FMO DATABASE

FMODB ID: Z2MRN

Calculation Name: 3DOS-B-Xray312

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3DOS

Chain ID: B

ChEMBL ID:

UniProt ID: P26926

Base Structure: X-ray

Registration Date: 2021-09-06

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	149
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1133761.249545
FMO2-HF: Nuclear repulsion	1079151.290328
FMO2-HF: Total energy	-54609.959217
FMO2-MP2: Total energy	-54770.499091

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(B:1:ALA )

Summations of interaction energy for fragment #1(B:1:ALA )

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.
-18.314	-16.951	0.011	-0.445	-0.929	-0.001

Interaction energy analysis for fragmet #1(B:1:ALA )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.806 / q_NPA : 0.886

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	B	3	LEU	0	-0.027	-0.020	3.431	3.428	4.791	0.011	-0.445	-0.929	-0.001
4	B	4	THR	0	-0.003	0.000	5.546	2.419	2.419	0.000	0.000	0.000	0.000
5	B	5	ALA	0	0.026	0.010	9.231	0.802	0.802	0.000	0.000	0.000	0.000
6	B	6	SER	0	-0.052	-0.022	12.577	0.398	0.398	0.000	0.000	0.000	0.000
7	B	7	PHE	0	0.051	0.008	16.141	0.319	0.319	0.000	0.000	0.000	0.000
8	B	8	THR	0	-0.012	0.011	19.699	-0.050	-0.050	0.000	0.000	0.000	0.000
9	B	9	VAL	0	-0.011	-0.001	22.231	0.366	0.366	0.000	0.000	0.000	0.000
10	B	10	THR	0	-0.002	-0.005	24.842	0.212	0.212	0.000	0.000	0.000	0.000
11	B	11	ALA	0	0.015	-0.001	28.648	-0.060	-0.060	0.000	0.000	0.000	0.000
12	B	12	THR	0	-0.015	0.000	31.864	0.139	0.139	0.000	0.000	0.000	0.000
13	B	13	LEU	0	-0.011	-0.006	35.025	-0.008	-0.008	0.000	0.000	0.000	0.000
14	B	14	VAL	0	0.007	-0.001	38.089	0.110	0.110	0.000	0.000	0.000	0.000
15	B	15	GLU	-1	-0.910	-0.959	41.755	-7.394	-7.394	0.000	0.000	0.000	0.000
16	B	16	PRO	0	-0.070	-0.032	44.879	0.108	0.108	0.000	0.000	0.000	0.000
17	B	17	ALA	0	0.053	0.032	47.786	0.022	0.022	0.000	0.000	0.000	0.000
18	B	18	ARG	1	0.899	0.950	45.868	6.906	6.906	0.000	0.000	0.000	0.000
19	B	19	ILE	0	0.048	0.029	53.126	0.016	0.016	0.000	0.000	0.000	0.000
20	B	20	THR	0	-0.058	-0.029	55.886	0.019	0.019	0.000	0.000	0.000	0.000
21	B	21	LEU	0	0.043	0.005	58.580	0.031	0.031	0.000	0.000	0.000	0.000
22	B	22	THR	0	-0.041	-0.005	61.723	-0.006	-0.006	0.000	0.000	0.000	0.000
23	B	23	TYR	0	0.040	0.027	64.108	0.033	0.033	0.000	0.000	0.000	0.000
24	B	24	LYS	1	0.931	0.965	67.898	4.750	4.750	0.000	0.000	0.000	0.000
25	B	25	GLU	-1	-0.917	-0.960	69.838	-4.360	-4.360	0.000	0.000	0.000	0.000
26	B	26	GLY	0	-0.013	0.007	73.625	-0.030	-0.030	0.000	0.000	0.000	0.000
27	B	27	ALA	0	-0.043	-0.028	75.855	0.022	0.022	0.000	0.000	0.000	0.000
28	B	28	PRO	0	0.024	0.019	79.185	0.005	0.005	0.000	0.000	0.000	0.000
29	B	29	ILE	0	0.013	0.001	80.503	0.023	0.023	0.000	0.000	0.000	0.000
30	B	30	THR	0	-0.030	-0.028	84.221	0.032	0.032	0.000	0.000	0.000	0.000
31	B	31	ILE	0	-0.035	-0.004	87.847	0.001	0.001	0.000	0.000	0.000	0.000
32	B	32	MET	0	-0.006	-0.016	90.396	0.011	0.011	0.000	0.000	0.000	0.000
33	B	33	ASP	-1	-0.948	-0.952	93.055	-3.301	-3.301	0.000	0.000	0.000	0.000
34	B	34	ASN	0	-0.033	-0.026	94.744	0.005	0.005	0.000	0.000	0.000	0.000
35	B	35	GLY	0	-0.050	-0.028	94.002	0.011	0.011	0.000	0.000	0.000	0.000
36	B	36	ASN	0	0.030	0.029	90.978	-0.021	-0.021	0.000	0.000	0.000	0.000
37	B	37	ILE	0	-0.007	-0.008	84.329	0.001	0.001	0.000	0.000	0.000	0.000
38	B	38	ASP	-1	-0.816	-0.929	85.536	-3.757	-3.757	0.000	0.000	0.000	0.000
39	B	39	THR	0	-0.033	0.001	84.211	-0.055	-0.055	0.000	0.000	0.000	0.000
40	B	40	GLU	-1	-0.879	-0.947	79.109	-4.162	-4.162	0.000	0.000	0.000	0.000
41	B	41	LEU	0	-0.006	0.004	80.002	-0.045	-0.045	0.000	0.000	0.000	0.000
42	B	42	LEU	0	-0.055	-0.033	73.151	-0.032	-0.032	0.000	0.000	0.000	0.000
43	B	43	VAL	0	0.009	0.007	76.278	0.003	0.003	0.000	0.000	0.000	0.000
44	B	44	GLY	0	0.050	0.015	73.312	-0.006	-0.006	0.000	0.000	0.000	0.000
45	B	45	THR	0	-0.103	-0.056	67.646	0.009	0.009	0.000	0.000	0.000	0.000
46	B	46	LEU	0	0.000	0.003	66.502	-0.037	-0.037	0.000	0.000	0.000	0.000
47	B	47	THR	0	-0.005	-0.026	60.932	0.006	0.006	0.000	0.000	0.000	0.000
48	B	48	LEU	0	-0.010	0.006	59.993	-0.033	-0.033	0.000	0.000	0.000	0.000
49	B	49	GLY	0	0.075	0.018	57.487	-0.037	-0.037	0.000	0.000	0.000	0.000
50	B	50	GLY	0	-0.067	-0.024	53.401	0.014	0.014	0.000	0.000	0.000	0.000
51	B	51	TYR	0	-0.019	-0.056	52.573	-0.117	-0.117	0.000	0.000	0.000	0.000
52	B	52	LYS	1	0.977	0.996	46.014	6.826	6.826	0.000	0.000	0.000	0.000
53	B	53	THR	0	0.037	0.000	50.709	0.134	0.134	0.000	0.000	0.000	0.000
54	B	54	GLY	0	0.001	0.003	51.824	-0.108	-0.108	0.000	0.000	0.000	0.000
55	B	55	THR	0	-0.010	-0.004	54.330	0.078	0.078	0.000	0.000	0.000	0.000
56	B	56	THR	0	0.017	0.027	56.657	0.012	0.012	0.000	0.000	0.000	0.000
57	B	57	SER	0	0.005	0.002	60.086	0.031	0.031	0.000	0.000	0.000	0.000
58	B	58	THR	0	-0.035	-0.021	63.566	0.045	0.045	0.000	0.000	0.000	0.000
59	B	59	SER	0	-0.086	-0.023	59.828	0.000	0.000	0.000	0.000	0.000	0.000
60	B	60	VAL	0	0.017	0.011	61.727	-0.040	-0.040	0.000	0.000	0.000	0.000
61	B	61	ASN	0	0.014	-0.002	63.827	0.125	0.125	0.000	0.000	0.000	0.000
62	B	62	PHE	0	-0.010	0.003	66.499	-0.046	-0.046	0.000	0.000	0.000	0.000
63	B	63	THR	0	0.001	0.005	69.451	0.056	0.056	0.000	0.000	0.000	0.000
64	B	64	ASP	-1	-0.738	-0.883	71.740	-4.322	-4.322	0.000	0.000	0.000	0.000
65	B	65	ALA	0	-0.023	-0.022	74.641	0.013	0.013	0.000	0.000	0.000	0.000
66	B	66	ALA	0	-0.038	-0.004	77.235	0.038	0.038	0.000	0.000	0.000	0.000
67	B	67	GLY	0	-0.001	0.005	76.440	0.033	0.033	0.000	0.000	0.000	0.000
68	B	68	ASP	-1	-0.944	-0.980	77.504	-4.014	-4.014	0.000	0.000	0.000	0.000
69	B	69	PRO	0	0.022	0.012	76.299	-0.048	-0.048	0.000	0.000	0.000	0.000
70	B	70	MET	0	-0.058	-0.038	75.129	0.047	0.047	0.000	0.000	0.000	0.000
71	B	71	TYR	0	-0.080	-0.040	76.162	0.002	0.002	0.000	0.000	0.000	0.000
72	B	72	LEU	0	0.005	0.016	72.592	-0.023	-0.023	0.000	0.000	0.000	0.000
73	B	73	THR	0	-0.026	-0.026	77.136	0.080	0.080	0.000	0.000	0.000	0.000
74	B	74	PHE	0	0.001	0.019	75.960	-0.025	-0.025	0.000	0.000	0.000	0.000
75	B	75	THR	0	0.031	0.003	81.248	0.082	0.082	0.000	0.000	0.000	0.000
76	B	76	SER	0	-0.040	-0.008	83.424	-0.045	-0.045	0.000	0.000	0.000	0.000
77	B	77	GLN	0	-0.054	-0.035	81.786	0.033	0.033	0.000	0.000	0.000	0.000
78	B	78	ASP	-1	-0.778	-0.871	85.447	-3.665	-3.665	0.000	0.000	0.000	0.000
79	B	79	GLY	0	0.000	-0.030	89.244	0.020	0.020	0.000	0.000	0.000	0.000
80	B	80	ASN	0	-0.109	-0.052	90.898	0.040	0.040	0.000	0.000	0.000	0.000
81	B	81	ASN	0	-0.034	-0.002	87.593	-0.013	-0.013	0.000	0.000	0.000	0.000
82	B	82	HIS	0	-0.002	0.008	89.333	0.026	0.026	0.000	0.000	0.000	0.000
83	B	83	GLN	0	-0.014	-0.026	84.512	-0.021	-0.021	0.000	0.000	0.000	0.000
84	B	84	PHE	0	-0.049	-0.033	81.116	0.045	0.045	0.000	0.000	0.000	0.000
85	B	85	THR	0	0.032	0.038	81.329	-0.027	-0.027	0.000	0.000	0.000	0.000
86	B	86	THR	0	-0.041	-0.022	77.369	-0.001	-0.001	0.000	0.000	0.000	0.000
87	B	87	LYS	1	0.948	0.982	76.261	4.186	4.186	0.000	0.000	0.000	0.000
88	B	88	VAL	0	0.021	0.014	69.869	-0.008	-0.008	0.000	0.000	0.000	0.000
89	B	89	ILE	0	0.000	-0.009	71.167	-0.012	-0.012	0.000	0.000	0.000	0.000
90	B	90	GLY	0	0.023	0.003	68.071	-0.023	-0.023	0.000	0.000	0.000	0.000
91	B	91	LYS	1	0.887	0.965	67.481	4.601	4.601	0.000	0.000	0.000	0.000
92	B	92	ASP	-1	-0.731	-0.865	63.975	-5.045	-5.045	0.000	0.000	0.000	0.000
93	B	93	SER	0	-0.053	-0.037	61.104	0.046	0.046	0.000	0.000	0.000	0.000
94	B	94	ARG	1	0.870	0.936	63.134	4.964	4.964	0.000	0.000	0.000	0.000
95	B	95	ASP	-1	-0.923	-0.951	66.138	-4.597	-4.597	0.000	0.000	0.000	0.000
96	B	96	PHE	0	-0.050	-0.038	68.166	0.107	0.107	0.000	0.000	0.000	0.000
97	B	97	ASP	-1	-0.923	-0.963	69.164	-4.503	-4.503	0.000	0.000	0.000	0.000
98	B	98	ILE	0	-0.006	0.002	65.169	-0.010	-0.010	0.000	0.000	0.000	0.000
99	B	99	SER	0	-0.010	-0.020	69.155	0.048	0.048	0.000	0.000	0.000	0.000
100	B	100	PRO	0	-0.031	0.011	66.376	-0.050	-0.050	0.000	0.000	0.000	0.000
101	B	101	LYS	1	0.934	0.966	66.494	4.911	4.911	0.000	0.000	0.000	0.000
102	B	102	VAL	0	0.018	0.014	69.404	-0.045	-0.045	0.000	0.000	0.000	0.000
103	B	103	ASN	0	-0.033	-0.027	72.122	0.006	0.006	0.000	0.000	0.000	0.000
104	B	104	GLY	0	-0.040	-0.022	70.443	0.042	0.042	0.000	0.000	0.000	0.000
105	B	105	GLU	-1	-0.928	-0.963	71.520	-4.452	-4.452	0.000	0.000	0.000	0.000
106	B	106	ASN	0	-0.017	-0.004	68.174	-0.013	-0.013	0.000	0.000	0.000	0.000
107	B	107	LEU	0	0.004	0.009	72.159	0.058	0.058	0.000	0.000	0.000	0.000
108	B	108	VAL	0	-0.044	-0.035	72.791	0.057	0.057	0.000	0.000	0.000	0.000
109	B	109	GLY	0	0.021	0.015	70.794	-0.065	-0.065	0.000	0.000	0.000	0.000
110	B	110	ASP	-1	-0.955	-0.966	67.230	-4.807	-4.807	0.000	0.000	0.000	0.000
111	B	111	ASP	-1	-0.849	-0.949	63.048	-5.214	-5.214	0.000	0.000	0.000	0.000
112	B	112	VAL	0	0.014	0.018	62.914	-0.037	-0.037	0.000	0.000	0.000	0.000
113	B	113	VAL	0	-0.051	-0.032	56.257	-0.042	-0.042	0.000	0.000	0.000	0.000
114	B	114	LEU	0	-0.041	-0.016	58.838	0.068	0.068	0.000	0.000	0.000	0.000
115	B	115	ALA	0	0.044	0.021	58.090	-0.101	-0.101	0.000	0.000	0.000	0.000
116	B	116	THR	0	-0.011	0.016	52.123	-0.040	-0.040	0.000	0.000	0.000	0.000
117	B	117	GLY	0	-0.023	0.001	53.784	0.040	0.040	0.000	0.000	0.000	0.000
118	B	118	SER	0	-0.022	-0.021	54.681	-0.030	-0.030	0.000	0.000	0.000	0.000
119	B	119	GLN	0	-0.001	0.025	58.303	-0.061	-0.061	0.000	0.000	0.000	0.000
120	B	120	ASP	-1	-0.861	-0.902	61.696	-5.095	-5.095	0.000	0.000	0.000	0.000
121	B	121	PHE	0	-0.010	-0.023	64.176	0.017	0.017	0.000	0.000	0.000	0.000
122	B	122	PHE	0	-0.034	-0.024	68.190	0.015	0.015	0.000	0.000	0.000	0.000
123	B	123	VAL	0	0.026	0.022	71.657	0.017	0.017	0.000	0.000	0.000	0.000
124	B	124	ARG	1	0.893	0.944	74.226	4.364	4.364	0.000	0.000	0.000	0.000
125	B	125	SER	0	0.011	-0.008	77.515	-0.009	-0.009	0.000	0.000	0.000	0.000
126	B	126	ILE	0	-0.014	0.008	80.337	0.007	0.007	0.000	0.000	0.000	0.000
127	B	127	GLY	0	0.028	-0.005	82.910	0.046	0.046	0.000	0.000	0.000	0.000
128	B	128	SER	0	0.008	-0.011	85.703	-0.031	-0.031	0.000	0.000	0.000	0.000
129	B	129	LYS	1	0.931	0.961	86.175	3.811	3.811	0.000	0.000	0.000	0.000
130	B	130	GLY	0	0.022	0.042	90.029	0.036	0.036	0.000	0.000	0.000	0.000
131	B	131	GLY	0	0.010	-0.003	91.812	0.045	0.045	0.000	0.000	0.000	0.000
132	B	132	LYS	1	0.947	0.976	92.792	3.317	3.317	0.000	0.000	0.000	0.000
133	B	133	LEU	0	0.025	0.021	87.549	0.004	0.004	0.000	0.000	0.000	0.000
134	B	134	ALA	0	0.075	0.068	91.295	0.031	0.031	0.000	0.000	0.000	0.000
135	B	135	ALA	0	-0.039	-0.059	87.898	-0.031	-0.031	0.000	0.000	0.000	0.000
136	B	136	GLY	0	-0.004	-0.013	87.914	-0.014	-0.014	0.000	0.000	0.000	0.000
137	B	137	LYS	1	0.918	0.967	82.471	3.945	3.945	0.000	0.000	0.000	0.000
138	B	138	TYR	0	0.010	0.017	82.643	0.047	0.047	0.000	0.000	0.000	0.000
139	B	139	THR	0	-0.092	-0.055	78.858	-0.052	-0.052	0.000	0.000	0.000	0.000
140	B	140	ASP	-1	-0.733	-0.894	76.148	-4.255	-4.255	0.000	0.000	0.000	0.000
141	B	141	ALA	0	-0.096	-0.038	73.545	-0.048	-0.048	0.000	0.000	0.000	0.000
142	B	142	VAL	0	-0.001	0.003	70.064	0.001	0.001	0.000	0.000	0.000	0.000
143	B	143	THR	0	-0.057	-0.019	66.569	-0.086	-0.086	0.000	0.000	0.000	0.000
144	B	144	VAL	0	0.000	-0.002	64.105	0.033	0.033	0.000	0.000	0.000	0.000
145	B	145	THR	0	-0.033	-0.011	62.755	-0.089	-0.089	0.000	0.000	0.000	0.000
146	B	146	VAL	0	0.011	-0.006	58.267	0.027	0.027	0.000	0.000	0.000	0.000
147	B	147	SER	0	-0.062	-0.036	59.118	-0.048	-0.048	0.000	0.000	0.000	0.000
148	B	148	ASN	0	-0.065	-0.046	53.686	-0.027	-0.027	0.000	0.000	0.000	0.000
149	B	149	GLN	-1	-0.888	-0.928	52.081	-6.349	-6.349	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:1:ALA )