FMO DATABASE

FMODB ID: ZYRMN

Calculation Name: 3WTD-A-Xray320

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3WTD

Chain ID: A

ChEMBL ID:

UniProt ID: Q9BUH6

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	134
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1016133.254809
FMO2-HF: Nuclear repulsion	966889.241065
FMO2-HF: Total energy	-49244.013744
FMO2-MP2: Total energy	-49386.64591

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:4:ACE )

Summations of interaction energy for fragment #1(A:4:ACE )

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.
2.994	3.897	-0.006	-0.39	-0.507	0

Interaction energy analysis for fragmet #1(A:4:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.055 / q_NPA : 0.020

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].
3	A	6	PRO	0	0.011	0.027	3.813	0.817	1.666	-0.006	-0.381	-0.463
4	A	7	PRO	0	0.005	0.017	6.516	-0.018	-0.018	0.000	0.000	0.000
5	A	8	LEU	0	0.033	-0.005	9.136	0.039	0.039	0.000	0.000	0.000
6	A	9	CYS	0	-0.010	0.008	12.742	0.000	0.000	0.000	0.000	0.000
7	A	10	THR	0	0.039	0.006	15.969	-0.001	-0.001	0.000	0.000	0.000
8	A	11	LEU	0	-0.009	0.020	19.510	0.011	0.011	0.000	0.000	0.000
9	A	12	PRO	0	0.030	0.011	22.879	-0.001	-0.001	0.000	0.000	0.000
10	A	13	PRO	0	0.045	0.018	22.165	-0.008	-0.008	0.000	0.000	0.000
11	A	14	GLY	0	-0.040	-0.005	23.397	-0.001	-0.001	0.000	0.000	0.000
12	A	15	PRO	0	0.021	0.001	25.492	-0.008	-0.008	0.000	0.000	0.000
13	A	16	GLU	-1	-0.854	-0.908	27.540	-0.073	-0.073	0.000	0.000	0.000
14	A	17	PRO	0	0.013	0.012	26.763	-0.009	-0.009	0.000	0.000	0.000
15	A	18	PRO	0	0.013	0.021	22.685	0.008	0.008	0.000	0.000	0.000
16	A	19	ARG	1	0.760	0.823	24.601	0.082	0.082	0.000	0.000	0.000
17	A	20	PHE	0	0.030	0.015	22.448	0.003	0.003	0.000	0.000	0.000
18	A	21	VAL	0	-0.022	0.002	16.483	-0.014	-0.014	0.000	0.000	0.000
19	A	22	CYS	0	-0.010	0.008	17.035	0.024	0.024	0.000	0.000	0.000
20	A	23	TYR	0	-0.042	-0.034	12.404	-0.039	-0.039	0.000	0.000	0.000
21	A	24	CYS	0	-0.016	0.008	10.266	0.030	0.030	0.000	0.000	0.000
22	A	25	GLU	-1	-0.907	-0.977	10.146	-0.229	-0.229	0.000	0.000	0.000
23	A	26	GLY	0	-0.007	-0.022	8.830	0.048	0.048	0.000	0.000	0.000
24	A	27	GLU	-1	-0.737	-0.774	9.286	0.299	0.299	0.000	0.000	0.000
25	A	28	NME	0	0.015	0.013	9.865	-0.051	-0.051	0.000	0.000	0.000
26	A	35	ACE	0	0.003	-0.012	14.519	0.005	0.005	0.000	0.000	0.000
27	A	36	GLY	0	0.000	-0.015	14.129	-0.015	-0.015	0.000	0.000	0.000
28	A	37	PHE	0	0.001	0.032	11.646	-0.021	-0.021	0.000	0.000	0.000
29	A	38	ASN	0	0.009	0.036	13.930	-0.002	-0.002	0.000	0.000	0.000
30	A	39	LEU	0	-0.008	0.004	14.201	-0.016	-0.016	0.000	0.000	0.000
31	A	40	TYR	0	0.009	-0.016	15.134	0.009	0.009	0.000	0.000	0.000
32	A	41	VAL	0	0.049	0.010	17.654	-0.013	-0.013	0.000	0.000	0.000
33	A	42	THR	0	-0.037	-0.035	19.523	0.006	0.006	0.000	0.000	0.000
34	A	43	ASP	-1	-0.749	-0.871	22.039	-0.090	-0.090	0.000	0.000	0.000
35	A	44	ALA	0	-0.089	-0.045	23.060	-0.002	-0.002	0.000	0.000	0.000
36	A	45	ALA	0	-0.051	-0.015	23.956	0.002	0.002	0.000	0.000	0.000
37	A	46	GLU	-1	-0.884	-0.948	26.473	-0.046	-0.046	0.000	0.000	0.000
38	A	47	LEU	0	-0.038	0.001	19.437	-0.011	-0.011	0.000	0.000	0.000
39	A	48	TRP	0	0.033	0.015	22.514	0.008	0.008	0.000	0.000	0.000
40	A	49	SER	0	0.030	-0.004	20.017	-0.007	-0.007	0.000	0.000	0.000
41	A	50	THR	0	0.040	0.013	18.942	0.002	0.002	0.000	0.000	0.000
42	A	51	CYS	0	-0.109	-0.045	20.894	0.005	0.005	0.000	0.000	0.000
43	A	52	PHE	0	-0.006	-0.021	17.677	0.006	0.006	0.000	0.000	0.000
44	A	53	THR	0	-0.022	-0.032	20.890	-0.003	-0.003	0.000	0.000	0.000
45	A	54	PRO	0	0.012	-0.018	20.178	0.007	0.007	0.000	0.000	0.000
46	A	55	ASP	-1	-0.812	-0.876	21.224	0.065	0.065	0.000	0.000	0.000
47	A	56	SER	0	-0.007	-0.010	23.693	0.005	0.005	0.000	0.000	0.000
48	A	57	LEU	0	0.033	0.027	16.315	0.000	0.000	0.000	0.000	0.000
49	A	58	ALA	0	0.019	0.007	20.850	0.007	0.007	0.000	0.000	0.000
50	A	59	ALA	0	-0.014	-0.012	22.248	0.000	0.000	0.000	0.000	0.000
51	A	60	LEU	0	-0.031	-0.003	20.176	-0.002	-0.002	0.000	0.000	0.000
52	A	61	LYS	1	0.939	0.960	15.664	-0.201	-0.201	0.000	0.000	0.000
53	A	62	ALA	0	-0.008	0.008	21.430	0.000	0.000	0.000	0.000	0.000
54	A	63	ARG	1	0.910	0.955	24.768	-0.043	-0.043	0.000	0.000	0.000
55	A	64	PHE	0	-0.026	-0.012	22.339	-0.007	-0.007	0.000	0.000	0.000
56	A	65	GLY	0	-0.022	0.009	23.999	0.001	0.001	0.000	0.000	0.000
57	A	66	LEU	0	-0.028	-0.033	16.708	0.005	0.005	0.000	0.000	0.000
58	A	67	SER	0	-0.045	-0.003	20.350	0.017	0.017	0.000	0.000	0.000
59	A	68	ALA	0	0.022	0.006	21.622	-0.001	-0.001	0.000	0.000	0.000
60	A	69	ALA	0	-0.036	-0.033	16.460	-0.002	-0.002	0.000	0.000	0.000
61	A	70	GLU	-1	-1.038	-0.963	14.993	0.264	0.264	0.000	0.000	0.000
62	A	71	ASP	-1	-0.781	-0.938	11.008	0.432	0.432	0.000	0.000	0.000
63	A	72	ILE	0	-0.022	-0.022	13.459	-0.020	-0.020	0.000	0.000	0.000
64	A	73	THR	0	-0.073	-0.119	7.180	-0.060	-0.060	0.000	0.000	0.000
65	A	74	PRO	0	-0.035	-0.017	9.416	-0.060	-0.060	0.000	0.000	0.000
66	A	75	ARG	1	1.000	1.008	10.454	-0.176	-0.176	0.000	0.000	0.000
67	A	76	PHE	0	0.022	0.009	11.319	-0.036	-0.036	0.000	0.000	0.000
68	A	77	ARG	1	0.878	0.920	4.753	0.187	0.241	0.000	-0.009	-0.044
69	A	78	ALA	0	0.026	0.022	10.623	-0.049	-0.049	0.000	0.000	0.000
70	A	79	ALA	0	0.024	0.009	13.168	-0.022	-0.022	0.000	0.000	0.000
71	A	80	CYS	0	-0.071	-0.027	12.341	-0.024	-0.024	0.000	0.000	0.000
72	A	81	GLU	-1	-0.967	-0.981	9.980	-0.160	-0.160	0.000	0.000	0.000
73	A	82	GLN	0	-0.055	-0.029	14.255	0.004	0.004	0.000	0.000	0.000
74	A	83	GLN	0	-0.026	-0.004	17.106	-0.003	-0.003	0.000	0.000	0.000
75	A	84	ALA	0	-0.012	0.005	18.479	0.010	0.010	0.000	0.000	0.000
76	A	85	VAL	0	-0.024	-0.025	17.237	0.013	0.013	0.000	0.000	0.000
77	A	86	ALA	0	-0.019	-0.005	20.417	-0.006	-0.006	0.000	0.000	0.000
78	A	87	LEU	0	0.011	-0.002	23.024	0.003	0.003	0.000	0.000	0.000
79	A	88	THR	0	-0.078	-0.021	25.081	0.000	0.000	0.000	0.000	0.000
80	A	89	LEU	0	0.045	-0.007	26.357	0.000	0.000	0.000	0.000	0.000
81	A	90	GLN	0	-0.038	-0.035	29.249	-0.002	-0.002	0.000	0.000	0.000
82	A	91	GLU	-1	-0.855	-0.898	32.169	-0.018	-0.018	0.000	0.000	0.000
83	A	92	ASP	-1	-0.910	-0.971	30.722	-0.031	-0.031	0.000	0.000	0.000
84	A	93	ARG	1	0.813	0.895	27.822	0.014	0.014	0.000	0.000	0.000
85	A	94	ALA	0	0.039	0.029	25.123	-0.004	-0.004	0.000	0.000	0.000
86	A	95	SER	0	0.024	0.024	25.166	0.004	0.004	0.000	0.000	0.000
87	A	96	LEU	0	-0.009	-0.003	18.259	-0.008	-0.008	0.000	0.000	0.000
88	A	97	THR	0	-0.016	-0.016	22.486	0.013	0.013	0.000	0.000	0.000
89	A	98	LEU	0	-0.027	-0.013	16.317	-0.010	-0.010	0.000	0.000	0.000
90	A	99	SER	0	0.015	-0.002	20.082	0.014	0.014	0.000	0.000	0.000
91	A	100	GLY	0	0.051	0.020	19.580	-0.006	-0.006	0.000	0.000	0.000
92	A	101	GLY	0	-0.038	-0.025	19.957	0.008	0.008	0.000	0.000	0.000
93	A	102	PRO	0	-0.001	-0.002	20.539	-0.007	-0.007	0.000	0.000	0.000
94	A	103	SER	0	-0.014	-0.008	22.945	-0.006	-0.006	0.000	0.000	0.000
95	A	104	ALA	0	-0.003	0.011	22.657	0.004	0.004	0.000	0.000	0.000
96	A	105	LEU	0	-0.038	-0.012	18.579	0.007	0.007	0.000	0.000	0.000
97	A	106	ALA	0	0.023	0.020	22.332	-0.010	-0.010	0.000	0.000	0.000
98	A	107	PHE	0	-0.037	-0.022	18.433	0.009	0.009	0.000	0.000	0.000
99	A	108	ASP	-1	-0.882	-0.939	22.898	-0.003	-0.003	0.000	0.000	0.000
100	A	109	LEU	0	-0.062	-0.039	20.069	0.002	0.002	0.000	0.000	0.000
101	A	110	SER	0	-0.011	-0.014	24.304	0.001	0.001	0.000	0.000	0.000
102	A	111	LYS	1	0.885	0.971	25.078	0.037	0.037	0.000	0.000	0.000
103	A	112	VAL	0	-0.020	-0.010	22.468	0.005	0.005	0.000	0.000	0.000
104	A	113	PRO	0	0.031	0.019	25.935	-0.004	-0.004	0.000	0.000	0.000
105	A	114	GLY	0	0.071	0.027	27.259	-0.004	-0.004	0.000	0.000	0.000
106	A	115	PRO	0	-0.034	-0.030	27.548	-0.006	-0.006	0.000	0.000	0.000
107	A	116	GLU	-1	-0.920	-0.953	23.176	-0.032	-0.032	0.000	0.000	0.000
108	A	117	ALA	0	0.015	0.000	23.059	-0.007	-0.007	0.000	0.000	0.000
109	A	118	ALA	0	0.022	0.014	22.726	-0.013	-0.013	0.000	0.000	0.000
110	A	119	PRO	0	-0.023	-0.021	21.727	-0.013	-0.013	0.000	0.000	0.000
111	A	120	ARG	1	0.958	0.984	16.156	0.054	0.054	0.000	0.000	0.000
112	A	121	LEU	0	0.059	0.037	18.516	-0.028	-0.028	0.000	0.000	0.000
113	A	122	ARG	1	0.933	0.973	20.346	0.081	0.081	0.000	0.000	0.000
114	A	123	ALA	0	0.006	-0.011	16.417	-0.016	-0.016	0.000	0.000	0.000
115	A	124	LEU	0	0.016	0.026	14.851	-0.047	-0.047	0.000	0.000	0.000
116	A	125	THR	0	0.009	0.004	16.332	-0.039	-0.039	0.000	0.000	0.000
117	A	126	LEU	0	-0.030	-0.023	18.313	-0.018	-0.018	0.000	0.000	0.000
118	A	127	GLY	0	-0.003	-0.003	13.996	-0.021	-0.021	0.000	0.000	0.000
119	A	128	LEU	0	-0.004	-0.010	13.558	-0.093	-0.093	0.000	0.000	0.000
120	A	129	ALA	0	0.030	0.027	15.026	-0.025	-0.025	0.000	0.000	0.000
121	A	130	LYS	1	0.963	0.984	13.273	0.331	0.331	0.000	0.000	0.000
122	A	131	ARG	1	0.888	0.934	8.439	0.936	0.936	0.000	0.000	0.000
123	A	132	VAL	0	0.057	0.041	12.569	-0.029	-0.029	0.000	0.000	0.000
124	A	133	TRP	0	0.042	0.028	15.477	-0.001	-0.001	0.000	0.000	0.000
125	A	134	SER	0	-0.030	-0.025	11.318	0.030	0.030	0.000	0.000	0.000
126	A	135	LEU	0	-0.040	-0.039	9.777	-0.024	-0.024	0.000	0.000	0.000
127	A	136	GLU	-1	-0.879	-0.932	13.383	-0.204	-0.204	0.000	0.000	0.000
128	A	137	ARG	1	0.899	0.959	15.533	0.276	0.276	0.000	0.000	0.000
129	A	138	ARG	1	0.872	0.926	7.296	0.938	0.938	0.000	0.000	0.000
130	A	139	LEU	0	-0.001	0.008	14.742	0.027	0.027	0.000	0.000	0.000
131	A	140	ALA	0	0.020	0.013	16.648	0.031	0.031	0.000	0.000	0.000
132	A	141	ALA	0	-0.085	-0.025	17.204	0.026	0.026	0.000	0.000	0.000
133	A	142	ALA	0	-0.010	-0.017	17.159	-0.006	-0.006	0.000	0.000	0.000
134	A	143	NME	0	-0.003	0.018	19.208	0.007	0.007	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:4:ACE )