FMO DATABASE

FMODB ID: ZY16N

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

Total energy (hartree)

FMO2-HF: Electronic energy	-701897.411401
FMO2-HF: Nuclear repulsion	663619.410841
FMO2-HF: Total energy	-38278.00056
FMO2-MP2: Total energy	-38389.21065

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.
-17.445	-14.69	8.937	-5.343	-6.347	0.01

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 : -0.041 / q_NPA : -0.013

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	0.050	-0.002	3.851	-0.182	1.462	-0.021	-0.766	-0.858	0.002
4	D	46	GLN	0	-0.038	-0.008	6.730	-0.102	-0.102	0.000	0.000	0.000	0.000
5	D	47	ILE	0	-0.002	-0.006	10.525	0.085	0.085	0.000	0.000	0.000	0.000
6	D	48	GLU	-1	-0.871	-0.910	13.579	0.130	0.130	0.000	0.000	0.000	0.000
7	D	49	ASP	-1	-0.800	-0.877	16.312	-0.056	-0.056	0.000	0.000	0.000	0.000
8	D	50	ASN	0	-0.058	-0.054	17.834	-0.024	-0.024	0.000	0.000	0.000	0.000
9	D	51	ARG	1	0.836	0.909	20.000	0.049	0.049	0.000	0.000	0.000	0.000
10	D	52	CYS	0	-0.014	-0.003	21.200	0.007	0.007	0.000	0.000	0.000	0.000
11	D	53	TYR	0	0.018	0.025	26.521	0.002	0.002	0.000	0.000	0.000	0.000
12	D	54	ILE	0	0.013	0.003	30.274	-0.002	-0.002	0.000	0.000	0.000	0.000
13	D	55	ASP	-1	-0.868	-0.924	32.967	-0.031	-0.031	0.000	0.000	0.000	0.000
14	D	56	ASN	0	-0.100	-0.070	35.994	-0.001	-0.001	0.000	0.000	0.000	0.000
15	D	57	GLY	0	0.017	0.023	37.083	0.002	0.002	0.000	0.000	0.000	0.000
16	D	58	LYS	1	0.839	0.932	33.259	0.033	0.033	0.000	0.000	0.000	0.000
17	D	59	LEU	0	-0.002	0.001	26.143	0.000	0.000	0.000	0.000	0.000	0.000
18	D	60	PHE	0	-0.030	-0.015	28.163	0.009	0.009	0.000	0.000	0.000	0.000
19	D	61	ALA	0	0.014	-0.007	23.492	-0.008	-0.008	0.000	0.000	0.000	0.000
20	D	62	ARG	1	0.841	0.921	22.144	0.018	0.018	0.000	0.000	0.000	0.000
21	D	63	GLY	0	0.031	0.006	18.866	-0.014	-0.014	0.000	0.000	0.000	0.000
22	D	64	SER	0	-0.090	-0.068	15.926	0.034	0.034	0.000	0.000	0.000	0.000
23	D	65	ILE	0	0.033	0.018	9.659	-0.055	-0.055	0.000	0.000	0.000	0.000
24	D	66	VAL	0	0.019	0.015	10.565	0.077	0.077	0.000	0.000	0.000	0.000
25	D	67	GLY	0	0.051	-0.007	6.442	-0.308	-0.308	0.000	0.000	0.000	0.000
26	D	68	ASN	0	-0.053	-0.004	2.074	-12.228	-12.964	8.818	-3.890	-4.191	0.013
27	D	69	MET	0	-0.019	0.004	5.093	-0.023	0.108	-0.001	-0.005	-0.125	0.000
28	D	70	SER	0	0.049	0.025	5.926	-0.039	-0.039	0.000	0.000	0.000	0.000
29	D	71	ARG	1	0.847	0.911	6.811	0.494	0.494	0.000	0.000	0.000	0.000
30	D	72	PHE	0	0.013	0.001	8.470	-0.116	-0.116	0.000	0.000	0.000	0.000
31	D	73	VAL	0	-0.015	0.001	10.924	0.042	0.042	0.000	0.000	0.000	0.000
32	D	74	PHE	0	0.043	0.010	13.598	-0.054	-0.054	0.000	0.000	0.000	0.000
33	D	75	ASP	-1	-0.812	-0.890	16.282	-0.246	-0.246	0.000	0.000	0.000	0.000
34	D	76	PRO	0	0.025	0.020	18.548	-0.023	-0.023	0.000	0.000	0.000	0.000
35	D	77	LYS	1	0.831	0.903	19.955	0.248	0.248	0.000	0.000	0.000	0.000
36	D	78	ALA	0	0.031	0.028	23.992	-0.001	-0.001	0.000	0.000	0.000	0.000
37	D	79	ASP	-1	-0.803	-0.889	26.200	-0.172	-0.172	0.000	0.000	0.000	0.000
38	D	80	TYR	0	-0.055	-0.070	28.036	0.009	0.009	0.000	0.000	0.000	0.000
39	D	81	GLY	0	0.065	0.055	30.433	0.008	0.008	0.000	0.000	0.000	0.000
40	D	82	GLY	0	-0.083	-0.044	28.613	0.001	0.001	0.000	0.000	0.000	0.000
41	D	83	VAL	0	-0.047	-0.025	29.402	-0.006	-0.006	0.000	0.000	0.000	0.000
42	D	84	GLY	0	0.038	0.013	28.019	0.003	0.003	0.000	0.000	0.000	0.000
43	D	85	GLU	-1	-0.906	-0.914	28.058	-0.106	-0.106	0.000	0.000	0.000	0.000
44	D	86	ASN	0	-0.040	-0.015	24.027	-0.021	-0.021	0.000	0.000	0.000	0.000
45	D	87	LEU	0	0.018	0.017	24.752	0.014	0.014	0.000	0.000	0.000	0.000
46	D	88	TYR	0	-0.009	-0.021	24.556	-0.013	-0.013	0.000	0.000	0.000	0.000
47	D	89	VAL	0	0.011	0.007	21.824	0.004	0.004	0.000	0.000	0.000	0.000
48	D	90	HIS	0	0.014	0.008	24.887	-0.006	-0.006	0.000	0.000	0.000	0.000
49	D	91	ALA	0	0.017	0.000	22.672	-0.004	-0.004	0.000	0.000	0.000	0.000
50	D	92	ASP	-1	-0.851	-0.926	22.376	0.020	0.020	0.000	0.000	0.000	0.000
51	D	93	ASP	-1	-0.836	-0.894	23.505	-0.025	-0.025	0.000	0.000	0.000	0.000
52	D	94	VAL	0	-0.060	-0.037	17.179	-0.016	-0.016	0.000	0.000	0.000	0.000
53	D	95	GLU	-1	-0.934	-0.948	18.082	0.088	0.088	0.000	0.000	0.000	0.000
54	D	96	PHE	0	-0.035	-0.042	9.794	-0.015	-0.015	0.000	0.000	0.000	0.000
55	D	97	VAL	0	0.021	0.021	13.119	-0.004	-0.004	0.000	0.000	0.000	0.000
56	D	98	PRO	0	-0.019	-0.012	10.585	0.081	0.081	0.000	0.000	0.000	0.000
57	D	99	GLY	0	-0.034	-0.015	7.927	0.058	0.058	0.000	0.000	0.000	0.000
58	D	100	GLU	-1	-0.941	-0.964	8.886	0.825	0.825	0.000	0.000	0.000	0.000
59	D	101	SER	0	-0.020	-0.030	10.356	-0.094	-0.094	0.000	0.000	0.000	0.000
60	D	102	LEU	0	-0.033	0.001	11.215	-0.010	-0.010	0.000	0.000	0.000	0.000
61	D	103	LYS	1	0.901	0.962	12.808	-0.182	-0.182	0.000	0.000	0.000	0.000
62	D	104	TRP	0	0.020	0.020	14.564	-0.008	-0.008	0.000	0.000	0.000	0.000
63	D	105	ASN	0	0.033	0.002	19.452	-0.004	-0.004	0.000	0.000	0.000	0.000
64	D	106	VAL	0	0.023	0.020	22.444	0.007	0.007	0.000	0.000	0.000	0.000
65	D	107	ARG	1	0.810	0.874	24.962	0.004	0.004	0.000	0.000	0.000	0.000
66	D	108	ASN	0	-0.001	-0.006	28.715	-0.001	-0.001	0.000	0.000	0.000	0.000
67	D	109	LEU	0	0.043	0.043	26.846	0.001	0.001	0.000	0.000	0.000	0.000
68	D	110	ASP	-1	-0.870	-0.943	30.606	-0.051	-0.051	0.000	0.000	0.000	0.000
69	D	111	VAL	0	-0.026	-0.009	29.912	-0.007	-0.007	0.000	0.000	0.000	0.000
70	D	112	MET	0	0.006	0.010	33.111	0.005	0.005	0.000	0.000	0.000	0.000
71	D	113	PRO	0	-0.016	-0.031	34.802	-0.004	-0.004	0.000	0.000	0.000	0.000
72	D	114	ILE	0	-0.017	0.004	34.916	0.001	0.001	0.000	0.000	0.000	0.000
73	D	115	PHE	0	-0.024	-0.014	27.113	-0.008	-0.008	0.000	0.000	0.000	0.000
74	D	116	GLU	-1	-0.911	-0.940	30.206	-0.122	-0.122	0.000	0.000	0.000	0.000
75	D	117	THR	0	-0.101	-0.079	25.798	-0.006	-0.006	0.000	0.000	0.000	0.000
76	D	118	LEU	0	0.017	0.024	21.890	0.001	0.001	0.000	0.000	0.000	0.000
77	D	119	ALA	0	0.001	-0.011	21.613	-0.014	-0.014	0.000	0.000	0.000	0.000
78	D	120	LEU	0	0.009	0.006	17.017	0.004	0.004	0.000	0.000	0.000	0.000
79	D	121	ARG	1	0.869	0.941	14.330	0.381	0.381	0.000	0.000	0.000	0.000
80	D	122	LEU	0	0.013	0.001	12.158	0.052	0.052	0.000	0.000	0.000	0.000
81	D	123	VAL	0	-0.044	-0.028	9.519	-0.080	-0.080	0.000	0.000	0.000	0.000
82	D	124	LEU	0	0.034	0.012	6.494	0.234	0.234	0.000	0.000	0.000	0.000
83	D	125	GLN	0	0.024	0.008	3.398	-0.800	-0.378	0.009	-0.073	-0.357	0.000
84	D	126	GLY	0	-0.033	-0.009	5.335	-0.086	-0.086	0.000	0.000	0.000	0.000
85	D	127	ASP	-1	-0.892	-0.928	3.132	-5.506	-4.212	0.132	-0.609	-0.816	-0.005
86	D	128	VAL	0	-0.037	-0.026	6.581	0.258	0.258	0.000	0.000	0.000	0.000
87	D	129	ILE	0	-0.014	-0.002	8.836	-0.064	-0.064	0.000	0.000	0.000	0.000
88	D	130	TRP	0	0.003	-0.012	11.656	0.097	0.097	0.000	0.000	0.000	0.000
89	D	131	LEU	0	-0.006	0.011	13.760	-0.021	-0.021	0.000	0.000	0.000	0.000
90	D	132	ARG	1	0.846	0.903	17.375	0.200	0.200	0.000	0.000	0.000	0.000
91	D	134	VAL	0	0.025	0.018	23.853	0.002	0.002	0.000	0.000	0.000	0.000
92	D	135	PRO	0	-0.020	-0.017	27.565	0.004	0.004	0.000	0.000	0.000	0.000
93	D	136	GLU	-1	-0.899	-0.958	27.469	-0.072	-0.072	0.000	0.000	0.000	0.000
94	D	137	LEU	0	-0.044	-0.015	31.168	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)