FMO DATABASE

FMODB ID: VRMN1

Calculation Name: 5C3L-A-Xray372

Preferred Name:
Warning: Undefined array key "pref_name" in /home/FMODBwui_src/fmodbwui/detail.php on line 446

Target Type:
Warning: Undefined array key "target_type" in /home/FMODBwui_src/fmodbwui/detail.php on line 447

Ligand Name:
Warning: Undefined variable $Ligand in /home/FMODBwui_src/fmodbwui/detail.php on line 448

Warning: Trying to access array offset on value of type null in /home/FMODBwui_src/fmodbwui/detail.php on line 448

Warning: Trying to access array offset on value of type null in /home/FMODBwui_src/fmodbwui/detail.php on line 448

ligand 3-letter code:
Warning: Undefined variable $Ligand in /home/FMODBwui_src/fmodbwui/detail.php on line 449

Warning: Trying to access array offset on value of type null in /home/FMODBwui_src/fmodbwui/detail.php on line 449

Warning: Trying to access array offset on value of type null in /home/FMODBwui_src/fmodbwui/detail.php on line 449

PDB ID: 5C3L

Chain ID: A

ChEMBL ID:
Warning: Undefined array key "chembl_id" in /home/FMODBwui_src/fmodbwui/detail.php on line 452

Warning: Undefined array key "chembl_id" in /home/FMODBwui_src/fmodbwui/detail.php on line 452

UniProt ID: Q91349

Base Structure: X-ray

Registration Date: 2023-06-20

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	134
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-823933.032457
FMO2-HF: Nuclear repulsion	769588.04334
FMO2-HF: Total energy	-54344.989116
FMO2-MP2: Total energy	-54503.542347

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:317:SER)

Summations of interaction energy for fragment #1(A:317: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.
-3.2	-1.169	2.898	-1.663	-3.265	-0.005

Interaction energy analysis for fragmet #1(A:317:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.011 / q_NPA : -0.007

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	319	VAL	0	-0.009	-0.019	3.902	-1.811	-0.782	-0.006	-0.467	-0.556	0.002
4	A	320	GLN	0	0.050	0.010	2.681	-0.734	-0.186	0.211	-0.131	-0.628	0.000
5	A	321	ILE	0	0.056	0.042	2.281	0.039	0.329	2.692	-1.036	-1.945	-0.007
6	A	322	LYS	1	0.971	0.966	4.089	1.717	1.814	0.002	-0.029	-0.070	0.000
7	A	323	GLN	0	-0.046	-0.017	6.647	0.106	0.106	0.000	0.000	0.000	0.000
8	A	324	LEU	0	0.004	0.016	4.773	0.188	0.255	-0.001	0.000	-0.066	0.000
9	A	325	ILE	0	-0.031	-0.005	7.397	-0.029	-0.029	0.000	0.000	0.000	0.000
10	A	326	GLN	0	0.044	0.034	9.708	-0.081	-0.081	0.000	0.000	0.000	0.000
11	A	327	ASN	0	-0.013	-0.006	12.045	0.025	0.025	0.000	0.000	0.000	0.000
12	A	328	PRO	0	0.039	0.016	14.083	-0.006	-0.006	0.000	0.000	0.000	0.000
13	A	329	LEU	0	0.019	0.016	11.899	0.037	0.037	0.000	0.000	0.000	0.000
14	A	330	SER	0	-0.040	-0.018	16.036	0.020	0.020	0.000	0.000	0.000	0.000
15	A	331	GLY	0	0.002	-0.003	19.185	-0.005	-0.005	0.000	0.000	0.000	0.000
16	A	332	VAL	0	-0.066	-0.025	18.689	-0.006	-0.006	0.000	0.000	0.000	0.000
17	A	333	ASP	-1	-0.819	-0.910	20.722	-0.139	-0.139	0.000	0.000	0.000	0.000
18	A	334	PRO	0	0.027	-0.015	20.027	-0.027	-0.027	0.000	0.000	0.000	0.000
19	A	335	ILE	0	0.025	0.023	20.302	-0.031	-0.031	0.000	0.000	0.000	0.000
20	A	336	ILE	0	-0.005	-0.002	21.231	-0.023	-0.023	0.000	0.000	0.000	0.000
21	A	337	TRP	0	-0.043	-0.038	12.138	-0.018	-0.018	0.000	0.000	0.000	0.000
22	A	338	GLU	-1	-0.819	-0.909	16.745	-0.441	-0.441	0.000	0.000	0.000	0.000
23	A	339	GLN	0	-0.058	-0.037	17.813	-0.028	-0.028	0.000	0.000	0.000	0.000
24	A	340	ALA	0	-0.003	-0.005	16.364	-0.034	-0.034	0.000	0.000	0.000	0.000
25	A	341	LYS	1	0.690	0.830	12.906	0.372	0.372	0.000	0.000	0.000	0.000
26	A	342	VAL	0	-0.050	-0.014	14.155	-0.097	-0.097	0.000	0.000	0.000	0.000
27	A	343	ASP	-1	-0.857	-0.913	16.954	-0.386	-0.386	0.000	0.000	0.000	0.000
28	A	344	ASN	0	-0.060	-0.039	10.289	0.048	0.048	0.000	0.000	0.000	0.000
29	A	345	PRO	0	-0.011	-0.005	14.733	-0.019	-0.019	0.000	0.000	0.000	0.000
30	A	346	ASP	-1	-0.827	-0.935	11.714	-1.204	-1.204	0.000	0.000	0.000	0.000
31	A	347	PRO	0	-0.014	-0.018	10.112	-0.245	-0.245	0.000	0.000	0.000	0.000
32	A	348	GLU	-1	-0.904	-0.918	8.563	-1.369	-1.369	0.000	0.000	0.000	0.000
33	A	349	ARG	1	0.759	0.871	6.954	0.385	0.385	0.000	0.000	0.000	0.000
34	A	350	LEU	0	-0.045	-0.006	8.351	-0.024	-0.024	0.000	0.000	0.000	0.000
35	A	351	ILE	0	0.014	0.014	5.798	-0.106	-0.106	0.000	0.000	0.000	0.000
36	A	352	PRO	0	0.022	0.023	8.954	0.154	0.154	0.000	0.000	0.000	0.000
37	A	353	VAL	0	0.027	0.005	10.209	0.067	0.067	0.000	0.000	0.000	0.000
38	A	354	PRO	0	0.005	0.010	12.847	-0.001	-0.001	0.000	0.000	0.000	0.000
39	A	355	MET	0	-0.029	-0.021	16.448	-0.004	-0.004	0.000	0.000	0.000	0.000
40	A	356	ILE	0	0.024	0.014	19.277	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	357	GLY	0	0.044	0.021	22.550	0.013	0.013	0.000	0.000	0.000	0.000
42	A	358	PHE	0	0.041	0.000	24.651	-0.012	-0.012	0.000	0.000	0.000	0.000
43	A	359	LYS	1	0.915	0.973	21.990	0.072	0.072	0.000	0.000	0.000	0.000
44	A	360	GLU	-1	-0.747	-0.872	18.840	-0.136	-0.136	0.000	0.000	0.000	0.000
45	A	361	LEU	0	-0.005	0.005	21.019	-0.026	-0.026	0.000	0.000	0.000	0.000
46	A	362	LEU	0	0.017	0.014	23.219	-0.016	-0.016	0.000	0.000	0.000	0.000
47	A	363	ARG	1	0.876	0.930	15.413	0.191	0.191	0.000	0.000	0.000	0.000
48	A	364	ARG	1	0.859	0.920	15.360	0.352	0.352	0.000	0.000	0.000	0.000
49	A	365	LEU	0	0.032	0.027	20.326	-0.018	-0.018	0.000	0.000	0.000	0.000
50	A	366	GLU	-1	-0.892	-0.958	23.499	-0.111	-0.111	0.000	0.000	0.000	0.000
51	A	367	VAL	0	-0.022	-0.017	17.337	0.001	0.001	0.000	0.000	0.000	0.000
52	A	368	GLN	0	0.012	0.005	20.352	0.011	0.011	0.000	0.000	0.000	0.000
53	A	369	ASP	-1	-0.791	-0.852	21.903	-0.140	-0.140	0.000	0.000	0.000	0.000
54	A	370	GLN	0	-0.014	-0.006	19.704	0.022	0.022	0.000	0.000	0.000	0.000
55	A	371	MET	0	-0.032	-0.026	17.805	0.009	0.009	0.000	0.000	0.000	0.000
56	A	372	THR	0	-0.010	-0.017	21.774	-0.003	-0.003	0.000	0.000	0.000	0.000
57	A	373	LYS	1	0.817	0.886	24.796	0.139	0.139	0.000	0.000	0.000	0.000
58	A	374	GLN	0	-0.011	-0.005	20.956	-0.002	-0.002	0.000	0.000	0.000	0.000
59	A	375	HIS	0	-0.010	-0.007	19.546	0.022	0.022	0.000	0.000	0.000	0.000
60	A	376	GLN	0	-0.022	-0.021	24.659	-0.002	-0.002	0.000	0.000	0.000	0.000
61	A	377	SER	0	0.001	0.012	27.519	0.009	0.009	0.000	0.000	0.000	0.000
62	A	378	ARG	1	0.907	0.941	20.293	0.234	0.234	0.000	0.000	0.000	0.000
63	A	379	LEU	0	-0.012	-0.004	26.887	0.004	0.004	0.000	0.000	0.000	0.000
64	A	380	ASP	-1	-0.838	-0.907	29.229	-0.103	-0.103	0.000	0.000	0.000	0.000
65	A	381	ILE	0	-0.026	-0.011	29.079	0.007	0.007	0.000	0.000	0.000	0.000
66	A	382	ILE	0	0.010	0.003	26.194	0.004	0.004	0.000	0.000	0.000	0.000
67	A	383	SER	0	-0.006	-0.006	30.853	0.003	0.003	0.000	0.000	0.000	0.000
68	A	384	GLU	-1	-0.937	-0.956	34.151	-0.062	-0.062	0.000	0.000	0.000	0.000
69	A	385	ASP	-1	-0.928	-0.965	31.368	-0.074	-0.074	0.000	0.000	0.000	0.000
70	A	386	ILE	0	-0.047	-0.030	32.216	0.004	0.004	0.000	0.000	0.000	0.000
71	A	387	GLY	0	0.044	0.030	35.429	0.004	0.004	0.000	0.000	0.000	0.000
72	A	388	GLU	-1	-0.794	-0.874	37.386	-0.040	-0.040	0.000	0.000	0.000	0.000
73	A	389	LEU	0	-0.017	0.007	34.032	0.005	0.005	0.000	0.000	0.000	0.000
74	A	390	GLN	0	0.038	0.012	37.903	0.006	0.006	0.000	0.000	0.000	0.000
75	A	391	LYS	1	0.881	0.935	40.631	0.046	0.046	0.000	0.000	0.000	0.000
76	A	392	ASN	0	-0.063	-0.042	40.175	0.007	0.007	0.000	0.000	0.000	0.000
77	A	393	GLN	0	0.003	0.014	40.220	0.002	0.002	0.000	0.000	0.000	0.000
78	A	394	THR	0	0.004	-0.014	42.279	0.003	0.003	0.000	0.000	0.000	0.000
79	A	395	THR	0	-0.052	-0.041	45.357	0.004	0.004	0.000	0.000	0.000	0.000
80	A	396	THR	0	-0.043	-0.034	43.230	0.004	0.004	0.000	0.000	0.000	0.000
81	A	397	MET	0	-0.015	-0.009	45.280	0.001	0.001	0.000	0.000	0.000	0.000
82	A	398	ALA	0	0.014	0.016	47.647	0.002	0.002	0.000	0.000	0.000	0.000
83	A	399	LYS	1	0.955	0.984	46.614	0.030	0.030	0.000	0.000	0.000	0.000
84	A	400	ILE	0	0.005	0.006	45.784	0.002	0.002	0.000	0.000	0.000	0.000
85	A	401	GLY	0	0.025	0.013	50.304	0.001	0.001	0.000	0.000	0.000	0.000
86	A	402	GLN	0	-0.077	-0.040	53.359	0.001	0.001	0.000	0.000	0.000	0.000
87	A	403	TYR	0	0.029	-0.003	49.289	0.001	0.001	0.000	0.000	0.000	0.000
88	A	404	LYS	1	0.970	0.989	50.716	0.033	0.033	0.000	0.000	0.000	0.000
89	A	405	ARG	1	0.986	1.001	55.067	0.028	0.028	0.000	0.000	0.000	0.000
90	A	406	LYS	1	0.846	0.902	57.265	0.017	0.017	0.000	0.000	0.000	0.000
91	A	407	LEU	0	0.030	0.013	54.776	0.001	0.001	0.000	0.000	0.000	0.000
92	A	408	MET	0	0.013	0.010	58.216	0.001	0.001	0.000	0.000	0.000	0.000
93	A	409	GLU	-1	-0.795	-0.865	60.768	-0.015	-0.015	0.000	0.000	0.000	0.000
94	A	410	LEU	0	-0.016	-0.025	59.241	0.001	0.001	0.000	0.000	0.000	0.000
95	A	411	SER	0	0.010	0.017	60.823	0.001	0.001	0.000	0.000	0.000	0.000
96	A	412	HIS	0	0.062	0.031	62.767	0.001	0.001	0.000	0.000	0.000	0.000
97	A	413	ARG	1	0.862	0.914	65.333	0.013	0.013	0.000	0.000	0.000	0.000
98	A	414	VAL	0	0.025	0.012	63.336	0.001	0.001	0.000	0.000	0.000	0.000
99	A	415	LEU	0	0.045	0.028	66.494	0.001	0.001	0.000	0.000	0.000	0.000
100	A	416	GLN	0	0.016	-0.007	68.237	0.001	0.001	0.000	0.000	0.000	0.000
101	A	417	VAL	0	-0.063	-0.016	69.449	0.001	0.001	0.000	0.000	0.000	0.000
102	A	418	LEU	0	0.036	0.016	66.660	0.001	0.001	0.000	0.000	0.000	0.000
103	A	419	ILE	0	0.033	0.019	71.212	0.000	0.000	0.000	0.000	0.000	0.000
104	A	420	LYS	1	0.852	0.939	73.838	0.011	0.011	0.000	0.000	0.000	0.000
105	A	421	GLN	0	0.022	-0.004	71.364	0.000	0.000	0.000	0.000	0.000	0.000
106	A	422	GLU	-1	-0.807	-0.888	74.474	-0.007	-0.007	0.000	0.000	0.000	0.000
107	A	423	ILE	0	0.011	-0.001	76.346	0.000	0.000	0.000	0.000	0.000	0.000
108	A	424	GLN	0	-0.043	-0.023	78.270	0.000	0.000	0.000	0.000	0.000	0.000
109	A	425	ARG	1	0.839	0.913	75.320	0.006	0.006	0.000	0.000	0.000	0.000
110	A	426	LYS	1	0.792	0.888	77.640	0.008	0.008	0.000	0.000	0.000	0.000
111	A	427	SER	0	-0.050	-0.042	81.821	0.000	0.000	0.000	0.000	0.000	0.000
112	A	428	GLY	0	-0.031	-0.009	84.801	0.000	0.000	0.000	0.000	0.000	0.000
113	A	429	PHE	0	-0.040	-0.003	82.027	0.000	0.000	0.000	0.000	0.000	0.000
114	A	430	ALA	0	0.008	-0.001	86.593	0.000	0.000	0.000	0.000	0.000	0.000
115	A	431	ILE	0	0.014	-0.002	83.879	0.000	0.000	0.000	0.000	0.000	0.000
116	A	432	GLN	0	0.001	0.000	81.399	0.000	0.000	0.000	0.000	0.000	0.000
117	A	433	ALA	0	0.023	0.006	81.130	0.000	0.000	0.000	0.000	0.000	0.000
118	A	434	GLU	-1	-0.882	-0.935	76.041	-0.009	-0.009	0.000	0.000	0.000	0.000
119	A	435	GLU	-1	-0.789	-0.887	76.931	-0.009	-0.009	0.000	0.000	0.000	0.000
120	A	436	GLU	-1	-0.894	-0.949	78.549	-0.012	-0.012	0.000	0.000	0.000	0.000
121	A	437	GLN	0	-0.052	-0.027	76.082	-0.001	-0.001	0.000	0.000	0.000	0.000
122	A	438	LEU	0	0.001	0.005	72.141	-0.001	-0.001	0.000	0.000	0.000	0.000
123	A	439	ARG	1	0.795	0.874	75.513	0.012	0.012	0.000	0.000	0.000	0.000
124	A	440	VAL	0	0.049	0.021	77.309	-0.001	-0.001	0.000	0.000	0.000	0.000
125	A	441	GLN	0	-0.010	0.007	71.894	-0.001	-0.001	0.000	0.000	0.000	0.000
126	A	442	LEU	0	-0.021	-0.008	72.136	-0.001	-0.001	0.000	0.000	0.000	0.000
127	A	443	ASP	-1	-0.798	-0.864	74.421	-0.015	-0.015	0.000	0.000	0.000	0.000
128	A	444	THR	0	-0.039	-0.031	74.682	-0.001	-0.001	0.000	0.000	0.000	0.000
129	A	445	ILE	0	0.009	0.016	69.133	-0.001	-0.001	0.000	0.000	0.000	0.000
130	A	446	GLN	0	-0.022	-0.013	72.095	-0.001	-0.001	0.000	0.000	0.000	0.000
131	A	447	SER	0	-0.067	-0.047	74.377	0.000	0.000	0.000	0.000	0.000	0.000
132	A	448	GLU	-1	-0.928	-0.960	69.980	-0.022	-0.022	0.000	0.000	0.000	0.000
133	A	449	LEU	0	-0.098	-0.039	69.702	-0.001	-0.001	0.000	0.000	0.000	0.000
134	A	450	ASN	0	-0.105	-0.047	71.567	0.000	0.000	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:317:SER)