FMO DATABASE

FMODB ID: 6YK2Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1037012.086545
FMO2-HF: Nuclear repulsion	988941.539958
FMO2-HF: Total energy	-48070.546588
FMO2-MP2: Total energy	-48211.690681

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.
-42.101	-38.603	14.302	-9.689	-8.11	-0.039

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 : -0.045 / q_NPA : -0.050

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	-0.119	-0.017	2.091	-8.919	-5.645	4.649	-3.655	-4.268	0.037
4	A	4	PRO	0	0.071	0.020	3.621	-2.705	-2.565	0.015	-0.195	0.040	0.000
5	A	5	ILE	0	-0.032	-0.011	6.365	0.310	0.310	0.000	0.000	0.000	0.000
6	A	6	THR	0	0.027	0.008	9.395	-0.205	-0.205	0.000	0.000	0.000	0.000
7	A	7	GLY	0	-0.008	-0.011	12.419	0.140	0.140	0.000	0.000	0.000	0.000
8	A	8	LYS	1	0.942	0.983	16.026	0.092	0.092	0.000	0.000	0.000	0.000
9	A	9	LEU	0	0.040	0.012	19.398	0.017	0.017	0.000	0.000	0.000	0.000
10	A	10	GLY	0	-0.036	-0.029	21.020	0.027	0.027	0.000	0.000	0.000	0.000
11	A	11	SER	0	-0.084	-0.047	19.273	0.039	0.039	0.000	0.000	0.000	0.000
12	A	12	GLU	-1	-0.866	-0.947	18.819	-0.098	-0.098	0.000	0.000	0.000	0.000
13	A	13	LEU	0	-0.037	-0.001	13.243	0.048	0.048	0.000	0.000	0.000	0.000
14	A	14	THR	0	-0.008	-0.015	14.680	-0.023	-0.023	0.000	0.000	0.000	0.000
15	A	15	MET	0	0.012	0.010	9.774	-0.014	-0.014	0.000	0.000	0.000	0.000
16	A	16	THR	0	-0.019	-0.014	10.909	-0.086	-0.086	0.000	0.000	0.000	0.000
17	A	17	ASP	-1	-0.826	-0.923	10.346	0.290	0.290	0.000	0.000	0.000	0.000
18	A	18	THR	0	0.000	-0.016	11.790	-0.083	-0.083	0.000	0.000	0.000	0.000
19	A	19	VAL	0	-0.029	-0.006	11.378	-0.011	-0.011	0.000	0.000	0.000	0.000
20	A	20	GLY	0	0.034	0.022	13.600	-0.052	-0.052	0.000	0.000	0.000	0.000
21	A	21	GLN	0	-0.103	-0.050	15.465	0.017	0.017	0.000	0.000	0.000	0.000
22	A	22	VAL	0	0.002	0.019	14.862	-0.027	-0.027	0.000	0.000	0.000	0.000
23	A	23	VAL	0	-0.033	-0.025	14.911	0.072	0.072	0.000	0.000	0.000	0.000
24	A	24	LEU	0	-0.023	-0.002	13.595	-0.043	-0.043	0.000	0.000	0.000	0.000
25	A	25	GLY	0	0.033	0.032	15.414	0.027	0.027	0.000	0.000	0.000	0.000
26	A	26	TRP	0	0.044	0.005	14.591	-0.029	-0.029	0.000	0.000	0.000	0.000
27	A	27	LYS	1	0.928	0.981	17.393	0.130	0.130	0.000	0.000	0.000	0.000
28	A	28	VAL	0	0.038	0.026	17.858	-0.008	-0.008	0.000	0.000	0.000	0.000
29	A	29	SER	0	-0.034	-0.036	20.444	0.010	0.010	0.000	0.000	0.000	0.000
30	A	30	ASP	-1	-0.906	-0.937	23.645	-0.179	-0.179	0.000	0.000	0.000	0.000
31	A	31	LEU	0	0.007	0.012	21.539	-0.002	-0.002	0.000	0.000	0.000	0.000
32	A	32	LYS	1	0.882	0.946	25.027	0.187	0.187	0.000	0.000	0.000	0.000
33	A	33	SER	0	0.023	0.010	28.229	-0.011	-0.011	0.000	0.000	0.000	0.000
34	A	34	SER	0	-0.012	-0.029	30.019	0.014	0.014	0.000	0.000	0.000	0.000
35	A	35	THR	0	-0.034	-0.025	31.904	-0.001	-0.001	0.000	0.000	0.000	0.000
36	A	36	ALA	0	0.003	0.010	32.052	0.008	0.008	0.000	0.000	0.000	0.000
37	A	37	VAL	0	0.015	0.016	34.103	-0.007	-0.007	0.000	0.000	0.000	0.000
38	A	38	ILE	0	-0.023	-0.023	29.184	0.005	0.005	0.000	0.000	0.000	0.000
39	A	39	PRO	0	0.025	-0.028	33.074	0.004	0.004	0.000	0.000	0.000	0.000
40	A	40	GLY	0	0.058	0.022	34.448	0.009	0.009	0.000	0.000	0.000	0.000
41	A	41	TYR	0	-0.083	-0.001	27.619	-0.002	-0.002	0.000	0.000	0.000	0.000
42	A	42	PRO	0	-0.013	-0.009	31.341	0.010	0.010	0.000	0.000	0.000	0.000
43	A	43	VAL	0	-0.034	-0.017	31.251	-0.014	-0.014	0.000	0.000	0.000	0.000
44	A	44	ALA	0	-0.045	-0.028	30.570	0.014	0.014	0.000	0.000	0.000	0.000
45	A	45	GLY	0	-0.040	-0.023	30.905	0.008	0.008	0.000	0.000	0.000	0.000
46	A	46	GLN	0	-0.056	-0.015	30.662	0.023	0.023	0.000	0.000	0.000	0.000
47	A	47	VAL	0	0.029	0.016	29.120	-0.021	-0.021	0.000	0.000	0.000	0.000
48	A	48	TRP	0	-0.001	0.004	25.894	0.011	0.011	0.000	0.000	0.000	0.000
49	A	49	GLU	-1	-0.859	-0.936	26.232	-0.201	-0.201	0.000	0.000	0.000	0.000
50	A	50	ALA	0	0.030	0.017	22.515	-0.011	-0.011	0.000	0.000	0.000	0.000
51	A	51	THR	0	-0.010	-0.003	24.598	0.012	0.012	0.000	0.000	0.000	0.000
52	A	52	ALA	0	-0.010	-0.002	20.468	-0.008	-0.008	0.000	0.000	0.000	0.000
53	A	53	THR	0	0.009	0.007	21.449	0.023	0.023	0.000	0.000	0.000	0.000
54	A	54	VAL	0	-0.014	0.011	18.420	-0.012	-0.012	0.000	0.000	0.000	0.000
55	A	55	ASN	0	-0.007	-0.017	19.799	0.022	0.022	0.000	0.000	0.000	0.000
56	A	56	ALA	0	0.046	0.031	19.735	0.005	0.005	0.000	0.000	0.000	0.000
57	A	57	ILE	0	0.012	0.008	18.103	0.020	0.020	0.000	0.000	0.000	0.000
58	A	58	ARG	1	0.868	0.930	18.044	-0.244	-0.244	0.000	0.000	0.000	0.000
59	A	59	GLY	0	0.046	0.016	19.478	-0.003	-0.003	0.000	0.000	0.000	0.000
60	A	60	SER	0	-0.031	-0.018	21.845	-0.008	-0.008	0.000	0.000	0.000	0.000
61	A	61	VAL	0	0.029	0.018	18.047	0.000	0.000	0.000	0.000	0.000	0.000
62	A	62	THR	0	0.052	0.044	19.645	0.013	0.013	0.000	0.000	0.000	0.000
63	A	63	PRO	0	-0.015	0.018	18.316	-0.034	-0.034	0.000	0.000	0.000	0.000
64	A	64	ALA	0	0.050	0.026	14.961	0.000	0.000	0.000	0.000	0.000	0.000
65	A	65	VAL	0	0.041	0.011	16.396	-0.077	-0.077	0.000	0.000	0.000	0.000
66	A	66	SER	0	0.015	0.009	18.153	-0.036	-0.036	0.000	0.000	0.000	0.000
67	A	67	GLN	0	0.028	0.001	11.575	-0.059	-0.059	0.000	0.000	0.000	0.000
68	A	68	PHE	0	-0.001	0.013	14.101	-0.124	-0.124	0.000	0.000	0.000	0.000
69	A	69	ASN	0	-0.001	-0.005	14.257	0.060	0.060	0.000	0.000	0.000	0.000
70	A	70	ALA	0	0.018	0.029	17.231	-0.002	-0.002	0.000	0.000	0.000	0.000
71	A	71	ARG	1	0.832	0.870	11.346	1.331	1.331	0.000	0.000	0.000	0.000
72	A	72	THR	0	0.006	-0.011	18.948	0.042	0.042	0.000	0.000	0.000	0.000
73	A	73	ALA	0	-0.013	-0.019	18.501	-0.056	-0.056	0.000	0.000	0.000	0.000
74	A	74	ASP	-1	-0.906	-0.940	17.753	-0.542	-0.542	0.000	0.000	0.000	0.000
75	A	75	GLY	0	0.027	0.021	16.653	-0.058	-0.058	0.000	0.000	0.000	0.000
76	A	76	ILE	0	-0.020	0.005	17.281	-0.043	-0.043	0.000	0.000	0.000	0.000
77	A	77	ASN	0	-0.021	-0.019	16.131	-0.085	-0.085	0.000	0.000	0.000	0.000
78	A	78	TYR	0	0.001	-0.026	19.019	0.034	0.034	0.000	0.000	0.000	0.000
79	A	79	ARG	1	0.833	0.911	17.166	0.646	0.646	0.000	0.000	0.000	0.000
80	A	80	VAL	0	-0.026	-0.020	19.092	0.048	0.048	0.000	0.000	0.000	0.000
81	A	81	LEU	0	-0.084	-0.043	21.220	-0.002	-0.002	0.000	0.000	0.000	0.000
82	A	82	TRP	0	-0.195	-0.227	21.337	0.007	0.007	0.000	0.000	0.000	0.000
83	A	83	GLN	0	0.198	0.245	23.389	-0.027	-0.027	0.000	0.000	0.000	0.000
84	A	84	ALA	0	0.025	0.003	25.728	-0.011	-0.011	0.000	0.000	0.000	0.000
85	A	85	ALA	0	-0.010	0.007	28.591	0.013	0.013	0.000	0.000	0.000	0.000
86	A	86	GLY	0	0.020	0.003	30.067	-0.002	-0.002	0.000	0.000	0.000	0.000
87	A	87	PRO	0	0.009	0.031	31.151	0.006	0.006	0.000	0.000	0.000	0.000
88	A	88	ASP	-1	-0.892	-0.921	31.093	-0.151	-0.151	0.000	0.000	0.000	0.000
89	A	89	THR	0	-0.019	0.005	26.293	-0.011	-0.011	0.000	0.000	0.000	0.000
90	A	90	ILE	0	-0.068	-0.012	22.191	0.013	0.013	0.000	0.000	0.000	0.000
91	A	91	SER	0	0.023	0.012	26.200	-0.011	-0.011	0.000	0.000	0.000	0.000
92	A	92	GLY	0	-0.005	-0.021	23.698	-0.012	-0.012	0.000	0.000	0.000	0.000
93	A	93	ALA	0	-0.044	-0.021	24.195	0.000	0.000	0.000	0.000	0.000	0.000
94	A	94	THR	0	-0.040	-0.055	23.543	-0.006	-0.006	0.000	0.000	0.000	0.000
95	A	95	ILE	0	-0.017	0.004	22.389	0.008	0.008	0.000	0.000	0.000	0.000
96	A	96	PRO	0	0.026	0.007	24.224	0.008	0.008	0.000	0.000	0.000	0.000
97	A	97	GLN	0	0.032	0.007	23.560	0.002	0.002	0.000	0.000	0.000	0.000
98	A	98	GLY	0	-0.062	-0.032	24.484	0.002	0.002	0.000	0.000	0.000	0.000
99	A	99	GLU	-1	-0.945	-0.957	26.092	-0.039	-0.039	0.000	0.000	0.000	0.000
100	A	100	GLN	0	-0.006	-0.028	24.443	-0.015	-0.015	0.000	0.000	0.000	0.000
101	A	101	SER	0	-0.033	-0.003	24.168	0.002	0.002	0.000	0.000	0.000	0.000
102	A	102	THR	0	-0.009	-0.037	24.196	-0.017	-0.017	0.000	0.000	0.000	0.000
103	A	103	GLY	0	0.044	0.027	25.711	0.010	0.010	0.000	0.000	0.000	0.000
104	A	104	LYS	1	0.864	0.945	25.548	0.160	0.160	0.000	0.000	0.000	0.000
105	A	105	ILE	0	-0.004	0.008	20.372	-0.007	-0.007	0.000	0.000	0.000	0.000
106	A	106	TYR	0	0.009	-0.059	24.316	0.006	0.006	0.000	0.000	0.000	0.000
107	A	107	PHE	0	0.024	0.009	19.715	-0.032	-0.032	0.000	0.000	0.000	0.000
108	A	108	ASP	-1	-0.758	-0.868	24.791	-0.259	-0.259	0.000	0.000	0.000	0.000
109	A	109	VAL	0	-0.042	-0.019	25.117	-0.026	-0.026	0.000	0.000	0.000	0.000
110	A	110	THR	0	0.026	0.016	26.777	0.019	0.019	0.000	0.000	0.000	0.000
111	A	111	GLY	0	0.020	0.005	26.948	0.012	0.012	0.000	0.000	0.000	0.000
112	A	112	PRO	0	-0.023	-0.004	25.400	0.019	0.019	0.000	0.000	0.000	0.000
113	A	113	SER	0	0.025	0.022	25.756	-0.023	-0.023	0.000	0.000	0.000	0.000
114	A	114	PRO	0	-0.019	0.012	22.022	-0.012	-0.012	0.000	0.000	0.000	0.000
115	A	115	THR	0	-0.032	-0.027	21.708	0.022	0.022	0.000	0.000	0.000	0.000
116	A	116	ILE	0	0.026	0.011	15.873	0.018	0.018	0.000	0.000	0.000	0.000
117	A	117	VAL	0	-0.025	0.002	16.536	0.009	0.009	0.000	0.000	0.000	0.000
118	A	118	ALA	0	0.015	0.006	12.000	-0.022	-0.022	0.000	0.000	0.000	0.000
119	A	119	MET	0	-0.064	-0.030	11.621	0.105	0.105	0.000	0.000	0.000	0.000
120	A	120	ASN	0	-0.030	-0.041	9.316	-0.035	-0.035	0.000	0.000	0.000	0.000
121	A	121	ASN	0	0.072	0.047	7.030	-0.025	-0.025	0.000	0.000	0.000	0.000
122	A	122	GLY	0	-0.046	-0.023	10.450	0.188	0.188	0.000	0.000	0.000	0.000
123	A	123	MET	0	-0.058	-0.028	7.221	0.219	0.219	0.000	0.000	0.000	0.000
124	A	124	GLU	-1	-0.858	-0.923	1.782	-30.024	-29.940	9.638	-5.839	-3.882	-0.076
125	A	125	ASP	-1	-0.770	-0.847	6.147	-1.071	-1.071	0.000	0.000	0.000	0.000
126	A	126	LEU	0	-0.002	-0.006	5.114	-0.664	-0.664	0.000	0.000	0.000	0.000
127	A	127	LEU	0	-0.003	-0.015	7.077	0.424	0.424	0.000	0.000	0.000	0.000
128	A	128	ILE	0	0.024	0.020	9.995	-0.098	-0.098	0.000	0.000	0.000	0.000
129	A	129	TRP	0	-0.028	-0.026	12.713	0.080	0.080	0.000	0.000	0.000	0.000
130	A	130	GLU	-1	-0.907	-0.955	16.172	-0.524	-0.524	0.000	0.000	0.000	0.000
131	A	131	PRO	0	-0.013	-0.009	18.538	0.048	0.048	0.000	0.000	0.000	0.000

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