FMO DATABASE

FMODB ID: GN361

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1136706.53458
FMO2-HF: Nuclear repulsion	1080396.330049
FMO2-HF: Total energy	-56310.204531
FMO2-MP2: Total energy	-56472.855191

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.
-1.997	1.123	-0.027	-1.609	-1.484	-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 : -0.018 / 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	3	ALA	0	0.031	0.026	3.821	-2.762	0.358	-0.027	-1.609	-1.484	-0.002
4	A	4	PRO	0	-0.029	-0.029	5.466	-0.134	-0.134	0.000	0.000	0.000	0.000
5	A	5	LYN	0	0.040	0.036	5.690	0.399	0.399	0.000	0.000	0.000	0.000
6	A	6	GLY	0	-0.035	-0.009	7.791	-0.156	-0.156	0.000	0.000	0.000	0.000
7	A	7	ASN	0	-0.041	-0.022	10.043	-0.146	-0.146	0.000	0.000	0.000	0.000
8	A	8	ARG	1	0.883	0.945	12.978	-0.528	-0.528	0.000	0.000	0.000	0.000
9	A	9	PHE	0	0.042	0.008	16.621	-0.019	-0.019	0.000	0.000	0.000	0.000
10	A	10	TRP	0	-0.034	-0.013	18.107	-0.010	-0.010	0.000	0.000	0.000	0.000
11	A	11	GLU	-1	-0.897	-0.960	18.261	0.407	0.407	0.000	0.000	0.000	0.000
12	A	12	ALA	0	-0.066	-0.011	16.747	0.003	0.003	0.000	0.000	0.000	0.000
13	A	13	ARG	1	0.931	0.965	18.245	-0.272	-0.272	0.000	0.000	0.000	0.000
14	A	14	SER	0	-0.029	0.006	18.388	0.024	0.024	0.000	0.000	0.000	0.000
15	A	15	SER	0	-0.060	-0.078	17.957	-0.008	-0.008	0.000	0.000	0.000	0.000
16	A	16	HIS	0	-0.012	-0.011	19.675	-0.021	-0.021	0.000	0.000	0.000	0.000
17	A	17	GLY	0	-0.043	-0.015	22.440	-0.012	-0.012	0.000	0.000	0.000	0.000
18	A	18	ARG	1	0.896	0.936	24.034	-0.153	-0.153	0.000	0.000	0.000	0.000
19	A	19	ASN	0	-0.081	-0.049	27.067	-0.010	-0.010	0.000	0.000	0.000	0.000
20	A	20	PRO	0	0.024	0.042	26.166	-0.011	-0.011	0.000	0.000	0.000	0.000
21	A	21	LYS	1	0.897	0.946	29.004	-0.073	-0.073	0.000	0.000	0.000	0.000
22	A	22	PHE	0	-0.007	-0.011	25.539	-0.005	-0.005	0.000	0.000	0.000	0.000
23	A	23	GLU	-1	-0.853	-0.945	31.007	0.058	0.058	0.000	0.000	0.000	0.000
24	A	24	SER	0	-0.020	-0.014	30.511	-0.004	-0.004	0.000	0.000	0.000	0.000
25	A	25	PRO	0	0.049	0.030	30.521	0.008	0.008	0.000	0.000	0.000	0.000
26	A	26	GLU	-1	-0.861	-0.940	27.825	0.041	0.041	0.000	0.000	0.000	0.000
27	A	27	ALA	0	-0.016	0.004	26.169	0.008	0.008	0.000	0.000	0.000	0.000
28	A	28	LEU	0	0.022	0.014	25.495	0.012	0.012	0.000	0.000	0.000	0.000
29	A	29	TRP	0	0.043	-0.001	23.418	0.009	0.009	0.000	0.000	0.000	0.000
30	A	30	ALA	0	0.022	0.013	22.031	0.004	0.004	0.000	0.000	0.000	0.000
31	A	31	ALA	0	0.018	0.015	20.860	0.019	0.019	0.000	0.000	0.000	0.000
32	A	32	CYS	0	-0.088	-0.047	21.187	0.016	0.016	0.000	0.000	0.000	0.000
33	A	33	CYS	0	-0.012	-0.018	18.967	-0.003	-0.003	0.000	0.000	0.000	0.000
34	A	34	GLU	-1	-0.728	-0.817	16.753	0.257	0.257	0.000	0.000	0.000	0.000
35	A	35	TYR	0	-0.005	0.004	16.411	0.028	0.028	0.000	0.000	0.000	0.000
36	A	36	PHE	0	-0.017	-0.037	17.074	0.012	0.012	0.000	0.000	0.000	0.000
37	A	37	GLU	-1	-0.860	-0.928	12.951	0.185	0.185	0.000	0.000	0.000	0.000
38	A	38	TRP	0	-0.011	0.000	12.329	0.013	0.013	0.000	0.000	0.000	0.000
39	A	39	VAL	0	-0.057	-0.043	12.939	0.041	0.041	0.000	0.000	0.000	0.000
40	A	40	GLU	-1	-0.965	-0.973	11.645	-0.070	-0.070	0.000	0.000	0.000	0.000
41	A	41	ALA	0	-0.024	-0.002	8.530	-0.084	-0.084	0.000	0.000	0.000	0.000
42	A	42	ASN	0	-0.067	-0.037	8.753	0.303	0.303	0.000	0.000	0.000	0.000
43	A	43	PRO	0	0.051	0.048	9.412	-0.028	-0.028	0.000	0.000	0.000	0.000
44	A	44	LEU	0	-0.047	-0.028	12.375	0.113	0.113	0.000	0.000	0.000	0.000
45	A	45	TRP	0	0.033	0.002	7.502	0.011	0.011	0.000	0.000	0.000	0.000
46	A	46	GLU	-1	-0.954	-0.974	14.051	0.119	0.119	0.000	0.000	0.000	0.000
47	A	47	MET	0	-0.034	-0.002	14.149	0.044	0.044	0.000	0.000	0.000	0.000
48	A	48	LYS	1	0.942	0.974	16.154	-0.142	-0.142	0.000	0.000	0.000	0.000
49	A	49	ALA	0	0.030	0.014	17.127	0.035	0.035	0.000	0.000	0.000	0.000
50	A	50	PHE	0	-0.012	-0.007	15.510	-0.046	-0.046	0.000	0.000	0.000	0.000
51	A	51	SER	0	-0.017	-0.016	19.921	0.016	0.016	0.000	0.000	0.000	0.000
52	A	52	TYR	0	0.005	0.006	21.019	-0.024	-0.024	0.000	0.000	0.000	0.000
53	A	53	GLN	0	-0.020	-0.016	22.859	-0.006	-0.006	0.000	0.000	0.000	0.000
54	A	54	GLY	0	0.012	0.013	25.895	0.004	0.004	0.000	0.000	0.000	0.000
55	A	55	GLU	-1	-0.924	-0.950	21.549	0.106	0.106	0.000	0.000	0.000	0.000
56	A	56	VAL	0	-0.053	-0.036	21.036	-0.007	-0.007	0.000	0.000	0.000	0.000
57	A	57	ILE	0	0.003	0.005	15.353	0.024	0.024	0.000	0.000	0.000	0.000
58	A	58	GLN	0	-0.021	-0.025	15.986	-0.030	-0.030	0.000	0.000	0.000	0.000
59	A	59	GLU	-1	-0.884	-0.956	9.430	0.867	0.867	0.000	0.000	0.000	0.000
60	A	60	PRO	0	-0.043	-0.003	9.769	-0.110	-0.110	0.000	0.000	0.000	0.000
61	A	61	ILE	0	0.003	-0.004	11.154	-0.010	-0.010	0.000	0.000	0.000	0.000
62	A	62	ALA	0	0.028	0.015	10.186	0.042	0.042	0.000	0.000	0.000	0.000
63	A	63	LYS	1	0.917	0.950	12.248	-0.124	-0.124	0.000	0.000	0.000	0.000
64	A	64	MET	0	0.044	0.034	15.028	0.028	0.028	0.000	0.000	0.000	0.000
65	A	65	ARG	1	0.897	0.946	14.374	-0.296	-0.296	0.000	0.000	0.000	0.000
66	A	66	ALA	0	0.004	0.012	17.471	-0.019	-0.019	0.000	0.000	0.000	0.000
67	A	67	MET	0	-0.003	0.024	17.999	0.023	0.023	0.000	0.000	0.000	0.000
68	A	68	THR	0	0.026	-0.002	21.449	-0.009	-0.009	0.000	0.000	0.000	0.000
69	A	69	ILE	0	0.068	0.039	24.538	0.010	0.010	0.000	0.000	0.000	0.000
70	A	70	THR	0	-0.013	-0.011	27.023	0.006	0.006	0.000	0.000	0.000	0.000
71	A	71	GLY	0	0.032	0.018	23.087	0.010	0.010	0.000	0.000	0.000	0.000
72	A	72	LEU	0	0.020	0.014	22.747	0.017	0.017	0.000	0.000	0.000	0.000
73	A	73	THR	0	-0.076	-0.044	23.782	0.006	0.006	0.000	0.000	0.000	0.000
74	A	74	LEU	0	0.014	-0.005	23.946	0.001	0.001	0.000	0.000	0.000	0.000
75	A	75	PHE	0	0.005	0.032	16.877	0.005	0.005	0.000	0.000	0.000	0.000
76	A	76	ILE	0	-0.047	-0.041	22.172	0.012	0.012	0.000	0.000	0.000	0.000
77	A	77	ASP	-1	-0.833	-0.905	23.991	0.162	0.162	0.000	0.000	0.000	0.000
78	A	78	VAL	0	-0.026	0.004	26.499	-0.012	-0.012	0.000	0.000	0.000	0.000
79	A	79	THR	0	0.058	0.029	29.694	0.002	0.002	0.000	0.000	0.000	0.000
80	A	80	LEU	0	0.061	0.002	30.897	-0.006	-0.006	0.000	0.000	0.000	0.000
81	A	81	GLU	-1	-0.939	-0.964	33.466	0.073	0.073	0.000	0.000	0.000	0.000
82	A	82	THR	0	0.002	0.005	33.024	-0.006	-0.006	0.000	0.000	0.000	0.000
83	A	83	TRP	0	-0.029	-0.023	27.742	-0.001	-0.001	0.000	0.000	0.000	0.000
84	A	84	ARG	1	0.915	0.946	33.032	-0.074	-0.074	0.000	0.000	0.000	0.000
85	A	85	THR	0	0.001	-0.018	36.317	-0.006	-0.006	0.000	0.000	0.000	0.000
86	A	86	TYR	0	0.027	0.012	30.348	-0.005	-0.005	0.000	0.000	0.000	0.000
87	A	87	ARG	1	0.855	0.916	34.690	-0.045	-0.045	0.000	0.000	0.000	0.000
88	A	88	LEU	0	-0.026	-0.005	38.088	-0.004	-0.004	0.000	0.000	0.000	0.000
89	A	89	ARG	1	0.803	0.897	36.243	-0.048	-0.048	0.000	0.000	0.000	0.000
90	A	90	GLH	0	-0.076	-0.082	37.880	0.002	0.002	0.000	0.000	0.000	0.000
91	A	91	ASP	-1	-0.769	-0.869	36.401	0.034	0.034	0.000	0.000	0.000	0.000
92	A	92	LEU	0	0.026	0.011	32.671	0.000	0.000	0.000	0.000	0.000	0.000
93	A	93	SER	0	-0.015	0.004	33.054	0.003	0.003	0.000	0.000	0.000	0.000
94	A	94	GLU	-1	-0.815	-0.887	33.259	0.016	0.016	0.000	0.000	0.000	0.000
95	A	95	VAL	0	-0.030	0.000	27.981	-0.002	-0.002	0.000	0.000	0.000	0.000
96	A	96	VAL	0	-0.005	-0.001	29.040	0.002	0.002	0.000	0.000	0.000	0.000
97	A	97	THR	0	0.018	0.014	30.125	0.002	0.002	0.000	0.000	0.000	0.000
98	A	98	ARG	1	0.935	0.986	26.153	-0.018	-0.018	0.000	0.000	0.000	0.000
99	A	99	ALA	0	0.012	0.003	25.585	-0.003	-0.003	0.000	0.000	0.000	0.000
100	A	100	GLU	-1	-0.880	-0.956	25.828	0.057	0.057	0.000	0.000	0.000	0.000
101	A	101	GLN	0	0.009	0.009	28.010	0.002	0.002	0.000	0.000	0.000	0.000
102	A	102	VAL	0	0.001	0.009	21.789	-0.007	-0.007	0.000	0.000	0.000	0.000
103	A	103	ILE	0	-0.025	-0.017	23.183	-0.003	-0.003	0.000	0.000	0.000	0.000
104	A	104	TYR	0	-0.017	-0.006	24.396	-0.002	-0.002	0.000	0.000	0.000	0.000
105	A	105	ASP	-1	-0.885	-0.954	24.672	-0.021	-0.021	0.000	0.000	0.000	0.000
106	A	106	GLN	0	0.015	0.019	17.642	-0.004	-0.004	0.000	0.000	0.000	0.000
107	A	107	LYS	1	0.796	0.886	21.893	-0.072	-0.072	0.000	0.000	0.000	0.000
108	A	108	PHE	0	0.013	0.017	23.834	-0.004	-0.004	0.000	0.000	0.000	0.000
109	A	109	SER	0	-0.012	-0.022	22.109	-0.009	-0.009	0.000	0.000	0.000	0.000
110	A	110	GLY	0	0.040	0.005	20.925	-0.012	-0.012	0.000	0.000	0.000	0.000
111	A	111	ALA	0	-0.059	-0.035	21.712	-0.003	-0.003	0.000	0.000	0.000	0.000
112	A	112	ALA	0	-0.017	-0.002	25.040	-0.002	-0.002	0.000	0.000	0.000	0.000
113	A	113	ALA	0	-0.044	-0.012	21.627	-0.006	-0.006	0.000	0.000	0.000	0.000
114	A	114	ASP	-1	-0.932	-0.956	22.645	-0.043	-0.043	0.000	0.000	0.000	0.000
115	A	115	LEU	0	-0.074	-0.037	17.358	0.002	0.002	0.000	0.000	0.000	0.000
116	A	116	LEU	0	-0.065	-0.031	20.000	0.027	0.027	0.000	0.000	0.000	0.000
117	A	117	ASN	0	-0.006	-0.009	22.625	-0.009	-0.009	0.000	0.000	0.000	0.000
118	A	118	ALA	0	0.139	0.065	26.011	0.004	0.004	0.000	0.000	0.000	0.000
119	A	119	ASN	0	0.025	0.019	28.642	0.007	0.007	0.000	0.000	0.000	0.000
120	A	120	ILE	0	0.012	-0.004	27.024	0.002	0.002	0.000	0.000	0.000	0.000
121	A	121	ILE	0	0.031	0.014	24.622	0.004	0.004	0.000	0.000	0.000	0.000
122	A	122	ALA	0	0.008	0.010	28.427	0.000	0.000	0.000	0.000	0.000	0.000
123	A	123	ARG	1	0.859	0.914	31.865	-0.045	-0.045	0.000	0.000	0.000	0.000
124	A	124	ASP	-1	-0.882	-0.928	28.028	0.065	0.065	0.000	0.000	0.000	0.000
125	A	125	LEU	0	-0.043	-0.019	27.747	0.000	0.000	0.000	0.000	0.000	0.000
126	A	126	GLY	0	-0.018	0.006	31.652	-0.003	-0.003	0.000	0.000	0.000	0.000
127	A	127	LEU	0	-0.055	-0.029	31.495	-0.004	-0.004	0.000	0.000	0.000	0.000
128	A	128	LYS	1	0.920	0.951	35.544	-0.015	-0.015	0.000	0.000	0.000	0.000
129	A	129	GLU	-1	-0.889	-0.937	38.662	0.004	0.004	0.000	0.000	0.000	0.000
130	A	130	GLN	0	-0.081	-0.041	40.851	0.002	0.002	0.000	0.000	0.000	0.000
131	A	131	SER	0	0.000	-0.003	43.957	-0.001	-0.001	0.000	0.000	0.000	0.000
132	A	132	GLN	0	-0.020	-0.017	46.983	0.000	0.000	0.000	0.000	0.000	0.000
133	A	133	VAL	0	-0.007	-0.004	50.500	0.000	0.000	0.000	0.000	0.000	0.000
134	A	134	GLU	-1	-0.943	-0.970	53.188	0.000	0.000	0.000	0.000	0.000	0.000
135	A	135	ASP	-1	-0.890	-0.919	56.684	0.007	0.007	0.000	0.000	0.000	0.000
136	A	136	VAL	0	-0.010	-0.006	59.061	-0.001	-0.001	0.000	0.000	0.000	0.000
137	A	137	THR	0	-0.075	-0.060	61.522	0.000	0.000	0.000	0.000	0.000	0.000
138	A	138	PRO	0	-0.084	-0.044	64.074	0.000	0.000	0.000	0.000	0.000	0.000
139	A	139	ASP	-1	-0.950	-0.961	65.873	0.006	0.006	0.000	0.000	0.000	0.000

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