FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2025-07-23

All entries: 44592

Number of unique PDB entries: 7794

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FMODB ID: ZNMRN

Calculation Name: 1V1H-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1V1H

Chain ID: A

ChEMBL ID:

UniProt ID: P03275

Base Structure: X-ray

Registration Date: 2025-07-11

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None


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 188
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -505223.734386
FMO2-HF: Nuclear repulsion 467767.444531
FMO2-HF: Total energy -37456.289854
FMO2-MP2: Total energy -37566.395345


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
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/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(A:319:VAL)


Summations of interaction energy for fragment #1(A:319:VAL)
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.
0.2412.970.008-1.41-1.3270.007
Interaction energy analysis for fragmet #1(A:319:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.136 / q_NPA : 0.030
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   
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].
4A320SER0-0.0550.0614.3410.1080.3560.000-0.111-0.1370.000
5A321ILE00.058-0.1143.880-1.7650.401-0.012-1.243-0.9110.006
6A321ILE0-0.0660.1324.7750.0840.140-0.001-0.006-0.0490.000
7A322LYS00.139-0.0686.9040.2300.2300.0000.0000.0000.000
8A322LYS10.7881.02211.0580.6890.6890.0000.0000.0000.000
9A323LYS00.104-0.10510.4940.1010.1010.0000.0000.0000.000
10A323LYS10.8211.0598.9931.5871.5870.0000.0000.0000.000
11A324SER00.029-0.06712.0570.0870.0870.0000.0000.0000.000
12A324SER0-0.0560.07115.069-0.012-0.0120.0000.0000.0000.000
13A325SER0-0.059-0.12914.0310.1190.1190.0000.0000.0000.000
14A325SER0-0.0290.09813.7660.0150.0150.0000.0000.0000.000
15A326GLY00.097-0.05814.592-0.012-0.0120.0000.0000.0000.000
16A327LEU00.0420.01110.5120.1250.1250.0000.0000.0000.000
17A327LEU0-0.0350.1118.764-0.077-0.0770.0000.0000.0000.000
18A328ASN00.123-0.07910.7560.0380.0380.0000.0000.0000.000
19A328ASN0-0.0780.08912.025-0.102-0.1020.0000.0000.0000.000
20A329PHE00.066-0.1178.541-0.299-0.2990.0000.0000.0000.000
21A329PHE0-0.0960.0824.0650.1770.345-0.001-0.053-0.1140.000
22A330ASP00.134-0.0779.5230.1640.1640.0000.0000.0000.000
23A330ASP-1-0.923-0.80212.571-0.640-0.6400.0000.0000.0000.000
24A331ASN00.070-0.07111.264-0.076-0.0760.0000.0000.0000.000
25A331ASN0-0.1530.03912.7450.0850.0850.0000.0000.0000.000
26A332THR0-0.004-0.1047.913-0.036-0.0360.0000.0000.0000.000
27A332THR0-0.0460.0576.8970.1970.1970.0000.0000.0000.000
28A333ALA00.092-0.1106.716-0.371-0.3710.0000.0000.0000.000
29A333ALA0-0.0450.1349.3420.0770.0770.0000.0000.0000.000
30A334ILE00.058-0.1036.8130.1160.1160.0000.0000.0000.000
31A334ILE0-0.0790.0823.601-0.243-0.1520.0220.003-0.1160.001
32A335ALA00.086-0.1077.6160.2420.2420.0000.0000.0000.000
33A335ALA0-0.0340.14411.9580.0370.0370.0000.0000.0000.000
34A336ILE00.056-0.10611.338-0.166-0.1660.0000.0000.0000.000
35A336ILE0-0.0450.11313.4040.0130.0130.0000.0000.0000.000
36A337ASN00.129-0.04913.8120.0850.0850.0000.0000.0000.000
37A337ASN0-0.1660.04514.272-0.053-0.0530.0000.0000.0000.000
38A338ALA00.088-0.13615.7830.0290.0290.0000.0000.0000.000
39A338ALA0-0.0530.13218.9100.0070.0070.0000.0000.0000.000
40A339GLY0-0.007-0.10519.1550.0020.0020.0000.0000.0000.000
41A340LYS00.0380.00122.4370.0110.0110.0000.0000.0000.000
42A340LYS10.8911.05026.4710.2790.2790.0000.0000.0000.000
43A341GLY00.048-0.07325.791-0.004-0.0040.0000.0000.0000.000
44A342LEU00.0500.02022.6910.0230.0230.0000.0000.0000.000
45A342LEU0-0.0610.08120.523-0.010-0.0100.0000.0000.0000.000
46A343GLU00.048-0.08922.985-0.003-0.0030.0000.0000.0000.000
47A343GLU-1-0.882-0.80824.854-0.238-0.2380.0000.0000.0000.000
48A344PHE00.075-0.09521.047-0.011-0.0110.0000.0000.0000.000
49A344PHE0-0.0960.08116.795-0.013-0.0130.0000.0000.0000.000
50A345ASP00.098-0.09422.1920.0120.0120.0000.0000.0000.000
51A345ASP-1-0.907-0.81524.992-0.215-0.2150.0000.0000.0000.000
52A346THR00.023-0.09224.306-0.008-0.0080.0000.0000.0000.000
53A346THR0-0.0780.05424.194-0.003-0.0030.0000.0000.0000.000
54A347ASN00.095-0.04325.6750.0110.0110.0000.0000.0000.000
55A347ASN0-0.1500.02328.5050.0080.0080.0000.0000.0000.000
56A348THR00.040-0.06826.2570.0180.0180.0000.0000.0000.000
57A348THR0-0.0530.03124.986-0.001-0.0010.0000.0000.0000.000
58A349SER00.061-0.07627.5370.0000.0000.0000.0000.0000.000
59A349SER0-0.0420.04927.7990.0000.0000.0000.0000.0000.000
60A350GLU00.093-0.03723.7550.0180.0180.0000.0000.0000.000
61A350GLU-1-1.033-0.87922.268-0.157-0.1570.0000.0000.0000.000
62A351SER00.002-0.10423.171-0.019-0.0190.0000.0000.0000.000
63A351SER0-0.0460.09724.0640.0040.0040.0000.0000.0000.000
64A352PRO0-0.043-0.11423.3570.0210.0210.0000.0000.0000.000
65A353ASP00.100-0.00120.378-0.043-0.0430.0000.0000.0000.000
66A353ASP-1-0.969-0.84220.370-0.180-0.1800.0000.0000.0000.000
67A354ILE00.033-0.11018.648-0.051-0.0510.0000.0000.0000.000
68A354ILE0-0.0920.08617.976-0.004-0.0040.0000.0000.0000.000
69A355ASN00.069-0.08019.1800.0340.0340.0000.0000.0000.000
70A355ASN0-0.1200.06120.1670.0280.0280.0000.0000.0000.000
71A356PRO00.021-0.08219.326-0.052-0.0520.0000.0000.0000.000
72A357ILE00.1220.02019.4300.0240.0240.0000.0000.0000.000
73A357ILE0-0.1110.07417.912-0.015-0.0150.0000.0000.0000.000
74A358LYS00.029-0.11920.5500.0100.0100.0000.0000.0000.000
75A358LYS10.7841.03224.4260.2400.2400.0000.0000.0000.000
76A359THR00.049-0.07024.006-0.026-0.0260.0000.0000.0000.000
77A359THR0-0.0010.03826.2480.0040.0040.0000.0000.0000.000
78A360LYS00.103-0.07526.4010.0080.0080.0000.0000.0000.000
79A360LYS10.7611.02526.7640.2470.2470.0000.0000.0000.000
80A361ILE0-0.039-0.13128.413-0.004-0.0040.0000.0000.0000.000
81A361ILE0-0.0450.12430.6020.0010.0010.0000.0000.0000.000
82A362GLY00.041-0.10732.1730.0000.0000.0000.0000.0000.000
83A363SER00.0350.01335.6580.0020.0020.0000.0000.0000.000
84A363SER0-0.0540.06339.7980.0000.0000.0000.0000.0000.000
85A364GLY00.050-0.06739.056-0.002-0.0020.0000.0000.0000.000
86A365ILE00.0330.01135.9740.0060.0060.0000.0000.0000.000
87A365ILE0-0.0690.07934.029-0.002-0.0020.0000.0000.0000.000
88A366ASP00.059-0.08536.131-0.001-0.0010.0000.0000.0000.000
89A366ASP-1-0.908-0.81636.948-0.128-0.1280.0000.0000.0000.000
90A367TYR00.073-0.11233.838-0.005-0.0050.0000.0000.0000.000
91A367TYR0-0.0780.07529.122-0.003-0.0030.0000.0000.0000.000
92A368ASN00.076-0.03934.9700.0070.0070.0000.0000.0000.000
93A368ASN0-0.1010.03535.148-0.008-0.0080.0000.0000.0000.000
94A369GLU00.085-0.09835.313-0.009-0.0090.0000.0000.0000.000
95A369GLU-1-0.867-0.78438.197-0.107-0.1070.0000.0000.0000.000
96A370ASN00.017-0.09033.9390.0010.0010.0000.0000.0000.000
97A370ASN0-0.1640.01933.751-0.001-0.0010.0000.0000.0000.000
98A371GLY00.039-0.10330.985-0.008-0.0080.0000.0000.0000.000
99A372ALA00.1000.00530.711-0.018-0.0180.0000.0000.0000.000
100A372ALA0-0.0630.11132.7500.0010.0010.0000.0000.0000.000
101A373MET00.065-0.09332.0270.0080.0080.0000.0000.0000.000
102A373MET0-0.0850.11129.844-0.007-0.0070.0000.0000.0000.000
103A374ILE0-0.007-0.11633.5090.0000.0000.0000.0000.0000.000
104A374ILE0-0.0390.12236.8580.0020.0020.0000.0000.0000.000
105A375THR00.071-0.09337.280-0.006-0.0060.0000.0000.0000.000
106A375THR0-0.0160.09039.0080.0000.0000.0000.0000.0000.000
107A376LYS00.113-0.07539.7190.0060.0060.0000.0000.0000.000
108A376LYS10.7421.01139.9170.1170.1170.0000.0000.0000.000
109A377LEU00.002-0.13241.5830.0000.0000.0000.0000.0000.000
110A377LEU0-0.0960.10543.8590.0010.0010.0000.0000.0000.000
111A378GLY00.030-0.10145.1700.0000.0000.0000.0000.0000.000
112A379ALA00.1000.00048.3570.0010.0010.0000.0000.0000.000
113A379ALA0-0.0830.10352.7280.0000.0000.0000.0000.0000.000
114A380GLY0-0.026-0.10852.153-0.001-0.0010.0000.0000.0000.000
115A381LEU00.0640.00248.7960.0020.0020.0000.0000.0000.000
116A381LEU0-0.0840.08446.811-0.001-0.0010.0000.0000.0000.000
117A382SER0-0.020-0.07448.8480.0000.0000.0000.0000.0000.000
118A382SER0-0.0190.06750.5740.0020.0020.0000.0000.0000.000
119A383PHE00.105-0.08446.170-0.002-0.0020.0000.0000.0000.000
120A383PHE0-0.0650.08741.9350.0000.0000.0000.0000.0000.000
121A384ASP00.041-0.06847.2770.0040.0040.0000.0000.0000.000
122A384ASP-1-0.856-0.80048.213-0.080-0.0800.0000.0000.0000.000
123A385ASN00.095-0.07147.297-0.003-0.0030.0000.0000.0000.000
124A385ASN0-0.1120.05649.5770.0010.0010.0000.0000.0000.000
125A386SER0-0.015-0.12945.8460.0010.0010.0000.0000.0000.000
126A386SER0-0.0620.04645.378-0.001-0.0010.0000.0000.0000.000
127A387GLY0-0.035-0.10542.860-0.004-0.0040.0000.0000.0000.000
128A388ALA00.071-0.00142.906-0.006-0.0060.0000.0000.0000.000
129A388ALA0-0.0650.11144.7690.0000.0000.0000.0000.0000.000
130A389ILE00.094-0.11544.5920.0030.0030.0000.0000.0000.000
131A389ILE0-0.0880.10641.7210.0000.0000.0000.0000.0000.000
132A390THR00.019-0.08046.016-0.001-0.0010.0000.0000.0000.000
133A390THR0-0.0240.08349.6560.0010.0010.0000.0000.0000.000
134A391ILE00.083-0.08849.760-0.001-0.0010.0000.0000.0000.000
135A391ILE0-0.0500.12151.4760.0000.0000.0000.0000.0000.000
136A392GLY0-0.013-0.08952.5400.0020.0020.0000.0000.0000.000
137A401GLY0-0.007-0.01254.0010.0010.0010.0000.0000.0000.000
138A402SER00.022-0.01455.8240.0010.0010.0000.0000.0000.000
139A402SER0-0.0160.06854.8380.0000.0000.0000.0000.0000.000
140A457GLY0-0.046-0.11057.2240.0010.0010.0000.0000.0000.000
141A458TYR00.040-0.00659.4820.0020.0020.0000.0000.0000.000
142A458TYR0-0.0790.10055.8780.0000.0000.0000.0000.0000.000
143A459ILE00.118-0.08560.739-0.001-0.0010.0000.0000.0000.000
144A459ILE0-0.1010.10164.8350.0000.0000.0000.0000.0000.000
145A460PRO0-0.019-0.10260.751-0.001-0.0010.0000.0000.0000.000
146A461GLU00.1880.02862.1970.0020.0020.0000.0000.0000.000
147A461GLU-1-0.919-0.78762.724-0.048-0.0480.0000.0000.0000.000
148A462ALA00.015-0.12664.1760.0000.0000.0000.0000.0000.000
149A462ALA0-0.0350.11968.8440.0000.0000.0000.0000.0000.000
150A463PRO0-0.036-0.12266.986-0.001-0.0010.0000.0000.0000.000
151A464ARG00.0770.04067.8280.0010.0010.0000.0000.0000.000
152A464ARG10.7380.97765.8990.0470.0470.0000.0000.0000.000
153A465ASP00.050-0.12469.0520.0000.0000.0000.0000.0000.000
154A465ASP-1-0.839-0.77671.725-0.037-0.0370.0000.0000.0000.000
155A466GLY0-0.018-0.11472.1490.0010.0010.0000.0000.0000.000
156A467GLN00.025-0.01874.5740.0010.0010.0000.0000.0000.000
157A467GLN0-0.0710.08875.3800.0010.0010.0000.0000.0000.000
158A468ALA00.130-0.06474.697-0.001-0.0010.0000.0000.0000.000
159A468ALA0-0.0880.09277.6890.0000.0000.0000.0000.0000.000
160A469TYR0-0.008-0.14073.0140.0010.0010.0000.0000.0000.000
161A469TYR0-0.0890.06172.4610.0000.0000.0000.0000.0000.000
162A470VAL00.045-0.10574.021-0.001-0.0010.0000.0000.0000.000
163A470VAL0-0.0610.10575.6280.0000.0000.0000.0000.0000.000
164A471ARG00.152-0.08270.7750.0000.0000.0000.0000.0000.000
165A471ARG10.7101.01665.3550.0440.0440.0000.0000.0000.000
166A472LYS00.061-0.11171.8120.0010.0010.0000.0000.0000.000
167A472LYS10.7480.98474.0650.0330.0330.0000.0000.0000.000
168A473ASP00.005-0.10971.530-0.001-0.0010.0000.0000.0000.000
169A473ASP-1-0.879-0.77872.037-0.034-0.0340.0000.0000.0000.000
170A474GLY00.046-0.09867.6350.0000.0000.0000.0000.0000.000
171A475GLU00.026-0.01566.598-0.002-0.0020.0000.0000.0000.000
172A475GLU-1-0.874-0.78666.069-0.044-0.0440.0000.0000.0000.000
173A476TRP00.084-0.13368.5610.0010.0010.0000.0000.0000.000
174A476TRP0-0.1040.08966.0240.0010.0010.0000.0000.0000.000
175A477VAL00.067-0.09070.3650.0000.0000.0000.0000.0000.000
176A477VAL0-0.0860.09673.1520.0000.0000.0000.0000.0000.000
177A478LEU00.146-0.08974.035-0.001-0.0010.0000.0000.0000.000
178A478LEU0-0.0690.13075.3750.0000.0000.0000.0000.0000.000
179A479LEU00.136-0.09776.5180.0010.0010.0000.0000.0000.000
180A479LEU0-0.0840.11478.1030.0000.0000.0000.0000.0000.000
181A480SER00.045-0.08478.9890.0010.0010.0000.0000.0000.000
182A480SER0-0.0160.06580.7700.0000.0000.0000.0000.0000.000
183A481THR0-0.105-0.09480.2800.0010.0010.0000.0000.0000.000
184A481THR0-0.0290.05478.8350.0000.0000.0000.0000.0000.000
185A482PHE00.048-0.07881.5850.0010.0010.0000.0000.0000.000
186A482PHE0-0.0910.07077.6990.0000.0000.0000.0000.0000.000
187A483LEU0-0.066-0.13083.2690.0010.0010.0000.0000.0000.000
188A483LEU00.0400.02983.1330.0000.0000.0000.0000.0000.000