FMO DATABASE

FMODB ID: 2JG1R

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1168936.715289
FMO2-HF: Nuclear repulsion	1118874.875121
FMO2-HF: Total energy	-50061.840168
FMO2-MP2: Total energy	-50212.049503

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.
11.681	-2.83	6.014	12.906	-4.411	-0.033

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 : -0.012 / q_NPA : 0.032

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	-0.021	-0.003	2.420	15.308	-0.534	-0.347	17.128	-0.939	-0.017
4	A	21	PHE	0	0.017	0.013	4.604	-0.260	-0.215	-0.001	-0.009	-0.035	0.000
5	A	22	GLY	0	0.029	-0.007	8.210	0.299	0.299	0.000	0.000	0.000	0.000
6	A	23	ASN	0	-0.069	-0.035	11.081	-0.037	-0.037	0.000	0.000	0.000	0.000
7	A	24	GLY	0	0.052	0.032	11.537	0.048	0.048	0.000	0.000	0.000	0.000
8	A	25	LYS	1	0.929	0.961	12.463	-0.059	-0.059	0.000	0.000	0.000	0.000
9	A	26	GLY	0	-0.001	0.004	15.654	-0.002	-0.002	0.000	0.000	0.000	0.000
10	A	27	SER	0	0.017	0.009	15.919	0.028	0.028	0.000	0.000	0.000	0.000
11	A	28	TYR	0	0.035	0.012	7.853	-0.109	-0.109	0.000	0.000	0.000	0.000
12	A	29	PHE	0	-0.030	-0.013	12.020	-0.067	-0.067	0.000	0.000	0.000	0.000
13	A	30	ILE	0	0.007	-0.014	8.616	0.180	0.180	0.000	0.000	0.000	0.000
14	A	31	THR	0	-0.026	0.007	11.364	-0.192	-0.192	0.000	0.000	0.000	0.000
15	A	32	SER	0	-0.012	-0.033	11.071	0.251	0.251	0.000	0.000	0.000	0.000
16	A	33	LYS	1	1.015	1.026	12.608	-0.601	-0.601	0.000	0.000	0.000	0.000
17	A	34	ASP	-1	-0.932	-0.966	14.776	0.546	0.546	0.000	0.000	0.000	0.000
18	A	35	ASN	0	-0.071	-0.029	17.872	-0.026	-0.026	0.000	0.000	0.000	0.000
19	A	36	GLU	-1	-0.760	-0.868	19.126	0.237	0.237	0.000	0.000	0.000	0.000
20	A	37	THR	0	-0.127	-0.068	19.915	-0.016	-0.016	0.000	0.000	0.000	0.000
21	A	38	GLY	0	-0.008	-0.016	15.947	0.049	0.049	0.000	0.000	0.000	0.000
22	A	39	ILE	0	0.007	-0.001	11.758	-0.024	-0.024	0.000	0.000	0.000	0.000
23	A	40	THR	0	0.026	-0.001	16.022	-0.043	-0.043	0.000	0.000	0.000	0.000
24	A	41	GLY	0	-0.029	-0.023	18.109	-0.042	-0.042	0.000	0.000	0.000	0.000
25	A	42	ILE	0	-0.007	0.015	13.665	0.051	0.051	0.000	0.000	0.000	0.000
26	A	43	ARG	1	0.798	0.875	17.456	-0.187	-0.187	0.000	0.000	0.000	0.000
27	A	44	VAL	0	0.021	0.013	16.377	0.033	0.033	0.000	0.000	0.000	0.000
28	A	45	PHE	0	-0.016	-0.008	19.116	-0.017	-0.017	0.000	0.000	0.000	0.000
29	A	46	VAL	0	0.030	0.024	20.780	-0.005	-0.005	0.000	0.000	0.000	0.000
30	A	47	GLY	0	-0.008	-0.004	23.020	0.007	0.007	0.000	0.000	0.000	0.000
31	A	48	PRO	0	0.020	-0.004	26.051	-0.010	-0.010	0.000	0.000	0.000	0.000
32	A	49	VAL	0	-0.018	-0.005	25.061	-0.006	-0.006	0.000	0.000	0.000	0.000
33	A	50	GLY	0	0.017	0.017	24.534	-0.012	-0.012	0.000	0.000	0.000	0.000
34	A	51	LEU	0	-0.030	0.000	20.325	-0.015	-0.015	0.000	0.000	0.000	0.000
35	A	52	ILE	0	0.004	-0.011	15.786	0.026	0.026	0.000	0.000	0.000	0.000
36	A	53	LYS	1	0.859	0.922	18.487	-0.050	-0.050	0.000	0.000	0.000	0.000
37	A	54	SER	0	0.010	-0.006	17.876	0.028	0.028	0.000	0.000	0.000	0.000
38	A	55	ILE	0	0.005	0.012	12.990	-0.042	-0.042	0.000	0.000	0.000	0.000
39	A	56	GLN	0	-0.036	-0.015	17.028	0.002	0.002	0.000	0.000	0.000	0.000
40	A	57	VAL	0	0.032	0.016	13.285	-0.045	-0.045	0.000	0.000	0.000	0.000
41	A	58	ARG	1	0.890	0.953	16.675	-0.151	-0.151	0.000	0.000	0.000	0.000
42	A	59	TYR	0	0.070	0.030	13.452	0.033	0.033	0.000	0.000	0.000	0.000
43	A	60	GLY	0	0.129	0.082	19.181	-0.019	-0.019	0.000	0.000	0.000	0.000
44	A	61	SER	0	-0.060	-0.037	22.291	-0.017	-0.017	0.000	0.000	0.000	0.000
45	A	62	SER	0	0.010	0.016	22.664	-0.022	-0.022	0.000	0.000	0.000	0.000
46	A	63	TRP	0	-0.055	-0.030	19.250	0.024	0.024	0.000	0.000	0.000	0.000
47	A	64	SER	0	0.049	0.038	17.685	-0.002	-0.002	0.000	0.000	0.000	0.000
48	A	65	GLU	-1	-0.897	-0.947	19.690	0.310	0.310	0.000	0.000	0.000	0.000
49	A	66	LYS	1	0.870	0.934	18.963	-0.147	-0.147	0.000	0.000	0.000	0.000
50	A	67	TYR	0	0.075	0.042	15.516	0.018	0.018	0.000	0.000	0.000	0.000
51	A	68	GLY	0	0.028	-0.016	17.023	-0.019	-0.019	0.000	0.000	0.000	0.000
52	A	69	ILE	0	-0.071	-0.017	18.709	-0.002	-0.002	0.000	0.000	0.000	0.000
53	A	70	PRO	0	-0.021	-0.014	22.123	-0.011	-0.011	0.000	0.000	0.000	0.000
54	A	71	GLY	0	0.046	0.010	25.236	-0.013	-0.013	0.000	0.000	0.000	0.000
55	A	72	GLY	0	-0.023	-0.020	25.083	0.004	0.004	0.000	0.000	0.000	0.000
56	A	73	LYS	1	0.937	0.966	25.961	-0.008	-0.008	0.000	0.000	0.000	0.000
57	A	74	ALA	0	0.016	0.006	23.861	-0.003	-0.003	0.000	0.000	0.000	0.000
58	A	75	HIS	0	-0.011	-0.001	22.220	-0.013	-0.013	0.000	0.000	0.000	0.000
59	A	76	GLU	-1	-0.804	-0.896	21.308	0.115	0.115	0.000	0.000	0.000	0.000
60	A	77	LEU	0	-0.005	0.015	16.971	-0.023	-0.023	0.000	0.000	0.000	0.000
61	A	78	ILE	0	-0.048	-0.023	19.920	0.029	0.029	0.000	0.000	0.000	0.000
62	A	79	LEU	0	-0.058	-0.026	16.739	-0.021	-0.021	0.000	0.000	0.000	0.000
63	A	80	HIS	0	0.025	0.016	21.218	0.020	0.020	0.000	0.000	0.000	0.000
64	A	81	PRO	0	0.034	0.000	22.679	0.009	0.009	0.000	0.000	0.000	0.000
65	A	82	GLY	0	0.008	0.013	22.360	-0.015	-0.015	0.000	0.000	0.000	0.000
66	A	83	GLU	-1	-0.822	-0.861	19.388	-0.044	-0.044	0.000	0.000	0.000	0.000
67	A	84	HIS	0	0.047	0.014	15.055	0.049	0.049	0.000	0.000	0.000	0.000
68	A	85	ILE	0	0.001	-0.005	11.695	-0.051	-0.051	0.000	0.000	0.000	0.000
69	A	86	ILE	0	-0.001	-0.008	12.064	0.043	0.043	0.000	0.000	0.000	0.000
70	A	87	SER	0	-0.018	-0.004	10.158	-0.140	-0.140	0.000	0.000	0.000	0.000
71	A	88	ILE	0	-0.009	-0.005	8.415	0.182	0.182	0.000	0.000	0.000	0.000
72	A	89	TYR	0	0.014	0.040	10.350	-0.229	-0.229	0.000	0.000	0.000	0.000
73	A	90	GLY	0	0.037	0.014	12.899	0.114	0.114	0.000	0.000	0.000	0.000
74	A	91	ARG	1	0.841	0.922	13.650	0.307	0.307	0.000	0.000	0.000	0.000
75	A	92	TYR	0	0.034	0.032	12.634	0.028	0.028	0.000	0.000	0.000	0.000
76	A	93	ARG	1	0.958	0.971	16.388	0.123	0.123	0.000	0.000	0.000	0.000
77	A	94	THR	0	0.008	0.010	17.441	-0.019	-0.019	0.000	0.000	0.000	0.000
78	A	95	PHE	0	0.006	-0.008	17.237	0.023	0.023	0.000	0.000	0.000	0.000
79	A	96	LEU	0	0.018	0.005	12.477	-0.051	-0.051	0.000	0.000	0.000	0.000
80	A	97	GLN	0	-0.060	-0.032	15.803	0.048	0.048	0.000	0.000	0.000	0.000
81	A	98	HIS	0	-0.016	-0.023	16.694	0.008	0.008	0.000	0.000	0.000	0.000
82	A	99	VAL	0	0.042	0.011	12.512	-0.051	-0.051	0.000	0.000	0.000	0.000
83	A	100	THR	0	-0.010	0.006	14.610	0.052	0.052	0.000	0.000	0.000	0.000
84	A	101	LEU	0	0.019	0.002	12.527	-0.071	-0.071	0.000	0.000	0.000	0.000
85	A	102	ILE	0	0.017	0.014	14.178	0.046	0.046	0.000	0.000	0.000	0.000
86	A	103	THR	0	-0.024	-0.054	14.698	-0.024	-0.024	0.000	0.000	0.000	0.000
87	A	104	ASN	0	0.025	-0.005	17.033	-0.031	-0.031	0.000	0.000	0.000	0.000
88	A	105	GLN	0	-0.008	0.000	18.408	-0.004	-0.004	0.000	0.000	0.000	0.000
89	A	106	GLY	0	-0.004	0.008	20.515	0.008	0.008	0.000	0.000	0.000	0.000
90	A	107	ARG	1	0.837	0.919	21.168	0.015	0.015	0.000	0.000	0.000	0.000
91	A	108	SER	0	0.007	-0.001	18.801	-0.022	-0.022	0.000	0.000	0.000	0.000
92	A	109	ALA	0	-0.007	0.012	18.457	0.018	0.018	0.000	0.000	0.000	0.000
93	A	110	SER	0	0.017	0.003	18.111	-0.029	-0.029	0.000	0.000	0.000	0.000
94	A	111	PHE	0	0.000	-0.008	17.293	0.032	0.032	0.000	0.000	0.000	0.000
95	A	112	GLY	0	0.031	0.015	18.743	-0.019	-0.019	0.000	0.000	0.000	0.000
96	A	113	LEU	0	0.018	0.009	21.042	-0.013	-0.013	0.000	0.000	0.000	0.000
97	A	114	GLU	-1	-0.862	-0.937	19.921	-0.266	-0.266	0.000	0.000	0.000	0.000
98	A	115	THR	0	-0.036	-0.012	20.875	0.002	0.002	0.000	0.000	0.000	0.000
99	A	116	GLY	0	-0.009	-0.019	19.616	-0.003	-0.003	0.000	0.000	0.000	0.000
100	A	117	LYS	1	0.939	0.985	14.473	0.600	0.600	0.000	0.000	0.000	0.000
101	A	118	GLY	0	0.016	0.002	15.464	0.012	0.012	0.000	0.000	0.000	0.000
102	A	119	PHE	0	-0.057	-0.031	9.123	-0.019	-0.019	0.000	0.000	0.000	0.000
103	A	120	PHE	0	0.044	0.003	10.486	0.161	0.161	0.000	0.000	0.000	0.000
104	A	121	ALA	0	-0.033	-0.002	5.721	-0.373	-0.373	0.000	0.000	0.000	0.000
105	A	122	ALA	0	0.044	0.011	7.253	0.526	0.526	0.000	0.000	0.000	0.000
106	A	123	PRO	0	-0.015	0.020	6.415	-0.665	-0.665	0.000	0.000	0.000	0.000
107	A	124	ASN	0	0.007	-0.006	5.630	0.035	0.035	0.000	0.000	0.000	0.000
108	A	125	LEU	0	-0.022	0.002	8.417	0.160	0.160	0.000	0.000	0.000	0.000
109	A	126	THR	0	0.056	0.012	11.192	0.013	0.013	0.000	0.000	0.000	0.000
110	A	127	GLY	0	-0.003	-0.004	13.864	0.052	0.052	0.000	0.000	0.000	0.000
111	A	128	GLN	0	-0.070	-0.018	8.294	-0.102	-0.102	0.000	0.000	0.000	0.000
112	A	129	VAL	0	0.019	0.008	11.509	-0.145	-0.145	0.000	0.000	0.000	0.000
113	A	130	LEU	0	-0.065	-0.033	7.632	0.134	0.134	0.000	0.000	0.000	0.000
114	A	131	GLU	-1	-0.877	-0.947	9.182	0.706	0.706	0.000	0.000	0.000	0.000
115	A	132	GLY	0	0.069	0.033	9.043	-0.051	-0.051	0.000	0.000	0.000	0.000
116	A	133	VAL	0	-0.062	-0.015	7.561	0.136	0.136	0.000	0.000	0.000	0.000
117	A	134	TYR	0	0.011	0.010	1.874	-4.888	-4.994	6.010	-3.586	-2.319	-0.011
118	A	135	GLY	0	0.030	-0.009	8.596	-0.248	-0.248	0.000	0.000	0.000	0.000
119	A	136	GLN	0	-0.001	-0.002	9.502	0.026	0.026	0.000	0.000	0.000	0.000
120	A	137	PHE	0	0.029	0.041	12.703	-0.092	-0.092	0.000	0.000	0.000	0.000
121	A	138	TRP	0	0.009	-0.015	16.196	0.000	0.000	0.000	0.000	0.000	0.000
122	A	139	LEU	0	0.009	0.023	19.236	0.005	0.005	0.000	0.000	0.000	0.000
123	A	140	TYR	0	0.012	-0.004	22.212	0.003	0.003	0.000	0.000	0.000	0.000
124	A	141	GLY	0	0.022	0.004	19.693	-0.003	-0.003	0.000	0.000	0.000	0.000
125	A	142	ILE	0	0.012	0.023	13.180	0.009	0.009	0.000	0.000	0.000	0.000
126	A	143	THR	0	-0.091	-0.054	14.559	-0.045	-0.045	0.000	0.000	0.000	0.000
127	A	144	GLY	0	0.006	0.011	10.627	-0.096	-0.096	0.000	0.000	0.000	0.000
128	A	145	ILE	0	-0.013	-0.006	8.640	0.166	0.166	0.000	0.000	0.000	0.000
129	A	146	GLY	0	0.044	0.016	4.861	-0.553	-0.553	0.000	0.000	0.000	0.000
130	A	147	PHE	0	-0.007	-0.012	3.302	0.184	0.388	0.003	-0.044	-0.162	0.000
131	A	148	THR	0	0.013	0.001	2.903	1.315	2.382	0.349	-0.561	-0.856	-0.005
132	A	149	TRP	0	0.016	-0.002	3.874	-0.717	-0.596	0.000	-0.022	-0.100	0.000
133	A	150	GLY	0	0.036	0.028	7.028	0.283	0.283	0.000	0.000	0.000	0.000
134	A	151	PHE	0	-0.042	-0.013	10.024	-0.181	-0.181	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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