FMO DATABASE

FMODB ID: 2N38R

Calculation Name: 2LIS-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2LIS

Chain ID: A

ChEMBL ID:

UniProt ID: P04552

Base Structure: X-ray

Registration Date: 2023-09-23

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	131
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1231834.485419
FMO2-HF: Nuclear repulsion	1176900.208604
FMO2-HF: Total energy	-54934.276816
FMO2-MP2: Total energy	-55093.553516

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:4:HIS)

Summations of interaction energy for fragment #1(A:4:HIS)

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.
-0.955	0.88	0.056	-0.931	-0.959	0.001

Interaction energy analysis for fragmet #1(A:4:HIS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.011 / q_NPA : -0.014

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	A	6	VAL	0	0.000	-0.006	3.253	-2.419	-0.584	0.056	-0.931	-0.959	0.001
4	A	7	GLU	-1	-0.889	-0.936	5.835	1.498	1.498	0.000	0.000	0.000	0.000
5	A	8	PRO	0	0.011	0.013	8.828	-0.233	-0.233	0.000	0.000	0.000	0.000
6	A	9	LYS	1	0.855	0.905	10.323	0.025	0.025	0.000	0.000	0.000	0.000
7	A	10	PHE	0	0.009	0.002	15.111	-0.026	-0.026	0.000	0.000	0.000	0.000
8	A	11	LEU	0	0.009	0.014	18.460	-0.008	-0.008	0.000	0.000	0.000	0.000
9	A	12	ASN	0	0.034	0.028	17.763	0.009	0.009	0.000	0.000	0.000	0.000
10	A	13	LYS	1	0.913	0.933	16.907	0.049	0.049	0.000	0.000	0.000	0.000
11	A	14	ALA	0	0.051	0.016	18.838	0.004	0.004	0.000	0.000	0.000	0.000
12	A	15	PHE	0	0.025	0.007	21.575	0.000	0.000	0.000	0.000	0.000	0.000
13	A	16	GLU	-1	-0.736	-0.823	20.512	-0.009	-0.009	0.000	0.000	0.000	0.000
14	A	17	VAL	0	-0.015	-0.008	21.854	0.005	0.005	0.000	0.000	0.000	0.000
15	A	18	ALA	0	0.002	0.002	24.434	0.004	0.004	0.000	0.000	0.000	0.000
16	A	19	LEU	0	-0.023	-0.009	25.892	0.005	0.005	0.000	0.000	0.000	0.000
17	A	20	LYS	1	0.792	0.867	22.670	0.057	0.057	0.000	0.000	0.000	0.000
18	A	21	VAL	0	-0.008	-0.003	27.602	0.001	0.001	0.000	0.000	0.000	0.000
19	A	22	GLN	0	0.028	0.010	30.011	0.007	0.007	0.000	0.000	0.000	0.000
20	A	23	ILE	0	-0.021	0.002	30.347	0.004	0.004	0.000	0.000	0.000	0.000
21	A	24	ILE	0	0.019	0.011	29.809	0.002	0.002	0.000	0.000	0.000	0.000
22	A	25	ALA	0	0.004	0.007	33.731	0.001	0.001	0.000	0.000	0.000	0.000
23	A	26	GLY	0	-0.057	-0.027	35.719	0.001	0.001	0.000	0.000	0.000	0.000
24	A	27	PHE	0	0.038	0.006	35.124	0.001	0.001	0.000	0.000	0.000	0.000
25	A	28	ASP	-1	-0.746	-0.845	36.374	-0.046	-0.046	0.000	0.000	0.000	0.000
26	A	29	ARG	1	0.861	0.935	36.356	0.050	0.050	0.000	0.000	0.000	0.000
27	A	30	GLY	0	-0.003	0.007	41.461	0.001	0.001	0.000	0.000	0.000	0.000
28	A	31	LEU	0	0.002	0.003	40.915	0.001	0.001	0.000	0.000	0.000	0.000
29	A	32	VAL	0	-0.012	-0.009	42.459	0.000	0.000	0.000	0.000	0.000	0.000
30	A	33	LYS	1	0.941	0.966	44.970	0.028	0.028	0.000	0.000	0.000	0.000
31	A	34	TRP	0	-0.005	-0.009	46.748	-0.001	-0.001	0.000	0.000	0.000	0.000
32	A	35	LEU	0	-0.011	-0.008	44.682	0.001	0.001	0.000	0.000	0.000	0.000
33	A	36	ARG	1	0.905	0.955	48.613	0.031	0.031	0.000	0.000	0.000	0.000
34	A	37	VAL	0	-0.004	0.015	51.104	0.000	0.000	0.000	0.000	0.000	0.000
35	A	38	HIS	0	0.077	0.026	50.727	0.000	0.000	0.000	0.000	0.000	0.000
36	A	39	GLY	0	0.031	0.026	49.787	0.000	0.000	0.000	0.000	0.000	0.000
37	A	40	ARG	1	0.925	0.956	50.639	0.027	0.027	0.000	0.000	0.000	0.000
38	A	41	THR	0	-0.037	-0.021	52.938	0.001	0.001	0.000	0.000	0.000	0.000
39	A	42	LEU	0	0.018	0.024	47.732	0.002	0.002	0.000	0.000	0.000	0.000
40	A	43	SER	0	0.050	-0.008	48.351	-0.004	-0.004	0.000	0.000	0.000	0.000
41	A	44	THR	0	0.010	-0.025	44.227	0.002	0.002	0.000	0.000	0.000	0.000
42	A	45	VAL	0	0.041	0.020	43.301	-0.002	-0.002	0.000	0.000	0.000	0.000
43	A	46	GLN	0	0.095	0.077	43.151	-0.001	-0.001	0.000	0.000	0.000	0.000
44	A	47	LYS	1	0.869	0.936	44.135	0.036	0.036	0.000	0.000	0.000	0.000
45	A	48	LYS	1	0.884	0.918	38.331	0.062	0.062	0.000	0.000	0.000	0.000
46	A	49	ALA	0	0.031	0.015	39.281	0.000	0.000	0.000	0.000	0.000	0.000
47	A	50	LEU	0	0.010	0.015	39.821	0.003	0.003	0.000	0.000	0.000	0.000
48	A	51	TYR	0	0.003	0.003	37.530	0.002	0.002	0.000	0.000	0.000	0.000
49	A	52	PHE	0	0.014	0.016	33.302	0.000	0.000	0.000	0.000	0.000	0.000
50	A	53	VAL	0	0.019	0.010	35.423	0.005	0.005	0.000	0.000	0.000	0.000
51	A	54	ASN	0	-0.003	0.014	36.560	0.010	0.010	0.000	0.000	0.000	0.000
52	A	55	ARG	1	0.816	0.884	31.595	0.056	0.056	0.000	0.000	0.000	0.000
53	A	56	ARG	1	0.896	0.946	30.338	-0.010	-0.010	0.000	0.000	0.000	0.000
54	A	57	TYR	0	0.051	0.026	33.435	0.012	0.012	0.000	0.000	0.000	0.000
55	A	58	MET	0	0.008	0.017	28.195	0.004	0.004	0.000	0.000	0.000	0.000
56	A	59	GLN	0	-0.029	-0.017	27.053	0.011	0.011	0.000	0.000	0.000	0.000
57	A	60	THR	0	-0.053	-0.040	29.708	0.011	0.011	0.000	0.000	0.000	0.000
58	A	61	HIS	1	0.883	0.950	32.203	-0.034	-0.034	0.000	0.000	0.000	0.000
59	A	62	TRP	0	0.005	0.012	24.173	-0.008	-0.008	0.000	0.000	0.000	0.000
60	A	63	ALA	0	0.043	0.013	28.313	0.001	0.001	0.000	0.000	0.000	0.000
61	A	64	ASN	0	0.005	0.007	29.210	-0.001	-0.001	0.000	0.000	0.000	0.000
62	A	65	TYR	0	0.035	0.005	30.711	-0.002	-0.002	0.000	0.000	0.000	0.000
63	A	66	MET	0	0.019	0.007	24.761	-0.008	-0.008	0.000	0.000	0.000	0.000
64	A	67	LEU	0	0.010	0.026	28.877	0.002	0.002	0.000	0.000	0.000	0.000
65	A	68	TRP	0	0.011	0.000	31.250	-0.003	-0.003	0.000	0.000	0.000	0.000
66	A	69	ILE	0	-0.010	-0.017	28.294	-0.005	-0.005	0.000	0.000	0.000	0.000
67	A	70	ASN	0	0.019	0.003	25.901	-0.015	-0.015	0.000	0.000	0.000	0.000
68	A	71	LYS	1	0.883	0.932	29.663	-0.087	-0.087	0.000	0.000	0.000	0.000
69	A	72	LYS	1	0.813	0.902	33.175	-0.018	-0.018	0.000	0.000	0.000	0.000
70	A	73	ILE	0	-0.038	-0.030	27.406	-0.007	-0.007	0.000	0.000	0.000	0.000
71	A	74	ASP	-1	-0.820	-0.895	30.132	0.084	0.084	0.000	0.000	0.000	0.000
72	A	75	ALA	0	-0.036	-0.016	31.957	0.000	0.000	0.000	0.000	0.000	0.000
73	A	76	LEU	0	-0.086	-0.035	30.600	-0.007	-0.007	0.000	0.000	0.000	0.000
74	A	77	GLY	0	0.024	0.023	34.071	-0.006	-0.006	0.000	0.000	0.000	0.000
75	A	78	ARG	1	0.810	0.882	30.355	0.011	0.011	0.000	0.000	0.000	0.000
76	A	79	THR	0	0.047	0.022	24.853	0.010	0.010	0.000	0.000	0.000	0.000
77	A	80	PRO	0	-0.008	0.021	25.365	-0.012	-0.012	0.000	0.000	0.000	0.000
78	A	81	VAL	0	0.041	0.008	26.016	-0.012	-0.012	0.000	0.000	0.000	0.000
79	A	82	VAL	0	0.053	0.013	25.016	0.010	0.010	0.000	0.000	0.000	0.000
80	A	83	GLY	0	0.042	0.038	26.735	0.004	0.004	0.000	0.000	0.000	0.000
81	A	84	ASP	-1	-0.727	-0.826	29.538	-0.017	-0.017	0.000	0.000	0.000	0.000
82	A	85	TYR	0	0.064	0.016	25.572	0.003	0.003	0.000	0.000	0.000	0.000
83	A	86	THR	0	-0.034	-0.028	29.087	-0.001	-0.001	0.000	0.000	0.000	0.000
84	A	87	ARG	1	0.865	0.924	31.006	0.025	0.025	0.000	0.000	0.000	0.000
85	A	88	LEU	0	0.010	0.004	30.844	0.003	0.003	0.000	0.000	0.000	0.000
86	A	89	GLY	0	0.035	0.016	31.691	0.005	0.005	0.000	0.000	0.000	0.000
87	A	90	ALA	0	0.014	0.001	32.482	0.001	0.001	0.000	0.000	0.000	0.000
88	A	91	GLU	-1	-0.855	-0.900	35.703	0.007	0.007	0.000	0.000	0.000	0.000
89	A	92	ILE	0	0.025	0.000	32.709	0.002	0.002	0.000	0.000	0.000	0.000
90	A	93	GLY	0	-0.008	-0.007	35.810	0.002	0.002	0.000	0.000	0.000	0.000
91	A	94	ARG	1	0.844	0.924	37.105	0.015	0.015	0.000	0.000	0.000	0.000
92	A	95	ARG	1	0.898	0.941	39.810	-0.012	-0.012	0.000	0.000	0.000	0.000
93	A	96	ILE	0	-0.036	0.000	38.036	0.004	0.004	0.000	0.000	0.000	0.000
94	A	97	ASP	-1	-0.817	-0.912	41.271	-0.007	-0.007	0.000	0.000	0.000	0.000
95	A	98	MET	0	-0.038	-0.026	38.872	0.004	0.004	0.000	0.000	0.000	0.000
96	A	99	ALA	0	-0.010	0.006	43.168	0.000	0.000	0.000	0.000	0.000	0.000
97	A	100	TYR	0	0.045	0.034	46.728	0.001	0.001	0.000	0.000	0.000	0.000
98	A	101	PHE	0	0.000	-0.004	40.186	0.002	0.002	0.000	0.000	0.000	0.000
99	A	102	TYR	0	0.008	-0.037	40.804	-0.001	-0.001	0.000	0.000	0.000	0.000
100	A	103	ASP	-1	-0.742	-0.856	46.377	-0.008	-0.008	0.000	0.000	0.000	0.000
101	A	104	PHE	0	-0.030	-0.004	46.693	0.001	0.001	0.000	0.000	0.000	0.000
102	A	105	LEU	0	-0.024	-0.027	43.088	0.000	0.000	0.000	0.000	0.000	0.000
103	A	106	LYS	1	0.793	0.880	47.743	0.007	0.007	0.000	0.000	0.000	0.000
104	A	107	ASP	-1	-0.830	-0.900	50.589	-0.001	-0.001	0.000	0.000	0.000	0.000
105	A	108	LYS	1	0.849	0.925	50.934	-0.006	-0.006	0.000	0.000	0.000	0.000
106	A	109	ASN	0	-0.053	-0.022	51.204	0.000	0.000	0.000	0.000	0.000	0.000
107	A	110	MET	0	0.026	0.019	45.923	0.000	0.000	0.000	0.000	0.000	0.000
108	A	111	ILE	0	-0.059	-0.020	44.482	0.000	0.000	0.000	0.000	0.000	0.000
109	A	112	PRO	0	-0.017	-0.006	40.633	0.000	0.000	0.000	0.000	0.000	0.000
110	A	113	LYS	1	0.968	0.979	42.956	0.006	0.006	0.000	0.000	0.000	0.000
111	A	114	TYR	0	-0.010	-0.035	37.548	0.003	0.003	0.000	0.000	0.000	0.000
112	A	115	LEU	0	0.050	0.019	37.239	0.000	0.000	0.000	0.000	0.000	0.000
113	A	116	PRO	0	0.053	0.021	34.550	-0.002	-0.002	0.000	0.000	0.000	0.000
114	A	117	TYR	0	0.086	0.037	31.233	-0.005	-0.005	0.000	0.000	0.000	0.000
115	A	118	MET	0	-0.049	-0.002	32.141	-0.001	-0.001	0.000	0.000	0.000	0.000
116	A	119	GLU	-1	-0.749	-0.810	34.470	-0.071	-0.071	0.000	0.000	0.000	0.000
117	A	120	GLU	-1	-0.924	-0.965	27.219	-0.058	-0.058	0.000	0.000	0.000	0.000
118	A	121	ILE	0	-0.005	-0.022	28.937	-0.007	-0.007	0.000	0.000	0.000	0.000
119	A	122	ASN	0	-0.054	-0.058	30.665	-0.002	-0.002	0.000	0.000	0.000	0.000
120	A	123	ARG	1	0.820	0.913	31.120	0.089	0.089	0.000	0.000	0.000	0.000
121	A	124	MET	0	-0.019	0.019	25.980	-0.009	-0.009	0.000	0.000	0.000	0.000
122	A	125	ARG	1	0.879	0.907	22.094	0.210	0.210	0.000	0.000	0.000	0.000
123	A	126	PRO	0	0.015	-0.006	27.044	0.005	0.005	0.000	0.000	0.000	0.000
124	A	127	ALA	0	0.008	-0.001	23.841	0.011	0.011	0.000	0.000	0.000	0.000
125	A	128	ASP	-1	-0.767	-0.846	22.538	-0.170	-0.170	0.000	0.000	0.000	0.000
126	A	129	VAL	0	-0.015	0.003	23.183	0.015	0.015	0.000	0.000	0.000	0.000
127	A	130	PRO	0	0.037	0.035	22.424	0.006	0.006	0.000	0.000	0.000	0.000
128	A	131	VAL	0	-0.004	-0.006	22.817	0.003	0.003	0.000	0.000	0.000	0.000
129	A	132	LYS	1	0.901	0.929	22.226	-0.189	-0.189	0.000	0.000	0.000	0.000
130	A	133	TYR	0	0.022	-0.009	20.265	-0.006	-0.006	0.000	0.000	0.000	0.000
131	A	134	MET	0	0.101	0.073	23.452	0.021	0.021	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:4:HIS)