FMO DATABASE

FMODB ID: 494YN

Calculation Name: 3D1N-L-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3D1N

Chain ID: L

ChEMBL ID:

UniProt ID: Q14863

Base Structure: X-ray

Registration Date: 2023-09-20

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	145
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1287087.558708
FMO2-HF: Nuclear repulsion	1228305.667476
FMO2-HF: Total energy	-58781.891233
FMO2-MP2: Total energy	-58954.442366

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(L:143:ASN)

Summations of interaction energy for fragment #1(L:143:ASN)

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.
-31.268	-31.01	13.321	-6.813	-6.767	-0.073

Interaction energy analysis for fragmet #1(L:143:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.032 / q_NPA : -0.038

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	L	145	GLU	-1	-0.860	-0.941	3.844	-3.540	-1.412	-0.032	-0.964	-1.132	-0.002
4	L	146	GLU	-1	-0.843	-0.904	1.738	-37.639	-40.680	13.309	-5.573	-4.695	-0.072
5	L	147	ILE	0	0.026	-0.008	3.797	1.822	2.194	0.001	-0.068	-0.305	0.000
6	L	148	ARG	1	0.798	0.880	5.958	2.757	2.757	0.000	0.000	0.000	0.000
7	L	149	GLU	-1	-0.801	-0.881	8.920	-1.414	-1.414	0.000	0.000	0.000	0.000
8	L	150	PHE	0	-0.035	-0.007	8.144	0.312	0.312	0.000	0.000	0.000	0.000
9	L	151	ALA	0	0.000	-0.003	9.880	0.498	0.498	0.000	0.000	0.000	0.000
10	L	152	LYS	1	0.959	0.986	11.931	1.587	1.587	0.000	0.000	0.000	0.000
11	L	153	ASN	0	0.011	-0.014	12.284	0.394	0.394	0.000	0.000	0.000	0.000
12	L	154	PHE	0	0.001	0.011	13.339	0.219	0.219	0.000	0.000	0.000	0.000
13	L	155	LYS	1	0.963	0.991	15.204	0.887	0.887	0.000	0.000	0.000	0.000
14	L	156	ILE	0	0.005	-0.002	17.736	0.120	0.120	0.000	0.000	0.000	0.000
15	L	157	ARG	1	0.950	0.976	15.565	1.422	1.422	0.000	0.000	0.000	0.000
16	L	158	ARG	1	0.818	0.915	19.118	0.813	0.813	0.000	0.000	0.000	0.000
17	L	159	LEU	0	-0.059	-0.045	20.809	0.082	0.082	0.000	0.000	0.000	0.000
18	L	160	SER	0	-0.035	-0.004	22.633	0.057	0.057	0.000	0.000	0.000	0.000
19	L	161	LEU	0	-0.068	-0.007	21.767	0.042	0.042	0.000	0.000	0.000	0.000
20	L	162	GLY	0	0.040	0.024	25.124	0.038	0.038	0.000	0.000	0.000	0.000
21	L	163	LEU	0	-0.014	0.002	23.091	0.029	0.029	0.000	0.000	0.000	0.000
22	L	164	THR	0	-0.018	-0.030	24.532	-0.016	-0.016	0.000	0.000	0.000	0.000
23	L	165	GLN	0	0.009	-0.016	20.823	0.047	0.047	0.000	0.000	0.000	0.000
24	L	166	THR	0	-0.010	-0.016	23.059	-0.014	-0.014	0.000	0.000	0.000	0.000
25	L	167	GLN	0	0.105	0.086	25.877	-0.013	-0.013	0.000	0.000	0.000	0.000
26	L	168	VAL	0	0.062	0.039	19.418	0.008	0.008	0.000	0.000	0.000	0.000
27	L	169	GLY	0	-0.006	-0.001	21.894	0.001	0.001	0.000	0.000	0.000	0.000
28	L	170	GLN	0	-0.088	-0.035	22.860	0.043	0.043	0.000	0.000	0.000	0.000
29	L	171	ALA	0	0.100	0.058	23.279	0.018	0.018	0.000	0.000	0.000	0.000
30	L	172	MET	0	-0.027	-0.003	16.663	-0.010	-0.010	0.000	0.000	0.000	0.000
31	L	173	THR	0	-0.159	-0.098	21.080	0.046	0.046	0.000	0.000	0.000	0.000
32	L	174	ALA	0	-0.033	0.000	22.646	0.036	0.036	0.000	0.000	0.000	0.000
33	L	175	THR	0	0.012	0.000	21.008	0.027	0.027	0.000	0.000	0.000	0.000
34	L	176	GLU	-1	-0.822	-0.877	17.048	-0.681	-0.681	0.000	0.000	0.000	0.000
35	L	177	GLY	0	0.062	0.025	19.894	0.061	0.061	0.000	0.000	0.000	0.000
36	L	178	PRO	0	-0.023	-0.035	20.380	-0.050	-0.050	0.000	0.000	0.000	0.000
37	L	179	ALA	0	-0.088	-0.039	16.128	0.010	0.010	0.000	0.000	0.000	0.000
38	L	180	TYR	0	0.045	0.018	13.626	-0.116	-0.116	0.000	0.000	0.000	0.000
39	L	181	SER	0	0.052	0.030	18.766	-0.007	-0.007	0.000	0.000	0.000	0.000
40	L	182	GLN	0	0.053	0.013	20.469	-0.021	-0.021	0.000	0.000	0.000	0.000
41	L	183	SER	0	-0.014	-0.010	21.630	-0.046	-0.046	0.000	0.000	0.000	0.000
42	L	184	ALA	0	0.017	0.019	17.277	-0.009	-0.009	0.000	0.000	0.000	0.000
43	L	185	ILE	0	0.049	0.031	17.026	-0.082	-0.082	0.000	0.000	0.000	0.000
44	L	186	SER	0	-0.021	-0.004	17.476	-0.077	-0.077	0.000	0.000	0.000	0.000
45	L	187	ARG	1	0.905	0.941	16.580	0.155	0.155	0.000	0.000	0.000	0.000
46	L	188	PHE	0	0.032	0.024	9.227	0.004	0.004	0.000	0.000	0.000	0.000
47	L	189	GLU	-1	-0.778	-0.903	13.545	-0.955	-0.955	0.000	0.000	0.000	0.000
48	L	190	LYS	1	0.825	0.909	15.495	0.382	0.382	0.000	0.000	0.000	0.000
49	L	191	LEU	0	0.016	0.006	10.012	-0.006	-0.006	0.000	0.000	0.000	0.000
50	L	192	ASP	-1	-0.987	-0.973	12.996	0.013	0.013	0.000	0.000	0.000	0.000
51	L	193	ILE	0	-0.047	-0.020	10.807	0.044	0.044	0.000	0.000	0.000	0.000
52	L	194	THR	0	0.036	0.018	10.523	0.026	0.026	0.000	0.000	0.000	0.000
53	L	195	PRO	0	0.093	0.019	5.255	-0.374	-0.374	0.000	0.000	0.000	0.000
54	L	196	LYS	1	0.883	0.941	5.887	-4.929	-4.929	0.000	0.000	0.000	0.000
55	L	197	SER	0	0.021	0.003	8.173	-0.241	-0.241	0.000	0.000	0.000	0.000
56	L	198	ALA	0	0.042	0.023	7.297	-0.250	-0.250	0.000	0.000	0.000	0.000
57	L	199	GLN	0	0.058	0.027	2.820	2.137	2.864	0.044	-0.207	-0.564	0.001
58	L	200	LYS	1	0.944	0.977	5.293	-0.361	-0.289	-0.001	-0.001	-0.071	0.000
59	L	201	LEU	0	0.023	0.011	8.372	-0.100	-0.100	0.000	0.000	0.000	0.000
60	L	202	LYS	1	0.957	0.982	4.858	7.532	7.532	0.000	0.000	0.000	0.000
61	L	203	PRO	0	0.026	0.024	6.785	0.104	0.104	0.000	0.000	0.000	0.000
62	L	204	VAL	0	-0.005	-0.002	9.219	0.281	0.281	0.000	0.000	0.000	0.000
63	L	205	LEU	0	-0.051	-0.021	11.771	0.181	0.181	0.000	0.000	0.000	0.000
64	L	206	GLU	-1	-0.931	-0.976	10.299	-2.637	-2.637	0.000	0.000	0.000	0.000
65	L	207	LYS	1	0.881	0.937	12.671	1.016	1.016	0.000	0.000	0.000	0.000
66	L	208	TRP	0	0.048	0.016	14.941	0.072	0.072	0.000	0.000	0.000	0.000
67	L	209	LEU	0	-0.052	-0.036	15.271	0.082	0.082	0.000	0.000	0.000	0.000
68	L	210	ASN	0	0.056	0.025	14.680	0.101	0.101	0.000	0.000	0.000	0.000
69	L	211	GLU	-1	-0.944	-0.958	18.293	-0.573	-0.573	0.000	0.000	0.000	0.000
70	L	212	ALA	0	0.001	-0.016	20.695	0.077	0.077	0.000	0.000	0.000	0.000
71	L	213	GLU	-1	-0.904	-0.981	18.839	-1.040	-1.040	0.000	0.000	0.000	0.000
72	L	214	LEU	0	-0.049	-0.015	22.543	0.039	0.039	0.000	0.000	0.000	0.000
73	L	215	ARG	1	0.956	0.968	24.419	0.545	0.545	0.000	0.000	0.000	0.000
74	L	216	ASN	0	0.000	-0.010	25.744	0.066	0.066	0.000	0.000	0.000	0.000
75	L	217	GLN	0	-0.060	-0.014	25.009	0.049	0.049	0.000	0.000	0.000	0.000
76	L	218	GLU	-1	-0.880	-0.948	28.396	-0.421	-0.421	0.000	0.000	0.000	0.000
77	L	219	GLY	0	0.104	0.073	31.499	0.008	0.008	0.000	0.000	0.000	0.000
78	L	220	GLN	0	0.022	0.012	30.375	0.009	0.009	0.000	0.000	0.000	0.000
79	L	221	GLN	0	-0.117	-0.067	31.971	0.013	0.013	0.000	0.000	0.000	0.000
80	L	222	ASN	0	0.019	-0.013	30.527	0.026	0.026	0.000	0.000	0.000	0.000
81	L	223	LEU	0	-0.026	0.000	25.186	-0.021	-0.021	0.000	0.000	0.000	0.000
82	L	224	MET	0	-0.078	-0.032	28.343	-0.016	-0.016	0.000	0.000	0.000	0.000
83	L	225	GLU	-1	-0.923	-0.952	30.882	-0.338	-0.338	0.000	0.000	0.000	0.000
84	L	226	PHE	0	-0.057	-0.014	21.836	0.008	0.008	0.000	0.000	0.000	0.000
85	L	227	VAL	0	-0.059	-0.026	25.534	-0.009	-0.009	0.000	0.000	0.000	0.000
86	L	228	GLY	0	-0.024	-0.005	27.278	0.008	0.008	0.000	0.000	0.000	0.000
87	L	229	GLY	0	0.049	0.012	30.206	0.017	0.017	0.000	0.000	0.000	0.000
88	L	230	GLU	-1	-0.954	-1.009	31.759	-0.244	-0.244	0.000	0.000	0.000	0.000
89	L	231	PRO	0	0.014	0.032	30.426	0.022	0.022	0.000	0.000	0.000	0.000
90	L	232	SER	0	0.036	0.009	32.256	-0.007	-0.007	0.000	0.000	0.000	0.000
91	L	233	LYS	1	0.927	0.976	34.631	0.134	0.134	0.000	0.000	0.000	0.000
92	L	234	LYS	1	0.886	0.943	29.889	0.271	0.271	0.000	0.000	0.000	0.000
93	L	235	ARG	1	0.965	0.982	34.166	0.122	0.122	0.000	0.000	0.000	0.000
94	L	236	LYS	1	0.939	0.968	35.436	0.057	0.057	0.000	0.000	0.000	0.000
95	L	237	ARG	1	0.898	0.966	30.318	0.098	0.098	0.000	0.000	0.000	0.000
96	L	238	ARG	1	0.959	1.003	36.636	0.063	0.063	0.000	0.000	0.000	0.000
97	L	239	THR	0	0.012	-0.005	38.914	0.001	0.001	0.000	0.000	0.000	0.000
98	L	240	SER	0	0.036	0.024	41.161	0.004	0.004	0.000	0.000	0.000	0.000
99	L	241	PHE	0	0.058	0.019	41.335	-0.006	-0.006	0.000	0.000	0.000	0.000
100	L	242	THR	0	-0.017	-0.003	45.578	0.000	0.000	0.000	0.000	0.000	0.000
101	L	243	PRO	0	0.097	0.026	46.886	0.001	0.001	0.000	0.000	0.000	0.000
102	L	244	GLN	0	0.065	0.030	46.058	0.001	0.001	0.000	0.000	0.000	0.000
103	L	245	ALA	0	-0.019	0.004	42.755	-0.001	-0.001	0.000	0.000	0.000	0.000
104	L	246	ILE	0	-0.020	-0.020	43.445	0.002	0.002	0.000	0.000	0.000	0.000
105	L	247	GLU	-1	-0.902	-0.943	45.608	-0.031	-0.031	0.000	0.000	0.000	0.000
106	L	248	ALA	0	0.009	0.007	41.267	0.001	0.001	0.000	0.000	0.000	0.000
107	L	249	LEU	0	-0.028	-0.022	39.398	0.002	0.002	0.000	0.000	0.000	0.000
108	L	250	ASN	0	0.024	0.003	41.648	0.011	0.011	0.000	0.000	0.000	0.000
109	L	251	ALA	0	0.055	0.053	42.547	0.004	0.004	0.000	0.000	0.000	0.000
110	L	252	TYR	0	-0.042	-0.057	36.201	0.002	0.002	0.000	0.000	0.000	0.000
111	L	253	PHE	0	-0.031	-0.008	39.448	0.006	0.006	0.000	0.000	0.000	0.000
112	L	254	GLU	-1	-0.898	-0.937	41.485	-0.010	-0.010	0.000	0.000	0.000	0.000
113	L	255	LYS	1	0.784	0.883	38.971	0.025	0.025	0.000	0.000	0.000	0.000
114	L	256	ASN	0	-0.049	-0.027	33.968	0.011	0.011	0.000	0.000	0.000	0.000
115	L	257	PRO	0	0.038	0.020	38.312	0.001	0.001	0.000	0.000	0.000	0.000
116	L	258	LEU	0	-0.068	-0.048	36.158	0.004	0.004	0.000	0.000	0.000	0.000
117	L	259	PRO	0	0.025	0.034	33.724	0.006	0.006	0.000	0.000	0.000	0.000
118	L	260	THR	0	0.030	0.022	28.606	0.014	0.014	0.000	0.000	0.000	0.000
119	L	261	GLY	0	0.010	-0.012	28.653	-0.014	-0.014	0.000	0.000	0.000	0.000
120	L	262	GLN	0	0.023	0.011	24.257	-0.030	-0.030	0.000	0.000	0.000	0.000
121	L	263	GLU	-1	-0.722	-0.863	26.945	0.004	0.004	0.000	0.000	0.000	0.000
122	L	264	ILE	0	0.025	0.015	30.108	-0.012	-0.012	0.000	0.000	0.000	0.000
123	L	265	THR	0	-0.136	-0.061	26.589	-0.012	-0.012	0.000	0.000	0.000	0.000
124	L	266	GLU	-1	-0.880	-0.931	26.335	-0.118	-0.118	0.000	0.000	0.000	0.000
125	L	267	MET	0	-0.003	0.002	29.735	-0.009	-0.009	0.000	0.000	0.000	0.000
126	L	268	ALA	0	0.018	0.010	32.301	-0.005	-0.005	0.000	0.000	0.000	0.000
127	L	269	LYS	1	0.866	0.900	25.844	0.184	0.184	0.000	0.000	0.000	0.000
128	L	270	GLU	-1	-0.850	-0.918	31.882	-0.092	-0.092	0.000	0.000	0.000	0.000
129	L	271	LEU	0	0.053	0.064	34.083	0.000	0.000	0.000	0.000	0.000	0.000
130	L	272	ASN	0	-0.118	-0.056	35.166	-0.007	-0.007	0.000	0.000	0.000	0.000
131	L	273	TYR	0	-0.007	-0.023	36.045	0.003	0.003	0.000	0.000	0.000	0.000
132	L	274	ASP	-1	-0.905	-0.974	35.090	-0.018	-0.018	0.000	0.000	0.000	0.000
133	L	275	ARG	1	0.910	0.924	29.003	-0.026	-0.026	0.000	0.000	0.000	0.000
134	L	276	GLU	-1	-0.860	-0.935	33.606	0.062	0.062	0.000	0.000	0.000	0.000
135	L	277	VAL	0	-0.034	-0.003	35.672	0.004	0.004	0.000	0.000	0.000	0.000
136	L	278	VAL	0	0.023	0.014	35.460	0.004	0.004	0.000	0.000	0.000	0.000
137	L	279	ARG	1	0.925	0.950	33.576	-0.068	-0.068	0.000	0.000	0.000	0.000
138	L	280	VAL	0	-0.027	-0.003	36.106	0.009	0.009	0.000	0.000	0.000	0.000
139	L	281	TRP	0	-0.021	0.004	39.319	0.003	0.003	0.000	0.000	0.000	0.000
140	L	282	PHE	0	0.024	-0.008	37.752	0.002	0.002	0.000	0.000	0.000	0.000
141	L	283	SER	0	-0.052	-0.026	38.622	0.007	0.007	0.000	0.000	0.000	0.000
142	L	284	ASN	0	0.006	-0.007	40.071	0.009	0.009	0.000	0.000	0.000	0.000
143	L	285	ARG	1	0.872	0.960	42.840	-0.014	-0.014	0.000	0.000	0.000	0.000
144	L	286	ARG	1	0.892	0.956	40.975	-0.060	-0.060	0.000	0.000	0.000	0.000
145	L	287	GLN	0	0.022	0.028	43.645	-0.003	-0.003	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(L:143:ASN)