FMO DATABASE

FMODB ID: RKY98

Calculation Name: 4NDH-A-Xray549

Preferred Name:

Target Type:

Ligand Name: adenosine monophosphate

Ligand 3-letter code: AMP

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4NDH

Chain ID: A

ChEMBL ID:

UniProt ID: Q7Z2E3

Base Structure: X-ray

Registration Date: 2025-10-12

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	180
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-2041492.46289
FMO2-HF: Nuclear repulsion	1967250.654746
FMO2-HF: Total energy	-74241.808144
FMO2-MP2: Total energy	-74455.857054

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:161:GLY)

Summations of interaction energy for fragment #1(A:161:GLY)

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.
102.586	103.255	-0.004	-0.246	-0.418	0

Interaction energy analysis for fragmet #1(A:161:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.879 / q_NPA : 0.928

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].
3	A	163	HIS	0	0.073	0.023	3.835	-3.786	-3.117	-0.004	-0.246	-0.418
4	A	164	MET	0	0.018	0.002	6.577	1.790	1.790	0.000	0.000	0.000
5	A	165	GLY	0	0.024	0.025	5.023	3.762	3.762	0.000	0.000	0.000
6	A	166	HIS	0	-0.001	0.033	4.976	-0.124	-0.124	0.000	0.000	0.000
7	A	167	TRP	0	0.037	0.009	5.798	5.397	5.397	0.000	0.000	0.000
8	A	168	SER	0	0.000	-0.019	8.864	3.309	3.309	0.000	0.000	0.000
9	A	169	GLN	0	0.008	-0.015	9.341	4.066	4.066	0.000	0.000	0.000
10	A	170	GLY	0	0.016	0.014	11.311	1.273	1.273	0.000	0.000	0.000
11	A	171	LEU	0	0.009	0.004	12.457	1.022	1.022	0.000	0.000	0.000
12	A	172	LYS	1	0.901	0.932	13.813	19.724	19.724	0.000	0.000	0.000
13	A	173	ILE	0	-0.022	0.004	10.757	0.499	0.499	0.000	0.000	0.000
14	A	174	SER	0	0.019	-0.033	15.364	0.648	0.648	0.000	0.000	0.000
15	A	175	MET	0	-0.051	-0.006	17.901	0.495	0.495	0.000	0.000	0.000
16	A	176	GLN	0	0.027	0.016	18.886	1.233	1.233	0.000	0.000	0.000
17	A	177	ASP	-1	-0.837	-0.908	19.370	-13.856	-13.856	0.000	0.000	0.000
18	A	178	PRO	0	0.011	-0.006	21.251	0.361	0.361	0.000	0.000	0.000
19	A	179	LYS	1	0.954	0.982	23.018	13.172	13.172	0.000	0.000	0.000
20	A	180	MET	0	-0.115	-0.038	17.956	-0.124	-0.124	0.000	0.000	0.000
21	A	181	GLN	0	0.022	0.000	23.444	0.711	0.711	0.000	0.000	0.000
22	A	182	VAL	0	-0.053	-0.020	25.858	0.209	0.209	0.000	0.000	0.000
23	A	183	TYR	0	-0.007	-0.025	28.864	0.458	0.458	0.000	0.000	0.000
24	A	184	LYS	1	0.864	0.925	26.843	10.631	10.631	0.000	0.000	0.000
25	A	185	ASP	-1	-0.710	-0.810	30.312	-9.363	-9.363	0.000	0.000	0.000
26	A	186	GLU	-1	-0.890	-0.940	30.569	-9.211	-9.211	0.000	0.000	0.000
27	A	187	GLN	0	-0.039	-0.009	30.221	-0.364	-0.364	0.000	0.000	0.000
28	A	188	VAL	0	-0.050	-0.035	27.569	-0.535	-0.535	0.000	0.000	0.000
29	A	189	VAL	0	-0.014	0.006	23.589	0.227	0.227	0.000	0.000	0.000
30	A	190	VAL	0	-0.004	0.007	26.231	-0.190	-0.190	0.000	0.000	0.000
31	A	191	ILE	0	-0.001	-0.002	20.520	-0.024	-0.024	0.000	0.000	0.000
32	A	192	LYS	1	0.917	0.962	24.456	11.974	11.974	0.000	0.000	0.000
33	A	193	ASP	-1	-0.840	-0.925	21.787	-14.883	-14.883	0.000	0.000	0.000
34	A	194	LYS	1	0.929	0.961	14.783	19.083	19.083	0.000	0.000	0.000
35	A	195	TYR	0	-0.065	-0.044	15.764	-0.585	-0.585	0.000	0.000	0.000
36	A	196	PRO	0	0.097	0.074	21.520	-0.060	-0.060	0.000	0.000	0.000
37	A	197	LYS	1	0.826	0.896	20.920	14.138	14.138	0.000	0.000	0.000
38	A	198	ALA	0	0.015	0.013	26.743	0.262	0.262	0.000	0.000	0.000
39	A	199	ARG	1	0.810	0.892	29.545	8.324	8.324	0.000	0.000	0.000
40	A	200	TYR	0	0.000	0.019	30.999	-0.010	-0.010	0.000	0.000	0.000
41	A	201	HIS	0	-0.019	-0.009	23.991	0.056	0.056	0.000	0.000	0.000
42	A	202	TRP	0	0.032	0.014	26.237	-0.280	-0.280	0.000	0.000	0.000
43	A	203	LEU	0	-0.047	-0.019	20.677	-0.111	-0.111	0.000	0.000	0.000
44	A	204	VAL	0	0.042	0.026	24.646	-0.062	-0.062	0.000	0.000	0.000
45	A	205	LEU	0	-0.031	-0.023	20.148	-0.410	-0.410	0.000	0.000	0.000
46	A	206	PRO	0	0.052	0.037	23.567	0.365	0.365	0.000	0.000	0.000
47	A	207	TRP	0	0.007	-0.017	23.324	-1.040	-1.040	0.000	0.000	0.000
48	A	208	THR	0	-0.009	0.007	22.960	-0.764	-0.764	0.000	0.000	0.000
49	A	209	SER	0	0.003	-0.016	19.198	-0.666	-0.666	0.000	0.000	0.000
50	A	210	ILE	0	0.050	0.047	21.120	-0.158	-0.158	0.000	0.000	0.000
51	A	211	SER	0	-0.007	-0.016	18.190	-0.205	-0.205	0.000	0.000	0.000
52	A	212	SER	0	0.020	-0.007	18.786	-0.498	-0.498	0.000	0.000	0.000
53	A	213	LEU	0	0.101	0.030	21.320	0.262	0.262	0.000	0.000	0.000
54	A	214	LYS	1	0.934	0.968	20.463	15.133	15.133	0.000	0.000	0.000
55	A	215	ALA	0	-0.049	-0.016	22.924	0.198	0.198	0.000	0.000	0.000
56	A	216	VAL	0	-0.019	0.011	24.895	0.083	0.083	0.000	0.000	0.000
57	A	217	ALA	0	0.028	0.008	27.826	0.195	0.195	0.000	0.000	0.000
58	A	218	ARG	1	0.873	0.923	31.264	8.438	8.438	0.000	0.000	0.000
59	A	219	GLU	-1	-0.888	-0.932	30.484	-10.464	-10.464	0.000	0.000	0.000
60	A	220	HIS	0	0.001	-0.006	28.013	-0.112	-0.112	0.000	0.000	0.000
61	A	221	LEU	0	-0.024	-0.005	31.556	-0.043	-0.043	0.000	0.000	0.000
62	A	222	GLU	-1	-0.896	-0.952	34.569	-8.309	-8.309	0.000	0.000	0.000
63	A	223	LEU	0	0.010	0.009	27.849	-0.063	-0.063	0.000	0.000	0.000
64	A	224	LEU	0	-0.011	-0.017	28.980	-0.151	-0.151	0.000	0.000	0.000
65	A	225	LYS	1	0.953	0.975	31.834	8.259	8.259	0.000	0.000	0.000
66	A	226	HIS	0	-0.022	-0.004	32.172	0.276	0.276	0.000	0.000	0.000
67	A	227	MET	0	-0.044	-0.030	26.060	-0.080	-0.080	0.000	0.000	0.000
68	A	228	HIS	0	-0.036	-0.006	31.265	-0.323	-0.323	0.000	0.000	0.000
69	A	229	THR	0	0.021	-0.001	33.682	0.140	0.140	0.000	0.000	0.000
70	A	230	VAL	0	-0.006	0.001	31.419	0.119	0.119	0.000	0.000	0.000
71	A	231	GLY	0	-0.008	-0.011	32.010	-0.056	-0.056	0.000	0.000	0.000
72	A	232	GLU	-1	-0.867	-0.935	32.745	-8.201	-8.201	0.000	0.000	0.000
73	A	233	LYS	1	0.866	0.914	36.025	8.363	8.363	0.000	0.000	0.000
74	A	234	VAL	0	-0.013	-0.004	31.062	0.104	0.104	0.000	0.000	0.000
75	A	235	ILE	0	-0.011	-0.008	34.299	0.048	0.048	0.000	0.000	0.000
76	A	236	VAL	0	-0.012	-0.011	36.145	0.170	0.170	0.000	0.000	0.000
77	A	237	ASP	-1	-0.859	-0.912	36.624	-8.117	-8.117	0.000	0.000	0.000
78	A	238	PHE	0	-0.044	-0.025	33.238	0.024	0.024	0.000	0.000	0.000
79	A	239	ALA	0	-0.012	0.000	36.047	-0.037	-0.037	0.000	0.000	0.000
80	A	240	GLY	0	0.044	0.055	38.030	0.146	0.146	0.000	0.000	0.000
81	A	241	SER	0	-0.067	-0.048	41.394	0.146	0.146	0.000	0.000	0.000
82	A	242	SER	0	-0.027	-0.033	39.743	0.124	0.124	0.000	0.000	0.000
83	A	243	LYS	1	0.902	0.955	42.007	6.985	6.985	0.000	0.000	0.000
84	A	244	LEU	0	0.020	0.029	36.813	0.021	0.021	0.000	0.000	0.000
85	A	245	ARG	1	0.859	0.923	37.427	8.218	8.218	0.000	0.000	0.000
86	A	246	PHE	0	0.029	-0.014	33.115	-0.262	-0.262	0.000	0.000	0.000
87	A	247	ARG	1	0.785	0.894	32.890	9.615	9.615	0.000	0.000	0.000
88	A	248	LEU	0	0.050	0.024	31.464	-0.269	-0.269	0.000	0.000	0.000
89	A	249	GLY	0	0.045	0.007	29.814	0.275	0.275	0.000	0.000	0.000
90	A	250	TYR	0	0.007	0.008	25.347	-0.343	-0.343	0.000	0.000	0.000
91	A	251	HIS	0	-0.034	-0.009	22.760	-0.310	-0.310	0.000	0.000	0.000
92	A	252	ALA	0	0.023	0.007	24.461	-0.315	-0.315	0.000	0.000	0.000
93	A	253	ILE	0	-0.019	-0.006	19.960	-0.222	-0.222	0.000	0.000	0.000
94	A	254	PRO	0	0.024	0.040	19.285	-0.202	-0.202	0.000	0.000	0.000
95	A	255	SER	0	-0.057	-0.053	15.651	-0.402	-0.402	0.000	0.000	0.000
96	A	256	MET	0	-0.034	0.002	13.308	-1.911	-1.911	0.000	0.000	0.000
97	A	257	SER	0	0.004	-0.009	13.959	0.669	0.669	0.000	0.000	0.000
98	A	258	HIS	0	-0.020	0.002	15.756	-1.072	-1.072	0.000	0.000	0.000
99	A	259	VAL	0	-0.033	-0.003	18.611	0.087	0.087	0.000	0.000	0.000
100	A	260	HIS	0	-0.035	-0.035	19.241	0.280	0.280	0.000	0.000	0.000
101	A	261	LEU	0	-0.003	0.021	23.069	-0.031	-0.031	0.000	0.000	0.000
102	A	262	HIS	0	0.004	-0.003	22.302	0.207	0.207	0.000	0.000	0.000
103	A	263	VAL	0	0.024	0.019	26.755	0.397	0.397	0.000	0.000	0.000
104	A	264	ILE	0	-0.027	-0.019	27.585	-0.226	-0.226	0.000	0.000	0.000
105	A	265	SER	0	0.009	-0.015	30.720	0.158	0.158	0.000	0.000	0.000
106	A	266	GLN	0	-0.023	-0.030	32.858	-0.105	-0.105	0.000	0.000	0.000
107	A	267	ASP	-1	-0.671	-0.805	33.781	-9.203	-9.203	0.000	0.000	0.000
108	A	268	PHE	0	-0.033	-0.026	29.680	-0.059	-0.059	0.000	0.000	0.000
109	A	269	ASP	-1	-0.865	-0.903	31.766	-9.282	-9.282	0.000	0.000	0.000
110	A	270	SER	0	0.044	-0.003	26.820	-0.166	-0.166	0.000	0.000	0.000
111	A	271	PRO	0	-0.005	-0.001	26.673	-0.050	-0.050	0.000	0.000	0.000
112	A	272	CYS	0	-0.075	-0.041	23.032	-0.600	-0.600	0.000	0.000	0.000
113	A	273	LEU	0	-0.024	0.013	23.753	-0.583	-0.583	0.000	0.000	0.000
114	A	274	LYS	1	0.965	0.972	21.920	13.889	13.889	0.000	0.000	0.000
115	A	275	ASN	0	0.014	0.002	21.528	0.395	0.395	0.000	0.000	0.000
116	A	276	LYS	1	0.947	0.971	25.881	10.447	10.447	0.000	0.000	0.000
117	A	277	LYS	1	0.967	1.009	18.656	16.340	16.340	0.000	0.000	0.000
118	A	278	HIS	0	-0.002	0.002	20.486	0.492	0.492	0.000	0.000	0.000
119	A	279	TRP	0	0.036	0.026	25.059	-0.056	-0.056	0.000	0.000	0.000
120	A	280	ASN	0	0.019	-0.010	28.235	0.294	0.294	0.000	0.000	0.000
121	A	281	SER	0	-0.075	-0.037	24.745	0.107	0.107	0.000	0.000	0.000
122	A	282	PHE	0	0.005	-0.013	24.436	-0.177	-0.177	0.000	0.000	0.000
123	A	283	ASN	0	-0.045	-0.022	29.189	0.565	0.565	0.000	0.000	0.000
124	A	284	THR	0	-0.022	-0.015	30.187	0.159	0.159	0.000	0.000	0.000
125	A	285	GLU	-1	-0.852	-0.936	32.046	-9.410	-9.410	0.000	0.000	0.000
126	A	286	TYR	0	-0.093	-0.057	22.016	-0.292	-0.292	0.000	0.000	0.000
127	A	287	PHE	0	-0.061	-0.013	27.755	-0.540	-0.540	0.000	0.000	0.000
128	A	288	LEU	0	-0.003	0.001	28.196	0.397	0.397	0.000	0.000	0.000
129	A	289	GLU	-1	-0.771	-0.876	30.802	-9.342	-9.342	0.000	0.000	0.000
130	A	290	SER	0	-0.012	-0.039	31.975	-0.119	-0.119	0.000	0.000	0.000
131	A	291	GLN	0	0.020	0.013	32.932	-0.090	-0.090	0.000	0.000	0.000
132	A	292	ALA	0	0.083	0.049	35.019	0.062	0.062	0.000	0.000	0.000
133	A	293	VAL	0	-0.068	-0.030	29.616	-0.092	-0.092	0.000	0.000	0.000
134	A	294	ILE	0	-0.009	-0.005	32.954	-0.023	-0.023	0.000	0.000	0.000
135	A	295	GLU	-1	-0.883	-0.949	35.037	-8.008	-8.008	0.000	0.000	0.000
136	A	296	MET	0	-0.014	0.019	33.123	-0.060	-0.060	0.000	0.000	0.000
137	A	297	VAL	0	-0.023	-0.015	31.561	0.015	0.015	0.000	0.000	0.000
138	A	298	GLN	0	0.046	0.028	34.640	0.008	0.008	0.000	0.000	0.000
139	A	299	GLU	-1	-0.923	-0.950	38.288	-7.553	-7.553	0.000	0.000	0.000
140	A	300	ALA	0	-0.013	-0.015	35.713	0.095	0.095	0.000	0.000	0.000
141	A	301	GLY	0	-0.045	-0.018	35.522	-0.094	-0.094	0.000	0.000	0.000
142	A	302	ARG	1	0.938	0.962	28.004	10.447	10.447	0.000	0.000	0.000
143	A	303	VAL	0	0.023	0.014	28.162	0.216	0.216	0.000	0.000	0.000
144	A	304	THR	0	-0.084	-0.054	29.141	-0.171	-0.171	0.000	0.000	0.000
145	A	305	VAL	0	0.007	-0.005	26.236	0.104	0.104	0.000	0.000	0.000
146	A	306	ARG	1	0.969	0.985	29.628	9.087	9.087	0.000	0.000	0.000
147	A	307	ASP	-1	-0.851	-0.922	28.988	-10.895	-10.895	0.000	0.000	0.000
148	A	308	GLY	0	0.017	0.006	29.051	0.252	0.252	0.000	0.000	0.000
149	A	309	MET	0	-0.011	-0.005	26.044	-0.016	-0.016	0.000	0.000	0.000
150	A	310	PRO	0	-0.017	-0.025	23.506	-0.177	-0.177	0.000	0.000	0.000
151	A	311	GLU	-1	-0.867	-0.945	25.337	-11.733	-11.733	0.000	0.000	0.000
152	A	312	LEU	0	0.066	0.042	28.754	0.182	0.182	0.000	0.000	0.000
153	A	313	LEU	0	-0.039	-0.016	23.199	0.036	0.036	0.000	0.000	0.000
154	A	314	LYS	1	0.904	0.947	24.529	12.405	12.405	0.000	0.000	0.000
155	A	315	LEU	0	0.041	0.039	29.083	0.262	0.262	0.000	0.000	0.000
156	A	316	PRO	0	-0.017	-0.025	32.330	-0.208	-0.208	0.000	0.000	0.000
157	A	317	LEU	0	-0.003	0.009	30.740	-0.098	-0.098	0.000	0.000	0.000
158	A	318	ARG	1	0.937	0.966	34.696	8.164	8.164	0.000	0.000	0.000
159	A	319	CYS	0	-0.031	0.000	36.093	-0.198	-0.198	0.000	0.000	0.000
160	A	320	HIS	0	0.030	0.002	35.763	0.145	0.145	0.000	0.000	0.000
161	A	321	GLU	-1	-0.786	-0.871	37.862	-7.889	-7.889	0.000	0.000	0.000
162	A	322	CYS	0	0.007	0.019	41.144	0.084	0.084	0.000	0.000	0.000
163	A	323	GLN	0	-0.010	0.002	40.654	0.261	0.261	0.000	0.000	0.000
164	A	324	GLN	0	0.004	0.007	41.713	0.071	0.071	0.000	0.000	0.000
165	A	325	LEU	0	-0.037	-0.015	38.019	-0.231	-0.231	0.000	0.000	0.000
166	A	326	LEU	0	0.016	0.005	37.236	0.170	0.170	0.000	0.000	0.000
167	A	327	PRO	0	-0.001	0.005	36.901	-0.237	-0.237	0.000	0.000	0.000
168	A	328	SER	0	-0.017	-0.017	33.584	-0.277	-0.277	0.000	0.000	0.000
169	A	329	ILE	0	0.032	0.017	28.805	0.161	0.161	0.000	0.000	0.000
170	A	330	PRO	0	0.019	-0.001	31.615	0.102	0.102	0.000	0.000	0.000
171	A	331	GLN	0	0.059	0.025	33.963	0.230	0.230	0.000	0.000	0.000
172	A	332	LEU	0	-0.005	0.006	32.548	0.191	0.191	0.000	0.000	0.000
173	A	333	LYS	1	0.827	0.894	29.315	10.567	10.567	0.000	0.000	0.000
174	A	334	GLU	-1	-0.870	-0.944	34.835	-8.146	-8.146	0.000	0.000	0.000
175	A	335	HIS	0	-0.023	-0.034	38.225	0.253	0.253	0.000	0.000	0.000
176	A	336	LEU	0	-0.009	-0.014	34.268	0.149	0.149	0.000	0.000	0.000
177	A	337	ARG	1	0.926	0.976	37.379	8.262	8.262	0.000	0.000	0.000
178	A	338	LYS	1	0.884	0.956	39.958	7.383	7.383	0.000	0.000	0.000
179	A	339	HIS	0	-0.059	-0.034	40.431	0.278	0.278	0.000	0.000	0.000
180	A	340	TRP	-1	-0.908	-0.938	36.607	-7.460	-7.460	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:161:GLY)