FMO DATABASE

FMODB ID: 52MLZ

Calculation Name: 2P9M-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2P9M

Chain ID: A

ChEMBL ID:

UniProt ID: Q58332

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:

Apendix: None

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
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	133
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1134061.921964
FMO2-HF: Nuclear repulsion	1082077.944828
FMO2-HF: Total energy	-51983.977137
FMO2-MP2: Total energy	-52136.083613

3D Structure Molmil

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:5:LEU)

Summations of interaction energy for fragment #1(A:5:LEU)

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.
-10.97	-3.423	4.847	-2.69	-9.703	-0.003

Interaction energy analysis for fragmet #1(A:5:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.067 / q_NPA : 0.019

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	7	ASN	0	-0.060	-0.041	3.607	-3.399	-1.692	0.003	-0.698	-1.013	0.003
4	A	8	ILE	0	-0.015	0.013	2.375	-1.781	-0.283	0.900	-0.581	-1.818	-0.001
5	A	9	LYS	1	0.985	0.985	4.709	-0.404	-0.383	-0.001	-0.006	-0.013	0.000
6	A	10	VAL	0	0.043	0.026	7.817	-0.107	-0.107	0.000	0.000	0.000	0.000
7	A	11	LYS	1	0.981	0.973	9.006	0.153	0.153	0.000	0.000	0.000	0.000
8	A	12	ASP	-1	-0.941	-0.962	8.103	-0.413	-0.413	0.000	0.000	0.000	0.000
9	A	13	VAL	0	-0.093	-0.053	5.992	-0.016	-0.016	0.000	0.000	0.000	0.000
10	A	14	MET	0	-0.024	0.017	9.426	0.019	0.019	0.000	0.000	0.000	0.000
11	A	15	THR	0	-0.017	-0.006	12.076	0.047	0.047	0.000	0.000	0.000	0.000
12	A	16	LYS	1	0.969	0.965	14.812	0.302	0.302	0.000	0.000	0.000	0.000
13	A	17	ASN	0	0.001	0.014	18.217	0.011	0.011	0.000	0.000	0.000	0.000
14	A	18	VAL	0	-0.009	-0.003	18.698	0.004	0.004	0.000	0.000	0.000	0.000
15	A	19	ILE	0	0.007	-0.001	21.864	0.016	0.016	0.000	0.000	0.000	0.000
16	A	20	THR	0	-0.019	-0.010	23.731	-0.008	-0.008	0.000	0.000	0.000	0.000
17	A	21	ALA	0	0.015	0.016	26.068	0.006	0.006	0.000	0.000	0.000	0.000
18	A	22	LYS	1	0.930	0.966	28.844	0.084	0.084	0.000	0.000	0.000	0.000
19	A	23	ARG	1	1.004	0.979	31.600	0.074	0.074	0.000	0.000	0.000	0.000
20	A	24	HIS	0	0.014	0.001	33.153	-0.001	-0.001	0.000	0.000	0.000	0.000
21	A	25	GLU	-1	-0.854	-0.912	32.394	-0.095	-0.095	0.000	0.000	0.000	0.000
22	A	26	GLY	0	0.086	0.050	35.149	-0.002	-0.002	0.000	0.000	0.000	0.000
23	A	27	VAL	0	-0.035	-0.029	31.839	-0.007	-0.007	0.000	0.000	0.000	0.000
24	A	28	VAL	0	0.024	0.007	33.284	-0.007	-0.007	0.000	0.000	0.000	0.000
25	A	29	GLU	-1	-0.871	-0.935	34.741	-0.086	-0.086	0.000	0.000	0.000	0.000
26	A	30	ALA	0	-0.034	-0.007	30.388	-0.006	-0.006	0.000	0.000	0.000	0.000
27	A	31	PHE	0	-0.006	-0.013	29.586	-0.011	-0.011	0.000	0.000	0.000	0.000
28	A	32	GLU	-1	-0.872	-0.943	30.864	-0.101	-0.101	0.000	0.000	0.000	0.000
29	A	33	LYS	1	0.924	0.971	29.995	0.114	0.114	0.000	0.000	0.000	0.000
30	A	34	MET	0	-0.054	-0.024	26.448	-0.011	-0.011	0.000	0.000	0.000	0.000
31	A	35	LEU	0	0.001	0.003	27.576	-0.011	-0.011	0.000	0.000	0.000	0.000
32	A	36	LYS	1	0.896	0.965	29.519	0.102	0.102	0.000	0.000	0.000	0.000
33	A	37	TYR	0	-0.049	-0.045	27.315	0.005	0.005	0.000	0.000	0.000	0.000
34	A	38	LYS	1	0.913	0.969	24.254	0.172	0.172	0.000	0.000	0.000	0.000
35	A	39	ILE	0	-0.024	0.009	22.781	-0.018	-0.018	0.000	0.000	0.000	0.000
36	A	40	SER	0	0.038	0.002	19.472	0.007	0.007	0.000	0.000	0.000	0.000
37	A	41	SER	0	-0.010	-0.014	19.618	0.005	0.005	0.000	0.000	0.000	0.000
38	A	42	LEU	0	0.021	-0.001	22.216	0.001	0.001	0.000	0.000	0.000	0.000
39	A	43	PRO	0	-0.006	0.002	20.543	0.008	0.008	0.000	0.000	0.000	0.000
40	A	44	VAL	0	-0.002	-0.007	23.239	0.008	0.008	0.000	0.000	0.000	0.000
41	A	45	ILE	0	-0.012	-0.005	25.267	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	46	ASP	-1	-0.819	-0.916	27.695	-0.072	-0.072	0.000	0.000	0.000	0.000
43	A	47	ASP	-1	-0.920	-0.978	30.355	-0.071	-0.071	0.000	0.000	0.000	0.000
44	A	48	GLU	-1	-0.954	-0.972	30.269	-0.049	-0.049	0.000	0.000	0.000	0.000
45	A	49	ASN	0	-0.052	-0.032	24.341	-0.005	-0.005	0.000	0.000	0.000	0.000
46	A	50	LYS	1	0.955	0.976	25.354	0.048	0.048	0.000	0.000	0.000	0.000
47	A	51	VAL	0	-0.003	0.000	21.010	-0.003	-0.003	0.000	0.000	0.000	0.000
48	A	52	ILE	0	-0.065	-0.040	24.341	0.007	0.007	0.000	0.000	0.000	0.000
49	A	53	GLY	0	0.040	0.012	25.037	0.006	0.006	0.000	0.000	0.000	0.000
50	A	54	ILE	0	-0.059	-0.019	19.912	-0.010	-0.010	0.000	0.000	0.000	0.000
51	A	55	VAL	0	0.044	0.048	24.052	0.007	0.007	0.000	0.000	0.000	0.000
52	A	56	THR	0	0.066	0.012	21.481	-0.009	-0.009	0.000	0.000	0.000	0.000
53	A	57	THR	0	0.000	-0.006	24.344	0.010	0.010	0.000	0.000	0.000	0.000
54	A	58	THR	0	0.013	0.005	22.865	0.013	0.013	0.000	0.000	0.000	0.000
55	A	59	ASP	-1	-0.853	-0.918	25.147	-0.148	-0.148	0.000	0.000	0.000	0.000
56	A	60	ILE	0	-0.049	-0.020	27.431	0.012	0.012	0.000	0.000	0.000	0.000
57	A	61	GLY	0	0.040	0.002	29.237	0.009	0.009	0.000	0.000	0.000	0.000
58	A	62	TYR	0	-0.022	-0.012	29.687	0.010	0.010	0.000	0.000	0.000	0.000
59	A	63	ASN	0	-0.020	-0.027	31.339	0.013	0.013	0.000	0.000	0.000	0.000
60	A	64	LEU	0	-0.007	0.013	33.551	0.006	0.006	0.000	0.000	0.000	0.000
61	A	65	ILE	0	-0.011	-0.005	34.627	0.005	0.005	0.000	0.000	0.000	0.000
62	A	66	ARG	1	0.846	0.935	33.901	0.101	0.101	0.000	0.000	0.000	0.000
63	A	67	ASP	-1	-0.877	-0.932	38.083	-0.069	-0.069	0.000	0.000	0.000	0.000
64	A	68	LYS	1	0.856	0.931	36.705	0.081	0.081	0.000	0.000	0.000	0.000
65	A	69	TYR	0	-0.035	-0.014	32.670	-0.003	-0.003	0.000	0.000	0.000	0.000
66	A	70	THR	0	0.028	0.004	38.802	0.002	0.002	0.000	0.000	0.000	0.000
67	A	71	LEU	0	0.015	-0.007	39.891	-0.003	-0.003	0.000	0.000	0.000	0.000
68	A	72	GLU	-1	-0.906	-0.950	41.071	-0.058	-0.058	0.000	0.000	0.000	0.000
69	A	73	THR	0	-0.078	-0.008	37.805	-0.002	-0.002	0.000	0.000	0.000	0.000
70	A	74	THR	0	0.068	0.032	36.357	-0.005	-0.005	0.000	0.000	0.000	0.000
71	A	75	ILE	0	-0.016	-0.023	29.803	-0.004	-0.004	0.000	0.000	0.000	0.000
72	A	76	GLY	0	-0.044	-0.044	32.148	-0.003	-0.003	0.000	0.000	0.000	0.000
73	A	77	ASP	-1	-0.930	-0.948	33.700	-0.069	-0.069	0.000	0.000	0.000	0.000
74	A	78	VAL	0	-0.040	-0.028	31.590	0.000	0.000	0.000	0.000	0.000	0.000
75	A	79	MET	0	-0.053	0.006	27.878	-0.008	-0.008	0.000	0.000	0.000	0.000
76	A	80	THR	0	-0.005	-0.016	25.691	0.009	0.009	0.000	0.000	0.000	0.000
77	A	81	LYS	1	0.983	0.982	27.142	0.072	0.072	0.000	0.000	0.000	0.000
78	A	82	ASP	-1	-0.948	-0.952	25.062	-0.080	-0.080	0.000	0.000	0.000	0.000
79	A	83	VAL	0	-0.051	-0.016	21.098	-0.011	-0.011	0.000	0.000	0.000	0.000
80	A	84	ILE	0	0.040	0.021	16.563	0.002	0.002	0.000	0.000	0.000	0.000
81	A	85	THR	0	0.013	0.015	17.058	-0.021	-0.021	0.000	0.000	0.000	0.000
82	A	86	ILE	0	-0.046	-0.029	10.324	0.017	0.017	0.000	0.000	0.000	0.000
83	A	87	HIS	0	0.057	0.048	14.234	-0.016	-0.016	0.000	0.000	0.000	0.000
84	A	88	GLU	-1	-0.867	-0.961	12.835	-0.202	-0.202	0.000	0.000	0.000	0.000
85	A	89	ASP	-1	-0.933	-0.996	11.966	-0.138	-0.138	0.000	0.000	0.000	0.000
86	A	90	ALA	0	-0.018	0.019	10.097	0.058	0.058	0.000	0.000	0.000	0.000
87	A	91	SER	0	-0.011	-0.008	4.927	-0.144	-0.144	0.000	0.000	0.000	0.000
88	A	92	ILE	0	0.070	0.020	2.383	-1.159	-0.462	1.663	-0.406	-1.953	0.000
89	A	93	LEU	0	-0.031	-0.013	3.387	-0.870	0.115	0.034	-0.231	-0.788	0.000
90	A	94	GLU	-1	-0.913	-0.961	4.599	0.081	0.197	-0.001	-0.019	-0.097	0.000
91	A	95	ALA	0	0.021	0.002	6.921	0.081	0.081	0.000	0.000	0.000	0.000
92	A	96	ILE	0	0.003	-0.002	3.383	-0.285	0.059	0.020	-0.065	-0.299	0.000
93	A	97	LYS	1	0.935	0.963	7.460	0.113	0.113	0.000	0.000	0.000	0.000
94	A	98	LYS	1	0.850	0.941	9.856	0.270	0.270	0.000	0.000	0.000	0.000
95	A	99	MET	0	0.009	-0.004	10.434	0.008	0.008	0.000	0.000	0.000	0.000
96	A	100	ASP	-1	-0.905	-0.931	11.419	-0.264	-0.264	0.000	0.000	0.000	0.000
97	A	101	ILE	0	-0.058	-0.019	13.256	0.055	0.055	0.000	0.000	0.000	0.000
98	A	102	SER	0	0.042	-0.010	16.528	-0.007	-0.007	0.000	0.000	0.000	0.000
99	A	103	GLY	0	-0.024	-0.013	19.410	0.015	0.015	0.000	0.000	0.000	0.000
100	A	104	LYS	1	0.706	0.849	15.461	0.239	0.239	0.000	0.000	0.000	0.000
101	A	105	LYS	1	0.800	0.881	20.513	0.117	0.117	0.000	0.000	0.000	0.000
102	A	106	GLU	-1	-0.789	-0.878	21.976	-0.130	-0.130	0.000	0.000	0.000	0.000
103	A	107	GLU	-1	-0.840	-0.904	17.730	-0.206	-0.206	0.000	0.000	0.000	0.000
104	A	108	ILE	0	0.024	0.009	13.599	0.001	0.001	0.000	0.000	0.000	0.000
105	A	109	ILE	0	-0.025	0.024	15.665	0.020	0.020	0.000	0.000	0.000	0.000
106	A	110	ASN	0	0.000	-0.008	14.911	-0.003	-0.003	0.000	0.000	0.000	0.000
107	A	111	GLN	0	-0.010	-0.030	14.360	-0.043	-0.043	0.000	0.000	0.000	0.000
108	A	112	LEU	0	-0.019	0.001	11.548	0.037	0.037	0.000	0.000	0.000	0.000
109	A	113	PRO	0	-0.001	0.005	14.915	-0.027	-0.027	0.000	0.000	0.000	0.000
110	A	114	VAL	0	-0.018	-0.008	13.313	-0.009	-0.009	0.000	0.000	0.000	0.000
111	A	115	VAL	0	0.008	0.012	15.906	0.026	0.026	0.000	0.000	0.000	0.000
112	A	116	ASP	-1	-0.803	-0.907	17.189	-0.102	-0.102	0.000	0.000	0.000	0.000
113	A	117	LYS	1	0.930	0.939	19.260	0.019	0.019	0.000	0.000	0.000	0.000
114	A	118	ASN	0	-0.056	-0.008	20.935	0.019	0.019	0.000	0.000	0.000	0.000
115	A	119	ASN	0	-0.012	-0.029	21.570	0.011	0.011	0.000	0.000	0.000	0.000
116	A	120	LYS	1	0.847	0.957	22.631	0.062	0.062	0.000	0.000	0.000	0.000
117	A	121	LEU	0	0.013	0.005	19.439	-0.011	-0.011	0.000	0.000	0.000	0.000
118	A	122	VAL	0	-0.034	-0.023	16.709	0.009	0.009	0.000	0.000	0.000	0.000
119	A	123	GLY	0	0.021	0.010	16.525	-0.007	-0.007	0.000	0.000	0.000	0.000
120	A	124	ILE	0	-0.033	-0.003	15.423	0.014	0.014	0.000	0.000	0.000	0.000
121	A	125	ILE	0	-0.016	-0.005	7.435	-0.038	-0.038	0.000	0.000	0.000	0.000
122	A	126	SER	0	-0.024	-0.027	11.547	0.035	0.035	0.000	0.000	0.000	0.000
123	A	127	ASP	-1	-0.742	-0.891	10.237	-0.629	-0.629	0.000	0.000	0.000	0.000
124	A	128	GLY	0	0.003	0.009	9.934	-0.123	-0.123	0.000	0.000	0.000	0.000
125	A	129	ASP	-1	-0.809	-0.896	9.393	-0.653	-0.653	0.000	0.000	0.000	0.000
126	A	130	ILE	0	0.024	0.012	4.868	-0.202	-0.202	0.000	0.000	0.000	0.000
127	A	131	ILE	0	0.014	0.018	5.318	-0.392	-0.392	0.000	0.000	0.000	0.000
128	A	132	ARG	1	0.848	0.923	7.355	0.607	0.607	0.000	0.000	0.000	0.000
129	A	133	THR	0	-0.068	-0.048	3.182	-0.241	0.115	0.073	-0.081	-0.347	0.000
130	A	134	ILE	0	-0.018	-0.025	2.422	-1.587	-0.433	0.731	-0.285	-1.599	-0.002
131	A	135	SER	0	-0.038	-0.008	4.095	0.215	0.295	0.001	-0.024	-0.057	0.000
132	A	136	LYS	1	0.902	0.954	6.570	0.844	0.844	0.000	0.000	0.000	0.000
133	A	137	ILE	0	-0.026	0.013	2.472	-0.818	-0.229	1.424	-0.294	-1.719	-0.003

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Interactive mode: IFIE and PIEDA for fragment #1(A:5:LEU)