FMO DATABASE

FMODB ID: Z7KNN

Calculation Name: 1NP8-A-Xray547

Preferred Name:

Target Type:

Ligand Name: cadmium ion

Ligand 3-letter code: CD

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1NP8

Chain ID: A

ChEMBL ID:

UniProt ID: Q64537

Base Structure: X-ray

Registration Date: 2025-10-03

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	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Homology Modeling
Water	No
Procedure	Manual calculation
Remarks	ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	149
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1472054.810836
FMO2-HF: Nuclear repulsion	1410489.634334
FMO2-HF: Total energy	-61565.176502
FMO2-MP2: Total energy	-61740.537547

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:11:SER)

Summations of interaction energy for fragment #1(A:11: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.
-57.08	-52.566	10.859	-8.35	-7.021	-0.099

Interaction energy analysis for fragmet #1(A:11:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.813 / q_NPA : 0.887

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	13	GLU	-1	-0.895	-0.955	3.882	-41.367	-39.961	-0.010	-0.509	-0.886	-0.001
4	A	14	GLU	-1	-0.845	-0.912	1.865	-111.314	-108.612	10.869	-7.735	-5.835	-0.098
5	A	15	ARG	1	0.980	0.989	4.125	54.861	55.267	0.000	-0.106	-0.300	0.000
6	A	16	GLN	0	-0.100	-0.074	6.351	7.799	7.799	0.000	0.000	0.000	0.000
7	A	17	PHE	0	0.046	0.038	7.359	3.459	3.459	0.000	0.000	0.000	0.000
8	A	18	ARG	1	0.923	0.974	8.044	28.155	28.155	0.000	0.000	0.000	0.000
9	A	19	LYS	1	0.923	0.965	9.866	30.403	30.403	0.000	0.000	0.000	0.000
10	A	20	LEU	0	-0.019	0.003	11.819	1.903	1.903	0.000	0.000	0.000	0.000
11	A	21	PHE	0	0.027	0.007	12.647	1.045	1.045	0.000	0.000	0.000	0.000
12	A	22	VAL	0	0.002	-0.007	14.048	1.150	1.150	0.000	0.000	0.000	0.000
13	A	23	GLN	0	-0.053	-0.017	16.007	1.005	1.005	0.000	0.000	0.000	0.000
14	A	24	LEU	0	-0.110	-0.061	17.261	0.934	0.934	0.000	0.000	0.000	0.000
15	A	25	ALA	0	0.026	0.013	18.432	0.679	0.679	0.000	0.000	0.000	0.000
16	A	26	GLY	0	0.019	0.030	20.190	0.518	0.518	0.000	0.000	0.000	0.000
17	A	27	ASP	-1	-0.899	-0.962	22.164	-12.299	-12.299	0.000	0.000	0.000	0.000
18	A	28	ASP	-1	-0.899	-0.942	24.436	-12.351	-12.351	0.000	0.000	0.000	0.000
19	A	29	MET	0	-0.077	-0.033	19.044	-0.193	-0.193	0.000	0.000	0.000	0.000
20	A	30	GLU	0	-0.029	-0.045	19.378	-1.159	-1.159	0.000	0.000	0.000	0.000
21	A	31	VAL	0	-0.042	-0.001	17.797	0.412	0.412	0.000	0.000	0.000	0.000
22	A	32	SER	0	0.024	-0.024	20.868	0.452	0.452	0.000	0.000	0.000	0.000
23	A	33	ALA	0	0.021	-0.003	23.900	-0.314	-0.314	0.000	0.000	0.000	0.000
24	A	34	THR	0	-0.005	-0.012	26.271	0.049	0.049	0.000	0.000	0.000	0.000
25	A	35	GLU	-1	-0.796	-0.855	21.892	-13.324	-13.324	0.000	0.000	0.000	0.000
26	A	36	LEU	0	0.013	0.008	20.527	-0.563	-0.563	0.000	0.000	0.000	0.000
27	A	37	MET	0	0.008	-0.003	22.560	-0.115	-0.115	0.000	0.000	0.000	0.000
28	A	38	ASN	0	-0.016	-0.015	24.135	0.232	0.232	0.000	0.000	0.000	0.000
29	A	39	ILE	0	-0.073	-0.034	17.390	-0.158	-0.158	0.000	0.000	0.000	0.000
30	A	40	LEU	0	0.008	0.005	20.150	-0.484	-0.484	0.000	0.000	0.000	0.000
31	A	41	ASN	0	0.057	0.029	22.245	0.169	0.169	0.000	0.000	0.000	0.000
32	A	42	LYS	1	0.919	0.982	19.939	15.118	15.118	0.000	0.000	0.000	0.000
33	A	43	VAL	0	-0.038	-0.014	18.641	-0.403	-0.403	0.000	0.000	0.000	0.000
34	A	44	VAL	0	0.077	0.029	21.218	-0.016	-0.016	0.000	0.000	0.000	0.000
35	A	45	THR	0	-0.075	-0.042	24.521	0.427	0.427	0.000	0.000	0.000	0.000
36	A	46	ARG	1	0.861	0.925	16.991	16.766	16.766	0.000	0.000	0.000	0.000
37	A	47	HIS	0	-0.066	-0.012	19.778	-1.074	-1.074	0.000	0.000	0.000	0.000
38	A	48	PRO	0	0.055	0.028	24.326	0.193	0.193	0.000	0.000	0.000	0.000
39	A	49	ASP	-1	-0.866	-0.918	24.465	-12.700	-12.700	0.000	0.000	0.000	0.000
40	A	50	LEU	0	-0.060	-0.022	22.727	-0.133	-0.133	0.000	0.000	0.000	0.000
41	A	51	LYS	1	0.970	0.998	27.426	9.125	9.125	0.000	0.000	0.000	0.000
42	A	52	THR	0	-0.083	-0.085	28.528	-0.447	-0.447	0.000	0.000	0.000	0.000
43	A	53	ASP	-1	-0.913	-0.943	30.643	-9.199	-9.199	0.000	0.000	0.000	0.000
44	A	54	GLY	0	-0.034	0.001	29.468	0.135	0.135	0.000	0.000	0.000	0.000
45	A	55	PHE	0	0.013	-0.010	24.062	-0.013	-0.013	0.000	0.000	0.000	0.000
46	A	56	GLY	0	0.090	0.036	28.338	0.074	0.074	0.000	0.000	0.000	0.000
47	A	57	ILE	0	0.024	-0.017	29.905	-0.250	-0.250	0.000	0.000	0.000	0.000
48	A	58	ASP	-1	-0.961	-0.973	30.815	-9.562	-9.562	0.000	0.000	0.000	0.000
49	A	59	THR	0	0.066	0.021	28.521	-0.220	-0.220	0.000	0.000	0.000	0.000
50	A	60	CYS	0	-0.009	0.010	26.247	-0.436	-0.436	0.000	0.000	0.000	0.000
51	A	61	ARG	1	0.957	0.969	26.646	9.359	9.359	0.000	0.000	0.000	0.000
52	A	62	SER	0	-0.070	-0.029	28.745	-0.087	-0.087	0.000	0.000	0.000	0.000
53	A	63	MET	0	-0.013	-0.011	24.085	-0.278	-0.278	0.000	0.000	0.000	0.000
54	A	64	VAL	0	0.005	-0.003	23.656	-0.400	-0.400	0.000	0.000	0.000	0.000
55	A	65	ALA	0	-0.002	-0.006	25.146	-0.214	-0.214	0.000	0.000	0.000	0.000
56	A	66	VAL	0	-0.047	-0.014	25.137	0.220	0.220	0.000	0.000	0.000	0.000
57	A	67	MET	0	-0.056	-0.029	20.948	-0.756	-0.756	0.000	0.000	0.000	0.000
58	A	68	ASP	-1	-0.843	-0.914	21.860	-12.802	-12.802	0.000	0.000	0.000	0.000
59	A	69	SER	0	-0.046	-0.021	21.814	0.510	0.510	0.000	0.000	0.000	0.000
60	A	70	ASP	-1	-0.922	-0.942	21.907	-13.571	-13.571	0.000	0.000	0.000	0.000
61	A	71	THR	0	-0.082	-0.033	24.491	0.676	0.676	0.000	0.000	0.000	0.000
62	A	72	THR	0	-0.016	-0.011	23.901	0.410	0.410	0.000	0.000	0.000	0.000
63	A	73	GLY	0	-0.038	-0.015	26.597	0.267	0.267	0.000	0.000	0.000	0.000
64	A	74	LYS	1	0.741	0.853	23.343	11.966	11.966	0.000	0.000	0.000	0.000
65	A	75	LEU	0	0.019	0.026	18.954	-0.237	-0.237	0.000	0.000	0.000	0.000
66	A	76	GLY	0	0.131	0.066	18.575	-0.432	-0.432	0.000	0.000	0.000	0.000
67	A	77	PHE	0	-0.082	-0.059	8.777	-1.297	-1.297	0.000	0.000	0.000	0.000
68	A	78	GLU	-1	-0.830	-0.926	11.551	-27.298	-27.298	0.000	0.000	0.000	0.000
69	A	79	GLU	-1	-0.733	-0.847	14.222	-15.662	-15.662	0.000	0.000	0.000	0.000
70	A	80	PHE	0	0.021	0.002	14.202	-0.190	-0.190	0.000	0.000	0.000	0.000
71	A	81	LYS	1	0.824	0.902	7.832	30.303	30.303	0.000	0.000	0.000	0.000
72	A	82	TYR	0	-0.088	-0.070	12.510	-1.367	-1.367	0.000	0.000	0.000	0.000
73	A	83	LEU	0	0.057	0.026	14.596	0.058	0.058	0.000	0.000	0.000	0.000
74	A	84	TRP	0	-0.010	-0.010	11.779	1.027	1.027	0.000	0.000	0.000	0.000
75	A	85	ASN	0	0.007	-0.011	8.811	0.308	0.308	0.000	0.000	0.000	0.000
76	A	86	ASN	0	0.003	0.009	12.842	-0.274	-0.274	0.000	0.000	0.000	0.000
77	A	87	ILE	0	0.007	0.009	16.399	0.615	0.615	0.000	0.000	0.000	0.000
78	A	88	LYS	1	0.866	0.928	13.003	20.042	20.042	0.000	0.000	0.000	0.000
79	A	89	LYS	1	0.918	0.975	14.683	18.852	18.852	0.000	0.000	0.000	0.000
80	A	90	TRP	0	0.023	-0.002	16.007	0.575	0.575	0.000	0.000	0.000	0.000
81	A	91	GLN	0	0.043	0.038	18.196	0.009	0.009	0.000	0.000	0.000	0.000
82	A	92	GLY	0	-0.026	-0.010	17.879	0.565	0.565	0.000	0.000	0.000	0.000
83	A	93	ILE	0	-0.072	-0.032	18.812	0.529	0.529	0.000	0.000	0.000	0.000
84	A	94	TYR	0	0.011	-0.020	21.473	0.459	0.459	0.000	0.000	0.000	0.000
85	A	95	LYS	1	0.873	0.902	21.812	13.372	13.372	0.000	0.000	0.000	0.000
86	A	96	ARG	1	0.878	0.939	20.245	14.817	14.817	0.000	0.000	0.000	0.000
87	A	97	PHE	0	-0.021	-0.011	23.838	0.231	0.231	0.000	0.000	0.000	0.000
88	A	98	ASP	-1	-0.766	-0.859	27.016	-10.178	-10.178	0.000	0.000	0.000	0.000
89	A	99	THR	0	-0.143	-0.085	29.040	-0.019	-0.019	0.000	0.000	0.000	0.000
90	A	100	ASP	-1	-0.888	-0.933	31.077	-9.118	-9.118	0.000	0.000	0.000	0.000
91	A	101	ARG	1	0.825	0.917	30.813	9.880	9.880	0.000	0.000	0.000	0.000
92	A	102	SER	0	0.001	0.008	32.139	0.095	0.095	0.000	0.000	0.000	0.000
93	A	103	GLY	0	0.008	0.008	29.506	0.109	0.109	0.000	0.000	0.000	0.000
94	A	104	THR	0	-0.092	-0.045	29.879	-0.079	-0.079	0.000	0.000	0.000	0.000
95	A	105	ILE	0	0.002	0.018	27.091	-0.211	-0.211	0.000	0.000	0.000	0.000
96	A	106	GLY	0	0.097	0.047	30.833	0.208	0.208	0.000	0.000	0.000	0.000
97	A	107	SER	0	0.021	-0.005	33.649	-0.267	-0.267	0.000	0.000	0.000	0.000
98	A	108	ASN	0	-0.030	-0.025	35.531	0.022	0.022	0.000	0.000	0.000	0.000
99	A	109	GLU	-1	-0.773	-0.855	30.390	-10.079	-10.079	0.000	0.000	0.000	0.000
100	A	110	LEU	0	-0.014	-0.005	29.656	-0.365	-0.365	0.000	0.000	0.000	0.000
101	A	111	PRO	0	-0.009	-0.011	29.723	-0.325	-0.325	0.000	0.000	0.000	0.000
102	A	112	GLY	0	0.062	0.038	28.938	-0.238	-0.238	0.000	0.000	0.000	0.000
103	A	113	ALA	0	0.013	-0.001	25.699	-0.537	-0.537	0.000	0.000	0.000	0.000
104	A	114	PHE	0	-0.006	-0.039	24.878	-0.543	-0.543	0.000	0.000	0.000	0.000
105	A	115	GLU	-1	-0.926	-0.943	25.706	-11.626	-11.626	0.000	0.000	0.000	0.000
106	A	116	ALA	0	-0.042	-0.026	22.361	-0.526	-0.526	0.000	0.000	0.000	0.000
107	A	117	ALA	0	-0.075	-0.036	21.254	-0.930	-0.930	0.000	0.000	0.000	0.000
108	A	118	GLY	0	-0.024	-0.006	21.616	-0.652	-0.652	0.000	0.000	0.000	0.000
109	A	119	PHE	0	-0.048	-0.019	23.076	0.338	0.338	0.000	0.000	0.000	0.000
110	A	120	HIS	0	0.033	0.016	27.025	0.380	0.380	0.000	0.000	0.000	0.000
111	A	121	LEU	0	0.002	0.002	29.918	0.118	0.118	0.000	0.000	0.000	0.000
112	A	122	ASN	0	0.031	0.014	33.372	0.135	0.135	0.000	0.000	0.000	0.000
113	A	123	GLN	0	0.082	0.023	37.163	-0.223	-0.223	0.000	0.000	0.000	0.000
114	A	124	HIS	0	-0.042	0.000	39.720	0.120	0.120	0.000	0.000	0.000	0.000
115	A	125	ILE	0	0.048	0.024	33.111	0.030	0.030	0.000	0.000	0.000	0.000
116	A	126	TYR	0	0.015	0.007	34.368	0.021	0.021	0.000	0.000	0.000	0.000
117	A	127	SER	0	-0.007	-0.023	36.191	0.018	0.018	0.000	0.000	0.000	0.000
118	A	128	MET	0	-0.054	-0.009	34.349	0.046	0.046	0.000	0.000	0.000	0.000
119	A	129	ILE	0	0.016	-0.019	31.939	-0.033	-0.033	0.000	0.000	0.000	0.000
120	A	130	ILE	0	0.000	0.004	34.921	-0.070	-0.070	0.000	0.000	0.000	0.000
121	A	131	ARG	1	0.930	0.959	36.796	7.471	7.471	0.000	0.000	0.000	0.000
122	A	132	ARG	1	0.871	0.944	33.907	9.383	9.383	0.000	0.000	0.000	0.000
123	A	133	TYR	0	-0.008	-0.017	31.895	-0.085	-0.085	0.000	0.000	0.000	0.000
124	A	134	SER	0	0.005	0.002	33.756	-0.309	-0.309	0.000	0.000	0.000	0.000
125	A	135	ASP	-1	-0.811	-0.901	36.099	-8.299	-8.299	0.000	0.000	0.000	0.000
126	A	136	GLU	-1	-0.931	-0.988	38.851	-7.647	-7.647	0.000	0.000	0.000	0.000
127	A	137	THR	0	-0.115	-0.043	39.267	0.262	0.262	0.000	0.000	0.000	0.000
128	A	138	GLY	0	-0.052	-0.018	38.567	0.028	0.028	0.000	0.000	0.000	0.000
129	A	139	ASN	0	-0.043	-0.036	34.630	-0.020	-0.020	0.000	0.000	0.000	0.000
130	A	140	MET	0	-0.014	0.019	30.276	-0.090	-0.090	0.000	0.000	0.000	0.000
131	A	141	ASP	-1	-0.800	-0.911	30.606	-10.383	-10.383	0.000	0.000	0.000	0.000
132	A	142	PHE	0	0.029	-0.002	21.046	-0.467	-0.467	0.000	0.000	0.000	0.000
133	A	143	ASP	-1	-0.775	-0.871	26.032	-11.203	-11.203	0.000	0.000	0.000	0.000
134	A	144	ASN	0	0.011	0.029	27.421	0.043	0.043	0.000	0.000	0.000	0.000
135	A	145	PHE	0	0.007	-0.006	23.225	-0.113	-0.113	0.000	0.000	0.000	0.000
136	A	146	ILE	0	-0.019	-0.015	22.029	-0.365	-0.365	0.000	0.000	0.000	0.000
137	A	147	SER	0	-0.030	-0.031	24.635	-0.163	-0.163	0.000	0.000	0.000	0.000
138	A	148	CYS	0	-0.061	-0.004	27.382	0.097	0.097	0.000	0.000	0.000	0.000
139	A	149	LEU	0	0.021	0.008	23.067	-0.028	-0.028	0.000	0.000	0.000	0.000
140	A	150	VAL	0	-0.010	-0.011	21.894	-0.277	-0.277	0.000	0.000	0.000	0.000
141	A	151	ARG	1	0.913	0.960	24.205	10.493	10.493	0.000	0.000	0.000	0.000
142	A	152	LEU	0	-0.015	0.002	26.957	0.289	0.289	0.000	0.000	0.000	0.000
143	A	153	ASP	-1	-0.747	-0.849	21.428	-14.927	-14.927	0.000	0.000	0.000	0.000
144	A	154	ALA	0	0.000	-0.004	24.724	0.126	0.126	0.000	0.000	0.000	0.000
145	A	155	MET	0	-0.079	-0.031	25.976	0.400	0.400	0.000	0.000	0.000	0.000
146	A	156	PHE	0	-0.014	-0.017	26.933	0.303	0.303	0.000	0.000	0.000	0.000
147	A	157	ARG	1	0.801	0.901	19.041	15.238	15.238	0.000	0.000	0.000	0.000
148	A	158	ALA	0	-0.033	-0.005	26.078	-0.045	-0.045	0.000	0.000	0.000	0.000
149	A	159	PHE	-1	-0.949	-0.963	29.228	-9.567	-9.567	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:11:SER)