000	0.000	0.000	0.000
26	D	68	ASN	0	-0.019	0.009	2.686	-3.413	-1.369	1.003	-1.406	-1.641	-0.011
27	D	69	MET	0	-0.003	0.016	5.087	0.025	0.025	0.000	0.000	0.000	0.000
28	D	70	SER	0	0.032	0.014	5.863	0.080	0.080	0.000	0.000	0.000	0.000
29	D	71	ARG	1	0.884	0.938	6.573	0.657	0.657	0.000	0.000	0.000	0.000
30	D	72	PHE	0	-0.006	-0.012	8.571	-0.122	-0.122	0.000	0.000	0.000	0.000
31	D	73	VAL	0	0.008	0.014	10.960	0.058	0.058	0.000	0.000	0.000	0.000
32	D	74	PHE	0	0.035	0.013	13.592	-0.048	-0.048	0.000	0.000	0.000	0.000
33	D	75	ASP	-1	-0.794	-0.886	16.151	-0.265	-0.265	0.000	0.000	0.000	0.000
34	D	76	PRO	0	0.014	0.017	18.229	-0.016	-0.016	0.000	0.000	0.000	0.000
35	D	77	LYS	1	0.816	0.884	19.537	0.267	0.267	0.000	0.000	0.000	0.000
36	D	78	ALA	0	0.037	0.023	23.550	-0.001	-0.001	0.000	0.000	0.000	0.000
37	D	79	ASP	-1	-0.832	-0.926	25.683	-0.168	-0.168	0.000	0.000	0.000	0.000
38	D	80	TYR	0	-0.075	-0.084	27.605	0.008	0.008	0.000	0.000	0.000	0.000
39	D	81	GLY	0	0.081	0.068	29.816	0.008	0.008	0.000	0.000	0.000	0.000
40	D	82	GLY	0	-0.098	-0.046	29.174	0.006	0.006	0.000	0.000	0.000	0.000
41	D	83	VAL	0	-0.040	-0.027	28.995	-0.009	-0.009	0.000	0.000	0.000	0.000
42	D	84	GLY	0	0.052	0.014	27.894	0.004	0.004	0.000	0.000	0.000	0.000
43	D	85	GLU	-1	-0.917	-0.918	27.649	-0.113	-0.113	0.000	0.000	0.000	0.000
44	D	86	ASN	0	-0.036	-0.012	23.806	-0.019	-0.019	0.000	0.000	0.000	0.000
45	D	87	LEU	0	0.015	0.025	24.280	0.014	0.014	0.000	0.000	0.000	0.000
46	D	88	TYR	0	-0.004	-0.022	24.041	-0.016	-0.016	0.000	0.000	0.000	0.000
47	D	89	VAL	0	0.010	0.008	21.870	0.008	0.008	0.000	0.000	0.000	0.000
48	D	90	HIS	0	0.032	0.025	24.289	-0.009	-0.009	0.000	0.000	0.000	0.000
49	D	91	ALA	0	0.030	0.004	22.622	-0.006	-0.006	0.000	0.000	0.000	0.000
50	D	92	ASP	-1	-0.861	-0.937	22.662	-0.045	-0.045	0.000	0.000	0.000	0.000
51	D	93	ASP	-1	-0.873	-0.907	23.781	-0.070	-0.070	0.000	0.000	0.000	0.000
52	D	94	VAL	0	-0.044	-0.033	17.580	-0.018	-0.018	0.000	0.000	0.000	0.000
53	D	95	GLU	-1	-0.935	-0.954	18.365	-0.008	-0.008	0.000	0.000	0.000	0.000
54	D	96	PHE	0	-0.025	-0.025	9.932	-0.015	-0.015	0.000	0.000	0.000	0.000
55	D	97	VAL	0	0.012	0.018	13.435	0.012	0.012	0.000	0.000	0.000	0.000
56	D	98	PRO	0	-0.010	-0.016	10.920	0.020	0.020	0.000	0.000	0.000	0.000
57	D	99	GLY	0	-0.043	-0.027	7.815	0.054	0.054	0.000	0.000	0.000	0.000
58	D	100	GLU	-1	-0.942	-0.963	8.760	0.406	0.406	0.000	0.000	0.000	0.000
59	D	101	SER	0	-0.010	-0.025	10.350	-0.035	-0.035	0.000	0.000	0.000	0.000
60	D	102	LEU	0	-0.026	0.011	11.694	-0.008	-0.008	0.000	0.000	0.000	0.000
61	D	103	LYS	1	0.922	0.954	13.360	-0.022	-0.022	0.000	0.000	0.000	0.000
62	D	104	TRP	0	0.023	0.032	15.056	-0.007	-0.007	0.000	0.000	0.000	0.000
63	D	105	ASN	0	0.015	-0.009	19.834	0.008	0.008	0.000	0.000	0.000	0.000
64	D	106	VAL	0	0.008	0.011	22.813	0.007	0.007	0.000	0.000	0.000	0.000
65	D	107	ARG	1	0.828	0.890	25.359	0.059	0.059	0.000	0.000	0.000	0.000
66	D	108	ASN	0	-0.031	-0.012	29.085	0.003	0.003	0.000	0.000	0.000	0.000
67	D	109	LEU	0	0.050	0.031	26.596	0.001	0.001	0.000	0.000	0.000	0.000
68	D	110	ASP	-1	-0.858	-0.932	30.507	-0.070	-0.070	0.000	0.000	0.000	0.000
69	D	111	VAL	0	-0.051	-0.005	29.486	-0.008	-0.008	0.000	0.000	0.000	0.000
70	D	112	MET	0	0.014	0.000	32.615	0.006	0.006	0.000	0.000	0.000	0.000
71	D	113	PRO	0	0.015	-0.015	34.532	-0.003	-0.003	0.000	0.000	0.000	0.000
72	D	114	ILE	0	-0.035	-0.012	34.737	0.001	0.001	0.000	0.000	0.000	0.000
73	D	115	PHE	0	-0.031	-0.007	26.721	-0.008	-0.008	0.000	0.000	0.000	0.000
74	D	116	GLU	-1	-0.899	-0.940	30.158	-0.112	-0.112	0.000	0.000	0.000	0.000
75	D	117	THR	0	-0.110	-0.067	25.791	-0.004	-0.004	0.000	0.000	0.000	0.000
76	D	118	LEU	0	0.020	0.015	22.028	-0.001	-0.001	0.000	0.000	0.000	0.000
77	D	119	ALA	0	-0.012	-0.006	21.248	-0.014	-0.014	0.000	0.000	0.000	0.000
78	D	120	LEU	0	0.013	0.000	16.665	0.005	0.005	0.000	0.000	0.000	0.000
79	D	121	ARG	1	0.866	0.945	14.757	0.384	0.384	0.000	0.000	0.000	0.000
80	D	122	LEU	0	0.011	0.006	12.016	0.037	0.037	0.000	0.000	0.000	0.000
81	D	123	VAL	0	-0.026	-0.025	9.648	-0.081	-0.081	0.000	0.000	0.000	0.000
82	D	124	LEU	0	0.021	0.008	6.557	0.190	0.190	0.000	0.000	0.000	0.000
83	D	125	GLN	0	0.016	0.008	3.184	-0.819	-0.382	0.023	-0.092	-0.367	0.000
84	D	126	GLY	0	-0.060	-0.034	4.940	-0.258	-0.174	-0.001	-0.002	-0.081	0.000
85	D	127	ASP	-1	-0.876	-0.912	3.192	-5.243	-4.168	0.076	-0.482	-0.669	-0.004
86	D	128	VAL	0	-0.059	-0.040	6.739	0.232	0.232	0.000	0.000	0.000	0.000
87	D	129	ILE	0	-0.006	0.005	8.705	-0.052	-0.052	0.000	0.000	0.000	0.000
88	D	130	TRP	0	0.010	-0.005	11.531	0.071	0.071	0.000	0.000	0.000	0.000
89	D	131	LEU	0	-0.007	0.004	13.401	-0.007	-0.007	0.000	0.000	0.000	0.000
90	D	132	ARG	1	0.901	0.938	17.078	0.189	0.189	0.000	0.000	0.000	0.000
91	D	134	VAL	0	0.000	0.004	23.323	0.001	0.001	0.000	0.000	0.000	0.000
92	D	135	PRO	0	0.003	-0.002	27.033	0.005	0.005	0.000	0.000	0.000	0.000
93	D	136	GLU	-1	-0.948	-0.984	28.053	-0.076	-0.076	0.000	0.000	0.000	0.000
94	D	137	LEU	0	-0.019	0.006	31.399	0.004	0.004	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:43:PRO)