FMO DATABASE

FMODB ID: 2NN7R

Calculation Name: 3NHM-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3NHM

Chain ID: A

ChEMBL ID:

UniProt ID: Q1CZZ7

Base Structure: X-ray

Registration Date: 2023-09-21

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	120
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-956320.375853
FMO2-HF: Nuclear repulsion	910684.435692
FMO2-HF: Total energy	-45635.940161
FMO2-MP2: Total energy	-45768.103299

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:19:PRO)

Summations of interaction energy for fragment #1(A:19: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.
-8.711	0.227	7.701	-5.623	-11.015	-0.033

Interaction energy analysis for fragmet #1(A:19:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.045 / q_NPA : 0.019

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	21	VAL	0	0.002	-0.003	3.779	-0.457	1.160	-0.008	-0.716	-0.893	0.003
4	A	22	LEU	0	-0.036	-0.003	5.883	0.232	0.232	0.000	0.000	0.000	0.000
5	A	23	ILE	0	-0.008	-0.001	9.629	0.088	0.088	0.000	0.000	0.000	0.000
6	A	24	VAL	0	0.000	0.007	12.059	0.057	0.057	0.000	0.000	0.000	0.000
7	A	25	GLU	-1	-0.764	-0.872	15.555	-0.256	-0.256	0.000	0.000	0.000	0.000
8	A	26	ASN	0	0.070	0.044	18.403	0.013	0.013	0.000	0.000	0.000	0.000
9	A	27	SER	0	-0.037	-0.024	21.817	0.013	0.013	0.000	0.000	0.000	0.000
10	A	28	TRP	0	0.053	0.004	20.757	-0.028	-0.028	0.000	0.000	0.000	0.000
11	A	29	THR	0	0.025	0.021	20.212	-0.024	-0.024	0.000	0.000	0.000	0.000
12	A	30	MET	0	-0.001	0.021	18.128	-0.024	-0.024	0.000	0.000	0.000	0.000
13	A	31	ARG	1	0.868	0.935	16.280	0.265	0.265	0.000	0.000	0.000	0.000
14	A	32	GLU	-1	-0.762	-0.843	15.279	-0.432	-0.432	0.000	0.000	0.000	0.000
15	A	33	THR	0	-0.057	-0.037	15.447	-0.021	-0.021	0.000	0.000	0.000	0.000
16	A	34	LEU	0	-0.019	-0.019	12.815	-0.023	-0.023	0.000	0.000	0.000	0.000
17	A	35	ARG	1	0.868	0.892	11.148	0.399	0.399	0.000	0.000	0.000	0.000
18	A	36	LEU	0	-0.032	0.002	10.696	-0.098	-0.098	0.000	0.000	0.000	0.000
19	A	37	LEU	0	-0.064	-0.048	11.687	-0.008	-0.008	0.000	0.000	0.000	0.000
20	A	38	LEU	0	-0.003	0.011	7.247	0.026	0.026	0.000	0.000	0.000	0.000
21	A	39	SER	0	-0.012	-0.045	6.638	-0.236	-0.236	0.000	0.000	0.000	0.000
22	A	40	GLY	0	-0.064	-0.016	8.219	0.081	0.081	0.000	0.000	0.000	0.000
23	A	41	GLU	-1	-0.912	-0.952	4.755	-0.642	-0.456	-0.001	-0.020	-0.165	0.000
24	A	42	PHE	0	0.011	-0.001	2.316	-3.780	-1.165	3.851	-1.968	-4.498	-0.012
25	A	43	ASP	-1	-0.898	-0.935	3.058	-0.547	0.256	0.019	-0.042	-0.779	-0.001
26	A	44	CYS	0	-0.065	-0.021	4.870	-0.007	0.006	-0.001	-0.012	-0.001	0.000
27	A	45	THR	0	0.031	0.020	8.162	0.389	0.389	0.000	0.000	0.000	0.000
28	A	46	THR	0	-0.040	-0.044	10.639	-0.014	-0.014	0.000	0.000	0.000	0.000
29	A	47	ALA	0	0.030	0.026	13.741	0.058	0.058	0.000	0.000	0.000	0.000
30	A	48	ALA	0	-0.021	-0.020	16.864	-0.008	-0.008	0.000	0.000	0.000	0.000
31	A	49	ASP	-1	-0.794	-0.907	19.842	-0.184	-0.184	0.000	0.000	0.000	0.000
32	A	50	GLY	0	0.082	0.032	18.984	-0.022	-0.022	0.000	0.000	0.000	0.000
33	A	51	ALA	0	0.021	0.009	19.430	-0.006	-0.006	0.000	0.000	0.000	0.000
34	A	52	SER	0	-0.021	-0.001	19.542	-0.013	-0.013	0.000	0.000	0.000	0.000
35	A	53	GLY	0	0.011	-0.011	15.901	-0.017	-0.017	0.000	0.000	0.000	0.000
36	A	54	LEU	0	0.030	0.009	15.725	-0.023	-0.023	0.000	0.000	0.000	0.000
37	A	55	GLN	0	-0.033	-0.020	17.598	0.004	0.004	0.000	0.000	0.000	0.000
38	A	56	GLN	0	-0.042	-0.039	14.218	-0.015	-0.015	0.000	0.000	0.000	0.000
39	A	57	ALA	0	-0.002	0.001	12.822	-0.008	-0.008	0.000	0.000	0.000	0.000
40	A	58	LEU	0	-0.012	-0.010	13.709	0.024	0.024	0.000	0.000	0.000	0.000
41	A	59	ALA	0	-0.063	-0.017	15.981	0.031	0.031	0.000	0.000	0.000	0.000
42	A	60	HIS	0	-0.030	-0.023	11.061	0.053	0.053	0.000	0.000	0.000	0.000
43	A	61	PRO	0	0.042	0.035	10.453	-0.115	-0.115	0.000	0.000	0.000	0.000
44	A	62	PRO	0	-0.053	-0.004	7.074	0.024	0.024	0.000	0.000	0.000	0.000
45	A	63	ASP	-1	-0.782	-0.890	2.562	-3.376	-0.507	1.491	-2.161	-2.198	-0.021
46	A	64	VAL	0	-0.041	-0.027	4.163	0.073	0.222	-0.001	-0.011	-0.138	0.000
47	A	65	LEU	0	-0.027	-0.004	6.711	-0.180	-0.180	0.000	0.000	0.000	0.000
48	A	66	ILE	0	-0.011	-0.011	8.641	0.057	0.057	0.000	0.000	0.000	0.000
49	A	67	SER	0	0.011	-0.007	11.675	0.009	0.009	0.000	0.000	0.000	0.000
50	A	68	ASP	-1	-0.792	-0.868	15.464	-0.216	-0.216	0.000	0.000	0.000	0.000
51	A	69	VAL	0	-0.010	0.000	18.829	0.000	0.000	0.000	0.000	0.000	0.000
52	A	70	ASN	0	-0.018	-0.028	21.446	0.005	0.005	0.000	0.000	0.000	0.000
53	A	71	MET	0	-0.055	-0.024	18.978	-0.005	-0.005	0.000	0.000	0.000	0.000
54	A	72	ASP	-1	-0.964	-0.985	23.909	-0.127	-0.127	0.000	0.000	0.000	0.000
55	A	73	GLY	0	0.041	0.025	25.644	0.012	0.012	0.000	0.000	0.000	0.000
56	A	74	MET	0	-0.098	-0.019	21.854	0.000	0.000	0.000	0.000	0.000	0.000
57	A	75	ASP	-1	-0.793	-0.893	22.778	-0.167	-0.167	0.000	0.000	0.000	0.000
58	A	76	GLY	0	0.034	0.006	19.499	-0.007	-0.007	0.000	0.000	0.000	0.000
59	A	77	TYR	0	-0.055	-0.065	19.477	-0.017	-0.017	0.000	0.000	0.000	0.000
60	A	78	ALA	0	0.019	0.012	21.803	0.004	0.004	0.000	0.000	0.000	0.000
61	A	79	LEU	0	-0.029	-0.013	16.046	0.006	0.006	0.000	0.000	0.000	0.000
62	A	80	CYS	0	-0.054	-0.015	17.302	-0.004	-0.004	0.000	0.000	0.000	0.000
63	A	81	GLY	0	0.027	0.009	18.329	0.010	0.010	0.000	0.000	0.000	0.000
64	A	82	HIS	0	0.006	-0.002	20.030	0.015	0.015	0.000	0.000	0.000	0.000
65	A	83	PHE	0	0.041	0.012	11.930	0.009	0.009	0.000	0.000	0.000	0.000
66	A	84	ARG	1	0.801	0.870	14.158	0.211	0.211	0.000	0.000	0.000	0.000
67	A	85	SER	0	-0.087	-0.043	18.713	0.022	0.022	0.000	0.000	0.000	0.000
68	A	86	GLU	-1	-0.846	-0.943	18.231	-0.067	-0.067	0.000	0.000	0.000	0.000
69	A	87	PRO	0	-0.081	-0.043	18.092	-0.002	-0.002	0.000	0.000	0.000	0.000
70	A	88	THR	0	-0.012	-0.005	14.833	0.024	0.024	0.000	0.000	0.000	0.000
71	A	89	LEU	0	-0.031	-0.019	13.615	-0.013	-0.013	0.000	0.000	0.000	0.000
72	A	90	LYS	1	0.933	0.987	13.801	0.017	0.017	0.000	0.000	0.000	0.000
73	A	91	HIS	0	-0.029	-0.012	10.058	0.005	0.005	0.000	0.000	0.000	0.000
74	A	92	ILE	0	-0.032	0.005	8.726	-0.001	-0.001	0.000	0.000	0.000	0.000
75	A	93	PRO	0	-0.020	0.001	8.037	0.010	0.010	0.000	0.000	0.000	0.000
76	A	94	VAL	0	-0.013	-0.022	9.982	-0.094	-0.094	0.000	0.000	0.000	0.000
77	A	95	ILE	0	-0.012	-0.004	9.174	0.052	0.052	0.000	0.000	0.000	0.000
78	A	96	PHE	0	0.003	-0.012	12.829	-0.013	-0.013	0.000	0.000	0.000	0.000
79	A	97	VAL	0	-0.002	-0.012	14.317	0.005	0.005	0.000	0.000	0.000	0.000
80	A	98	SER	0	0.071	0.046	17.305	0.006	0.006	0.000	0.000	0.000	0.000
81	A	99	GLY	0	-0.016	-0.007	21.104	-0.001	-0.001	0.000	0.000	0.000	0.000
82	A	100	TYR	0	-0.018	-0.006	24.168	0.014	0.014	0.000	0.000	0.000	0.000
83	A	101	ALA	0	0.038	0.026	23.755	-0.012	-0.012	0.000	0.000	0.000	0.000
84	A	102	PRO	0	0.034	0.041	22.004	0.004	0.004	0.000	0.000	0.000	0.000
85	A	103	ARG	1	0.783	0.846	24.275	0.134	0.134	0.000	0.000	0.000	0.000
86	A	104	THR	0	-0.004	-0.006	26.100	-0.006	-0.006	0.000	0.000	0.000	0.000
87	A	105	GLU	-1	-0.808	-0.856	24.444	-0.118	-0.118	0.000	0.000	0.000	0.000
88	A	106	GLY	0	0.017	0.018	26.748	0.001	0.001	0.000	0.000	0.000	0.000
89	A	107	PRO	0	-0.034	-0.012	28.097	0.005	0.005	0.000	0.000	0.000	0.000
90	A	108	ALA	0	0.034	0.005	27.238	-0.005	-0.005	0.000	0.000	0.000	0.000
91	A	109	ASP	-1	-0.905	-0.936	27.119	-0.067	-0.067	0.000	0.000	0.000	0.000
92	A	110	GLN	0	-0.073	-0.043	25.982	-0.008	-0.008	0.000	0.000	0.000	0.000
93	A	111	PRO	0	-0.016	0.005	20.693	0.000	0.000	0.000	0.000	0.000	0.000
94	A	112	VAL	0	0.038	0.010	19.921	-0.002	-0.002	0.000	0.000	0.000	0.000
95	A	113	PRO	0	-0.028	0.000	15.866	-0.003	-0.003	0.000	0.000	0.000	0.000
96	A	114	ASP	-1	-0.790	-0.875	12.924	-0.202	-0.202	0.000	0.000	0.000	0.000
97	A	115	ALA	0	-0.016	-0.001	13.392	0.016	0.016	0.000	0.000	0.000	0.000
98	A	116	TYR	0	-0.014	-0.031	15.329	-0.020	-0.020	0.000	0.000	0.000	0.000
99	A	117	LEU	0	-0.049	-0.020	13.838	0.015	0.015	0.000	0.000	0.000	0.000
100	A	118	VAL	0	-0.006	-0.008	17.989	0.000	0.000	0.000	0.000	0.000	0.000
101	A	119	LYS	1	0.761	0.861	19.368	0.255	0.255	0.000	0.000	0.000	0.000
102	A	120	PRO	0	-0.019	-0.019	21.370	0.016	0.016	0.000	0.000	0.000	0.000
103	A	121	VAL	0	0.039	0.020	15.148	0.012	0.012	0.000	0.000	0.000	0.000
104	A	122	LYS	1	0.964	0.972	17.639	0.156	0.156	0.000	0.000	0.000	0.000
105	A	123	PRO	0	0.068	0.033	13.829	-0.006	-0.006	0.000	0.000	0.000	0.000
106	A	124	PRO	0	0.038	0.010	12.804	-0.046	-0.046	0.000	0.000	0.000	0.000
107	A	125	VAL	0	-0.021	-0.006	12.481	-0.006	-0.006	0.000	0.000	0.000	0.000
108	A	126	LEU	0	0.012	0.013	10.256	0.020	0.020	0.000	0.000	0.000	0.000
109	A	127	ILE	0	0.027	0.023	7.513	-0.054	-0.054	0.000	0.000	0.000	0.000
110	A	128	ALA	0	-0.001	-0.002	7.718	-0.041	-0.041	0.000	0.000	0.000	0.000
111	A	129	GLN	0	-0.033	-0.028	9.535	0.027	0.027	0.000	0.000	0.000	0.000
112	A	130	LEU	0	0.006	0.012	5.413	0.072	0.072	0.000	0.000	0.000	0.000
113	A	131	HIS	0	0.010	-0.009	3.430	-0.387	0.072	0.010	-0.111	-0.358	0.000
114	A	132	ALA	0	-0.045	-0.012	5.902	0.148	0.148	0.000	0.000	0.000	0.000
115	A	133	LEU	0	-0.012	-0.018	8.501	0.077	0.077	0.000	0.000	0.000	0.000
116	A	134	LEU	0	0.008	0.013	2.496	-0.669	-0.442	2.341	-0.582	-1.985	-0.002
117	A	135	ALA	0	0.045	0.030	5.992	0.130	0.130	0.000	0.000	0.000	0.000
118	A	136	ARG	1	0.853	0.929	8.446	0.087	0.087	0.000	0.000	0.000	0.000
119	A	137	ALA	0	-0.030	-0.015	7.727	0.027	0.027	0.000	0.000	0.000	0.000
120	A	138	GLU	-1	-1.051	-1.020	7.359	0.714	0.714	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:19:PRO)