FMO DATABASE

FMODB ID: V5711

Calculation Name: 2P9M-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

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:

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	133
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1140573.161141
FMO2-HF: Nuclear repulsion	1088583.89712
FMO2-HF: Total energy	-51989.264021
FMO2-MP2: Total energy	-52141.333348

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: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.
-9.866	-1.162	5.216	-3.2	-10.717	-0.007

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 : 0.058 / q_NPA : 0.011

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	-0.035	-0.021	3.068	-2.173	-0.111	0.008	-0.914	-1.155	0.002
4	A	8	ILE	0	0.005	0.018	2.520	-1.716	-0.022	0.704	-0.611	-1.787	-0.001
5	A	9	LYS	1	0.882	0.930	4.590	-0.052	-0.052	-0.001	-0.010	0.011	0.000
6	A	10	VAL	0	0.022	0.006	7.453	-0.047	-0.047	0.000	0.000	0.000	0.000
7	A	11	LYS	1	0.824	0.881	9.235	0.248	0.248	0.000	0.000	0.000	0.000
8	A	12	ASP	-1	-0.829	-0.910	7.905	-0.667	-0.667	0.000	0.000	0.000	0.000
9	A	13	VAL	0	-0.085	-0.053	6.123	0.063	0.063	0.000	0.000	0.000	0.000
10	A	14	MET	0	-0.044	0.012	9.356	0.037	0.037	0.000	0.000	0.000	0.000
11	A	15	THR	0	0.040	0.024	11.833	0.034	0.034	0.000	0.000	0.000	0.000
12	A	16	LYS	1	0.831	0.911	12.843	0.439	0.439	0.000	0.000	0.000	0.000
13	A	17	ASN	0	0.008	0.008	17.776	0.016	0.016	0.000	0.000	0.000	0.000
14	A	18	VAL	0	-0.017	-0.010	18.372	0.006	0.006	0.000	0.000	0.000	0.000
15	A	19	ILE	0	0.015	0.008	21.419	0.014	0.014	0.000	0.000	0.000	0.000
16	A	20	THR	0	-0.011	-0.012	23.631	-0.006	-0.006	0.000	0.000	0.000	0.000
17	A	21	ALA	0	0.003	0.002	25.917	0.005	0.005	0.000	0.000	0.000	0.000
18	A	22	LYS	1	0.839	0.896	28.862	0.086	0.086	0.000	0.000	0.000	0.000
19	A	23	ARG	1	0.991	0.971	31.696	0.069	0.069	0.000	0.000	0.000	0.000
20	A	24	HIS	0	0.015	0.005	32.916	0.001	0.001	0.000	0.000	0.000	0.000
21	A	25	GLU	-1	-0.782	-0.854	31.731	-0.099	-0.099	0.000	0.000	0.000	0.000
22	A	26	GLY	0	0.106	0.059	35.059	-0.001	-0.001	0.000	0.000	0.000	0.000
23	A	27	VAL	0	-0.058	-0.043	32.099	-0.006	-0.006	0.000	0.000	0.000	0.000
24	A	28	VAL	0	0.025	0.013	33.097	-0.006	-0.006	0.000	0.000	0.000	0.000
25	A	29	GLU	-1	-0.833	-0.916	34.585	-0.078	-0.078	0.000	0.000	0.000	0.000
26	A	30	ALA	0	-0.014	-0.014	30.256	-0.006	-0.006	0.000	0.000	0.000	0.000
27	A	31	PHE	0	-0.012	-0.007	29.338	-0.010	-0.010	0.000	0.000	0.000	0.000
28	A	32	GLU	-1	-0.901	-0.954	30.636	-0.088	-0.088	0.000	0.000	0.000	0.000
29	A	33	LYS	1	0.774	0.878	29.283	0.108	0.108	0.000	0.000	0.000	0.000
30	A	34	MET	0	-0.052	-0.023	26.017	-0.010	-0.010	0.000	0.000	0.000	0.000
31	A	35	LEU	0	0.010	0.011	27.240	-0.009	-0.009	0.000	0.000	0.000	0.000
32	A	36	LYS	1	0.893	0.957	29.133	0.094	0.094	0.000	0.000	0.000	0.000
33	A	37	TYR	0	-0.021	-0.015	27.236	0.005	0.005	0.000	0.000	0.000	0.000
34	A	38	LYS	1	0.905	0.956	24.454	0.153	0.153	0.000	0.000	0.000	0.000
35	A	39	ILE	0	-0.004	0.017	22.497	-0.017	-0.017	0.000	0.000	0.000	0.000
36	A	40	SER	0	0.025	0.009	18.813	0.009	0.009	0.000	0.000	0.000	0.000
37	A	41	SER	0	-0.007	-0.016	19.718	0.001	0.001	0.000	0.000	0.000	0.000
38	A	42	LEU	0	0.017	0.007	22.136	-0.003	-0.003	0.000	0.000	0.000	0.000
39	A	43	PRO	0	-0.001	0.003	20.520	0.008	0.008	0.000	0.000	0.000	0.000
40	A	44	VAL	0	-0.016	-0.004	23.307	0.007	0.007	0.000	0.000	0.000	0.000
41	A	45	ILE	0	-0.003	-0.001	25.430	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	46	ASP	-1	-0.763	-0.888	27.962	-0.076	-0.076	0.000	0.000	0.000	0.000
43	A	47	ASP	-1	-0.886	-0.939	30.525	-0.078	-0.078	0.000	0.000	0.000	0.000
44	A	48	GLU	-1	-0.808	-0.889	30.469	-0.065	-0.065	0.000	0.000	0.000	0.000
45	A	49	ASN	0	-0.044	-0.026	24.125	-0.003	-0.003	0.000	0.000	0.000	0.000
46	A	50	LYS	1	0.892	0.947	25.290	0.055	0.055	0.000	0.000	0.000	0.000
47	A	51	VAL	0	-0.013	-0.014	20.974	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	52	ILE	0	-0.043	-0.029	24.374	0.008	0.008	0.000	0.000	0.000	0.000
49	A	53	GLY	0	0.050	0.019	25.652	0.007	0.007	0.000	0.000	0.000	0.000
50	A	54	ILE	0	-0.037	-0.018	20.003	-0.011	-0.011	0.000	0.000	0.000	0.000
51	A	55	VAL	0	0.023	0.025	24.106	0.010	0.010	0.000	0.000	0.000	0.000
52	A	56	THR	0	0.022	-0.029	21.538	-0.012	-0.012	0.000	0.000	0.000	0.000
53	A	57	THR	0	0.035	-0.002	24.228	0.009	0.009	0.000	0.000	0.000	0.000
54	A	58	THR	0	0.018	0.013	22.679	0.011	0.011	0.000	0.000	0.000	0.000
55	A	59	ASP	-1	-0.820	-0.881	24.330	-0.131	-0.131	0.000	0.000	0.000	0.000
56	A	60	ILE	0	-0.010	0.004	27.305	0.010	0.010	0.000	0.000	0.000	0.000
57	A	61	GLY	0	0.067	0.030	29.117	0.008	0.008	0.000	0.000	0.000	0.000
58	A	62	TYR	0	-0.011	-0.006	29.132	0.008	0.008	0.000	0.000	0.000	0.000
59	A	63	ASN	0	-0.016	-0.020	30.702	0.013	0.013	0.000	0.000	0.000	0.000
60	A	64	LEU	0	0.049	0.030	33.465	0.005	0.005	0.000	0.000	0.000	0.000
61	A	65	ILE	0	-0.060	-0.021	33.696	0.004	0.004	0.000	0.000	0.000	0.000
62	A	66	ARG	1	0.812	0.893	32.237	0.081	0.081	0.000	0.000	0.000	0.000
63	A	67	ASP	-1	-0.872	-0.924	38.047	-0.056	-0.056	0.000	0.000	0.000	0.000
64	A	68	LYS	1	0.815	0.912	34.475	0.070	0.070	0.000	0.000	0.000	0.000
65	A	69	TYR	0	-0.054	-0.030	32.424	-0.003	-0.003	0.000	0.000	0.000	0.000
66	A	70	THR	0	0.015	0.003	38.605	0.002	0.002	0.000	0.000	0.000	0.000
67	A	71	LEU	0	-0.003	-0.013	39.458	-0.003	-0.003	0.000	0.000	0.000	0.000
68	A	72	GLU	-1	-0.880	-0.936	40.396	-0.054	-0.054	0.000	0.000	0.000	0.000
69	A	73	THR	0	-0.058	-0.006	37.416	0.000	0.000	0.000	0.000	0.000	0.000
70	A	74	THR	0	0.031	-0.006	36.016	-0.005	-0.005	0.000	0.000	0.000	0.000
71	A	75	ILE	0	0.009	-0.015	29.554	-0.002	-0.002	0.000	0.000	0.000	0.000
72	A	76	GLY	0	0.009	-0.014	31.606	-0.003	-0.003	0.000	0.000	0.000	0.000
73	A	77	ASP	-1	-0.890	-0.914	33.340	-0.061	-0.061	0.000	0.000	0.000	0.000
74	A	78	VAL	0	-0.048	-0.030	30.725	0.001	0.001	0.000	0.000	0.000	0.000
75	A	79	MET	0	-0.071	0.013	27.695	-0.005	-0.005	0.000	0.000	0.000	0.000
76	A	80	THR	0	0.022	0.005	24.710	0.010	0.010	0.000	0.000	0.000	0.000
77	A	81	LYS	1	0.849	0.919	26.527	0.071	0.071	0.000	0.000	0.000	0.000
78	A	82	ASP	-1	-0.908	-0.937	24.958	-0.071	-0.071	0.000	0.000	0.000	0.000
79	A	83	VAL	0	-0.058	-0.027	21.418	-0.009	-0.009	0.000	0.000	0.000	0.000
80	A	84	ILE	0	0.035	0.020	16.471	0.000	0.000	0.000	0.000	0.000	0.000
81	A	85	THR	0	0.008	0.008	17.160	-0.016	-0.016	0.000	0.000	0.000	0.000
82	A	86	ILE	0	-0.051	-0.022	10.099	0.008	0.008	0.000	0.000	0.000	0.000
83	A	87	HIS	0	0.054	0.037	13.815	-0.008	-0.008	0.000	0.000	0.000	0.000
84	A	88	GLU	-1	-0.774	-0.900	12.671	-0.235	-0.235	0.000	0.000	0.000	0.000
85	A	89	ASP	-1	-0.850	-0.930	11.784	-0.273	-0.273	0.000	0.000	0.000	0.000
86	A	90	ALA	0	0.030	0.042	9.776	0.031	0.031	0.000	0.000	0.000	0.000
87	A	91	SER	0	-0.042	-0.064	4.580	-0.211	-0.125	-0.001	-0.012	-0.072	0.000
88	A	92	ILE	0	0.024	-0.006	2.416	-1.483	-0.257	1.635	-0.541	-2.319	-0.001
89	A	93	LEU	0	-0.013	0.000	3.520	-0.808	0.118	0.025	-0.221	-0.731	-0.001
90	A	94	GLU	-1	-0.817	-0.878	4.620	-0.069	0.019	-0.001	-0.014	-0.073	0.000
91	A	95	ALA	0	0.012	-0.001	6.840	0.066	0.066	0.000	0.000	0.000	0.000
92	A	96	ILE	0	0.014	0.006	3.078	-0.393	0.060	0.113	-0.098	-0.468	-0.001
93	A	97	LYS	1	0.925	0.956	7.101	-0.006	-0.006	0.000	0.000	0.000	0.000
94	A	98	LYS	1	0.875	0.947	9.727	0.230	0.230	0.000	0.000	0.000	0.000
95	A	99	MET	0	-0.001	0.008	10.424	-0.006	-0.006	0.000	0.000	0.000	0.000
96	A	100	ASP	-1	-0.876	-0.935	11.058	-0.131	-0.131	0.000	0.000	0.000	0.000
97	A	101	ILE	0	-0.047	-0.005	12.918	0.039	0.039	0.000	0.000	0.000	0.000
98	A	102	SER	0	-0.025	-0.034	16.144	-0.003	-0.003	0.000	0.000	0.000	0.000
99	A	103	GLY	0	-0.035	-0.019	18.763	0.011	0.011	0.000	0.000	0.000	0.000
100	A	104	LYS	1	0.707	0.831	14.898	0.145	0.145	0.000	0.000	0.000	0.000
101	A	105	LYS	1	0.801	0.877	20.120	0.077	0.077	0.000	0.000	0.000	0.000
102	A	106	GLU	-1	-0.774	-0.871	21.249	-0.088	-0.088	0.000	0.000	0.000	0.000
103	A	107	GLU	-1	-0.810	-0.867	16.992	-0.139	-0.139	0.000	0.000	0.000	0.000
104	A	108	ILE	0	0.017	0.012	12.811	0.000	0.000	0.000	0.000	0.000	0.000
105	A	109	ILE	0	-0.024	0.009	15.281	0.010	0.010	0.000	0.000	0.000	0.000
106	A	110	ASN	0	-0.021	-0.022	14.368	-0.012	-0.012	0.000	0.000	0.000	0.000
107	A	111	GLN	0	-0.041	-0.043	14.366	-0.042	-0.042	0.000	0.000	0.000	0.000
108	A	112	LEU	0	0.004	0.008	11.878	0.029	0.029	0.000	0.000	0.000	0.000
109	A	113	PRO	0	0.008	0.003	14.856	-0.031	-0.031	0.000	0.000	0.000	0.000
110	A	114	VAL	0	-0.034	-0.013	13.234	-0.007	-0.007	0.000	0.000	0.000	0.000
111	A	115	VAL	0	0.009	0.004	16.016	0.021	0.021	0.000	0.000	0.000	0.000
112	A	116	ASP	-1	-0.754	-0.888	17.334	-0.122	-0.122	0.000	0.000	0.000	0.000
113	A	117	LYS	1	0.858	0.932	19.316	0.101	0.101	0.000	0.000	0.000	0.000
114	A	118	ASN	0	-0.071	-0.030	20.791	0.021	0.021	0.000	0.000	0.000	0.000
115	A	119	ASN	0	-0.023	-0.022	21.557	0.013	0.013	0.000	0.000	0.000	0.000
116	A	120	LYS	1	0.806	0.920	22.713	0.077	0.077	0.000	0.000	0.000	0.000
117	A	121	LEU	0	0.005	0.002	19.644	-0.015	-0.015	0.000	0.000	0.000	0.000
118	A	122	VAL	0	-0.042	-0.026	16.993	0.009	0.009	0.000	0.000	0.000	0.000
119	A	123	GLY	0	0.030	0.009	16.345	-0.015	-0.015	0.000	0.000	0.000	0.000
120	A	124	ILE	0	-0.031	-0.009	15.177	0.019	0.019	0.000	0.000	0.000	0.000
121	A	125	ILE	0	-0.033	-0.005	7.362	-0.041	-0.041	0.000	0.000	0.000	0.000
122	A	126	SER	0	0.014	-0.030	11.256	0.047	0.047	0.000	0.000	0.000	0.000
123	A	127	ASP	-1	-0.741	-0.874	10.100	-0.511	-0.511	0.000	0.000	0.000	0.000
124	A	128	GLY	0	-0.001	0.000	9.942	-0.093	-0.093	0.000	0.000	0.000	0.000
125	A	129	ASP	-1	-0.791	-0.864	9.299	-0.559	-0.559	0.000	0.000	0.000	0.000
126	A	130	ILE	0	0.013	0.021	4.597	-0.277	-0.173	-0.001	-0.004	-0.099	0.000
127	A	131	ILE	0	0.019	0.012	5.230	-0.304	-0.304	0.000	0.000	0.000	0.000
128	A	132	ARG	1	0.842	0.916	7.132	0.525	0.525	0.000	0.000	0.000	0.000
129	A	133	THR	0	-0.056	-0.049	3.023	-0.356	0.041	0.106	-0.089	-0.413	0.000
130	A	134	ILE	0	-0.006	-0.016	2.481	-1.493	-0.465	0.998	-0.349	-1.677	-0.002
131	A	135	SER	0	-0.013	-0.001	3.739	0.197	0.271	0.005	0.009	-0.088	0.000
132	A	136	LYS	1	0.921	0.976	6.307	0.917	0.917	0.000	0.000	0.000	0.000
133	A	137	ILE	0	-0.078	-0.028	2.385	-0.854	-0.288	1.626	-0.346	-1.846	-0.003

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