FMO DATABASE

FMODB ID: ZVK8N

Calculation Name: 1LMI-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1LMI

Chain ID: A

ChEMBL ID:

UniProt ID: P9WIP1

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1037168.420032
FMO2-HF: Nuclear repulsion	989097.394251
FMO2-HF: Total energy	-48071.025782
FMO2-MP2: Total energy	-48212.095431

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:SER)

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

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.
-41.784	-39.644	15.966	-10.048	-8.059	-0.044

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.053 / q_NPA : -0.056

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	TYR	0	-0.081	-0.002	2.250	-8.527	-3.728	2.723	-3.435	-4.088	0.033
4	A	4	PRO	0	0.006	-0.008	3.489	-3.076	-2.582	0.023	-0.268	-0.250	-0.001
5	A	5	ILE	0	-0.004	-0.002	6.597	0.301	0.301	0.000	0.000	0.000	0.000
6	A	6	THR	0	0.025	0.005	9.575	-0.191	-0.191	0.000	0.000	0.000	0.000
7	A	7	GLY	0	-0.006	-0.003	12.588	0.139	0.139	0.000	0.000	0.000	0.000
8	A	8	LYS	1	0.946	0.980	16.247	0.077	0.077	0.000	0.000	0.000	0.000
9	A	9	LEU	0	0.033	0.011	19.619	0.017	0.017	0.000	0.000	0.000	0.000
10	A	10	GLY	0	-0.037	-0.031	21.228	0.026	0.026	0.000	0.000	0.000	0.000
11	A	11	SER	0	-0.073	-0.039	19.220	0.039	0.039	0.000	0.000	0.000	0.000
12	A	12	GLU	-1	-0.855	-0.937	18.814	-0.076	-0.076	0.000	0.000	0.000	0.000
13	A	13	LEU	0	-0.030	0.005	13.386	0.046	0.046	0.000	0.000	0.000	0.000
14	A	14	THR	0	0.000	-0.012	14.766	-0.033	-0.033	0.000	0.000	0.000	0.000
15	A	15	MET	0	0.006	0.012	9.280	-0.029	-0.029	0.000	0.000	0.000	0.000
16	A	16	THR	0	-0.010	-0.015	10.970	-0.115	-0.115	0.000	0.000	0.000	0.000
17	A	17	ASP	-1	-0.829	-0.924	10.285	0.303	0.303	0.000	0.000	0.000	0.000
18	A	18	THR	0	-0.016	-0.021	11.648	-0.083	-0.083	0.000	0.000	0.000	0.000
19	A	19	VAL	0	-0.046	-0.022	10.850	-0.012	-0.012	0.000	0.000	0.000	0.000
20	A	20	GLY	0	0.042	0.028	13.450	-0.052	-0.052	0.000	0.000	0.000	0.000
21	A	21	GLN	0	-0.071	-0.021	15.338	0.013	0.013	0.000	0.000	0.000	0.000
22	A	22	VAL	0	0.009	0.022	14.770	-0.026	-0.026	0.000	0.000	0.000	0.000
23	A	23	VAL	0	-0.033	-0.024	14.841	0.072	0.072	0.000	0.000	0.000	0.000
24	A	24	LEU	0	-0.023	0.000	13.303	-0.045	-0.045	0.000	0.000	0.000	0.000
25	A	25	GLY	0	0.025	0.028	15.460	0.029	0.029	0.000	0.000	0.000	0.000
26	A	26	TRP	0	0.031	-0.001	14.810	-0.031	-0.031	0.000	0.000	0.000	0.000
27	A	27	LYS	1	0.934	0.980	17.525	0.128	0.128	0.000	0.000	0.000	0.000
28	A	28	VAL	0	0.052	0.035	17.927	-0.010	-0.010	0.000	0.000	0.000	0.000
29	A	29	SER	0	-0.040	-0.032	20.604	0.014	0.014	0.000	0.000	0.000	0.000
30	A	30	ASP	-1	-0.858	-0.913	23.822	-0.167	-0.167	0.000	0.000	0.000	0.000
31	A	31	LEU	0	0.013	0.011	21.717	-0.002	-0.002	0.000	0.000	0.000	0.000
32	A	32	LYS	1	0.810	0.911	25.214	0.180	0.180	0.000	0.000	0.000	0.000
33	A	33	SER	0	0.044	0.015	28.418	-0.012	-0.012	0.000	0.000	0.000	0.000
34	A	34	SER	0	-0.041	-0.056	30.162	0.015	0.015	0.000	0.000	0.000	0.000
35	A	35	THR	0	0.004	-0.010	32.064	0.001	0.001	0.000	0.000	0.000	0.000
36	A	36	ALA	0	-0.050	-0.012	32.151	0.008	0.008	0.000	0.000	0.000	0.000
37	A	37	VAL	0	0.026	0.021	34.232	-0.007	-0.007	0.000	0.000	0.000	0.000
38	A	38	ILE	0	-0.023	-0.037	29.590	0.005	0.005	0.000	0.000	0.000	0.000
39	A	39	PRO	0	0.016	-0.016	33.168	0.004	0.004	0.000	0.000	0.000	0.000
40	A	40	GLY	0	0.062	0.024	34.525	0.008	0.008	0.000	0.000	0.000	0.000
41	A	41	TYR	0	-0.081	-0.002	27.666	-0.004	-0.004	0.000	0.000	0.000	0.000
42	A	42	PRO	0	-0.012	-0.007	31.479	0.009	0.009	0.000	0.000	0.000	0.000
43	A	43	VAL	0	-0.039	-0.020	31.357	-0.013	-0.013	0.000	0.000	0.000	0.000
44	A	44	ALA	0	-0.045	-0.027	30.633	0.014	0.014	0.000	0.000	0.000	0.000
45	A	45	GLY	0	-0.031	-0.018	31.053	0.008	0.008	0.000	0.000	0.000	0.000
46	A	46	GLN	0	-0.071	-0.031	30.828	0.024	0.024	0.000	0.000	0.000	0.000
47	A	47	VAL	0	0.030	0.020	29.506	-0.021	-0.021	0.000	0.000	0.000	0.000
48	A	48	TRP	0	0.013	0.015	26.082	0.011	0.011	0.000	0.000	0.000	0.000
49	A	49	GLU	-1	-0.844	-0.911	26.416	-0.194	-0.194	0.000	0.000	0.000	0.000
50	A	50	ALA	0	0.025	0.015	22.689	-0.009	-0.009	0.000	0.000	0.000	0.000
51	A	51	THR	0	-0.024	-0.011	24.754	0.012	0.012	0.000	0.000	0.000	0.000
52	A	52	ALA	0	-0.009	-0.003	20.563	-0.007	-0.007	0.000	0.000	0.000	0.000
53	A	53	THR	0	-0.019	-0.028	21.597	0.017	0.017	0.000	0.000	0.000	0.000
54	A	54	VAL	0	-0.007	0.014	18.472	-0.010	-0.010	0.000	0.000	0.000	0.000
55	A	55	ASN	0	-0.018	-0.040	19.847	0.020	0.020	0.000	0.000	0.000	0.000
56	A	56	ALA	0	0.047	0.036	19.762	0.006	0.006	0.000	0.000	0.000	0.000
57	A	57	ILE	0	0.005	0.007	18.048	0.021	0.021	0.000	0.000	0.000	0.000
58	A	58	ARG	1	0.835	0.901	17.789	-0.251	-0.251	0.000	0.000	0.000	0.000
59	A	59	GLY	0	0.054	0.018	19.421	-0.004	-0.004	0.000	0.000	0.000	0.000
60	A	60	SER	0	-0.032	-0.018	21.771	-0.007	-0.007	0.000	0.000	0.000	0.000
61	A	61	VAL	0	0.029	0.013	17.984	-0.001	-0.001	0.000	0.000	0.000	0.000
62	A	62	THR	0	0.008	-0.005	19.612	0.009	0.009	0.000	0.000	0.000	0.000
63	A	63	PRO	0	-0.023	0.007	18.319	-0.034	-0.034	0.000	0.000	0.000	0.000
64	A	64	ALA	0	0.045	0.022	14.967	-0.003	-0.003	0.000	0.000	0.000	0.000
65	A	65	VAL	0	0.033	0.009	16.423	-0.072	-0.072	0.000	0.000	0.000	0.000
66	A	66	SER	0	0.025	0.014	18.204	-0.035	-0.035	0.000	0.000	0.000	0.000
67	A	67	GLN	0	0.034	0.008	12.039	-0.103	-0.103	0.000	0.000	0.000	0.000
68	A	68	PHE	0	-0.008	0.013	14.187	-0.117	-0.117	0.000	0.000	0.000	0.000
69	A	69	ASN	0	0.003	-0.002	14.275	0.058	0.058	0.000	0.000	0.000	0.000
70	A	70	ALA	0	0.023	0.032	17.393	0.000	0.000	0.000	0.000	0.000	0.000
71	A	71	ARG	1	0.813	0.843	11.254	1.286	1.286	0.000	0.000	0.000	0.000
72	A	72	THR	0	-0.001	-0.028	18.909	0.042	0.042	0.000	0.000	0.000	0.000
73	A	73	ALA	0	-0.018	-0.019	18.445	-0.054	-0.054	0.000	0.000	0.000	0.000
74	A	74	ASP	-1	-0.875	-0.909	17.708	-0.510	-0.510	0.000	0.000	0.000	0.000
75	A	75	GLY	0	0.017	0.011	16.618	-0.054	-0.054	0.000	0.000	0.000	0.000
76	A	76	ILE	0	-0.033	-0.003	17.253	-0.042	-0.042	0.000	0.000	0.000	0.000
77	A	77	ASN	0	-0.011	-0.008	16.125	-0.090	-0.090	0.000	0.000	0.000	0.000
78	A	78	TYR	0	0.004	-0.018	18.988	0.030	0.030	0.000	0.000	0.000	0.000
79	A	79	ARG	1	0.813	0.896	17.033	0.631	0.631	0.000	0.000	0.000	0.000
80	A	80	VAL	0	-0.025	-0.018	19.150	0.049	0.049	0.000	0.000	0.000	0.000
81	A	81	LEU	0	-0.084	-0.047	21.317	-0.004	-0.004	0.000	0.000	0.000	0.000
82	A	82	TRP	0	-0.169	-0.203	21.320	0.002	0.002	0.000	0.000	0.000	0.000
83	A	83	GLN	0	0.172	0.224	23.083	-0.037	-0.037	0.000	0.000	0.000	0.000
84	A	84	ALA	0	0.032	0.005	25.765	-0.010	-0.010	0.000	0.000	0.000	0.000
85	A	85	ALA	0	-0.008	0.000	28.630	0.013	0.013	0.000	0.000	0.000	0.000
86	A	86	GLY	0	0.042	0.020	30.150	-0.001	-0.001	0.000	0.000	0.000	0.000
87	A	87	PRO	0	-0.009	0.026	31.234	0.005	0.005	0.000	0.000	0.000	0.000
88	A	88	ASP	-1	-0.830	-0.909	31.192	-0.156	-0.156	0.000	0.000	0.000	0.000
89	A	89	THR	0	-0.021	-0.001	26.530	-0.009	-0.009	0.000	0.000	0.000	0.000
90	A	90	ILE	0	-0.061	-0.007	22.241	0.013	0.013	0.000	0.000	0.000	0.000
91	A	91	SER	0	0.021	0.007	26.260	-0.012	-0.012	0.000	0.000	0.000	0.000
92	A	92	GLY	0	0.002	-0.011	23.704	-0.011	-0.011	0.000	0.000	0.000	0.000
93	A	93	ALA	0	-0.043	-0.021	24.173	-0.001	-0.001	0.000	0.000	0.000	0.000
94	A	94	THR	0	0.005	-0.006	23.336	-0.012	-0.012	0.000	0.000	0.000	0.000
95	A	95	ILE	0	0.000	0.021	22.559	0.008	0.008	0.000	0.000	0.000	0.000
96	A	96	PRO	0	0.011	0.004	24.187	0.007	0.007	0.000	0.000	0.000	0.000
97	A	97	GLN	0	0.036	0.008	23.272	0.003	0.003	0.000	0.000	0.000	0.000
98	A	98	GLY	0	-0.056	-0.026	24.475	0.002	0.002	0.000	0.000	0.000	0.000
99	A	99	GLU	-1	-0.938	-0.955	26.093	-0.037	-0.037	0.000	0.000	0.000	0.000
100	A	100	GLN	0	-0.019	-0.033	24.483	-0.012	-0.012	0.000	0.000	0.000	0.000
101	A	101	SER	0	-0.031	0.003	24.175	0.001	0.001	0.000	0.000	0.000	0.000
102	A	102	THR	0	0.016	-0.004	24.262	-0.020	-0.020	0.000	0.000	0.000	0.000
103	A	103	GLY	0	0.039	0.023	25.788	0.009	0.009	0.000	0.000	0.000	0.000
104	A	104	LYS	1	0.822	0.920	25.656	0.151	0.151	0.000	0.000	0.000	0.000
105	A	105	ILE	0	-0.012	0.004	20.393	-0.007	-0.007	0.000	0.000	0.000	0.000
106	A	106	TYR	0	0.018	-0.036	24.424	0.006	0.006	0.000	0.000	0.000	0.000
107	A	107	PHE	0	0.027	0.012	19.856	-0.031	-0.031	0.000	0.000	0.000	0.000
108	A	108	ASP	-1	-0.758	-0.872	24.922	-0.252	-0.252	0.000	0.000	0.000	0.000
109	A	109	VAL	0	-0.050	-0.019	25.235	-0.025	-0.025	0.000	0.000	0.000	0.000
110	A	110	THR	0	0.035	0.016	26.861	0.018	0.018	0.000	0.000	0.000	0.000
111	A	111	GLY	0	0.008	0.005	26.916	0.011	0.011	0.000	0.000	0.000	0.000
112	A	112	PRO	0	-0.030	-0.006	25.432	0.018	0.018	0.000	0.000	0.000	0.000
113	A	113	SER	0	0.033	0.023	25.700	-0.022	-0.022	0.000	0.000	0.000	0.000
114	A	114	PRO	0	-0.026	0.005	22.064	-0.009	-0.009	0.000	0.000	0.000	0.000
115	A	115	THR	0	-0.038	-0.031	21.618	0.022	0.022	0.000	0.000	0.000	0.000
116	A	116	ILE	0	0.017	0.011	15.763	0.019	0.019	0.000	0.000	0.000	0.000
117	A	117	VAL	0	-0.023	0.003	16.737	0.006	0.006	0.000	0.000	0.000	0.000
118	A	118	ALA	0	0.017	0.006	12.239	-0.018	-0.018	0.000	0.000	0.000	0.000
119	A	119	MET	0	-0.045	-0.018	11.841	0.098	0.098	0.000	0.000	0.000	0.000
120	A	120	ASN	0	-0.040	-0.043	9.400	-0.087	-0.087	0.000	0.000	0.000	0.000
121	A	121	ASN	0	0.075	0.044	6.834	0.000	0.000	0.000	0.000	0.000	0.000
122	A	122	GLY	0	-0.044	-0.020	10.438	0.172	0.172	0.000	0.000	0.000	0.000
123	A	123	MET	0	-0.050	-0.020	7.070	0.235	0.235	0.000	0.000	0.000	0.000
124	A	124	GLU	-1	-0.875	-0.930	1.690	-29.731	-32.884	13.220	-6.345	-3.721	-0.076
125	A	125	ASP	-1	-0.749	-0.828	6.198	-0.999	-0.999	0.000	0.000	0.000	0.000
126	A	126	LEU	0	-0.013	-0.010	5.105	-0.600	-0.600	0.000	0.000	0.000	0.000
127	A	127	LEU	0	0.001	-0.009	7.209	0.409	0.409	0.000	0.000	0.000	0.000
128	A	128	ILE	0	0.014	0.013	9.896	-0.093	-0.093	0.000	0.000	0.000	0.000
129	A	129	TRP	0	-0.028	-0.027	12.925	0.079	0.079	0.000	0.000	0.000	0.000
130	A	130	GLU	-1	-0.895	-0.952	15.771	-0.485	-0.485	0.000	0.000	0.000	0.000
131	A	131	PRO	0	0.006	-0.002	18.550	0.047	0.047	0.000	0.000	0.000	0.000

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