FMO DATABASE

FMODB ID: 43VKN

Calculation Name: 4IM9-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4IM9

Chain ID: A

ChEMBL ID:

UniProt ID:

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	132
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1156053.55105
FMO2-HF: Nuclear repulsion	1102916.083663
FMO2-HF: Total energy	-53137.467387
FMO2-MP2: Total energy	-53292.820162

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:12:THR)

Summations of interaction energy for fragment #1(A:12:THR)

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.
-39.264	-32.743	8.118	-7.249	-7.39	-0.076

Interaction energy analysis for fragmet #1(A:12:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.038 / q_NPA : -0.036

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	14	MET	0	0.015	0.026	3.915	-1.010	0.590	-0.007	-0.641	-0.952	0.001
4	A	15	ARG	1	0.917	0.940	2.938	-1.002	-0.043	0.118	-0.335	-0.742	0.001
5	A	16	ASP	-1	-0.755	-0.867	1.884	-37.381	-33.953	7.998	-6.192	-5.235	-0.078
6	A	17	VAL	0	0.044	0.024	4.900	1.479	1.587	-0.001	-0.009	-0.098	0.000
7	A	18	ILE	0	-0.059	-0.031	7.260	0.590	0.590	0.000	0.000	0.000	0.000
8	A	19	ALA	0	-0.023	-0.013	7.442	0.367	0.367	0.000	0.000	0.000	0.000
9	A	20	LEU	0	0.037	0.025	8.682	0.436	0.436	0.000	0.000	0.000	0.000
10	A	21	LEU	0	-0.018	0.001	10.939	0.297	0.297	0.000	0.000	0.000	0.000
11	A	22	ILE	0	-0.037	-0.023	11.294	0.194	0.194	0.000	0.000	0.000	0.000
12	A	23	GLN	0	-0.046	-0.033	10.240	0.176	0.176	0.000	0.000	0.000	0.000
13	A	24	ASN	0	-0.033	0.004	14.743	0.200	0.200	0.000	0.000	0.000	0.000
14	A	25	PRO	0	0.033	0.017	16.868	0.010	0.010	0.000	0.000	0.000	0.000
15	A	26	SER	0	0.043	0.006	18.405	0.014	0.014	0.000	0.000	0.000	0.000
16	A	27	TYR	0	0.034	0.011	14.214	0.016	0.016	0.000	0.000	0.000	0.000
17	A	28	ALA	0	-0.019	-0.017	17.712	0.009	0.009	0.000	0.000	0.000	0.000
18	A	29	GLU	-1	-1.011	-1.010	18.826	-0.303	-0.303	0.000	0.000	0.000	0.000
19	A	30	LEU	0	-0.017	0.004	17.143	0.045	0.045	0.000	0.000	0.000	0.000
20	A	31	VAL	0	-0.030	0.009	15.888	0.014	0.014	0.000	0.000	0.000	0.000
21	A	32	PRO	0	0.016	0.020	17.817	0.047	0.047	0.000	0.000	0.000	0.000
22	A	33	ASP	-1	-0.802	-0.912	19.957	-0.074	-0.074	0.000	0.000	0.000	0.000
23	A	34	LEU	0	-0.007	-0.016	15.707	0.017	0.017	0.000	0.000	0.000	0.000
24	A	35	ALA	0	-0.022	-0.014	19.873	0.049	0.049	0.000	0.000	0.000	0.000
25	A	36	SER	0	-0.029	-0.009	22.674	0.018	0.018	0.000	0.000	0.000	0.000
26	A	37	VAL	0	0.017	-0.007	17.297	0.035	0.035	0.000	0.000	0.000	0.000
27	A	38	ARG	1	0.907	0.957	16.899	0.078	0.078	0.000	0.000	0.000	0.000
28	A	39	HIS	0	-0.024	0.002	17.824	0.009	0.009	0.000	0.000	0.000	0.000
29	A	40	LEU	0	-0.057	-0.010	15.423	0.055	0.055	0.000	0.000	0.000	0.000
30	A	41	MET	0	0.027	0.004	15.031	0.064	0.064	0.000	0.000	0.000	0.000
31	A	42	ILE	0	0.033	0.022	9.436	0.126	0.126	0.000	0.000	0.000	0.000
32	A	43	PRO	0	-0.025	-0.026	7.554	-0.242	-0.242	0.000	0.000	0.000	0.000
33	A	44	GLY	0	0.048	0.032	7.642	0.401	0.401	0.000	0.000	0.000	0.000
34	A	45	LEU	0	0.055	0.028	8.993	-0.347	-0.347	0.000	0.000	0.000	0.000
35	A	46	ASP	-1	-0.829	-0.901	11.591	0.235	0.235	0.000	0.000	0.000	0.000
36	A	47	THR	0	-0.037	-0.028	10.229	-0.101	-0.101	0.000	0.000	0.000	0.000
37	A	48	PHE	0	0.032	0.003	10.322	-0.109	-0.109	0.000	0.000	0.000	0.000
38	A	49	SER	0	-0.030	-0.019	12.127	-0.063	-0.063	0.000	0.000	0.000	0.000
39	A	50	GLU	-1	-0.832	-0.892	15.113	-0.092	-0.092	0.000	0.000	0.000	0.000
40	A	51	VAL	0	0.021	0.001	13.169	-0.018	-0.018	0.000	0.000	0.000	0.000
41	A	52	LEU	0	0.025	0.020	15.764	-0.013	-0.013	0.000	0.000	0.000	0.000
42	A	53	GLU	-1	-0.945	-0.963	17.309	-0.107	-0.107	0.000	0.000	0.000	0.000
43	A	54	LYS	1	0.854	0.930	19.378	0.182	0.182	0.000	0.000	0.000	0.000
44	A	55	CYS	0	-0.038	-0.018	17.740	-0.016	-0.016	0.000	0.000	0.000	0.000
45	A	56	ARG	1	0.831	0.909	20.485	0.296	0.296	0.000	0.000	0.000	0.000
46	A	57	GLN	0	-0.061	-0.027	22.966	0.016	0.016	0.000	0.000	0.000	0.000
47	A	58	TYR	0	-0.067	-0.030	23.836	0.027	0.027	0.000	0.000	0.000	0.000
48	A	59	PRO	0	0.052	0.024	23.584	-0.028	-0.028	0.000	0.000	0.000	0.000
49	A	60	HIS	0	0.009	0.012	23.729	-0.043	-0.043	0.000	0.000	0.000	0.000
50	A	61	ILE	0	-0.073	-0.011	21.353	0.010	0.010	0.000	0.000	0.000	0.000
51	A	62	THR	0	0.027	-0.015	22.063	-0.043	-0.043	0.000	0.000	0.000	0.000
52	A	63	THR	0	0.050	-0.010	16.439	0.041	0.041	0.000	0.000	0.000	0.000
53	A	64	GLY	0	-0.016	-0.006	19.269	0.011	0.011	0.000	0.000	0.000	0.000
54	A	65	GLN	0	0.020	0.019	21.754	0.010	0.010	0.000	0.000	0.000	0.000
55	A	66	LEU	0	0.003	0.010	17.083	0.036	0.036	0.000	0.000	0.000	0.000
56	A	67	LEU	0	0.015	-0.003	16.023	0.030	0.030	0.000	0.000	0.000	0.000
57	A	68	GLU	-1	-0.799	-0.865	19.843	-0.188	-0.188	0.000	0.000	0.000	0.000
58	A	69	HIS	0	-0.036	-0.014	21.508	0.052	0.052	0.000	0.000	0.000	0.000
59	A	70	TRP	0	-0.097	-0.067	17.095	-0.006	-0.006	0.000	0.000	0.000	0.000
60	A	71	ARG	1	0.829	0.890	20.561	0.194	0.194	0.000	0.000	0.000	0.000
61	A	72	ASP	-1	-0.922	-0.947	23.052	-0.086	-0.086	0.000	0.000	0.000	0.000
62	A	73	SER	0	-0.050	-0.025	20.490	0.037	0.037	0.000	0.000	0.000	0.000
63	A	74	LYS	1	0.787	0.879	14.431	-0.208	-0.208	0.000	0.000	0.000	0.000
64	A	75	ASN	0	0.000	-0.011	13.772	0.100	0.100	0.000	0.000	0.000	0.000
65	A	76	GLU	-1	-0.784	-0.878	14.594	-0.269	-0.269	0.000	0.000	0.000	0.000
66	A	77	THR	0	0.019	0.010	14.870	-0.063	-0.063	0.000	0.000	0.000	0.000
67	A	78	LEU	0	-0.071	-0.028	8.085	-0.058	-0.058	0.000	0.000	0.000	0.000
68	A	79	LEU	0	0.048	0.009	11.402	-0.220	-0.220	0.000	0.000	0.000	0.000
69	A	80	SER	0	0.005	-0.009	13.193	-0.118	-0.118	0.000	0.000	0.000	0.000
70	A	81	ARG	1	0.839	0.931	6.185	1.366	1.366	0.000	0.000	0.000	0.000
71	A	82	LEU	0	-0.041	-0.030	6.752	-0.163	-0.163	0.000	0.000	0.000	0.000
72	A	83	ALA	0	0.044	0.024	10.074	-0.224	-0.224	0.000	0.000	0.000	0.000
73	A	84	SER	0	-0.052	-0.036	12.163	0.144	0.144	0.000	0.000	0.000	0.000
74	A	85	TRP	0	-0.068	-0.030	3.395	1.822	2.248	0.010	-0.072	-0.363	0.000
75	A	86	GLU	-1	-0.933	-0.970	6.560	-3.501	-3.501	0.000	0.000	0.000	0.000
76	A	87	ILE	0	0.013	0.035	9.878	0.015	0.015	0.000	0.000	0.000	0.000
77	A	88	PRO	0	-0.022	0.009	12.900	0.115	0.115	0.000	0.000	0.000	0.000
78	A	89	LEU	0	-0.061	-0.043	15.093	0.085	0.085	0.000	0.000	0.000	0.000
79	A	90	VAL	0	-0.034	-0.023	17.830	0.077	0.077	0.000	0.000	0.000	0.000
80	A	91	GLU	-1	-0.786	-0.898	15.796	-1.162	-1.162	0.000	0.000	0.000	0.000
81	A	92	ASP	-1	-0.948	-0.976	17.781	-0.600	-0.600	0.000	0.000	0.000	0.000
82	A	93	ASN	0	-0.044	-0.022	14.432	0.136	0.136	0.000	0.000	0.000	0.000
83	A	94	GLN	0	-0.015	-0.020	12.054	-0.285	-0.285	0.000	0.000	0.000	0.000
84	A	95	GLU	-1	-0.900	-0.949	13.553	-0.765	-0.765	0.000	0.000	0.000	0.000
85	A	96	GLU	-1	-0.921	-0.966	14.685	-0.693	-0.693	0.000	0.000	0.000	0.000
86	A	97	LEU	0	-0.011	0.007	8.244	-0.019	-0.019	0.000	0.000	0.000	0.000
87	A	98	PHE	0	0.020	0.013	9.900	-0.366	-0.366	0.000	0.000	0.000	0.000
88	A	99	LEU	0	0.021	0.005	11.290	-0.027	-0.027	0.000	0.000	0.000	0.000
89	A	100	ASP	-1	-0.804	-0.891	9.666	-1.152	-1.152	0.000	0.000	0.000	0.000
90	A	101	SER	0	-0.068	-0.043	7.083	-0.285	-0.285	0.000	0.000	0.000	0.000
91	A	102	LEU	0	-0.013	-0.008	8.460	0.272	0.272	0.000	0.000	0.000	0.000
92	A	103	ASP	-1	-0.856	-0.921	11.304	-0.148	-0.148	0.000	0.000	0.000	0.000
93	A	104	LYS	1	0.738	0.847	7.710	1.293	1.293	0.000	0.000	0.000	0.000
94	A	105	ILE	0	-0.039	-0.017	6.538	0.543	0.543	0.000	0.000	0.000	0.000
95	A	106	LEU	0	0.001	0.003	10.471	0.210	0.210	0.000	0.000	0.000	0.000
96	A	107	ALA	0	0.020	0.004	13.184	0.089	0.089	0.000	0.000	0.000	0.000
97	A	108	GLN	0	0.018	0.012	7.347	0.188	0.188	0.000	0.000	0.000	0.000
98	A	109	CYS	0	-0.059	-0.041	12.573	0.058	0.058	0.000	0.000	0.000	0.000
99	A	110	VAL	0	-0.025	-0.011	15.043	-0.013	-0.013	0.000	0.000	0.000	0.000
100	A	111	GLU	-1	-0.938	-0.960	14.013	0.686	0.686	0.000	0.000	0.000	0.000
101	A	112	LYS	1	0.924	0.950	14.053	-0.955	-0.955	0.000	0.000	0.000	0.000
102	A	113	GLN	0	0.020	0.000	17.166	0.017	0.017	0.000	0.000	0.000	0.000
103	A	114	ILE	0	0.003	-0.010	20.115	-0.036	-0.036	0.000	0.000	0.000	0.000
104	A	115	GLU	-1	-0.972	-0.974	19.171	0.520	0.520	0.000	0.000	0.000	0.000
105	A	116	ASN	0	-0.037	-0.028	19.328	0.002	0.002	0.000	0.000	0.000	0.000
106	A	117	LEU	0	-0.022	0.000	22.734	-0.026	-0.026	0.000	0.000	0.000	0.000
107	A	118	GLN	0	0.010	-0.002	23.894	-0.027	-0.027	0.000	0.000	0.000	0.000
108	A	119	ALA	0	-0.049	-0.020	24.498	-0.014	-0.014	0.000	0.000	0.000	0.000
109	A	120	LYS	1	0.849	0.918	26.512	-0.172	-0.172	0.000	0.000	0.000	0.000
110	A	121	GLU	-1	-0.849	-0.904	28.901	0.141	0.141	0.000	0.000	0.000	0.000
111	A	122	ARG	1	0.905	0.939	24.654	-0.311	-0.311	0.000	0.000	0.000	0.000
112	A	123	SER	0	-0.034	-0.001	30.704	-0.002	-0.002	0.000	0.000	0.000	0.000
113	A	124	VAL	0	-0.084	-0.046	32.139	-0.009	-0.009	0.000	0.000	0.000	0.000
114	A	125	GLY	0	0.013	0.030	33.636	-0.013	-0.013	0.000	0.000	0.000	0.000
115	A	126	LEU	0	-0.055	-0.035	29.087	0.007	0.007	0.000	0.000	0.000	0.000
116	A	127	SER	0	-0.009	-0.033	32.705	-0.014	-0.014	0.000	0.000	0.000	0.000
117	A	128	THR	0	0.023	-0.018	33.813	0.005	0.005	0.000	0.000	0.000	0.000
118	A	129	GLU	-1	-0.816	-0.864	31.676	0.045	0.045	0.000	0.000	0.000	0.000
119	A	130	GLU	-1	-0.708	-0.821	28.998	0.146	0.146	0.000	0.000	0.000	0.000
120	A	131	LYS	1	0.834	0.907	29.123	-0.129	-0.129	0.000	0.000	0.000	0.000
121	A	132	ARG	1	0.793	0.858	30.666	-0.049	-0.049	0.000	0.000	0.000	0.000
122	A	133	GLU	-1	-0.831	-0.901	24.211	0.150	0.150	0.000	0.000	0.000	0.000
123	A	134	LEU	0	0.019	0.008	25.221	0.000	0.000	0.000	0.000	0.000	0.000
124	A	135	GLN	0	0.015	-0.010	26.119	0.007	0.007	0.000	0.000	0.000	0.000
125	A	136	ASP	-1	-0.814	-0.885	26.901	0.010	0.010	0.000	0.000	0.000	0.000
126	A	137	LEU	0	-0.030	-0.007	20.910	-0.012	-0.012	0.000	0.000	0.000	0.000
127	A	138	ILE	0	-0.019	-0.017	22.853	0.001	0.001	0.000	0.000	0.000	0.000
128	A	139	LEU	0	-0.080	-0.026	24.859	-0.008	-0.008	0.000	0.000	0.000	0.000
129	A	140	LYS	1	0.834	0.898	24.543	-0.015	-0.015	0.000	0.000	0.000	0.000
130	A	141	GLY	0	0.061	0.044	20.612	-0.026	-0.026	0.000	0.000	0.000	0.000
131	A	142	LEU	0	-0.019	-0.042	17.312	0.012	0.012	0.000	0.000	0.000	0.000
132	A	143	LYS	1	0.876	0.964	18.360	-0.020	-0.020	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:12:THR)