FMO DATABASE

FMODB ID: Z69QN

Calculation Name: 3WOB-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3WOB

Chain ID: A

ChEMBL ID:

UniProt ID: A0A0A8

Base Structure: X-ray

Registration Date: 2023-06-26

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	134
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1168979.19616
FMO2-HF: Nuclear repulsion	1118916.718299
FMO2-HF: Total energy	-50062.477861
FMO2-MP2: Total energy	-50212.772795

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:18:GLY)

Summations of interaction energy for fragment #1(A:18:GLY)

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.
-2.846	-5.074	9.855	-1.527	-6.102	-0.054

Interaction energy analysis for fragmet #1(A:18:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.021 / q_NPA : -0.009

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	20	MET	0	-0.013	-0.021	2.377	3.483	-0.215	3.399	2.198	-1.900	-0.021
4	A	21	PHE	0	0.012	0.009	3.862	0.013	0.085	0.001	-0.026	-0.047	0.000
5	A	22	GLY	0	0.029	-0.012	7.782	0.185	0.185	0.000	0.000	0.000	0.000
6	A	23	ASN	0	-0.082	-0.043	11.281	-0.026	-0.026	0.000	0.000	0.000	0.000
7	A	24	GLY	0	0.013	0.012	11.942	0.048	0.048	0.000	0.000	0.000	0.000
8	A	25	LYS	1	0.958	0.985	12.685	0.147	0.147	0.000	0.000	0.000	0.000
9	A	26	GLY	0	0.008	0.018	16.059	-0.010	-0.010	0.000	0.000	0.000	0.000
10	A	27	SER	0	0.031	0.023	16.241	0.018	0.018	0.000	0.000	0.000	0.000
11	A	28	TYR	0	0.042	0.018	7.853	-0.054	-0.054	0.000	0.000	0.000	0.000
12	A	29	PHE	0	-0.035	-0.008	11.301	-0.003	-0.003	0.000	0.000	0.000	0.000
13	A	30	ILE	0	0.012	-0.010	8.748	0.016	0.016	0.000	0.000	0.000	0.000
14	A	31	THR	0	-0.030	-0.006	10.674	-0.034	-0.034	0.000	0.000	0.000	0.000
15	A	32	SER	0	-0.038	-0.052	9.739	0.039	0.039	0.000	0.000	0.000	0.000
16	A	33	LYS	1	0.885	0.949	11.457	-0.209	-0.209	0.000	0.000	0.000	0.000
17	A	34	ASP	-1	-0.857	-0.926	13.704	0.206	0.206	0.000	0.000	0.000	0.000
18	A	35	ASN	0	-0.085	-0.045	16.643	0.010	0.010	0.000	0.000	0.000	0.000
19	A	36	GLU	-1	-0.784	-0.840	18.431	0.040	0.040	0.000	0.000	0.000	0.000
20	A	37	THR	0	-0.089	-0.089	18.310	0.005	0.005	0.000	0.000	0.000	0.000
21	A	38	GLY	0	0.010	-0.005	14.706	0.020	0.020	0.000	0.000	0.000	0.000
22	A	39	ILE	0	-0.017	-0.012	10.850	-0.004	-0.004	0.000	0.000	0.000	0.000
23	A	40	THR	0	0.000	0.008	14.889	-0.027	-0.027	0.000	0.000	0.000	0.000
24	A	41	GLY	0	-0.013	-0.014	17.390	-0.004	-0.004	0.000	0.000	0.000	0.000
25	A	42	ILE	0	-0.005	0.012	13.019	0.002	0.002	0.000	0.000	0.000	0.000
26	A	43	ARG	1	0.780	0.871	17.044	0.073	0.073	0.000	0.000	0.000	0.000
27	A	44	VAL	0	-0.001	0.002	16.495	-0.009	-0.009	0.000	0.000	0.000	0.000
28	A	45	PHE	0	0.028	0.009	18.907	0.022	0.022	0.000	0.000	0.000	0.000
29	A	46	VAL	0	0.013	0.012	20.317	-0.014	-0.014	0.000	0.000	0.000	0.000
30	A	47	GLY	0	0.008	0.001	22.601	0.017	0.017	0.000	0.000	0.000	0.000
31	A	48	PRO	0	0.016	-0.005	25.591	-0.010	-0.010	0.000	0.000	0.000	0.000
32	A	49	VAL	0	0.003	0.007	24.592	-0.002	-0.002	0.000	0.000	0.000	0.000
33	A	50	GLY	0	0.006	0.008	23.883	-0.009	-0.009	0.000	0.000	0.000	0.000
34	A	51	LEU	0	-0.053	-0.016	19.901	-0.019	-0.019	0.000	0.000	0.000	0.000
35	A	52	ILE	0	0.023	0.001	15.348	0.024	0.024	0.000	0.000	0.000	0.000
36	A	53	LYS	1	0.835	0.929	17.684	0.105	0.105	0.000	0.000	0.000	0.000
37	A	54	SER	0	0.006	-0.020	17.313	0.013	0.013	0.000	0.000	0.000	0.000
38	A	55	ILE	0	-0.043	-0.009	13.237	-0.019	-0.019	0.000	0.000	0.000	0.000
39	A	56	GLN	0	-0.033	-0.017	16.781	0.020	0.020	0.000	0.000	0.000	0.000
40	A	57	VAL	0	0.023	0.006	12.775	-0.036	-0.036	0.000	0.000	0.000	0.000
41	A	58	ARG	1	0.894	0.949	16.111	0.067	0.067	0.000	0.000	0.000	0.000
42	A	59	TYR	0	0.083	0.038	13.042	-0.005	-0.005	0.000	0.000	0.000	0.000
43	A	60	GLY	0	0.125	0.064	18.294	0.003	0.003	0.000	0.000	0.000	0.000
44	A	61	SER	0	-0.044	-0.015	21.483	-0.015	-0.015	0.000	0.000	0.000	0.000
45	A	62	SER	0	-0.002	0.008	21.254	-0.010	-0.010	0.000	0.000	0.000	0.000
46	A	63	TRP	0	-0.061	-0.034	18.704	-0.003	-0.003	0.000	0.000	0.000	0.000
47	A	64	SER	0	0.007	0.011	17.061	0.003	0.003	0.000	0.000	0.000	0.000
48	A	65	GLU	-1	-0.887	-0.936	19.100	0.044	0.044	0.000	0.000	0.000	0.000
49	A	66	LYS	1	0.827	0.928	18.799	0.057	0.057	0.000	0.000	0.000	0.000
50	A	67	TYR	0	0.084	0.039	15.076	0.004	0.004	0.000	0.000	0.000	0.000
51	A	68	GLY	0	0.045	0.005	16.729	-0.037	-0.037	0.000	0.000	0.000	0.000
52	A	69	ILE	0	-0.054	-0.005	18.220	0.017	0.017	0.000	0.000	0.000	0.000
53	A	70	PRO	0	0.029	0.024	21.643	-0.011	-0.011	0.000	0.000	0.000	0.000
54	A	71	GLY	0	0.044	0.008	24.467	-0.005	-0.005	0.000	0.000	0.000	0.000
55	A	72	GLY	0	-0.007	-0.020	24.600	-0.009	-0.009	0.000	0.000	0.000	0.000
56	A	73	LYS	1	0.940	0.977	26.095	0.101	0.101	0.000	0.000	0.000	0.000
57	A	74	ALA	0	0.028	0.015	23.607	-0.012	-0.012	0.000	0.000	0.000	0.000
58	A	75	HIS	0	-0.018	-0.011	21.949	0.007	0.007	0.000	0.000	0.000	0.000
59	A	76	GLU	-1	-0.792	-0.892	20.925	-0.085	-0.085	0.000	0.000	0.000	0.000
60	A	77	LEU	0	-0.008	0.008	16.599	-0.006	-0.006	0.000	0.000	0.000	0.000
61	A	78	ILE	0	-0.003	0.006	19.213	0.001	0.001	0.000	0.000	0.000	0.000
62	A	79	LEU	0	-0.045	-0.009	16.343	-0.012	-0.012	0.000	0.000	0.000	0.000
63	A	80	HIS	0	0.041	0.012	20.439	0.020	0.020	0.000	0.000	0.000	0.000
64	A	81	PRO	0	0.027	-0.005	21.980	0.003	0.003	0.000	0.000	0.000	0.000
65	A	82	GLY	0	0.016	0.017	21.678	-0.004	-0.004	0.000	0.000	0.000	0.000
66	A	83	GLU	-1	-0.788	-0.842	18.675	-0.145	-0.145	0.000	0.000	0.000	0.000
67	A	84	HIS	0	0.061	0.018	14.080	0.008	0.008	0.000	0.000	0.000	0.000
68	A	85	ILE	0	-0.009	-0.008	11.227	-0.015	-0.015	0.000	0.000	0.000	0.000
69	A	86	ILE	0	0.004	-0.008	11.221	0.012	0.012	0.000	0.000	0.000	0.000
70	A	87	SER	0	-0.026	-0.011	9.605	-0.060	-0.060	0.000	0.000	0.000	0.000
71	A	88	ILE	0	-0.019	-0.005	8.390	0.129	0.129	0.000	0.000	0.000	0.000
72	A	89	TYR	0	-0.038	-0.032	10.611	-0.147	-0.147	0.000	0.000	0.000	0.000
73	A	90	GLY	0	0.033	0.011	12.975	0.060	0.060	0.000	0.000	0.000	0.000
74	A	91	ARG	1	0.788	0.895	13.778	0.343	0.343	0.000	0.000	0.000	0.000
75	A	92	TYR	0	0.001	0.009	12.049	-0.014	-0.014	0.000	0.000	0.000	0.000
76	A	93	ARG	1	0.935	0.945	15.680	0.228	0.228	0.000	0.000	0.000	0.000
77	A	94	THR	0	0.008	0.013	17.094	-0.024	-0.024	0.000	0.000	0.000	0.000
78	A	95	PHE	0	0.015	0.008	16.813	0.015	0.015	0.000	0.000	0.000	0.000
79	A	96	LEU	0	0.040	0.019	11.821	-0.020	-0.020	0.000	0.000	0.000	0.000
80	A	97	GLN	0	-0.071	-0.028	15.235	0.069	0.069	0.000	0.000	0.000	0.000
81	A	98	HIS	0	-0.019	-0.025	16.354	0.016	0.016	0.000	0.000	0.000	0.000
82	A	99	VAL	0	0.030	0.011	12.514	-0.069	-0.069	0.000	0.000	0.000	0.000
83	A	100	THR	0	0.005	0.029	14.523	0.079	0.079	0.000	0.000	0.000	0.000
84	A	101	LEU	0	0.008	0.001	12.550	-0.091	-0.091	0.000	0.000	0.000	0.000
85	A	102	ILE	0	0.031	0.018	13.888	0.059	0.059	0.000	0.000	0.000	0.000
86	A	103	THR	0	-0.013	-0.037	14.296	-0.042	-0.042	0.000	0.000	0.000	0.000
87	A	104	ASN	0	0.008	-0.003	16.644	-0.014	-0.014	0.000	0.000	0.000	0.000
88	A	105	GLN	0	-0.046	-0.018	17.892	0.016	0.016	0.000	0.000	0.000	0.000
89	A	106	GLY	0	-0.002	0.007	19.785	0.009	0.009	0.000	0.000	0.000	0.000
90	A	107	ARG	1	0.796	0.888	20.800	0.124	0.124	0.000	0.000	0.000	0.000
91	A	108	SER	0	0.032	0.002	18.835	-0.025	-0.025	0.000	0.000	0.000	0.000
92	A	109	ALA	0	-0.034	-0.007	18.703	0.028	0.028	0.000	0.000	0.000	0.000
93	A	110	SER	0	-0.007	-0.025	18.173	-0.031	-0.031	0.000	0.000	0.000	0.000
94	A	111	PHE	0	-0.001	-0.004	17.262	0.036	0.036	0.000	0.000	0.000	0.000
95	A	112	GLY	0	0.060	0.027	18.526	-0.031	-0.031	0.000	0.000	0.000	0.000
96	A	113	LEU	0	0.002	0.014	20.709	0.002	0.002	0.000	0.000	0.000	0.000
97	A	114	GLU	-1	-0.745	-0.852	19.388	-0.360	-0.360	0.000	0.000	0.000	0.000
98	A	115	THR	0	-0.029	-0.009	20.295	0.020	0.020	0.000	0.000	0.000	0.000
99	A	116	GLY	0	0.016	-0.005	19.300	-0.014	-0.014	0.000	0.000	0.000	0.000
100	A	117	LYS	1	0.918	0.972	13.340	0.634	0.634	0.000	0.000	0.000	0.000
101	A	118	GLY	0	0.039	0.021	15.231	-0.014	-0.014	0.000	0.000	0.000	0.000
102	A	119	PHE	0	-0.070	-0.040	8.789	0.009	0.009	0.000	0.000	0.000	0.000
103	A	120	PHE	0	0.052	0.008	10.305	0.107	0.107	0.000	0.000	0.000	0.000
104	A	121	ALA	0	-0.027	0.001	5.488	-0.315	-0.315	0.000	0.000	0.000	0.000
105	A	122	ALA	0	0.044	0.010	6.182	0.383	0.383	0.000	0.000	0.000	0.000
106	A	123	PRO	0	-0.010	0.020	5.599	-0.426	-0.426	0.000	0.000	0.000	0.000
107	A	124	ASN	0	-0.003	-0.007	4.941	-0.506	-0.506	0.000	0.000	0.000	0.000
108	A	125	LEU	0	-0.014	0.005	7.864	-0.003	-0.003	0.000	0.000	0.000	0.000
109	A	126	THR	0	0.007	-0.006	10.978	-0.040	-0.040	0.000	0.000	0.000	0.000
110	A	127	GLY	0	0.032	0.009	13.177	0.039	0.039	0.000	0.000	0.000	0.000
111	A	128	GLN	0	-0.056	-0.012	8.358	-0.055	-0.055	0.000	0.000	0.000	0.000
112	A	129	VAL	0	0.008	-0.001	10.739	-0.117	-0.117	0.000	0.000	0.000	0.000
113	A	130	LEU	0	-0.038	-0.019	6.868	0.029	0.029	0.000	0.000	0.000	0.000
114	A	131	GLU	-1	-0.767	-0.854	8.156	0.343	0.343	0.000	0.000	0.000	0.000
115	A	132	GLY	0	0.042	0.024	8.029	0.127	0.127	0.000	0.000	0.000	0.000
116	A	133	VAL	0	-0.071	-0.017	7.058	-0.276	-0.276	0.000	0.000	0.000	0.000
117	A	134	TYR	0	0.027	0.012	2.160	-1.376	-1.539	3.149	-1.640	-1.345	-0.009
118	A	135	GLY	0	0.039	0.002	7.958	-0.212	-0.212	0.000	0.000	0.000	0.000
119	A	136	GLN	0	-0.031	-0.016	9.392	0.060	0.060	0.000	0.000	0.000	0.000
120	A	137	PHE	0	0.017	0.015	12.760	-0.061	-0.061	0.000	0.000	0.000	0.000
121	A	138	TRP	0	0.034	0.006	16.129	0.019	0.019	0.000	0.000	0.000	0.000
122	A	139	LEU	0	0.024	-0.004	19.501	-0.007	-0.007	0.000	0.000	0.000	0.000
123	A	140	TYR	0	0.027	0.016	21.838	0.006	0.006	0.000	0.000	0.000	0.000
124	A	141	GLY	0	-0.004	-0.006	19.114	0.002	0.002	0.000	0.000	0.000	0.000
125	A	142	ILE	0	0.015	0.021	12.363	0.014	0.014	0.000	0.000	0.000	0.000
126	A	143	THR	0	-0.072	-0.055	14.188	-0.025	-0.025	0.000	0.000	0.000	0.000
127	A	144	GLY	0	-0.002	0.002	10.384	-0.046	-0.046	0.000	0.000	0.000	0.000
128	A	145	ILE	0	-0.017	-0.007	8.016	0.156	0.156	0.000	0.000	0.000	0.000
129	A	146	GLY	0	0.037	0.019	4.173	-0.386	-0.360	0.000	-0.020	-0.006	0.000
130	A	147	PHE	0	0.002	0.000	2.762	0.082	0.608	0.074	-0.218	-0.382	0.000
131	A	148	THR	0	0.002	0.001	2.106	-5.393	-4.743	3.198	-1.707	-2.142	-0.024
132	A	149	TRP	0	0.025	0.013	3.142	-0.255	0.104	0.034	-0.114	-0.280	0.000
133	A	150	GLY	0	0.027	0.018	6.053	0.527	0.527	0.000	0.000	0.000	0.000
134	A	151	PHE	0	-0.045	-0.047	9.404	-0.151	-0.151	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:18:GLY)