FMO DATABASE

FMODB ID: 5G1NZ

Calculation Name: 1NN4-A-Xray549

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1NN4

Chain ID: A

ChEMBL ID:

UniProt ID: P37351

Base Structure: X-ray

Registration Date: 2025-10-11

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
Protonation	MOE:Protonate 3D
Complement	ac.sh, 23 2024 Oct
Water	No
Procedure	Manual calculation
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	159
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1462079.207459
FMO2-HF: Nuclear repulsion	1402250.172813
FMO2-HF: Total energy	-59829.034646
FMO2-MP2: Total energy	-60003.651797

3D Structure Molmil

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:-12:HIS)

Summations of interaction energy for fragment #1(A:-12:HIS)

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.
-45.942	-44.019	0.01	-0.858	-1.075	-0.003

Interaction energy analysis for fragmet #1(A:-12:HIS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.869 / q_NPA : 0.923

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	-10	HIS	0	0.027	0.014	3.476	-1.630	0.293	0.010	-0.858	-1.075	-0.003
4	A	-9	SER	0	0.007	0.002	6.313	2.958	2.958	0.000	0.000	0.000	0.000
5	A	-8	SER	0	-0.014	0.001	8.503	1.520	1.520	0.000	0.000	0.000	0.000
6	A	-7	GLY	0	0.019	0.008	10.358	0.086	0.086	0.000	0.000	0.000	0.000
7	A	-6	LEU	0	0.002	0.002	13.242	0.948	0.948	0.000	0.000	0.000	0.000
8	A	-5	THR	0	0.005	0.003	9.859	-2.226	-2.226	0.000	0.000	0.000	0.000
9	A	-4	PRO	0	0.009	0.006	10.094	1.495	1.495	0.000	0.000	0.000	0.000
10	A	-3	ARG	1	0.947	0.993	12.201	14.877	14.877	0.000	0.000	0.000	0.000
11	A	-2	GLY	0	0.011	0.010	14.075	-0.159	-0.159	0.000	0.000	0.000	0.000
12	A	-1	SER	0	-0.006	-0.020	14.933	0.875	0.875	0.000	0.000	0.000	0.000
13	A	0	GLN	0	-0.016	-0.003	17.354	0.174	0.174	0.000	0.000	0.000	0.000
14	A	1	MET	0	-0.076	-0.015	20.189	0.570	0.570	0.000	0.000	0.000	0.000
15	A	2	LYS	1	0.975	0.991	18.739	14.216	14.216	0.000	0.000	0.000	0.000
16	A	3	LYS	1	0.790	0.891	20.576	10.996	10.996	0.000	0.000	0.000	0.000
17	A	4	ILE	0	0.010	0.004	20.431	0.275	0.275	0.000	0.000	0.000	0.000
18	A	5	ALA	0	0.004	0.015	23.195	-0.007	-0.007	0.000	0.000	0.000	0.000
19	A	6	PHE	0	0.010	-0.007	22.109	-0.140	-0.140	0.000	0.000	0.000	0.000
20	A	7	GLY	0	0.071	0.024	24.963	0.382	0.382	0.000	0.000	0.000	0.000
21	A	8	CYS	0	-0.101	-0.036	26.186	-0.307	-0.307	0.000	0.000	0.000	0.000
22	A	9	ASP	-1	-0.749	-0.864	28.320	-9.237	-9.237	0.000	0.000	0.000	0.000
23	A	10	HIS	0	0.057	0.029	29.301	-0.385	-0.385	0.000	0.000	0.000	0.000
24	A	11	VAL	0	-0.059	-0.034	29.428	-0.100	-0.100	0.000	0.000	0.000	0.000
25	A	12	GLY	0	-0.007	0.006	26.526	-0.334	-0.334	0.000	0.000	0.000	0.000
26	A	13	PHE	0	-0.002	-0.005	24.897	-0.523	-0.523	0.000	0.000	0.000	0.000
27	A	14	ILE	0	-0.037	-0.024	23.542	-0.313	-0.313	0.000	0.000	0.000	0.000
28	A	15	LEU	0	0.022	0.009	19.782	-0.389	-0.389	0.000	0.000	0.000	0.000
29	A	16	LYS	1	0.779	0.899	19.959	10.791	10.791	0.000	0.000	0.000	0.000
30	A	17	HIS	0	0.029	0.004	18.692	-0.610	-0.610	0.000	0.000	0.000	0.000
31	A	18	GLU	-1	-0.893	-0.949	15.446	-16.839	-16.839	0.000	0.000	0.000	0.000
32	A	19	ILE	0	-0.014	-0.004	14.985	-1.049	-1.049	0.000	0.000	0.000	0.000
33	A	20	VAL	0	-0.002	-0.004	16.338	-0.451	-0.451	0.000	0.000	0.000	0.000
34	A	21	ALA	0	-0.003	0.003	13.018	-0.346	-0.346	0.000	0.000	0.000	0.000
35	A	22	HIS	0	-0.006	-0.016	10.739	-1.583	-1.583	0.000	0.000	0.000	0.000
36	A	23	LEU	0	-0.026	-0.018	12.484	-0.645	-0.645	0.000	0.000	0.000	0.000
37	A	24	VAL	0	0.012	0.008	14.022	-0.087	-0.087	0.000	0.000	0.000	0.000
38	A	25	GLU	-1	-0.998	-0.988	6.830	-31.399	-31.399	0.000	0.000	0.000	0.000
39	A	26	ARG	1	0.766	0.859	9.986	20.506	20.506	0.000	0.000	0.000	0.000
40	A	27	GLY	0	-0.029	-0.005	11.746	0.609	0.609	0.000	0.000	0.000	0.000
41	A	28	VAL	0	-0.071	-0.033	14.355	0.916	0.916	0.000	0.000	0.000	0.000
42	A	29	GLU	-1	-0.841	-0.914	17.687	-12.174	-12.174	0.000	0.000	0.000	0.000
43	A	30	VAL	0	-0.004	-0.011	18.881	0.390	0.390	0.000	0.000	0.000	0.000
44	A	31	ILE	0	0.002	-0.001	21.677	0.281	0.281	0.000	0.000	0.000	0.000
45	A	32	ASP	-1	-0.779	-0.879	24.100	-11.123	-11.123	0.000	0.000	0.000	0.000
46	A	33	LYS	1	0.845	0.934	25.875	9.951	9.951	0.000	0.000	0.000	0.000
47	A	34	GLY	0	0.005	0.008	27.887	0.374	0.374	0.000	0.000	0.000	0.000
48	A	35	THR	0	-0.001	-0.003	28.683	-0.127	-0.127	0.000	0.000	0.000	0.000
49	A	36	TRP	0	0.002	-0.031	26.408	-0.296	-0.296	0.000	0.000	0.000	0.000
50	A	37	SER	0	-0.027	-0.029	28.334	-0.124	-0.124	0.000	0.000	0.000	0.000
51	A	38	SER	0	0.010	-0.001	29.313	-0.104	-0.104	0.000	0.000	0.000	0.000
52	A	39	GLU	-1	-0.896	-0.916	30.881	-8.256	-8.256	0.000	0.000	0.000	0.000
53	A	40	ARG	1	0.893	0.939	34.481	7.505	7.505	0.000	0.000	0.000	0.000
54	A	41	THR	0	0.029	0.028	33.298	0.106	0.106	0.000	0.000	0.000	0.000
55	A	42	ASP	-1	-0.868	-0.951	36.201	-7.954	-7.954	0.000	0.000	0.000	0.000
56	A	43	TYR	0	0.023	-0.002	33.280	-0.102	-0.102	0.000	0.000	0.000	0.000
57	A	44	PRO	0	-0.004	-0.013	34.272	-0.163	-0.163	0.000	0.000	0.000	0.000
58	A	45	HIS	0	0.040	0.048	34.409	0.077	0.077	0.000	0.000	0.000	0.000
59	A	46	TYR	0	-0.005	-0.023	30.642	-0.089	-0.089	0.000	0.000	0.000	0.000
60	A	47	ALA	0	0.005	-0.006	31.709	-0.213	-0.213	0.000	0.000	0.000	0.000
61	A	48	SER	0	0.002	0.008	33.099	-0.088	-0.088	0.000	0.000	0.000	0.000
62	A	49	GLN	0	-0.022	-0.018	32.380	-0.131	-0.131	0.000	0.000	0.000	0.000
63	A	50	VAL	0	-0.026	-0.001	28.050	-0.125	-0.125	0.000	0.000	0.000	0.000
64	A	51	ALA	0	0.009	0.006	30.708	-0.103	-0.103	0.000	0.000	0.000	0.000
65	A	52	LEU	0	0.001	-0.005	33.193	0.082	0.082	0.000	0.000	0.000	0.000
66	A	53	ALA	0	0.002	0.014	30.679	0.050	0.050	0.000	0.000	0.000	0.000
67	A	54	VAL	0	-0.047	-0.033	28.599	-0.063	-0.063	0.000	0.000	0.000	0.000
68	A	55	ALA	0	-0.005	0.002	31.306	0.018	0.018	0.000	0.000	0.000	0.000
69	A	56	GLY	0	-0.023	-0.003	34.792	0.173	0.173	0.000	0.000	0.000	0.000
70	A	57	GLY	0	-0.010	0.006	32.078	0.085	0.085	0.000	0.000	0.000	0.000
71	A	58	GLU	-1	-0.934	-0.956	30.695	-9.364	-9.364	0.000	0.000	0.000	0.000
72	A	59	VAL	0	-0.062	-0.055	25.771	-0.385	-0.385	0.000	0.000	0.000	0.000
73	A	60	ASP	-1	-0.795	-0.883	24.154	-11.835	-11.835	0.000	0.000	0.000	0.000
74	A	61	GLY	0	0.030	0.003	25.389	0.113	0.113	0.000	0.000	0.000	0.000
75	A	62	GLY	0	0.000	-0.005	25.712	-0.067	-0.067	0.000	0.000	0.000	0.000
76	A	63	ILE	0	-0.037	-0.021	20.275	-0.183	-0.183	0.000	0.000	0.000	0.000
77	A	64	LEU	0	-0.008	0.003	24.406	0.163	0.163	0.000	0.000	0.000	0.000
78	A	65	ILE	0	-0.009	0.006	21.892	-0.085	-0.085	0.000	0.000	0.000	0.000
79	A	66	CYS	0	-0.014	0.011	26.477	0.295	0.295	0.000	0.000	0.000	0.000
80	A	67	GLY	0	0.050	0.024	28.255	-0.253	-0.253	0.000	0.000	0.000	0.000
81	A	68	THR	0	-0.014	-0.031	29.429	-0.249	-0.249	0.000	0.000	0.000	0.000
82	A	69	GLY	0	0.074	0.047	28.793	-0.107	-0.107	0.000	0.000	0.000	0.000
83	A	70	VAL	0	0.030	-0.001	29.566	0.134	0.134	0.000	0.000	0.000	0.000
84	A	71	GLY	0	0.011	0.008	32.926	0.134	0.134	0.000	0.000	0.000	0.000
85	A	72	ILE	0	-0.001	-0.011	29.653	0.182	0.182	0.000	0.000	0.000	0.000
86	A	73	SER	0	0.024	0.024	30.773	0.099	0.099	0.000	0.000	0.000	0.000
87	A	74	ILE	0	-0.018	-0.019	32.411	0.137	0.137	0.000	0.000	0.000	0.000
88	A	75	ALA	0	-0.027	-0.019	35.408	0.158	0.158	0.000	0.000	0.000	0.000
89	A	76	ALA	0	0.060	0.020	32.478	0.118	0.118	0.000	0.000	0.000	0.000
90	A	77	ASN	0	-0.015	-0.011	33.414	0.022	0.022	0.000	0.000	0.000	0.000
91	A	78	LYS	1	0.881	0.950	36.183	7.558	7.558	0.000	0.000	0.000	0.000
92	A	79	PHE	0	-0.033	-0.003	36.487	0.190	0.190	0.000	0.000	0.000	0.000
93	A	80	ALA	0	0.058	0.029	37.784	-0.132	-0.132	0.000	0.000	0.000	0.000
94	A	81	GLY	0	0.005	-0.004	37.024	-0.131	-0.131	0.000	0.000	0.000	0.000
95	A	82	ILE	0	-0.108	-0.039	32.302	-0.364	-0.364	0.000	0.000	0.000	0.000
96	A	83	ARG	1	0.874	0.938	32.220	9.289	9.289	0.000	0.000	0.000	0.000
97	A	84	ALA	0	0.004	-0.013	29.918	-0.395	-0.395	0.000	0.000	0.000	0.000
98	A	85	VAL	0	-0.006	0.008	26.167	0.264	0.264	0.000	0.000	0.000	0.000
99	A	86	VAL	0	-0.001	-0.016	27.968	-0.174	-0.174	0.000	0.000	0.000	0.000
100	A	87	CYS	0	-0.094	-0.033	24.311	0.132	0.132	0.000	0.000	0.000	0.000
101	A	88	SER	0	0.011	-0.007	24.988	-0.097	-0.097	0.000	0.000	0.000	0.000
102	A	89	GLU	-1	-0.762	-0.858	22.630	-12.042	-12.042	0.000	0.000	0.000	0.000
103	A	90	PRO	0	0.061	0.008	19.238	0.204	0.204	0.000	0.000	0.000	0.000
104	A	91	TYR	0	-0.012	0.018	21.405	0.040	0.040	0.000	0.000	0.000	0.000
105	A	92	SER	0	0.000	-0.046	24.138	0.291	0.291	0.000	0.000	0.000	0.000
106	A	93	ALA	0	-0.001	0.005	22.479	0.248	0.248	0.000	0.000	0.000	0.000
107	A	94	GLN	0	-0.007	0.010	20.490	-0.421	-0.421	0.000	0.000	0.000	0.000
108	A	95	LEU	0	0.021	0.008	23.495	0.235	0.235	0.000	0.000	0.000	0.000
109	A	96	SER	0	-0.012	-0.006	26.465	0.358	0.358	0.000	0.000	0.000	0.000
110	A	97	ARG	1	0.812	0.904	23.414	12.010	12.010	0.000	0.000	0.000	0.000
111	A	98	GLN	0	-0.006	-0.017	25.481	0.117	0.117	0.000	0.000	0.000	0.000
112	A	99	HIS	0	-0.029	-0.035	28.032	0.497	0.497	0.000	0.000	0.000	0.000
113	A	100	ASN	0	-0.061	-0.040	30.601	0.241	0.241	0.000	0.000	0.000	0.000
114	A	101	ASP	-1	-0.805	-0.875	29.277	-10.062	-10.062	0.000	0.000	0.000	0.000
115	A	102	THR	0	-0.011	-0.002	27.529	0.056	0.056	0.000	0.000	0.000	0.000
116	A	103	ASN	0	0.061	0.028	27.384	-0.424	-0.424	0.000	0.000	0.000	0.000
117	A	104	VAL	0	0.014	0.007	27.183	-0.174	-0.174	0.000	0.000	0.000	0.000
118	A	105	LEU	0	-0.004	0.016	21.652	0.035	0.035	0.000	0.000	0.000	0.000
119	A	106	ALA	0	0.004	-0.002	25.831	0.062	0.062	0.000	0.000	0.000	0.000
120	A	107	PHE	0	0.039	0.008	20.650	-0.077	-0.077	0.000	0.000	0.000	0.000
121	A	108	GLY	0	0.019	0.006	25.725	0.190	0.190	0.000	0.000	0.000	0.000
122	A	109	SER	0	-0.001	-0.030	24.618	-0.185	-0.185	0.000	0.000	0.000	0.000
123	A	110	ARG	1	0.851	0.923	25.659	10.277	10.277	0.000	0.000	0.000	0.000
124	A	111	VAL	0	-0.033	-0.004	26.723	0.255	0.255	0.000	0.000	0.000	0.000
125	A	112	VAL	0	-0.010	0.003	21.782	-0.109	-0.109	0.000	0.000	0.000	0.000
126	A	113	GLY	0	0.024	0.016	20.567	0.084	0.084	0.000	0.000	0.000	0.000
127	A	114	LEU	0	0.033	0.013	14.950	-0.165	-0.165	0.000	0.000	0.000	0.000
128	A	115	GLU	-1	-0.807	-0.905	12.241	-21.539	-21.539	0.000	0.000	0.000	0.000
129	A	116	LEU	0	-0.019	-0.002	15.264	-0.396	-0.396	0.000	0.000	0.000	0.000
130	A	117	ALA	0	0.020	0.007	18.144	0.050	0.050	0.000	0.000	0.000	0.000
131	A	118	LYS	1	0.879	0.932	10.894	21.940	21.940	0.000	0.000	0.000	0.000
132	A	119	MET	0	0.009	0.004	14.163	0.099	0.099	0.000	0.000	0.000	0.000
133	A	120	ILE	0	-0.039	-0.017	15.661	0.282	0.282	0.000	0.000	0.000	0.000
134	A	121	VAL	0	0.003	0.000	15.649	0.393	0.393	0.000	0.000	0.000	0.000
135	A	122	ASP	-1	-0.819	-0.891	12.140	-21.330	-21.330	0.000	0.000	0.000	0.000
136	A	123	ALA	0	-0.050	-0.025	15.540	0.046	0.046	0.000	0.000	0.000	0.000
137	A	124	TRP	0	-0.049	-0.026	18.445	0.365	0.365	0.000	0.000	0.000	0.000
138	A	125	LEU	0	0.057	0.015	16.520	0.311	0.311	0.000	0.000	0.000	0.000
139	A	126	GLY	0	-0.032	0.005	17.286	0.036	0.036	0.000	0.000	0.000	0.000
140	A	127	ALA	0	-0.045	-0.020	18.004	0.144	0.144	0.000	0.000	0.000	0.000
141	A	128	GLN	0	-0.007	-0.014	21.658	-0.189	-0.189	0.000	0.000	0.000	0.000
142	A	129	TYR	0	-0.020	-0.016	24.793	0.087	0.087	0.000	0.000	0.000	0.000
143	A	130	GLU	-1	-0.853	-0.941	28.195	-10.720	-10.720	0.000	0.000	0.000	0.000
144	A	131	GLY	0	0.005	0.021	30.592	0.215	0.215	0.000	0.000	0.000	0.000
145	A	132	GLY	0	0.030	-0.001	34.136	0.067	0.067	0.000	0.000	0.000	0.000
146	A	133	ARG	1	0.936	0.965	33.964	9.027	9.027	0.000	0.000	0.000	0.000
147	A	134	HIS	0	-0.075	-0.032	32.200	0.440	0.440	0.000	0.000	0.000	0.000
148	A	135	GLN	0	0.022	0.027	36.387	-0.212	-0.212	0.000	0.000	0.000	0.000
149	A	136	GLN	0	0.021	0.000	38.022	-0.002	-0.002	0.000	0.000	0.000	0.000
150	A	137	ARG	1	0.876	0.944	38.036	8.048	8.048	0.000	0.000	0.000	0.000
151	A	138	VAL	0	0.049	0.033	34.552	0.060	0.060	0.000	0.000	0.000	0.000
152	A	139	GLU	-1	-0.834	-0.904	37.816	-7.647	-7.647	0.000	0.000	0.000	0.000
153	A	140	ALA	0	-0.048	-0.023	41.260	0.133	0.133	0.000	0.000	0.000	0.000
154	A	141	ILE	0	-0.035	-0.025	36.623	0.081	0.081	0.000	0.000	0.000	0.000
155	A	142	THR	0	0.010	-0.012	39.546	0.038	0.038	0.000	0.000	0.000	0.000
156	A	143	ALA	0	-0.055	-0.025	41.404	0.128	0.128	0.000	0.000	0.000	0.000
157	A	144	ILE	0	-0.045	-0.019	42.956	0.155	0.155	0.000	0.000	0.000	0.000
158	A	145	GLU	-1	-0.917	-0.932	39.397	-7.733	-7.733	0.000	0.000	0.000	0.000
159	A	146	GLN	-1	-0.996	-0.991	44.131	-6.319	-6.319	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:-12:HIS)