FMO DATABASE

FMODB ID: YZK12

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1287889.465996
FMO2-HF: Nuclear repulsion	1229105.152344
FMO2-HF: Total energy	-58784.313653
FMO2-MP2: Total energy	-58956.526189

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.
-40.914	-37.096	11.605	-7.318	-8.105	-0.06

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 : -0.014 / q_NPA : -0.030

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	-0.782	-0.881	3.877	-3.632	-1.906	-0.012	-0.755	-0.960	0.001
4	L	146	GLU	-1	-0.836	-0.895	1.775	-37.645	-38.453	11.213	-5.548	-4.856	-0.069
5	L	147	ILE	0	0.004	-0.005	2.777	0.269	1.841	0.327	-0.573	-1.326	0.005
6	L	148	ARG	1	0.801	0.874	5.774	1.668	1.668	0.000	0.000	0.000	0.000
7	L	149	GLU	-1	-0.762	-0.858	8.440	-1.022	-1.022	0.000	0.000	0.000	0.000
8	L	150	PHE	0	0.020	0.018	7.511	0.304	0.304	0.000	0.000	0.000	0.000
9	L	151	ALA	0	-0.003	-0.002	9.285	0.420	0.420	0.000	0.000	0.000	0.000
10	L	152	LYS	1	0.835	0.903	11.547	1.384	1.384	0.000	0.000	0.000	0.000
11	L	153	ASN	0	-0.007	-0.022	11.821	0.338	0.338	0.000	0.000	0.000	0.000
12	L	154	PHE	0	-0.011	0.001	12.685	0.168	0.168	0.000	0.000	0.000	0.000
13	L	155	LYS	1	0.887	0.946	14.519	0.506	0.506	0.000	0.000	0.000	0.000
14	L	156	ILE	0	0.001	0.002	16.889	0.090	0.090	0.000	0.000	0.000	0.000
15	L	157	ARG	1	0.810	0.871	13.811	1.450	1.450	0.000	0.000	0.000	0.000
16	L	158	ARG	1	0.807	0.860	18.485	0.560	0.560	0.000	0.000	0.000	0.000
17	L	159	LEU	0	-0.063	-0.039	20.321	0.072	0.072	0.000	0.000	0.000	0.000
18	L	160	SER	0	-0.031	-0.020	21.751	0.050	0.050	0.000	0.000	0.000	0.000
19	L	161	LEU	0	-0.020	0.001	21.417	0.023	0.023	0.000	0.000	0.000	0.000
20	L	162	GLY	0	-0.001	0.014	24.552	0.035	0.035	0.000	0.000	0.000	0.000
21	L	163	LEU	0	-0.023	0.010	22.493	0.039	0.039	0.000	0.000	0.000	0.000
22	L	164	THR	0	0.010	-0.024	24.031	-0.008	-0.008	0.000	0.000	0.000	0.000
23	L	165	GLN	0	0.010	-0.017	20.021	0.028	0.028	0.000	0.000	0.000	0.000
24	L	166	THR	0	-0.019	-0.025	22.422	0.000	0.000	0.000	0.000	0.000	0.000
25	L	167	GLN	0	0.088	0.077	25.221	0.007	0.007	0.000	0.000	0.000	0.000
26	L	168	VAL	0	0.069	0.043	18.678	0.001	0.001	0.000	0.000	0.000	0.000
27	L	169	GLY	0	0.008	0.012	20.835	-0.008	-0.008	0.000	0.000	0.000	0.000
28	L	170	GLN	0	-0.073	-0.029	21.831	0.046	0.046	0.000	0.000	0.000	0.000
29	L	171	ALA	0	0.079	0.056	22.518	0.016	0.016	0.000	0.000	0.000	0.000
30	L	172	MET	0	0.013	0.023	15.731	-0.006	-0.006	0.000	0.000	0.000	0.000
31	L	173	THR	0	-0.137	-0.088	20.347	0.039	0.039	0.000	0.000	0.000	0.000
32	L	174	ALA	0	-0.043	-0.009	22.260	0.039	0.039	0.000	0.000	0.000	0.000
33	L	175	THR	0	-0.012	-0.035	20.314	0.020	0.020	0.000	0.000	0.000	0.000
34	L	176	GLU	-1	-0.824	-0.889	16.464	-0.600	-0.600	0.000	0.000	0.000	0.000
35	L	177	GLY	0	0.014	0.013	19.281	0.055	0.055	0.000	0.000	0.000	0.000
36	L	178	PRO	0	-0.033	-0.050	19.922	-0.018	-0.018	0.000	0.000	0.000	0.000
37	L	179	ALA	0	-0.067	-0.027	15.706	0.019	0.019	0.000	0.000	0.000	0.000
38	L	180	TYR	0	0.055	0.026	12.271	0.057	0.057	0.000	0.000	0.000	0.000
39	L	181	SER	0	0.035	0.024	17.720	-0.039	-0.039	0.000	0.000	0.000	0.000
40	L	182	GLN	0	0.060	0.019	19.625	0.002	0.002	0.000	0.000	0.000	0.000
41	L	183	SER	0	0.010	0.005	20.750	-0.026	-0.026	0.000	0.000	0.000	0.000
42	L	184	ALA	0	0.002	0.010	16.387	0.036	0.036	0.000	0.000	0.000	0.000
43	L	185	ILE	0	0.042	0.022	15.951	-0.009	-0.009	0.000	0.000	0.000	0.000
44	L	186	SER	0	-0.025	-0.023	16.742	-0.021	-0.021	0.000	0.000	0.000	0.000
45	L	187	ARG	1	0.784	0.894	16.404	-0.295	-0.295	0.000	0.000	0.000	0.000
46	L	188	PHE	0	0.040	0.022	8.441	0.122	0.122	0.000	0.000	0.000	0.000
47	L	189	GLU	-1	-0.731	-0.841	13.204	-0.562	-0.562	0.000	0.000	0.000	0.000
48	L	190	LYS	1	0.762	0.859	15.557	-0.089	-0.089	0.000	0.000	0.000	0.000
49	L	191	LEU	0	0.024	0.014	9.045	0.091	0.091	0.000	0.000	0.000	0.000
50	L	192	ASP	-1	-0.810	-0.849	13.140	0.600	0.600	0.000	0.000	0.000	0.000
51	L	193	ILE	0	-0.010	-0.015	10.559	-0.070	-0.070	0.000	0.000	0.000	0.000
52	L	194	THR	0	0.055	0.038	11.371	0.186	0.186	0.000	0.000	0.000	0.000
53	L	195	PRO	0	0.073	0.018	5.836	-0.299	-0.299	0.000	0.000	0.000	0.000
54	L	196	LYS	1	0.905	0.947	6.045	-4.996	-4.996	0.000	0.000	0.000	0.000
55	L	197	SER	0	0.006	-0.004	8.103	-0.484	-0.484	0.000	0.000	0.000	0.000
56	L	198	ALA	0	0.029	0.008	7.161	-0.437	-0.437	0.000	0.000	0.000	0.000
57	L	199	GLN	0	0.053	0.030	2.780	-0.577	0.586	0.079	-0.437	-0.805	0.003
58	L	200	LYS	1	0.951	0.976	4.900	-1.628	-1.559	-0.001	-0.001	-0.067	0.000
59	L	201	LEU	0	-0.010	-0.004	8.119	-0.290	-0.290	0.000	0.000	0.000	0.000
60	L	202	LYS	1	0.838	0.925	4.507	7.166	7.262	-0.001	-0.004	-0.091	0.000
61	L	203	PRO	0	0.048	0.018	5.934	0.145	0.145	0.000	0.000	0.000	0.000
62	L	204	VAL	0	-0.021	0.006	8.706	0.234	0.234	0.000	0.000	0.000	0.000
63	L	205	LEU	0	-0.005	-0.011	10.610	0.130	0.130	0.000	0.000	0.000	0.000
64	L	206	GLU	-1	-0.871	-0.933	8.183	-4.214	-4.214	0.000	0.000	0.000	0.000
65	L	207	LYS	1	0.874	0.948	11.957	0.899	0.899	0.000	0.000	0.000	0.000
66	L	208	TRP	0	0.040	0.009	14.475	0.074	0.074	0.000	0.000	0.000	0.000
67	L	209	LEU	0	-0.012	-0.006	15.113	0.072	0.072	0.000	0.000	0.000	0.000
68	L	210	ASN	0	0.029	0.021	13.499	0.065	0.065	0.000	0.000	0.000	0.000
69	L	211	GLU	-1	-0.864	-0.912	17.430	-0.544	-0.544	0.000	0.000	0.000	0.000
70	L	212	ALA	0	0.003	-0.002	19.930	0.077	0.077	0.000	0.000	0.000	0.000
71	L	213	GLU	-1	-0.798	-0.885	18.918	-0.981	-0.981	0.000	0.000	0.000	0.000
72	L	214	LEU	0	-0.044	-0.010	21.705	0.037	0.037	0.000	0.000	0.000	0.000
73	L	215	ARG	1	0.915	0.933	23.568	0.538	0.538	0.000	0.000	0.000	0.000
74	L	216	ASN	0	-0.029	-0.017	24.989	0.075	0.075	0.000	0.000	0.000	0.000
75	L	217	GLN	0	-0.080	-0.027	24.284	0.041	0.041	0.000	0.000	0.000	0.000
76	L	218	GLU	-1	-0.851	-0.930	27.802	-0.416	-0.416	0.000	0.000	0.000	0.000
77	L	219	GLY	0	0.059	0.028	30.281	0.033	0.033	0.000	0.000	0.000	0.000
78	L	220	GLN	0	-0.066	-0.033	29.745	0.013	0.013	0.000	0.000	0.000	0.000
79	L	221	GLN	0	-0.082	-0.039	31.242	0.019	0.019	0.000	0.000	0.000	0.000
80	L	222	ASN	0	0.038	0.017	30.030	0.026	0.026	0.000	0.000	0.000	0.000
81	L	223	LEU	0	0.021	0.006	24.385	-0.013	-0.013	0.000	0.000	0.000	0.000
82	L	224	MET	0	-0.043	-0.013	27.522	-0.005	-0.005	0.000	0.000	0.000	0.000
83	L	225	GLU	-1	-0.898	-0.948	30.166	-0.281	-0.281	0.000	0.000	0.000	0.000
84	L	226	PHE	0	-0.061	-0.020	21.207	0.010	0.010	0.000	0.000	0.000	0.000
85	L	227	VAL	0	-0.063	-0.030	24.796	-0.003	-0.003	0.000	0.000	0.000	0.000
86	L	228	GLY	0	-0.019	-0.003	26.534	0.018	0.018	0.000	0.000	0.000	0.000
87	L	229	GLY	0	0.040	0.019	29.651	0.014	0.014	0.000	0.000	0.000	0.000
88	L	230	GLU	-1	-0.918	-0.971	30.779	-0.150	-0.150	0.000	0.000	0.000	0.000
89	L	231	PRO	0	0.039	0.025	29.099	0.020	0.020	0.000	0.000	0.000	0.000
90	L	232	SER	0	-0.003	-0.004	31.164	0.007	0.007	0.000	0.000	0.000	0.000
91	L	233	LYS	1	0.940	0.968	33.588	0.063	0.063	0.000	0.000	0.000	0.000
92	L	234	LYS	1	0.850	0.927	29.209	0.130	0.130	0.000	0.000	0.000	0.000
93	L	235	ARG	1	0.900	0.938	33.620	0.030	0.030	0.000	0.000	0.000	0.000
94	L	236	LYS	1	0.892	0.956	34.565	-0.059	-0.059	0.000	0.000	0.000	0.000
95	L	237	ARG	1	0.897	0.957	29.005	-0.054	-0.054	0.000	0.000	0.000	0.000
96	L	238	ARG	1	0.935	0.972	35.858	-0.009	-0.009	0.000	0.000	0.000	0.000
97	L	239	THR	0	0.029	0.003	38.695	0.003	0.003	0.000	0.000	0.000	0.000
98	L	240	SER	0	0.060	0.037	40.945	0.003	0.003	0.000	0.000	0.000	0.000
99	L	241	PHE	0	0.015	0.022	41.408	-0.006	-0.006	0.000	0.000	0.000	0.000
100	L	242	THR	0	0.011	-0.002	44.889	-0.004	-0.004	0.000	0.000	0.000	0.000
101	L	243	PRO	0	0.074	0.030	46.737	0.003	0.003	0.000	0.000	0.000	0.000
102	L	244	GLN	0	0.053	0.005	45.454	0.003	0.003	0.000	0.000	0.000	0.000
103	L	245	ALA	0	-0.032	0.005	42.366	-0.001	-0.001	0.000	0.000	0.000	0.000
104	L	246	ILE	0	0.001	-0.010	42.880	0.003	0.003	0.000	0.000	0.000	0.000
105	L	247	GLU	-1	-0.861	-0.893	45.192	0.003	0.003	0.000	0.000	0.000	0.000
106	L	248	ALA	0	0.043	0.018	40.934	0.000	0.000	0.000	0.000	0.000	0.000
107	L	249	LEU	0	-0.014	-0.010	38.605	0.002	0.002	0.000	0.000	0.000	0.000
108	L	250	ASN	0	-0.035	-0.012	41.532	0.009	0.009	0.000	0.000	0.000	0.000
109	L	251	ALA	0	0.053	0.044	42.595	0.002	0.002	0.000	0.000	0.000	0.000
110	L	252	TYR	0	-0.028	-0.057	35.779	-0.001	-0.001	0.000	0.000	0.000	0.000
111	L	253	PHE	0	0.002	-0.008	39.659	0.003	0.003	0.000	0.000	0.000	0.000
112	L	254	GLU	-1	-0.862	-0.940	41.257	0.019	0.019	0.000	0.000	0.000	0.000
113	L	255	LYS	1	0.768	0.871	38.988	-0.012	-0.012	0.000	0.000	0.000	0.000
114	L	256	ASN	0	-0.044	-0.021	33.548	0.006	0.006	0.000	0.000	0.000	0.000
115	L	257	PRO	0	0.026	0.009	38.041	0.006	0.006	0.000	0.000	0.000	0.000
116	L	258	LEU	0	-0.055	-0.027	36.171	0.006	0.006	0.000	0.000	0.000	0.000
117	L	259	PRO	0	-0.002	0.024	33.520	0.006	0.006	0.000	0.000	0.000	0.000
118	L	260	THR	0	0.006	-0.037	28.430	0.026	0.026	0.000	0.000	0.000	0.000
119	L	261	GLY	0	-0.016	-0.020	28.088	-0.009	-0.009	0.000	0.000	0.000	0.000
120	L	262	GLN	0	0.006	0.007	23.621	-0.025	-0.025	0.000	0.000	0.000	0.000
121	L	263	GLU	-1	-0.697	-0.830	26.847	0.084	0.084	0.000	0.000	0.000	0.000
122	L	264	ILE	0	0.021	0.016	30.115	-0.011	-0.011	0.000	0.000	0.000	0.000
123	L	265	THR	0	-0.126	-0.065	25.613	0.000	0.000	0.000	0.000	0.000	0.000
124	L	266	GLU	-1	-0.797	-0.895	26.332	-0.005	-0.005	0.000	0.000	0.000	0.000
125	L	267	MET	0	0.032	0.028	29.577	-0.011	-0.011	0.000	0.000	0.000	0.000
126	L	268	ALA	0	0.007	0.000	32.223	-0.007	-0.007	0.000	0.000	0.000	0.000
127	L	269	LYS	1	0.798	0.895	25.393	0.042	0.042	0.000	0.000	0.000	0.000
128	L	270	GLU	-1	-0.844	-0.888	31.497	-0.023	-0.023	0.000	0.000	0.000	0.000
129	L	271	LEU	0	0.032	0.029	33.649	-0.003	-0.003	0.000	0.000	0.000	0.000
130	L	272	ASN	0	-0.051	-0.020	34.850	-0.007	-0.007	0.000	0.000	0.000	0.000
131	L	273	TYR	0	0.000	-0.024	35.463	0.001	0.001	0.000	0.000	0.000	0.000
132	L	274	ASP	-1	-0.887	-0.960	34.437	0.096	0.096	0.000	0.000	0.000	0.000
133	L	275	ARG	1	0.899	0.941	28.446	-0.170	-0.170	0.000	0.000	0.000	0.000
134	L	276	GLU	-1	-0.810	-0.897	33.278	0.169	0.169	0.000	0.000	0.000	0.000
135	L	277	VAL	0	-0.020	-0.003	35.446	-0.002	-0.002	0.000	0.000	0.000	0.000
136	L	278	VAL	0	0.042	0.019	35.476	-0.003	-0.003	0.000	0.000	0.000	0.000
137	L	279	ARG	1	0.882	0.930	33.730	-0.160	-0.160	0.000	0.000	0.000	0.000
138	L	280	VAL	0	-0.017	-0.005	36.162	0.005	0.005	0.000	0.000	0.000	0.000
139	L	281	TRP	0	-0.003	0.007	39.380	-0.001	-0.001	0.000	0.000	0.000	0.000
140	L	282	PHE	0	0.032	-0.002	37.644	-0.001	-0.001	0.000	0.000	0.000	0.000
141	L	283	SER	0	-0.032	-0.008	38.388	0.004	0.004	0.000	0.000	0.000	0.000
142	L	284	ASN	0	0.005	-0.003	40.030	0.005	0.005	0.000	0.000	0.000	0.000
143	L	285	ARG	1	0.843	0.936	42.963	-0.055	-0.055	0.000	0.000	0.000	0.000
144	L	286	ARG	1	0.905	0.957	40.639	-0.092	-0.092	0.000	0.000	0.000	0.000
145	L	287	GLN	0	-0.061	-0.026	43.375	0.000	0.000	0.000	0.000	0.000	0.000

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