FMO DATABASE

FMODB ID: V5L41

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1181097.511917
FMO2-HF: Nuclear repulsion	1126559.177465
FMO2-HF: Total energy	-54538.334451
FMO2-MP2: Total energy	-54691.310814

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.
-9.119	-4.903	0.105	-1.586	-2.733	0.005

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 : 0.006 / q_NPA : 0.003

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	-0.031	-0.012	3.141	0.199	2.834	0.027	-1.220	-1.441	0.006
4	A	3	TRP	0	-0.042	-0.025	5.233	1.386	1.493	-0.001	-0.005	-0.100	0.000
5	A	4	LYS	1	0.884	0.945	8.789	0.945	0.945	0.000	0.000	0.000	0.000
6	A	5	ARG	1	0.811	0.913	11.394	0.850	0.850	0.000	0.000	0.000	0.000
7	A	6	HIS	0	-0.024	-0.018	9.259	0.092	0.092	0.000	0.000	0.000	0.000
8	A	7	LEU	0	0.005	0.015	13.652	0.156	0.156	0.000	0.000	0.000	0.000
9	A	8	THR	0	-0.014	-0.042	14.758	-0.135	-0.135	0.000	0.000	0.000	0.000
10	A	9	LEU	0	0.039	-0.001	15.361	0.020	0.020	0.000	0.000	0.000	0.000
11	A	10	ASP	-1	-0.908	-0.942	17.975	-0.497	-0.497	0.000	0.000	0.000	0.000
12	A	11	GLU	-1	-0.838	-0.891	19.378	-0.640	-0.640	0.000	0.000	0.000	0.000
13	A	12	LEU	0	-0.016	-0.017	15.435	0.028	0.028	0.000	0.000	0.000	0.000
14	A	13	ASN	0	-0.034	-0.023	20.119	0.063	0.063	0.000	0.000	0.000	0.000
15	A	14	ALA	0	0.037	0.038	22.907	0.040	0.040	0.000	0.000	0.000	0.000
16	A	15	THR	0	-0.094	-0.054	22.307	0.033	0.033	0.000	0.000	0.000	0.000
17	A	16	SER	0	-0.009	-0.009	24.628	0.013	0.013	0.000	0.000	0.000	0.000
18	A	17	ASP	-1	-0.904	-0.936	26.529	-0.300	-0.300	0.000	0.000	0.000	0.000
19	A	18	ASN	0	-0.077	-0.039	29.888	0.017	0.017	0.000	0.000	0.000	0.000
20	A	19	THR	0	0.008	-0.002	28.038	0.005	0.005	0.000	0.000	0.000	0.000
21	A	20	MET	0	0.004	-0.016	27.864	0.016	0.016	0.000	0.000	0.000	0.000
22	A	21	VAL	0	0.031	0.012	24.249	0.009	0.009	0.000	0.000	0.000	0.000
23	A	22	ALA	0	0.049	0.025	27.350	-0.001	-0.001	0.000	0.000	0.000	0.000
24	A	23	HIS	0	-0.056	-0.015	29.453	0.010	0.010	0.000	0.000	0.000	0.000
25	A	24	LEU	0	-0.027	-0.020	28.957	0.017	0.017	0.000	0.000	0.000	0.000
26	A	25	GLY	0	-0.041	-0.020	29.071	0.003	0.003	0.000	0.000	0.000	0.000
27	A	26	ILE	0	-0.053	-0.024	23.084	-0.009	-0.009	0.000	0.000	0.000	0.000
28	A	27	VAL	0	0.017	0.015	22.131	-0.002	-0.002	0.000	0.000	0.000	0.000
29	A	28	TYR	0	0.014	-0.002	17.789	-0.047	-0.047	0.000	0.000	0.000	0.000
30	A	29	THR	0	0.009	-0.026	17.935	0.000	0.000	0.000	0.000	0.000	0.000
31	A	30	ARG	1	0.871	0.928	9.148	1.344	1.344	0.000	0.000	0.000	0.000
32	A	31	LEU	0	0.013	0.006	10.663	0.027	0.027	0.000	0.000	0.000	0.000
33	A	32	GLY	0	-0.009	0.012	7.658	0.148	0.148	0.000	0.000	0.000	0.000
34	A	33	ASP	-1	-0.909	-0.962	2.952	-6.503	-5.426	0.079	-0.281	-0.875	-0.001
35	A	34	ASP	-1	-0.885	-0.956	3.656	-6.267	-5.870	0.000	-0.080	-0.317	0.000
36	A	35	VAL	0	-0.025	-0.011	5.751	1.416	1.416	0.000	0.000	0.000	0.000
37	A	36	LEU	0	-0.018	-0.001	9.263	-0.081	-0.081	0.000	0.000	0.000	0.000
38	A	37	GLU	-1	-0.812	-0.886	12.705	-0.707	-0.707	0.000	0.000	0.000	0.000
39	A	38	ALA	0	0.054	0.034	15.572	-0.008	-0.008	0.000	0.000	0.000	0.000
40	A	39	GLU	-1	-0.886	-0.918	19.250	-0.385	-0.385	0.000	0.000	0.000	0.000
41	A	40	MET	0	0.001	0.013	22.415	0.001	0.001	0.000	0.000	0.000	0.000
42	A	41	PRO	0	0.009	0.017	25.934	0.011	0.011	0.000	0.000	0.000	0.000
43	A	42	VAL	0	-0.012	0.010	29.342	0.002	0.002	0.000	0.000	0.000	0.000
44	A	43	ASP	-1	-0.763	-0.861	31.876	-0.199	-0.199	0.000	0.000	0.000	0.000
45	A	44	THR	0	0.024	-0.004	35.161	0.001	0.001	0.000	0.000	0.000	0.000
46	A	45	ARG	1	0.811	0.887	32.070	0.238	0.238	0.000	0.000	0.000	0.000
47	A	46	THR	0	-0.032	-0.033	30.428	0.002	0.002	0.000	0.000	0.000	0.000
48	A	47	HIS	0	0.013	0.017	33.635	0.005	0.005	0.000	0.000	0.000	0.000
49	A	48	GLN	0	-0.065	-0.035	34.807	0.010	0.010	0.000	0.000	0.000	0.000
50	A	49	PRO	0	-0.002	-0.017	38.291	0.002	0.002	0.000	0.000	0.000	0.000
51	A	50	PHE	0	-0.014	-0.013	40.218	0.002	0.002	0.000	0.000	0.000	0.000
52	A	51	GLY	0	0.027	0.031	39.401	0.004	0.004	0.000	0.000	0.000	0.000
53	A	52	LEU	0	-0.050	-0.017	35.337	-0.006	-0.006	0.000	0.000	0.000	0.000
54	A	53	LEU	0	0.013	0.000	28.272	-0.001	-0.001	0.000	0.000	0.000	0.000
55	A	54	HIS	0	0.025	0.020	33.000	0.003	0.003	0.000	0.000	0.000	0.000
56	A	55	GLY	0	0.034	0.012	30.985	-0.014	-0.014	0.000	0.000	0.000	0.000
57	A	56	GLY	0	-0.014	-0.022	29.904	-0.012	-0.012	0.000	0.000	0.000	0.000
58	A	57	ALA	0	0.034	0.018	29.509	-0.015	-0.015	0.000	0.000	0.000	0.000
59	A	58	SER	0	0.016	0.001	26.109	-0.028	-0.028	0.000	0.000	0.000	0.000
60	A	59	ALA	0	-0.001	0.005	24.889	-0.029	-0.029	0.000	0.000	0.000	0.000
61	A	60	ALA	0	0.026	0.017	24.975	-0.023	-0.023	0.000	0.000	0.000	0.000
62	A	61	LEU	0	0.017	0.017	21.843	-0.029	-0.029	0.000	0.000	0.000	0.000
63	A	62	ALA	0	-0.017	-0.018	20.561	-0.057	-0.057	0.000	0.000	0.000	0.000
64	A	63	GLU	-1	-0.862	-0.947	20.160	-0.393	-0.393	0.000	0.000	0.000	0.000
65	A	64	THR	0	-0.039	-0.031	21.308	-0.020	-0.020	0.000	0.000	0.000	0.000
66	A	65	LEU	0	-0.023	-0.016	16.390	-0.050	-0.050	0.000	0.000	0.000	0.000
67	A	66	GLY	0	0.031	0.008	16.188	-0.101	-0.101	0.000	0.000	0.000	0.000
68	A	67	SER	0	-0.017	-0.010	16.601	-0.032	-0.032	0.000	0.000	0.000	0.000
69	A	68	MET	0	-0.005	0.013	16.445	-0.029	-0.029	0.000	0.000	0.000	0.000
70	A	69	ALA	0	0.027	0.013	12.227	-0.089	-0.089	0.000	0.000	0.000	0.000
71	A	70	GLY	0	0.057	0.017	12.971	-0.100	-0.100	0.000	0.000	0.000	0.000
72	A	71	PHE	0	0.028	0.002	14.976	0.008	0.008	0.000	0.000	0.000	0.000
73	A	72	MET	0	0.028	0.030	12.222	0.045	0.045	0.000	0.000	0.000	0.000
74	A	73	MET	0	-0.023	0.011	8.153	-0.271	-0.271	0.000	0.000	0.000	0.000
75	A	74	THR	0	-0.125	-0.054	12.397	0.170	0.170	0.000	0.000	0.000	0.000
76	A	75	ARG	1	0.949	0.957	15.705	0.228	0.228	0.000	0.000	0.000	0.000
77	A	76	ASP	-1	-0.868	-0.947	17.418	-0.458	-0.458	0.000	0.000	0.000	0.000
78	A	77	GLY	0	-0.012	-0.011	20.847	0.030	0.030	0.000	0.000	0.000	0.000
79	A	78	GLN	0	-0.054	-0.022	17.758	-0.020	-0.020	0.000	0.000	0.000	0.000
80	A	79	CYS	0	0.010	0.012	21.452	-0.035	-0.035	0.000	0.000	0.000	0.000
81	A	80	VAL	0	0.001	0.011	17.298	0.014	0.014	0.000	0.000	0.000	0.000
82	A	81	VAL	0	0.011	0.011	20.734	0.003	0.003	0.000	0.000	0.000	0.000
83	A	82	GLY	0	0.059	0.041	21.872	-0.001	-0.001	0.000	0.000	0.000	0.000
84	A	83	THR	0	-0.085	-0.056	22.502	0.034	0.034	0.000	0.000	0.000	0.000
85	A	84	GLU	-1	-0.894	-0.936	23.348	-0.143	-0.143	0.000	0.000	0.000	0.000
86	A	85	LEU	0	0.026	0.026	22.818	-0.029	-0.029	0.000	0.000	0.000	0.000
87	A	86	ASN	0	-0.057	-0.033	23.394	0.028	0.028	0.000	0.000	0.000	0.000
88	A	87	ALA	0	0.037	-0.004	24.001	-0.027	-0.027	0.000	0.000	0.000	0.000
89	A	88	THR	0	-0.031	-0.002	25.629	0.028	0.028	0.000	0.000	0.000	0.000
90	A	89	HIS	0	0.030	-0.002	26.815	-0.018	-0.018	0.000	0.000	0.000	0.000
91	A	90	HIS	0	-0.018	0.024	25.196	0.001	0.001	0.000	0.000	0.000	0.000
92	A	91	ARG	1	0.884	0.928	28.071	0.155	0.155	0.000	0.000	0.000	0.000
93	A	92	PRO	0	-0.003	0.014	30.275	-0.013	-0.013	0.000	0.000	0.000	0.000
94	A	93	VAL	0	0.021	-0.009	28.422	0.000	0.000	0.000	0.000	0.000	0.000
95	A	94	SER	0	0.021	0.002	31.899	0.001	0.001	0.000	0.000	0.000	0.000
96	A	95	GLU	-1	-0.960	-0.966	32.941	-0.134	-0.134	0.000	0.000	0.000	0.000
97	A	96	GLY	0	0.024	0.032	30.413	-0.006	-0.006	0.000	0.000	0.000	0.000
98	A	97	LYS	1	0.765	0.862	23.656	0.330	0.330	0.000	0.000	0.000	0.000
99	A	98	VAL	0	-0.013	-0.014	24.760	0.010	0.010	0.000	0.000	0.000	0.000
100	A	99	ARG	1	0.872	0.908	15.244	0.568	0.568	0.000	0.000	0.000	0.000
101	A	100	GLY	0	-0.011	-0.004	19.327	0.033	0.033	0.000	0.000	0.000	0.000
102	A	101	VAL	0	-0.021	-0.017	13.311	-0.073	-0.073	0.000	0.000	0.000	0.000
103	A	102	CYS	0	-0.044	-0.011	13.998	0.082	0.082	0.000	0.000	0.000	0.000
104	A	103	GLN	0	0.036	0.011	9.910	-0.392	-0.392	0.000	0.000	0.000	0.000
105	A	104	PRO	0	0.017	0.017	7.249	0.309	0.309	0.000	0.000	0.000	0.000
106	A	105	LEU	0	-0.046	-0.017	10.038	0.134	0.134	0.000	0.000	0.000	0.000
107	A	106	HIS	0	-0.009	-0.019	12.030	0.201	0.201	0.000	0.000	0.000	0.000
108	A	107	LEU	0	0.025	0.014	7.684	-0.125	-0.125	0.000	0.000	0.000	0.000
109	A	108	GLY	0	0.017	0.022	11.797	0.136	0.136	0.000	0.000	0.000	0.000
110	A	109	ARG	1	0.924	0.947	14.887	0.007	0.007	0.000	0.000	0.000	0.000
111	A	110	GLN	0	-0.004	-0.004	16.555	-0.016	-0.016	0.000	0.000	0.000	0.000
112	A	111	ASN	0	-0.024	-0.015	17.770	-0.001	-0.001	0.000	0.000	0.000	0.000
113	A	112	GLN	0	0.037	0.045	13.897	-0.006	-0.006	0.000	0.000	0.000	0.000
114	A	113	SER	0	-0.024	-0.004	14.404	0.032	0.032	0.000	0.000	0.000	0.000
115	A	114	TRP	0	0.065	0.013	10.038	-0.073	-0.073	0.000	0.000	0.000	0.000
116	A	115	GLU	-1	-0.884	-0.940	13.940	-0.331	-0.331	0.000	0.000	0.000	0.000
117	A	116	ILE	0	-0.002	-0.015	15.027	-0.118	-0.118	0.000	0.000	0.000	0.000
118	A	117	VAL	0	-0.047	-0.009	16.951	0.095	0.095	0.000	0.000	0.000	0.000
119	A	118	VAL	0	0.032	0.007	18.981	-0.051	-0.051	0.000	0.000	0.000	0.000
120	A	119	PHE	0	-0.026	-0.019	17.425	0.057	0.057	0.000	0.000	0.000	0.000
121	A	120	ASP	-1	-0.663	-0.822	22.675	-0.196	-0.196	0.000	0.000	0.000	0.000
122	A	121	GLU	-1	-0.773	-0.888	24.581	-0.263	-0.263	0.000	0.000	0.000	0.000
123	A	122	GLN	0	-0.076	-0.036	26.023	0.011	0.011	0.000	0.000	0.000	0.000
124	A	123	GLY	0	-0.003	0.003	22.641	0.015	0.015	0.000	0.000	0.000	0.000
125	A	124	ARG	1	0.823	0.901	22.711	0.150	0.150	0.000	0.000	0.000	0.000
126	A	125	ARG	1	0.947	0.970	18.134	0.197	0.197	0.000	0.000	0.000	0.000
127	A	126	CYS	0	-0.060	-0.025	23.645	0.033	0.033	0.000	0.000	0.000	0.000
128	A	127	CYS	0	-0.024	-0.010	24.181	0.014	0.014	0.000	0.000	0.000	0.000
129	A	128	THR	0	0.014	0.003	20.326	-0.036	-0.036	0.000	0.000	0.000	0.000
130	A	129	CYS	0	-0.021	-0.005	20.811	0.040	0.040	0.000	0.000	0.000	0.000
131	A	130	ARG	1	0.920	0.964	17.999	0.153	0.153	0.000	0.000	0.000	0.000
132	A	131	LEU	0	0.003	0.023	18.420	0.023	0.023	0.000	0.000	0.000	0.000
133	A	132	GLY	0	-0.022	0.000	18.148	-0.036	-0.036	0.000	0.000	0.000	0.000
134	A	133	THR	0	0.004	-0.011	16.974	0.018	0.018	0.000	0.000	0.000	0.000
135	A	134	ALA	0	0.018	-0.001	19.568	0.028	0.028	0.000	0.000	0.000	0.000
136	A	135	VAL	0	-0.002	-0.005	16.997	-0.028	-0.028	0.000	0.000	0.000	0.000
137	A	136	LEU	0	-0.054	-0.033	20.265	0.042	0.042	0.000	0.000	0.000	0.000
138	A	137	GLY	0	-0.013	0.001	21.544	0.009	0.009	0.000	0.000	0.000	0.000

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