FMO DATABASE

FMODB ID: VRMY1

Calculation Name: 1B9L-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1B9L

Chain ID: A

ChEMBL ID:

UniProt ID: P0AC19

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	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	119
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1003621.885887
FMO2-HF: Nuclear repulsion	955538.373148
FMO2-HF: Total energy	-48083.51274
FMO2-MP2: Total energy	-48227.010777

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:2:ALA)

Summations of interaction energy for fragment #1(A:2:ALA)

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.
-0.507	2.452	0.029	-1.43	-1.558	0.006

Interaction energy analysis for fragmet #1(A:2:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.046 / q_NPA : 0.024

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	4	PRO	0	-0.004	-0.019	3.315	-0.795	2.055	0.030	-1.419	-1.461	0.006
4	A	5	ALA	0	0.030	0.020	4.782	0.197	0.306	-0.001	-0.011	-0.097	0.000
5	A	6	ALA	0	-0.022	-0.001	7.827	0.080	0.080	0.000	0.000	0.000	0.000
6	A	7	ILE	0	-0.017	-0.018	9.431	-0.034	-0.034	0.000	0.000	0.000	0.000
7	A	8	ILE	0	-0.027	-0.008	12.591	0.072	0.072	0.000	0.000	0.000	0.000
8	A	9	ARG	1	0.940	0.957	14.116	0.100	0.100	0.000	0.000	0.000	0.000
9	A	10	ILE	0	-0.010	0.009	18.800	0.025	0.025	0.000	0.000	0.000	0.000
10	A	11	LYS	1	0.960	0.958	18.758	-0.018	-0.018	0.000	0.000	0.000	0.000
11	A	12	ASN	0	-0.021	-0.017	24.086	0.001	0.001	0.000	0.000	0.000	0.000
12	A	13	LEU	0	0.015	0.026	27.623	0.009	0.009	0.000	0.000	0.000	0.000
13	A	14	ARG	1	0.938	0.962	29.216	0.006	0.006	0.000	0.000	0.000	0.000
14	A	15	LEU	0	0.045	0.024	32.361	0.004	0.004	0.000	0.000	0.000	0.000
15	A	16	ARG	1	0.918	0.944	35.299	0.013	0.013	0.000	0.000	0.000	0.000
16	A	17	THR	0	-0.016	-0.030	37.493	0.001	0.001	0.000	0.000	0.000	0.000
17	A	18	PHE	0	-0.019	0.004	40.047	0.001	0.001	0.000	0.000	0.000	0.000
18	A	19	ILE	0	0.036	0.016	37.244	-0.003	-0.003	0.000	0.000	0.000	0.000
19	A	20	GLY	0	0.026	0.023	41.425	0.001	0.001	0.000	0.000	0.000	0.000
20	A	21	ILE	0	-0.016	-0.026	44.045	0.001	0.001	0.000	0.000	0.000	0.000
21	A	22	LYS	1	0.945	0.978	47.455	0.039	0.039	0.000	0.000	0.000	0.000
22	A	23	GLU	-1	-0.855	-0.941	49.294	-0.025	-0.025	0.000	0.000	0.000	0.000
23	A	24	GLU	-1	-0.940	-0.967	48.880	-0.025	-0.025	0.000	0.000	0.000	0.000
24	A	25	GLU	-1	-0.868	-0.935	44.255	-0.040	-0.040	0.000	0.000	0.000	0.000
25	A	26	ILE	0	-0.041	-0.003	45.800	0.000	0.000	0.000	0.000	0.000	0.000
26	A	27	ASN	0	-0.026	-0.018	47.913	0.002	0.002	0.000	0.000	0.000	0.000
27	A	28	ASN	0	-0.034	-0.011	47.534	0.003	0.003	0.000	0.000	0.000	0.000
28	A	29	ARG	1	0.811	0.911	40.403	0.022	0.022	0.000	0.000	0.000	0.000
29	A	30	GLN	0	0.020	-0.003	40.703	0.000	0.000	0.000	0.000	0.000	0.000
30	A	31	ASP	-1	-0.843	-0.900	37.810	-0.019	-0.019	0.000	0.000	0.000	0.000
31	A	32	ILE	0	0.004	-0.002	34.065	-0.003	-0.003	0.000	0.000	0.000	0.000
32	A	33	VAL	0	-0.057	-0.024	29.353	0.006	0.006	0.000	0.000	0.000	0.000
33	A	34	ILE	0	0.028	0.015	27.140	-0.006	-0.006	0.000	0.000	0.000	0.000
34	A	35	ASN	0	0.005	0.006	23.824	0.015	0.015	0.000	0.000	0.000	0.000
35	A	36	VAL	0	0.023	0.021	21.122	-0.012	-0.012	0.000	0.000	0.000	0.000
36	A	37	THR	0	-0.020	-0.008	16.729	0.021	0.021	0.000	0.000	0.000	0.000
37	A	38	ILE	0	0.028	0.015	16.151	-0.019	-0.019	0.000	0.000	0.000	0.000
38	A	39	HIS	0	-0.003	0.007	12.523	-0.042	-0.042	0.000	0.000	0.000	0.000
39	A	40	TYR	0	0.042	0.004	11.695	0.035	0.035	0.000	0.000	0.000	0.000
40	A	41	PRO	0	0.021	0.028	8.997	-0.029	-0.029	0.000	0.000	0.000	0.000
41	A	42	ALA	0	0.018	0.005	5.107	0.125	0.125	0.000	0.000	0.000	0.000
42	A	43	ASP	-1	-0.882	-0.934	7.192	-0.077	-0.077	0.000	0.000	0.000	0.000
43	A	44	LYS	1	0.970	0.977	8.197	0.258	0.258	0.000	0.000	0.000	0.000
44	A	45	ALA	0	-0.043	-0.011	9.731	0.032	0.032	0.000	0.000	0.000	0.000
45	A	46	ARG	1	0.897	0.937	7.961	-0.389	-0.389	0.000	0.000	0.000	0.000
46	A	47	THR	0	-0.014	0.025	11.878	0.017	0.017	0.000	0.000	0.000	0.000
47	A	48	SER	0	0.017	-0.015	14.523	-0.038	-0.038	0.000	0.000	0.000	0.000
48	A	49	GLU	-1	-1.034	-0.992	16.520	0.214	0.214	0.000	0.000	0.000	0.000
49	A	50	ASP	-1	-0.959	-0.977	17.590	0.108	0.108	0.000	0.000	0.000	0.000
50	A	51	ILE	0	-0.010	-0.009	16.479	-0.021	-0.021	0.000	0.000	0.000	0.000
51	A	52	ASN	0	0.006	-0.004	20.255	0.009	0.009	0.000	0.000	0.000	0.000
52	A	53	ASP	-1	-0.958	-0.968	21.378	-0.024	-0.024	0.000	0.000	0.000	0.000
53	A	54	ALA	0	0.000	-0.001	18.608	-0.017	-0.017	0.000	0.000	0.000	0.000
54	A	55	LEU	0	-0.017	0.006	16.220	-0.004	-0.004	0.000	0.000	0.000	0.000
55	A	56	ASN	0	0.086	0.031	19.042	0.023	0.023	0.000	0.000	0.000	0.000
56	A	57	TYR	0	0.056	0.015	19.049	-0.010	-0.010	0.000	0.000	0.000	0.000
57	A	58	ARG	1	0.968	0.982	21.782	-0.052	-0.052	0.000	0.000	0.000	0.000
58	A	59	THR	0	-0.032	-0.003	24.808	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	60	VAL	0	0.036	0.026	21.859	-0.002	-0.002	0.000	0.000	0.000	0.000
60	A	61	THR	0	0.020	-0.005	24.957	-0.003	-0.003	0.000	0.000	0.000	0.000
61	A	62	LYS	1	0.911	0.970	27.094	0.018	0.018	0.000	0.000	0.000	0.000
62	A	63	ASN	0	0.015	-0.009	27.867	0.007	0.007	0.000	0.000	0.000	0.000
63	A	64	ILE	0	0.035	0.025	25.796	-0.001	-0.001	0.000	0.000	0.000	0.000
64	A	65	ILE	0	0.011	-0.001	30.184	0.000	0.000	0.000	0.000	0.000	0.000
65	A	66	GLN	0	-0.029	-0.014	32.835	0.001	0.001	0.000	0.000	0.000	0.000
66	A	67	HIS	0	-0.036	-0.018	33.084	0.004	0.004	0.000	0.000	0.000	0.000
67	A	68	VAL	0	0.025	0.011	32.462	-0.001	-0.001	0.000	0.000	0.000	0.000
68	A	69	GLU	-1	-0.940	-0.963	35.508	-0.017	-0.017	0.000	0.000	0.000	0.000
69	A	70	ASN	0	-0.048	-0.005	38.210	0.003	0.003	0.000	0.000	0.000	0.000
70	A	71	ASN	0	-0.022	-0.010	38.048	0.000	0.000	0.000	0.000	0.000	0.000
71	A	72	ARG	1	0.849	0.930	40.743	0.031	0.031	0.000	0.000	0.000	0.000
72	A	73	PHE	0	-0.013	0.001	36.304	-0.003	-0.003	0.000	0.000	0.000	0.000
73	A	74	SER	0	0.005	0.005	40.635	0.001	0.001	0.000	0.000	0.000	0.000
74	A	75	LEU	0	0.009	-0.011	38.737	0.002	0.002	0.000	0.000	0.000	0.000
75	A	76	LEU	0	0.062	0.029	34.198	0.000	0.000	0.000	0.000	0.000	0.000
76	A	77	GLU	-1	-0.846	-0.921	33.876	-0.079	-0.079	0.000	0.000	0.000	0.000
77	A	78	LYS	1	0.922	0.962	33.575	0.067	0.067	0.000	0.000	0.000	0.000
78	A	79	LEU	0	0.025	0.029	33.432	-0.002	-0.002	0.000	0.000	0.000	0.000
79	A	80	THR	0	0.019	-0.028	28.808	0.001	0.001	0.000	0.000	0.000	0.000
80	A	81	GLN	0	-0.042	-0.010	28.581	-0.008	-0.008	0.000	0.000	0.000	0.000
81	A	82	ASP	-1	-0.822	-0.917	29.584	-0.076	-0.076	0.000	0.000	0.000	0.000
82	A	83	VAL	0	-0.018	-0.012	27.215	0.001	0.001	0.000	0.000	0.000	0.000
83	A	84	LEU	0	-0.030	-0.020	23.483	-0.004	-0.004	0.000	0.000	0.000	0.000
84	A	85	ASP	-1	-0.873	-0.954	25.074	-0.124	-0.124	0.000	0.000	0.000	0.000
85	A	86	ILE	0	-0.004	-0.001	26.087	-0.001	-0.001	0.000	0.000	0.000	0.000
86	A	87	ALA	0	-0.084	-0.041	22.523	0.004	0.004	0.000	0.000	0.000	0.000
87	A	88	ARG	1	0.801	0.894	21.252	0.144	0.144	0.000	0.000	0.000	0.000
88	A	89	GLU	-1	-0.954	-0.960	22.283	-0.079	-0.079	0.000	0.000	0.000	0.000
89	A	90	HIS	0	0.010	0.004	18.795	-0.017	-0.017	0.000	0.000	0.000	0.000
90	A	91	HIS	0	0.069	0.027	19.494	-0.024	-0.024	0.000	0.000	0.000	0.000
91	A	92	TRP	0	-0.060	-0.038	15.128	-0.029	-0.029	0.000	0.000	0.000	0.000
92	A	93	VAL	0	-0.055	-0.026	15.146	-0.046	-0.046	0.000	0.000	0.000	0.000
93	A	94	THR	0	-0.026	-0.013	12.794	-0.031	-0.031	0.000	0.000	0.000	0.000
94	A	95	TYR	0	-0.069	-0.051	15.184	-0.026	-0.026	0.000	0.000	0.000	0.000
95	A	96	ALA	0	-0.005	-0.001	16.925	0.018	0.018	0.000	0.000	0.000	0.000
96	A	97	GLU	-1	-0.869	-0.942	19.604	-0.224	-0.224	0.000	0.000	0.000	0.000
97	A	98	VAL	0	-0.030	-0.013	21.669	0.014	0.014	0.000	0.000	0.000	0.000
98	A	99	GLU	-1	-0.817	-0.864	24.850	-0.098	-0.098	0.000	0.000	0.000	0.000
99	A	100	ILE	0	-0.052	-0.029	26.892	0.010	0.010	0.000	0.000	0.000	0.000
100	A	101	ASP	-1	-0.830	-0.900	29.960	-0.063	-0.063	0.000	0.000	0.000	0.000
101	A	102	LYS	1	0.870	0.928	32.598	0.050	0.050	0.000	0.000	0.000	0.000
102	A	103	LEU	0	-0.025	-0.046	34.183	0.000	0.000	0.000	0.000	0.000	0.000
103	A	104	HIS	0	-0.013	0.003	37.543	0.000	0.000	0.000	0.000	0.000	0.000
104	A	105	ALA	0	0.017	0.020	39.284	0.001	0.001	0.000	0.000	0.000	0.000
105	A	106	LEU	0	-0.045	-0.010	38.950	0.000	0.000	0.000	0.000	0.000	0.000
106	A	107	ARG	1	0.946	0.974	42.247	0.029	0.029	0.000	0.000	0.000	0.000
107	A	108	TYR	0	-0.043	-0.059	43.723	-0.001	-0.001	0.000	0.000	0.000	0.000
108	A	109	ALA	0	0.032	0.032	38.539	-0.001	-0.001	0.000	0.000	0.000	0.000
109	A	110	ASP	-1	-0.893	-0.938	35.729	-0.029	-0.029	0.000	0.000	0.000	0.000
110	A	111	SER	0	-0.114	-0.072	33.303	0.002	0.002	0.000	0.000	0.000	0.000
111	A	112	VAL	0	0.002	0.016	35.021	-0.002	-0.002	0.000	0.000	0.000	0.000
112	A	113	SER	0	-0.037	-0.050	29.422	0.002	0.002	0.000	0.000	0.000	0.000
113	A	114	MET	0	-0.016	0.008	30.877	-0.002	-0.002	0.000	0.000	0.000	0.000
114	A	115	THR	0	0.022	-0.002	24.598	0.001	0.001	0.000	0.000	0.000	0.000
115	A	116	LEU	0	-0.038	-0.007	26.342	-0.002	-0.002	0.000	0.000	0.000	0.000
116	A	117	SER	0	0.002	-0.003	21.404	0.001	0.001	0.000	0.000	0.000	0.000
117	A	118	TRP	0	-0.034	-0.015	19.188	0.005	0.005	0.000	0.000	0.000	0.000
118	A	119	GLN	0	0.017	-0.011	16.368	-0.024	-0.024	0.000	0.000	0.000	0.000
119	A	120	ARG	1	1.012	1.031	18.035	0.358	0.358	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:2:ALA)