FMO DATABASE

FMODB ID: ZY3QN

Calculation Name: 4L3R-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4L3R

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-06-20

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	OptH
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	143
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1308282.827279
FMO2-HF: Nuclear repulsion	1252490.822411
FMO2-HF: Total energy	-55792.004868
FMO2-MP2: Total energy	-55955.939545

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:30:ASP)

Summations of interaction energy for fragment #1(A:30:ASP)

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.
-31.612	-29.401	3.171	-1.938	-3.443	0.012

Interaction energy analysis for fragmet #1(A:30:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.946 / q_NPA : -0.977

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	32	VAL	0	-0.029	-0.010	3.214	-7.947	-5.603	0.034	-1.045	-1.332	0.006
4	A	33	MET	0	0.038	0.010	2.594	-10.433	-10.566	3.137	-0.893	-2.111	0.006
5	A	34	GLU	-1	-0.777	-0.881	5.141	23.530	23.530	0.000	0.000	0.000	0.000
6	A	35	ILE	0	-0.060	-0.036	6.904	-3.846	-3.846	0.000	0.000	0.000	0.000
7	A	36	PHE	0	-0.021	-0.022	8.591	-2.513	-2.513	0.000	0.000	0.000	0.000
8	A	37	ASN	0	-0.077	-0.023	8.548	-2.066	-2.066	0.000	0.000	0.000	0.000
9	A	38	ASP	-1	-0.940	-0.957	10.493	16.126	16.126	0.000	0.000	0.000	0.000
10	A	39	LYS	1	0.777	0.899	10.663	-24.309	-24.309	0.000	0.000	0.000	0.000
11	A	40	THR	0	-0.036	-0.011	15.565	-0.216	-0.216	0.000	0.000	0.000	0.000
12	A	41	TRP	0	-0.024	-0.010	12.050	-1.016	-1.016	0.000	0.000	0.000	0.000
13	A	42	LYS	1	0.811	0.899	18.291	-11.629	-11.629	0.000	0.000	0.000	0.000
14	A	43	LEU	0	-0.009	0.002	21.703	0.215	0.215	0.000	0.000	0.000	0.000
15	A	44	SER	0	-0.032	-0.021	22.180	-0.410	-0.410	0.000	0.000	0.000	0.000
16	A	45	ARG	1	0.941	0.972	20.988	-13.473	-13.473	0.000	0.000	0.000	0.000
17	A	46	ILE	0	0.015	0.015	24.564	0.432	0.432	0.000	0.000	0.000	0.000
18	A	47	THR	0	0.005	0.016	25.635	-0.534	-0.534	0.000	0.000	0.000	0.000
19	A	48	THR	0	0.020	0.001	26.444	0.287	0.287	0.000	0.000	0.000	0.000
20	A	49	GLU	-1	-0.928	-0.964	23.185	12.312	12.312	0.000	0.000	0.000	0.000
21	A	50	LYS	1	0.936	0.962	23.998	-11.244	-11.244	0.000	0.000	0.000	0.000
22	A	51	GLY	0	0.013	0.034	26.289	-0.258	-0.258	0.000	0.000	0.000	0.000
23	A	52	LYS	1	0.930	0.944	26.649	-10.498	-10.498	0.000	0.000	0.000	0.000
24	A	53	GLU	-1	-0.862	-0.919	29.275	9.752	9.752	0.000	0.000	0.000	0.000
25	A	54	GLN	0	-0.011	-0.007	28.408	-0.047	-0.047	0.000	0.000	0.000	0.000
26	A	55	PHE	0	0.021	-0.018	28.654	0.322	0.322	0.000	0.000	0.000	0.000
27	A	56	TYR	0	0.018	0.019	29.228	-0.274	-0.274	0.000	0.000	0.000	0.000
28	A	57	GLN	0	0.004	-0.004	32.051	-0.251	-0.251	0.000	0.000	0.000	0.000
29	A	58	GLY	0	0.036	0.007	35.650	0.054	0.054	0.000	0.000	0.000	0.000
30	A	59	LEU	0	-0.058	0.001	30.787	-0.012	-0.012	0.000	0.000	0.000	0.000
31	A	60	TRP	0	-0.008	-0.025	32.992	-0.019	-0.019	0.000	0.000	0.000	0.000
32	A	61	SER	0	-0.039	-0.035	38.197	-0.015	-0.015	0.000	0.000	0.000	0.000
33	A	62	ASN	0	-0.013	-0.008	41.735	-0.129	-0.129	0.000	0.000	0.000	0.000
34	A	63	GLU	-1	-0.848	-0.929	41.648	7.135	7.135	0.000	0.000	0.000	0.000
35	A	64	ALA	0	-0.010	-0.002	41.834	0.124	0.124	0.000	0.000	0.000	0.000
36	A	65	GLU	-1	-0.827	-0.928	39.663	7.579	7.579	0.000	0.000	0.000	0.000
37	A	66	GLU	-1	-0.804	-0.889	36.356	8.454	8.454	0.000	0.000	0.000	0.000
38	A	67	LYS	1	0.936	0.964	37.120	-7.016	-7.016	0.000	0.000	0.000	0.000
39	A	68	ALA	0	0.009	-0.004	38.344	0.117	0.117	0.000	0.000	0.000	0.000
40	A	69	SER	0	0.032	0.000	34.118	0.106	0.106	0.000	0.000	0.000	0.000
41	A	70	ARG	1	0.795	0.887	32.618	-8.645	-8.645	0.000	0.000	0.000	0.000
42	A	71	GLU	-1	-0.938	-0.963	34.074	8.222	8.222	0.000	0.000	0.000	0.000
43	A	72	LEU	0	-0.021	-0.002	33.632	0.137	0.137	0.000	0.000	0.000	0.000
44	A	73	LEU	0	-0.010	-0.007	27.465	0.228	0.228	0.000	0.000	0.000	0.000
45	A	74	LYS	1	0.870	0.939	29.743	-8.215	-8.215	0.000	0.000	0.000	0.000
46	A	75	ILE	0	-0.011	0.022	31.118	0.078	0.078	0.000	0.000	0.000	0.000
47	A	76	THR	0	-0.004	-0.017	26.618	0.242	0.242	0.000	0.000	0.000	0.000
48	A	77	GLU	-1	-0.854	-0.932	26.612	10.192	10.192	0.000	0.000	0.000	0.000
49	A	78	ASN	0	-0.037	-0.003	27.127	0.248	0.248	0.000	0.000	0.000	0.000
50	A	79	PHE	0	-0.023	-0.014	26.022	0.156	0.156	0.000	0.000	0.000	0.000
51	A	80	THR	0	-0.025	-0.004	22.244	0.471	0.471	0.000	0.000	0.000	0.000
52	A	81	LEU	0	0.001	-0.004	16.910	-0.335	-0.335	0.000	0.000	0.000	0.000
53	A	82	ASN	0	0.001	-0.004	16.860	0.832	0.832	0.000	0.000	0.000	0.000
54	A	83	PHE	0	0.052	0.036	12.217	-0.604	-0.604	0.000	0.000	0.000	0.000
55	A	84	ASN	0	0.015	-0.001	13.731	-0.097	-0.097	0.000	0.000	0.000	0.000
56	A	85	CYS	0	0.009	0.005	12.069	0.881	0.881	0.000	0.000	0.000	0.000
57	A	86	ALA	0	0.034	0.019	14.971	-0.708	-0.708	0.000	0.000	0.000	0.000
58	A	87	ASP	-1	-0.925	-0.966	18.381	14.067	14.067	0.000	0.000	0.000	0.000
59	A	88	VAL	0	-0.035	-0.010	19.859	-0.809	-0.809	0.000	0.000	0.000	0.000
60	A	89	ASN	0	-0.057	-0.043	21.982	-0.330	-0.330	0.000	0.000	0.000	0.000
61	A	90	GLY	0	0.011	0.002	23.949	-0.003	-0.003	0.000	0.000	0.000	0.000
62	A	91	GLU	-1	-0.940	-0.951	18.848	15.355	15.355	0.000	0.000	0.000	0.000
63	A	92	VAL	0	-0.020	-0.008	14.914	-0.071	-0.071	0.000	0.000	0.000	0.000
64	A	93	THR	0	-0.026	-0.006	14.793	0.957	0.957	0.000	0.000	0.000	0.000
65	A	94	GLY	0	0.030	0.007	12.379	-0.081	-0.081	0.000	0.000	0.000	0.000
66	A	95	THR	0	-0.076	-0.037	13.405	-0.336	-0.336	0.000	0.000	0.000	0.000
67	A	96	VAL	0	0.023	0.005	15.352	0.706	0.706	0.000	0.000	0.000	0.000
68	A	97	SER	0	0.042	0.028	17.404	-1.107	-1.107	0.000	0.000	0.000	0.000
69	A	98	ALA	0	-0.022	-0.017	19.958	0.462	0.462	0.000	0.000	0.000	0.000
70	A	99	HIS	1	0.829	0.913	22.554	-10.947	-10.947	0.000	0.000	0.000	0.000
71	A	100	ALA	0	0.012	0.026	25.983	0.170	0.170	0.000	0.000	0.000	0.000
72	A	101	VAL	0	-0.015	-0.011	28.245	-0.058	-0.058	0.000	0.000	0.000	0.000
73	A	102	LYS	1	0.904	0.950	31.812	-8.073	-8.073	0.000	0.000	0.000	0.000
74	A	103	ALA	0	-0.043	-0.003	30.423	-0.079	-0.079	0.000	0.000	0.000	0.000
75	A	104	ASN	0	-0.012	-0.024	27.054	0.476	0.476	0.000	0.000	0.000	0.000
76	A	105	ILE	0	-0.008	0.005	22.309	-0.328	-0.328	0.000	0.000	0.000	0.000
77	A	106	SER	0	-0.008	-0.014	23.398	0.126	0.126	0.000	0.000	0.000	0.000
78	A	107	ASP	-1	-0.857	-0.913	19.980	13.784	13.784	0.000	0.000	0.000	0.000
79	A	108	ALA	0	-0.029	-0.016	20.189	-0.300	-0.300	0.000	0.000	0.000	0.000
80	A	109	ILE	0	0.018	-0.005	18.646	0.739	0.739	0.000	0.000	0.000	0.000
81	A	110	LEU	0	-0.009	0.004	11.877	-0.343	-0.343	0.000	0.000	0.000	0.000
82	A	111	LYS	1	0.916	0.962	13.745	-16.326	-16.326	0.000	0.000	0.000	0.000
83	A	112	ILE	0	0.024	-0.003	8.706	-0.817	-0.817	0.000	0.000	0.000	0.000
84	A	113	ASP	-1	-0.843	-0.923	8.544	27.315	27.315	0.000	0.000	0.000	0.000
85	A	114	GLY	0	0.036	-0.005	4.967	-0.747	-0.747	0.000	0.000	0.000	0.000
86	A	115	LYS	1	0.890	0.960	6.038	-32.004	-32.004	0.000	0.000	0.000	0.000
87	A	116	GLU	-1	-0.896	-0.933	7.977	17.965	17.965	0.000	0.000	0.000	0.000
88	A	117	HIS	0	-0.051	-0.009	8.595	-0.795	-0.795	0.000	0.000	0.000	0.000
89	A	118	THR	0	-0.041	-0.039	10.644	-1.432	-1.432	0.000	0.000	0.000	0.000
90	A	119	ILE	0	-0.013	-0.026	11.735	1.435	1.435	0.000	0.000	0.000	0.000
91	A	120	SER	0	-0.048	-0.011	14.095	-0.989	-0.989	0.000	0.000	0.000	0.000
92	A	121	ILE	0	0.050	0.024	16.713	0.603	0.603	0.000	0.000	0.000	0.000
93	A	122	SER	0	-0.010	-0.003	19.073	-0.841	-0.841	0.000	0.000	0.000	0.000
94	A	123	GLY	0	0.025	0.004	22.107	0.231	0.231	0.000	0.000	0.000	0.000
95	A	124	LYS	1	0.939	0.968	24.989	-9.774	-9.774	0.000	0.000	0.000	0.000
96	A	125	ALA	0	0.031	0.020	27.442	0.183	0.183	0.000	0.000	0.000	0.000
97	A	126	TYR	0	-0.024	0.001	28.540	-0.395	-0.395	0.000	0.000	0.000	0.000
98	A	127	GLY	0	0.048	0.017	30.973	0.055	0.055	0.000	0.000	0.000	0.000
99	A	128	SER	0	-0.018	-0.018	33.082	0.167	0.167	0.000	0.000	0.000	0.000
100	A	129	GLU	-1	-0.706	-0.868	31.501	9.322	9.322	0.000	0.000	0.000	0.000
101	A	130	SER	0	-0.059	-0.047	35.109	-0.145	-0.145	0.000	0.000	0.000	0.000
102	A	131	ASP	-1	-0.818	-0.902	34.477	8.550	8.550	0.000	0.000	0.000	0.000
103	A	132	LYS	1	0.905	0.952	34.622	-7.485	-7.485	0.000	0.000	0.000	0.000
104	A	133	LEU	0	0.038	0.037	29.473	0.185	0.185	0.000	0.000	0.000	0.000
105	A	134	ALA	0	0.007	0.002	30.139	0.361	0.361	0.000	0.000	0.000	0.000
106	A	135	LYS	1	0.903	0.952	29.999	-7.899	-7.899	0.000	0.000	0.000	0.000
107	A	136	VAL	0	0.005	0.007	28.295	0.189	0.189	0.000	0.000	0.000	0.000
108	A	137	PHE	0	-0.001	-0.003	23.107	0.254	0.254	0.000	0.000	0.000	0.000
109	A	138	ILE	0	0.015	0.001	25.279	0.388	0.388	0.000	0.000	0.000	0.000
110	A	139	SER	0	-0.023	-0.020	26.017	0.172	0.172	0.000	0.000	0.000	0.000
111	A	140	GLY	0	0.008	0.006	25.104	0.123	0.123	0.000	0.000	0.000	0.000
112	A	141	LEU	0	-0.016	-0.016	20.001	0.470	0.470	0.000	0.000	0.000	0.000
113	A	142	PHE	0	-0.007	-0.005	21.029	0.456	0.456	0.000	0.000	0.000	0.000
114	A	143	ASN	0	-0.018	0.012	23.149	-0.028	-0.028	0.000	0.000	0.000	0.000
115	A	144	VAL	0	-0.044	-0.025	17.497	-0.057	-0.057	0.000	0.000	0.000	0.000
116	A	145	PHE	0	-0.031	-0.014	18.348	-0.113	-0.113	0.000	0.000	0.000	0.000
117	A	146	LYS	1	0.955	0.985	14.893	-14.319	-14.319	0.000	0.000	0.000	0.000
118	A	147	TYR	0	-0.029	-0.017	7.385	-1.146	-1.146	0.000	0.000	0.000	0.000
119	A	148	GLU	-1	-0.840	-0.913	12.066	17.291	17.291	0.000	0.000	0.000	0.000
120	A	149	GLY	0	-0.023	-0.025	11.756	-1.266	-1.266	0.000	0.000	0.000	0.000
121	A	150	ASP	-1	-0.789	-0.880	10.044	20.912	20.912	0.000	0.000	0.000	0.000
122	A	151	VAL	0	0.017	0.010	9.526	-0.274	-0.274	0.000	0.000	0.000	0.000
123	A	152	HIS	1	0.852	0.923	11.492	-18.180	-18.180	0.000	0.000	0.000	0.000
124	A	153	ASN	0	-0.042	-0.028	14.380	-1.978	-1.978	0.000	0.000	0.000	0.000
125	A	154	LEU	0	0.047	0.038	12.479	1.171	1.171	0.000	0.000	0.000	0.000
126	A	155	THR	0	-0.046	-0.024	15.227	-1.607	-1.607	0.000	0.000	0.000	0.000
127	A	156	LEU	0	0.017	0.008	15.057	0.764	0.764	0.000	0.000	0.000	0.000
128	A	157	TYR	0	-0.036	-0.028	17.333	-1.287	-1.287	0.000	0.000	0.000	0.000
129	A	158	PHE	0	0.021	0.005	19.586	0.201	0.201	0.000	0.000	0.000	0.000
130	A	159	LYS	1	0.957	0.981	22.346	-11.826	-11.826	0.000	0.000	0.000	0.000
131	A	160	ASP	-1	-0.880	-0.929	25.468	9.578	9.578	0.000	0.000	0.000	0.000
132	A	161	GLY	0	0.040	0.024	28.847	-0.292	-0.292	0.000	0.000	0.000	0.000
133	A	162	ASN	0	-0.016	-0.022	29.868	0.301	0.301	0.000	0.000	0.000	0.000
134	A	163	THR	0	-0.081	-0.039	29.625	0.108	0.108	0.000	0.000	0.000	0.000
135	A	164	THR	0	0.040	0.012	23.269	0.176	0.176	0.000	0.000	0.000	0.000
136	A	165	LYS	1	0.838	0.928	25.114	-9.927	-9.927	0.000	0.000	0.000	0.000
137	A	166	VAL	0	0.001	0.003	21.081	0.472	0.472	0.000	0.000	0.000	0.000
138	A	167	MET	0	-0.034	-0.006	20.963	-0.691	-0.691	0.000	0.000	0.000	0.000
139	A	168	GLY	0	-0.003	0.007	20.041	0.718	0.718	0.000	0.000	0.000	0.000
140	A	169	PHE	0	0.005	-0.020	17.824	-0.728	-0.728	0.000	0.000	0.000	0.000
141	A	170	THR	0	0.012	0.003	18.504	0.293	0.293	0.000	0.000	0.000	0.000
142	A	171	ALA	0	0.043	0.035	15.681	-0.421	-0.421	0.000	0.000	0.000	0.000
143	A	172	ARG	1	0.883	0.943	17.784	-13.682	-13.682	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:30:ASP)