FMO DATABASE

FMODB ID: 66L9Z

Calculation Name: 3P9A-A-Xray320

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: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	140
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1137543.21551
FMO2-HF: Nuclear repulsion	1081213.89796
FMO2-HF: Total energy	-56329.31755
FMO2-MP2: Total energy	-56492.067455

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.
-1.943	1.096	-0.016	-1.578	-1.445	-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 : -0.017 / q_NPA : -0.018

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	0.025	3.821	-2.677	0.362	-0.016	-1.578	-1.445	-0.002
4	A	4	PRO	0	-0.030	-0.029	5.466	-0.162	-0.162	0.000	0.000	0.000	0.000
5	A	5	LYN	0	0.041	0.037	5.690	0.398	0.398	0.000	0.000	0.000	0.000
6	A	6	GLY	0	-0.037	-0.009	7.791	-0.176	-0.176	0.000	0.000	0.000	0.000
7	A	7	ASN	0	-0.040	-0.022	10.043	-0.155	-0.155	0.000	0.000	0.000	0.000
8	A	8	ARG	1	0.882	0.944	12.978	-0.536	-0.536	0.000	0.000	0.000	0.000
9	A	9	PHE	0	0.044	0.008	16.621	-0.022	-0.022	0.000	0.000	0.000	0.000
10	A	10	TRP	0	-0.035	-0.012	18.107	-0.011	-0.011	0.000	0.000	0.000	0.000
11	A	11	GLU	-1	-0.897	-0.959	18.261	0.410	0.410	0.000	0.000	0.000	0.000
12	A	12	ALA	0	-0.069	-0.011	16.747	0.003	0.003	0.000	0.000	0.000	0.000
13	A	13	ARG	1	0.932	0.965	18.245	-0.273	-0.273	0.000	0.000	0.000	0.000
14	A	14	SER	0	-0.027	0.006	18.388	0.024	0.024	0.000	0.000	0.000	0.000
15	A	15	SER	0	-0.059	-0.077	17.956	-0.009	-0.009	0.000	0.000	0.000	0.000
16	A	16	HIS	0	-0.014	-0.011	19.675	-0.022	-0.022	0.000	0.000	0.000	0.000
17	A	17	GLY	0	-0.046	-0.016	22.440	-0.012	-0.012	0.000	0.000	0.000	0.000
18	A	18	ARG	1	0.895	0.936	24.034	-0.153	-0.153	0.000	0.000	0.000	0.000
19	A	19	ASN	0	-0.081	-0.050	27.067	-0.011	-0.011	0.000	0.000	0.000	0.000
20	A	20	PRO	0	0.028	0.044	26.166	-0.011	-0.011	0.000	0.000	0.000	0.000
21	A	21	LYS	1	0.898	0.946	29.004	-0.073	-0.073	0.000	0.000	0.000	0.000
22	A	22	PHE	0	-0.011	-0.012	25.539	-0.005	-0.005	0.000	0.000	0.000	0.000
23	A	23	GLU	-1	-0.852	-0.945	31.007	0.057	0.057	0.000	0.000	0.000	0.000
24	A	24	SER	0	-0.019	-0.014	30.515	-0.004	-0.004	0.000	0.000	0.000	0.000
25	A	25	PRO	0	0.051	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	0.040	0.040	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	0.013	0.010	25.495	0.012	0.012	0.000	0.000	0.000	0.000
29	A	29	TRP	0	0.049	0.001	23.418	0.009	0.009	0.000	0.000	0.000	0.000
30	A	30	ALA	0	0.027	0.016	22.031	0.004	0.004	0.000	0.000	0.000	0.000
31	A	31	ALA	0	0.019	0.016	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	-0.013	-0.019	18.967	-0.002	-0.002	0.000	0.000	0.000	0.000
34	A	34	GLU	-1	-0.728	-0.817	16.753	0.255	0.255	0.000	0.000	0.000	0.000
35	A	35	TYR	0	-0.003	0.005	16.411	0.030	0.030	0.000	0.000	0.000	0.000
36	A	36	PHE	0	-0.019	-0.037	17.074	0.013	0.013	0.000	0.000	0.000	0.000
37	A	37	GLU	-1	-0.861	-0.928	12.951	0.182	0.182	0.000	0.000	0.000	0.000
38	A	38	TRP	0	-0.010	0.000	12.329	0.018	0.018	0.000	0.000	0.000	0.000
39	A	39	VAL	0	-0.058	-0.043	12.939	0.043	0.043	0.000	0.000	0.000	0.000
40	A	40	GLU	-1	-0.965	-0.972	11.645	-0.066	-0.066	0.000	0.000	0.000	0.000
41	A	41	ALA	0	-0.023	-0.002	8.530	-0.079	-0.079	0.000	0.000	0.000	0.000
42	A	42	ASN	0	-0.068	-0.038	8.753	0.316	0.316	0.000	0.000	0.000	0.000
43	A	43	PRO	0	0.049	0.047	9.412	-0.035	-0.035	0.000	0.000	0.000	0.000
44	A	44	LEU	0	-0.045	-0.027	12.375	0.115	0.115	0.000	0.000	0.000	0.000
45	A	45	TRP	0	0.033	0.003	7.502	0.013	0.013	0.000	0.000	0.000	0.000
46	A	46	GLU	-1	-0.955	-0.975	14.051	0.128	0.128	0.000	0.000	0.000	0.000
47	A	47	MET	0	-0.030	0.000	14.149	0.048	0.048	0.000	0.000	0.000	0.000
48	A	48	LYS	1	0.939	0.973	16.154	-0.159	-0.159	0.000	0.000	0.000	0.000
49	A	49	ALA	0	0.028	0.013	17.139	0.035	0.035	0.000	0.000	0.000	0.000
50	A	50	PHE	0	-0.011	-0.006	15.523	-0.048	-0.048	0.000	0.000	0.000	0.000
51	A	51	SER	0	-0.019	-0.016	19.933	0.015	0.015	0.000	0.000	0.000	0.000
52	A	52	TYR	0	0.007	0.006	21.028	-0.025	-0.025	0.000	0.000	0.000	0.000
53	A	53	GLN	0	-0.021	-0.016	22.869	-0.006	-0.006	0.000	0.000	0.000	0.000
54	A	54	GLY	0	0.011	0.014	25.904	0.004	0.004	0.000	0.000	0.000	0.000
55	A	55	GLU	-1	-0.923	-0.950	21.558	0.112	0.112	0.000	0.000	0.000	0.000
56	A	56	VAL	0	-0.053	-0.036	21.047	-0.006	-0.006	0.000	0.000	0.000	0.000
57	A	57	ILE	0	0.003	0.005	15.364	0.025	0.025	0.000	0.000	0.000	0.000
58	A	58	GLN	0	-0.019	-0.024	15.986	-0.028	-0.028	0.000	0.000	0.000	0.000
59	A	59	GLU	-1	-0.885	-0.957	9.442	0.906	0.906	0.000	0.000	0.000	0.000
60	A	60	PRO	0	-0.045	-0.004	9.769	-0.113	-0.113	0.000	0.000	0.000	0.000
61	A	61	ILE	0	0.006	-0.003	11.154	-0.008	-0.008	0.000	0.000	0.000	0.000
62	A	62	ALA	0	0.025	0.014	10.186	0.038	0.038	0.000	0.000	0.000	0.000
63	A	63	LYS	1	0.917	0.950	12.248	-0.142	-0.142	0.000	0.000	0.000	0.000
64	A	64	MET	0	0.045	0.034	15.028	0.028	0.028	0.000	0.000	0.000	0.000
65	A	65	ARG	1	0.895	0.946	14.374	-0.307	-0.307	0.000	0.000	0.000	0.000
66	A	66	ALA	0	0.004	0.012	17.471	-0.020	-0.020	0.000	0.000	0.000	0.000
67	A	67	MET	0	-0.003	0.025	17.999	0.023	0.023	0.000	0.000	0.000	0.000
68	A	68	THR	0	0.028	-0.002	21.449	-0.010	-0.010	0.000	0.000	0.000	0.000
69	A	69	ILE	0	0.073	0.040	24.538	0.010	0.010	0.000	0.000	0.000	0.000
70	A	70	THR	0	-0.018	-0.013	27.023	0.007	0.007	0.000	0.000	0.000	0.000
71	A	71	GLY	0	0.029	0.019	23.087	0.010	0.010	0.000	0.000	0.000	0.000
72	A	72	LEU	0	0.016	0.013	22.747	0.017	0.017	0.000	0.000	0.000	0.000
73	A	73	THR	0	-0.075	-0.044	23.782	0.006	0.006	0.000	0.000	0.000	0.000
74	A	74	LEU	0	0.018	-0.002	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	-0.046	-0.041	22.172	0.011	0.011	0.000	0.000	0.000	0.000
77	A	77	ASP	-1	-0.833	-0.904	23.991	0.162	0.162	0.000	0.000	0.000	0.000
78	A	78	VAL	0	-0.025	0.003	26.499	-0.013	-0.013	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	0.060	0.001	30.897	-0.006	-0.006	0.000	0.000	0.000	0.000
81	A	81	GLU	-1	-0.938	-0.964	33.466	0.073	0.073	0.000	0.000	0.000	0.000
82	A	82	THR	0	0.004	0.006	33.024	-0.006	-0.006	0.000	0.000	0.000	0.000
83	A	83	TRP	0	-0.030	-0.023	27.742	-0.001	-0.001	0.000	0.000	0.000	0.000
84	A	84	ARG	1	0.916	0.947	33.032	-0.075	-0.075	0.000	0.000	0.000	0.000
85	A	85	THR	0	0.000	-0.018	36.317	-0.006	-0.006	0.000	0.000	0.000	0.000
86	A	86	TYR	0	0.025	0.012	30.348	-0.005	-0.005	0.000	0.000	0.000	0.000
87	A	87	ARG	1	0.856	0.917	34.690	-0.045	-0.045	0.000	0.000	0.000	0.000
88	A	88	LEU	0	-0.028	-0.005	38.088	-0.004	-0.004	0.000	0.000	0.000	0.000
89	A	89	ARG	1	0.805	0.897	36.243	-0.048	-0.048	0.000	0.000	0.000	0.000
90	A	90	GLH	0	-0.075	-0.082	37.880	0.002	0.002	0.000	0.000	0.000	0.000
91	A	91	ASP	-1	-0.767	-0.868	36.401	0.033	0.033	0.000	0.000	0.000	0.000
92	A	92	LEU	0	0.024	0.010	32.671	0.000	0.000	0.000	0.000	0.000	0.000
93	A	93	SER	0	-0.015	0.005	33.054	0.004	0.004	0.000	0.000	0.000	0.000
94	A	94	GLU	-1	-0.813	-0.886	33.259	0.016	0.016	0.000	0.000	0.000	0.000
95	A	95	VAL	0	-0.034	-0.002	27.980	-0.002	-0.002	0.000	0.000	0.000	0.000
96	A	96	VAL	0	0.002	0.001	29.040	0.002	0.002	0.000	0.000	0.000	0.000
97	A	97	THR	0	0.012	0.013	30.125	0.003	0.003	0.000	0.000	0.000	0.000
98	A	98	ARG	1	0.939	0.987	26.153	-0.018	-0.018	0.000	0.000	0.000	0.000
99	A	99	ALA	0	0.010	0.002	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	0.059	0.059	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	-0.029	-0.019	23.183	-0.002	-0.002	0.000	0.000	0.000	0.000
104	A	104	TYR	0	-0.014	-0.005	24.396	-0.001	-0.001	0.000	0.000	0.000	0.000
105	A	105	ASP	-1	-0.884	-0.954	24.672	-0.019	-0.019	0.000	0.000	0.000	0.000
106	A	106	GLN	0	0.012	0.018	17.642	-0.004	-0.004	0.000	0.000	0.000	0.000
107	A	107	LYS	1	0.799	0.887	21.893	-0.074	-0.074	0.000	0.000	0.000	0.000
108	A	108	PHE	0	0.012	0.016	23.834	-0.004	-0.004	0.000	0.000	0.000	0.000
109	A	109	SER	0	-0.014	-0.022	22.109	-0.009	-0.009	0.000	0.000	0.000	0.000
110	A	110	GLY	0	0.037	0.004	20.925	-0.012	-0.012	0.000	0.000	0.000	0.000
111	A	111	ALA	0	-0.055	-0.033	21.712	-0.002	-0.002	0.000	0.000	0.000	0.000
112	A	112	ALA	0	-0.022	-0.004	25.040	-0.003	-0.003	0.000	0.000	0.000	0.000
113	A	113	ALA	0	-0.040	-0.011	21.627	-0.006	-0.006	0.000	0.000	0.000	0.000
114	A	114	ASP	-1	-0.930	-0.955	22.645	-0.036	-0.036	0.000	0.000	0.000	0.000
115	A	115	LEU	0	-0.076	-0.038	17.357	0.004	0.004	0.000	0.000	0.000	0.000
116	A	116	LEU	0	-0.068	-0.033	20.000	0.028	0.028	0.000	0.000	0.000	0.000
117	A	117	ASN	0	-0.004	-0.009	22.625	-0.010	-0.010	0.000	0.000	0.000	0.000
118	A	118	ALA	0	0.141	0.065	26.011	0.004	0.004	0.000	0.000	0.000	0.000
119	A	119	ASN	0	0.024	0.019	28.642	0.007	0.007	0.000	0.000	0.000	0.000
120	A	120	ILE	0	0.011	-0.004	27.024	0.002	0.002	0.000	0.000	0.000	0.000
121	A	121	ILE	0	0.030	0.014	24.621	0.004	0.004	0.000	0.000	0.000	0.000
122	A	122	ALA	0	0.010	0.011	28.427	-0.001	-0.001	0.000	0.000	0.000	0.000
123	A	123	ARG	1	0.857	0.913	31.865	-0.048	-0.048	0.000	0.000	0.000	0.000
124	A	124	ASP	-1	-0.882	-0.927	28.028	0.068	0.068	0.000	0.000	0.000	0.000
125	A	125	LEU	0	-0.041	-0.019	27.747	0.000	0.000	0.000	0.000	0.000	0.000
126	A	126	GLY	0	-0.020	0.006	31.652	-0.003	-0.003	0.000	0.000	0.000	0.000
127	A	127	LEU	0	-0.056	-0.030	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	-0.017	-0.017	0.000	0.000	0.000	0.000
129	A	129	GLU	-1	-0.890	-0.937	38.662	0.006	0.006	0.000	0.000	0.000	0.000
130	A	130	GLN	0	-0.081	-0.040	40.851	0.001	0.001	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	-0.021	-0.017	46.983	0.000	0.000	0.000	0.000	0.000	0.000
133	A	133	VAL	0	-0.008	-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	0.001	0.001	0.000	0.000	0.000	0.000
135	A	135	ASP	-1	-0.892	-0.919	56.684	0.008	0.008	0.000	0.000	0.000	0.000
136	A	136	VAL	0	-0.009	-0.005	59.061	-0.001	-0.001	0.000	0.000	0.000	0.000
137	A	137	THR	0	-0.073	-0.061	61.522	0.000	0.000	0.000	0.000	0.000	0.000
138	A	138	PRO	0	-0.085	-0.044	64.074	0.000	0.000	0.000	0.000	0.000	0.000
139	A	139	ASP	-1	-0.858	-0.907	65.873	0.007	0.007	0.000	0.000	0.000	0.000
140	A	140	NME	0	-0.095	-0.055	68.917	-0.001	-0.001	0.000	0.000	0.000	0.000

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