FMO DATABASE

FMODB ID: LN399

Calculation Name: 2NML-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2NML

Chain ID: A

ChEMBL ID:

UniProt ID: P84090

Base Structure: X-ray

Registration Date: 2023-09-23

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	100
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-783022.15757
FMO2-HF: Nuclear repulsion	740531.466571
FMO2-HF: Total energy	-42490.690998
FMO2-MP2: Total energy	-42611.832614

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:2:SER)

Summations of interaction energy for fragment #1(A:2: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.
-26.076	-28.163	26.171	-12.727	-11.355	-0.069

Interaction energy analysis for fragmet #1(A:2:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.058 / q_NPA : -0.048

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	4	THR	0	-0.022	-0.033	3.817	-0.283	1.423	-0.006	-0.777	-0.923	0.005
4	A	5	ILE	0	-0.001	0.006	5.778	0.467	0.467	0.000	0.000	0.000	0.000
5	A	6	LEU	0	-0.013	-0.012	9.401	-0.006	-0.006	0.000	0.000	0.000	0.000
6	A	7	LEU	0	-0.016	-0.007	12.034	0.124	0.124	0.000	0.000	0.000	0.000
7	A	8	VAL	0	0.048	0.005	15.278	0.011	0.011	0.000	0.000	0.000	0.000
8	A	9	GLN	0	-0.020	-0.024	18.398	0.029	0.029	0.000	0.000	0.000	0.000
9	A	10	PRO	0	0.028	0.016	22.001	0.015	0.015	0.000	0.000	0.000	0.000
10	A	11	THR	0	0.075	0.034	24.289	0.017	0.017	0.000	0.000	0.000	0.000
11	A	12	LYS	1	1.005	0.989	26.630	0.182	0.182	0.000	0.000	0.000	0.000
12	A	13	ARG	1	0.816	0.893	28.924	0.190	0.190	0.000	0.000	0.000	0.000
13	A	14	PRO	0	0.049	0.027	26.531	-0.018	-0.018	0.000	0.000	0.000	0.000
14	A	15	GLU	-1	-0.803	-0.883	25.819	-0.219	-0.219	0.000	0.000	0.000	0.000
15	A	16	GLY	0	-0.012	0.004	25.659	-0.003	-0.003	0.000	0.000	0.000	0.000
16	A	17	ARG	1	0.851	0.925	21.409	0.269	0.269	0.000	0.000	0.000	0.000
17	A	18	THR	0	-0.005	-0.001	19.226	0.011	0.011	0.000	0.000	0.000	0.000
18	A	19	TYR	0	-0.014	-0.009	14.011	0.000	0.000	0.000	0.000	0.000	0.000
19	A	20	ALA	0	0.006	0.014	13.729	0.074	0.074	0.000	0.000	0.000	0.000
20	A	21	ASP	-1	-0.883	-0.926	9.214	-1.114	-1.114	0.000	0.000	0.000	0.000
21	A	22	TYR	0	0.022	0.011	6.861	0.343	0.343	0.000	0.000	0.000	0.000
22	A	23	GLU	-1	-0.879	-0.933	4.433	-2.147	-1.889	-0.001	-0.098	-0.159	0.000
23	A	24	SER	0	-0.069	-0.077	2.103	-9.601	-8.818	5.948	-3.664	-3.066	-0.031
24	A	25	VAL	0	0.044	0.010	2.978	2.495	2.157	0.048	0.832	-0.541	0.000
25	A	26	ASN	0	0.011	0.001	4.992	0.592	0.655	-0.001	-0.003	-0.059	0.000
26	A	27	GLU	-1	-0.747	-0.833	5.756	-2.227	-2.227	0.000	0.000	0.000	0.000
27	A	28	CYS	0	-0.047	-0.005	7.121	0.352	0.352	0.000	0.000	0.000	0.000
28	A	29	MET	0	-0.068	-0.035	8.865	0.353	0.353	0.000	0.000	0.000	0.000
29	A	30	GLU	-1	-0.825	-0.901	10.662	-0.478	-0.478	0.000	0.000	0.000	0.000
30	A	31	GLY	0	0.003	0.003	11.659	0.132	0.132	0.000	0.000	0.000	0.000
31	A	32	VAL	0	-0.021	-0.015	12.902	0.108	0.108	0.000	0.000	0.000	0.000
32	A	33	CYS	0	-0.030	-0.011	15.039	0.073	0.073	0.000	0.000	0.000	0.000
33	A	34	LYS	1	0.920	0.951	14.439	0.670	0.670	0.000	0.000	0.000	0.000
34	A	35	MET	0	-0.045	-0.002	17.577	0.046	0.046	0.000	0.000	0.000	0.000
35	A	36	TYR	0	0.002	0.003	19.420	0.049	0.049	0.000	0.000	0.000	0.000
36	A	37	GLU	-1	-0.823	-0.908	19.973	-0.322	-0.322	0.000	0.000	0.000	0.000
37	A	38	GLU	-1	-0.821	-0.881	22.065	-0.233	-0.233	0.000	0.000	0.000	0.000
38	A	39	HIS	0	-0.031	-0.019	23.798	0.026	0.026	0.000	0.000	0.000	0.000
39	A	40	LEU	0	0.020	0.003	25.000	0.028	0.028	0.000	0.000	0.000	0.000
40	A	41	LYS	1	0.850	0.933	26.590	0.197	0.197	0.000	0.000	0.000	0.000
41	A	42	ARG	1	0.794	0.861	25.824	0.279	0.279	0.000	0.000	0.000	0.000
42	A	43	MET	0	-0.027	-0.003	29.923	0.014	0.014	0.000	0.000	0.000	0.000
43	A	44	ASN	0	-0.063	-0.020	30.399	0.021	0.021	0.000	0.000	0.000	0.000
44	A	45	PRO	0	0.044	0.008	32.486	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	46	ASN	0	-0.028	-0.011	33.792	-0.002	-0.002	0.000	0.000	0.000	0.000
46	A	47	SER	0	0.007	0.002	32.267	0.011	0.011	0.000	0.000	0.000	0.000
47	A	48	PRO	0	-0.020	-0.010	31.017	-0.012	-0.012	0.000	0.000	0.000	0.000
48	A	49	SER	0	-0.018	-0.015	28.752	-0.004	-0.004	0.000	0.000	0.000	0.000
49	A	50	ILE	0	-0.012	0.018	26.323	0.009	0.009	0.000	0.000	0.000	0.000
50	A	51	THR	0	-0.025	-0.013	26.336	-0.010	-0.010	0.000	0.000	0.000	0.000
51	A	52	TYR	0	-0.045	-0.046	20.067	0.000	0.000	0.000	0.000	0.000	0.000
52	A	53	ASP	-1	-0.820	-0.871	25.223	-0.182	-0.182	0.000	0.000	0.000	0.000
53	A	54	ILE	0	0.003	-0.024	19.222	-0.015	-0.015	0.000	0.000	0.000	0.000
54	A	55	SER	0	-0.057	-0.054	22.910	-0.020	-0.020	0.000	0.000	0.000	0.000
55	A	56	GLN	0	0.093	0.047	25.492	-0.014	-0.014	0.000	0.000	0.000	0.000
56	A	57	LEU	0	-0.023	0.000	18.033	-0.014	-0.014	0.000	0.000	0.000	0.000
57	A	58	PHE	0	-0.035	-0.044	18.704	-0.032	-0.032	0.000	0.000	0.000	0.000
58	A	59	ASP	-1	-0.857	-0.919	22.485	-0.225	-0.225	0.000	0.000	0.000	0.000
59	A	60	PHE	0	-0.009	-0.005	20.506	-0.008	-0.008	0.000	0.000	0.000	0.000
60	A	61	ILE	0	-0.023	-0.023	17.791	-0.020	-0.020	0.000	0.000	0.000	0.000
61	A	62	ASP	-1	-0.832	-0.912	21.553	-0.323	-0.323	0.000	0.000	0.000	0.000
62	A	63	ASP	-1	-0.936	-0.959	24.034	-0.227	-0.227	0.000	0.000	0.000	0.000
63	A	64	LEU	0	-0.119	-0.031	20.092	0.002	0.002	0.000	0.000	0.000	0.000
64	A	65	ALA	0	-0.069	-0.032	23.740	0.005	0.005	0.000	0.000	0.000	0.000
65	A	66	ASP	-1	-0.924	-0.970	19.504	-0.461	-0.461	0.000	0.000	0.000	0.000
66	A	67	LEU	0	-0.031	-0.005	15.792	-0.015	-0.015	0.000	0.000	0.000	0.000
67	A	68	SER	0	-0.016	0.000	14.239	-0.003	-0.003	0.000	0.000	0.000	0.000
68	A	69	CYS	0	-0.042	-0.013	9.271	-0.107	-0.107	0.000	0.000	0.000	0.000
69	A	70	LEU	0	0.027	0.014	8.504	0.128	0.128	0.000	0.000	0.000	0.000
70	A	71	VAL	0	0.000	-0.004	2.563	-0.578	-0.172	0.561	-0.287	-0.680	-0.001
71	A	72	TYR	0	0.027	0.032	2.533	-4.056	-1.324	1.398	-1.600	-2.530	0.015
72	A	73	ARG	1	0.904	0.955	1.650	-12.890	-20.725	18.225	-7.101	-3.289	-0.057
73	A	74	ALA	0	0.060	0.015	4.145	0.784	0.922	-0.001	-0.029	-0.108	0.000
74	A	75	ASP	-1	-0.932	-0.955	5.849	0.433	0.433	0.000	0.000	0.000	0.000
75	A	76	THR	0	-0.017	-0.019	8.043	-0.044	-0.044	0.000	0.000	0.000	0.000
76	A	77	GLN	0	-0.045	-0.007	7.255	0.129	0.129	0.000	0.000	0.000	0.000
77	A	78	THR	0	-0.035	-0.011	7.261	-0.071	-0.071	0.000	0.000	0.000	0.000
78	A	79	TYR	0	-0.026	-0.044	6.185	-0.168	-0.168	0.000	0.000	0.000	0.000
79	A	80	GLN	0	-0.055	-0.025	6.437	0.371	0.371	0.000	0.000	0.000	0.000
80	A	81	PRO	0	0.005	0.012	8.341	-0.246	-0.246	0.000	0.000	0.000	0.000
81	A	82	TYR	0	-0.002	0.000	6.863	0.043	0.043	0.000	0.000	0.000	0.000
82	A	83	ASN	0	0.039	-0.001	11.877	-0.046	-0.046	0.000	0.000	0.000	0.000
83	A	84	LYS	1	0.917	0.940	14.583	0.309	0.309	0.000	0.000	0.000	0.000
84	A	85	ASP	-1	-0.811	-0.899	16.802	-0.374	-0.374	0.000	0.000	0.000	0.000
85	A	86	TRP	0	0.022	0.006	6.966	0.016	0.016	0.000	0.000	0.000	0.000
86	A	87	ILE	0	-0.001	-0.013	11.892	-0.034	-0.034	0.000	0.000	0.000	0.000
87	A	88	LYS	1	0.829	0.916	13.649	0.340	0.340	0.000	0.000	0.000	0.000
88	A	89	GLU	-1	-0.904	-0.957	15.340	-0.265	-0.265	0.000	0.000	0.000	0.000
89	A	90	LYS	1	0.811	0.911	9.766	0.663	0.663	0.000	0.000	0.000	0.000
90	A	91	ILE	0	0.059	0.023	12.557	0.020	0.020	0.000	0.000	0.000	0.000
91	A	92	TYR	0	0.038	0.032	14.334	0.069	0.069	0.000	0.000	0.000	0.000
92	A	93	VAL	0	-0.043	-0.039	12.414	0.052	0.052	0.000	0.000	0.000	0.000
93	A	94	LEU	0	-0.061	-0.019	11.206	0.070	0.070	0.000	0.000	0.000	0.000
94	A	95	LEU	0	0.083	0.025	13.718	0.053	0.053	0.000	0.000	0.000	0.000
95	A	96	ARG	1	0.882	0.948	17.240	0.132	0.132	0.000	0.000	0.000	0.000
96	A	97	ARG	1	0.842	0.919	10.505	0.210	0.210	0.000	0.000	0.000	0.000
97	A	98	GLN	0	0.027	-0.005	14.823	0.019	0.019	0.000	0.000	0.000	0.000
98	A	99	ALA	0	-0.011	0.015	17.826	0.015	0.015	0.000	0.000	0.000	0.000
99	A	100	GLN	0	-0.037	-0.003	19.666	0.002	0.002	0.000	0.000	0.000	0.000
100	A	101	GLN	0	-0.028	-0.001	15.325	-0.010	-0.010	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:2:SER)