FMO DATABASE

FMODB ID: 16NMZ

Calculation Name: 2P4V-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2P4V

Chain ID: A

ChEMBL ID:

UniProt ID: P30128

Base Structure: X-ray

Registration Date: 2023-09-27

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	156
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1439995.314905
FMO2-HF: Nuclear repulsion	1376125.166902
FMO2-HF: Total energy	-63870.148003
FMO2-MP2: Total energy	-64057.711776

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:MET)

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

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.
-10.752	-6.167	0.597	-2.282	-2.898	-0.015

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.037 / q_NPA : 0.027

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	THR	0	-0.003	-0.023	3.876	-0.399	1.421	0.018	-0.665	-1.173	0.001
4	A	4	PRO	0	0.015	0.009	5.356	-0.273	-0.214	-0.001	-0.001	-0.056	0.000
5	A	5	LEU	0	-0.042	-0.002	8.730	-0.109	-0.109	0.000	0.000	0.000	0.000
6	A	6	VAL	0	0.018	-0.001	10.771	-0.158	-0.158	0.000	0.000	0.000	0.000
7	A	7	THR	0	0.069	0.044	13.561	0.034	0.034	0.000	0.000	0.000	0.000
8	A	8	ARG	1	0.851	0.910	16.977	-0.046	-0.046	0.000	0.000	0.000	0.000
9	A	9	GLU	-1	-0.761	-0.889	20.174	-0.062	-0.062	0.000	0.000	0.000	0.000
10	A	10	GLY	0	0.046	0.026	17.235	-0.014	-0.014	0.000	0.000	0.000	0.000
11	A	11	TYR	0	-0.017	-0.038	17.126	0.020	0.020	0.000	0.000	0.000	0.000
12	A	12	GLU	-1	-0.882	-0.953	18.988	0.078	0.078	0.000	0.000	0.000	0.000
13	A	13	LYN	0	-0.003	0.004	18.473	0.019	0.019	0.000	0.000	0.000	0.000
14	A	14	LEU	0	0.018	0.021	14.608	0.019	0.019	0.000	0.000	0.000	0.000
15	A	15	LYS	1	0.895	0.917	18.790	-0.368	-0.368	0.000	0.000	0.000	0.000
16	A	16	GLN	0	-0.039	-0.003	22.322	-0.011	-0.011	0.000	0.000	0.000	0.000
17	A	17	GLU	-1	-0.765	-0.861	18.411	0.245	0.245	0.000	0.000	0.000	0.000
18	A	18	LEU	0	0.019	0.013	19.633	0.000	0.000	0.000	0.000	0.000	0.000
19	A	19	ASN	0	-0.058	-0.041	21.819	-0.015	-0.015	0.000	0.000	0.000	0.000
20	A	20	TYR	0	0.029	0.011	23.737	-0.003	-0.003	0.000	0.000	0.000	0.000
21	A	21	LEU	0	-0.025	-0.021	19.151	-0.004	-0.004	0.000	0.000	0.000	0.000
22	A	22	TRP	0	-0.019	-0.019	23.848	-0.005	-0.005	0.000	0.000	0.000	0.000
23	A	23	ARG	1	0.841	0.913	25.929	-0.246	-0.246	0.000	0.000	0.000	0.000
24	A	24	GLU	-1	-0.888	-0.931	28.171	0.110	0.110	0.000	0.000	0.000	0.000
25	A	25	GLU	-1	-0.755	-0.849	24.370	0.140	0.140	0.000	0.000	0.000	0.000
26	A	26	ARG	1	0.801	0.861	24.861	-0.299	-0.299	0.000	0.000	0.000	0.000
27	A	27	PRO	0	-0.021	0.007	27.605	-0.006	-0.006	0.000	0.000	0.000	0.000
28	A	28	GLU	-1	-0.897	-0.932	30.342	0.093	0.093	0.000	0.000	0.000	0.000
29	A	29	VAL	0	0.004	-0.004	26.228	-0.006	-0.006	0.000	0.000	0.000	0.000
30	A	30	THR	0	-0.044	-0.049	29.435	0.005	0.005	0.000	0.000	0.000	0.000
31	A	31	LYS	1	0.968	0.996	31.081	-0.145	-0.145	0.000	0.000	0.000	0.000
32	A	32	LYS	1	0.854	0.927	31.525	-0.086	-0.086	0.000	0.000	0.000	0.000
33	A	33	VAL	0	-0.040	-0.026	29.158	-0.005	-0.005	0.000	0.000	0.000	0.000
34	A	34	THR	0	-0.046	-0.031	32.503	-0.001	-0.001	0.000	0.000	0.000	0.000
35	A	35	TRP	0	0.030	0.011	35.765	-0.003	-0.003	0.000	0.000	0.000	0.000
36	A	36	ALA	0	0.001	-0.002	34.452	-0.005	-0.005	0.000	0.000	0.000	0.000
37	A	37	ALA	0	-0.039	-0.025	35.464	-0.004	-0.004	0.000	0.000	0.000	0.000
38	A	38	SER	0	0.004	0.006	37.193	-0.001	-0.001	0.000	0.000	0.000	0.000
39	A	39	LEU	0	-0.017	0.007	38.937	-0.005	-0.005	0.000	0.000	0.000	0.000
40	A	40	GLY	0	0.047	0.032	40.320	-0.006	-0.006	0.000	0.000	0.000	0.000
41	A	41	ASH	0	-0.087	-0.076	39.576	0.010	0.010	0.000	0.000	0.000	0.000
42	A	42	ARG	1	0.876	0.906	34.509	-0.110	-0.110	0.000	0.000	0.000	0.000
43	A	43	SER	0	-0.010	-0.003	33.740	0.007	0.007	0.000	0.000	0.000	0.000
44	A	44	GLU	-1	-0.799	-0.859	34.114	0.052	0.052	0.000	0.000	0.000	0.000
45	A	45	ASN	0	0.023	0.030	35.539	-0.007	-0.007	0.000	0.000	0.000	0.000
46	A	46	ALA	0	0.061	0.008	31.823	0.011	0.011	0.000	0.000	0.000	0.000
47	A	47	ASP	-1	-0.776	-0.870	30.895	0.085	0.085	0.000	0.000	0.000	0.000
48	A	48	TYR	0	0.020	0.020	31.230	0.021	0.021	0.000	0.000	0.000	0.000
49	A	49	GLN	0	-0.053	-0.021	28.793	0.018	0.018	0.000	0.000	0.000	0.000
50	A	50	TYR	0	0.039	0.026	24.348	0.022	0.022	0.000	0.000	0.000	0.000
51	A	51	ASN	0	-0.009	-0.021	26.115	0.018	0.018	0.000	0.000	0.000	0.000
52	A	52	LYS	1	0.934	0.967	26.754	-0.165	-0.165	0.000	0.000	0.000	0.000
53	A	53	LYS	1	0.786	0.877	19.385	-0.106	-0.106	0.000	0.000	0.000	0.000
54	A	54	ARG	1	0.891	0.920	22.063	-0.090	-0.090	0.000	0.000	0.000	0.000
55	A	55	LEU	0	0.022	0.009	22.449	0.024	0.024	0.000	0.000	0.000	0.000
56	A	56	ARG	1	0.935	0.960	20.519	-0.225	-0.225	0.000	0.000	0.000	0.000
57	A	57	GLU	-1	-0.858	-0.915	17.647	0.252	0.252	0.000	0.000	0.000	0.000
58	A	58	ILE	0	0.022	0.027	17.911	0.050	0.050	0.000	0.000	0.000	0.000
59	A	59	ASP	-1	-0.737	-0.835	19.575	0.407	0.407	0.000	0.000	0.000	0.000
60	A	60	ARG	1	0.851	0.925	15.063	-0.446	-0.446	0.000	0.000	0.000	0.000
61	A	61	ARG	1	0.759	0.822	13.391	-0.206	-0.206	0.000	0.000	0.000	0.000
62	A	62	VAL	0	0.060	0.034	15.964	0.054	0.054	0.000	0.000	0.000	0.000
63	A	63	ARG	1	0.930	0.977	15.094	-0.875	-0.875	0.000	0.000	0.000	0.000
64	A	64	TYR	0	-0.111	-0.079	8.212	0.310	0.310	0.000	0.000	0.000	0.000
65	A	65	LEU	0	0.051	0.013	13.714	0.126	0.126	0.000	0.000	0.000	0.000
66	A	66	THR	0	-0.039	-0.023	15.893	-0.023	-0.023	0.000	0.000	0.000	0.000
67	A	67	LYS	1	0.981	1.000	9.895	-2.391	-2.391	0.000	0.000	0.000	0.000
68	A	68	CYS	0	-0.044	-0.021	10.768	0.183	0.183	0.000	0.000	0.000	0.000
69	A	69	MET	0	-0.010	0.026	13.887	-0.112	-0.112	0.000	0.000	0.000	0.000
70	A	70	GLU	-1	-0.913	-0.941	16.967	0.794	0.794	0.000	0.000	0.000	0.000
71	A	71	ASN	0	-0.082	-0.045	12.535	0.116	0.116	0.000	0.000	0.000	0.000
72	A	72	LEU	0	-0.042	-0.006	11.095	0.115	0.115	0.000	0.000	0.000	0.000
73	A	73	LYS	1	0.914	0.961	12.764	-0.369	-0.369	0.000	0.000	0.000	0.000
74	A	74	ILE	0	0.023	0.003	14.045	-0.091	-0.091	0.000	0.000	0.000	0.000
75	A	75	VAL	0	-0.074	-0.041	13.531	0.016	0.016	0.000	0.000	0.000	0.000
76	A	76	ASP	-1	-0.832	-0.899	16.726	0.020	0.020	0.000	0.000	0.000	0.000
77	A	77	TYR	0	-0.055	-0.027	19.705	0.006	0.006	0.000	0.000	0.000	0.000
78	A	78	SER	0	0.019	0.015	21.448	-0.011	-0.011	0.000	0.000	0.000	0.000
79	A	79	PRO	0	0.076	0.017	23.993	-0.003	-0.003	0.000	0.000	0.000	0.000
80	A	80	GLN	0	-0.052	0.004	25.896	-0.007	-0.007	0.000	0.000	0.000	0.000
81	A	81	GLN	0	-0.038	-0.030	22.658	0.015	0.015	0.000	0.000	0.000	0.000
82	A	82	GLU	-1	-0.806	-0.896	22.445	-0.241	-0.241	0.000	0.000	0.000	0.000
83	A	83	GLY	0	-0.009	0.000	24.190	0.006	0.006	0.000	0.000	0.000	0.000
84	A	84	LYS	1	0.770	0.859	19.237	0.326	0.326	0.000	0.000	0.000	0.000
85	A	85	VAL	0	0.031	0.020	15.682	0.018	0.018	0.000	0.000	0.000	0.000
86	A	86	PHE	0	-0.076	-0.020	14.622	-0.021	-0.021	0.000	0.000	0.000	0.000
87	A	87	PHE	0	-0.020	-0.028	10.930	-0.095	-0.095	0.000	0.000	0.000	0.000
88	A	88	GLY	0	0.024	0.018	14.964	0.067	0.067	0.000	0.000	0.000	0.000
89	A	89	ALA	0	0.023	0.028	17.394	0.052	0.052	0.000	0.000	0.000	0.000
90	A	90	TRP	0	-0.029	-0.022	18.394	-0.086	-0.086	0.000	0.000	0.000	0.000
91	A	91	VAL	0	-0.005	-0.005	18.144	0.008	0.008	0.000	0.000	0.000	0.000
92	A	92	GLU	-1	-0.927	-0.958	20.716	-0.334	-0.334	0.000	0.000	0.000	0.000
93	A	93	ILE	0	-0.076	-0.035	19.315	-0.015	-0.015	0.000	0.000	0.000	0.000
94	A	94	GLU	-1	-0.833	-0.917	22.614	-0.315	-0.315	0.000	0.000	0.000	0.000
95	A	95	ASN	0	-0.039	-0.043	24.625	-0.016	-0.016	0.000	0.000	0.000	0.000
96	A	96	ASP	-1	-0.879	-0.938	26.189	-0.351	-0.351	0.000	0.000	0.000	0.000
97	A	97	ASP	-1	-0.920	-0.940	28.949	-0.329	-0.329	0.000	0.000	0.000	0.000
98	A	98	GLY	0	-0.017	-0.002	29.569	0.020	0.020	0.000	0.000	0.000	0.000
99	A	99	VAL	0	-0.090	-0.044	24.109	0.002	0.002	0.000	0.000	0.000	0.000
100	A	100	THR	0	0.030	0.024	25.139	-0.031	-0.031	0.000	0.000	0.000	0.000
101	A	101	HIS	0	-0.040	-0.026	20.004	-0.011	-0.011	0.000	0.000	0.000	0.000
102	A	102	ARG	1	1.017	1.018	21.582	0.305	0.305	0.000	0.000	0.000	0.000
103	A	103	PHE	0	-0.033	-0.031	15.949	-0.045	-0.045	0.000	0.000	0.000	0.000
104	A	104	ARG	1	0.802	0.878	17.236	0.297	0.297	0.000	0.000	0.000	0.000
105	A	105	ILE	0	-0.030	0.001	11.340	-0.080	-0.080	0.000	0.000	0.000	0.000
106	A	106	VAL	0	0.018	0.011	12.412	0.132	0.132	0.000	0.000	0.000	0.000
107	A	107	GLY	0	0.032	0.009	9.329	-0.288	-0.288	0.000	0.000	0.000	0.000
108	A	108	TYR	0	-0.023	-0.031	6.511	-0.309	-0.309	0.000	0.000	0.000	0.000
109	A	109	ASP	-1	-0.856	-0.910	8.881	1.615	1.615	0.000	0.000	0.000	0.000
110	A	110	GLU	-1	-0.807	-0.886	10.602	0.322	0.322	0.000	0.000	0.000	0.000
111	A	111	ILE	0	-0.042	0.021	10.989	-0.059	-0.059	0.000	0.000	0.000	0.000
112	A	112	PHE	0	0.037	-0.016	14.004	0.000	0.000	0.000	0.000	0.000	0.000
113	A	113	GLY	0	0.016	0.014	16.777	0.008	0.008	0.000	0.000	0.000	0.000
114	A	114	ARG	1	0.884	0.954	19.898	0.057	0.057	0.000	0.000	0.000	0.000
115	A	115	LYS	1	0.804	0.906	19.817	0.074	0.074	0.000	0.000	0.000	0.000
116	A	116	ASP	-1	-0.752	-0.847	16.501	-0.300	-0.300	0.000	0.000	0.000	0.000
117	A	117	TYR	0	-0.042	-0.050	15.474	0.028	0.028	0.000	0.000	0.000	0.000
118	A	118	ILE	0	0.030	0.023	11.674	-0.098	-0.098	0.000	0.000	0.000	0.000
119	A	119	SER	0	0.019	0.023	7.681	0.075	0.075	0.000	0.000	0.000	0.000
120	A	120	ILE	0	0.021	-0.008	6.576	-0.301	-0.301	0.000	0.000	0.000	0.000
121	A	121	ASP	-1	-0.832	-0.888	2.956	-10.296	-7.775	0.582	-1.608	-1.495	-0.016
122	A	122	SER	0	-0.037	-0.007	4.828	-0.531	-0.425	-0.001	-0.003	-0.101	0.000
123	A	123	PRO	0	0.045	0.000	7.600	0.142	0.142	0.000	0.000	0.000	0.000
124	A	124	MET	0	0.050	0.048	9.683	0.140	0.140	0.000	0.000	0.000	0.000
125	A	125	ALA	0	0.025	0.016	9.372	0.145	0.145	0.000	0.000	0.000	0.000
126	A	126	ARG	1	0.821	0.892	4.061	3.653	3.732	-0.001	-0.005	-0.073	0.000
127	A	127	ALA	0	0.013	0.022	10.114	0.159	0.159	0.000	0.000	0.000	0.000
128	A	128	LEU	0	0.047	0.013	13.594	0.135	0.135	0.000	0.000	0.000	0.000
129	A	129	LEU	0	-0.043	-0.007	10.049	0.106	0.106	0.000	0.000	0.000	0.000
130	A	130	LYS	1	0.902	0.930	13.740	0.577	0.577	0.000	0.000	0.000	0.000
131	A	131	LYS	1	0.895	0.969	16.717	0.775	0.775	0.000	0.000	0.000	0.000
132	A	132	GLU	-1	-0.752	-0.866	19.554	-0.324	-0.324	0.000	0.000	0.000	0.000
133	A	133	VAL	0	-0.001	-0.013	23.201	-0.026	-0.026	0.000	0.000	0.000	0.000
134	A	134	GLY	0	0.032	0.024	24.988	0.021	0.021	0.000	0.000	0.000	0.000
135	A	135	ASP	-1	-0.909	-0.940	21.405	-0.497	-0.497	0.000	0.000	0.000	0.000
136	A	136	LEU	0	0.024	0.006	23.100	-0.011	-0.011	0.000	0.000	0.000	0.000
137	A	137	ALA	0	-0.050	-0.017	17.666	-0.040	-0.040	0.000	0.000	0.000	0.000
138	A	138	VAL	0	0.007	0.000	17.643	0.036	0.036	0.000	0.000	0.000	0.000
139	A	139	VAL	0	-0.039	-0.026	13.313	-0.128	-0.128	0.000	0.000	0.000	0.000
140	A	140	ASN	0	-0.028	-0.007	14.197	0.029	0.029	0.000	0.000	0.000	0.000
141	A	141	THR	0	0.005	0.000	13.292	-0.186	-0.186	0.000	0.000	0.000	0.000
142	A	142	PRO	0	-0.007	-0.023	13.390	0.094	0.094	0.000	0.000	0.000	0.000
143	A	143	ALA	0	-0.005	0.005	16.485	0.075	0.075	0.000	0.000	0.000	0.000
144	A	144	GLY	0	0.004	0.007	18.228	0.055	0.055	0.000	0.000	0.000	0.000
145	A	145	GLU	-1	-0.969	-0.972	17.645	-0.645	-0.645	0.000	0.000	0.000	0.000
146	A	146	ALA	0	0.003	-0.006	18.679	0.037	0.037	0.000	0.000	0.000	0.000
147	A	147	SER	0	-0.005	-0.011	19.567	-0.046	-0.046	0.000	0.000	0.000	0.000
148	A	148	TRP	0	-0.026	-0.015	17.946	-0.028	-0.028	0.000	0.000	0.000	0.000
149	A	149	TYR	0	0.034	0.024	21.815	-0.020	-0.020	0.000	0.000	0.000	0.000
150	A	150	VAL	0	-0.060	-0.038	20.476	-0.021	-0.021	0.000	0.000	0.000	0.000
151	A	151	ASN	0	-0.067	-0.022	23.063	0.036	0.036	0.000	0.000	0.000	0.000
152	A	152	ALA	0	0.060	0.025	24.875	0.021	0.021	0.000	0.000	0.000	0.000
153	A	153	ILE	0	-0.053	-0.053	21.147	-0.043	-0.043	0.000	0.000	0.000	0.000
154	A	154	GLU	-1	-0.925	-0.945	23.073	-0.209	-0.209	0.000	0.000	0.000	0.000
155	A	155	TYR	0	-0.072	-0.061	19.111	-0.022	-0.022	0.000	0.000	0.000	0.000
156	A	156	VAL	0	-0.026	-0.013	23.668	0.025	0.025	0.000	0.000	0.000	0.000

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