FMO DATABASE

FMODB ID: 6NQ2Z

Calculation Name: 3L1P-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3L1P

Chain ID: A

ChEMBL ID:

UniProt ID: P20263

Base Structure: X-ray

Registration Date: 2023-09-20

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	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	150
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1330420.627882
FMO2-HF: Nuclear repulsion	1269919.554486
FMO2-HF: Total energy	-60501.073396
FMO2-MP2: Total energy	-60680.270113

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:1:ASP)

Summations of interaction energy for fragment #1(A:1: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.
-353.477	-353.296	29.318	-13.894	-15.604	0.168

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.753 / q_NPA : -0.889

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	3	LYS	1	0.908	0.929	1.803	-76.587	-76.565	12.906	-6.784	-6.143	0.069
4	A	4	ALA	0	-0.019	-0.013	2.306	-11.617	-10.678	7.204	-2.872	-5.272	0.034
5	A	5	LEU	0	0.035	0.035	3.435	-13.577	-12.960	0.190	-0.104	-0.702	0.008
6	A	6	GLN	0	0.011	-0.005	6.483	-1.908	-1.908	0.000	0.000	0.000	0.000
7	A	7	LYS	1	0.935	0.983	1.857	-112.485	-113.882	9.018	-4.134	-3.487	0.057
8	A	8	GLU	-1	-0.818	-0.882	7.573	22.806	22.806	0.000	0.000	0.000	0.000
9	A	9	LEU	0	-0.041	-0.045	9.739	-3.185	-3.185	0.000	0.000	0.000	0.000
10	A	10	GLU	-1	-0.821	-0.901	10.964	19.254	19.254	0.000	0.000	0.000	0.000
11	A	11	GLN	0	0.003	0.012	11.958	-1.596	-1.596	0.000	0.000	0.000	0.000
12	A	12	PHE	0	0.044	0.025	13.738	-1.609	-1.609	0.000	0.000	0.000	0.000
13	A	13	ALA	0	-0.003	-0.008	15.481	-1.396	-1.396	0.000	0.000	0.000	0.000
14	A	14	LYS	1	0.798	0.892	14.234	-22.098	-22.098	0.000	0.000	0.000	0.000
15	A	15	LEU	0	0.024	0.018	17.979	-0.946	-0.946	0.000	0.000	0.000	0.000
16	A	16	LEU	0	-0.021	-0.006	19.675	-0.823	-0.823	0.000	0.000	0.000	0.000
17	A	17	LYS	1	0.934	0.969	21.018	-15.733	-15.733	0.000	0.000	0.000	0.000
18	A	18	GLN	0	0.007	0.004	22.507	-0.313	-0.313	0.000	0.000	0.000	0.000
19	A	19	LYS	1	0.811	0.901	23.714	-13.052	-13.052	0.000	0.000	0.000	0.000
20	A	20	ARG	1	0.787	0.852	25.618	-12.476	-12.476	0.000	0.000	0.000	0.000
21	A	21	ILE	0	-0.057	-0.032	26.709	-0.406	-0.406	0.000	0.000	0.000	0.000
22	A	22	THR	0	-0.034	-0.020	27.791	-0.389	-0.389	0.000	0.000	0.000	0.000
23	A	23	LEU	0	0.002	0.005	28.758	-0.227	-0.227	0.000	0.000	0.000	0.000
24	A	24	GLY	0	0.008	0.025	31.823	-0.283	-0.283	0.000	0.000	0.000	0.000
25	A	25	TYR	0	0.013	0.029	30.645	-0.100	-0.100	0.000	0.000	0.000	0.000
26	A	26	THR	0	-0.001	-0.052	30.957	0.433	0.433	0.000	0.000	0.000	0.000
27	A	27	GLN	0	-0.045	-0.055	25.845	-0.108	-0.108	0.000	0.000	0.000	0.000
28	A	28	ALA	0	-0.045	-0.029	29.607	0.169	0.169	0.000	0.000	0.000	0.000
29	A	29	ASP	-1	-0.721	-0.820	32.414	9.383	9.383	0.000	0.000	0.000	0.000
30	A	30	VAL	0	0.037	0.033	26.130	0.013	0.013	0.000	0.000	0.000	0.000
31	A	31	GLY	0	-0.012	-0.019	28.221	0.087	0.087	0.000	0.000	0.000	0.000
32	A	32	LEU	0	0.018	-0.004	29.212	-0.015	-0.015	0.000	0.000	0.000	0.000
33	A	33	THR	0	0.053	0.010	31.055	-0.081	-0.081	0.000	0.000	0.000	0.000
34	A	34	LEU	0	0.016	0.029	25.151	0.157	0.157	0.000	0.000	0.000	0.000
35	A	35	GLY	0	-0.074	-0.044	28.823	-0.095	-0.095	0.000	0.000	0.000	0.000
36	A	36	VAL	0	-0.043	-0.020	31.720	-0.126	-0.126	0.000	0.000	0.000	0.000
37	A	37	LEU	0	0.077	0.066	28.630	-0.134	-0.134	0.000	0.000	0.000	0.000
38	A	38	PHE	0	0.038	0.002	25.701	0.072	0.072	0.000	0.000	0.000	0.000
39	A	39	GLY	0	0.005	0.016	28.967	-0.014	-0.014	0.000	0.000	0.000	0.000
40	A	40	LYS	1	0.743	0.847	26.960	-11.036	-11.036	0.000	0.000	0.000	0.000
41	A	41	VAL	0	0.053	0.044	28.973	0.285	0.285	0.000	0.000	0.000	0.000
42	A	42	PHE	0	-0.104	-0.052	25.036	0.233	0.233	0.000	0.000	0.000	0.000
43	A	43	SER	0	-0.033	-0.015	28.863	-0.217	-0.217	0.000	0.000	0.000	0.000
44	A	44	GLN	0	0.172	0.064	28.636	0.495	0.495	0.000	0.000	0.000	0.000
45	A	45	THR	0	0.017	0.010	27.358	0.345	0.345	0.000	0.000	0.000	0.000
46	A	46	THR	0	-0.093	-0.044	24.100	0.258	0.258	0.000	0.000	0.000	0.000
47	A	47	ILE	0	0.098	0.053	24.022	0.707	0.707	0.000	0.000	0.000	0.000
48	A	48	SER	0	0.017	0.014	23.593	0.702	0.702	0.000	0.000	0.000	0.000
49	A	49	ARG	1	0.914	0.943	21.975	-12.431	-12.431	0.000	0.000	0.000	0.000
50	A	50	PHE	0	-0.005	-0.016	17.473	0.846	0.846	0.000	0.000	0.000	0.000
51	A	51	GLU	-1	-0.705	-0.820	18.744	14.153	14.153	0.000	0.000	0.000	0.000
52	A	52	ALA	0	-0.054	-0.015	19.437	0.315	0.315	0.000	0.000	0.000	0.000
53	A	53	LEU	0	-0.009	0.007	12.739	0.747	0.747	0.000	0.000	0.000	0.000
54	A	54	GLN	0	0.016	0.006	16.505	0.473	0.473	0.000	0.000	0.000	0.000
55	A	55	LEU	0	-0.111	-0.044	18.135	-0.757	-0.757	0.000	0.000	0.000	0.000
56	A	56	SER	0	0.033	0.007	15.894	1.157	1.157	0.000	0.000	0.000	0.000
57	A	57	LEU	0	0.121	0.040	8.773	-0.864	-0.864	0.000	0.000	0.000	0.000
58	A	58	LYS	1	0.970	0.998	13.022	-19.183	-19.183	0.000	0.000	0.000	0.000
59	A	59	ASN	0	-0.030	-0.051	14.574	-0.993	-0.993	0.000	0.000	0.000	0.000
60	A	60	MET	0	0.026	0.041	14.141	-1.188	-1.188	0.000	0.000	0.000	0.000
61	A	61	SER	0	0.055	0.018	12.145	-0.069	-0.069	0.000	0.000	0.000	0.000
62	A	62	LYS	1	0.854	0.943	14.387	-15.637	-15.637	0.000	0.000	0.000	0.000
63	A	63	LEU	0	-0.036	-0.017	17.733	-0.696	-0.696	0.000	0.000	0.000	0.000
64	A	64	ARG	1	0.783	0.863	11.247	-22.528	-22.528	0.000	0.000	0.000	0.000
65	A	65	PRO	0	0.015	0.026	16.343	-0.409	-0.409	0.000	0.000	0.000	0.000
66	A	66	LEU	0	-0.057	-0.022	18.745	-0.634	-0.634	0.000	0.000	0.000	0.000
67	A	67	LEU	0	-0.010	-0.012	20.018	-0.519	-0.519	0.000	0.000	0.000	0.000
68	A	68	GLU	-1	-0.786	-0.886	16.163	18.412	18.412	0.000	0.000	0.000	0.000
69	A	69	LYS	1	0.836	0.888	20.424	-13.497	-13.497	0.000	0.000	0.000	0.000
70	A	70	TRP	0	-0.008	0.005	23.520	-0.212	-0.212	0.000	0.000	0.000	0.000
71	A	71	VAL	0	-0.011	-0.017	22.204	-0.291	-0.291	0.000	0.000	0.000	0.000
72	A	72	GLU	-1	-0.817	-0.884	22.003	13.087	13.087	0.000	0.000	0.000	0.000
73	A	73	GLU	-1	-0.920	-0.951	25.414	9.870	9.870	0.000	0.000	0.000	0.000
74	A	74	ALA	0	-0.055	-0.041	28.209	-0.375	-0.375	0.000	0.000	0.000	0.000
75	A	75	ASP	-1	-0.765	-0.857	26.618	11.748	11.748	0.000	0.000	0.000	0.000
76	A	76	ASN	0	-0.079	-0.031	29.946	-0.197	-0.197	0.000	0.000	0.000	0.000
77	A	77	ASN	0	-0.009	-0.007	32.413	-0.485	-0.485	0.000	0.000	0.000	0.000
78	A	78	GLU	-1	-0.923	-0.968	33.394	9.277	9.277	0.000	0.000	0.000	0.000
79	A	79	ASN	0	-0.019	-0.018	35.305	-0.202	-0.202	0.000	0.000	0.000	0.000
80	A	80	LEU	0	0.048	0.005	37.910	-0.129	-0.129	0.000	0.000	0.000	0.000
81	A	81	GLN	0	-0.098	-0.046	31.177	0.174	0.174	0.000	0.000	0.000	0.000
82	A	82	GLU	-1	-0.901	-0.943	36.052	8.224	8.224	0.000	0.000	0.000	0.000
83	A	83	ILE	0	-0.018	0.001	38.266	-0.186	-0.186	0.000	0.000	0.000	0.000
84	A	84	SER	0	-0.094	-0.022	38.359	-0.157	-0.157	0.000	0.000	0.000	0.000
85	A	85	LYS	1	0.736	0.867	36.873	-8.542	-8.542	0.000	0.000	0.000	0.000
86	A	86	SER	0	0.130	0.053	39.735	0.126	0.126	0.000	0.000	0.000	0.000
87	A	87	GLU	-1	-0.843	-0.862	41.405	7.116	7.116	0.000	0.000	0.000	0.000
88	A	88	THR	0	-0.120	-0.115	39.898	0.262	0.262	0.000	0.000	0.000	0.000
89	A	89	LEU	0	0.044	0.030	39.954	0.205	0.205	0.000	0.000	0.000	0.000
90	A	90	VAL	0	0.074	0.045	38.073	0.165	0.165	0.000	0.000	0.000	0.000
91	A	91	GLN	0	0.023	0.007	37.857	0.281	0.281	0.000	0.000	0.000	0.000
92	A	92	ALA	0	0.021	0.005	34.918	-0.193	-0.193	0.000	0.000	0.000	0.000
93	A	93	ARG	1	0.958	0.994	33.900	-8.651	-8.651	0.000	0.000	0.000	0.000
94	A	94	LYS	1	0.952	0.953	30.550	-9.560	-9.560	0.000	0.000	0.000	0.000
95	A	95	ARG	1	1.004	0.991	28.627	-10.804	-10.804	0.000	0.000	0.000	0.000
96	A	96	LYS	1	0.907	0.972	34.489	-8.066	-8.066	0.000	0.000	0.000	0.000
97	A	97	ARG	1	0.981	0.980	33.904	-9.237	-9.237	0.000	0.000	0.000	0.000
98	A	98	THR	0	0.033	0.020	37.220	-0.017	-0.017	0.000	0.000	0.000	0.000
99	A	99	SER	0	-0.023	0.004	40.042	0.168	0.168	0.000	0.000	0.000	0.000
100	A	100	ILE	0	0.022	0.015	41.326	-0.137	-0.137	0.000	0.000	0.000	0.000
101	A	101	GLU	-1	-0.717	-0.821	43.909	6.711	6.711	0.000	0.000	0.000	0.000
102	A	102	ASN	0	0.041	0.007	44.919	0.218	0.218	0.000	0.000	0.000	0.000
103	A	103	ARG	1	0.935	0.925	46.796	-6.249	-6.249	0.000	0.000	0.000	0.000
104	A	104	VAL	0	0.040	0.045	46.622	-0.022	-0.022	0.000	0.000	0.000	0.000
105	A	105	ARG	1	0.893	0.939	40.969	-7.705	-7.705	0.000	0.000	0.000	0.000
106	A	106	TRP	0	0.031	0.026	45.391	0.122	0.122	0.000	0.000	0.000	0.000
107	A	107	SER	0	0.007	-0.022	47.463	-0.014	-0.014	0.000	0.000	0.000	0.000
108	A	108	LEU	0	-0.058	-0.030	44.418	-0.045	-0.045	0.000	0.000	0.000	0.000
109	A	109	GLU	-1	-0.854	-0.927	42.949	7.709	7.709	0.000	0.000	0.000	0.000
110	A	110	THR	0	0.112	0.071	45.809	-0.063	-0.063	0.000	0.000	0.000	0.000
111	A	111	MET	0	-0.090	-0.026	47.694	-0.101	-0.101	0.000	0.000	0.000	0.000
112	A	112	PHE	0	-0.133	-0.072	41.008	0.179	0.179	0.000	0.000	0.000	0.000
113	A	113	LEU	0	0.047	0.030	43.515	0.021	0.021	0.000	0.000	0.000	0.000
114	A	114	LYS	1	1.003	1.000	46.542	-6.258	-6.258	0.000	0.000	0.000	0.000
115	A	115	SER	0	-0.006	-0.019	48.062	-0.087	-0.087	0.000	0.000	0.000	0.000
116	A	116	PRO	0	0.058	0.031	42.464	0.069	0.069	0.000	0.000	0.000	0.000
117	A	117	LYS	1	0.915	0.950	40.846	-7.550	-7.550	0.000	0.000	0.000	0.000
118	A	118	PRO	0	-0.010	0.010	44.533	-0.081	-0.081	0.000	0.000	0.000	0.000
119	A	119	SER	0	0.077	0.038	46.151	-0.067	-0.067	0.000	0.000	0.000	0.000
120	A	120	LEU	0	0.022	0.002	47.500	-0.035	-0.035	0.000	0.000	0.000	0.000
121	A	121	GLN	0	0.085	0.046	48.911	0.084	0.084	0.000	0.000	0.000	0.000
122	A	122	GLN	0	0.051	0.016	49.888	-0.128	-0.128	0.000	0.000	0.000	0.000
123	A	123	ILE	0	-0.098	-0.053	45.115	0.050	0.050	0.000	0.000	0.000	0.000
124	A	124	THR	0	-0.003	0.008	48.609	0.053	0.053	0.000	0.000	0.000	0.000
125	A	125	HIS	0	0.039	0.014	51.440	0.007	0.007	0.000	0.000	0.000	0.000
126	A	126	ILE	0	0.012	-0.001	48.746	-0.014	-0.014	0.000	0.000	0.000	0.000
127	A	127	ALA	0	-0.039	-0.009	48.599	0.035	0.035	0.000	0.000	0.000	0.000
128	A	128	ASN	0	0.020	0.004	49.942	0.002	0.002	0.000	0.000	0.000	0.000
129	A	129	GLN	0	0.007	0.024	53.195	-0.018	-0.018	0.000	0.000	0.000	0.000
130	A	130	LEU	0	-0.051	-0.030	49.276	-0.030	-0.030	0.000	0.000	0.000	0.000
131	A	131	GLY	0	0.032	0.033	50.719	0.089	0.089	0.000	0.000	0.000	0.000
132	A	132	LEU	0	-0.079	-0.044	45.506	0.189	0.189	0.000	0.000	0.000	0.000
133	A	133	GLU	-1	-0.813	-0.903	44.472	6.776	6.776	0.000	0.000	0.000	0.000
134	A	134	LYS	1	0.944	0.945	45.451	-6.711	-6.711	0.000	0.000	0.000	0.000
135	A	135	ASP	-1	-0.832	-0.915	40.969	7.560	7.560	0.000	0.000	0.000	0.000
136	A	136	VAL	0	0.013	0.003	40.932	0.210	0.210	0.000	0.000	0.000	0.000
137	A	137	VAL	0	0.070	0.046	41.477	0.202	0.202	0.000	0.000	0.000	0.000
138	A	138	ARG	1	0.894	0.946	40.142	-7.562	-7.562	0.000	0.000	0.000	0.000
139	A	139	VAL	0	0.022	0.011	36.268	0.191	0.191	0.000	0.000	0.000	0.000
140	A	140	TRP	0	0.001	0.016	38.034	0.297	0.297	0.000	0.000	0.000	0.000
141	A	141	PHE	0	0.057	0.007	39.353	0.176	0.176	0.000	0.000	0.000	0.000
142	A	142	SER	0	-0.087	-0.045	36.464	0.044	0.044	0.000	0.000	0.000	0.000
143	A	143	ASN	0	-0.046	-0.036	33.636	0.430	0.430	0.000	0.000	0.000	0.000
144	A	144	ARG	1	0.777	0.882	35.394	-7.782	-7.782	0.000	0.000	0.000	0.000
145	A	145	ARG	1	0.914	0.947	37.673	-8.098	-8.098	0.000	0.000	0.000	0.000
146	A	146	GLN	0	-0.021	-0.012	30.640	-0.063	-0.063	0.000	0.000	0.000	0.000
147	A	147	LYS	1	0.926	0.963	33.108	-8.903	-8.903	0.000	0.000	0.000	0.000
148	A	148	GLY	0	0.050	0.036	34.365	0.029	0.029	0.000	0.000	0.000	0.000
149	A	149	LYS	1	0.953	1.002	32.464	-9.648	-9.648	0.000	0.000	0.000	0.000
150	A	150	ARG	1	0.899	0.947	28.717	-10.423	-10.423	0.000	0.000	0.000	0.000

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