FMO DATABASE

FMODB ID: N1Y9Q

Calculation Name: 3P9A-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3P9A

Chain ID: A

ChEMBL ID:

UniProt ID: P04893

Base Structure: X-ray

Registration Date: 2023-06-20

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	139
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1139532.378024
FMO2-HF: Nuclear repulsion	1083221.285474
FMO2-HF: Total energy	-56311.09255
FMO2-MP2: Total energy	-56473.741993

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:MET)

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

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.
-1.527	1.353	-0.021	-1.504	-1.355	-0.002

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.020 / q_NPA : -0.024

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	ALA	0	0.028	0.023	3.872	-2.562	0.318	-0.021	-1.504	-1.355	-0.002
4	A	4	PRO	0	-0.022	-0.018	5.405	0.225	0.225	0.000	0.000	0.000	0.000
5	A	5	LYN	0	0.018	0.016	5.253	0.412	0.412	0.000	0.000	0.000	0.000
6	A	6	GLY	0	-0.035	-0.011	7.624	-0.276	-0.276	0.000	0.000	0.000	0.000
7	A	7	ASN	0	-0.059	-0.038	9.732	-0.305	-0.305	0.000	0.000	0.000	0.000
8	A	8	ARG	1	0.883	0.934	12.694	-0.599	-0.599	0.000	0.000	0.000	0.000
9	A	9	PHE	0	0.030	-0.002	16.336	-0.027	-0.027	0.000	0.000	0.000	0.000
10	A	10	TRP	0	-0.052	-0.025	17.866	-0.024	-0.024	0.000	0.000	0.000	0.000
11	A	11	GLU	-1	-0.858	-0.915	18.527	0.439	0.439	0.000	0.000	0.000	0.000
12	A	12	ALA	0	-0.051	-0.008	16.181	-0.002	-0.002	0.000	0.000	0.000	0.000
13	A	13	ARG	1	0.806	0.881	17.564	-0.315	-0.315	0.000	0.000	0.000	0.000
14	A	14	SER	0	-0.042	-0.009	17.601	0.025	0.025	0.000	0.000	0.000	0.000
15	A	15	SER	0	-0.064	-0.075	17.451	-0.015	-0.015	0.000	0.000	0.000	0.000
16	A	16	HIS	0	-0.029	-0.021	19.008	-0.026	-0.026	0.000	0.000	0.000	0.000
17	A	17	GLY	0	0.008	0.019	21.949	-0.016	-0.016	0.000	0.000	0.000	0.000
18	A	18	ARG	1	0.866	0.911	23.529	-0.160	-0.160	0.000	0.000	0.000	0.000
19	A	19	ASN	0	-0.102	-0.043	26.431	-0.015	-0.015	0.000	0.000	0.000	0.000
20	A	20	PRO	0	0.031	0.053	25.498	-0.014	-0.014	0.000	0.000	0.000	0.000
21	A	21	LYS	1	0.812	0.878	28.518	-0.075	-0.075	0.000	0.000	0.000	0.000
22	A	22	PHE	0	-0.001	-0.010	24.506	-0.008	-0.008	0.000	0.000	0.000	0.000
23	A	23	GLU	-1	-0.804	-0.879	30.232	0.061	0.061	0.000	0.000	0.000	0.000
24	A	24	SER	0	-0.068	-0.057	30.671	-0.005	-0.005	0.000	0.000	0.000	0.000
25	A	25	PRO	0	0.045	0.023	30.270	0.009	0.009	0.000	0.000	0.000	0.000
26	A	26	GLU	-1	-0.810	-0.896	26.904	0.044	0.044	0.000	0.000	0.000	0.000
27	A	27	ALA	0	-0.002	0.010	25.640	0.008	0.008	0.000	0.000	0.000	0.000
28	A	28	LEU	0	0.033	0.018	25.113	0.013	0.013	0.000	0.000	0.000	0.000
29	A	29	TRP	0	0.053	0.011	23.643	0.013	0.013	0.000	0.000	0.000	0.000
30	A	30	ALA	0	0.027	0.020	21.493	0.006	0.006	0.000	0.000	0.000	0.000
31	A	31	ALA	0	0.021	0.020	20.327	0.022	0.022	0.000	0.000	0.000	0.000
32	A	32	CYS	0	-0.095	-0.050	20.830	0.021	0.021	0.000	0.000	0.000	0.000
33	A	33	CYS	0	-0.040	-0.016	18.562	0.002	0.002	0.000	0.000	0.000	0.000
34	A	34	GLU	-1	-0.691	-0.824	16.072	0.279	0.279	0.000	0.000	0.000	0.000
35	A	35	TYR	0	-0.001	0.007	15.847	0.047	0.047	0.000	0.000	0.000	0.000
36	A	36	PHE	0	-0.003	-0.024	16.917	0.026	0.026	0.000	0.000	0.000	0.000
37	A	37	GLU	-1	-0.856	-0.935	12.810	0.210	0.210	0.000	0.000	0.000	0.000
38	A	38	TRP	0	-0.028	-0.010	12.095	0.059	0.059	0.000	0.000	0.000	0.000
39	A	39	VAL	0	-0.040	-0.038	12.783	0.084	0.084	0.000	0.000	0.000	0.000
40	A	40	GLU	-1	-0.950	-0.973	11.921	0.039	0.039	0.000	0.000	0.000	0.000
41	A	41	ALA	0	-0.020	-0.006	8.298	-0.063	-0.063	0.000	0.000	0.000	0.000
42	A	42	ASN	0	-0.046	-0.016	8.347	0.513	0.513	0.000	0.000	0.000	0.000
43	A	43	PRO	0	0.058	0.051	9.162	-0.062	-0.062	0.000	0.000	0.000	0.000
44	A	44	LEU	0	-0.032	-0.016	12.295	0.124	0.124	0.000	0.000	0.000	0.000
45	A	45	TRP	0	0.034	-0.005	6.889	0.056	0.056	0.000	0.000	0.000	0.000
46	A	46	GLU	-1	-0.835	-0.890	13.926	0.148	0.148	0.000	0.000	0.000	0.000
47	A	47	MET	0	-0.032	-0.001	13.956	0.037	0.037	0.000	0.000	0.000	0.000
48	A	48	LYS	1	0.841	0.914	16.033	-0.222	-0.222	0.000	0.000	0.000	0.000
49	A	49	ALA	0	0.036	0.021	17.031	0.027	0.027	0.000	0.000	0.000	0.000
50	A	50	PHE	0	0.000	-0.006	15.578	-0.046	-0.046	0.000	0.000	0.000	0.000
51	A	51	SER	0	-0.026	-0.018	19.884	0.015	0.015	0.000	0.000	0.000	0.000
52	A	52	TYR	0	0.001	0.001	21.107	-0.027	-0.027	0.000	0.000	0.000	0.000
53	A	53	GLN	0	-0.032	-0.021	22.959	-0.004	-0.004	0.000	0.000	0.000	0.000
54	A	54	GLY	0	0.008	0.017	25.680	-0.002	-0.002	0.000	0.000	0.000	0.000
55	A	55	GLU	-1	-0.918	-0.942	21.638	0.111	0.111	0.000	0.000	0.000	0.000
56	A	56	VAL	0	-0.033	-0.031	21.239	-0.009	-0.009	0.000	0.000	0.000	0.000
57	A	57	ILE	0	0.003	0.001	15.434	0.025	0.025	0.000	0.000	0.000	0.000
58	A	58	GLN	0	-0.018	-0.027	16.000	-0.024	-0.024	0.000	0.000	0.000	0.000
59	A	59	GLU	-1	-0.861	-0.929	10.077	0.833	0.833	0.000	0.000	0.000	0.000
60	A	60	PRO	0	-0.043	-0.017	9.573	-0.110	-0.110	0.000	0.000	0.000	0.000
61	A	61	ILE	0	0.015	0.002	10.967	0.008	0.008	0.000	0.000	0.000	0.000
62	A	62	ALA	0	0.030	0.018	10.080	0.044	0.044	0.000	0.000	0.000	0.000
63	A	63	LYS	1	0.838	0.899	12.152	-0.227	-0.227	0.000	0.000	0.000	0.000
64	A	64	MET	0	0.039	0.038	14.719	0.038	0.038	0.000	0.000	0.000	0.000
65	A	65	ARG	1	0.838	0.919	13.823	-0.442	-0.442	0.000	0.000	0.000	0.000
66	A	66	ALA	0	0.020	0.018	17.234	-0.023	-0.023	0.000	0.000	0.000	0.000
67	A	67	MET	0	-0.019	0.019	17.296	0.026	0.026	0.000	0.000	0.000	0.000
68	A	68	THR	0	0.030	-0.010	21.155	-0.014	-0.014	0.000	0.000	0.000	0.000
69	A	69	ILE	0	0.053	0.031	24.314	0.011	0.011	0.000	0.000	0.000	0.000
70	A	70	THR	0	-0.001	-0.003	26.689	0.006	0.006	0.000	0.000	0.000	0.000
71	A	71	GLY	0	0.010	0.009	22.691	0.010	0.010	0.000	0.000	0.000	0.000
72	A	72	LEU	0	0.034	0.017	22.407	0.019	0.019	0.000	0.000	0.000	0.000
73	A	73	THR	0	-0.020	-0.018	23.444	0.004	0.004	0.000	0.000	0.000	0.000
74	A	74	LEU	0	-0.016	-0.007	23.981	-0.002	-0.002	0.000	0.000	0.000	0.000
75	A	75	PHE	0	0.032	0.042	15.951	0.003	0.003	0.000	0.000	0.000	0.000
76	A	76	ILE	0	-0.042	-0.021	21.350	0.010	0.010	0.000	0.000	0.000	0.000
77	A	77	ASP	-1	-0.755	-0.869	23.666	0.185	0.185	0.000	0.000	0.000	0.000
78	A	78	VAL	0	-0.015	-0.004	26.020	-0.016	-0.016	0.000	0.000	0.000	0.000
79	A	79	THR	0	0.008	-0.011	29.252	0.004	0.004	0.000	0.000	0.000	0.000
80	A	80	LEU	0	0.048	0.007	30.493	-0.005	-0.005	0.000	0.000	0.000	0.000
81	A	81	GLU	-1	-0.852	-0.913	33.178	0.097	0.097	0.000	0.000	0.000	0.000
82	A	82	THR	0	-0.037	-0.009	32.455	-0.008	-0.008	0.000	0.000	0.000	0.000
83	A	83	TRP	0	-0.011	-0.023	27.208	-0.002	-0.002	0.000	0.000	0.000	0.000
84	A	84	ARG	1	0.922	0.957	32.417	-0.093	-0.093	0.000	0.000	0.000	0.000
85	A	85	THR	0	-0.013	-0.023	35.832	-0.008	-0.008	0.000	0.000	0.000	0.000
86	A	86	TYR	0	0.044	0.014	29.865	-0.003	-0.003	0.000	0.000	0.000	0.000
87	A	87	ARG	1	0.818	0.897	33.703	-0.058	-0.058	0.000	0.000	0.000	0.000
88	A	88	LEU	0	-0.040	-0.011	37.505	-0.005	-0.005	0.000	0.000	0.000	0.000
89	A	89	ARG	1	0.758	0.878	35.543	-0.054	-0.054	0.000	0.000	0.000	0.000
90	A	90	GLH	0	-0.048	-0.070	37.292	0.003	0.003	0.000	0.000	0.000	0.000
91	A	91	ASP	-1	-0.758	-0.883	35.823	0.040	0.040	0.000	0.000	0.000	0.000
92	A	92	LEU	0	0.032	0.025	31.768	0.001	0.001	0.000	0.000	0.000	0.000
93	A	93	SER	0	-0.016	0.005	32.758	0.005	0.005	0.000	0.000	0.000	0.000
94	A	94	GLU	-1	-0.841	-0.873	32.965	0.019	0.019	0.000	0.000	0.000	0.000
95	A	95	VAL	0	-0.041	-0.007	27.731	-0.001	-0.001	0.000	0.000	0.000	0.000
96	A	96	VAL	0	-0.014	-0.006	28.752	0.004	0.004	0.000	0.000	0.000	0.000
97	A	97	THR	0	0.003	-0.015	29.788	0.003	0.003	0.000	0.000	0.000	0.000
98	A	98	ARG	1	0.907	0.965	26.602	-0.030	-0.030	0.000	0.000	0.000	0.000
99	A	99	ALA	0	0.020	0.008	25.303	-0.002	-0.002	0.000	0.000	0.000	0.000
100	A	100	GLU	-1	-0.811	-0.909	25.647	0.078	0.078	0.000	0.000	0.000	0.000
101	A	101	GLN	0	-0.054	-0.033	27.875	0.004	0.004	0.000	0.000	0.000	0.000
102	A	102	VAL	0	0.008	0.009	21.532	-0.005	-0.005	0.000	0.000	0.000	0.000
103	A	103	ILE	0	-0.039	-0.022	23.311	0.002	0.002	0.000	0.000	0.000	0.000
104	A	104	TYR	0	-0.044	-0.027	24.384	0.002	0.002	0.000	0.000	0.000	0.000
105	A	105	ASP	-1	-0.804	-0.907	24.856	0.006	0.006	0.000	0.000	0.000	0.000
106	A	106	GLN	0	0.012	0.016	17.164	-0.007	-0.007	0.000	0.000	0.000	0.000
107	A	107	LYS	1	0.794	0.881	21.495	-0.096	-0.096	0.000	0.000	0.000	0.000
108	A	108	PHE	0	-0.004	0.000	23.536	-0.006	-0.006	0.000	0.000	0.000	0.000
109	A	109	SER	0	-0.019	-0.036	22.056	-0.008	-0.008	0.000	0.000	0.000	0.000
110	A	110	GLY	0	0.043	0.010	20.894	-0.013	-0.013	0.000	0.000	0.000	0.000
111	A	111	ALA	0	-0.052	-0.034	21.655	-0.003	-0.003	0.000	0.000	0.000	0.000
112	A	112	ALA	0	-0.043	-0.018	25.059	-0.002	-0.002	0.000	0.000	0.000	0.000
113	A	113	ALA	0	-0.017	-0.005	21.864	-0.012	-0.012	0.000	0.000	0.000	0.000
114	A	114	ASP	-1	-0.948	-0.965	22.466	-0.005	-0.005	0.000	0.000	0.000	0.000
115	A	115	LEU	0	-0.047	-0.013	17.506	0.010	0.010	0.000	0.000	0.000	0.000
116	A	116	LEU	0	-0.056	-0.029	19.805	0.034	0.034	0.000	0.000	0.000	0.000
117	A	117	ASN	0	0.003	-0.010	22.544	-0.018	-0.018	0.000	0.000	0.000	0.000
118	A	118	ALA	0	0.156	0.073	26.043	0.006	0.006	0.000	0.000	0.000	0.000
119	A	119	ASN	0	0.018	0.020	28.460	0.005	0.005	0.000	0.000	0.000	0.000
120	A	120	ILE	0	-0.026	-0.018	27.205	0.002	0.002	0.000	0.000	0.000	0.000
121	A	121	ILE	0	0.037	0.009	24.441	0.003	0.003	0.000	0.000	0.000	0.000
122	A	122	ALA	0	0.014	0.016	28.346	-0.002	-0.002	0.000	0.000	0.000	0.000
123	A	123	ARG	1	0.856	0.923	31.816	-0.068	-0.068	0.000	0.000	0.000	0.000
124	A	124	ASP	-1	-0.831	-0.903	28.089	0.093	0.093	0.000	0.000	0.000	0.000
125	A	125	LEU	0	-0.023	0.009	27.468	0.001	0.001	0.000	0.000	0.000	0.000
126	A	126	GLY	0	-0.026	-0.002	31.354	-0.006	-0.006	0.000	0.000	0.000	0.000
127	A	127	LEU	0	-0.045	-0.019	31.355	-0.005	-0.005	0.000	0.000	0.000	0.000
128	A	128	LYS	1	0.905	0.944	35.426	-0.029	-0.029	0.000	0.000	0.000	0.000
129	A	129	GLU	-1	-0.873	-0.934	38.582	0.018	0.018	0.000	0.000	0.000	0.000
130	A	130	GLN	0	-0.083	-0.043	40.534	0.001	0.001	0.000	0.000	0.000	0.000
131	A	131	SER	0	-0.014	-0.002	43.675	-0.001	-0.001	0.000	0.000	0.000	0.000
132	A	132	GLN	0	-0.021	-0.017	46.788	-0.001	-0.001	0.000	0.000	0.000	0.000
133	A	133	VAL	0	-0.007	-0.008	50.481	0.000	0.000	0.000	0.000	0.000	0.000
134	A	134	GLU	-1	-0.938	-0.960	53.372	0.005	0.005	0.000	0.000	0.000	0.000
135	A	135	ASP	-1	-0.874	-0.917	56.942	0.014	0.014	0.000	0.000	0.000	0.000
136	A	136	VAL	0	-0.018	-0.011	58.816	-0.001	-0.001	0.000	0.000	0.000	0.000
137	A	137	THR	0	-0.067	-0.052	61.367	0.000	0.000	0.000	0.000	0.000	0.000
138	A	138	PRO	0	-0.087	-0.052	63.997	0.000	0.000	0.000	0.000	0.000	0.000
139	A	139	ASP	-1	-0.965	-0.962	67.270	0.010	0.010	0.000	0.000	0.000	0.000

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