FMO DATABASE

FMODB ID: 17KQZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1187523.24787
FMO2-HF: Nuclear repulsion	1132984.712184
FMO2-HF: Total energy	-54538.535686
FMO2-MP2: Total energy	-54691.581978

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.
-13.387	-7.964	2.757	-3.896	-4.285	-0.032

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 : -0.036 / q_NPA : -0.020

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	-0.013	0.003	3.538	0.479	2.230	-0.007	-0.772	-0.973	0.003
4	A	3	TRP	0	-0.040	-0.020	5.461	1.502	1.502	0.000	0.000	0.000	0.000
5	A	4	LYS	1	0.831	0.928	9.112	0.989	0.989	0.000	0.000	0.000	0.000
6	A	5	ARG	1	0.783	0.892	12.079	1.054	1.054	0.000	0.000	0.000	0.000
7	A	6	HIS	0	-0.027	-0.027	9.446	0.050	0.050	0.000	0.000	0.000	0.000
8	A	7	LEU	0	-0.003	0.012	13.388	0.159	0.159	0.000	0.000	0.000	0.000
9	A	8	THR	0	-0.013	-0.040	14.316	-0.115	-0.115	0.000	0.000	0.000	0.000
10	A	9	LEU	0	0.028	-0.003	14.992	-0.005	-0.005	0.000	0.000	0.000	0.000
11	A	10	ASP	-1	-0.900	-0.935	17.453	-0.474	-0.474	0.000	0.000	0.000	0.000
12	A	11	GLU	-1	-0.832	-0.890	18.787	-0.664	-0.664	0.000	0.000	0.000	0.000
13	A	12	LEU	0	0.006	0.000	14.940	0.025	0.025	0.000	0.000	0.000	0.000
14	A	13	ASN	0	-0.039	-0.022	19.611	0.067	0.067	0.000	0.000	0.000	0.000
15	A	14	ALA	0	0.041	0.042	22.373	0.037	0.037	0.000	0.000	0.000	0.000
16	A	15	THR	0	-0.099	-0.056	22.100	0.024	0.024	0.000	0.000	0.000	0.000
17	A	16	SER	0	-0.018	-0.026	24.342	0.013	0.013	0.000	0.000	0.000	0.000
18	A	17	ASP	-1	-0.885	-0.937	26.448	-0.291	-0.291	0.000	0.000	0.000	0.000
19	A	18	ASN	0	-0.078	-0.043	29.789	0.015	0.015	0.000	0.000	0.000	0.000
20	A	19	THR	0	-0.011	-0.009	28.506	0.005	0.005	0.000	0.000	0.000	0.000
21	A	20	MET	0	0.003	-0.018	27.684	0.016	0.016	0.000	0.000	0.000	0.000
22	A	21	VAL	0	0.016	0.020	24.255	0.013	0.013	0.000	0.000	0.000	0.000
23	A	22	ALA	0	0.070	0.034	27.437	0.006	0.006	0.000	0.000	0.000	0.000
24	A	23	HIS	0	-0.053	-0.011	29.302	0.013	0.013	0.000	0.000	0.000	0.000
25	A	24	LEU	0	-0.022	-0.028	29.169	0.016	0.016	0.000	0.000	0.000	0.000
26	A	25	GLY	0	-0.033	-0.015	29.090	0.007	0.007	0.000	0.000	0.000	0.000
27	A	26	ILE	0	-0.054	-0.023	23.257	-0.002	-0.002	0.000	0.000	0.000	0.000
28	A	27	VAL	0	0.017	0.013	21.881	-0.004	-0.004	0.000	0.000	0.000	0.000
29	A	28	TYR	0	0.025	0.003	17.513	-0.027	-0.027	0.000	0.000	0.000	0.000
30	A	29	THR	0	-0.006	-0.015	17.763	-0.005	-0.005	0.000	0.000	0.000	0.000
31	A	30	ARG	1	0.879	0.929	8.984	0.966	0.966	0.000	0.000	0.000	0.000
32	A	31	LEU	0	0.031	0.015	10.122	0.014	0.014	0.000	0.000	0.000	0.000
33	A	32	GLY	0	-0.005	0.002	7.445	0.281	0.281	0.000	0.000	0.000	0.000
34	A	33	ASP	-1	-0.875	-0.941	2.330	-13.438	-10.103	2.765	-3.068	-3.032	-0.035
35	A	34	ASP	-1	-0.869	-0.942	3.927	-3.951	-3.614	-0.001	-0.056	-0.280	0.000
36	A	35	VAL	0	-0.033	-0.012	5.834	1.264	1.264	0.000	0.000	0.000	0.000
37	A	36	LEU	0	-0.009	0.003	9.164	-0.110	-0.110	0.000	0.000	0.000	0.000
38	A	37	GLU	-1	-0.821	-0.893	12.633	-0.481	-0.481	0.000	0.000	0.000	0.000
39	A	38	ALA	0	0.041	0.025	15.564	-0.026	-0.026	0.000	0.000	0.000	0.000
40	A	39	GLU	-1	-0.880	-0.924	19.233	-0.274	-0.274	0.000	0.000	0.000	0.000
41	A	40	MET	0	0.011	0.018	22.524	-0.013	-0.013	0.000	0.000	0.000	0.000
42	A	41	PRO	0	0.022	0.025	26.111	0.014	0.014	0.000	0.000	0.000	0.000
43	A	42	VAL	0	-0.027	0.007	29.478	-0.003	-0.003	0.000	0.000	0.000	0.000
44	A	43	ASP	-1	-0.752	-0.854	31.990	-0.167	-0.167	0.000	0.000	0.000	0.000
45	A	44	THR	0	0.019	-0.007	35.195	0.000	0.000	0.000	0.000	0.000	0.000
46	A	45	ARG	1	0.786	0.883	31.763	0.208	0.208	0.000	0.000	0.000	0.000
47	A	46	THR	0	-0.034	-0.043	30.380	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	47	HIS	0	-0.010	-0.002	33.372	0.002	0.002	0.000	0.000	0.000	0.000
49	A	48	GLN	0	-0.071	-0.043	34.964	0.004	0.004	0.000	0.000	0.000	0.000
50	A	49	PRO	0	0.007	-0.027	38.133	0.003	0.003	0.000	0.000	0.000	0.000
51	A	50	PHE	0	-0.033	-0.008	40.066	0.004	0.004	0.000	0.000	0.000	0.000
52	A	51	GLY	0	0.016	0.033	39.409	0.004	0.004	0.000	0.000	0.000	0.000
53	A	52	LEU	0	-0.022	-0.006	35.591	-0.001	-0.001	0.000	0.000	0.000	0.000
54	A	53	LEU	0	0.018	0.002	28.278	-0.003	-0.003	0.000	0.000	0.000	0.000
55	A	54	HIS	0	0.022	0.022	32.981	0.006	0.006	0.000	0.000	0.000	0.000
56	A	55	GLY	0	0.032	0.012	30.779	-0.013	-0.013	0.000	0.000	0.000	0.000
57	A	56	GLY	0	-0.006	-0.016	29.862	-0.012	-0.012	0.000	0.000	0.000	0.000
58	A	57	ALA	0	0.041	0.020	29.723	-0.017	-0.017	0.000	0.000	0.000	0.000
59	A	58	SER	0	-0.004	-0.008	26.378	-0.025	-0.025	0.000	0.000	0.000	0.000
60	A	59	ALA	0	0.008	0.007	25.160	-0.026	-0.026	0.000	0.000	0.000	0.000
61	A	60	ALA	0	0.017	0.015	25.247	-0.025	-0.025	0.000	0.000	0.000	0.000
62	A	61	LEU	0	0.019	0.018	21.831	-0.032	-0.032	0.000	0.000	0.000	0.000
63	A	62	ALA	0	-0.006	-0.011	21.000	-0.052	-0.052	0.000	0.000	0.000	0.000
64	A	63	GLU	-1	-0.836	-0.920	20.471	-0.430	-0.430	0.000	0.000	0.000	0.000
65	A	64	THR	0	-0.025	-0.026	21.260	-0.036	-0.036	0.000	0.000	0.000	0.000
66	A	65	LEU	0	-0.023	-0.011	16.538	-0.057	-0.057	0.000	0.000	0.000	0.000
67	A	66	GLY	0	0.040	0.012	16.538	-0.104	-0.104	0.000	0.000	0.000	0.000
68	A	67	SER	0	-0.017	-0.033	16.851	-0.068	-0.068	0.000	0.000	0.000	0.000
69	A	68	MET	0	-0.041	0.006	16.849	-0.056	-0.056	0.000	0.000	0.000	0.000
70	A	69	ALA	0	0.019	-0.001	12.685	-0.103	-0.103	0.000	0.000	0.000	0.000
71	A	70	GLY	0	0.054	0.009	13.333	-0.138	-0.138	0.000	0.000	0.000	0.000
72	A	71	PHE	0	0.022	0.001	15.256	-0.028	-0.028	0.000	0.000	0.000	0.000
73	A	72	MET	0	0.033	0.034	12.343	0.023	0.023	0.000	0.000	0.000	0.000
74	A	73	MET	0	-0.002	0.016	8.294	-0.288	-0.288	0.000	0.000	0.000	0.000
75	A	74	THR	0	-0.118	-0.046	12.378	0.119	0.119	0.000	0.000	0.000	0.000
76	A	75	ARG	1	0.959	0.961	15.756	0.391	0.391	0.000	0.000	0.000	0.000
77	A	76	ASP	-1	-0.835	-0.927	17.484	-0.639	-0.639	0.000	0.000	0.000	0.000
78	A	77	GLY	0	-0.004	-0.006	20.836	0.031	0.031	0.000	0.000	0.000	0.000
79	A	78	GLN	0	-0.059	-0.024	17.987	-0.030	-0.030	0.000	0.000	0.000	0.000
80	A	79	CYS	0	0.003	0.016	21.688	-0.033	-0.033	0.000	0.000	0.000	0.000
81	A	80	VAL	0	-0.016	-0.016	17.719	-0.007	-0.007	0.000	0.000	0.000	0.000
82	A	81	VAL	0	0.006	0.013	21.149	0.016	0.016	0.000	0.000	0.000	0.000
83	A	82	GLY	0	0.075	0.042	21.986	-0.010	-0.010	0.000	0.000	0.000	0.000
84	A	83	THR	0	-0.093	-0.063	22.914	0.030	0.030	0.000	0.000	0.000	0.000
85	A	84	GLU	-1	-0.864	-0.920	23.742	-0.154	-0.154	0.000	0.000	0.000	0.000
86	A	85	LEU	0	0.001	0.017	22.901	-0.032	-0.032	0.000	0.000	0.000	0.000
87	A	86	ASN	0	-0.052	-0.019	23.300	0.036	0.036	0.000	0.000	0.000	0.000
88	A	87	ALA	0	0.044	-0.002	24.163	-0.022	-0.022	0.000	0.000	0.000	0.000
89	A	88	THR	0	-0.037	-0.012	25.787	0.025	0.025	0.000	0.000	0.000	0.000
90	A	89	HIS	0	0.066	0.014	26.914	-0.005	-0.005	0.000	0.000	0.000	0.000
91	A	90	HIS	0	0.009	0.033	25.122	0.003	0.003	0.000	0.000	0.000	0.000
92	A	91	ARG	1	0.854	0.908	27.984	0.098	0.098	0.000	0.000	0.000	0.000
93	A	92	PRO	0	-0.006	0.017	30.526	-0.012	-0.012	0.000	0.000	0.000	0.000
94	A	93	VAL	0	0.002	-0.014	28.554	0.004	0.004	0.000	0.000	0.000	0.000
95	A	94	SER	0	0.001	-0.027	32.055	-0.003	-0.003	0.000	0.000	0.000	0.000
96	A	95	GLU	-1	-0.887	-0.912	33.150	-0.093	-0.093	0.000	0.000	0.000	0.000
97	A	96	GLY	0	0.012	0.018	30.648	-0.004	-0.004	0.000	0.000	0.000	0.000
98	A	97	LYS	1	0.758	0.852	23.721	0.238	0.238	0.000	0.000	0.000	0.000
99	A	98	VAL	0	-0.019	-0.015	24.957	0.016	0.016	0.000	0.000	0.000	0.000
100	A	99	ARG	1	0.870	0.916	15.318	0.381	0.381	0.000	0.000	0.000	0.000
101	A	100	GLY	0	-0.002	0.003	19.627	0.036	0.036	0.000	0.000	0.000	0.000
102	A	101	VAL	0	-0.014	-0.020	13.641	-0.057	-0.057	0.000	0.000	0.000	0.000
103	A	102	CYS	0	-0.056	-0.015	14.317	0.066	0.066	0.000	0.000	0.000	0.000
104	A	103	GLN	0	0.022	0.006	10.590	-0.237	-0.237	0.000	0.000	0.000	0.000
105	A	104	PRO	0	0.021	0.018	7.370	0.241	0.241	0.000	0.000	0.000	0.000
106	A	105	LEU	0	-0.058	-0.032	10.583	0.183	0.183	0.000	0.000	0.000	0.000
107	A	106	HIS	0	-0.025	-0.021	12.585	0.142	0.142	0.000	0.000	0.000	0.000
108	A	107	LEU	0	0.037	0.020	7.978	-0.107	-0.107	0.000	0.000	0.000	0.000
109	A	108	GLY	0	0.023	0.027	12.111	0.060	0.060	0.000	0.000	0.000	0.000
110	A	109	ARG	1	0.920	0.941	15.139	0.206	0.206	0.000	0.000	0.000	0.000
111	A	110	GLN	0	-0.013	-0.004	16.770	0.003	0.003	0.000	0.000	0.000	0.000
112	A	111	ASN	0	-0.005	-0.003	17.950	0.006	0.006	0.000	0.000	0.000	0.000
113	A	112	GLN	0	0.022	0.045	14.341	-0.005	-0.005	0.000	0.000	0.000	0.000
114	A	113	SER	0	-0.038	-0.018	14.682	0.073	0.073	0.000	0.000	0.000	0.000
115	A	114	TRP	0	0.085	0.032	10.343	-0.077	-0.077	0.000	0.000	0.000	0.000
116	A	115	GLU	-1	-0.775	-0.891	14.350	-0.148	-0.148	0.000	0.000	0.000	0.000
117	A	116	ILE	0	-0.014	-0.019	15.529	-0.102	-0.102	0.000	0.000	0.000	0.000
118	A	117	VAL	0	-0.035	0.004	16.799	0.074	0.074	0.000	0.000	0.000	0.000
119	A	118	VAL	0	0.033	0.011	19.301	-0.045	-0.045	0.000	0.000	0.000	0.000
120	A	119	PHE	0	-0.022	-0.014	17.430	0.048	0.048	0.000	0.000	0.000	0.000
121	A	120	ASP	-1	-0.642	-0.808	22.814	-0.120	-0.120	0.000	0.000	0.000	0.000
122	A	121	GLU	-1	-0.797	-0.897	24.422	-0.182	-0.182	0.000	0.000	0.000	0.000
123	A	122	GLN	0	-0.056	-0.026	26.105	0.019	0.019	0.000	0.000	0.000	0.000
124	A	123	GLY	0	0.002	0.009	22.372	0.019	0.019	0.000	0.000	0.000	0.000
125	A	124	ARG	1	0.804	0.881	22.593	0.087	0.087	0.000	0.000	0.000	0.000
126	A	125	ARG	1	0.877	0.925	17.815	0.106	0.106	0.000	0.000	0.000	0.000
127	A	126	CYS	0	-0.068	-0.012	23.456	0.024	0.024	0.000	0.000	0.000	0.000
128	A	127	CYS	0	-0.067	-0.034	24.408	0.008	0.008	0.000	0.000	0.000	0.000
129	A	128	THR	0	0.001	0.000	20.291	-0.018	-0.018	0.000	0.000	0.000	0.000
130	A	129	CYS	0	-0.023	-0.004	21.220	0.030	0.030	0.000	0.000	0.000	0.000
131	A	130	ARG	1	0.886	0.945	18.290	0.166	0.166	0.000	0.000	0.000	0.000
132	A	131	LEU	0	0.011	0.031	18.781	0.025	0.025	0.000	0.000	0.000	0.000
133	A	132	GLY	0	-0.018	-0.002	18.339	-0.035	-0.035	0.000	0.000	0.000	0.000
134	A	133	THR	0	-0.002	-0.025	17.382	0.024	0.024	0.000	0.000	0.000	0.000
135	A	134	ALA	0	0.017	0.001	20.111	0.022	0.022	0.000	0.000	0.000	0.000
136	A	135	VAL	0	-0.001	-0.005	17.224	-0.026	-0.026	0.000	0.000	0.000	0.000
137	A	136	LEU	0	-0.024	-0.011	20.454	0.047	0.047	0.000	0.000	0.000	0.000
138	A	137	GLY	0	0.002	0.009	22.121	-0.005	-0.005	0.000	0.000	0.000	0.000

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