FMO DATABASE

FMODB ID: YZ822

Calculation Name: 1VH9-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1VH9

Chain ID: A

ChEMBL ID:

UniProt ID: P0A8Y8

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	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	138
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1179402.613011
FMO2-HF: Nuclear repulsion	1124864.796895
FMO2-HF: Total energy	-54537.816117
FMO2-MP2: Total energy	-54690.811325

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:0:SER)

Summations of interaction energy for fragment #1(A:0: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.
-9.637	-5.268	0.121	-1.653	-2.836	0.004

Interaction energy analysis for fragmet #1(A:0:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.009 / q_NPA : 0.000

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	2	ILE	0	-0.036	-0.016	3.128	0.355	2.942	0.026	-1.192	-1.422	0.006
4	A	3	TRP	0	-0.050	-0.029	5.186	1.325	1.435	-0.001	-0.005	-0.104	0.000
5	A	4	LYS	1	0.907	0.965	8.719	0.845	0.845	0.000	0.000	0.000	0.000
6	A	5	ARG	1	0.824	0.918	11.437	0.831	0.831	0.000	0.000	0.000	0.000
7	A	6	HIS	0	0.003	-0.005	8.923	0.071	0.071	0.000	0.000	0.000	0.000
8	A	7	LEU	0	0.012	0.014	13.643	0.161	0.161	0.000	0.000	0.000	0.000
9	A	8	THR	0	0.005	-0.002	14.715	-0.133	-0.133	0.000	0.000	0.000	0.000
10	A	9	LEU	0	0.055	0.004	15.211	0.016	0.016	0.000	0.000	0.000	0.000
11	A	10	ASP	-1	-0.914	-0.945	17.923	-0.458	-0.458	0.000	0.000	0.000	0.000
12	A	11	GLU	-1	-0.888	-0.946	19.497	-0.600	-0.600	0.000	0.000	0.000	0.000
13	A	12	LEU	0	-0.023	-0.015	15.324	0.026	0.026	0.000	0.000	0.000	0.000
14	A	13	ASN	0	-0.019	-0.005	20.049	0.055	0.055	0.000	0.000	0.000	0.000
15	A	14	ALA	0	0.024	0.034	22.837	0.038	0.038	0.000	0.000	0.000	0.000
16	A	15	THR	0	-0.098	-0.070	22.310	0.028	0.028	0.000	0.000	0.000	0.000
17	A	16	SER	0	0.007	-0.002	24.346	0.013	0.013	0.000	0.000	0.000	0.000
18	A	17	ASP	-1	-0.878	-0.920	26.438	-0.297	-0.297	0.000	0.000	0.000	0.000
19	A	18	ASN	0	-0.073	-0.037	29.808	0.016	0.016	0.000	0.000	0.000	0.000
20	A	19	THR	0	0.002	-0.004	28.012	0.005	0.005	0.000	0.000	0.000	0.000
21	A	20	MET	0	0.003	-0.020	27.738	0.015	0.015	0.000	0.000	0.000	0.000
22	A	21	VAL	0	0.028	0.014	24.270	0.009	0.009	0.000	0.000	0.000	0.000
23	A	22	ALA	0	0.041	0.020	27.270	-0.001	-0.001	0.000	0.000	0.000	0.000
24	A	23	HIS	0	-0.059	-0.017	29.365	0.009	0.009	0.000	0.000	0.000	0.000
25	A	24	LEU	0	-0.023	-0.018	28.647	0.016	0.016	0.000	0.000	0.000	0.000
26	A	25	GLY	0	-0.038	-0.018	28.985	0.002	0.002	0.000	0.000	0.000	0.000
27	A	26	ILE	0	-0.049	-0.020	23.017	-0.010	-0.010	0.000	0.000	0.000	0.000
28	A	27	VAL	0	0.010	0.009	21.967	-0.001	-0.001	0.000	0.000	0.000	0.000
29	A	28	TYR	0	0.005	-0.008	17.772	-0.046	-0.046	0.000	0.000	0.000	0.000
30	A	29	THR	0	-0.004	-0.022	17.865	-0.002	-0.002	0.000	0.000	0.000	0.000
31	A	30	ARG	1	0.884	0.928	9.051	1.335	1.335	0.000	0.000	0.000	0.000
32	A	31	LEU	0	0.015	0.014	10.178	0.021	0.021	0.000	0.000	0.000	0.000
33	A	32	GLY	0	-0.022	0.005	7.594	0.161	0.161	0.000	0.000	0.000	0.000
34	A	33	ASP	-1	-0.892	-0.962	2.908	-6.191	-4.990	0.095	-0.330	-0.965	-0.001
35	A	34	ASP	-1	-0.876	-0.950	3.611	-7.106	-6.635	0.001	-0.126	-0.345	-0.001
36	A	35	VAL	0	-0.013	-0.007	5.667	1.430	1.430	0.000	0.000	0.000	0.000
37	A	36	LEU	0	-0.022	-0.005	9.278	-0.075	-0.075	0.000	0.000	0.000	0.000
38	A	37	GLU	-1	-0.817	-0.893	12.606	-0.710	-0.710	0.000	0.000	0.000	0.000
39	A	38	ALA	0	0.048	0.028	15.482	-0.005	-0.005	0.000	0.000	0.000	0.000
40	A	39	GLU	-1	-0.918	-0.949	19.162	-0.392	-0.392	0.000	0.000	0.000	0.000
41	A	40	MET	0	0.007	0.012	22.332	0.001	0.001	0.000	0.000	0.000	0.000
42	A	41	PRO	0	-0.004	0.009	25.845	0.012	0.012	0.000	0.000	0.000	0.000
43	A	42	VAL	0	-0.005	0.016	29.258	0.001	0.001	0.000	0.000	0.000	0.000
44	A	43	ASP	-1	-0.774	-0.872	31.788	-0.195	-0.195	0.000	0.000	0.000	0.000
45	A	44	THR	0	-0.001	-0.017	35.074	-0.002	-0.002	0.000	0.000	0.000	0.000
46	A	45	ARG	1	0.844	0.908	32.223	0.230	0.230	0.000	0.000	0.000	0.000
47	A	46	THR	0	-0.026	-0.027	30.359	0.002	0.002	0.000	0.000	0.000	0.000
48	A	47	HIS	0	0.017	0.020	33.596	0.004	0.004	0.000	0.000	0.000	0.000
49	A	48	GLN	0	-0.078	-0.048	34.874	0.010	0.010	0.000	0.000	0.000	0.000
50	A	49	PRO	0	-0.008	-0.019	38.287	0.002	0.002	0.000	0.000	0.000	0.000
51	A	50	PHE	0	-0.015	-0.015	40.287	0.002	0.002	0.000	0.000	0.000	0.000
52	A	51	GLY	0	0.031	0.033	39.403	0.004	0.004	0.000	0.000	0.000	0.000
53	A	52	LEU	0	-0.048	-0.018	35.377	-0.006	-0.006	0.000	0.000	0.000	0.000
54	A	53	LEU	0	0.018	0.004	28.403	0.000	0.000	0.000	0.000	0.000	0.000
55	A	54	HIS	0	0.039	0.050	33.083	0.001	0.001	0.000	0.000	0.000	0.000
56	A	55	GLY	0	0.029	0.006	30.947	-0.014	-0.014	0.000	0.000	0.000	0.000
57	A	56	GLY	0	-0.013	-0.037	29.867	-0.011	-0.011	0.000	0.000	0.000	0.000
58	A	57	ALA	0	0.034	0.019	29.463	-0.015	-0.015	0.000	0.000	0.000	0.000
59	A	58	SER	0	0.005	-0.006	26.091	-0.029	-0.029	0.000	0.000	0.000	0.000
60	A	59	ALA	0	0.009	0.010	24.844	-0.029	-0.029	0.000	0.000	0.000	0.000
61	A	60	ALA	0	0.026	0.017	24.936	-0.023	-0.023	0.000	0.000	0.000	0.000
62	A	61	LEU	0	0.014	0.017	21.739	-0.029	-0.029	0.000	0.000	0.000	0.000
63	A	62	ALA	0	-0.010	-0.017	20.517	-0.057	-0.057	0.000	0.000	0.000	0.000
64	A	63	GLU	-1	-0.904	-0.961	20.118	-0.373	-0.373	0.000	0.000	0.000	0.000
65	A	64	THR	0	-0.032	-0.023	21.073	-0.019	-0.019	0.000	0.000	0.000	0.000
66	A	65	LEU	0	-0.009	-0.014	16.273	-0.049	-0.049	0.000	0.000	0.000	0.000
67	A	66	GLY	0	0.020	0.004	16.154	-0.103	-0.103	0.000	0.000	0.000	0.000
68	A	67	SER	0	-0.025	-0.014	16.566	-0.030	-0.030	0.000	0.000	0.000	0.000
69	A	68	MET	0	0.005	0.019	16.230	-0.027	-0.027	0.000	0.000	0.000	0.000
70	A	69	ALA	0	0.028	0.014	12.140	-0.083	-0.083	0.000	0.000	0.000	0.000
71	A	70	GLY	0	0.046	0.010	12.924	-0.096	-0.096	0.000	0.000	0.000	0.000
72	A	71	PHE	0	0.029	0.007	14.945	0.012	0.012	0.000	0.000	0.000	0.000
73	A	72	MET	0	0.018	0.030	12.159	0.048	0.048	0.000	0.000	0.000	0.000
74	A	73	MET	0	-0.009	0.018	8.274	-0.269	-0.269	0.000	0.000	0.000	0.000
75	A	74	THR	0	-0.132	-0.064	12.366	0.169	0.169	0.000	0.000	0.000	0.000
76	A	75	ARG	1	0.944	0.957	15.666	0.223	0.223	0.000	0.000	0.000	0.000
77	A	76	ASP	-1	-0.894	-0.964	17.459	-0.410	-0.410	0.000	0.000	0.000	0.000
78	A	77	GLY	0	-0.013	-0.010	20.889	0.030	0.030	0.000	0.000	0.000	0.000
79	A	78	GLN	0	-0.060	-0.035	17.910	-0.017	-0.017	0.000	0.000	0.000	0.000
80	A	79	CYS	0	0.045	0.029	21.438	-0.031	-0.031	0.000	0.000	0.000	0.000
81	A	80	VAL	0	-0.028	-0.005	17.274	0.015	0.015	0.000	0.000	0.000	0.000
82	A	81	VAL	0	-0.001	0.005	20.715	0.002	0.002	0.000	0.000	0.000	0.000
83	A	82	GLY	0	0.054	0.034	21.872	-0.002	-0.002	0.000	0.000	0.000	0.000
84	A	83	THR	0	-0.069	-0.038	22.372	0.032	0.032	0.000	0.000	0.000	0.000
85	A	84	GLU	-1	-0.955	-0.969	23.355	-0.135	-0.135	0.000	0.000	0.000	0.000
86	A	85	LEU	0	0.043	0.029	22.927	-0.029	-0.029	0.000	0.000	0.000	0.000
87	A	86	ASN	0	-0.054	-0.020	23.466	0.019	0.019	0.000	0.000	0.000	0.000
88	A	87	ALA	0	0.049	-0.001	23.998	-0.027	-0.027	0.000	0.000	0.000	0.000
89	A	88	THR	0	-0.031	-0.001	25.619	0.028	0.028	0.000	0.000	0.000	0.000
90	A	89	HIS	0	0.014	-0.002	26.802	-0.019	-0.019	0.000	0.000	0.000	0.000
91	A	90	HIS	0	-0.010	0.039	25.188	0.001	0.001	0.000	0.000	0.000	0.000
92	A	91	ARG	1	0.922	0.955	28.063	0.149	0.149	0.000	0.000	0.000	0.000
93	A	92	PRO	0	-0.005	0.016	30.338	-0.013	-0.013	0.000	0.000	0.000	0.000
94	A	93	VAL	0	0.042	0.004	28.578	0.001	0.001	0.000	0.000	0.000	0.000
95	A	94	SER	0	0.021	-0.006	31.974	0.002	0.002	0.000	0.000	0.000	0.000
96	A	95	GLU	-1	-0.969	-0.967	32.851	-0.134	-0.134	0.000	0.000	0.000	0.000
97	A	96	GLY	0	0.034	0.037	30.352	-0.006	-0.006	0.000	0.000	0.000	0.000
98	A	97	LYS	1	0.838	0.916	23.627	0.321	0.321	0.000	0.000	0.000	0.000
99	A	98	VAL	0	-0.012	-0.011	24.766	0.009	0.009	0.000	0.000	0.000	0.000
100	A	99	ARG	1	0.886	0.911	15.356	0.537	0.537	0.000	0.000	0.000	0.000
101	A	100	GLY	0	-0.015	-0.004	19.376	0.032	0.032	0.000	0.000	0.000	0.000
102	A	101	VAL	0	-0.023	-0.019	13.321	-0.073	-0.073	0.000	0.000	0.000	0.000
103	A	102	CYS	0	-0.045	-0.010	13.949	0.092	0.092	0.000	0.000	0.000	0.000
104	A	103	GLN	0	0.045	0.018	9.386	-0.440	-0.440	0.000	0.000	0.000	0.000
105	A	104	PRO	0	0.008	0.013	7.209	0.320	0.320	0.000	0.000	0.000	0.000
106	A	105	LEU	0	-0.042	-0.014	10.068	0.126	0.126	0.000	0.000	0.000	0.000
107	A	106	HIS	0	-0.014	-0.017	12.102	0.194	0.194	0.000	0.000	0.000	0.000
108	A	107	LEU	0	0.024	0.012	7.694	-0.119	-0.119	0.000	0.000	0.000	0.000
109	A	108	GLY	0	0.014	0.021	11.848	0.133	0.133	0.000	0.000	0.000	0.000
110	A	109	ARG	1	0.923	0.944	14.945	0.019	0.019	0.000	0.000	0.000	0.000
111	A	110	GLN	0	0.015	0.010	16.600	-0.025	-0.025	0.000	0.000	0.000	0.000
112	A	111	ASN	0	-0.041	-0.023	17.793	-0.005	-0.005	0.000	0.000	0.000	0.000
113	A	112	GLN	0	0.053	0.045	13.783	-0.003	-0.003	0.000	0.000	0.000	0.000
114	A	113	SER	0	-0.017	0.007	14.434	0.030	0.030	0.000	0.000	0.000	0.000
115	A	114	TRP	0	0.071	0.029	9.935	-0.081	-0.081	0.000	0.000	0.000	0.000
116	A	115	GLU	-1	-0.914	-0.959	13.940	-0.336	-0.336	0.000	0.000	0.000	0.000
117	A	116	ILE	0	0.000	-0.008	15.005	-0.112	-0.112	0.000	0.000	0.000	0.000
118	A	117	VAL	0	-0.051	-0.016	17.096	0.095	0.095	0.000	0.000	0.000	0.000
119	A	118	VAL	0	0.036	0.012	19.054	-0.050	-0.050	0.000	0.000	0.000	0.000
120	A	119	PHE	0	-0.030	-0.025	17.453	0.055	0.055	0.000	0.000	0.000	0.000
121	A	120	ASP	-1	-0.687	-0.844	22.746	-0.206	-0.206	0.000	0.000	0.000	0.000
122	A	121	GLU	-1	-0.812	-0.917	24.508	-0.246	-0.246	0.000	0.000	0.000	0.000
123	A	122	GLN	0	-0.085	-0.037	25.964	0.005	0.005	0.000	0.000	0.000	0.000
124	A	123	GLY	0	-0.015	-0.002	22.591	0.014	0.014	0.000	0.000	0.000	0.000
125	A	124	ARG	1	0.816	0.908	22.766	0.149	0.149	0.000	0.000	0.000	0.000
126	A	125	ARG	1	0.944	0.964	18.585	0.199	0.199	0.000	0.000	0.000	0.000
127	A	126	CYS	0	-0.063	-0.028	23.699	0.033	0.033	0.000	0.000	0.000	0.000
128	A	127	CYS	0	-0.022	-0.009	24.246	0.013	0.013	0.000	0.000	0.000	0.000
129	A	128	THR	0	0.012	-0.012	20.403	-0.036	-0.036	0.000	0.000	0.000	0.000
130	A	129	CYS	0	-0.016	-0.004	20.798	0.041	0.041	0.000	0.000	0.000	0.000
131	A	130	ARG	1	0.955	0.984	18.066	0.154	0.154	0.000	0.000	0.000	0.000
132	A	131	LEU	0	0.017	0.018	18.421	0.024	0.024	0.000	0.000	0.000	0.000
133	A	132	GLY	0	-0.023	0.003	18.153	-0.036	-0.036	0.000	0.000	0.000	0.000
134	A	133	THR	0	0.005	-0.028	16.954	0.014	0.014	0.000	0.000	0.000	0.000
135	A	134	ALA	0	0.015	-0.002	19.587	0.026	0.026	0.000	0.000	0.000	0.000
136	A	135	VAL	0	0.008	-0.003	17.038	-0.028	-0.028	0.000	0.000	0.000	0.000
137	A	136	LEU	0	-0.063	-0.036	20.271	0.040	0.040	0.000	0.000	0.000	0.000
138	A	137	GLY	0	-0.012	0.004	21.507	0.010	0.010	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:0:SER)