FMO DATABASE

FMODB ID: JL339

Calculation Name: 2V4X-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2V4X

Chain ID: A

ChEMBL ID:

UniProt ID: P31622

Base Structure: X-ray

Registration Date: 2023-06-21

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	131
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1182517.097132
FMO2-HF: Nuclear repulsion	1130181.80247
FMO2-HF: Total energy	-52335.294662
FMO2-MP2: Total energy	-52487.465595

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:PRO)

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

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.
-21.139	-10.137	18.821	-10.398	-19.422	-0.064

Interaction energy analysis for fragmet #1(A:1:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.032 / q_NPA : -0.031

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	3	PHE	0	-0.031	-0.009	2.349	-3.105	0.371	2.480	-2.026	-3.930	-0.011
4	A	4	GLU	-1	-0.825	-0.903	5.576	-0.288	-0.288	0.000	0.000	0.000	0.000
5	A	5	ASN	0	0.027	0.019	9.364	0.133	0.133	0.000	0.000	0.000	0.000
6	A	6	ASN	0	-0.007	-0.015	12.432	0.016	0.016	0.000	0.000	0.000	0.000
7	A	7	ASN	0	-0.050	-0.011	15.228	0.042	0.042	0.000	0.000	0.000	0.000
8	A	8	GLN	0	-0.021	-0.011	12.641	-0.026	-0.026	0.000	0.000	0.000	0.000
9	A	9	ARG	1	0.778	0.869	8.889	0.672	0.672	0.000	0.000	0.000	0.000
10	A	10	TYR	0	-0.029	-0.020	7.672	0.255	0.255	0.000	0.000	0.000	0.000
11	A	11	TYR	0	-0.035	-0.058	2.662	-5.658	-4.056	1.259	-0.885	-1.975	-0.002
12	A	12	GLU	-1	-0.869	-0.903	3.032	-0.761	-0.042	0.007	-0.221	-0.505	0.000
13	A	13	SER	0	0.000	-0.030	1.976	-9.575	-10.147	6.939	-3.311	-3.055	-0.039
14	A	14	LEU	0	-0.030	-0.008	2.264	-2.623	-0.733	1.858	-1.206	-2.543	0.004
15	A	15	PRO	0	0.014	-0.001	2.744	-0.388	-0.636	0.181	0.710	-0.643	0.000
16	A	16	PHE	0	0.037	0.018	5.729	0.238	0.238	0.000	0.000	0.000	0.000
17	A	17	LYS	1	0.825	0.889	8.701	-0.200	-0.200	0.000	0.000	0.000	0.000
18	A	18	GLN	0	0.083	0.046	5.759	-0.170	-0.170	0.000	0.000	0.000	0.000
19	A	19	LEU	0	0.021	0.019	7.374	0.013	0.013	0.000	0.000	0.000	0.000
20	A	20	LYS	1	0.939	0.972	9.356	-0.290	-0.290	0.000	0.000	0.000	0.000
21	A	21	GLU	-1	-0.811	-0.896	12.641	0.332	0.332	0.000	0.000	0.000	0.000
22	A	22	LEU	0	0.056	0.032	10.235	-0.044	-0.044	0.000	0.000	0.000	0.000
23	A	23	LYS	1	0.921	0.955	13.269	-0.531	-0.531	0.000	0.000	0.000	0.000
24	A	24	ILE	0	-0.038	-0.016	15.096	-0.055	-0.055	0.000	0.000	0.000	0.000
25	A	25	ALA	0	0.034	0.013	16.228	-0.032	-0.032	0.000	0.000	0.000	0.000
26	A	26	CYS	0	-0.034	-0.016	15.517	-0.010	-0.010	0.000	0.000	0.000	0.000
27	A	27	SER	0	-0.094	-0.038	18.484	-0.043	-0.043	0.000	0.000	0.000	0.000
28	A	28	GLN	0	-0.048	-0.028	21.115	-0.047	-0.047	0.000	0.000	0.000	0.000
29	A	29	TYR	0	-0.044	-0.014	19.789	-0.029	-0.029	0.000	0.000	0.000	0.000
30	A	30	GLY	0	0.075	0.053	21.375	-0.021	-0.021	0.000	0.000	0.000	0.000
31	A	31	PRO	0	-0.004	-0.009	18.212	0.028	0.028	0.000	0.000	0.000	0.000
32	A	32	THR	0	0.018	-0.001	17.731	0.053	0.053	0.000	0.000	0.000	0.000
33	A	33	ALA	0	0.021	0.035	20.154	-0.028	-0.028	0.000	0.000	0.000	0.000
34	A	34	PRO	0	0.033	-0.004	19.651	0.038	0.038	0.000	0.000	0.000	0.000
35	A	35	PHE	0	0.020	0.015	16.782	0.025	0.025	0.000	0.000	0.000	0.000
36	A	36	THR	0	0.040	-0.003	15.767	0.032	0.032	0.000	0.000	0.000	0.000
37	A	37	ILE	0	0.006	0.013	14.834	0.092	0.092	0.000	0.000	0.000	0.000
38	A	38	ALA	0	0.006	0.007	14.840	0.055	0.055	0.000	0.000	0.000	0.000
39	A	39	MET	0	-0.032	-0.011	11.464	0.026	0.026	0.000	0.000	0.000	0.000
40	A	40	ILE	0	-0.014	0.008	10.590	0.185	0.185	0.000	0.000	0.000	0.000
41	A	41	GLU	-1	-0.764	-0.885	10.412	0.769	0.769	0.000	0.000	0.000	0.000
42	A	42	ASN	0	-0.039	-0.008	9.135	-0.074	-0.074	0.000	0.000	0.000	0.000
43	A	43	LEU	0	-0.011	0.008	4.578	-0.098	-0.004	-0.001	-0.005	-0.087	0.000
44	A	44	GLY	0	0.009	-0.014	6.092	0.400	0.400	0.000	0.000	0.000	0.000
45	A	45	THR	0	-0.066	-0.025	8.329	-0.100	-0.100	0.000	0.000	0.000	0.000
46	A	46	GLN	0	-0.038	-0.017	3.185	-1.166	-0.576	0.078	-0.127	-0.541	0.000
47	A	47	ALA	0	0.034	0.026	3.206	-0.377	0.499	0.084	-0.278	-0.682	-0.001
48	A	48	LEU	0	-0.011	-0.009	2.212	-1.882	-0.086	4.025	-2.431	-3.390	-0.014
49	A	49	PRO	0	0.016	0.027	2.399	-1.789	-2.093	1.537	-0.177	-1.056	0.000
50	A	50	PRO	0	-0.004	-0.008	5.205	0.641	0.699	-0.001	-0.001	-0.056	0.000
51	A	51	ASN	0	-0.023	-0.035	7.964	0.022	0.022	0.000	0.000	0.000	0.000
52	A	52	ASP	-1	-0.753	-0.846	3.370	8.741	9.766	0.375	-0.440	-0.959	-0.001
53	A	53	TRP	0	0.054	0.027	6.274	-0.533	-0.533	0.000	0.000	0.000	0.000
54	A	54	LYS	1	0.765	0.885	8.621	-1.174	-1.174	0.000	0.000	0.000	0.000
55	A	55	GLN	0	-0.035	-0.010	7.379	-0.363	-0.363	0.000	0.000	0.000	0.000
56	A	56	THR	0	0.013	-0.022	7.400	-0.280	-0.280	0.000	0.000	0.000	0.000
57	A	57	ALA	0	0.015	0.008	9.871	-0.259	-0.259	0.000	0.000	0.000	0.000
58	A	58	ARG	1	0.903	0.949	13.256	-0.844	-0.844	0.000	0.000	0.000	0.000
59	A	59	ALA	0	-0.011	0.009	11.467	-0.118	-0.118	0.000	0.000	0.000	0.000
60	A	60	CYS	0	-0.101	-0.054	11.950	-0.112	-0.112	0.000	0.000	0.000	0.000
61	A	61	LEU	0	0.012	0.023	14.952	-0.076	-0.076	0.000	0.000	0.000	0.000
62	A	62	SER	0	0.000	-0.030	17.791	-0.028	-0.028	0.000	0.000	0.000	0.000
63	A	63	GLY	0	0.026	-0.003	20.554	0.031	0.031	0.000	0.000	0.000	0.000
64	A	64	GLY	0	0.013	0.011	22.225	0.001	0.001	0.000	0.000	0.000	0.000
65	A	65	ASP	-1	-0.802	-0.885	20.021	0.386	0.386	0.000	0.000	0.000	0.000
66	A	66	TYR	0	0.000	0.001	14.823	0.001	0.001	0.000	0.000	0.000	0.000
67	A	67	LEU	0	-0.005	-0.003	18.807	0.032	0.032	0.000	0.000	0.000	0.000
68	A	68	LEU	0	-0.004	0.002	21.522	-0.002	-0.002	0.000	0.000	0.000	0.000
69	A	69	TRP	0	-0.005	-0.008	12.117	0.016	0.016	0.000	0.000	0.000	0.000
70	A	70	LYS	1	0.819	0.900	15.612	-0.512	-0.512	0.000	0.000	0.000	0.000
71	A	71	SER	0	-0.023	-0.008	17.940	-0.010	-0.010	0.000	0.000	0.000	0.000
72	A	72	GLU	-1	-0.733	-0.853	19.958	0.360	0.360	0.000	0.000	0.000	0.000
73	A	73	PHE	0	0.024	-0.001	11.441	0.016	0.016	0.000	0.000	0.000	0.000
74	A	74	PHE	0	-0.006	-0.011	15.262	0.006	0.006	0.000	0.000	0.000	0.000
75	A	75	GLU	-1	-0.839	-0.908	18.445	0.275	0.275	0.000	0.000	0.000	0.000
76	A	76	GLN	0	-0.051	-0.022	17.590	-0.037	-0.037	0.000	0.000	0.000	0.000
77	A	77	CYS	0	-0.048	-0.021	14.917	0.002	0.002	0.000	0.000	0.000	0.000
78	A	78	ALA	0	-0.009	-0.008	17.343	-0.038	-0.038	0.000	0.000	0.000	0.000
79	A	79	ARG	1	0.841	0.912	18.358	-0.380	-0.380	0.000	0.000	0.000	0.000
80	A	80	ILE	0	-0.033	-0.015	16.024	-0.027	-0.027	0.000	0.000	0.000	0.000
81	A	81	ALA	0	0.002	0.008	19.128	-0.031	-0.031	0.000	0.000	0.000	0.000
82	A	82	ASP	-1	-0.814	-0.894	20.133	0.108	0.108	0.000	0.000	0.000	0.000
83	A	83	VAL	0	0.014	0.013	21.741	-0.020	-0.020	0.000	0.000	0.000	0.000
84	A	84	ASN	0	-0.001	-0.019	16.745	-0.029	-0.029	0.000	0.000	0.000	0.000
85	A	85	ARG	1	0.867	0.934	21.281	-0.130	-0.130	0.000	0.000	0.000	0.000
86	A	86	GLN	0	-0.078	-0.054	24.139	-0.023	-0.023	0.000	0.000	0.000	0.000
87	A	87	GLN	0	-0.038	-0.015	22.512	-0.004	-0.004	0.000	0.000	0.000	0.000
88	A	88	GLY	0	0.001	0.017	24.652	-0.012	-0.012	0.000	0.000	0.000	0.000
89	A	89	ILE	0	-0.043	-0.009	18.153	-0.019	-0.019	0.000	0.000	0.000	0.000
90	A	90	GLN	0	0.019	0.009	18.581	0.014	0.014	0.000	0.000	0.000	0.000
91	A	91	THR	0	-0.035	-0.050	14.081	-0.011	-0.011	0.000	0.000	0.000	0.000
92	A	92	SER	0	0.023	0.006	16.787	0.036	0.036	0.000	0.000	0.000	0.000
93	A	93	TYR	0	0.046	0.005	16.558	0.033	0.033	0.000	0.000	0.000	0.000
94	A	94	GLU	-1	-0.881	-0.956	16.481	0.224	0.224	0.000	0.000	0.000	0.000
95	A	95	MET	0	-0.020	0.026	13.366	0.044	0.044	0.000	0.000	0.000	0.000
96	A	96	LEU	0	-0.012	-0.005	12.015	0.108	0.108	0.000	0.000	0.000	0.000
97	A	97	ILE	0	0.034	0.015	12.123	0.148	0.148	0.000	0.000	0.000	0.000
98	A	98	GLY	0	0.008	0.012	11.480	0.108	0.108	0.000	0.000	0.000	0.000
99	A	99	GLU	-1	-0.797	-0.901	12.454	0.537	0.537	0.000	0.000	0.000	0.000
100	A	100	GLY	0	0.063	0.035	15.955	-0.034	-0.034	0.000	0.000	0.000	0.000
101	A	101	PRO	0	-0.022	-0.018	18.122	-0.005	-0.005	0.000	0.000	0.000	0.000
102	A	102	TYR	0	0.003	-0.001	13.416	-0.038	-0.038	0.000	0.000	0.000	0.000
103	A	103	GLN	0	-0.028	0.000	12.915	0.046	0.046	0.000	0.000	0.000	0.000
104	A	104	ALA	0	0.032	0.031	12.889	0.100	0.100	0.000	0.000	0.000	0.000
105	A	105	THR	0	0.059	0.028	6.188	0.029	0.029	0.000	0.000	0.000	0.000
106	A	106	ASP	-1	-0.848	-0.921	8.642	-0.566	-0.566	0.000	0.000	0.000	0.000
107	A	107	THR	0	-0.086	-0.059	10.629	-0.054	-0.054	0.000	0.000	0.000	0.000
108	A	108	GLN	0	-0.027	-0.034	8.044	0.346	0.346	0.000	0.000	0.000	0.000
109	A	109	LEU	0	0.015	0.033	6.144	0.050	0.050	0.000	0.000	0.000	0.000
110	A	110	ASN	0	0.001	-0.002	8.368	-0.168	-0.168	0.000	0.000	0.000	0.000
111	A	111	PHE	0	0.032	0.032	9.713	0.082	0.082	0.000	0.000	0.000	0.000
112	A	112	LEU	0	0.050	0.023	11.913	-0.107	-0.107	0.000	0.000	0.000	0.000
113	A	113	PRO	0	0.038	0.009	10.322	0.071	0.071	0.000	0.000	0.000	0.000
114	A	114	GLY	0	0.011	0.008	10.178	0.076	0.076	0.000	0.000	0.000	0.000
115	A	115	ALA	0	0.025	0.018	10.958	0.092	0.092	0.000	0.000	0.000	0.000
116	A	116	TYR	0	0.002	-0.021	6.148	0.016	0.016	0.000	0.000	0.000	0.000
117	A	117	ALA	0	0.023	0.018	8.314	0.241	0.241	0.000	0.000	0.000	0.000
118	A	118	GLN	0	-0.013	-0.016	10.398	0.052	0.052	0.000	0.000	0.000	0.000
119	A	119	ILE	0	0.020	0.013	8.170	0.003	0.003	0.000	0.000	0.000	0.000
120	A	120	SER	0	-0.010	0.003	8.214	0.027	0.027	0.000	0.000	0.000	0.000
121	A	121	ASN	0	-0.023	-0.016	10.058	-0.081	-0.081	0.000	0.000	0.000	0.000
122	A	122	ALA	0	0.039	0.010	13.792	-0.028	-0.028	0.000	0.000	0.000	0.000
123	A	123	ALA	0	0.006	0.004	10.986	-0.055	-0.055	0.000	0.000	0.000	0.000
124	A	124	ARG	1	0.831	0.917	10.317	-0.905	-0.905	0.000	0.000	0.000	0.000
125	A	125	GLN	0	-0.029	-0.022	13.924	-0.060	-0.060	0.000	0.000	0.000	0.000
126	A	126	ALA	0	0.026	0.025	16.161	-0.066	-0.066	0.000	0.000	0.000	0.000
127	A	127	TRP	0	-0.020	-0.027	11.920	0.000	0.000	0.000	0.000	0.000	0.000
128	A	128	LYS	1	0.797	0.879	15.880	-0.558	-0.558	0.000	0.000	0.000	0.000
129	A	129	ARG	1	0.808	0.917	19.017	-0.406	-0.406	0.000	0.000	0.000	0.000
130	A	130	LEU	0	-0.032	0.010	17.710	-0.023	-0.023	0.000	0.000	0.000	0.000
131	A	131	PRO	0	-0.025	-0.006	21.822	-0.028	-0.028	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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