FMO DATABASE

FMODB ID: 52K5Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1285952.13401
FMO2-HF: Nuclear repulsion	1227168.747626
FMO2-HF: Total energy	-58783.386384
FMO2-MP2: Total energy	-58955.742835

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.
-35.929	-34.715	11.797	-6.568	-6.445	-0.061

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 : -0.039 / q_NPA : -0.037

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	-0.816	-0.910	3.841	-3.627	-1.504	-0.034	-0.976	-1.114	-0.001
4	L	146	GLU	-1	-0.856	-0.915	1.756	-35.307	-37.781	11.792	-5.109	-4.209	-0.063
5	L	147	ILE	0	0.033	-0.003	3.687	1.380	2.036	0.013	-0.191	-0.478	0.001
6	L	148	ARG	1	0.771	0.865	6.042	2.120	2.120	0.000	0.000	0.000	0.000
7	L	149	GLU	-1	-0.740	-0.842	8.857	-1.141	-1.141	0.000	0.000	0.000	0.000
8	L	150	PHE	0	-0.006	0.010	8.039	0.323	0.323	0.000	0.000	0.000	0.000
9	L	151	ALA	0	0.000	-0.002	9.804	0.432	0.432	0.000	0.000	0.000	0.000
10	L	152	LYS	1	0.863	0.919	12.001	1.556	1.556	0.000	0.000	0.000	0.000
11	L	153	ASN	0	0.011	-0.013	11.884	0.390	0.390	0.000	0.000	0.000	0.000
12	L	154	PHE	0	-0.009	0.006	13.323	0.193	0.193	0.000	0.000	0.000	0.000
13	L	155	LYS	1	0.982	0.997	15.171	0.646	0.646	0.000	0.000	0.000	0.000
14	L	156	ILE	0	-0.006	-0.005	17.503	0.097	0.097	0.000	0.000	0.000	0.000
15	L	157	ARG	1	0.856	0.878	14.259	1.384	1.384	0.000	0.000	0.000	0.000
16	L	158	ARG	1	0.773	0.850	19.066	0.622	0.622	0.000	0.000	0.000	0.000
17	L	159	LEU	0	-0.050	-0.040	20.781	0.072	0.072	0.000	0.000	0.000	0.000
18	L	160	SER	0	-0.037	-0.012	22.275	0.043	0.043	0.000	0.000	0.000	0.000
19	L	161	LEU	0	-0.068	-0.011	21.638	0.035	0.035	0.000	0.000	0.000	0.000
20	L	162	GLY	0	0.039	0.026	25.035	0.036	0.036	0.000	0.000	0.000	0.000
21	L	163	LEU	0	-0.031	-0.001	22.826	0.033	0.033	0.000	0.000	0.000	0.000
22	L	164	THR	0	-0.004	-0.020	24.578	-0.008	-0.008	0.000	0.000	0.000	0.000
23	L	165	GLN	0	-0.011	-0.031	20.717	0.042	0.042	0.000	0.000	0.000	0.000
24	L	166	THR	0	-0.005	-0.012	23.050	-0.002	-0.002	0.000	0.000	0.000	0.000
25	L	167	GLN	0	0.097	0.079	25.747	0.002	0.002	0.000	0.000	0.000	0.000
26	L	168	VAL	0	0.069	0.041	19.211	0.006	0.006	0.000	0.000	0.000	0.000
27	L	169	GLY	0	0.000	0.002	21.757	0.006	0.006	0.000	0.000	0.000	0.000
28	L	170	GLN	0	-0.063	-0.012	22.713	0.043	0.043	0.000	0.000	0.000	0.000
29	L	171	ALA	0	0.093	0.058	23.086	0.016	0.016	0.000	0.000	0.000	0.000
30	L	172	MET	0	-0.016	-0.002	16.300	-0.012	-0.012	0.000	0.000	0.000	0.000
31	L	173	THR	0	-0.151	-0.100	20.866	0.039	0.039	0.000	0.000	0.000	0.000
32	L	174	ALA	0	-0.055	-0.010	22.567	0.033	0.033	0.000	0.000	0.000	0.000
33	L	175	THR	0	0.016	-0.009	20.734	0.026	0.026	0.000	0.000	0.000	0.000
34	L	176	GLU	-1	-0.830	-0.875	16.740	-0.528	-0.528	0.000	0.000	0.000	0.000
35	L	177	GLY	0	0.056	0.027	19.827	0.060	0.060	0.000	0.000	0.000	0.000
36	L	178	PRO	0	-0.014	-0.030	20.358	-0.035	-0.035	0.000	0.000	0.000	0.000
37	L	179	ALA	0	-0.098	-0.040	16.189	0.014	0.014	0.000	0.000	0.000	0.000
38	L	180	TYR	0	0.040	0.010	12.883	0.037	0.037	0.000	0.000	0.000	0.000
39	L	181	SER	0	0.061	0.038	18.706	-0.028	-0.028	0.000	0.000	0.000	0.000
40	L	182	GLN	0	0.061	0.012	20.382	-0.007	-0.007	0.000	0.000	0.000	0.000
41	L	183	SER	0	0.000	0.004	21.521	-0.022	-0.022	0.000	0.000	0.000	0.000
42	L	184	ALA	0	-0.016	0.001	17.206	0.013	0.013	0.000	0.000	0.000	0.000
43	L	185	ILE	0	0.059	0.033	16.952	-0.037	-0.037	0.000	0.000	0.000	0.000
44	L	186	SER	0	-0.020	-0.005	17.528	-0.052	-0.052	0.000	0.000	0.000	0.000
45	L	187	ARG	1	0.852	0.920	16.891	-0.138	-0.138	0.000	0.000	0.000	0.000
46	L	188	PHE	0	0.029	0.019	9.282	0.059	0.059	0.000	0.000	0.000	0.000
47	L	189	GLU	-1	-0.739	-0.833	13.793	-0.677	-0.677	0.000	0.000	0.000	0.000
48	L	190	LYS	1	0.765	0.870	15.674	0.042	0.042	0.000	0.000	0.000	0.000
49	L	191	LEU	0	0.017	0.001	9.611	0.036	0.036	0.000	0.000	0.000	0.000
50	L	192	ASP	-1	-0.879	-0.911	13.314	0.334	0.334	0.000	0.000	0.000	0.000
51	L	193	ILE	0	-0.036	-0.014	11.033	0.013	0.013	0.000	0.000	0.000	0.000
52	L	194	THR	0	0.049	0.035	10.830	0.123	0.123	0.000	0.000	0.000	0.000
53	L	195	PRO	0	0.096	0.021	5.419	-0.364	-0.364	0.000	0.000	0.000	0.000
54	L	196	LYS	1	0.893	0.937	5.969	-5.612	-5.612	0.000	0.000	0.000	0.000
55	L	197	SER	0	0.007	-0.005	8.239	-0.317	-0.317	0.000	0.000	0.000	0.000
56	L	198	ALA	0	0.031	0.011	7.467	-0.324	-0.324	0.000	0.000	0.000	0.000
57	L	199	GLN	0	0.044	0.030	3.070	0.154	0.998	0.027	-0.291	-0.580	0.002
58	L	200	LYS	1	0.951	0.980	5.397	-1.163	-1.098	-0.001	-0.001	-0.064	0.000
59	L	201	LEU	0	0.002	0.000	8.478	-0.252	-0.252	0.000	0.000	0.000	0.000
60	L	202	LYS	1	0.904	0.958	4.940	6.673	6.673	0.000	0.000	0.000	0.000
61	L	203	PRO	0	0.028	0.019	6.488	0.054	0.054	0.000	0.000	0.000	0.000
62	L	204	VAL	0	-0.005	-0.002	8.993	0.176	0.176	0.000	0.000	0.000	0.000
63	L	205	LEU	0	-0.034	-0.015	11.468	0.139	0.139	0.000	0.000	0.000	0.000
64	L	206	GLU	-1	-0.902	-0.948	8.753	-3.402	-3.402	0.000	0.000	0.000	0.000
65	L	207	LYS	1	0.883	0.934	12.506	0.826	0.826	0.000	0.000	0.000	0.000
66	L	208	TRP	0	0.044	0.012	14.645	0.056	0.056	0.000	0.000	0.000	0.000
67	L	209	LEU	0	-0.035	-0.024	15.140	0.059	0.059	0.000	0.000	0.000	0.000
68	L	210	ASN	0	0.016	0.018	14.208	0.039	0.039	0.000	0.000	0.000	0.000
69	L	211	GLU	-1	-0.861	-0.907	18.123	-0.463	-0.463	0.000	0.000	0.000	0.000
70	L	212	ALA	0	0.004	-0.002	20.492	0.065	0.065	0.000	0.000	0.000	0.000
71	L	213	GLU	-1	-0.778	-0.873	19.208	-0.947	-0.947	0.000	0.000	0.000	0.000
72	L	214	LEU	0	-0.069	-0.023	22.377	0.031	0.031	0.000	0.000	0.000	0.000
73	L	215	ARG	1	0.896	0.923	24.222	0.472	0.472	0.000	0.000	0.000	0.000
74	L	216	ASN	0	-0.025	-0.010	25.556	0.062	0.062	0.000	0.000	0.000	0.000
75	L	217	GLN	0	-0.055	-0.011	24.850	0.042	0.042	0.000	0.000	0.000	0.000
76	L	218	GLU	-1	-0.863	-0.936	28.182	-0.378	-0.378	0.000	0.000	0.000	0.000
77	L	219	GLY	0	0.101	0.069	31.300	0.010	0.010	0.000	0.000	0.000	0.000
78	L	220	GLN	0	0.023	0.009	30.227	0.012	0.012	0.000	0.000	0.000	0.000
79	L	221	GLN	0	-0.131	-0.080	31.844	0.022	0.022	0.000	0.000	0.000	0.000
80	L	222	ASN	0	0.007	-0.008	30.511	0.029	0.029	0.000	0.000	0.000	0.000
81	L	223	LEU	0	0.008	0.003	24.875	-0.015	-0.015	0.000	0.000	0.000	0.000
82	L	224	MET	0	-0.071	-0.030	28.148	-0.007	-0.007	0.000	0.000	0.000	0.000
83	L	225	GLU	-1	-0.933	-0.957	30.784	-0.271	-0.271	0.000	0.000	0.000	0.000
84	L	226	PHE	0	-0.051	-0.015	21.747	0.008	0.008	0.000	0.000	0.000	0.000
85	L	227	VAL	0	-0.066	-0.034	25.122	-0.001	-0.001	0.000	0.000	0.000	0.000
86	L	228	GLY	0	-0.018	0.001	27.030	0.014	0.014	0.000	0.000	0.000	0.000
87	L	229	GLY	0	0.046	0.012	29.992	0.012	0.012	0.000	0.000	0.000	0.000
88	L	230	GLU	-1	-0.955	-1.010	31.522	-0.170	-0.170	0.000	0.000	0.000	0.000
89	L	231	PRO	0	0.026	0.041	30.102	0.019	0.019	0.000	0.000	0.000	0.000
90	L	232	SER	0	0.038	0.007	32.100	-0.002	-0.002	0.000	0.000	0.000	0.000
91	L	233	LYS	1	0.942	0.973	34.487	0.072	0.072	0.000	0.000	0.000	0.000
92	L	234	LYS	1	0.864	0.929	29.909	0.159	0.159	0.000	0.000	0.000	0.000
93	L	235	ARG	1	0.949	0.983	34.092	0.044	0.044	0.000	0.000	0.000	0.000
94	L	236	LYS	1	0.937	0.962	35.423	-0.028	-0.028	0.000	0.000	0.000	0.000
95	L	237	ARG	1	0.895	0.957	29.891	-0.025	-0.025	0.000	0.000	0.000	0.000
96	L	238	ARG	1	0.972	1.004	36.681	0.003	0.003	0.000	0.000	0.000	0.000
97	L	239	THR	0	0.031	0.016	38.998	0.003	0.003	0.000	0.000	0.000	0.000
98	L	240	SER	0	0.074	0.038	41.262	0.004	0.004	0.000	0.000	0.000	0.000
99	L	241	PHE	0	0.005	0.010	41.538	-0.006	-0.006	0.000	0.000	0.000	0.000
100	L	242	THR	0	-0.005	0.002	45.405	-0.003	-0.003	0.000	0.000	0.000	0.000
101	L	243	PRO	0	0.084	0.022	46.976	0.003	0.003	0.000	0.000	0.000	0.000
102	L	244	GLN	0	0.051	0.015	46.069	0.001	0.001	0.000	0.000	0.000	0.000
103	L	245	ALA	0	-0.020	0.005	42.800	0.000	0.000	0.000	0.000	0.000	0.000
104	L	246	ILE	0	-0.011	-0.012	43.545	0.003	0.003	0.000	0.000	0.000	0.000
105	L	247	GLU	-1	-0.874	-0.908	45.724	0.007	0.007	0.000	0.000	0.000	0.000
106	L	248	ALA	0	0.033	0.014	41.381	0.001	0.001	0.000	0.000	0.000	0.000
107	L	249	LEU	0	-0.029	-0.021	39.296	0.003	0.003	0.000	0.000	0.000	0.000
108	L	250	ASN	0	0.000	-0.008	41.794	0.010	0.010	0.000	0.000	0.000	0.000
109	L	251	ALA	0	0.062	0.053	42.778	0.003	0.003	0.000	0.000	0.000	0.000
110	L	252	TYR	0	-0.042	-0.076	36.063	0.003	0.003	0.000	0.000	0.000	0.000
111	L	253	PHE	0	-0.020	-0.006	39.605	0.007	0.007	0.000	0.000	0.000	0.000
112	L	254	GLU	-1	-0.891	-0.937	41.657	0.030	0.030	0.000	0.000	0.000	0.000
113	L	255	LYS	1	0.789	0.885	39.114	-0.021	-0.021	0.000	0.000	0.000	0.000
114	L	256	ASN	0	-0.044	-0.027	34.007	0.008	0.008	0.000	0.000	0.000	0.000
115	L	257	PRO	0	0.021	0.011	38.499	0.004	0.004	0.000	0.000	0.000	0.000
116	L	258	LEU	0	-0.056	-0.035	36.454	0.004	0.004	0.000	0.000	0.000	0.000
117	L	259	PRO	0	0.005	0.025	33.743	0.009	0.009	0.000	0.000	0.000	0.000
118	L	260	THR	0	0.019	-0.018	28.879	0.021	0.021	0.000	0.000	0.000	0.000
119	L	261	GLY	0	0.017	-0.010	28.897	-0.013	-0.013	0.000	0.000	0.000	0.000
120	L	262	GLN	0	0.013	0.000	23.937	-0.033	-0.033	0.000	0.000	0.000	0.000
121	L	263	GLU	-1	-0.707	-0.828	27.134	0.095	0.095	0.000	0.000	0.000	0.000
122	L	264	ILE	0	0.009	0.012	30.275	-0.014	-0.014	0.000	0.000	0.000	0.000
123	L	265	THR	0	-0.145	-0.060	26.182	-0.008	-0.008	0.000	0.000	0.000	0.000
124	L	266	GLU	-1	-0.812	-0.895	26.741	-0.003	-0.003	0.000	0.000	0.000	0.000
125	L	267	MET	0	0.037	0.026	29.837	-0.012	-0.012	0.000	0.000	0.000	0.000
126	L	268	ALA	0	0.002	-0.005	32.397	-0.009	-0.009	0.000	0.000	0.000	0.000
127	L	269	LYS	1	0.805	0.876	25.737	0.031	0.031	0.000	0.000	0.000	0.000
128	L	270	GLU	-1	-0.858	-0.898	31.939	-0.021	-0.021	0.000	0.000	0.000	0.000
129	L	271	LEU	0	0.038	0.045	34.117	-0.004	-0.004	0.000	0.000	0.000	0.000
130	L	272	ASN	0	-0.102	-0.056	35.194	-0.004	-0.004	0.000	0.000	0.000	0.000
131	L	273	TYR	0	-0.024	-0.040	36.120	-0.001	-0.001	0.000	0.000	0.000	0.000
132	L	274	ASP	-1	-0.921	-0.979	35.186	0.076	0.076	0.000	0.000	0.000	0.000
133	L	275	ARG	1	0.922	0.940	29.143	-0.150	-0.150	0.000	0.000	0.000	0.000
134	L	276	GLU	-1	-0.823	-0.901	33.751	0.149	0.149	0.000	0.000	0.000	0.000
135	L	277	VAL	0	-0.024	-0.005	35.853	0.000	0.000	0.000	0.000	0.000	0.000
136	L	278	VAL	0	0.027	0.014	35.660	0.000	0.000	0.000	0.000	0.000	0.000
137	L	279	ARG	1	0.885	0.924	33.776	-0.149	-0.149	0.000	0.000	0.000	0.000
138	L	280	VAL	0	-0.017	-0.001	36.310	0.005	0.005	0.000	0.000	0.000	0.000
139	L	281	TRP	0	-0.008	0.008	39.537	0.000	0.000	0.000	0.000	0.000	0.000
140	L	282	PHE	0	0.029	-0.004	37.946	-0.001	-0.001	0.000	0.000	0.000	0.000
141	L	283	SER	0	-0.047	-0.024	38.764	0.005	0.005	0.000	0.000	0.000	0.000
142	L	284	ASN	0	-0.002	-0.006	40.320	0.007	0.007	0.000	0.000	0.000	0.000
143	L	285	ARG	1	0.848	0.956	43.139	-0.059	-0.059	0.000	0.000	0.000	0.000
144	L	286	ARG	1	0.915	0.967	41.082	-0.103	-0.103	0.000	0.000	0.000	0.000
145	L	287	GLN	0	-0.023	-0.017	43.871	-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)