FMO DATABASE

FMODB ID: 6YV1Z

Calculation Name: 2VWR-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2VWR

Chain ID: A

ChEMBL ID:

UniProt ID: Q8N448

Base Structure: X-ray

Registration Date: 2023-09-23

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	95
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-631567.430485
FMO2-HF: Nuclear repulsion	595949.168646
FMO2-HF: Total energy	-35618.261839
FMO2-MP2: Total energy	-35723.806849

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:-1:SER)

Summations of interaction energy for fragment #1(A:-1: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.
-6.323	-1.458	-0.032	-2.439	-2.395	0.003

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.036 / q_NPA : 0.017

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	336	GLU	-1	-0.844	-0.893	3.757	-4.023	-0.299	-0.037	-2.042	-1.646	0.004
4	A	337	ILE	0	-0.034	-0.019	6.272	0.294	0.294	0.000	0.000	0.000	0.000
5	A	338	LEU	0	0.000	0.011	9.417	0.240	0.240	0.000	0.000	0.000	0.000
6	A	339	GLN	0	-0.003	-0.001	12.554	0.075	0.075	0.000	0.000	0.000	0.000
7	A	340	VAL	0	0.002	0.006	15.886	0.028	0.028	0.000	0.000	0.000	0.000
8	A	341	ALA	0	-0.058	-0.022	18.526	0.023	0.023	0.000	0.000	0.000	0.000
9	A	342	LEU	0	0.018	0.013	21.727	0.009	0.009	0.000	0.000	0.000	0.000
10	A	343	HIS	0	-0.041	-0.058	24.595	-0.007	-0.007	0.000	0.000	0.000	0.000
11	A	344	LYS	1	0.801	0.927	28.367	0.264	0.264	0.000	0.000	0.000	0.000
12	A	345	ARG	1	0.947	0.959	30.860	0.238	0.238	0.000	0.000	0.000	0.000
13	A	346	ASP	-1	-0.860	-0.922	33.998	-0.182	-0.182	0.000	0.000	0.000	0.000
14	A	347	SER	0	-0.006	-0.017	34.144	-0.011	-0.011	0.000	0.000	0.000	0.000
15	A	348	GLY	0	-0.037	-0.022	34.405	-0.008	-0.008	0.000	0.000	0.000	0.000
16	A	349	GLU	-1	-0.845	-0.905	31.203	-0.257	-0.257	0.000	0.000	0.000	0.000
17	A	350	GLN	0	-0.031	-0.021	29.129	-0.018	-0.018	0.000	0.000	0.000	0.000
18	A	351	LEU	0	0.056	0.012	23.755	-0.003	-0.003	0.000	0.000	0.000	0.000
19	A	352	GLY	0	0.002	0.005	25.161	-0.014	-0.014	0.000	0.000	0.000	0.000
20	A	353	ILE	0	0.012	-0.001	20.317	-0.026	-0.026	0.000	0.000	0.000	0.000
21	A	354	LYS	1	0.811	0.904	22.339	0.391	0.391	0.000	0.000	0.000	0.000
22	A	355	LEU	0	-0.004	0.000	19.610	-0.053	-0.053	0.000	0.000	0.000	0.000
23	A	356	VAL	0	-0.019	-0.011	18.287	0.060	0.060	0.000	0.000	0.000	0.000
24	A	357	ARG	1	0.902	0.931	18.785	0.232	0.232	0.000	0.000	0.000	0.000
25	A	358	ARG	1	0.863	0.918	11.318	0.965	0.965	0.000	0.000	0.000	0.000
26	A	359	THR	0	-0.010	-0.016	17.912	0.015	0.015	0.000	0.000	0.000	0.000
27	A	360	ASP	-1	-0.925	-0.956	14.959	-0.371	-0.371	0.000	0.000	0.000	0.000
28	A	361	GLU	-1	-0.866	-0.920	10.769	-1.077	-1.077	0.000	0.000	0.000	0.000
29	A	362	PRO	0	-0.034	-0.011	13.296	-0.004	-0.004	0.000	0.000	0.000	0.000
30	A	363	GLY	0	0.018	-0.005	13.910	-0.112	-0.112	0.000	0.000	0.000	0.000
31	A	364	VAL	0	-0.028	0.001	15.775	0.064	0.064	0.000	0.000	0.000	0.000
32	A	365	PHE	0	-0.007	-0.009	11.118	-0.109	-0.109	0.000	0.000	0.000	0.000
33	A	366	ILE	0	0.017	0.014	15.745	0.138	0.138	0.000	0.000	0.000	0.000
34	A	367	LEU	0	-0.016	0.006	16.595	-0.064	-0.064	0.000	0.000	0.000	0.000
35	A	368	ASP	-1	-0.797	-0.881	18.627	-0.422	-0.422	0.000	0.000	0.000	0.000
36	A	369	LEU	0	0.023	0.011	18.962	0.000	0.000	0.000	0.000	0.000	0.000
37	A	370	LEU	0	-0.048	-0.028	22.066	0.029	0.029	0.000	0.000	0.000	0.000
38	A	371	GLU	-1	-0.894	-0.957	25.825	-0.246	-0.246	0.000	0.000	0.000	0.000
39	A	372	GLY	0	0.012	0.007	27.273	0.012	0.012	0.000	0.000	0.000	0.000
40	A	373	GLY	0	0.015	0.023	27.049	0.012	0.012	0.000	0.000	0.000	0.000
41	A	374	LEU	0	-0.002	-0.002	26.117	-0.017	-0.017	0.000	0.000	0.000	0.000
42	A	375	ALA	0	-0.003	-0.007	21.071	-0.014	-0.014	0.000	0.000	0.000	0.000
43	A	376	ALA	0	-0.002	0.001	21.526	-0.032	-0.032	0.000	0.000	0.000	0.000
44	A	377	GLN	0	-0.102	-0.058	22.996	0.006	0.006	0.000	0.000	0.000	0.000
45	A	378	ASP	-1	-0.833	-0.881	19.934	-0.542	-0.542	0.000	0.000	0.000	0.000
46	A	379	GLY	0	0.008	0.009	19.964	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	380	ARG	1	0.787	0.869	15.822	0.521	0.521	0.000	0.000	0.000	0.000
48	A	381	LEU	0	-0.017	-0.004	14.888	-0.122	-0.122	0.000	0.000	0.000	0.000
49	A	382	SER	0	0.030	0.008	12.904	0.130	0.130	0.000	0.000	0.000	0.000
50	A	383	SER	0	-0.047	-0.033	14.574	-0.071	-0.071	0.000	0.000	0.000	0.000
51	A	384	ASN	0	-0.018	-0.027	11.428	-0.076	-0.076	0.000	0.000	0.000	0.000
52	A	385	ASP	-1	-0.736	-0.821	11.364	-1.761	-1.761	0.000	0.000	0.000	0.000
53	A	386	ARG	1	0.887	0.939	10.848	1.229	1.229	0.000	0.000	0.000	0.000
54	A	387	VAL	0	0.006	-0.010	12.834	-0.078	-0.078	0.000	0.000	0.000	0.000
55	A	388	LEU	0	-0.046	-0.020	10.768	0.080	0.080	0.000	0.000	0.000	0.000
56	A	389	ALA	0	0.013	-0.001	15.215	0.100	0.100	0.000	0.000	0.000	0.000
57	A	390	ILE	0	0.032	0.018	18.587	-0.052	-0.052	0.000	0.000	0.000	0.000
58	A	391	ASN	0	-0.023	-0.018	21.617	0.018	0.018	0.000	0.000	0.000	0.000
59	A	392	GLY	0	0.002	0.009	21.695	0.034	0.034	0.000	0.000	0.000	0.000
60	A	393	HIS	0	-0.066	-0.021	22.621	0.037	0.037	0.000	0.000	0.000	0.000
61	A	394	ASP	-1	-0.845	-0.924	17.995	-0.533	-0.533	0.000	0.000	0.000	0.000
62	A	395	LEU	0	0.028	-0.003	18.628	0.039	0.039	0.000	0.000	0.000	0.000
63	A	396	LYS	1	0.873	0.952	13.667	0.523	0.523	0.000	0.000	0.000	0.000
64	A	397	TYR	0	-0.008	-0.022	15.291	-0.059	-0.059	0.000	0.000	0.000	0.000
65	A	398	GLY	0	-0.001	0.021	18.592	0.051	0.051	0.000	0.000	0.000	0.000
66	A	399	THR	0	-0.017	-0.041	20.429	-0.012	-0.012	0.000	0.000	0.000	0.000
67	A	400	PRO	0	0.047	0.012	21.774	-0.009	-0.009	0.000	0.000	0.000	0.000
68	A	401	GLU	-1	-0.785	-0.864	23.603	-0.284	-0.284	0.000	0.000	0.000	0.000
69	A	402	LEU	0	0.019	0.022	23.704	0.008	0.008	0.000	0.000	0.000	0.000
70	A	403	ALA	0	0.025	0.003	22.286	0.002	0.002	0.000	0.000	0.000	0.000
71	A	404	ALA	0	-0.009	-0.003	24.356	0.006	0.006	0.000	0.000	0.000	0.000
72	A	405	GLN	0	0.000	-0.002	27.542	0.006	0.006	0.000	0.000	0.000	0.000
73	A	406	ILE	0	-0.018	-0.008	24.306	0.011	0.011	0.000	0.000	0.000	0.000
74	A	407	ILE	0	-0.013	-0.017	23.872	0.006	0.006	0.000	0.000	0.000	0.000
75	A	408	GLN	0	-0.052	-0.033	27.964	0.021	0.021	0.000	0.000	0.000	0.000
76	A	409	ALA	0	-0.006	0.008	31.231	0.014	0.014	0.000	0.000	0.000	0.000
77	A	410	SER	0	-0.074	-0.018	28.817	0.005	0.005	0.000	0.000	0.000	0.000
78	A	411	GLY	0	0.042	0.017	30.699	0.015	0.015	0.000	0.000	0.000	0.000
79	A	412	GLU	-1	-0.809	-0.913	30.762	-0.270	-0.270	0.000	0.000	0.000	0.000
80	A	413	ARG	1	0.919	1.003	22.661	0.355	0.355	0.000	0.000	0.000	0.000
81	A	414	VAL	0	0.016	0.008	23.744	0.001	0.001	0.000	0.000	0.000	0.000
82	A	415	ASN	0	-0.033	-0.033	19.683	-0.008	-0.008	0.000	0.000	0.000	0.000
83	A	416	LEU	0	0.018	0.007	18.346	0.016	0.016	0.000	0.000	0.000	0.000
84	A	417	THR	0	-0.030	-0.013	13.941	-0.019	-0.019	0.000	0.000	0.000	0.000
85	A	418	ILE	0	-0.002	0.000	11.378	0.052	0.052	0.000	0.000	0.000	0.000
86	A	419	ALA	0	0.002	-0.005	8.271	-0.066	-0.066	0.000	0.000	0.000	0.000
87	A	420	ARG	1	0.810	0.868	7.177	2.068	2.068	0.000	0.000	0.000	0.000
88	A	421	PRO	0	-0.022	-0.025	4.932	-1.705	-1.705	0.000	0.000	0.000	0.000
89	A	422	GLY	0	-0.001	0.006	3.615	0.828	1.514	0.005	-0.268	-0.423	0.000
90	A	423	LYS	1	0.926	0.961	3.868	-3.382	-2.969	0.001	-0.128	-0.286	-0.001
91	A	424	PRO	0	0.017	0.010	5.317	-0.095	-0.053	-0.001	-0.001	-0.040	0.000
92	A	425	GLU	-1	-0.910	-0.949	8.403	0.045	0.045	0.000	0.000	0.000	0.000
93	A	426	ILE	0	-0.075	-0.054	8.107	0.271	0.271	0.000	0.000	0.000	0.000
94	A	427	GLU	-1	-0.918	-0.937	11.485	0.226	0.226	0.000	0.000	0.000	0.000
95	A	428	LEU	0	-0.048	-0.026	13.487	0.079	0.079	0.000	0.000	0.000	0.000

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