FMO DATABASE

FMODB ID: K3LZ3

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1152383.457224
FMO2-HF: Nuclear repulsion	1099246.375853
FMO2-HF: Total energy	-53137.081371
FMO2-MP2: Total energy	-53292.470031

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.
-17.476	-12.621	0.822	-2.042	-3.634	-0.002

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 : -0.025 / q_NPA : -0.035

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	0.003	0.018	3.219	-2.103	-0.243	0.067	-0.747	-1.180	0.001
4	A	15	ARG	1	0.913	0.929	2.501	-2.435	-1.149	0.736	-0.581	-1.441	0.001
5	A	16	ASP	-1	-0.807	-0.885	3.616	-12.040	-10.689	0.020	-0.685	-0.686	-0.004
6	A	17	VAL	0	0.029	0.026	5.248	0.984	1.069	-0.001	-0.003	-0.081	0.000
7	A	18	ILE	0	-0.058	-0.042	6.595	0.346	0.346	0.000	0.000	0.000	0.000
8	A	19	ALA	0	-0.028	-0.014	7.581	0.222	0.222	0.000	0.000	0.000	0.000
9	A	20	LEU	0	0.054	0.023	9.128	0.314	0.314	0.000	0.000	0.000	0.000
10	A	21	LEU	0	-0.005	0.008	11.149	0.210	0.210	0.000	0.000	0.000	0.000
11	A	22	ILE	0	-0.038	-0.022	11.415	0.128	0.128	0.000	0.000	0.000	0.000
12	A	23	GLN	0	-0.040	-0.019	10.571	0.112	0.112	0.000	0.000	0.000	0.000
13	A	24	ASN	0	-0.052	-0.010	14.602	0.133	0.133	0.000	0.000	0.000	0.000
14	A	25	PRO	0	0.037	0.016	17.108	0.021	0.021	0.000	0.000	0.000	0.000
15	A	26	SER	0	0.058	0.016	18.649	0.029	0.029	0.000	0.000	0.000	0.000
16	A	27	TYR	0	0.036	0.011	14.646	0.020	0.020	0.000	0.000	0.000	0.000
17	A	28	ALA	0	0.004	0.002	17.633	0.025	0.025	0.000	0.000	0.000	0.000
18	A	29	GLU	-1	-1.015	-1.004	18.581	-0.165	-0.165	0.000	0.000	0.000	0.000
19	A	30	LEU	0	-0.018	0.003	17.906	0.036	0.036	0.000	0.000	0.000	0.000
20	A	31	VAL	0	-0.047	-0.009	15.324	0.024	0.024	0.000	0.000	0.000	0.000
21	A	32	PRO	0	0.001	0.016	17.163	0.018	0.018	0.000	0.000	0.000	0.000
22	A	33	ASP	-1	-0.836	-0.948	19.009	0.119	0.119	0.000	0.000	0.000	0.000
23	A	34	LEU	0	0.026	0.013	14.735	0.031	0.031	0.000	0.000	0.000	0.000
24	A	35	ALA	0	-0.069	-0.039	18.895	0.056	0.056	0.000	0.000	0.000	0.000
25	A	36	SER	0	-0.032	-0.015	21.617	0.024	0.024	0.000	0.000	0.000	0.000
26	A	37	VAL	0	0.042	0.004	16.537	0.028	0.028	0.000	0.000	0.000	0.000
27	A	38	ARG	1	0.934	0.984	16.391	-0.112	-0.112	0.000	0.000	0.000	0.000
28	A	39	HIS	0	-0.024	0.003	16.924	0.024	0.024	0.000	0.000	0.000	0.000
29	A	40	LEU	0	-0.049	-0.011	15.097	0.040	0.040	0.000	0.000	0.000	0.000
30	A	41	MET	0	0.038	0.015	14.720	0.062	0.062	0.000	0.000	0.000	0.000
31	A	42	ILE	0	0.011	0.011	8.994	0.079	0.079	0.000	0.000	0.000	0.000
32	A	43	PRO	0	0.008	-0.012	7.303	-0.189	-0.189	0.000	0.000	0.000	0.000
33	A	44	GLY	0	0.034	0.020	7.359	0.570	0.570	0.000	0.000	0.000	0.000
34	A	45	LEU	0	0.044	0.029	8.427	-0.336	-0.336	0.000	0.000	0.000	0.000
35	A	46	ASP	-1	-0.857	-0.932	10.817	0.509	0.509	0.000	0.000	0.000	0.000
36	A	47	THR	0	-0.041	-0.022	9.976	-0.122	-0.122	0.000	0.000	0.000	0.000
37	A	48	PHE	0	0.038	0.005	9.597	-0.116	-0.116	0.000	0.000	0.000	0.000
38	A	49	SER	0	-0.044	-0.024	11.482	-0.111	-0.111	0.000	0.000	0.000	0.000
39	A	50	GLU	-1	-0.849	-0.900	14.708	0.078	0.078	0.000	0.000	0.000	0.000
40	A	51	VAL	0	0.002	-0.008	12.901	-0.044	-0.044	0.000	0.000	0.000	0.000
41	A	52	LEU	0	0.034	0.015	15.063	-0.034	-0.034	0.000	0.000	0.000	0.000
42	A	53	GLU	-1	-0.958	-0.964	16.664	0.022	0.022	0.000	0.000	0.000	0.000
43	A	54	LYS	1	0.900	0.951	19.309	0.033	0.033	0.000	0.000	0.000	0.000
44	A	55	CYS	0	-0.043	-0.023	17.517	-0.029	-0.029	0.000	0.000	0.000	0.000
45	A	56	ARG	1	0.833	0.909	19.571	0.062	0.062	0.000	0.000	0.000	0.000
46	A	57	GLN	0	-0.070	-0.037	22.403	-0.009	-0.009	0.000	0.000	0.000	0.000
47	A	58	TYR	0	-0.080	-0.037	23.567	0.010	0.010	0.000	0.000	0.000	0.000
48	A	59	PRO	0	0.060	0.029	23.712	-0.023	-0.023	0.000	0.000	0.000	0.000
49	A	60	HIS	0	-0.021	-0.008	23.899	-0.035	-0.035	0.000	0.000	0.000	0.000
50	A	61	ILE	0	-0.062	-0.007	21.398	-0.003	-0.003	0.000	0.000	0.000	0.000
51	A	62	THR	0	0.034	-0.007	22.332	-0.032	-0.032	0.000	0.000	0.000	0.000
52	A	63	THR	0	0.066	0.009	16.790	0.032	0.032	0.000	0.000	0.000	0.000
53	A	64	GLY	0	-0.019	-0.009	19.487	0.017	0.017	0.000	0.000	0.000	0.000
54	A	65	GLN	0	0.025	0.015	21.859	0.012	0.012	0.000	0.000	0.000	0.000
55	A	66	LEU	0	0.011	0.010	17.054	0.034	0.034	0.000	0.000	0.000	0.000
56	A	67	LEU	0	0.005	-0.005	16.042	0.032	0.032	0.000	0.000	0.000	0.000
57	A	68	GLU	-1	-0.826	-0.883	19.808	-0.117	-0.117	0.000	0.000	0.000	0.000
58	A	69	HIS	0	-0.043	-0.012	21.302	0.046	0.046	0.000	0.000	0.000	0.000
59	A	70	TRP	0	-0.084	-0.062	16.857	0.002	0.002	0.000	0.000	0.000	0.000
60	A	71	ARG	1	0.841	0.906	20.449	0.122	0.122	0.000	0.000	0.000	0.000
61	A	72	ASP	-1	-0.939	-0.971	22.291	-0.022	-0.022	0.000	0.000	0.000	0.000
62	A	73	SER	0	-0.055	-0.018	19.860	0.032	0.032	0.000	0.000	0.000	0.000
63	A	74	LYS	1	0.880	0.918	14.630	-0.355	-0.355	0.000	0.000	0.000	0.000
64	A	75	ASN	0	-0.028	-0.024	13.662	0.075	0.075	0.000	0.000	0.000	0.000
65	A	76	GLU	-1	-0.758	-0.856	14.459	-0.158	-0.158	0.000	0.000	0.000	0.000
66	A	77	THR	0	0.010	0.008	14.318	-0.053	-0.053	0.000	0.000	0.000	0.000
67	A	78	LEU	0	-0.070	-0.036	7.721	-0.062	-0.062	0.000	0.000	0.000	0.000
68	A	79	LEU	0	0.047	0.008	10.899	-0.163	-0.163	0.000	0.000	0.000	0.000
69	A	80	SER	0	0.004	-0.003	12.998	-0.107	-0.107	0.000	0.000	0.000	0.000
70	A	81	ARG	1	0.858	0.947	6.107	1.032	1.032	0.000	0.000	0.000	0.000
71	A	82	LEU	0	-0.037	-0.034	6.322	-0.126	-0.126	0.000	0.000	0.000	0.000
72	A	83	ALA	0	0.041	0.029	10.252	-0.190	-0.190	0.000	0.000	0.000	0.000
73	A	84	SER	0	-0.029	-0.024	12.633	0.055	0.055	0.000	0.000	0.000	0.000
74	A	85	TRP	0	-0.099	-0.051	3.932	1.383	1.656	0.000	-0.026	-0.246	0.000
75	A	86	GLU	-1	-0.949	-0.979	6.872	-3.962	-3.962	0.000	0.000	0.000	0.000
76	A	87	ILE	0	0.027	0.040	10.323	-0.032	-0.032	0.000	0.000	0.000	0.000
77	A	88	PRO	0	-0.037	0.003	13.227	0.062	0.062	0.000	0.000	0.000	0.000
78	A	89	LEU	0	-0.049	-0.037	15.421	0.089	0.089	0.000	0.000	0.000	0.000
79	A	90	VAL	0	-0.040	-0.030	18.813	0.066	0.066	0.000	0.000	0.000	0.000
80	A	91	GLU	-1	-0.862	-0.941	16.604	-0.920	-0.920	0.000	0.000	0.000	0.000
81	A	92	ASP	-1	-0.942	-0.970	18.726	-0.521	-0.521	0.000	0.000	0.000	0.000
82	A	93	ASN	0	-0.041	-0.027	15.754	0.109	0.109	0.000	0.000	0.000	0.000
83	A	94	GLN	0	0.052	0.028	12.595	-0.093	-0.093	0.000	0.000	0.000	0.000
84	A	95	GLU	-1	-0.897	-0.957	14.306	-0.551	-0.551	0.000	0.000	0.000	0.000
85	A	96	GLU	-1	-0.938	-0.970	15.797	-0.513	-0.513	0.000	0.000	0.000	0.000
86	A	97	LEU	0	0.008	0.011	9.019	-0.013	-0.013	0.000	0.000	0.000	0.000
87	A	98	PHE	0	0.008	0.009	11.159	-0.199	-0.199	0.000	0.000	0.000	0.000
88	A	99	LEU	0	0.013	0.007	12.094	0.041	0.041	0.000	0.000	0.000	0.000
89	A	100	ASP	-1	-0.783	-0.865	11.176	-0.794	-0.794	0.000	0.000	0.000	0.000
90	A	101	SER	0	-0.059	-0.043	7.708	-0.143	-0.143	0.000	0.000	0.000	0.000
91	A	102	LEU	0	-0.025	-0.029	9.185	0.381	0.381	0.000	0.000	0.000	0.000
92	A	103	ASP	-1	-0.874	-0.929	11.448	0.137	0.137	0.000	0.000	0.000	0.000
93	A	104	LYS	1	0.742	0.853	7.954	0.917	0.917	0.000	0.000	0.000	0.000
94	A	105	ILE	0	-0.014	-0.006	5.891	0.570	0.570	0.000	0.000	0.000	0.000
95	A	106	LEU	0	0.010	0.005	9.799	0.137	0.137	0.000	0.000	0.000	0.000
96	A	107	ALA	0	0.000	0.002	12.779	0.042	0.042	0.000	0.000	0.000	0.000
97	A	108	GLN	0	0.011	0.003	6.745	0.063	0.063	0.000	0.000	0.000	0.000
98	A	109	CYS	0	-0.072	-0.037	12.004	0.005	0.005	0.000	0.000	0.000	0.000
99	A	110	VAL	0	-0.003	-0.006	14.333	-0.052	-0.052	0.000	0.000	0.000	0.000
100	A	111	GLU	-1	-0.946	-0.959	14.280	0.765	0.765	0.000	0.000	0.000	0.000
101	A	112	LYS	1	0.930	0.947	13.433	-1.142	-1.142	0.000	0.000	0.000	0.000
102	A	113	GLN	0	0.012	-0.011	16.566	-0.005	-0.005	0.000	0.000	0.000	0.000
103	A	114	ILE	0	0.010	0.003	19.453	-0.058	-0.058	0.000	0.000	0.000	0.000
104	A	115	GLU	-1	-0.981	-0.982	18.305	0.591	0.591	0.000	0.000	0.000	0.000
105	A	116	ASN	0	-0.036	-0.014	18.758	-0.013	-0.013	0.000	0.000	0.000	0.000
106	A	117	LEU	0	-0.030	-0.007	22.211	-0.039	-0.039	0.000	0.000	0.000	0.000
107	A	118	GLN	0	0.006	-0.014	23.215	-0.050	-0.050	0.000	0.000	0.000	0.000
108	A	119	ALA	0	-0.052	-0.019	24.220	-0.023	-0.023	0.000	0.000	0.000	0.000
109	A	120	LYS	1	0.864	0.918	26.171	-0.243	-0.243	0.000	0.000	0.000	0.000
110	A	121	GLU	-1	-0.850	-0.900	28.386	0.184	0.184	0.000	0.000	0.000	0.000
111	A	122	ARG	1	0.929	0.964	24.513	-0.348	-0.348	0.000	0.000	0.000	0.000
112	A	123	SER	0	-0.081	-0.020	29.961	-0.011	-0.011	0.000	0.000	0.000	0.000
113	A	124	VAL	0	-0.034	-0.034	31.596	-0.012	-0.012	0.000	0.000	0.000	0.000
114	A	125	GLY	0	0.004	0.028	32.805	-0.014	-0.014	0.000	0.000	0.000	0.000
115	A	126	LEU	0	-0.056	-0.029	28.695	0.007	0.007	0.000	0.000	0.000	0.000
116	A	127	SER	0	-0.009	-0.027	32.278	-0.017	-0.017	0.000	0.000	0.000	0.000
117	A	128	THR	0	0.025	-0.022	33.363	0.006	0.006	0.000	0.000	0.000	0.000
118	A	129	GLU	-1	-0.824	-0.895	31.035	0.118	0.118	0.000	0.000	0.000	0.000
119	A	130	GLU	-1	-0.726	-0.828	28.563	0.216	0.216	0.000	0.000	0.000	0.000
120	A	131	LYS	1	0.834	0.911	28.710	-0.175	-0.175	0.000	0.000	0.000	0.000
121	A	132	ARG	1	0.807	0.887	30.353	-0.116	-0.116	0.000	0.000	0.000	0.000
122	A	133	GLU	-1	-0.835	-0.910	23.927	0.263	0.263	0.000	0.000	0.000	0.000
123	A	134	LEU	0	0.005	0.001	24.928	0.006	0.006	0.000	0.000	0.000	0.000
124	A	135	GLN	0	0.010	-0.021	25.873	0.006	0.006	0.000	0.000	0.000	0.000
125	A	136	ASP	-1	-0.804	-0.885	26.510	0.111	0.111	0.000	0.000	0.000	0.000
126	A	137	LEU	0	-0.019	-0.007	20.539	-0.006	-0.006	0.000	0.000	0.000	0.000
127	A	138	ILE	0	-0.014	-0.009	22.559	0.006	0.006	0.000	0.000	0.000	0.000
128	A	139	LEU	0	-0.080	-0.025	24.572	-0.012	-0.012	0.000	0.000	0.000	0.000
129	A	140	LYS	1	0.832	0.883	24.553	-0.106	-0.106	0.000	0.000	0.000	0.000
130	A	141	GLY	0	0.044	0.052	20.373	-0.015	-0.015	0.000	0.000	0.000	0.000
131	A	142	LEU	0	-0.063	-0.072	16.878	-0.006	-0.006	0.000	0.000	0.000	0.000
132	A	143	LYS	1	0.923	1.003	17.929	-0.122	-0.122	0.000	0.000	0.000	0.000

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