FMO DATABASE

FMODB ID: QYLJY

Calculation Name: 5J08-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5J08

Chain ID: A

ChEMBL ID:

UniProt ID: Q03769

Base Structure: X-ray

Registration Date: 2023-06-22

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	OptHSide
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	163
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1772275.232643
FMO2-HF: Nuclear repulsion	1705500.650284
FMO2-HF: Total energy	-66774.582359
FMO2-MP2: Total energy	-66972.146197

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:30:SER)

Summations of interaction energy for fragment #1(A:30:SER)

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.
-36.677	-38.306	16.297	-7.519	-7.151	0.039

Interaction energy analysis for fragmet #1(A:30:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.006 / q_NPA : 0.003

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	32	PRO	0	0.055	0.012	3.827	4.221	5.164	-0.006	-0.395	-0.543	0.001
4	A	33	TYR	0	0.100	0.045	6.449	1.241	1.241	0.000	0.000	0.000	0.000
5	A	34	GLN	0	0.045	0.021	2.214	1.074	1.142	3.253	-1.434	-1.887	-0.018
6	A	35	ILE	0	-0.051	-0.007	3.310	0.966	1.351	0.028	-0.084	-0.329	0.000
7	A	36	ASP	-1	-0.762	-0.844	6.032	0.148	0.148	0.000	0.000	0.000	0.000
8	A	37	ILE	0	0.027	0.018	8.826	-0.156	-0.156	0.000	0.000	0.000	0.000
9	A	38	ARG	1	0.845	0.906	1.917	-35.929	-38.954	13.022	-5.606	-4.392	0.056
10	A	39	ARG	1	0.814	0.899	9.534	-1.564	-1.564	0.000	0.000	0.000	0.000
11	A	40	ALA	0	-0.027	-0.009	11.620	-0.235	-0.235	0.000	0.000	0.000	0.000
12	A	41	THR	0	0.005	-0.018	12.167	-0.094	-0.094	0.000	0.000	0.000	0.000
13	A	42	ASN	0	0.056	0.047	13.211	0.038	0.038	0.000	0.000	0.000	0.000
14	A	43	THR	0	0.033	0.004	14.361	-0.098	-0.098	0.000	0.000	0.000	0.000
15	A	44	ASP	-1	-0.836	-0.904	17.028	0.608	0.608	0.000	0.000	0.000	0.000
16	A	45	ALA	0	-0.047	-0.025	18.972	0.008	0.008	0.000	0.000	0.000	0.000
17	A	46	TRP	0	0.015	0.019	21.432	-0.048	-0.048	0.000	0.000	0.000	0.000
18	A	47	GLY	0	-0.019	0.010	19.474	0.077	0.077	0.000	0.000	0.000	0.000
19	A	48	PRO	0	-0.014	-0.014	17.387	0.010	0.010	0.000	0.000	0.000	0.000
20	A	49	THR	0	0.029	-0.013	19.027	-0.086	-0.086	0.000	0.000	0.000	0.000
21	A	50	PRO	0	0.101	0.026	19.955	0.042	0.042	0.000	0.000	0.000	0.000
22	A	51	LYS	1	0.998	1.005	18.266	-0.275	-0.275	0.000	0.000	0.000	0.000
23	A	52	HIS	0	-0.009	0.002	15.716	0.017	0.017	0.000	0.000	0.000	0.000
24	A	53	LEU	0	0.060	0.035	15.676	0.071	0.071	0.000	0.000	0.000	0.000
25	A	54	ALA	0	0.019	0.015	17.587	-0.019	-0.019	0.000	0.000	0.000	0.000
26	A	55	LYS	1	0.804	0.890	11.310	-0.358	-0.358	0.000	0.000	0.000	0.000
27	A	56	VAL	0	0.007	0.003	12.327	-0.037	-0.037	0.000	0.000	0.000	0.000
28	A	57	LEU	0	0.043	0.021	13.966	-0.068	-0.068	0.000	0.000	0.000	0.000
29	A	58	ARG	1	0.932	0.962	16.064	-0.130	-0.130	0.000	0.000	0.000	0.000
30	A	59	ASN	0	-0.011	-0.033	10.789	-0.235	-0.235	0.000	0.000	0.000	0.000
31	A	60	ARG	1	0.807	0.882	13.508	-0.172	-0.172	0.000	0.000	0.000	0.000
32	A	61	TYR	0	-0.040	-0.014	16.063	-0.006	-0.006	0.000	0.000	0.000	0.000
33	A	62	GLN	0	-0.018	-0.013	12.773	-0.002	-0.002	0.000	0.000	0.000	0.000
34	A	63	VAL	0	-0.028	-0.003	9.658	-0.126	-0.126	0.000	0.000	0.000	0.000
35	A	64	PRO	0	0.059	0.035	12.666	0.110	0.110	0.000	0.000	0.000	0.000
36	A	65	LEU	0	0.102	0.023	13.653	0.085	0.085	0.000	0.000	0.000	0.000
37	A	66	TYR	0	0.003	0.029	14.952	0.126	0.126	0.000	0.000	0.000	0.000
38	A	67	LEU	0	0.077	0.035	10.108	0.101	0.101	0.000	0.000	0.000	0.000
39	A	68	MET	0	-0.061	-0.011	10.746	0.230	0.230	0.000	0.000	0.000	0.000
40	A	69	THR	0	-0.007	-0.023	11.809	0.247	0.247	0.000	0.000	0.000	0.000
41	A	70	GLU	-1	-0.875	-0.950	12.217	0.414	0.414	0.000	0.000	0.000	0.000
42	A	71	TYR	0	-0.022	-0.012	4.972	0.541	0.541	0.000	0.000	0.000	0.000
43	A	72	THR	0	-0.042	-0.030	9.931	0.348	0.348	0.000	0.000	0.000	0.000
44	A	73	LEU	0	-0.011	-0.009	12.458	0.040	0.040	0.000	0.000	0.000	0.000
45	A	74	LYS	1	0.883	0.937	9.398	-1.461	-1.461	0.000	0.000	0.000	0.000
46	A	75	ARG	1	0.883	0.933	9.733	-2.462	-2.462	0.000	0.000	0.000	0.000
47	A	76	LEU	0	0.004	-0.008	12.012	-0.079	-0.079	0.000	0.000	0.000	0.000
48	A	77	VAL	0	0.045	0.013	15.511	-0.050	-0.050	0.000	0.000	0.000	0.000
49	A	78	ASP	-1	-0.835	-0.900	11.141	1.563	1.563	0.000	0.000	0.000	0.000
50	A	79	HIS	1	0.778	0.851	11.612	-1.753	-1.753	0.000	0.000	0.000	0.000
51	A	80	ILE	0	-0.012	0.004	16.203	-0.098	-0.098	0.000	0.000	0.000	0.000
52	A	81	ALA	0	0.026	0.014	17.505	-0.076	-0.076	0.000	0.000	0.000	0.000
53	A	82	THR	0	0.001	0.012	15.318	-0.074	-0.074	0.000	0.000	0.000	0.000
54	A	83	ARG	1	0.830	0.927	18.555	-0.621	-0.621	0.000	0.000	0.000	0.000
55	A	84	PRO	0	0.012	0.023	21.991	-0.028	-0.028	0.000	0.000	0.000	0.000
56	A	85	LYS	1	0.935	0.957	25.089	-0.351	-0.351	0.000	0.000	0.000	0.000
57	A	86	ASN	0	-0.003	-0.009	27.733	-0.022	-0.022	0.000	0.000	0.000	0.000
58	A	87	LEU	0	0.089	0.032	29.646	0.023	0.023	0.000	0.000	0.000	0.000
59	A	88	TYR	0	0.066	0.036	30.803	0.007	0.007	0.000	0.000	0.000	0.000
60	A	89	GLU	-1	-0.741	-0.868	26.377	0.373	0.373	0.000	0.000	0.000	0.000
61	A	90	LYS	1	0.871	0.936	26.672	-0.383	-0.383	0.000	0.000	0.000	0.000
62	A	91	ALA	0	-0.041	-0.034	27.209	0.023	0.023	0.000	0.000	0.000	0.000
63	A	92	ARG	1	0.922	0.979	27.829	-0.263	-0.263	0.000	0.000	0.000	0.000
64	A	93	LYS	1	0.854	0.950	20.487	-0.642	-0.642	0.000	0.000	0.000	0.000
65	A	94	ASP	-1	-0.830	-0.912	19.151	0.698	0.698	0.000	0.000	0.000	0.000
66	A	95	TYR	0	-0.100	-0.068	19.073	-0.060	-0.060	0.000	0.000	0.000	0.000
67	A	96	VAL	0	0.124	0.063	15.944	-0.037	-0.037	0.000	0.000	0.000	0.000
68	A	97	ASN	0	-0.025	-0.030	15.050	0.052	0.052	0.000	0.000	0.000	0.000
69	A	98	TYR	0	0.061	0.038	19.513	-0.024	-0.024	0.000	0.000	0.000	0.000
70	A	99	GLY	0	0.011	0.022	22.703	-0.022	-0.022	0.000	0.000	0.000	0.000
71	A	100	SER	0	-0.069	-0.061	20.864	-0.014	-0.014	0.000	0.000	0.000	0.000
72	A	101	GLU	-1	-0.705	-0.840	16.727	1.277	1.277	0.000	0.000	0.000	0.000
73	A	102	TRP	0	-0.002	-0.004	19.594	0.046	0.046	0.000	0.000	0.000	0.000
74	A	103	ARG	1	0.898	0.952	19.780	-0.711	-0.711	0.000	0.000	0.000	0.000
75	A	104	VAL	0	0.021	0.029	14.358	0.010	0.010	0.000	0.000	0.000	0.000
76	A	105	VAL	0	0.037	0.029	17.188	0.025	0.025	0.000	0.000	0.000	0.000
77	A	106	LEU	0	0.018	0.002	19.192	-0.025	-0.025	0.000	0.000	0.000	0.000
78	A	107	LYS	1	0.816	0.918	17.293	-0.964	-0.964	0.000	0.000	0.000	0.000
79	A	108	CYS	0	-0.055	-0.024	14.914	0.068	0.068	0.000	0.000	0.000	0.000
80	A	109	LEU	0	0.008	0.005	16.865	-0.053	-0.053	0.000	0.000	0.000	0.000
81	A	110	VAL	0	0.004	0.005	20.224	-0.057	-0.057	0.000	0.000	0.000	0.000
82	A	111	VAL	0	-0.009	-0.008	14.473	-0.051	-0.051	0.000	0.000	0.000	0.000
83	A	112	ILE	0	0.015	0.010	17.184	-0.061	-0.061	0.000	0.000	0.000	0.000
84	A	113	GLU	-1	-0.788	-0.881	19.116	0.332	0.332	0.000	0.000	0.000	0.000
85	A	114	PHE	0	0.009	-0.002	19.197	-0.044	-0.044	0.000	0.000	0.000	0.000
86	A	115	LEU	0	0.022	0.010	15.269	-0.054	-0.054	0.000	0.000	0.000	0.000
87	A	116	LEU	0	0.006	0.006	19.982	-0.060	-0.060	0.000	0.000	0.000	0.000
88	A	117	LEU	0	-0.008	-0.001	23.068	-0.043	-0.043	0.000	0.000	0.000	0.000
89	A	118	ASN	0	-0.083	-0.048	22.073	-0.052	-0.052	0.000	0.000	0.000	0.000
90	A	119	VAL	0	-0.012	0.029	19.447	-0.020	-0.020	0.000	0.000	0.000	0.000
91	A	120	ASP	-1	-0.811	-0.875	22.367	0.049	0.049	0.000	0.000	0.000	0.000
92	A	121	THR	0	-0.048	-0.046	24.689	0.018	0.018	0.000	0.000	0.000	0.000
93	A	122	GLY	0	0.030	0.029	26.971	-0.016	-0.016	0.000	0.000	0.000	0.000
94	A	123	ASP	-1	-0.824	-0.909	21.766	-0.026	-0.026	0.000	0.000	0.000	0.000
95	A	124	GLU	-1	-0.722	-0.843	20.289	0.078	0.078	0.000	0.000	0.000	0.000
96	A	125	LEU	0	0.002	-0.004	20.895	0.035	0.035	0.000	0.000	0.000	0.000
97	A	126	ASN	0	0.012	-0.009	23.127	0.042	0.042	0.000	0.000	0.000	0.000
98	A	127	GLN	0	0.022	0.014	17.790	0.028	0.028	0.000	0.000	0.000	0.000
99	A	128	ILE	0	-0.002	0.012	18.409	0.028	0.028	0.000	0.000	0.000	0.000
100	A	129	ARG	1	0.902	0.939	19.869	-0.113	-0.113	0.000	0.000	0.000	0.000
101	A	130	SER	0	0.019	0.008	21.688	0.010	0.010	0.000	0.000	0.000	0.000
102	A	131	CYS	0	-0.046	0.013	16.638	0.036	0.036	0.000	0.000	0.000	0.000
103	A	132	LEU	0	0.018	-0.009	19.446	0.028	0.028	0.000	0.000	0.000	0.000
104	A	133	LEU	0	-0.002	-0.005	21.242	0.003	0.003	0.000	0.000	0.000	0.000
105	A	134	THR	0	-0.039	-0.031	20.522	-0.021	-0.021	0.000	0.000	0.000	0.000
106	A	135	HIS	0	-0.009	-0.001	16.833	0.002	0.002	0.000	0.000	0.000	0.000
107	A	136	LYS	1	0.966	0.991	21.431	-0.160	-0.160	0.000	0.000	0.000	0.000
108	A	137	HIS	0	-0.012	-0.002	21.109	-0.019	-0.019	0.000	0.000	0.000	0.000
109	A	138	ILE	0	0.047	0.038	18.297	0.007	0.007	0.000	0.000	0.000	0.000
110	A	139	LEU	0	0.002	-0.012	22.627	0.018	0.018	0.000	0.000	0.000	0.000
111	A	140	THR	0	-0.016	-0.023	24.936	-0.013	-0.013	0.000	0.000	0.000	0.000
112	A	141	ARG	1	0.947	0.980	26.759	-0.248	-0.248	0.000	0.000	0.000	0.000
113	A	142	GLU	-1	-0.906	-0.952	21.492	0.536	0.536	0.000	0.000	0.000	0.000
114	A	143	ILE	0	-0.034	-0.028	21.659	0.012	0.012	0.000	0.000	0.000	0.000
115	A	144	ALA	0	0.029	0.029	25.500	-0.008	-0.008	0.000	0.000	0.000	0.000
116	A	145	GLN	0	-0.037	-0.024	28.719	-0.023	-0.023	0.000	0.000	0.000	0.000
117	A	146	PHE	0	-0.016	0.007	22.936	0.012	0.012	0.000	0.000	0.000	0.000
118	A	147	LYS	1	0.883	0.917	27.584	-0.330	-0.330	0.000	0.000	0.000	0.000
119	A	148	VAL	0	-0.079	-0.034	26.413	0.043	0.043	0.000	0.000	0.000	0.000
120	A	149	LYS	1	0.831	0.906	27.806	-0.410	-0.410	0.000	0.000	0.000	0.000
121	A	150	PHE	0	0.055	0.012	27.462	-0.018	-0.018	0.000	0.000	0.000	0.000
122	A	151	SER	0	-0.019	-0.027	26.976	0.038	0.038	0.000	0.000	0.000	0.000
123	A	152	ASN	0	-0.022	-0.034	24.801	-0.054	-0.054	0.000	0.000	0.000	0.000
124	A	153	ASP	-1	-0.760	-0.842	28.559	0.394	0.394	0.000	0.000	0.000	0.000
125	A	154	GLY	0	0.054	0.032	31.207	-0.020	-0.020	0.000	0.000	0.000	0.000
126	A	155	LYS	1	0.845	0.919	31.062	-0.366	-0.366	0.000	0.000	0.000	0.000
127	A	156	MET	0	0.012	0.013	30.060	0.019	0.019	0.000	0.000	0.000	0.000
128	A	157	GLU	-1	-0.852	-0.919	30.828	0.292	0.292	0.000	0.000	0.000	0.000
129	A	158	ILE	0	-0.003	-0.008	31.055	0.004	0.004	0.000	0.000	0.000	0.000
130	A	159	HIS	1	0.795	0.883	26.852	-0.425	-0.425	0.000	0.000	0.000	0.000
131	A	160	GLU	-1	-0.704	-0.827	27.669	0.357	0.357	0.000	0.000	0.000	0.000
132	A	161	ARG	1	0.978	0.998	29.256	-0.268	-0.268	0.000	0.000	0.000	0.000
133	A	162	GLY	0	-0.014	-0.006	28.352	-0.007	-0.007	0.000	0.000	0.000	0.000
134	A	163	ILE	0	-0.029	-0.019	23.724	0.010	0.010	0.000	0.000	0.000	0.000
135	A	164	ARG	1	0.882	0.937	26.203	-0.308	-0.308	0.000	0.000	0.000	0.000
136	A	165	LYS	1	0.885	0.932	28.775	-0.274	-0.274	0.000	0.000	0.000	0.000
137	A	166	LYS	1	0.775	0.876	23.724	-0.418	-0.418	0.000	0.000	0.000	0.000
138	A	167	GLY	0	0.035	0.003	25.244	0.002	0.002	0.000	0.000	0.000	0.000
139	A	168	GLU	-1	-0.836	-0.906	26.193	0.258	0.258	0.000	0.000	0.000	0.000
140	A	169	LEU	0	-0.009	0.009	27.868	-0.017	-0.017	0.000	0.000	0.000	0.000
141	A	170	ILE	0	-0.025	-0.022	22.154	-0.013	-0.013	0.000	0.000	0.000	0.000
142	A	171	LEU	0	-0.003	-0.004	26.195	-0.014	-0.014	0.000	0.000	0.000	0.000
143	A	172	GLN	0	0.057	0.032	28.477	-0.010	-0.010	0.000	0.000	0.000	0.000
144	A	173	TYR	0	-0.070	-0.036	26.138	-0.028	-0.028	0.000	0.000	0.000	0.000
145	A	174	LEU	0	-0.064	-0.036	24.435	-0.015	-0.015	0.000	0.000	0.000	0.000
146	A	175	GLU	-1	-0.945	-0.963	28.564	0.186	0.186	0.000	0.000	0.000	0.000
147	A	176	ASP	-1	-0.823	-0.909	32.189	0.116	0.116	0.000	0.000	0.000	0.000
148	A	177	SER	0	0.031	-0.011	31.872	0.004	0.004	0.000	0.000	0.000	0.000
149	A	178	GLN	0	0.024	0.015	32.924	-0.004	-0.004	0.000	0.000	0.000	0.000
150	A	179	PHE	0	0.054	0.028	31.458	-0.004	-0.004	0.000	0.000	0.000	0.000
151	A	180	LEU	0	0.033	0.016	26.993	0.003	0.003	0.000	0.000	0.000	0.000
152	A	181	LYS	1	0.887	0.940	30.844	-0.079	-0.079	0.000	0.000	0.000	0.000
153	A	182	LYS	1	0.801	0.901	32.678	-0.152	-0.152	0.000	0.000	0.000	0.000
154	A	183	GLU	-1	-0.779	-0.863	30.931	0.168	0.168	0.000	0.000	0.000	0.000
155	A	184	ARG	1	0.809	0.878	25.134	-0.151	-0.151	0.000	0.000	0.000	0.000
156	A	185	ALA	0	-0.042	-0.013	30.170	-0.005	-0.005	0.000	0.000	0.000	0.000
157	A	186	LYS	1	0.840	0.896	33.372	-0.162	-0.162	0.000	0.000	0.000	0.000
158	A	187	ASN	0	-0.062	-0.037	26.451	0.008	0.008	0.000	0.000	0.000	0.000
159	A	188	LYS	1	0.962	0.985	28.914	-0.091	-0.091	0.000	0.000	0.000	0.000
160	A	189	LYS	1	0.926	0.985	31.569	-0.137	-0.137	0.000	0.000	0.000	0.000
161	A	190	ASN	0	-0.005	-0.021	33.013	-0.005	-0.005	0.000	0.000	0.000	0.000
162	A	191	ALA	0	0.014	0.010	29.700	0.008	0.008	0.000	0.000	0.000	0.000
163	A	192	LEU	0	-0.033	0.004	29.460	-0.004	-0.004	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:30:SER)